Source code for emdbXMLTranslator.emdb_da

#!/usr/bin/env python
# -*- coding: utf-8 -*-

#
# Generated Fri Dec 11 16:55:58 2015 by generateDS.py version 2.17a.
#
# Command line options:
#   ('--user-methods', 'emdb_user_methods')
#   ('--external-encoding', 'utf-8')
#   ('-f', '')
#   ('-o', 'emdb_da.py')
#
# Command line arguments:
#   ../schema/emdb_da.xsd
#
# Command line:
#   ../generateDS-2.17a0/build/scripts-2.7/generateDS.py --user-methods="emdb_user_methods" --external-encoding="utf-8" -f -o "emdb_da.py" ../schema/emdb_da.xsd
#
# Current working directory (os.getcwd()):
#   emdbXMLTranslator
#

import sys
import re as re_
import base64
import datetime as datetime_
import warnings as warnings_
from lxml import etree as etree_


Validate_simpletypes_ = True


def parsexml_(infile, parser=None, **kwargs):
    if parser is None:
        # Use the lxml ElementTree compatible parser so that, e.g.,
        #   we ignore comments.
        parser = etree_.ETCompatXMLParser()
    doc = etree_.parse(infile, parser=parser, **kwargs)
    return doc

#
# User methods
#
# Calls to the methods in these classes are generated by generateDS.py.
# You can replace these methods by re-implementing the following class
#   in a module named generatedssuper.py.

try:
    from generatedssuper import GeneratedsSuper
except ImportError as exp:

    class GeneratedsSuper(object):
        tzoff_pattern = re_.compile(r'(\+|-)((0\d|1[0-3]):[0-5]\d|14:00)$')
        class _FixedOffsetTZ(datetime_.tzinfo):
            def __init__(self, offset, name):
                self.__offset = datetime_.timedelta(minutes=offset)
                self.__name = name
            def utcoffset(self, dt):
                return self.__offset
            def tzname(self, dt):
                return self.__name
            def dst(self, dt):
                return None
        def gds_format_string(self, input_data, input_name=''):
            return input_data
        def gds_validate_string(self, input_data, node=None, input_name=''):
            if not input_data:
                return ''
            else:
                return input_data
        def gds_format_base64(self, input_data, input_name=''):
            return base64.b64encode(input_data)
        def gds_validate_base64(self, input_data, node=None, input_name=''):
            return input_data
        def gds_format_integer(self, input_data, input_name=''):
            return '%d' % input_data
        def gds_validate_integer(self, input_data, node=None, input_name=''):
            return input_data
        def gds_format_integer_list(self, input_data, input_name=''):
            return '%s' % ' '.join(input_data)
        def gds_validate_integer_list(
                self, input_data, node=None, input_name=''):
            values = input_data.split()
            for value in values:
                try:
                    int(value)
                except (TypeError, ValueError):
                    raise_parse_error(node, 'Requires sequence of integers')
            return values
        def gds_format_float(self, input_data, input_name=''):
            return ('%.15f' % input_data).rstrip('0')
        def gds_validate_float(self, input_data, node=None, input_name=''):
            return input_data
        def gds_format_float_list(self, input_data, input_name=''):
            return '%s' % ' '.join(input_data)
        def gds_validate_float_list(
                self, input_data, node=None, input_name=''):
            values = input_data.split()
            for value in values:
                try:
                    float(value)
                except (TypeError, ValueError):
                    raise_parse_error(node, 'Requires sequence of floats')
            return values
        def gds_format_double(self, input_data, input_name=''):
            return '%e' % input_data
        def gds_validate_double(self, input_data, node=None, input_name=''):
            return input_data
        def gds_format_double_list(self, input_data, input_name=''):
            return '%s' % ' '.join(input_data)
        def gds_validate_double_list(
                self, input_data, node=None, input_name=''):
            values = input_data.split()
            for value in values:
                try:
                    float(value)
                except (TypeError, ValueError):
                    raise_parse_error(node, 'Requires sequence of doubles')
            return values
        def gds_format_boolean(self, input_data, input_name=''):
            return ('%s' % input_data).lower()
        def gds_validate_boolean(self, input_data, node=None, input_name=''):
            return input_data
        def gds_format_boolean_list(self, input_data, input_name=''):
            return '%s' % ' '.join(input_data)
        def gds_validate_boolean_list(
                self, input_data, node=None, input_name=''):
            values = input_data.split()
            for value in values:
                if value not in ('true', '1', 'false', '0', ):
                    raise_parse_error(
                        node,
                        'Requires sequence of booleans '
                        '("true", "1", "false", "0")')
            return values
        def gds_validate_datetime(self, input_data, node=None, input_name=''):
            return input_data
        def gds_format_datetime(self, input_data, input_name=''):
            if input_data.microsecond == 0:
                _svalue = '%04d-%02d-%02dT%02d:%02d:%02d' % (
                    input_data.year,
                    input_data.month,
                    input_data.day,
                    input_data.hour,
                    input_data.minute,
                    input_data.second,
                )
            else:
                _svalue = '%04d-%02d-%02dT%02d:%02d:%02d.%s' % (
                    input_data.year,
                    input_data.month,
                    input_data.day,
                    input_data.hour,
                    input_data.minute,
                    input_data.second,
                    ('%f' % (float(input_data.microsecond) / 1000000))[2:],
                )
            if input_data.tzinfo is not None:
                tzoff = input_data.tzinfo.utcoffset(input_data)
                if tzoff is not None:
                    total_seconds = tzoff.seconds + (86400 * tzoff.days)
                    if total_seconds == 0:
                        _svalue += 'Z'
                    else:
                        if total_seconds < 0:
                            _svalue += '-'
                            total_seconds *= -1
                        else:
                            _svalue += '+'
                        hours = total_seconds // 3600
                        minutes = (total_seconds - (hours * 3600)) // 60
                        _svalue += '{0:02d}:{1:02d}'.format(hours, minutes)
            return _svalue
        @classmethod
        def gds_parse_datetime(cls, input_data):
            tz = None
            if input_data[-1] == 'Z':
                tz = GeneratedsSuper._FixedOffsetTZ(0, 'UTC')
                input_data = input_data[:-1]
            else:
                results = GeneratedsSuper.tzoff_pattern.search(input_data)
                if results is not None:
                    tzoff_parts = results.group(2).split(':')
                    tzoff = int(tzoff_parts[0]) * 60 + int(tzoff_parts[1])
                    if results.group(1) == '-':
                        tzoff *= -1
                    tz = GeneratedsSuper._FixedOffsetTZ(
                        tzoff, results.group(0))
                    input_data = input_data[:-6]
            time_parts = input_data.split('.')
            if len(time_parts) > 1:
                micro_seconds = int(float('0.' + time_parts[1]) * 1000000)
                input_data = '%s.%s' % (time_parts[0], micro_seconds, )
                dt = datetime_.datetime.strptime(
                    input_data, '%Y-%m-%dT%H:%M:%S.%f')
            else:
                dt = datetime_.datetime.strptime(
                    input_data, '%Y-%m-%dT%H:%M:%S')
            dt = dt.replace(tzinfo=tz)
            return dt
        def gds_validate_date(self, input_data, node=None, input_name=''):
            return input_data
        def gds_format_date(self, input_data, input_name=''):
            _svalue = '%04d-%02d-%02d' % (
                input_data.year,
                input_data.month,
                input_data.day,
            )
            try:
                if input_data.tzinfo is not None:
                    tzoff = input_data.tzinfo.utcoffset(input_data)
                    if tzoff is not None:
                        total_seconds = tzoff.seconds + (86400 * tzoff.days)
                        if total_seconds == 0:
                            _svalue += 'Z'
                        else:
                            if total_seconds < 0:
                                _svalue += '-'
                                total_seconds *= -1
                            else:
                                _svalue += '+'
                            hours = total_seconds // 3600
                            minutes = (total_seconds - (hours * 3600)) // 60
                            _svalue += '{0:02d}:{1:02d}'.format(hours, minutes)
            except AttributeError:
                pass
            return _svalue
        @classmethod
        def gds_parse_date(cls, input_data):
            tz = None
            if input_data[-1] == 'Z':
                tz = GeneratedsSuper._FixedOffsetTZ(0, 'UTC')
                input_data = input_data[:-1]
            else:
                results = GeneratedsSuper.tzoff_pattern.search(input_data)
                if results is not None:
                    tzoff_parts = results.group(2).split(':')
                    tzoff = int(tzoff_parts[0]) * 60 + int(tzoff_parts[1])
                    if results.group(1) == '-':
                        tzoff *= -1
                    tz = GeneratedsSuper._FixedOffsetTZ(
                        tzoff, results.group(0))
                    input_data = input_data[:-6]
            dt = datetime_.datetime.strptime(input_data, '%Y-%m-%d')
            dt = dt.replace(tzinfo=tz)
            return dt.date()
        def gds_validate_time(self, input_data, node=None, input_name=''):
            return input_data
        def gds_format_time(self, input_data, input_name=''):
            if input_data.microsecond == 0:
                _svalue = '%02d:%02d:%02d' % (
                    input_data.hour,
                    input_data.minute,
                    input_data.second,
                )
            else:
                _svalue = '%02d:%02d:%02d.%s' % (
                    input_data.hour,
                    input_data.minute,
                    input_data.second,
                    ('%f' % (float(input_data.microsecond) / 1000000))[2:],
                )
            if input_data.tzinfo is not None:
                tzoff = input_data.tzinfo.utcoffset(input_data)
                if tzoff is not None:
                    total_seconds = tzoff.seconds + (86400 * tzoff.days)
                    if total_seconds == 0:
                        _svalue += 'Z'
                    else:
                        if total_seconds < 0:
                            _svalue += '-'
                            total_seconds *= -1
                        else:
                            _svalue += '+'
                        hours = total_seconds // 3600
                        minutes = (total_seconds - (hours * 3600)) // 60
                        _svalue += '{0:02d}:{1:02d}'.format(hours, minutes)
            return _svalue
        def gds_validate_simple_patterns(self, patterns, target):
            # pat is a list of lists of strings/patterns.  We should:
            # - AND the outer elements
            # - OR the inner elements
            found1 = True
            for patterns1 in patterns:
                found2 = False
                for patterns2 in patterns1:
                    if re_.search(patterns2, target) is not None:
                        found2 = True
                        break
                if not found2:
                    found1 = False
                    break
            return found1
        @classmethod
        def gds_parse_time(cls, input_data):
            tz = None
            if input_data[-1] == 'Z':
                tz = GeneratedsSuper._FixedOffsetTZ(0, 'UTC')
                input_data = input_data[:-1]
            else:
                results = GeneratedsSuper.tzoff_pattern.search(input_data)
                if results is not None:
                    tzoff_parts = results.group(2).split(':')
                    tzoff = int(tzoff_parts[0]) * 60 + int(tzoff_parts[1])
                    if results.group(1) == '-':
                        tzoff *= -1
                    tz = GeneratedsSuper._FixedOffsetTZ(
                        tzoff, results.group(0))
                    input_data = input_data[:-6]
            if len(input_data.split('.')) > 1:
                dt = datetime_.datetime.strptime(input_data, '%H:%M:%S.%f')
            else:
                dt = datetime_.datetime.strptime(input_data, '%H:%M:%S')
            dt = dt.replace(tzinfo=tz)
            return dt.time()
        def gds_str_lower(self, instring):
            return instring.lower()
        def get_path_(self, node):
            path_list = []
            self.get_path_list_(node, path_list)
            path_list.reverse()
            path = '/'.join(path_list)
            return path
        Tag_strip_pattern_ = re_.compile(r'\{.*\}')
        def get_path_list_(self, node, path_list):
            if node is None:
                return
            tag = GeneratedsSuper.Tag_strip_pattern_.sub('', node.tag)
            if tag:
                path_list.append(tag)
            self.get_path_list_(node.getparent(), path_list)
        def get_class_obj_(self, node, default_class=None):
            class_obj1 = default_class
            if 'xsi' in node.nsmap:
                classname = node.get('{%s}type' % node.nsmap['xsi'])
                if classname is not None:
                    names = classname.split(':')
                    if len(names) == 2:
                        classname = names[1]
                    class_obj2 = globals().get(classname)
                    if class_obj2 is not None:
                        class_obj1 = class_obj2
            return class_obj1
        def gds_build_any(self, node, type_name=None):
            return None
        @classmethod
        def gds_reverse_node_mapping(cls, mapping):
            return dict(((v, k) for k, v in mapping.iteritems()))


#
# If you have installed IPython you can uncomment and use the following.
# IPython is available from http://ipython.scipy.org/.
#

## from IPython.Shell import IPShellEmbed
## args = ''
## ipshell = IPShellEmbed(args,
##     banner = 'Dropping into IPython',
##     exit_msg = 'Leaving Interpreter, back to program.')

# Then use the following line where and when you want to drop into the
# IPython shell:
#    ipshell('<some message> -- Entering ipshell.\nHit Ctrl-D to exit')

#
# Globals
#

ExternalEncoding = 'utf-8'
Tag_pattern_ = re_.compile(r'({.*})?(.*)')
String_cleanup_pat_ = re_.compile(r"[\n\r\s]+")
Namespace_extract_pat_ = re_.compile(r'{(.*)}(.*)')
CDATA_pattern_ = re_.compile(r"<!\[CDATA\[.*?\]\]>", re_.DOTALL)

#
# Support/utility functions.
#


def showIndent(outfile, level, pretty_print=True):
    if pretty_print:
        for idx in range(level):
            outfile.write('    ')


def quote_xml(inStr):
    "Escape markup chars, but do not modify CDATA sections."
    if not inStr:
        return ''
    s1 = (isinstance(inStr, basestring) and inStr or
          '%s' % inStr)
    s2 = ''
    pos = 0
    matchobjects = CDATA_pattern_.finditer(s1)
    for mo in matchobjects:
        s3 = s1[pos:mo.start()]
        s2 += quote_xml_aux(s3)
        s2 += s1[mo.start():mo.end()]
        pos = mo.end()
    s3 = s1[pos:]
    s2 += quote_xml_aux(s3)
    return s2


def quote_xml_aux(inStr):
    s1 = inStr.replace('&', '&amp;')
    s1 = s1.replace('<', '&lt;')
    s1 = s1.replace('>', '&gt;')
    return s1


def quote_attrib(inStr):
    s1 = (isinstance(inStr, basestring) and inStr or
          '%s' % inStr)
    s1 = s1.replace('&', '&amp;')
    s1 = s1.replace('<', '&lt;')
    s1 = s1.replace('>', '&gt;')
    if '"' in s1:
        if "'" in s1:
            s1 = '"%s"' % s1.replace('"', "&quot;")
        else:
            s1 = "'%s'" % s1
    else:
        s1 = '"%s"' % s1
    return s1


def quote_python(inStr):
    s1 = inStr
    if s1.find("'") == -1:
        if s1.find('\n') == -1:
            return "'%s'" % s1
        else:
            return "'''%s'''" % s1
    else:
        if s1.find('"') != -1:
            s1 = s1.replace('"', '\\"')
        if s1.find('\n') == -1:
            return '"%s"' % s1
        else:
            return '"""%s"""' % s1


def get_all_text_(node):
    if node.text is not None:
        text = node.text
    else:
        text = ''
    for child in node:
        if child.tail is not None:
            text += child.tail
    return text


def find_attr_value_(attr_name, node):
    attrs = node.attrib
    attr_parts = attr_name.split(':')
    value = None
    if len(attr_parts) == 1:
        value = attrs.get(attr_name)
    elif len(attr_parts) == 2:
        prefix, name = attr_parts
        namespace = node.nsmap.get(prefix)
        if namespace is not None:
            value = attrs.get('{%s}%s' % (namespace, name, ))
    return value


class GDSParseError(Exception):
    pass


def raise_parse_error(node, msg):
    msg = '%s (element %s/line %d)' % (msg, node.tag, node.sourceline, )
    raise GDSParseError(msg)


class MixedContainer:
    # Constants for category:
    CategoryNone = 0
    CategoryText = 1
    CategorySimple = 2
    CategoryComplex = 3
    # Constants for content_type:
    TypeNone = 0
    TypeText = 1
    TypeString = 2
    TypeInteger = 3
    TypeFloat = 4
    TypeDecimal = 5
    TypeDouble = 6
    TypeBoolean = 7
    TypeBase64 = 8
    def __init__(self, category, content_type, name, value):
        self.category = category
        self.content_type = content_type
        self.name = name
        self.value = value
    def getCategory(self):
        return self.category
    def getContenttype(self, content_type):
        return self.content_type
    def getValue(self):
        return self.value
    def getName(self):
        return self.name
    def export(self, outfile, level, name, namespace, pretty_print=True):
        if self.category == MixedContainer.CategoryText:
            # Prevent exporting empty content as empty lines.
            if self.value.strip():
                outfile.write(self.value)
        elif self.category == MixedContainer.CategorySimple:
            self.exportSimple(outfile, level, name)
        else:    # category == MixedContainer.CategoryComplex
            self.value.export(outfile, level, namespace, name, pretty_print)
    def exportSimple(self, outfile, level, name):
        if self.content_type == MixedContainer.TypeString:
            outfile.write('<%s>%s</%s>' % (
                self.name, self.value, self.name))
        elif self.content_type == MixedContainer.TypeInteger or \
                self.content_type == MixedContainer.TypeBoolean:
            outfile.write('<%s>%d</%s>' % (
                self.name, self.value, self.name))
        elif self.content_type == MixedContainer.TypeFloat or \
                self.content_type == MixedContainer.TypeDecimal:
            outfile.write('<%s>%f</%s>' % (
                self.name, self.value, self.name))
        elif self.content_type == MixedContainer.TypeDouble:
            outfile.write('<%s>%g</%s>' % (
                self.name, self.value, self.name))
        elif self.content_type == MixedContainer.TypeBase64:
            outfile.write('<%s>%s</%s>' % (
                self.name, base64.b64encode(self.value), self.name))
    def to_etree(self, element):
        if self.category == MixedContainer.CategoryText:
            # Prevent exporting empty content as empty lines.
            if self.value.strip():
                if len(element) > 0:
                    if element[-1].tail is None:
                        element[-1].tail = self.value
                    else:
                        element[-1].tail += self.value
                else:
                    if element.text is None:
                        element.text = self.value
                    else:
                        element.text += self.value
        elif self.category == MixedContainer.CategorySimple:
            subelement = etree_.SubElement(element, '%s' % self.name)
            subelement.text = self.to_etree_simple()
        else:    # category == MixedContainer.CategoryComplex
            self.value.to_etree(element)
    def to_etree_simple(self):
        if self.content_type == MixedContainer.TypeString:
            text = self.value
        elif (self.content_type == MixedContainer.TypeInteger or
                self.content_type == MixedContainer.TypeBoolean):
            text = '%d' % self.value
        elif (self.content_type == MixedContainer.TypeFloat or
                self.content_type == MixedContainer.TypeDecimal):
            text = '%f' % self.value
        elif self.content_type == MixedContainer.TypeDouble:
            text = '%g' % self.value
        elif self.content_type == MixedContainer.TypeBase64:
            text = '%s' % base64.b64encode(self.value)
        return text
    def exportLiteral(self, outfile, level, name):
        if self.category == MixedContainer.CategoryText:
            showIndent(outfile, level)
            outfile.write(
                'model_.MixedContainer(%d, %d, "%s", "%s"),\n' % (
                    self.category, self.content_type, self.name, self.value))
        elif self.category == MixedContainer.CategorySimple:
            showIndent(outfile, level)
            outfile.write(
                'model_.MixedContainer(%d, %d, "%s", "%s"),\n' % (
                    self.category, self.content_type, self.name, self.value))
        else:    # category == MixedContainer.CategoryComplex
            showIndent(outfile, level)
            outfile.write(
                'model_.MixedContainer(%d, %d, "%s",\n' % (
                    self.category, self.content_type, self.name,))
            self.value.exportLiteral(outfile, level + 1)
            showIndent(outfile, level)
            outfile.write(')\n')


class MemberSpec_(object):
    def __init__(self, name='', data_type='', container=0):
        self.name = name
        self.data_type = data_type
        self.container = container
    def set_name(self, name): self.name = name
    def get_name(self): return self.name
    def set_data_type(self, data_type): self.data_type = data_type
    def get_data_type_chain(self): return self.data_type
    def get_data_type(self):
        if isinstance(self.data_type, list):
            if len(self.data_type) > 0:
                return self.data_type[-1]
            else:
                return 'xs:string'
        else:
            return self.data_type
    def set_container(self, container): self.container = container
    def get_container(self): return self.container


def _cast(typ, value):
    if typ is None or value is None:
        return value
    return typ(value)

#
# Data representation classes.
#


[docs]class entry_type(GeneratedsSuper): """For example: EMD-1001The XML schema version that validates the header file. This attribute should contain a default value: the current schema version.""" member_data_items_ = [ MemberSpec_('emdb_id', 'emdb_id_type', 0), MemberSpec_('version', 'xs:token', 0), MemberSpec_('admin', 'admin_type', 0), MemberSpec_('crossreferences', 'crossreferences_type', 0), MemberSpec_('sample', 'sample', 0), MemberSpec_('structure_determination_list', 'structure_determination_listType', 0), MemberSpec_('map', 'map_type', 0), MemberSpec_('interpretation', 'interpretation_type', 0), MemberSpec_('validation', 'validationType', 0), ] subclass = None superclass = None def __init__(self, emdb_id=None, version=None, admin=None, crossreferences=None, sample=None, structure_determination_list=None, map=None, interpretation=None, validation=None): self.original_tagname_ = None self.emdb_id = _cast(None, emdb_id) self.version = _cast(None, version) self.admin = admin self.crossreferences = crossreferences self.sample = sample self.structure_determination_list = structure_determination_list self.map = map self.interpretation = interpretation self.validation = validation
[docs] def factory(*args_, **kwargs_): if entry_type.subclass: return entry_type.subclass(*args_, **kwargs_) else: return entry_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_admin(self): return self.admin
[docs] def set_admin(self, admin): self.admin = admin
[docs] def get_crossreferences(self): return self.crossreferences
[docs] def set_crossreferences(self, crossreferences): self.crossreferences = crossreferences
[docs] def get_sample(self): return self.sample
[docs] def set_sample(self, sample): self.sample = sample
[docs] def get_structure_determination_list(self): return self.structure_determination_list
[docs] def set_structure_determination_list(self, structure_determination_list): self.structure_determination_list = structure_determination_list
[docs] def get_map(self): return self.map
[docs] def set_map(self, map): self.map = map
[docs] def get_interpretation(self): return self.interpretation
[docs] def set_interpretation(self, interpretation): self.interpretation = interpretation
[docs] def get_validation(self): return self.validation
[docs] def set_validation(self, validation): self.validation = validation
[docs] def get_emdb_id(self): return self.emdb_id
[docs] def set_emdb_id(self, emdb_id): self.emdb_id = emdb_id
[docs] def get_version(self): return self.version
[docs] def set_version(self, version): self.version = version
[docs] def validate_emdb_id_type(self, value): # Validate type emdb_id_type, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_emdb_id_type_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_emdb_id_type_patterns_, ))
validate_emdb_id_type_patterns_ = [['^EMD-\\d{4,}$']]
[docs] def hasContent_(self): if ( self.admin is not None or self.crossreferences is not None or self.sample is not None or self.structure_determination_list is not None or self.map is not None or self.interpretation is not None or self.validation is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='entry_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='entry_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='entry_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='entry_type'): if self.emdb_id is not None and 'emdb_id' not in already_processed: already_processed.add('emdb_id') outfile.write(' emdb_id=%s' % (quote_attrib(self.emdb_id), )) if self.version is not None and 'version' not in already_processed: already_processed.add('version') outfile.write(' version=%s' % (self.gds_format_string(quote_attrib(self.version).encode(ExternalEncoding), input_name='version'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='entry_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.admin is not None: self.admin.export(outfile, level, namespace_, name_='admin', pretty_print=pretty_print) if self.crossreferences is not None: self.crossreferences.export(outfile, level, namespace_, name_='crossreferences', pretty_print=pretty_print) if self.sample is not None: self.sample.export(outfile, level, namespace_, name_='sample', pretty_print=pretty_print) if self.structure_determination_list is not None: self.structure_determination_list.export(outfile, level, namespace_, name_='structure_determination_list', pretty_print=pretty_print) if self.map is not None: self.map.export(outfile, level, namespace_, name_='map', pretty_print=pretty_print) if self.interpretation is not None: self.interpretation.export(outfile, level, namespace_, name_='interpretation', pretty_print=pretty_print) if self.validation is not None: self.validation.export(outfile, level, namespace_, name_='validation', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('emdb_id', node) if value is not None and 'emdb_id' not in already_processed: already_processed.add('emdb_id') self.emdb_id = value self.emdb_id = ' '.join(self.emdb_id.split()) self.validate_emdb_id_type(self.emdb_id) # validate type emdb_id_type value = find_attr_value_('version', node) if value is not None and 'version' not in already_processed: already_processed.add('version') self.version = value self.version = ' '.join(self.version.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'admin': obj_ = admin_type.factory() obj_.build(child_) self.admin = obj_ obj_.original_tagname_ = 'admin' elif nodeName_ == 'crossreferences': obj_ = crossreferences_type.factory() obj_.build(child_) self.crossreferences = obj_ obj_.original_tagname_ = 'crossreferences' elif nodeName_ == 'sample': obj_ = sample_type.factory() obj_.build(child_) self.sample = obj_ obj_.original_tagname_ = 'sample' elif nodeName_ == 'structure_determination_list': obj_ = structure_determination_listType.factory() obj_.build(child_) self.structure_determination_list = obj_ obj_.original_tagname_ = 'structure_determination_list' elif nodeName_ == 'map': obj_ = map_type.factory() obj_.build(child_) self.map = obj_ obj_.original_tagname_ = 'map' elif nodeName_ == 'interpretation': obj_ = interpretation_type.factory() obj_.build(child_) self.interpretation = obj_ obj_.original_tagname_ = 'interpretation' elif nodeName_ == 'validation': obj_ = validationType.factory() obj_.build(child_) self.validation = obj_ obj_.original_tagname_ = 'validation' # end class entry_type
[docs]class admin_type(GeneratedsSuper): """for pdbx categories with "PDB" in name, we should request duplicate categories with "EMDB" substituted""" member_data_items_ = [ MemberSpec_('status_history_list', 'version_list_type', 0), MemberSpec_('current_status', 'version_type', 0), MemberSpec_('sites', 'sitesType', 0), MemberSpec_('key_dates', 'key_datesType', 0), MemberSpec_('obsolete_list', 'obsolete_listType', 0), MemberSpec_('superseded_by_list', 'superseded_by_listType', 0), MemberSpec_('grant_support', 'grant_supportType', 0), MemberSpec_('contact_author', 'contact_authorType', 1), MemberSpec_('title', 'xs:token', 0), MemberSpec_('authors_list', 'authors_listType', 0), MemberSpec_('details', 'xs:token', 0), MemberSpec_('keywords', 'xs:string', 0), MemberSpec_('replace_existing_entry', 'xs:boolean', 0), ] subclass = None superclass = None def __init__(self, status_history_list=None, current_status=None, sites=None, key_dates=None, obsolete_list=None, superseded_by_list=None, grant_support=None, contact_author=None, title=None, authors_list=None, details=None, keywords=None, replace_existing_entry=None): self.original_tagname_ = None self.status_history_list = status_history_list self.current_status = current_status self.sites = sites self.key_dates = key_dates self.obsolete_list = obsolete_list self.superseded_by_list = superseded_by_list self.grant_support = grant_support if contact_author is None: self.contact_author = [] else: self.contact_author = contact_author self.title = title self.authors_list = authors_list self.details = details self.keywords = keywords self.replace_existing_entry = replace_existing_entry
[docs] def factory(*args_, **kwargs_): if admin_type.subclass: return admin_type.subclass(*args_, **kwargs_) else: return admin_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_status_history_list(self): return self.status_history_list
[docs] def set_status_history_list(self, status_history_list): self.status_history_list = status_history_list
[docs] def get_current_status(self): return self.current_status
[docs] def set_current_status(self, current_status): self.current_status = current_status
[docs] def get_sites(self): return self.sites
[docs] def set_sites(self, sites): self.sites = sites
[docs] def get_key_dates(self): return self.key_dates
[docs] def set_key_dates(self, key_dates): self.key_dates = key_dates
[docs] def get_obsolete_list(self): return self.obsolete_list
[docs] def set_obsolete_list(self, obsolete_list): self.obsolete_list = obsolete_list
[docs] def get_superseded_by_list(self): return self.superseded_by_list
[docs] def set_superseded_by_list(self, superseded_by_list): self.superseded_by_list = superseded_by_list
[docs] def get_grant_support(self): return self.grant_support
[docs] def set_grant_support(self, grant_support): self.grant_support = grant_support
[docs] def get_contact_author(self): return self.contact_author
[docs] def set_contact_author(self, contact_author): self.contact_author = contact_author
[docs] def add_contact_author(self, value): self.contact_author.append(value)
[docs] def insert_contact_author_at(self, index, value): self.contact_author.insert(index, value)
[docs] def replace_contact_author_at(self, index, value): self.contact_author[index] = value
[docs] def get_title(self): return self.title
[docs] def set_title(self, title): self.title = title
[docs] def get_authors_list(self): return self.authors_list
[docs] def set_authors_list(self, authors_list): self.authors_list = authors_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def get_keywords(self): return self.keywords
[docs] def set_keywords(self, keywords): self.keywords = keywords
[docs] def get_replace_existing_entry(self): return self.replace_existing_entry
[docs] def set_replace_existing_entry(self, replace_existing_entry): self.replace_existing_entry = replace_existing_entry
[docs] def hasContent_(self): if ( self.status_history_list is not None or self.current_status is not None or self.sites is not None or self.key_dates is not None or self.obsolete_list is not None or self.superseded_by_list is not None or self.grant_support is not None or self.contact_author or self.title is not None or self.authors_list is not None or self.details is not None or self.keywords is not None or self.replace_existing_entry is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='admin_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='admin_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='admin_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='admin_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='admin_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.status_history_list is not None: self.status_history_list.export(outfile, level, namespace_, name_='status_history_list', pretty_print=pretty_print) if self.current_status is not None: self.current_status.export(outfile, level, namespace_, name_='current_status', pretty_print=pretty_print) if self.sites is not None: self.sites.export(outfile, level, namespace_, name_='sites', pretty_print=pretty_print) if self.key_dates is not None: self.key_dates.export(outfile, level, namespace_, name_='key_dates', pretty_print=pretty_print) if self.obsolete_list is not None: self.obsolete_list.export(outfile, level, namespace_, name_='obsolete_list', pretty_print=pretty_print) if self.superseded_by_list is not None: self.superseded_by_list.export(outfile, level, namespace_, name_='superseded_by_list', pretty_print=pretty_print) if self.grant_support is not None: self.grant_support.export(outfile, level, namespace_, name_='grant_support', pretty_print=pretty_print) for contact_author_ in self.contact_author: contact_author_.export(outfile, level, namespace_, name_='contact_author', pretty_print=pretty_print) if self.title is not None: showIndent(outfile, level, pretty_print) outfile.write('<%stitle>%s</%stitle>%s' % (namespace_, self.gds_format_string(quote_xml(self.title).encode(ExternalEncoding), input_name='title'), namespace_, eol_)) if self.authors_list is not None: self.authors_list.export(outfile, level, namespace_, name_='authors_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_)) if self.keywords is not None: showIndent(outfile, level, pretty_print) outfile.write('<%skeywords>%s</%skeywords>%s' % (namespace_, self.gds_format_string(quote_xml(self.keywords).encode(ExternalEncoding), input_name='keywords'), namespace_, eol_)) if self.replace_existing_entry is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sreplace_existing_entry>%s</%sreplace_existing_entry>%s' % (namespace_, self.gds_format_boolean(self.replace_existing_entry, input_name='replace_existing_entry'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'status_history_list': obj_ = version_list_type.factory() obj_.build(child_) self.status_history_list = obj_ obj_.original_tagname_ = 'status_history_list' elif nodeName_ == 'current_status': class_obj_ = self.get_class_obj_(child_, version_type) obj_ = class_obj_.factory() obj_.build(child_) self.current_status = obj_ obj_.original_tagname_ = 'current_status' elif nodeName_ == 'sites': obj_ = sitesType.factory() obj_.build(child_) self.sites = obj_ obj_.original_tagname_ = 'sites' elif nodeName_ == 'key_dates': obj_ = key_datesType.factory() obj_.build(child_) self.key_dates = obj_ obj_.original_tagname_ = 'key_dates' elif nodeName_ == 'obsolete_list': obj_ = obsolete_listType.factory() obj_.build(child_) self.obsolete_list = obj_ obj_.original_tagname_ = 'obsolete_list' elif nodeName_ == 'superseded_by_list': obj_ = superseded_by_listType.factory() obj_.build(child_) self.superseded_by_list = obj_ obj_.original_tagname_ = 'superseded_by_list' elif nodeName_ == 'grant_support': obj_ = grant_supportType.factory() obj_.build(child_) self.grant_support = obj_ obj_.original_tagname_ = 'grant_support' elif nodeName_ == 'contact_author': obj_ = contact_authorType.factory() obj_.build(child_) self.contact_author.append(obj_) obj_.original_tagname_ = 'contact_author' elif nodeName_ == 'title': title_ = child_.text title_ = re_.sub(String_cleanup_pat_, " ", title_).strip() title_ = self.gds_validate_string(title_, node, 'title') self.title = title_ elif nodeName_ == 'authors_list': obj_ = authors_listType.factory() obj_.build(child_) self.authors_list = obj_ obj_.original_tagname_ = 'authors_list' elif nodeName_ == 'details': details_ = child_.text details_ = re_.sub(String_cleanup_pat_, " ", details_).strip() details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ elif nodeName_ == 'keywords': keywords_ = child_.text keywords_ = self.gds_validate_string(keywords_, node, 'keywords') self.keywords = keywords_ elif nodeName_ == 'replace_existing_entry': sval_ = child_.text if sval_ in ('true', '1'): ival_ = True elif sval_ in ('false', '0'): ival_ = False else: raise_parse_error(child_, 'requires boolean') ival_ = self.gds_validate_boolean(ival_, node, 'replace_existing_entry') self.replace_existing_entry = ival_ # end class admin_type
[docs]class version_list_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('status', 'statusType', 1), ] subclass = None superclass = None def __init__(self, status=None): self.original_tagname_ = None if status is None: self.status = [] else: self.status = status
[docs] def factory(*args_, **kwargs_): if version_list_type.subclass: return version_list_type.subclass(*args_, **kwargs_) else: return version_list_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_status(self): return self.status
[docs] def set_status(self, status): self.status = status
[docs] def add_status(self, value): self.status.append(value)
[docs] def insert_status_at(self, index, value): self.status.insert(index, value)
[docs] def replace_status_at(self, index, value): self.status[index] = value
[docs] def hasContent_(self): if ( self.status ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='version_list_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='version_list_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='version_list_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='version_list_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='version_list_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for status_ in self.status: status_.export(outfile, level, namespace_, name_='status', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'status': obj_ = statusType.factory() obj_.build(child_) self.status.append(obj_) obj_.original_tagname_ = 'status' # end class version_list_type
[docs]class version_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('date', ['dateType', 'xs:date'], 0), MemberSpec_('code', 'code_type', 0), MemberSpec_('processing_site', ['processing_siteType', 'xs:token'], 0), MemberSpec_('annotator', 'annotatorType', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, date=None, code=None, processing_site=None, annotator=None, details=None, extensiontype_=None): self.original_tagname_ = None if isinstance(date, basestring): initvalue_ = datetime_.datetime.strptime(date, '%Y-%m-%d').date() else: initvalue_ = date self.date = initvalue_ self.code = code self.processing_site = processing_site self.validate_processing_siteType(self.processing_site) self.annotator = annotator self.details = details self.extensiontype_ = extensiontype_
[docs] def factory(*args_, **kwargs_): if version_type.subclass: return version_type.subclass(*args_, **kwargs_) else: return version_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_date(self): return self.date
[docs] def set_date(self, date): self.date = date
[docs] def get_code(self): return self.code
[docs] def set_code(self, code): self.code = code
[docs] def get_processing_site(self): return self.processing_site
[docs] def set_processing_site(self, processing_site): self.processing_site = processing_site
[docs] def get_annotator(self): return self.annotator
[docs] def set_annotator(self, annotator): self.annotator = annotator
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def get_extensiontype_(self): return self.extensiontype_
[docs] def set_extensiontype_(self, extensiontype_): self.extensiontype_ = extensiontype_
[docs] def validate_dateType(self, value): # Validate type dateType, a restriction on xs:date. if value is not None and Validate_simpletypes_: if value < 2002-01-01: warnings_.warn('Value "%(value)s" does not match xsd minInclusive restriction on dateType' % {"value" : value} )
[docs] def validate_processing_siteType(self, value): # Validate type processing_siteType, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['PDBe', 'RCSB', 'PDBj'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on processing_siteType' % {"value" : value.encode("utf-8")} )
[docs] def hasContent_(self): if ( self.date is not None or self.code is not None or self.processing_site is not None or self.annotator is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='version_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='version_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='version_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='version_type'): if self.extensiontype_ is not None and 'xsi:type' not in already_processed: already_processed.add('xsi:type') outfile.write(' xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"') outfile.write(' xsi:type="%s"' % self.extensiontype_) pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='version_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.date is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdate>%s</%sdate>%s' % (namespace_, self.gds_format_date(self.date, input_name='date'), namespace_, eol_)) if self.code is not None: self.code.export(outfile, level, namespace_, name_='code', pretty_print=pretty_print) if self.processing_site is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sprocessing_site>%s</%sprocessing_site>%s' % (namespace_, self.gds_format_string(quote_xml(self.processing_site).encode(ExternalEncoding), input_name='processing_site'), namespace_, eol_)) if self.annotator is not None: self.annotator.export(outfile, level, namespace_, name_='annotator', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('xsi:type', node) if value is not None and 'xsi:type' not in already_processed: already_processed.add('xsi:type') self.extensiontype_ = value
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'date': sval_ = child_.text dval_ = self.gds_parse_date(sval_) self.date = dval_ # validate type dateType self.validate_dateType(self.date) elif nodeName_ == 'code': obj_ = code_type.factory() obj_.build(child_) self.code = obj_ obj_.original_tagname_ = 'code' elif nodeName_ == 'processing_site': processing_site_ = child_.text processing_site_ = re_.sub(String_cleanup_pat_, " ", processing_site_).strip() processing_site_ = self.gds_validate_string(processing_site_, node, 'processing_site') self.processing_site = processing_site_ # validate type processing_siteType self.validate_processing_siteType(self.processing_site) elif nodeName_ == 'annotator': obj_ = annotatorType.factory() obj_.build(child_) self.annotator = obj_ obj_.original_tagname_ = 'annotator' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class version_type
[docs]class status_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('date', 'xs:date', 0), MemberSpec_('code', 'code_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, date=None, code=None, details=None): self.original_tagname_ = None if isinstance(date, basestring): initvalue_ = datetime_.datetime.strptime(date, '%Y-%m-%d').date() else: initvalue_ = date self.date = initvalue_ self.code = code self.details = details
[docs] def factory(*args_, **kwargs_): if status_type.subclass: return status_type.subclass(*args_, **kwargs_) else: return status_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_date(self): return self.date
[docs] def set_date(self, date): self.date = date
[docs] def get_code(self): return self.code
[docs] def set_code(self, code): self.code = code
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def hasContent_(self): if ( self.date is not None or self.code is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='status_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='status_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='status_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='status_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='status_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.date is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdate>%s</%sdate>%s' % (namespace_, self.gds_format_date(self.date, input_name='date'), namespace_, eol_)) if self.code is not None: self.code.export(outfile, level, namespace_, name_='code', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'date': sval_ = child_.text dval_ = self.gds_parse_date(sval_) self.date = dval_ elif nodeName_ == 'code': obj_ = code_type.factory() obj_.build(child_) self.code = obj_ obj_.original_tagname_ = 'code' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class status_type
[docs]class supersedes_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('date', 'xs:date', 0), MemberSpec_('entry', ['emdb_id_type', 'xs:token'], 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, date=None, entry=None, details=None): self.original_tagname_ = None if isinstance(date, basestring): initvalue_ = datetime_.datetime.strptime(date, '%Y-%m-%d').date() else: initvalue_ = date self.date = initvalue_ self.entry = entry self.validate_emdb_id_type(self.entry) self.details = details
[docs] def factory(*args_, **kwargs_): if supersedes_type.subclass: return supersedes_type.subclass(*args_, **kwargs_) else: return supersedes_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_date(self): return self.date
[docs] def set_date(self, date): self.date = date
[docs] def get_entry(self): return self.entry
[docs] def set_entry(self, entry): self.entry = entry
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def validate_emdb_id_type(self, value): # Validate type emdb_id_type, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_emdb_id_type_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_emdb_id_type_patterns_, ))
validate_emdb_id_type_patterns_ = [['^EMD-\\d{4,}$']]
[docs] def hasContent_(self): if ( self.date is not None or self.entry is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='supersedes_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='supersedes_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='supersedes_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='supersedes_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='supersedes_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.date is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdate>%s</%sdate>%s' % (namespace_, self.gds_format_date(self.date, input_name='date'), namespace_, eol_)) if self.entry is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sentry>%s</%sentry>%s' % (namespace_, self.gds_format_string(quote_xml(self.entry).encode(ExternalEncoding), input_name='entry'), namespace_, eol_)) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'date': sval_ = child_.text dval_ = self.gds_parse_date(sval_) self.date = dval_ elif nodeName_ == 'entry': entry_ = child_.text entry_ = re_.sub(String_cleanup_pat_, " ", entry_).strip() entry_ = self.gds_validate_string(entry_, node, 'entry') self.entry = entry_ # validate type emdb_id_type self.validate_emdb_id_type(self.entry) elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class supersedes_type
[docs]class contact_details_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('role', ['roleType', 'xs:token'], 0), MemberSpec_('title', ['titleType', 'xs:token'], 0), MemberSpec_('first_name', 'xs:token', 0), MemberSpec_('middle_name', ['middle_nameType', 'xs:token'], 0), MemberSpec_('last_name', 'xs:token', 0), MemberSpec_('organization', 'organizationType', 0), MemberSpec_('street', 'xs:string', 0), MemberSpec_('town_or_city', 'xs:token', 0), MemberSpec_('state_or_province', 'xs:token', 0), MemberSpec_('country', 'xs:token', 0), MemberSpec_('post_or_zip_code', 'xs:token', 0), MemberSpec_('email', ['emailType', 'xs:token'], 0), MemberSpec_('telephone', 'telephone_number_type', 0), MemberSpec_('fax', 'telephone_number_type', 0), ] subclass = None superclass = None def __init__(self, role=None, title=None, first_name=None, middle_name=None, last_name=None, organization=None, street=None, town_or_city=None, state_or_province=None, country=None, post_or_zip_code=None, email=None, telephone=None, fax=None, extensiontype_=None): self.original_tagname_ = None self.role = role self.validate_roleType(self.role) self.title = title self.validate_titleType(self.title) self.first_name = first_name self.middle_name = middle_name self.validate_middle_nameType(self.middle_name) self.last_name = last_name self.organization = organization self.street = street self.town_or_city = town_or_city self.state_or_province = state_or_province self.country = country self.post_or_zip_code = post_or_zip_code self.email = email self.validate_emailType(self.email) self.telephone = telephone self.fax = fax self.extensiontype_ = extensiontype_
[docs] def factory(*args_, **kwargs_): if contact_details_type.subclass: return contact_details_type.subclass(*args_, **kwargs_) else: return contact_details_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_role(self): return self.role
[docs] def set_role(self, role): self.role = role
[docs] def get_title(self): return self.title
[docs] def set_title(self, title): self.title = title
[docs] def get_first_name(self): return self.first_name
[docs] def set_first_name(self, first_name): self.first_name = first_name
[docs] def get_middle_name(self): return self.middle_name
[docs] def set_middle_name(self, middle_name): self.middle_name = middle_name
[docs] def get_last_name(self): return self.last_name
[docs] def set_last_name(self, last_name): self.last_name = last_name
[docs] def get_organization(self): return self.organization
[docs] def set_organization(self, organization): self.organization = organization
[docs] def get_street(self): return self.street
[docs] def set_street(self, street): self.street = street
[docs] def get_town_or_city(self): return self.town_or_city
[docs] def set_town_or_city(self, town_or_city): self.town_or_city = town_or_city
[docs] def get_state_or_province(self): return self.state_or_province
[docs] def set_state_or_province(self, state_or_province): self.state_or_province = state_or_province
[docs] def get_country(self): return self.country
[docs] def set_country(self, country): self.country = country
[docs] def get_post_or_zip_code(self): return self.post_or_zip_code
[docs] def set_post_or_zip_code(self, post_or_zip_code): self.post_or_zip_code = post_or_zip_code
[docs] def get_email(self): return self.email
[docs] def set_email(self, email): self.email = email
[docs] def get_telephone(self): return self.telephone
[docs] def set_telephone(self, telephone): self.telephone = telephone
[docs] def get_fax(self): return self.fax
[docs] def set_fax(self, fax): self.fax = fax
[docs] def get_extensiontype_(self): return self.extensiontype_
[docs] def set_extensiontype_(self, extensiontype_): self.extensiontype_ = extensiontype_
[docs] def validate_roleType(self, value): # Validate type roleType, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['PRINCIPAL INVESTIGATOR', 'RESPONSIBLE SCIENTIST'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on roleType' % {"value" : value.encode("utf-8")} )
[docs] def validate_titleType(self, value): # Validate type titleType, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['PROF.', 'DR.'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on titleType' % {"value" : value.encode("utf-8")} )
[docs] def validate_middle_nameType(self, value): # Validate type middle_nameType, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_middle_nameType_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_middle_nameType_patterns_, ))
validate_middle_nameType_patterns_ = [['^[A-Z]$']]
[docs] def validate_emailType(self, value): # Validate type emailType, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_emailType_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_emailType_patterns_, ))
validate_emailType_patterns_ = [['^[A-Za-z0-9._%+-]+@[A-Za-z0-9.-]+\\.[A-Za-z]{2,4}$']]
[docs] def hasContent_(self): if ( self.role is not None or self.title is not None or self.first_name is not None or self.middle_name is not None or self.last_name is not None or self.organization is not None or self.street is not None or self.town_or_city is not None or self.state_or_province is not None or self.country is not None or self.post_or_zip_code is not None or self.email is not None or self.telephone is not None or self.fax is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='contact_details_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='contact_details_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='contact_details_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='contact_details_type'): if self.extensiontype_ is not None and 'xsi:type' not in already_processed: already_processed.add('xsi:type') outfile.write(' xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"') outfile.write(' xsi:type="%s"' % self.extensiontype_) pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='contact_details_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.role is not None: showIndent(outfile, level, pretty_print) outfile.write('<%srole>%s</%srole>%s' % (namespace_, self.gds_format_string(quote_xml(self.role).encode(ExternalEncoding), input_name='role'), namespace_, eol_)) if self.title is not None: showIndent(outfile, level, pretty_print) outfile.write('<%stitle>%s</%stitle>%s' % (namespace_, self.gds_format_string(quote_xml(self.title).encode(ExternalEncoding), input_name='title'), namespace_, eol_)) if self.first_name is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sfirst_name>%s</%sfirst_name>%s' % (namespace_, self.gds_format_string(quote_xml(self.first_name).encode(ExternalEncoding), input_name='first_name'), namespace_, eol_)) if self.middle_name is not None: showIndent(outfile, level, pretty_print) outfile.write('<%smiddle_name>%s</%smiddle_name>%s' % (namespace_, self.gds_format_string(quote_xml(self.middle_name).encode(ExternalEncoding), input_name='middle_name'), namespace_, eol_)) if self.last_name is not None: showIndent(outfile, level, pretty_print) outfile.write('<%slast_name>%s</%slast_name>%s' % (namespace_, self.gds_format_string(quote_xml(self.last_name).encode(ExternalEncoding), input_name='last_name'), namespace_, eol_)) if self.organization is not None: self.organization.export(outfile, level, namespace_, name_='organization', pretty_print=pretty_print) if self.street is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sstreet>%s</%sstreet>%s' % (namespace_, self.gds_format_string(quote_xml(self.street).encode(ExternalEncoding), input_name='street'), namespace_, eol_)) if self.town_or_city is not None: showIndent(outfile, level, pretty_print) outfile.write('<%stown_or_city>%s</%stown_or_city>%s' % (namespace_, self.gds_format_string(quote_xml(self.town_or_city).encode(ExternalEncoding), input_name='town_or_city'), namespace_, eol_)) if self.state_or_province is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sstate_or_province>%s</%sstate_or_province>%s' % (namespace_, self.gds_format_string(quote_xml(self.state_or_province).encode(ExternalEncoding), input_name='state_or_province'), namespace_, eol_)) if self.country is not None: showIndent(outfile, level, pretty_print) outfile.write('<%scountry>%s</%scountry>%s' % (namespace_, self.gds_format_string(quote_xml(self.country).encode(ExternalEncoding), input_name='country'), namespace_, eol_)) if self.post_or_zip_code is not None: showIndent(outfile, level, pretty_print) outfile.write('<%spost_or_zip_code>%s</%spost_or_zip_code>%s' % (namespace_, self.gds_format_string(quote_xml(self.post_or_zip_code).encode(ExternalEncoding), input_name='post_or_zip_code'), namespace_, eol_)) if self.email is not None: showIndent(outfile, level, pretty_print) outfile.write('<%semail>%s</%semail>%s' % (namespace_, self.gds_format_string(quote_xml(self.email).encode(ExternalEncoding), input_name='email'), namespace_, eol_)) if self.telephone is not None: self.telephone.export(outfile, level, namespace_, name_='telephone', pretty_print=pretty_print) if self.fax is not None: self.fax.export(outfile, level, namespace_, name_='fax', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('xsi:type', node) if value is not None and 'xsi:type' not in already_processed: already_processed.add('xsi:type') self.extensiontype_ = value
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'role': role_ = child_.text role_ = re_.sub(String_cleanup_pat_, " ", role_).strip() role_ = self.gds_validate_string(role_, node, 'role') self.role = role_ # validate type roleType self.validate_roleType(self.role) elif nodeName_ == 'title': title_ = child_.text title_ = re_.sub(String_cleanup_pat_, " ", title_).strip() title_ = self.gds_validate_string(title_, node, 'title') self.title = title_ # validate type titleType self.validate_titleType(self.title) elif nodeName_ == 'first_name': first_name_ = child_.text first_name_ = re_.sub(String_cleanup_pat_, " ", first_name_).strip() first_name_ = self.gds_validate_string(first_name_, node, 'first_name') self.first_name = first_name_ elif nodeName_ == 'middle_name': middle_name_ = child_.text middle_name_ = re_.sub(String_cleanup_pat_, " ", middle_name_).strip() middle_name_ = self.gds_validate_string(middle_name_, node, 'middle_name') self.middle_name = middle_name_ # validate type middle_nameType self.validate_middle_nameType(self.middle_name) elif nodeName_ == 'last_name': last_name_ = child_.text last_name_ = re_.sub(String_cleanup_pat_, " ", last_name_).strip() last_name_ = self.gds_validate_string(last_name_, node, 'last_name') self.last_name = last_name_ elif nodeName_ == 'organization': obj_ = organizationType.factory() obj_.build(child_) self.organization = obj_ obj_.original_tagname_ = 'organization' elif nodeName_ == 'street': street_ = child_.text street_ = self.gds_validate_string(street_, node, 'street') self.street = street_ elif nodeName_ == 'town_or_city': town_or_city_ = child_.text town_or_city_ = re_.sub(String_cleanup_pat_, " ", town_or_city_).strip() town_or_city_ = self.gds_validate_string(town_or_city_, node, 'town_or_city') self.town_or_city = town_or_city_ elif nodeName_ == 'state_or_province': state_or_province_ = child_.text state_or_province_ = re_.sub(String_cleanup_pat_, " ", state_or_province_).strip() state_or_province_ = self.gds_validate_string(state_or_province_, node, 'state_or_province') self.state_or_province = state_or_province_ elif nodeName_ == 'country': country_ = child_.text country_ = re_.sub(String_cleanup_pat_, " ", country_).strip() country_ = self.gds_validate_string(country_, node, 'country') self.country = country_ elif nodeName_ == 'post_or_zip_code': post_or_zip_code_ = child_.text post_or_zip_code_ = re_.sub(String_cleanup_pat_, " ", post_or_zip_code_).strip() post_or_zip_code_ = self.gds_validate_string(post_or_zip_code_, node, 'post_or_zip_code') self.post_or_zip_code = post_or_zip_code_ elif nodeName_ == 'email': email_ = child_.text email_ = re_.sub(String_cleanup_pat_, " ", email_).strip() email_ = self.gds_validate_string(email_, node, 'email') self.email = email_ # validate type emailType self.validate_emailType(self.email) elif nodeName_ == 'telephone': obj_ = telephone_number_type.factory() obj_.build(child_) self.telephone = obj_ obj_.original_tagname_ = 'telephone' elif nodeName_ == 'fax': obj_ = telephone_number_type.factory() obj_.build(child_) self.fax = obj_ obj_.original_tagname_ = 'fax' # end class contact_details_type
[docs]class name_type(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if name_type.subclass: return name_type.subclass(*args_, **kwargs_) else: return name_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='name_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='name_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='name_type', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='name_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='name_type', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class name_type
[docs]class address_type(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if address_type.subclass: return address_type.subclass(*args_, **kwargs_) else: return address_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='address_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='address_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='address_type', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='address_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='address_type', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class address_type
[docs]class crossreferences_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('citation_list', 'citation_listType', 0), MemberSpec_('emdb_list', 'emdb_cross_reference_list_type', 0), MemberSpec_('pdb_list', 'pdb_cross_reference_list_type', 0), MemberSpec_('auxiliary_link_list', 'auxiliary_link_listType', 0), ] subclass = None superclass = None def __init__(self, citation_list=None, emdb_list=None, pdb_list=None, auxiliary_link_list=None): self.original_tagname_ = None self.citation_list = citation_list self.emdb_list = emdb_list self.pdb_list = pdb_list self.auxiliary_link_list = auxiliary_link_list
[docs] def factory(*args_, **kwargs_): if crossreferences_type.subclass: return crossreferences_type.subclass(*args_, **kwargs_) else: return crossreferences_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_citation_list(self): return self.citation_list
[docs] def set_citation_list(self, citation_list): self.citation_list = citation_list
[docs] def get_emdb_list(self): return self.emdb_list
[docs] def set_emdb_list(self, emdb_list): self.emdb_list = emdb_list
[docs] def get_pdb_list(self): return self.pdb_list
[docs] def set_pdb_list(self, pdb_list): self.pdb_list = pdb_list
[docs] def hasContent_(self): if ( self.citation_list is not None or self.emdb_list is not None or self.pdb_list is not None or self.auxiliary_link_list is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='crossreferences_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='crossreferences_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='crossreferences_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='crossreferences_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='crossreferences_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.citation_list is not None: self.citation_list.export(outfile, level, namespace_, name_='citation_list', pretty_print=pretty_print) if self.emdb_list is not None: self.emdb_list.export(outfile, level, namespace_, name_='emdb_list', pretty_print=pretty_print) if self.pdb_list is not None: self.pdb_list.export(outfile, level, namespace_, name_='pdb_list', pretty_print=pretty_print) if self.auxiliary_link_list is not None: self.auxiliary_link_list.export(outfile, level, namespace_, name_='auxiliary_link_list', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'citation_list': obj_ = citation_listType.factory() obj_.build(child_) self.citation_list = obj_ obj_.original_tagname_ = 'citation_list' elif nodeName_ == 'emdb_list': obj_ = emdb_cross_reference_list_type.factory() obj_.build(child_) self.emdb_list = obj_ obj_.original_tagname_ = 'emdb_list' elif nodeName_ == 'pdb_list': obj_ = pdb_cross_reference_list_type.factory() obj_.build(child_) self.pdb_list = obj_ obj_.original_tagname_ = 'pdb_list' elif nodeName_ == 'auxiliary_link_list': obj_ = auxiliary_link_listType.factory() obj_.build(child_) self.auxiliary_link_list = obj_ obj_.original_tagname_ = 'auxiliary_link_list' # end class crossreferences_type
[docs]class citation_list_type(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if citation_list_type.subclass: return citation_list_type.subclass(*args_, **kwargs_) else: return citation_list_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='citation_list_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='citation_list_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='citation_list_type', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='citation_list_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='citation_list_type', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class citation_list_type
[docs]class emdb_cross_reference_type(GeneratedsSuper): """EMDB entries related to this entry""" member_data_items_ = [ MemberSpec_('id', 'xs:positiveInteger', 0), MemberSpec_('emdb_id', ['emdb_id_type', 'xs:token'], 0), MemberSpec_('relationship', 'relationshipType', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, id=None, emdb_id=None, relationship=None, details=None): self.original_tagname_ = None self.id = _cast(int, id) self.emdb_id = emdb_id self.validate_emdb_id_type(self.emdb_id) self.relationship = relationship self.details = details
[docs] def factory(*args_, **kwargs_): if emdb_cross_reference_type.subclass: return emdb_cross_reference_type.subclass(*args_, **kwargs_) else: return emdb_cross_reference_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_emdb_id(self): return self.emdb_id
[docs] def set_emdb_id(self, emdb_id): self.emdb_id = emdb_id
[docs] def get_relationship(self): return self.relationship
[docs] def set_relationship(self, relationship): self.relationship = relationship
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def get_id(self): return self.id
[docs] def set_id(self, id): self.id = id
[docs] def validate_emdb_id_type(self, value): # Validate type emdb_id_type, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_emdb_id_type_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_emdb_id_type_patterns_, ))
validate_emdb_id_type_patterns_ = [['^EMD-\\d{4,}$']]
[docs] def hasContent_(self): if ( self.emdb_id is not None or self.relationship is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='emdb_cross_reference_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='emdb_cross_reference_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='emdb_cross_reference_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='emdb_cross_reference_type'): if self.id is not None and 'id' not in already_processed: already_processed.add('id') outfile.write(' id="%s"' % self.gds_format_integer(self.id, input_name='id'))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='emdb_cross_reference_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.emdb_id is not None: showIndent(outfile, level, pretty_print) outfile.write('<%semdb_id>%s</%semdb_id>%s' % (namespace_, self.gds_format_string(quote_xml(self.emdb_id).encode(ExternalEncoding), input_name='emdb_id'), namespace_, eol_)) if self.relationship is not None: self.relationship.export(outfile, level, namespace_, name_='relationship', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('id', node) if value is not None and 'id' not in already_processed: already_processed.add('id') try: self.id = int(value) except ValueError as exp: raise_parse_error(node, 'Bad integer attribute: %s' % exp) if self.id <= 0: raise_parse_error(node, 'Invalid PositiveInteger')
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'emdb_id': emdb_id_ = child_.text emdb_id_ = re_.sub(String_cleanup_pat_, " ", emdb_id_).strip() emdb_id_ = self.gds_validate_string(emdb_id_, node, 'emdb_id') self.emdb_id = emdb_id_ # validate type emdb_id_type self.validate_emdb_id_type(self.emdb_id) elif nodeName_ == 'relationship': obj_ = relationshipType.factory() obj_.build(child_) self.relationship = obj_ obj_.original_tagname_ = 'relationship' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class emdb_cross_reference_type
[docs]class emdb_cross_reference_list_type(GeneratedsSuper): """List of related EMDB entries Maybe it can be combined with pdbReference into one datatype.""" member_data_items_ = [ MemberSpec_('emdb_reference', 'emdb_cross_reference_type', 1), ] subclass = None superclass = None def __init__(self, emdb_reference=None): self.original_tagname_ = None if emdb_reference is None: self.emdb_reference = [] else: self.emdb_reference = emdb_reference
[docs] def factory(*args_, **kwargs_): if emdb_cross_reference_list_type.subclass: return emdb_cross_reference_list_type.subclass(*args_, **kwargs_) else: return emdb_cross_reference_list_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_emdb_reference(self): return self.emdb_reference
[docs] def set_emdb_reference(self, emdb_reference): self.emdb_reference = emdb_reference
[docs] def add_emdb_reference(self, value): self.emdb_reference.append(value)
[docs] def insert_emdb_reference_at(self, index, value): self.emdb_reference.insert(index, value)
[docs] def replace_emdb_reference_at(self, index, value): self.emdb_reference[index] = value
[docs] def hasContent_(self): if ( self.emdb_reference ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='emdb_cross_reference_list_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='emdb_cross_reference_list_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='emdb_cross_reference_list_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='emdb_cross_reference_list_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='emdb_cross_reference_list_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for emdb_reference_ in self.emdb_reference: emdb_reference_.export(outfile, level, namespace_, name_='emdb_reference', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'emdb_reference': obj_ = emdb_cross_reference_type.factory() obj_.build(child_) self.emdb_reference.append(obj_) obj_.original_tagname_ = 'emdb_reference' # end class emdb_cross_reference_list_type
[docs]class pdb_cross_reference_type(GeneratedsSuper): """PDB entries related to this entry. The chainID list can be used to specify which specific chains are related to this map.""" member_data_items_ = [ MemberSpec_('id', 'xs:positiveInteger', 0), MemberSpec_('pdb_id', ['pdb_code_type', 'xs:token'], 0), MemberSpec_('relationship', 'relationshipType1', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, id=None, pdb_id=None, relationship=None, details=None): self.original_tagname_ = None self.id = _cast(int, id) self.pdb_id = pdb_id self.validate_pdb_code_type(self.pdb_id) self.relationship = relationship self.details = details
[docs] def factory(*args_, **kwargs_): if pdb_cross_reference_type.subclass: return pdb_cross_reference_type.subclass(*args_, **kwargs_) else: return pdb_cross_reference_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_pdb_id(self): return self.pdb_id
[docs] def set_pdb_id(self, pdb_id): self.pdb_id = pdb_id
[docs] def get_relationship(self): return self.relationship
[docs] def set_relationship(self, relationship): self.relationship = relationship
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def get_id(self): return self.id
[docs] def set_id(self, id): self.id = id
[docs] def validate_pdb_code_type(self, value): # Validate type pdb_code_type, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_pdb_code_type_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_pdb_code_type_patterns_, ))
validate_pdb_code_type_patterns_ = [['^\\d[\\dA-Za-z]{3}$']]
[docs] def hasContent_(self): if ( self.pdb_id is not None or self.relationship is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='pdb_cross_reference_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='pdb_cross_reference_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='pdb_cross_reference_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='pdb_cross_reference_type'): if self.id is not None and 'id' not in already_processed: already_processed.add('id') outfile.write(' id="%s"' % self.gds_format_integer(self.id, input_name='id'))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='pdb_cross_reference_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.pdb_id is not None: showIndent(outfile, level, pretty_print) outfile.write('<%spdb_id>%s</%spdb_id>%s' % (namespace_, self.gds_format_string(quote_xml(self.pdb_id).encode(ExternalEncoding), input_name='pdb_id'), namespace_, eol_)) if self.relationship is not None: self.relationship.export(outfile, level, namespace_, name_='relationship', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('id', node) if value is not None and 'id' not in already_processed: already_processed.add('id') try: self.id = int(value) except ValueError as exp: raise_parse_error(node, 'Bad integer attribute: %s' % exp) if self.id <= 0: raise_parse_error(node, 'Invalid PositiveInteger')
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'pdb_id': pdb_id_ = child_.text pdb_id_ = re_.sub(String_cleanup_pat_, " ", pdb_id_).strip() pdb_id_ = self.gds_validate_string(pdb_id_, node, 'pdb_id') self.pdb_id = pdb_id_ # validate type pdb_code_type self.validate_pdb_code_type(self.pdb_id) elif nodeName_ == 'relationship': obj_ = relationshipType1.factory() obj_.build(child_) self.relationship = obj_ obj_.original_tagname_ = 'relationship' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class pdb_cross_reference_type
[docs]class pdb_cross_reference_list_type(GeneratedsSuper): """List of related PDB entries""" member_data_items_ = [ MemberSpec_('pdb_reference', 'pdb_cross_reference_type', 1), ] subclass = None superclass = None def __init__(self, pdb_reference=None): self.original_tagname_ = None if pdb_reference is None: self.pdb_reference = [] else: self.pdb_reference = pdb_reference
[docs] def factory(*args_, **kwargs_): if pdb_cross_reference_list_type.subclass: return pdb_cross_reference_list_type.subclass(*args_, **kwargs_) else: return pdb_cross_reference_list_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_pdb_reference(self): return self.pdb_reference
[docs] def set_pdb_reference(self, pdb_reference): self.pdb_reference = pdb_reference
[docs] def add_pdb_reference(self, value): self.pdb_reference.append(value)
[docs] def insert_pdb_reference_at(self, index, value): self.pdb_reference.insert(index, value)
[docs] def replace_pdb_reference_at(self, index, value): self.pdb_reference[index] = value
[docs] def hasContent_(self): if ( self.pdb_reference ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='pdb_cross_reference_list_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='pdb_cross_reference_list_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='pdb_cross_reference_list_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='pdb_cross_reference_list_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='pdb_cross_reference_list_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for pdb_reference_ in self.pdb_reference: pdb_reference_.export(outfile, level, namespace_, name_='pdb_reference', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'pdb_reference': obj_ = pdb_cross_reference_type.factory() obj_.build(child_) self.pdb_reference.append(obj_) obj_.original_tagname_ = 'pdb_reference' # end class pdb_cross_reference_list_type
[docs]class structure_determination_type(GeneratedsSuper): """Unique identifier that will allow the DA system to be refactored in terms of experiments rather than maps. Can be autogenerated unless user wants to specify a previously existing one.""" member_data_items_ = [ MemberSpec_('id', 'xs:positiveInteger', 0), MemberSpec_('method', ['methodType', 'xs:token'], 0), MemberSpec_('aggregation_state', ['aggregation_stateType', 'xs:token'], 0), MemberSpec_('macromolecules_and_complexes', 'macromolecules_and_complexes_type', 0), MemberSpec_('specimen_preparation_list', 'specimen_preparation_listType', 0), MemberSpec_('microscopy_list', 'microscopy_listType', 0), MemberSpec_('image_processing', 'base_processing_type', 1), ] subclass = None superclass = None def __init__(self, id=None, method=None, aggregation_state=None, macromolecules_and_complexes=None, specimen_preparation_list=None, microscopy_list=None, image_processing=None): self.original_tagname_ = None self.id = _cast(int, id) self.method = method self.validate_methodType(self.method) self.aggregation_state = aggregation_state self.validate_aggregation_stateType(self.aggregation_state) self.macromolecules_and_complexes = macromolecules_and_complexes self.specimen_preparation_list = specimen_preparation_list self.microscopy_list = microscopy_list if image_processing is None: self.image_processing = [] else: self.image_processing = image_processing
[docs] def factory(*args_, **kwargs_): if structure_determination_type.subclass: return structure_determination_type.subclass(*args_, **kwargs_) else: return structure_determination_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_method(self): return self.method
[docs] def set_method(self, method): self.method = method
[docs] def get_aggregation_state(self): return self.aggregation_state
[docs] def set_aggregation_state(self, aggregation_state): self.aggregation_state = aggregation_state
[docs] def get_macromolecules_and_complexes(self): return self.macromolecules_and_complexes
[docs] def set_macromolecules_and_complexes(self, macromolecules_and_complexes): self.macromolecules_and_complexes = macromolecules_and_complexes
[docs] def get_specimen_preparation_list(self): return self.specimen_preparation_list
[docs] def set_specimen_preparation_list(self, specimen_preparation_list): self.specimen_preparation_list = specimen_preparation_list
[docs] def get_microscopy_list(self): return self.microscopy_list
[docs] def set_microscopy_list(self, microscopy_list): self.microscopy_list = microscopy_list
[docs] def get_image_processing(self): return self.image_processing
[docs] def set_image_processing(self, image_processing): self.image_processing = image_processing
[docs] def add_image_processing(self, value): self.image_processing.append(value)
[docs] def insert_image_processing_at(self, index, value): self.image_processing.insert(index, value)
[docs] def replace_image_processing_at(self, index, value): self.image_processing[index] = value
[docs] def get_id(self): return self.id
[docs] def set_id(self, id): self.id = id
[docs] def validate_methodType(self, value): # Validate type methodType, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['singleParticle', 'subtomogramAveraging', 'tomography', 'electronCrystallography', 'helical'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on methodType' % {"value" : value.encode("utf-8")} )
[docs] def validate_aggregation_stateType(self, value): # Validate type aggregation_stateType, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['particle', 'filament', 'twoDArray', 'threeDArray', 'helicalArray', 'cell', 'tissue'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on aggregation_stateType' % {"value" : value.encode("utf-8")} )
[docs] def hasContent_(self): if ( self.method is not None or self.aggregation_state is not None or self.macromolecules_and_complexes is not None or self.specimen_preparation_list is not None or self.microscopy_list is not None or self.image_processing ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='structure_determination_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='structure_determination_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='structure_determination_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='structure_determination_type'): if self.id is not None and 'id' not in already_processed: already_processed.add('id') outfile.write(' id="%s"' % self.gds_format_integer(self.id, input_name='id'))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='structure_determination_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.method is not None: showIndent(outfile, level, pretty_print) outfile.write('<%smethod>%s</%smethod>%s' % (namespace_, self.gds_format_string(quote_xml(self.method).encode(ExternalEncoding), input_name='method'), namespace_, eol_)) if self.aggregation_state is not None: showIndent(outfile, level, pretty_print) outfile.write('<%saggregation_state>%s</%saggregation_state>%s' % (namespace_, self.gds_format_string(quote_xml(self.aggregation_state).encode(ExternalEncoding), input_name='aggregation_state'), namespace_, eol_)) if self.macromolecules_and_complexes is not None: self.macromolecules_and_complexes.export(outfile, level, namespace_, name_='macromolecules_and_complexes', pretty_print=pretty_print) if self.specimen_preparation_list is not None: self.specimen_preparation_list.export(outfile, level, namespace_, name_='specimen_preparation_list', pretty_print=pretty_print) if self.microscopy_list is not None: self.microscopy_list.export(outfile, level, namespace_, name_='microscopy_list', pretty_print=pretty_print) for image_processing_ in self.image_processing: image_processing_.export(outfile, level, namespace_, name_='image_processing', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('id', node) if value is not None and 'id' not in already_processed: already_processed.add('id') try: self.id = int(value) except ValueError as exp: raise_parse_error(node, 'Bad integer attribute: %s' % exp) if self.id <= 0: raise_parse_error(node, 'Invalid PositiveInteger')
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'method': method_ = child_.text method_ = re_.sub(String_cleanup_pat_, " ", method_).strip() method_ = self.gds_validate_string(method_, node, 'method') self.method = method_ # validate type methodType self.validate_methodType(self.method) elif nodeName_ == 'aggregation_state': aggregation_state_ = child_.text aggregation_state_ = re_.sub(String_cleanup_pat_, " ", aggregation_state_).strip() aggregation_state_ = self.gds_validate_string(aggregation_state_, node, 'aggregation_state') self.aggregation_state = aggregation_state_ # validate type aggregation_stateType self.validate_aggregation_stateType(self.aggregation_state) elif nodeName_ == 'macromolecules_and_complexes': obj_ = macromolecules_and_complexes_type.factory() obj_.build(child_) self.macromolecules_and_complexes = obj_ obj_.original_tagname_ = 'macromolecules_and_complexes' elif nodeName_ == 'specimen_preparation_list': obj_ = specimen_preparation_listType.factory() obj_.build(child_) self.specimen_preparation_list = obj_ obj_.original_tagname_ = 'specimen_preparation_list' elif nodeName_ == 'microscopy_list': obj_ = microscopy_listType.factory() obj_.build(child_) self.microscopy_list = obj_ obj_.original_tagname_ = 'microscopy_list' elif nodeName_ == 'image_processing': type_name_ = child_.attrib.get( '{http://www.w3.org/2001/XMLSchema-instance}type') if type_name_ is None: type_name_ = child_.attrib.get('type') if type_name_ is not None: type_names_ = type_name_.split(':') if len(type_names_) == 1: type_name_ = type_names_[0] else: type_name_ = type_names_[1] class_ = globals()[type_name_] obj_ = class_.factory() obj_.build(child_) else: raise NotImplementedError( 'Class not implemented for <image_processing> element') self.image_processing.append(obj_) obj_.original_tagname_ = 'image_processing' elif nodeName_ == 'singleparticle_processing': obj_ = singleparticle_processing_type.factory() obj_.build(child_) self.image_processing.append(obj_) obj_.original_tagname_ = 'singleparticle_processing' elif nodeName_ == 'subtomogram_averaging_processing': obj_ = subtomogram_averaging_processing_type.factory() obj_.build(child_) self.image_processing.append(obj_) obj_.original_tagname_ = 'subtomogram_averaging_processing' elif nodeName_ == 'tomography_processing': obj_ = tomography_processing_type.factory() obj_.build(child_) self.image_processing.append(obj_) obj_.original_tagname_ = 'tomography_processing' elif nodeName_ == 'crystallography_processing': obj_ = crystallography_processing_type.factory() obj_.build(child_) self.image_processing.append(obj_) obj_.original_tagname_ = 'crystallography_processing' elif nodeName_ == 'helical_processing': obj_ = helical_processing_type.factory() obj_.build(child_) self.image_processing.append(obj_) obj_.original_tagname_ = 'helical_processing' # end class structure_determination_type
[docs]class sample_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('name', 'xs:token', 0), MemberSpec_('supramolecule_list', 'supramolecule_listType', 0), MemberSpec_('macromolecule_list', 'macromolecule_list_type', 0), ] subclass = None superclass = None def __init__(self, name=None, supramolecule_list=None, macromolecule_list=None): self.original_tagname_ = None self.name = name self.supramolecule_list = supramolecule_list self.macromolecule_list = macromolecule_list
[docs] def factory(*args_, **kwargs_): if sample_type.subclass: return sample_type.subclass(*args_, **kwargs_) else: return sample_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_name(self): return self.name
[docs] def set_name(self, name): self.name = name
[docs] def get_supramolecule_list(self): return self.supramolecule_list
[docs] def set_supramolecule_list(self, supramolecule_list): self.supramolecule_list = supramolecule_list
[docs] def get_macromolecule_list(self): return self.macromolecule_list
[docs] def set_macromolecule_list(self, macromolecule_list): self.macromolecule_list = macromolecule_list
[docs] def hasContent_(self): if ( self.name is not None or self.supramolecule_list is not None or self.macromolecule_list is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='sample_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='sample_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='sample_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='sample_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='sample_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.name is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sname>%s</%sname>%s' % (namespace_, self.gds_format_string(quote_xml(self.name).encode(ExternalEncoding), input_name='name'), namespace_, eol_)) if self.supramolecule_list is not None: self.supramolecule_list.export(outfile, level, namespace_, name_='supramolecule_list', pretty_print=pretty_print) if self.macromolecule_list is not None: self.macromolecule_list.export(outfile, level, namespace_, name_='macromolecule_list', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'name': name_ = child_.text name_ = re_.sub(String_cleanup_pat_, " ", name_).strip() name_ = self.gds_validate_string(name_, node, 'name') self.name = name_ elif nodeName_ == 'supramolecule_list': obj_ = supramolecule_listType.factory() obj_.build(child_) self.supramolecule_list = obj_ obj_.original_tagname_ = 'supramolecule_list' elif nodeName_ == 'macromolecule_list': obj_ = macromolecule_list_type.factory() obj_.build(child_) self.macromolecule_list = obj_ obj_.original_tagname_ = 'macromolecule_list' # end class sample_type
[docs]class particle_selection_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('number_particles_selected', 'xs:positiveInteger', 0), MemberSpec_('reference_model', 'xs:token', 0), MemberSpec_('method', 'xs:string', 0), MemberSpec_('software_list', 'software_list_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, number_particles_selected=None, reference_model=None, method=None, software_list=None, details=None): self.original_tagname_ = None self.number_particles_selected = number_particles_selected self.reference_model = reference_model self.method = method self.software_list = software_list self.details = details
[docs] def factory(*args_, **kwargs_): if particle_selection_type.subclass: return particle_selection_type.subclass(*args_, **kwargs_) else: return particle_selection_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_number_particles_selected(self): return self.number_particles_selected
[docs] def set_number_particles_selected(self, number_particles_selected): self.number_particles_selected = number_particles_selected
[docs] def get_reference_model(self): return self.reference_model
[docs] def set_reference_model(self, reference_model): self.reference_model = reference_model
[docs] def get_method(self): return self.method
[docs] def set_method(self, method): self.method = method
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def hasContent_(self): if ( self.number_particles_selected is not None or self.reference_model is not None or self.method is not None or self.software_list is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='particle_selection_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='particle_selection_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='particle_selection_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='particle_selection_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='particle_selection_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.number_particles_selected is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_particles_selected>%s</%snumber_particles_selected>%s' % (namespace_, self.gds_format_integer(self.number_particles_selected, input_name='number_particles_selected'), namespace_, eol_)) if self.reference_model is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sreference_model>%s</%sreference_model>%s' % (namespace_, self.gds_format_string(quote_xml(self.reference_model).encode(ExternalEncoding), input_name='reference_model'), namespace_, eol_)) if self.method is not None: showIndent(outfile, level, pretty_print) outfile.write('<%smethod>%s</%smethod>%s' % (namespace_, self.gds_format_string(quote_xml(self.method).encode(ExternalEncoding), input_name='method'), namespace_, eol_)) if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'number_particles_selected': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'number_particles_selected') self.number_particles_selected = ival_ elif nodeName_ == 'reference_model': reference_model_ = child_.text reference_model_ = re_.sub(String_cleanup_pat_, " ", reference_model_).strip() reference_model_ = self.gds_validate_string(reference_model_, node, 'reference_model') self.reference_model = reference_model_ elif nodeName_ == 'method': method_ = child_.text method_ = self.gds_validate_string(method_, node, 'method') self.method = method_ elif nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class particle_selection_type
[docs]class grid_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('model', ['modelType', 'xs:token'], 0), MemberSpec_('material', ['materialType', 'xs:token'], 0), MemberSpec_('mesh', 'xs:positiveInteger', 0), MemberSpec_('support_film', 'film_type', 1), MemberSpec_('glow_discharge', 'glow_dischargeType', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, model=None, material=None, mesh=None, support_film=None, glow_discharge=None, details=None): self.original_tagname_ = None self.model = model self.validate_modelType(self.model) self.material = material self.validate_materialType(self.material) self.mesh = mesh if support_film is None: self.support_film = [] else: self.support_film = support_film self.glow_discharge = glow_discharge self.details = details
[docs] def factory(*args_, **kwargs_): if grid_type.subclass: return grid_type.subclass(*args_, **kwargs_) else: return grid_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_model(self): return self.model
[docs] def set_model(self, model): self.model = model
[docs] def get_material(self): return self.material
[docs] def set_material(self, material): self.material = material
[docs] def get_mesh(self): return self.mesh
[docs] def set_mesh(self, mesh): self.mesh = mesh
[docs] def get_support_film(self): return self.support_film
[docs] def set_support_film(self, support_film): self.support_film = support_film
[docs] def add_support_film(self, value): self.support_film.append(value)
[docs] def insert_support_film_at(self, index, value): self.support_film.insert(index, value)
[docs] def replace_support_film_at(self, index, value): self.support_film[index] = value
[docs] def get_glow_discharge(self): return self.glow_discharge
[docs] def set_glow_discharge(self, glow_discharge): self.glow_discharge = glow_discharge
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def validate_modelType(self, value): # Validate type modelType, a restriction on xs:token. if value is not None and Validate_simpletypes_: pass
[docs] def validate_materialType(self, value): # Validate type materialType, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['GOLD', 'COPPER', 'MOLYBDENUM'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on materialType' % {"value" : value.encode("utf-8")} )
[docs] def hasContent_(self): if ( self.model is not None or self.material is not None or self.mesh is not None or self.support_film or self.glow_discharge is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='grid_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='grid_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='grid_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='grid_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='grid_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.model is not None: showIndent(outfile, level, pretty_print) outfile.write('<%smodel>%s</%smodel>%s' % (namespace_, self.gds_format_string(quote_xml(self.model).encode(ExternalEncoding), input_name='model'), namespace_, eol_)) if self.material is not None: showIndent(outfile, level, pretty_print) outfile.write('<%smaterial>%s</%smaterial>%s' % (namespace_, self.gds_format_string(quote_xml(self.material).encode(ExternalEncoding), input_name='material'), namespace_, eol_)) if self.mesh is not None: showIndent(outfile, level, pretty_print) outfile.write('<%smesh>%s</%smesh>%s' % (namespace_, self.gds_format_integer(self.mesh, input_name='mesh'), namespace_, eol_)) for support_film_ in self.support_film: support_film_.export(outfile, level, namespace_, name_='support_film', pretty_print=pretty_print) if self.glow_discharge is not None: self.glow_discharge.export(outfile, level, namespace_, name_='glow_discharge', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'model': model_ = child_.text model_ = re_.sub(String_cleanup_pat_, " ", model_).strip() model_ = self.gds_validate_string(model_, node, 'model') self.model = model_ # validate type modelType self.validate_modelType(self.model) elif nodeName_ == 'material': material_ = child_.text material_ = re_.sub(String_cleanup_pat_, " ", material_).strip() material_ = self.gds_validate_string(material_, node, 'material') self.material = material_ # validate type materialType self.validate_materialType(self.material) elif nodeName_ == 'mesh': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'mesh') self.mesh = ival_ elif nodeName_ == 'support_film': obj_ = film_type.factory() obj_.build(child_) self.support_film.append(obj_) obj_.original_tagname_ = 'support_film' elif nodeName_ == 'glow_discharge': obj_ = glow_dischargeType.factory() obj_.build(child_) self.glow_discharge = obj_ obj_.original_tagname_ = 'glow_discharge' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class grid_type
[docs]class glow_discharge_params_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('time', 'timeType', 0), MemberSpec_('atmosphere', ['atmosphereType', 'xs:token'], 0), MemberSpec_('pressure', 'pressureType', 0), ] subclass = None superclass = None def __init__(self, time=None, atmosphere=None, pressure=None): self.original_tagname_ = None self.time = time self.atmosphere = atmosphere self.validate_atmosphereType(self.atmosphere) self.pressure = pressure
[docs] def factory(*args_, **kwargs_): if glow_discharge_params_type.subclass: return glow_discharge_params_type.subclass(*args_, **kwargs_) else: return glow_discharge_params_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_time(self): return self.time
[docs] def set_time(self, time): self.time = time
[docs] def get_atmosphere(self): return self.atmosphere
[docs] def set_atmosphere(self, atmosphere): self.atmosphere = atmosphere
[docs] def get_pressure(self): return self.pressure
[docs] def set_pressure(self, pressure): self.pressure = pressure
[docs] def validate_atmosphereType(self, value): # Validate type atmosphereType, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['AIR', 'AMYLAMINE'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on atmosphereType' % {"value" : value.encode("utf-8")} )
[docs] def hasContent_(self): if ( self.time is not None or self.atmosphere is not None or self.pressure is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='glow_discharge_params_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='glow_discharge_params_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='glow_discharge_params_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='glow_discharge_params_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='glow_discharge_params_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.time is not None: self.time.export(outfile, level, namespace_, name_='time', pretty_print=pretty_print) if self.atmosphere is not None: showIndent(outfile, level, pretty_print) outfile.write('<%satmosphere>%s</%satmosphere>%s' % (namespace_, self.gds_format_string(quote_xml(self.atmosphere).encode(ExternalEncoding), input_name='atmosphere'), namespace_, eol_)) if self.pressure is not None: self.pressure.export(outfile, level, namespace_, name_='pressure', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'time': obj_ = timeType.factory() obj_.build(child_) self.time = obj_ obj_.original_tagname_ = 'time' elif nodeName_ == 'atmosphere': atmosphere_ = child_.text atmosphere_ = re_.sub(String_cleanup_pat_, " ", atmosphere_).strip() atmosphere_ = self.gds_validate_string(atmosphere_, node, 'atmosphere') self.atmosphere = atmosphere_ # validate type atmosphereType self.validate_atmosphereType(self.atmosphere) elif nodeName_ == 'pressure': obj_ = pressureType.factory() obj_.build(child_) self.pressure = obj_ obj_.original_tagname_ = 'pressure' # end class glow_discharge_params_type
[docs]class stain_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('ammonium_molybdate', 'xs:string', 0), MemberSpec_('uranyl_acetate', 'xs:string', 0), MemberSpec_('uranyl_formate', 'xs:string', 0), MemberSpec_('phophotungstic_acid', 'xs:string', 0), MemberSpec_('osmium_tetroxide', 'xs:string', 0), MemberSpec_('osmium_ferricyanide', 'xs:string', 0), MemberSpec_('auro_glucothionate', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, ammonium_molybdate=None, uranyl_acetate=None, uranyl_formate=None, phophotungstic_acid=None, osmium_tetroxide=None, osmium_ferricyanide=None, auro_glucothionate=None): self.original_tagname_ = None self.ammonium_molybdate = ammonium_molybdate self.uranyl_acetate = uranyl_acetate self.uranyl_formate = uranyl_formate self.phophotungstic_acid = phophotungstic_acid self.osmium_tetroxide = osmium_tetroxide self.osmium_ferricyanide = osmium_ferricyanide self.auro_glucothionate = auro_glucothionate
[docs] def factory(*args_, **kwargs_): if stain_type.subclass: return stain_type.subclass(*args_, **kwargs_) else: return stain_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_ammonium_molybdate(self): return self.ammonium_molybdate
[docs] def set_ammonium_molybdate(self, ammonium_molybdate): self.ammonium_molybdate = ammonium_molybdate
[docs] def get_uranyl_acetate(self): return self.uranyl_acetate
[docs] def set_uranyl_acetate(self, uranyl_acetate): self.uranyl_acetate = uranyl_acetate
[docs] def get_uranyl_formate(self): return self.uranyl_formate
[docs] def set_uranyl_formate(self, uranyl_formate): self.uranyl_formate = uranyl_formate
[docs] def get_phophotungstic_acid(self): return self.phophotungstic_acid
[docs] def set_phophotungstic_acid(self, phophotungstic_acid): self.phophotungstic_acid = phophotungstic_acid
[docs] def get_osmium_tetroxide(self): return self.osmium_tetroxide
[docs] def set_osmium_tetroxide(self, osmium_tetroxide): self.osmium_tetroxide = osmium_tetroxide
[docs] def get_osmium_ferricyanide(self): return self.osmium_ferricyanide
[docs] def set_osmium_ferricyanide(self, osmium_ferricyanide): self.osmium_ferricyanide = osmium_ferricyanide
[docs] def get_auro_glucothionate(self): return self.auro_glucothionate
[docs] def set_auro_glucothionate(self, auro_glucothionate): self.auro_glucothionate = auro_glucothionate
[docs] def hasContent_(self): if ( self.ammonium_molybdate is not None or self.uranyl_acetate is not None or self.uranyl_formate is not None or self.phophotungstic_acid is not None or self.osmium_tetroxide is not None or self.osmium_ferricyanide is not None or self.auro_glucothionate is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='stain_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='stain_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='stain_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='stain_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='stain_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.ammonium_molybdate is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sammonium_molybdate>%s</%sammonium_molybdate>%s' % (namespace_, self.gds_format_string(quote_xml(self.ammonium_molybdate).encode(ExternalEncoding), input_name='ammonium_molybdate'), namespace_, eol_)) if self.uranyl_acetate is not None: showIndent(outfile, level, pretty_print) outfile.write('<%suranyl_acetate>%s</%suranyl_acetate>%s' % (namespace_, self.gds_format_string(quote_xml(self.uranyl_acetate).encode(ExternalEncoding), input_name='uranyl_acetate'), namespace_, eol_)) if self.uranyl_formate is not None: showIndent(outfile, level, pretty_print) outfile.write('<%suranyl_formate>%s</%suranyl_formate>%s' % (namespace_, self.gds_format_string(quote_xml(self.uranyl_formate).encode(ExternalEncoding), input_name='uranyl_formate'), namespace_, eol_)) if self.phophotungstic_acid is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sphophotungstic_acid>%s</%sphophotungstic_acid>%s' % (namespace_, self.gds_format_string(quote_xml(self.phophotungstic_acid).encode(ExternalEncoding), input_name='phophotungstic_acid'), namespace_, eol_)) if self.osmium_tetroxide is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sosmium_tetroxide>%s</%sosmium_tetroxide>%s' % (namespace_, self.gds_format_string(quote_xml(self.osmium_tetroxide).encode(ExternalEncoding), input_name='osmium_tetroxide'), namespace_, eol_)) if self.osmium_ferricyanide is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sosmium_ferricyanide>%s</%sosmium_ferricyanide>%s' % (namespace_, self.gds_format_string(quote_xml(self.osmium_ferricyanide).encode(ExternalEncoding), input_name='osmium_ferricyanide'), namespace_, eol_)) if self.auro_glucothionate is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sauro_glucothionate>%s</%sauro_glucothionate>%s' % (namespace_, self.gds_format_string(quote_xml(self.auro_glucothionate).encode(ExternalEncoding), input_name='auro_glucothionate'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'ammonium_molybdate': ammonium_molybdate_ = child_.text ammonium_molybdate_ = self.gds_validate_string(ammonium_molybdate_, node, 'ammonium_molybdate') self.ammonium_molybdate = ammonium_molybdate_ elif nodeName_ == 'uranyl_acetate': uranyl_acetate_ = child_.text uranyl_acetate_ = self.gds_validate_string(uranyl_acetate_, node, 'uranyl_acetate') self.uranyl_acetate = uranyl_acetate_ elif nodeName_ == 'uranyl_formate': uranyl_formate_ = child_.text uranyl_formate_ = self.gds_validate_string(uranyl_formate_, node, 'uranyl_formate') self.uranyl_formate = uranyl_formate_ elif nodeName_ == 'phophotungstic_acid': phophotungstic_acid_ = child_.text phophotungstic_acid_ = self.gds_validate_string(phophotungstic_acid_, node, 'phophotungstic_acid') self.phophotungstic_acid = phophotungstic_acid_ elif nodeName_ == 'osmium_tetroxide': osmium_tetroxide_ = child_.text osmium_tetroxide_ = self.gds_validate_string(osmium_tetroxide_, node, 'osmium_tetroxide') self.osmium_tetroxide = osmium_tetroxide_ elif nodeName_ == 'osmium_ferricyanide': osmium_ferricyanide_ = child_.text osmium_ferricyanide_ = self.gds_validate_string(osmium_ferricyanide_, node, 'osmium_ferricyanide') self.osmium_ferricyanide = osmium_ferricyanide_ elif nodeName_ == 'auro_glucothionate': auro_glucothionate_ = child_.text auro_glucothionate_ = self.gds_validate_string(auro_glucothionate_, node, 'auro_glucothionate') self.auro_glucothionate = auro_glucothionate_ # end class stain_type
[docs]class ammonium_molybdate(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if ammonium_molybdate.subclass: return ammonium_molybdate.subclass(*args_, **kwargs_) else: return ammonium_molybdate(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='ammonium_molybdate', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='ammonium_molybdate') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='ammonium_molybdate', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='ammonium_molybdate'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='ammonium_molybdate', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class ammonium_molybdate
[docs]class uranyl_acetate(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if uranyl_acetate.subclass: return uranyl_acetate.subclass(*args_, **kwargs_) else: return uranyl_acetate(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='uranyl_acetate', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='uranyl_acetate') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='uranyl_acetate', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='uranyl_acetate'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='uranyl_acetate', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class uranyl_acetate
[docs]class uranyl_formate(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if uranyl_formate.subclass: return uranyl_formate.subclass(*args_, **kwargs_) else: return uranyl_formate(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='uranyl_formate', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='uranyl_formate') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='uranyl_formate', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='uranyl_formate'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='uranyl_formate', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class uranyl_formate
[docs]class phophotungstic_acid(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if phophotungstic_acid.subclass: return phophotungstic_acid.subclass(*args_, **kwargs_) else: return phophotungstic_acid(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='phophotungstic_acid', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='phophotungstic_acid') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='phophotungstic_acid', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='phophotungstic_acid'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='phophotungstic_acid', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class phophotungstic_acid
[docs]class osmium_tetroxide(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if osmium_tetroxide.subclass: return osmium_tetroxide.subclass(*args_, **kwargs_) else: return osmium_tetroxide(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='osmium_tetroxide', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='osmium_tetroxide') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='osmium_tetroxide', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='osmium_tetroxide'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='osmium_tetroxide', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class osmium_tetroxide
[docs]class osmium_ferricyanide(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if osmium_ferricyanide.subclass: return osmium_ferricyanide.subclass(*args_, **kwargs_) else: return osmium_ferricyanide(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='osmium_ferricyanide', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='osmium_ferricyanide') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='osmium_ferricyanide', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='osmium_ferricyanide'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='osmium_ferricyanide', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class osmium_ferricyanide
[docs]class auro_glucothionate(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if auro_glucothionate.subclass: return auro_glucothionate.subclass(*args_, **kwargs_) else: return auro_glucothionate(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='auro_glucothionate', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='auro_glucothionate') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='auro_glucothionate', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='auro_glucothionate'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='auro_glucothionate', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class auro_glucothionate
[docs]class specialist_optics_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('phase_plate', 'xs:token', 0), MemberSpec_('sph_aberration_corrector', 'xs:token', 0), MemberSpec_('chr_aberration_corrector', 'xs:token', 0), MemberSpec_('energy_filter', 'energy_filterType', 0), ] subclass = None superclass = None def __init__(self, phase_plate=None, sph_aberration_corrector=None, chr_aberration_corrector=None, energy_filter=None): self.original_tagname_ = None self.phase_plate = phase_plate self.sph_aberration_corrector = sph_aberration_corrector self.chr_aberration_corrector = chr_aberration_corrector self.energy_filter = energy_filter
[docs] def factory(*args_, **kwargs_): if specialist_optics_type.subclass: return specialist_optics_type.subclass(*args_, **kwargs_) else: return specialist_optics_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_phase_plate(self): return self.phase_plate
[docs] def set_phase_plate(self, phase_plate): self.phase_plate = phase_plate
[docs] def get_sph_aberration_corrector(self): return self.sph_aberration_corrector
[docs] def set_sph_aberration_corrector(self, sph_aberration_corrector): self.sph_aberration_corrector = sph_aberration_corrector
[docs] def get_chr_aberration_corrector(self): return self.chr_aberration_corrector
[docs] def set_chr_aberration_corrector(self, chr_aberration_corrector): self.chr_aberration_corrector = chr_aberration_corrector
[docs] def get_energy_filter(self): return self.energy_filter
[docs] def set_energy_filter(self, energy_filter): self.energy_filter = energy_filter
[docs] def hasContent_(self): if ( self.phase_plate is not None or self.sph_aberration_corrector is not None or self.chr_aberration_corrector is not None or self.energy_filter is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='specialist_optics_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='specialist_optics_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='specialist_optics_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='specialist_optics_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='specialist_optics_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.phase_plate is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sphase_plate>%s</%sphase_plate>%s' % (namespace_, self.gds_format_string(quote_xml(self.phase_plate).encode(ExternalEncoding), input_name='phase_plate'), namespace_, eol_)) if self.sph_aberration_corrector is not None: showIndent(outfile, level, pretty_print) outfile.write('<%ssph_aberration_corrector>%s</%ssph_aberration_corrector>%s' % (namespace_, self.gds_format_string(quote_xml(self.sph_aberration_corrector).encode(ExternalEncoding), input_name='sph_aberration_corrector'), namespace_, eol_)) if self.chr_aberration_corrector is not None: showIndent(outfile, level, pretty_print) outfile.write('<%schr_aberration_corrector>%s</%schr_aberration_corrector>%s' % (namespace_, self.gds_format_string(quote_xml(self.chr_aberration_corrector).encode(ExternalEncoding), input_name='chr_aberration_corrector'), namespace_, eol_)) if self.energy_filter is not None: self.energy_filter.export(outfile, level, namespace_, name_='energy_filter', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'phase_plate': phase_plate_ = child_.text phase_plate_ = re_.sub(String_cleanup_pat_, " ", phase_plate_).strip() phase_plate_ = self.gds_validate_string(phase_plate_, node, 'phase_plate') self.phase_plate = phase_plate_ elif nodeName_ == 'sph_aberration_corrector': sph_aberration_corrector_ = child_.text sph_aberration_corrector_ = re_.sub(String_cleanup_pat_, " ", sph_aberration_corrector_).strip() sph_aberration_corrector_ = self.gds_validate_string(sph_aberration_corrector_, node, 'sph_aberration_corrector') self.sph_aberration_corrector = sph_aberration_corrector_ elif nodeName_ == 'chr_aberration_corrector': chr_aberration_corrector_ = child_.text chr_aberration_corrector_ = re_.sub(String_cleanup_pat_, " ", chr_aberration_corrector_).strip() chr_aberration_corrector_ = self.gds_validate_string(chr_aberration_corrector_, node, 'chr_aberration_corrector') self.chr_aberration_corrector = chr_aberration_corrector_ elif nodeName_ == 'energy_filter': obj_ = energy_filterType.factory() obj_.build(child_) self.energy_filter = obj_ obj_.original_tagname_ = 'energy_filter' # end class specialist_optics_type
[docs]class results_type(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if results_type.subclass: return results_type.subclass(*args_, **kwargs_) else: return results_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='results_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='results_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='results_type', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='results_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='results_type', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class results_type
[docs]class regexp_string(GeneratedsSuper): member_data_items_ = [ MemberSpec_('help_text', 'xs:string', 0), MemberSpec_('string', 'xs:string', 0), MemberSpec_('validation_list', 'validation_listType', 0), ] subclass = None superclass = None def __init__(self, help_text=None, string=None, validation_list=None): self.original_tagname_ = None self.help_text = help_text self.string = string self.validation_list = validation_list
[docs] def factory(*args_, **kwargs_): if regexp_string.subclass: return regexp_string.subclass(*args_, **kwargs_) else: return regexp_string(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_help_text(self): return self.help_text
[docs] def set_help_text(self, help_text): self.help_text = help_text
[docs] def get_string(self): return self.string
[docs] def set_string(self, string): self.string = string
[docs] def get_validation_list(self): return self.validation_list
[docs] def set_validation_list(self, validation_list): self.validation_list = validation_list
[docs] def hasContent_(self): if ( self.help_text is not None or self.string is not None or self.validation_list is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='regexp_string', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='regexp_string') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='regexp_string', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='regexp_string'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='regexp_string', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.help_text is not None: showIndent(outfile, level, pretty_print) outfile.write('<%shelp_text>%s</%shelp_text>%s' % (namespace_, self.gds_format_string(quote_xml(self.help_text).encode(ExternalEncoding), input_name='help_text'), namespace_, eol_)) if self.string is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sstring>%s</%sstring>%s' % (namespace_, self.gds_format_string(quote_xml(self.string).encode(ExternalEncoding), input_name='string'), namespace_, eol_)) if self.validation_list is not None: self.validation_list.export(outfile, level, namespace_, name_='validation_list', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'help_text': help_text_ = child_.text help_text_ = self.gds_validate_string(help_text_, node, 'help_text') self.help_text = help_text_ elif nodeName_ == 'string': string_ = child_.text string_ = self.gds_validate_string(string_, node, 'string') self.string = string_ elif nodeName_ == 'validation_list': obj_ = validation_listType.factory() obj_.build(child_) self.validation_list = obj_ obj_.original_tagname_ = 'validation_list' # end class regexp_string
[docs]class string_validation_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('regular_expression', 'xs:string', 0), MemberSpec_('enum', 'xs:string', 1), MemberSpec_('controlled_vocabulary_link', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, regular_expression=None, enum=None, controlled_vocabulary_link=None): self.original_tagname_ = None self.regular_expression = regular_expression if enum is None: self.enum = [] else: self.enum = enum self.controlled_vocabulary_link = controlled_vocabulary_link
[docs] def factory(*args_, **kwargs_): if string_validation_type.subclass: return string_validation_type.subclass(*args_, **kwargs_) else: return string_validation_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_regular_expression(self): return self.regular_expression
[docs] def set_regular_expression(self, regular_expression): self.regular_expression = regular_expression
[docs] def get_enum(self): return self.enum
[docs] def set_enum(self, enum): self.enum = enum
[docs] def add_enum(self, value): self.enum.append(value)
[docs] def insert_enum_at(self, index, value): self.enum.insert(index, value)
[docs] def replace_enum_at(self, index, value): self.enum[index] = value
[docs] def hasContent_(self): if ( self.regular_expression is not None or self.enum or self.controlled_vocabulary_link is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='string_validation_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='string_validation_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='string_validation_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='string_validation_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='string_validation_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.regular_expression is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sregular_expression>%s</%sregular_expression>%s' % (namespace_, self.gds_format_string(quote_xml(self.regular_expression).encode(ExternalEncoding), input_name='regular_expression'), namespace_, eol_)) for enum_ in self.enum: showIndent(outfile, level, pretty_print) outfile.write('<%senum>%s</%senum>%s' % (namespace_, self.gds_format_string(quote_xml(enum_).encode(ExternalEncoding), input_name='enum'), namespace_, eol_)) if self.controlled_vocabulary_link is not None: showIndent(outfile, level, pretty_print) outfile.write('<%scontrolled_vocabulary_link>%s</%scontrolled_vocabulary_link>%s' % (namespace_, self.gds_format_string(quote_xml(self.controlled_vocabulary_link).encode(ExternalEncoding), input_name='controlled_vocabulary_link'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'regular_expression': regular_expression_ = child_.text regular_expression_ = self.gds_validate_string(regular_expression_, node, 'regular_expression') self.regular_expression = regular_expression_ elif nodeName_ == 'enum': enum_ = child_.text enum_ = self.gds_validate_string(enum_, node, 'enum') self.enum.append(enum_) elif nodeName_ == 'controlled_vocabulary_link': controlled_vocabulary_link_ = child_.text controlled_vocabulary_link_ = self.gds_validate_string(controlled_vocabulary_link_, node, 'controlled_vocabulary_link') self.controlled_vocabulary_link = controlled_vocabulary_link_ # end class string_validation_type
[docs]class base_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('help_text', 'xs:string', 0), MemberSpec_('warning_text', 'xs:string', 0), MemberSpec_('error_text', 'xs:string', 0), MemberSpec_('validation_rules', 'string_validation_type', 1), MemberSpec_('label', 'xs:string', 0), MemberSpec_('value', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, help_text=None, warning_text=None, error_text=None, validation_rules=None, label=None, value=None, extensiontype_=None): self.original_tagname_ = None self.help_text = help_text self.warning_text = warning_text self.error_text = error_text if validation_rules is None: self.validation_rules = [] else: self.validation_rules = validation_rules self.label = label self.value = value self.extensiontype_ = extensiontype_
[docs] def factory(*args_, **kwargs_): if base_type.subclass: return base_type.subclass(*args_, **kwargs_) else: return base_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_help_text(self): return self.help_text
[docs] def set_help_text(self, help_text): self.help_text = help_text
[docs] def get_warning_text(self): return self.warning_text
[docs] def set_warning_text(self, warning_text): self.warning_text = warning_text
[docs] def get_error_text(self): return self.error_text
[docs] def set_error_text(self, error_text): self.error_text = error_text
[docs] def get_validation_rules(self): return self.validation_rules
[docs] def set_validation_rules(self, validation_rules): self.validation_rules = validation_rules
[docs] def add_validation_rules(self, value): self.validation_rules.append(value)
[docs] def insert_validation_rules_at(self, index, value): self.validation_rules.insert(index, value)
[docs] def replace_validation_rules_at(self, index, value): self.validation_rules[index] = value
[docs] def get_label(self): return self.label
[docs] def set_label(self, label): self.label = label
[docs] def get_value(self): return self.value
[docs] def set_value(self, value): self.value = value
[docs] def get_extensiontype_(self): return self.extensiontype_
[docs] def set_extensiontype_(self, extensiontype_): self.extensiontype_ = extensiontype_
[docs] def hasContent_(self): if ( self.help_text is not None or self.warning_text is not None or self.error_text is not None or self.validation_rules or self.label is not None or self.value is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='base_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='base_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='base_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='base_type'): if self.extensiontype_ is not None and 'xsi:type' not in already_processed: already_processed.add('xsi:type') outfile.write(' xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"') outfile.write(' xsi:type="%s"' % self.extensiontype_) pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='base_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.help_text is not None: showIndent(outfile, level, pretty_print) outfile.write('<%shelp_text>%s</%shelp_text>%s' % (namespace_, self.gds_format_string(quote_xml(self.help_text).encode(ExternalEncoding), input_name='help_text'), namespace_, eol_)) if self.warning_text is not None: showIndent(outfile, level, pretty_print) outfile.write('<%swarning_text>%s</%swarning_text>%s' % (namespace_, self.gds_format_string(quote_xml(self.warning_text).encode(ExternalEncoding), input_name='warning_text'), namespace_, eol_)) if self.error_text is not None: showIndent(outfile, level, pretty_print) outfile.write('<%serror_text>%s</%serror_text>%s' % (namespace_, self.gds_format_string(quote_xml(self.error_text).encode(ExternalEncoding), input_name='error_text'), namespace_, eol_)) for validation_rules_ in self.validation_rules: validation_rules_.export(outfile, level, namespace_, name_='validation_rules', pretty_print=pretty_print) if self.label is not None: showIndent(outfile, level, pretty_print) outfile.write('<%slabel>%s</%slabel>%s' % (namespace_, self.gds_format_string(quote_xml(self.label).encode(ExternalEncoding), input_name='label'), namespace_, eol_)) if self.value is not None: showIndent(outfile, level, pretty_print) outfile.write('<%svalue>%s</%svalue>%s' % (namespace_, self.gds_format_string(quote_xml(self.value).encode(ExternalEncoding), input_name='value'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('xsi:type', node) if value is not None and 'xsi:type' not in already_processed: already_processed.add('xsi:type') self.extensiontype_ = value
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'help_text': help_text_ = child_.text help_text_ = self.gds_validate_string(help_text_, node, 'help_text') self.help_text = help_text_ elif nodeName_ == 'warning_text': warning_text_ = child_.text warning_text_ = self.gds_validate_string(warning_text_, node, 'warning_text') self.warning_text = warning_text_ elif nodeName_ == 'error_text': error_text_ = child_.text error_text_ = self.gds_validate_string(error_text_, node, 'error_text') self.error_text = error_text_ elif nodeName_ == 'validation_rules': obj_ = string_validation_type.factory() obj_.build(child_) self.validation_rules.append(obj_) obj_.original_tagname_ = 'validation_rules' elif nodeName_ == 'label': label_ = child_.text label_ = self.gds_validate_string(label_, node, 'label') self.label = label_ elif nodeName_ == 'value': value_ = child_.text value_ = self.gds_validate_string(value_, node, 'value') self.value = value_ # end class base_type
[docs]class buffer_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('ph', ['phType', 'xs:float'], 0), MemberSpec_('component', 'componentType', 1), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, ph=None, component=None, details=None): self.original_tagname_ = None self.ph = ph self.validate_phType(self.ph) if component is None: self.component = [] else: self.component = component self.details = details
[docs] def factory(*args_, **kwargs_): if buffer_type.subclass: return buffer_type.subclass(*args_, **kwargs_) else: return buffer_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_ph(self): return self.ph
[docs] def set_ph(self, ph): self.ph = ph
[docs] def get_component(self): return self.component
[docs] def set_component(self, component): self.component = component
[docs] def add_component(self, value): self.component.append(value)
[docs] def insert_component_at(self, index, value): self.component.insert(index, value)
[docs] def replace_component_at(self, index, value): self.component[index] = value
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def validate_phType(self, value): # Validate type phType, a restriction on xs:float. if value is not None and Validate_simpletypes_: if value < 0: warnings_.warn('Value "%(value)s" does not match xsd minInclusive restriction on phType' % {"value" : value} ) if value > 14: warnings_.warn('Value "%(value)s" does not match xsd maxInclusive restriction on phType' % {"value" : value} )
[docs] def hasContent_(self): if ( self.ph is not None or self.component or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='buffer_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='buffer_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='buffer_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='buffer_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='buffer_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.ph is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sph>%s</%sph>%s' % (namespace_, self.gds_format_float(self.ph, input_name='ph'), namespace_, eol_)) for component_ in self.component: component_.export(outfile, level, namespace_, name_='component', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'ph': sval_ = child_.text try: fval_ = float(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires float or double: %s' % exp) fval_ = self.gds_validate_float(fval_, node, 'ph') self.ph = fval_ # validate type phType self.validate_phType(self.ph) elif nodeName_ == 'component': obj_ = componentType.factory() obj_.build(child_) self.component.append(obj_) obj_.original_tagname_ = 'component' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class buffer_type
[docs]class vitrification_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('cryogen_name', ['cryogen_nameType', 'xs:token'], 0), MemberSpec_('chamber_humidity', 'chamber_humidityType', 0), MemberSpec_('chamber_temperature', 'chamber_temperatureType', 0), MemberSpec_('instrument', ['instrumentType', 'xs:token'], 0), MemberSpec_('details', 'xs:string', 0), MemberSpec_('timed_resolved_state', 'xs:token', 0), MemberSpec_('method', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, cryogen_name=None, chamber_humidity=None, chamber_temperature=None, instrument=None, details=None, timed_resolved_state=None, method=None): self.original_tagname_ = None self.cryogen_name = cryogen_name self.validate_cryogen_nameType(self.cryogen_name) self.chamber_humidity = chamber_humidity self.chamber_temperature = chamber_temperature self.instrument = instrument self.validate_instrumentType(self.instrument) self.details = details self.timed_resolved_state = timed_resolved_state self.method = method
[docs] def factory(*args_, **kwargs_): if vitrification_type.subclass: return vitrification_type.subclass(*args_, **kwargs_) else: return vitrification_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_cryogen_name(self): return self.cryogen_name
[docs] def set_cryogen_name(self, cryogen_name): self.cryogen_name = cryogen_name
[docs] def get_chamber_humidity(self): return self.chamber_humidity
[docs] def set_chamber_humidity(self, chamber_humidity): self.chamber_humidity = chamber_humidity
[docs] def get_chamber_temperature(self): return self.chamber_temperature
[docs] def set_chamber_temperature(self, chamber_temperature): self.chamber_temperature = chamber_temperature
[docs] def get_instrument(self): return self.instrument
[docs] def set_instrument(self, instrument): self.instrument = instrument
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def get_timed_resolved_state(self): return self.timed_resolved_state
[docs] def set_timed_resolved_state(self, timed_resolved_state): self.timed_resolved_state = timed_resolved_state
[docs] def get_method(self): return self.method
[docs] def set_method(self, method): self.method = method
[docs] def validate_cryogen_nameType(self, value): # Validate type cryogen_nameType, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['ETHANE', 'FREON 12', 'FREON 22', 'HELIUM', 'METHANE', 'NITROGEN', 'PROPANE', 'ETHANE-PROPANE'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on cryogen_nameType' % {"value" : value.encode("utf-8")} )
[docs] def validate_instrumentType(self, value): # Validate type instrumentType, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['EMS-002 RAPID IMMERSION FREEZER', 'FEI VITROBOT MARK I', 'FEI VITROBOT MARK II', 'FEI VITROBOT MARK III', 'FEI VITROBOT MARK IV', 'GATAN CRYOPLUNGE 3', 'HOMEMADE PLUNGER', 'LEICA PLUNGER', 'LEICA EM GP', 'LEICA EM CPC', 'LEICA KF80', 'REICHERT-JUNG PLUNGER'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on instrumentType' % {"value" : value.encode("utf-8")} )
[docs] def hasContent_(self): if ( self.cryogen_name is not None or self.chamber_humidity is not None or self.chamber_temperature is not None or self.instrument is not None or self.details is not None or self.timed_resolved_state is not None or self.method is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='vitrification_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='vitrification_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='vitrification_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='vitrification_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='vitrification_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.cryogen_name is not None: showIndent(outfile, level, pretty_print) outfile.write('<%scryogen_name>%s</%scryogen_name>%s' % (namespace_, self.gds_format_string(quote_xml(self.cryogen_name).encode(ExternalEncoding), input_name='cryogen_name'), namespace_, eol_)) if self.chamber_humidity is not None: self.chamber_humidity.export(outfile, level, namespace_, name_='chamber_humidity', pretty_print=pretty_print) if self.chamber_temperature is not None: self.chamber_temperature.export(outfile, level, namespace_, name_='chamber_temperature', pretty_print=pretty_print) if self.instrument is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sinstrument>%s</%sinstrument>%s' % (namespace_, self.gds_format_string(quote_xml(self.instrument).encode(ExternalEncoding), input_name='instrument'), namespace_, eol_)) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_)) if self.timed_resolved_state is not None: showIndent(outfile, level, pretty_print) outfile.write('<%stimed_resolved_state>%s</%stimed_resolved_state>%s' % (namespace_, self.gds_format_string(quote_xml(self.timed_resolved_state).encode(ExternalEncoding), input_name='timed_resolved_state'), namespace_, eol_)) if self.method is not None: showIndent(outfile, level, pretty_print) outfile.write('<%smethod>%s</%smethod>%s' % (namespace_, self.gds_format_string(quote_xml(self.method).encode(ExternalEncoding), input_name='method'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'cryogen_name': cryogen_name_ = child_.text cryogen_name_ = re_.sub(String_cleanup_pat_, " ", cryogen_name_).strip() cryogen_name_ = self.gds_validate_string(cryogen_name_, node, 'cryogen_name') self.cryogen_name = cryogen_name_ # validate type cryogen_nameType self.validate_cryogen_nameType(self.cryogen_name) elif nodeName_ == 'chamber_humidity': obj_ = chamber_humidityType.factory() obj_.build(child_) self.chamber_humidity = obj_ obj_.original_tagname_ = 'chamber_humidity' elif nodeName_ == 'chamber_temperature': obj_ = chamber_temperatureType.factory() obj_.build(child_) self.chamber_temperature = obj_ obj_.original_tagname_ = 'chamber_temperature' elif nodeName_ == 'instrument': instrument_ = child_.text instrument_ = re_.sub(String_cleanup_pat_, " ", instrument_).strip() instrument_ = self.gds_validate_string(instrument_, node, 'instrument') self.instrument = instrument_ # validate type instrumentType self.validate_instrumentType(self.instrument) elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ elif nodeName_ == 'timed_resolved_state': timed_resolved_state_ = child_.text timed_resolved_state_ = re_.sub(String_cleanup_pat_, " ", timed_resolved_state_).strip() timed_resolved_state_ = self.gds_validate_string(timed_resolved_state_, node, 'timed_resolved_state') self.timed_resolved_state = timed_resolved_state_ elif nodeName_ == 'method': method_ = child_.text method_ = self.gds_validate_string(method_, node, 'method') self.method = method_ # end class vitrification_type
[docs]class base_preparation_type(GeneratedsSuper): """Unique identifier. Autogenerated""" member_data_items_ = [ MemberSpec_('id', 'xs:positiveInteger', 0), MemberSpec_('concentration', 'concentrationType3', 0), MemberSpec_('buffer', 'buffer_type', 0), MemberSpec_('staining', 'stainingType', 0), MemberSpec_('sugar_embedding', 'sugar_embeddingType', 0), MemberSpec_('shadowing', 'shadowingType', 0), MemberSpec_('grid', 'grid_type', 0), MemberSpec_('vitrification', 'vitrification_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, id=None, concentration=None, buffer=None, staining=None, sugar_embedding=None, shadowing=None, grid=None, vitrification=None, details=None, extensiontype_=None): self.original_tagname_ = None self.id = _cast(int, id) self.concentration = concentration self.buffer = buffer self.staining = staining self.sugar_embedding = sugar_embedding self.shadowing = shadowing self.grid = grid self.vitrification = vitrification self.details = details self.extensiontype_ = extensiontype_
[docs] def factory(*args_, **kwargs_): if base_preparation_type.subclass: return base_preparation_type.subclass(*args_, **kwargs_) else: return base_preparation_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_concentration(self): return self.concentration
[docs] def set_concentration(self, concentration): self.concentration = concentration
[docs] def get_buffer(self): return self.buffer
[docs] def set_buffer(self, buffer): self.buffer = buffer
[docs] def get_staining(self): return self.staining
[docs] def set_staining(self, staining): self.staining = staining
[docs] def get_sugar_embedding(self): return self.sugar_embedding
[docs] def set_sugar_embedding(self, sugar_embedding): self.sugar_embedding = sugar_embedding
[docs] def get_shadowing(self): return self.shadowing
[docs] def set_shadowing(self, shadowing): self.shadowing = shadowing
[docs] def get_grid(self): return self.grid
[docs] def set_grid(self, grid): self.grid = grid
[docs] def get_vitrification(self): return self.vitrification
[docs] def set_vitrification(self, vitrification): self.vitrification = vitrification
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def get_id(self): return self.id
[docs] def set_id(self, id): self.id = id
[docs] def get_extensiontype_(self): return self.extensiontype_
[docs] def set_extensiontype_(self, extensiontype_): self.extensiontype_ = extensiontype_
[docs] def hasContent_(self): if ( self.concentration is not None or self.buffer is not None or self.staining is not None or self.sugar_embedding is not None or self.shadowing is not None or self.grid is not None or self.vitrification is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='base_preparation_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='base_preparation_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='base_preparation_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='base_preparation_type'): if self.id is not None and 'id' not in already_processed: already_processed.add('id') outfile.write(' id="%s"' % self.gds_format_integer(self.id, input_name='id')) if self.extensiontype_ is not None and 'xsi:type' not in already_processed: already_processed.add('xsi:type') outfile.write(' xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"') outfile.write(' xsi:type="%s"' % self.extensiontype_)
[docs] def exportChildren(self, outfile, level, namespace_='', name_='base_preparation_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.concentration is not None: self.concentration.export(outfile, level, namespace_, name_='concentration', pretty_print=pretty_print) if self.buffer is not None: self.buffer.export(outfile, level, namespace_, name_='buffer', pretty_print=pretty_print) if self.staining is not None: self.staining.export(outfile, level, namespace_, name_='staining', pretty_print=pretty_print) if self.sugar_embedding is not None: self.sugar_embedding.export(outfile, level, namespace_, name_='sugar_embedding', pretty_print=pretty_print) if self.shadowing is not None: self.shadowing.export(outfile, level, namespace_, name_='shadowing', pretty_print=pretty_print) if self.grid is not None: self.grid.export(outfile, level, namespace_, name_='grid', pretty_print=pretty_print) if self.vitrification is not None: self.vitrification.export(outfile, level, namespace_, name_='vitrification', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('id', node) if value is not None and 'id' not in already_processed: already_processed.add('id') try: self.id = int(value) except ValueError as exp: raise_parse_error(node, 'Bad integer attribute: %s' % exp) if self.id <= 0: raise_parse_error(node, 'Invalid PositiveInteger') value = find_attr_value_('xsi:type', node) if value is not None and 'xsi:type' not in already_processed: already_processed.add('xsi:type') self.extensiontype_ = value
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'concentration': obj_ = concentrationType3.factory() obj_.build(child_) self.concentration = obj_ obj_.original_tagname_ = 'concentration' elif nodeName_ == 'buffer': obj_ = buffer_type.factory() obj_.build(child_) self.buffer = obj_ obj_.original_tagname_ = 'buffer' elif nodeName_ == 'staining': obj_ = stainingType.factory() obj_.build(child_) self.staining = obj_ obj_.original_tagname_ = 'staining' elif nodeName_ == 'sugar_embedding': obj_ = sugar_embeddingType.factory() obj_.build(child_) self.sugar_embedding = obj_ obj_.original_tagname_ = 'sugar_embedding' elif nodeName_ == 'shadowing': obj_ = shadowingType.factory() obj_.build(child_) self.shadowing = obj_ obj_.original_tagname_ = 'shadowing' elif nodeName_ == 'grid': obj_ = grid_type.factory() obj_.build(child_) self.grid = obj_ obj_.original_tagname_ = 'grid' elif nodeName_ == 'vitrification': obj_ = vitrification_type.factory() obj_.build(child_) self.vitrification = obj_ obj_.original_tagname_ = 'vitrification' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class base_preparation_type
[docs]class tomography_preparation_type(base_preparation_type): """TODO: add limits and units.""" member_data_items_ = [ MemberSpec_('fiducial_markers_list', 'fiducial_markers_listType', 0), MemberSpec_('high_pressure_freezing', 'high_pressure_freezingType', 0), MemberSpec_('embedding_material', 'xs:token', 0), MemberSpec_('cryo_protectant', 'xs:token', 0), MemberSpec_('sectioning', 'sectioningType', 0), ] subclass = None superclass = base_preparation_type def __init__(self, id=None, concentration=None, buffer=None, staining=None, sugar_embedding=None, shadowing=None, grid=None, vitrification=None, details=None, fiducial_markers_list=None, high_pressure_freezing=None, embedding_material=None, cryo_protectant=None, sectioning=None): self.original_tagname_ = None super(tomography_preparation_type, self).__init__(id, concentration, buffer, staining, sugar_embedding, shadowing, grid, vitrification, details, ) self.fiducial_markers_list = fiducial_markers_list self.high_pressure_freezing = high_pressure_freezing self.embedding_material = embedding_material self.cryo_protectant = cryo_protectant self.sectioning = sectioning
[docs] def factory(*args_, **kwargs_): if tomography_preparation_type.subclass: return tomography_preparation_type.subclass(*args_, **kwargs_) else: return tomography_preparation_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_fiducial_markers_list(self): return self.fiducial_markers_list
[docs] def set_fiducial_markers_list(self, fiducial_markers_list): self.fiducial_markers_list = fiducial_markers_list
[docs] def get_high_pressure_freezing(self): return self.high_pressure_freezing
[docs] def set_high_pressure_freezing(self, high_pressure_freezing): self.high_pressure_freezing = high_pressure_freezing
[docs] def get_embedding_material(self): return self.embedding_material
[docs] def set_embedding_material(self, embedding_material): self.embedding_material = embedding_material
[docs] def get_cryo_protectant(self): return self.cryo_protectant
[docs] def set_cryo_protectant(self, cryo_protectant): self.cryo_protectant = cryo_protectant
[docs] def get_sectioning(self): return self.sectioning
[docs] def set_sectioning(self, sectioning): self.sectioning = sectioning
[docs] def hasContent_(self): if ( self.fiducial_markers_list is not None or self.high_pressure_freezing is not None or self.embedding_material is not None or self.cryo_protectant is not None or self.sectioning is not None or super(tomography_preparation_type, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='tomography_preparation_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='tomography_preparation_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='tomography_preparation_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='tomography_preparation_type'): super(tomography_preparation_type, self).exportAttributes(outfile, level, already_processed, namespace_, name_='tomography_preparation_type')
[docs] def exportChildren(self, outfile, level, namespace_='', name_='tomography_preparation_type', fromsubclass_=False, pretty_print=True): super(tomography_preparation_type, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print) if pretty_print: eol_ = '\n' else: eol_ = '' if self.fiducial_markers_list is not None: self.fiducial_markers_list.export(outfile, level, namespace_, name_='fiducial_markers_list', pretty_print=pretty_print) if self.high_pressure_freezing is not None: self.high_pressure_freezing.export(outfile, level, namespace_, name_='high_pressure_freezing', pretty_print=pretty_print) if self.embedding_material is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sembedding_material>%s</%sembedding_material>%s' % (namespace_, self.gds_format_string(quote_xml(self.embedding_material).encode(ExternalEncoding), input_name='embedding_material'), namespace_, eol_)) if self.cryo_protectant is not None: showIndent(outfile, level, pretty_print) outfile.write('<%scryo_protectant>%s</%scryo_protectant>%s' % (namespace_, self.gds_format_string(quote_xml(self.cryo_protectant).encode(ExternalEncoding), input_name='cryo_protectant'), namespace_, eol_)) if self.sectioning is not None: self.sectioning.export(outfile, level, namespace_, name_='sectioning', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): super(tomography_preparation_type, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'fiducial_markers_list': obj_ = fiducial_markers_listType.factory() obj_.build(child_) self.fiducial_markers_list = obj_ obj_.original_tagname_ = 'fiducial_markers_list' elif nodeName_ == 'high_pressure_freezing': obj_ = high_pressure_freezingType.factory() obj_.build(child_) self.high_pressure_freezing = obj_ obj_.original_tagname_ = 'high_pressure_freezing' elif nodeName_ == 'embedding_material': embedding_material_ = child_.text embedding_material_ = re_.sub(String_cleanup_pat_, " ", embedding_material_).strip() embedding_material_ = self.gds_validate_string(embedding_material_, node, 'embedding_material') self.embedding_material = embedding_material_ elif nodeName_ == 'cryo_protectant': cryo_protectant_ = child_.text cryo_protectant_ = re_.sub(String_cleanup_pat_, " ", cryo_protectant_).strip() cryo_protectant_ = self.gds_validate_string(cryo_protectant_, node, 'cryo_protectant') self.cryo_protectant = cryo_protectant_ elif nodeName_ == 'sectioning': obj_ = sectioningType.factory() obj_.build(child_) self.sectioning = obj_ obj_.original_tagname_ = 'sectioning' super(tomography_preparation_type, self).buildChildren(child_, node, nodeName_, True) # end class tomography_preparation_type
[docs]class base_microscopy_type(GeneratedsSuper): """Auto generated by application""" member_data_items_ = [ MemberSpec_('id', 'xs:positiveInteger', 0), MemberSpec_('specimen_preparations', 'specimen_preparationsType', 0), MemberSpec_('microscope', ['microscopeType', 'xs:token'], 0), MemberSpec_('illumination_mode', ['illumination_modeType', 'xs:token'], 0), MemberSpec_('imaging_mode', ['imaging_modeType', 'xs:token'], 0), MemberSpec_('electron_source', ['electron_sourceType', 'xs:token'], 0), MemberSpec_('acceleration_voltage', 'acceleration_voltageType', 0), MemberSpec_('c2_aperture_diameter', 'c2_aperture_diameterType', 0), MemberSpec_('nominal_cs', 'nominal_csType', 0), MemberSpec_('nominal_defocus_min', 'nominal_defocus_minType', 0), MemberSpec_('calibrated_defocus_min', 'calibrated_defocus_minType', 0), MemberSpec_('nominal_defocus_max', 'nominal_defocus_maxType', 0), MemberSpec_('calibrated_defocus_max', 'calibrated_defocus_maxType', 0), MemberSpec_('nominal_magnification', ['allowed_magnification', 'xs:float'], 0), MemberSpec_('calibrated_magnification', ['allowed_magnification', 'xs:float'], 0), MemberSpec_('specimen_holder_model', ['specimen_holder_modelType', 'xs:token'], 0), MemberSpec_('cooling_holder_cryogen', ['cooling_holder_cryogenType', 'xs:token'], 0), MemberSpec_('temperature', 'temperatureType', 0), MemberSpec_('alignment_procedure', 'alignment_procedureType', 0), MemberSpec_('specialist_optics', 'specialist_optics_type', 0), MemberSpec_('software_list', 'software_list_type', 0), MemberSpec_('details', 'xs:string', 0), MemberSpec_('date', 'xs:date', 0), MemberSpec_('image_recording_list', 'image_recording_listType', 0), MemberSpec_('specimen_holder', 'xs:string', 0), MemberSpec_('tilt_angle_min', 'xs:string', 0), MemberSpec_('tilt_angle_max', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, id=None, specimen_preparations=None, microscope=None, illumination_mode=None, imaging_mode=None, electron_source=None, acceleration_voltage=None, c2_aperture_diameter=None, nominal_cs=None, nominal_defocus_min=None, calibrated_defocus_min=None, nominal_defocus_max=None, calibrated_defocus_max=None, nominal_magnification=None, calibrated_magnification=None, specimen_holder_model=None, cooling_holder_cryogen=None, temperature=None, alignment_procedure=None, specialist_optics=None, software_list=None, details=None, date=None, image_recording_list=None, specimen_holder=None, tilt_angle_min=None, tilt_angle_max=None, extensiontype_=None): self.original_tagname_ = None self.id = _cast(int, id) self.specimen_preparations = specimen_preparations self.microscope = microscope self.validate_microscopeType(self.microscope) self.illumination_mode = illumination_mode self.validate_illumination_modeType(self.illumination_mode) self.imaging_mode = imaging_mode self.validate_imaging_modeType(self.imaging_mode) self.electron_source = electron_source self.validate_electron_sourceType(self.electron_source) self.acceleration_voltage = acceleration_voltage self.c2_aperture_diameter = c2_aperture_diameter self.nominal_cs = nominal_cs self.nominal_defocus_min = nominal_defocus_min self.calibrated_defocus_min = calibrated_defocus_min self.nominal_defocus_max = nominal_defocus_max self.calibrated_defocus_max = calibrated_defocus_max self.nominal_magnification = nominal_magnification self.validate_allowed_magnification(self.nominal_magnification) self.calibrated_magnification = calibrated_magnification self.validate_allowed_magnification(self.calibrated_magnification) self.specimen_holder_model = specimen_holder_model self.validate_specimen_holder_modelType(self.specimen_holder_model) self.cooling_holder_cryogen = cooling_holder_cryogen self.validate_cooling_holder_cryogenType(self.cooling_holder_cryogen) self.temperature = temperature self.alignment_procedure = alignment_procedure self.specialist_optics = specialist_optics self.software_list = software_list self.details = details if isinstance(date, basestring): initvalue_ = datetime_.datetime.strptime(date, '%Y-%m-%d').date() else: initvalue_ = date self.date = initvalue_ self.image_recording_list = image_recording_list self.specimen_holder = specimen_holder self.tilt_angle_min = tilt_angle_min self.tilt_angle_max = tilt_angle_max self.extensiontype_ = extensiontype_
[docs] def factory(*args_, **kwargs_): if base_microscopy_type.subclass: return base_microscopy_type.subclass(*args_, **kwargs_) else: return base_microscopy_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_specimen_preparations(self): return self.specimen_preparations
[docs] def set_specimen_preparations(self, specimen_preparations): self.specimen_preparations = specimen_preparations
[docs] def get_microscope(self): return self.microscope
[docs] def set_microscope(self, microscope): self.microscope = microscope
[docs] def get_illumination_mode(self): return self.illumination_mode
[docs] def set_illumination_mode(self, illumination_mode): self.illumination_mode = illumination_mode
[docs] def get_imaging_mode(self): return self.imaging_mode
[docs] def set_imaging_mode(self, imaging_mode): self.imaging_mode = imaging_mode
[docs] def get_electron_source(self): return self.electron_source
[docs] def set_electron_source(self, electron_source): self.electron_source = electron_source
[docs] def get_acceleration_voltage(self): return self.acceleration_voltage
[docs] def set_acceleration_voltage(self, acceleration_voltage): self.acceleration_voltage = acceleration_voltage
[docs] def get_c2_aperture_diameter(self): return self.c2_aperture_diameter
[docs] def set_c2_aperture_diameter(self, c2_aperture_diameter): self.c2_aperture_diameter = c2_aperture_diameter
[docs] def get_nominal_cs(self): return self.nominal_cs
[docs] def set_nominal_cs(self, nominal_cs): self.nominal_cs = nominal_cs
[docs] def get_nominal_defocus_min(self): return self.nominal_defocus_min
[docs] def set_nominal_defocus_min(self, nominal_defocus_min): self.nominal_defocus_min = nominal_defocus_min
[docs] def get_calibrated_defocus_min(self): return self.calibrated_defocus_min
[docs] def set_calibrated_defocus_min(self, calibrated_defocus_min): self.calibrated_defocus_min = calibrated_defocus_min
[docs] def get_nominal_defocus_max(self): return self.nominal_defocus_max
[docs] def set_nominal_defocus_max(self, nominal_defocus_max): self.nominal_defocus_max = nominal_defocus_max
[docs] def get_calibrated_defocus_max(self): return self.calibrated_defocus_max
[docs] def set_calibrated_defocus_max(self, calibrated_defocus_max): self.calibrated_defocus_max = calibrated_defocus_max
[docs] def get_nominal_magnification(self): return self.nominal_magnification
[docs] def set_nominal_magnification(self, nominal_magnification): self.nominal_magnification = nominal_magnification
[docs] def get_calibrated_magnification(self): return self.calibrated_magnification
[docs] def set_calibrated_magnification(self, calibrated_magnification): self.calibrated_magnification = calibrated_magnification
[docs] def get_specimen_holder_model(self): return self.specimen_holder_model
[docs] def set_specimen_holder_model(self, specimen_holder_model): self.specimen_holder_model = specimen_holder_model
[docs] def get_cooling_holder_cryogen(self): return self.cooling_holder_cryogen
[docs] def set_cooling_holder_cryogen(self, cooling_holder_cryogen): self.cooling_holder_cryogen = cooling_holder_cryogen
[docs] def get_temperature(self): return self.temperature
[docs] def set_temperature(self, temperature): self.temperature = temperature
[docs] def get_alignment_procedure(self): return self.alignment_procedure
[docs] def set_alignment_procedure(self, alignment_procedure): self.alignment_procedure = alignment_procedure
[docs] def get_specialist_optics(self): return self.specialist_optics
[docs] def set_specialist_optics(self, specialist_optics): self.specialist_optics = specialist_optics
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def get_date(self): return self.date
[docs] def set_date(self, date): self.date = date
[docs] def get_image_recording_list(self): return self.image_recording_list
[docs] def set_image_recording_list(self, image_recording_list): self.image_recording_list = image_recording_list
[docs] def get_specimen_holder(self): return self.specimen_holder
[docs] def set_specimen_holder(self, specimen_holder): self.specimen_holder = specimen_holder
[docs] def get_tilt_angle_min(self): return self.tilt_angle_min
[docs] def set_tilt_angle_min(self, tilt_angle_min): self.tilt_angle_min = tilt_angle_min
[docs] def get_tilt_angle_max(self): return self.tilt_angle_max
[docs] def set_tilt_angle_max(self, tilt_angle_max): self.tilt_angle_max = tilt_angle_max
[docs] def get_id(self): return self.id
[docs] def set_id(self, id): self.id = id
[docs] def get_extensiontype_(self): return self.extensiontype_
[docs] def set_extensiontype_(self, extensiontype_): self.extensiontype_ = extensiontype_
[docs] def validate_microscopeType(self, value): # Validate type microscopeType, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['FEI MORGAGNI', 'FEI POLARA 300', 'FEI TECNAI 12', 'FEI TECNAI 20', 'FEI TECNAI F20', 'FEI TECNAI F30', 'FEI TECNAI SPHERA', 'FEI TITAN KRIOS', 'FEI/PHILIPS CM120T', 'FEI/PHILIPS CM200FEG', 'FEI/PHILIPS CM2000FEG/SOPHIE', 'FEI/PHILIPS CM200FEG/ST', 'FEI/PHILIPS CM200FEG/UT', 'FEI/PHILIPS CM200T', 'FEI/PHILIPS CM300FEG/HE', 'FEI/PHIILIPS CM300FEG/ST', 'FEI/PHILIPS CM300FEG/T', 'FEI/PHILIPS EM400', 'FEI/PHILIPS EM420', 'HITACHI EF2000', 'HITACHI HF2000', 'HITACHI HF3000', 'HITACHI H-95000SD', 'JEOL100CX', 'JEOL 1010', 'JEOL 1200', 'JEOL 1200EX', 'JEOL 1200EXII', 'JEOL 1230', 'JEOL 2000EX', 'JEOL 2000EXII', 'JEOL 2010F', 'JEOL 2010HT', 'JEOL 2010UHR', 'JEOL 2100', 'JEOL 2100F', 'JEOL 2200FS', 'JEOL 2200FSC', 'JEOL 3000SFF', 'JEOL KYOTO-3000SFF', 'JEOL 3200FSC', 'JEOL 4000EX'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on microscopeType' % {"value" : value.encode("utf-8")} )
[docs] def validate_illumination_modeType(self, value): # Validate type illumination_modeType, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['FLOOD BEAM', 'SPOT SCAN', 'OTHER'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on illumination_modeType' % {"value" : value.encode("utf-8")} )
[docs] def validate_imaging_modeType(self, value): # Validate type imaging_modeType, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['BRIGHT FIELD', 'DARK FIELD', 'DIFFRACTION', 'OTHER'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on imaging_modeType' % {"value" : value.encode("utf-8")} )
[docs] def validate_electron_sourceType(self, value): # Validate type electron_sourceType, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['TUNGSTEN HAIRPIN', 'LAB6', 'FIELD EMISSION GUN'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on electron_sourceType' % {"value" : value.encode("utf-8")} )
[docs] def validate_allowed_magnification(self, value): # Validate type allowed_magnification, a restriction on xs:float. if value is not None and Validate_simpletypes_: if value < 100: warnings_.warn('Value "%(value)s" does not match xsd minInclusive restriction on allowed_magnification' % {"value" : value} ) if value > 100000: warnings_.warn('Value "%(value)s" does not match xsd maxInclusive restriction on allowed_magnification' % {"value" : value} )
[docs] def validate_specimen_holder_modelType(self, value): # Validate type specimen_holder_modelType, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['GATAN HELIUM', 'GATAN LIQUID NITROGEN', 'HOME BUILD', 'JEM3400FSC CRYOHOLDER', 'JEOL', 'PHILIPS ROTATION HOLDER', 'SIDE ENTRY, EUCENTRIC', 'GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER', 'GATAN CT3500 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER', 'GATAN CT3500TR SINGLE TILT ROTATION LIQUID NITROGEN CRYO TRANSFER HOLDER', 'GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER', 'GATAN 914 HIGH TILT LIQUID NITROGEN CRYO TRANSFER TOMOGRAPHY HOLDER', 'GATAN 915 DOUBLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER', 'GATAN UHRST 3500 SINGLE TILT ULTRA HIGH RESOLUTION NITROGEN COOLING HOLDER', 'GATAN CHDT 3504 DOUBLE TILT HIGH RESOLUTION NITROGEN COOLING HOLDER', 'GATAN HC 3500 SINGLE TILT HEATING/NITROGEN COOLING HOLDER', 'GATAN HCHST 3008 SINGLE TILT HIGH RESOLUTION HELIUM COOLING HOLDER', 'GATAN ULTST ULTRA LOW TEMPERATURE SINGLE TILT HELIUM COOLING HOLDER', 'GATAN HCHDT 3010 DOUBLE TILT HIGH RESOLUTION HELIUM COOLING HOLDER', 'GATAN ULTDT ULTRA LOW TEMPERATURE DOUBLE TILT HELIUM COOLING HOLDER'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on specimen_holder_modelType' % {"value" : value.encode("utf-8")} )
[docs] def validate_cooling_holder_cryogenType(self, value): # Validate type cooling_holder_cryogenType, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['HELIUM', 'NITROGEN'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on cooling_holder_cryogenType' % {"value" : value.encode("utf-8")} )
[docs] def hasContent_(self): if ( self.specimen_preparations is not None or self.microscope is not None or self.illumination_mode is not None or self.imaging_mode is not None or self.electron_source is not None or self.acceleration_voltage is not None or self.c2_aperture_diameter is not None or self.nominal_cs is not None or self.nominal_defocus_min is not None or self.calibrated_defocus_min is not None or self.nominal_defocus_max is not None or self.calibrated_defocus_max is not None or self.nominal_magnification is not None or self.calibrated_magnification is not None or self.specimen_holder_model is not None or self.cooling_holder_cryogen is not None or self.temperature is not None or self.alignment_procedure is not None or self.specialist_optics is not None or self.software_list is not None or self.details is not None or self.date is not None or self.image_recording_list is not None or self.specimen_holder is not None or self.tilt_angle_min is not None or self.tilt_angle_max is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='base_microscopy_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='base_microscopy_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='base_microscopy_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='base_microscopy_type'): if self.id is not None and 'id' not in already_processed: already_processed.add('id') outfile.write(' id="%s"' % self.gds_format_integer(self.id, input_name='id')) if self.extensiontype_ is not None and 'xsi:type' not in already_processed: already_processed.add('xsi:type') outfile.write(' xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"') outfile.write(' xsi:type="%s"' % self.extensiontype_)
[docs] def exportChildren(self, outfile, level, namespace_='', name_='base_microscopy_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.specimen_preparations is not None: self.specimen_preparations.export(outfile, level, namespace_, name_='specimen_preparations', pretty_print=pretty_print) if self.microscope is not None: showIndent(outfile, level, pretty_print) outfile.write('<%smicroscope>%s</%smicroscope>%s' % (namespace_, self.gds_format_string(quote_xml(self.microscope).encode(ExternalEncoding), input_name='microscope'), namespace_, eol_)) if self.illumination_mode is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sillumination_mode>%s</%sillumination_mode>%s' % (namespace_, self.gds_format_string(quote_xml(self.illumination_mode).encode(ExternalEncoding), input_name='illumination_mode'), namespace_, eol_)) if self.imaging_mode is not None: showIndent(outfile, level, pretty_print) outfile.write('<%simaging_mode>%s</%simaging_mode>%s' % (namespace_, self.gds_format_string(quote_xml(self.imaging_mode).encode(ExternalEncoding), input_name='imaging_mode'), namespace_, eol_)) if self.electron_source is not None: showIndent(outfile, level, pretty_print) outfile.write('<%selectron_source>%s</%selectron_source>%s' % (namespace_, self.gds_format_string(quote_xml(self.electron_source).encode(ExternalEncoding), input_name='electron_source'), namespace_, eol_)) if self.acceleration_voltage is not None: self.acceleration_voltage.export(outfile, level, namespace_, name_='acceleration_voltage', pretty_print=pretty_print) if self.c2_aperture_diameter is not None: self.c2_aperture_diameter.export(outfile, level, namespace_, name_='c2_aperture_diameter', pretty_print=pretty_print) if self.nominal_cs is not None: self.nominal_cs.export(outfile, level, namespace_, name_='nominal_cs', pretty_print=pretty_print) if self.nominal_defocus_min is not None: self.nominal_defocus_min.export(outfile, level, namespace_, name_='nominal_defocus_min', pretty_print=pretty_print) if self.calibrated_defocus_min is not None: self.calibrated_defocus_min.export(outfile, level, namespace_, name_='calibrated_defocus_min', pretty_print=pretty_print) if self.nominal_defocus_max is not None: self.nominal_defocus_max.export(outfile, level, namespace_, name_='nominal_defocus_max', pretty_print=pretty_print) if self.calibrated_defocus_max is not None: self.calibrated_defocus_max.export(outfile, level, namespace_, name_='calibrated_defocus_max', pretty_print=pretty_print) if self.nominal_magnification is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snominal_magnification>%s</%snominal_magnification>%s' % (namespace_, self.gds_format_float(self.nominal_magnification, input_name='nominal_magnification'), namespace_, eol_)) if self.calibrated_magnification is not None: showIndent(outfile, level, pretty_print) outfile.write('<%scalibrated_magnification>%s</%scalibrated_magnification>%s' % (namespace_, self.gds_format_float(self.calibrated_magnification, input_name='calibrated_magnification'), namespace_, eol_)) if self.specimen_holder_model is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sspecimen_holder_model>%s</%sspecimen_holder_model>%s' % (namespace_, self.gds_format_string(quote_xml(self.specimen_holder_model).encode(ExternalEncoding), input_name='specimen_holder_model'), namespace_, eol_)) if self.cooling_holder_cryogen is not None: showIndent(outfile, level, pretty_print) outfile.write('<%scooling_holder_cryogen>%s</%scooling_holder_cryogen>%s' % (namespace_, self.gds_format_string(quote_xml(self.cooling_holder_cryogen).encode(ExternalEncoding), input_name='cooling_holder_cryogen'), namespace_, eol_)) if self.temperature is not None: self.temperature.export(outfile, level, namespace_, name_='temperature', pretty_print=pretty_print) if self.alignment_procedure is not None: self.alignment_procedure.export(outfile, level, namespace_, name_='alignment_procedure', pretty_print=pretty_print) if self.specialist_optics is not None: self.specialist_optics.export(outfile, level, namespace_, name_='specialist_optics', pretty_print=pretty_print) if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_)) if self.date is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdate>%s</%sdate>%s' % (namespace_, self.gds_format_date(self.date, input_name='date'), namespace_, eol_)) if self.image_recording_list is not None: self.image_recording_list.export(outfile, level, namespace_, name_='image_recording_list', pretty_print=pretty_print) if self.specimen_holder is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sspecimen_holder>%s</%sspecimen_holder>%s' % (namespace_, self.gds_format_string(quote_xml(self.specimen_holder).encode(ExternalEncoding), input_name='specimen_holder'), namespace_, eol_)) if self.tilt_angle_min is not None: showIndent(outfile, level, pretty_print) outfile.write('<%stilt_angle_min>%s</%stilt_angle_min>%s' % (namespace_, self.gds_format_string(quote_xml(self.tilt_angle_min).encode(ExternalEncoding), input_name='tilt_angle_min'), namespace_, eol_)) if self.tilt_angle_max is not None: showIndent(outfile, level, pretty_print) outfile.write('<%stilt_angle_max>%s</%stilt_angle_max>%s' % (namespace_, self.gds_format_string(quote_xml(self.tilt_angle_max).encode(ExternalEncoding), input_name='tilt_angle_max'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('id', node) if value is not None and 'id' not in already_processed: already_processed.add('id') try: self.id = int(value) except ValueError as exp: raise_parse_error(node, 'Bad integer attribute: %s' % exp) if self.id <= 0: raise_parse_error(node, 'Invalid PositiveInteger') value = find_attr_value_('xsi:type', node) if value is not None and 'xsi:type' not in already_processed: already_processed.add('xsi:type') self.extensiontype_ = value
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'specimen_preparations': obj_ = specimen_preparationsType.factory() obj_.build(child_) self.specimen_preparations = obj_ obj_.original_tagname_ = 'specimen_preparations' elif nodeName_ == 'microscope': microscope_ = child_.text microscope_ = re_.sub(String_cleanup_pat_, " ", microscope_).strip() microscope_ = self.gds_validate_string(microscope_, node, 'microscope') self.microscope = microscope_ # validate type microscopeType self.validate_microscopeType(self.microscope) elif nodeName_ == 'illumination_mode': illumination_mode_ = child_.text illumination_mode_ = re_.sub(String_cleanup_pat_, " ", illumination_mode_).strip() illumination_mode_ = self.gds_validate_string(illumination_mode_, node, 'illumination_mode') self.illumination_mode = illumination_mode_ # validate type illumination_modeType self.validate_illumination_modeType(self.illumination_mode) elif nodeName_ == 'imaging_mode': imaging_mode_ = child_.text imaging_mode_ = re_.sub(String_cleanup_pat_, " ", imaging_mode_).strip() imaging_mode_ = self.gds_validate_string(imaging_mode_, node, 'imaging_mode') self.imaging_mode = imaging_mode_ # validate type imaging_modeType self.validate_imaging_modeType(self.imaging_mode) elif nodeName_ == 'electron_source': electron_source_ = child_.text electron_source_ = re_.sub(String_cleanup_pat_, " ", electron_source_).strip() electron_source_ = self.gds_validate_string(electron_source_, node, 'electron_source') self.electron_source = electron_source_ # validate type electron_sourceType self.validate_electron_sourceType(self.electron_source) elif nodeName_ == 'acceleration_voltage': obj_ = acceleration_voltageType.factory() obj_.build(child_) self.acceleration_voltage = obj_ obj_.original_tagname_ = 'acceleration_voltage' elif nodeName_ == 'c2_aperture_diameter': obj_ = c2_aperture_diameterType.factory() obj_.build(child_) self.c2_aperture_diameter = obj_ obj_.original_tagname_ = 'c2_aperture_diameter' elif nodeName_ == 'nominal_cs': obj_ = nominal_csType.factory() obj_.build(child_) self.nominal_cs = obj_ obj_.original_tagname_ = 'nominal_cs' elif nodeName_ == 'nominal_defocus_min': obj_ = nominal_defocus_minType.factory() obj_.build(child_) self.nominal_defocus_min = obj_ obj_.original_tagname_ = 'nominal_defocus_min' elif nodeName_ == 'calibrated_defocus_min': obj_ = calibrated_defocus_minType.factory() obj_.build(child_) self.calibrated_defocus_min = obj_ obj_.original_tagname_ = 'calibrated_defocus_min' elif nodeName_ == 'nominal_defocus_max': obj_ = nominal_defocus_maxType.factory() obj_.build(child_) self.nominal_defocus_max = obj_ obj_.original_tagname_ = 'nominal_defocus_max' elif nodeName_ == 'calibrated_defocus_max': obj_ = calibrated_defocus_maxType.factory() obj_.build(child_) self.calibrated_defocus_max = obj_ obj_.original_tagname_ = 'calibrated_defocus_max' elif nodeName_ == 'nominal_magnification': sval_ = child_.text try: fval_ = float(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires float or double: %s' % exp) fval_ = self.gds_validate_float(fval_, node, 'nominal_magnification') self.nominal_magnification = fval_ # validate type allowed_magnification self.validate_allowed_magnification(self.nominal_magnification) elif nodeName_ == 'calibrated_magnification': sval_ = child_.text try: fval_ = float(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires float or double: %s' % exp) fval_ = self.gds_validate_float(fval_, node, 'calibrated_magnification') self.calibrated_magnification = fval_ # validate type allowed_magnification self.validate_allowed_magnification(self.calibrated_magnification) elif nodeName_ == 'specimen_holder_model': specimen_holder_model_ = child_.text specimen_holder_model_ = re_.sub(String_cleanup_pat_, " ", specimen_holder_model_).strip() specimen_holder_model_ = self.gds_validate_string(specimen_holder_model_, node, 'specimen_holder_model') self.specimen_holder_model = specimen_holder_model_ # validate type specimen_holder_modelType self.validate_specimen_holder_modelType(self.specimen_holder_model) elif nodeName_ == 'cooling_holder_cryogen': cooling_holder_cryogen_ = child_.text cooling_holder_cryogen_ = re_.sub(String_cleanup_pat_, " ", cooling_holder_cryogen_).strip() cooling_holder_cryogen_ = self.gds_validate_string(cooling_holder_cryogen_, node, 'cooling_holder_cryogen') self.cooling_holder_cryogen = cooling_holder_cryogen_ # validate type cooling_holder_cryogenType self.validate_cooling_holder_cryogenType(self.cooling_holder_cryogen) elif nodeName_ == 'temperature': obj_ = temperatureType.factory() obj_.build(child_) self.temperature = obj_ obj_.original_tagname_ = 'temperature' elif nodeName_ == 'alignment_procedure': obj_ = alignment_procedureType.factory() obj_.build(child_) self.alignment_procedure = obj_ obj_.original_tagname_ = 'alignment_procedure' elif nodeName_ == 'specialist_optics': obj_ = specialist_optics_type.factory() obj_.build(child_) self.specialist_optics = obj_ obj_.original_tagname_ = 'specialist_optics' elif nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ elif nodeName_ == 'date': sval_ = child_.text dval_ = self.gds_parse_date(sval_) self.date = dval_ elif nodeName_ == 'image_recording_list': obj_ = image_recording_listType.factory() obj_.build(child_) self.image_recording_list = obj_ obj_.original_tagname_ = 'image_recording_list' elif nodeName_ == 'specimen_holder': specimen_holder_ = child_.text specimen_holder_ = self.gds_validate_string(specimen_holder_, node, 'specimen_holder') self.specimen_holder = specimen_holder_ elif nodeName_ == 'tilt_angle_min': tilt_angle_min_ = child_.text tilt_angle_min_ = self.gds_validate_string(tilt_angle_min_, node, 'tilt_angle_min') self.tilt_angle_min = tilt_angle_min_ elif nodeName_ == 'tilt_angle_max': tilt_angle_max_ = child_.text tilt_angle_max_ = self.gds_validate_string(tilt_angle_max_, node, 'tilt_angle_max') self.tilt_angle_max = tilt_angle_max_ # end class base_microscopy_type
[docs]class tilt_angle_min(GeneratedsSuper): """Deprecated (2014/11/14)SHOULD NOT BE USED FOR TOMOGRAPHY - only for compatibility purposes with v1.9!! Use tomography microscopy instead. Angle is assumed in degrees""" member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if tilt_angle_min.subclass: return tilt_angle_min.subclass(*args_, **kwargs_) else: return tilt_angle_min(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='tilt_angle_min', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='tilt_angle_min') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='tilt_angle_min', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='tilt_angle_min'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='tilt_angle_min', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class tilt_angle_min
[docs]class tilt_angle_max(GeneratedsSuper): """Deprecated (2014/11/14)SHOULD NOT BE USED FOR TOMOGRAPHY - only for compatibility purposes with v1.9!! Use tomography microscopy instead. Angle is assumed in degrees""" member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if tilt_angle_max.subclass: return tilt_angle_max.subclass(*args_, **kwargs_) else: return tilt_angle_max(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='tilt_angle_max', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='tilt_angle_max') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='tilt_angle_max', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='tilt_angle_max'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='tilt_angle_max', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class tilt_angle_max
[docs]class tomography_microscopy_type(base_microscopy_type): member_data_items_ = [ MemberSpec_('tilt_series', 'tilt_series_type', 1), ] subclass = None superclass = base_microscopy_type def __init__(self, id=None, specimen_preparations=None, microscope=None, illumination_mode=None, imaging_mode=None, electron_source=None, acceleration_voltage=None, c2_aperture_diameter=None, nominal_cs=None, nominal_defocus_min=None, calibrated_defocus_min=None, nominal_defocus_max=None, calibrated_defocus_max=None, nominal_magnification=None, calibrated_magnification=None, specimen_holder_model=None, cooling_holder_cryogen=None, temperature=None, alignment_procedure=None, specialist_optics=None, software_list=None, details=None, date=None, image_recording_list=None, specimen_holder=None, tilt_angle_min=None, tilt_angle_max=None, tilt_series=None): self.original_tagname_ = None super(tomography_microscopy_type, self).__init__(id, specimen_preparations, microscope, illumination_mode, imaging_mode, electron_source, acceleration_voltage, c2_aperture_diameter, nominal_cs, nominal_defocus_min, calibrated_defocus_min, nominal_defocus_max, calibrated_defocus_max, nominal_magnification, calibrated_magnification, specimen_holder_model, cooling_holder_cryogen, temperature, alignment_procedure, specialist_optics, software_list, details, date, image_recording_list, specimen_holder, tilt_angle_min, tilt_angle_max, ) if tilt_series is None: self.tilt_series = [] else: self.tilt_series = tilt_series
[docs] def factory(*args_, **kwargs_): if tomography_microscopy_type.subclass: return tomography_microscopy_type.subclass(*args_, **kwargs_) else: return tomography_microscopy_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_tilt_series(self): return self.tilt_series
[docs] def set_tilt_series(self, tilt_series): self.tilt_series = tilt_series
[docs] def add_tilt_series(self, value): self.tilt_series.append(value)
[docs] def insert_tilt_series_at(self, index, value): self.tilt_series.insert(index, value)
[docs] def replace_tilt_series_at(self, index, value): self.tilt_series[index] = value
[docs] def hasContent_(self): if ( self.tilt_series or super(tomography_microscopy_type, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='tomography_microscopy_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='tomography_microscopy_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='tomography_microscopy_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='tomography_microscopy_type'): super(tomography_microscopy_type, self).exportAttributes(outfile, level, already_processed, namespace_, name_='tomography_microscopy_type')
[docs] def exportChildren(self, outfile, level, namespace_='', name_='tomography_microscopy_type', fromsubclass_=False, pretty_print=True): super(tomography_microscopy_type, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print) if pretty_print: eol_ = '\n' else: eol_ = '' for tilt_series_ in self.tilt_series: tilt_series_.export(outfile, level, namespace_, name_='tilt_series', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): super(tomography_microscopy_type, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'tilt_series': obj_ = tilt_series_type.factory() obj_.build(child_) self.tilt_series.append(obj_) obj_.original_tagname_ = 'tilt_series' super(tomography_microscopy_type, self).buildChildren(child_, node, nodeName_, True) # end class tomography_microscopy_type
[docs]class axis_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('min_angle', 'min_angleType', 0), MemberSpec_('max_angle', 'max_angleType', 0), MemberSpec_('angle_increment', 'angle_incrementType', 0), ] subclass = None superclass = None def __init__(self, min_angle=None, max_angle=None, angle_increment=None, extensiontype_=None): self.original_tagname_ = None self.min_angle = min_angle self.max_angle = max_angle self.angle_increment = angle_increment self.extensiontype_ = extensiontype_
[docs] def factory(*args_, **kwargs_): if axis_type.subclass: return axis_type.subclass(*args_, **kwargs_) else: return axis_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_min_angle(self): return self.min_angle
[docs] def set_min_angle(self, min_angle): self.min_angle = min_angle
[docs] def get_max_angle(self): return self.max_angle
[docs] def set_max_angle(self, max_angle): self.max_angle = max_angle
[docs] def get_angle_increment(self): return self.angle_increment
[docs] def set_angle_increment(self, angle_increment): self.angle_increment = angle_increment
[docs] def get_extensiontype_(self): return self.extensiontype_
[docs] def set_extensiontype_(self, extensiontype_): self.extensiontype_ = extensiontype_
[docs] def hasContent_(self): if ( self.min_angle is not None or self.max_angle is not None or self.angle_increment is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='axis_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='axis_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='axis_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='axis_type'): if self.extensiontype_ is not None and 'xsi:type' not in already_processed: already_processed.add('xsi:type') outfile.write(' xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"') outfile.write(' xsi:type="%s"' % self.extensiontype_) pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='axis_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.min_angle is not None: self.min_angle.export(outfile, level, namespace_, name_='min_angle', pretty_print=pretty_print) if self.max_angle is not None: self.max_angle.export(outfile, level, namespace_, name_='max_angle', pretty_print=pretty_print) if self.angle_increment is not None: self.angle_increment.export(outfile, level, namespace_, name_='angle_increment', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('xsi:type', node) if value is not None and 'xsi:type' not in already_processed: already_processed.add('xsi:type') self.extensiontype_ = value
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'min_angle': obj_ = min_angleType.factory() obj_.build(child_) self.min_angle = obj_ obj_.original_tagname_ = 'min_angle' elif nodeName_ == 'max_angle': obj_ = max_angleType.factory() obj_.build(child_) self.max_angle = obj_ obj_.original_tagname_ = 'max_angle' elif nodeName_ == 'angle_increment': obj_ = angle_incrementType.factory() obj_.build(child_) self.angle_increment = obj_ obj_.original_tagname_ = 'angle_increment' # end class axis_type
[docs]class tilt_series_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('axis1', 'axis_type', 0), MemberSpec_('axis2', 'axis2Type', 0), MemberSpec_('axis_rotation', 'axis_rotationType', 0), ] subclass = None superclass = None def __init__(self, axis1=None, axis2=None, axis_rotation=None): self.original_tagname_ = None self.axis1 = axis1 self.axis2 = axis2 self.axis_rotation = axis_rotation
[docs] def factory(*args_, **kwargs_): if tilt_series_type.subclass: return tilt_series_type.subclass(*args_, **kwargs_) else: return tilt_series_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_axis1(self): return self.axis1
[docs] def set_axis1(self, axis1): self.axis1 = axis1
[docs] def get_axis2(self): return self.axis2
[docs] def set_axis2(self, axis2): self.axis2 = axis2
[docs] def get_axis_rotation(self): return self.axis_rotation
[docs] def set_axis_rotation(self, axis_rotation): self.axis_rotation = axis_rotation
[docs] def hasContent_(self): if ( self.axis1 is not None or self.axis2 is not None or self.axis_rotation is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='tilt_series_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='tilt_series_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='tilt_series_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='tilt_series_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='tilt_series_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.axis1 is not None: self.axis1.export(outfile, level, namespace_, name_='axis1', pretty_print=pretty_print) if self.axis2 is not None: self.axis2.export(outfile, level, namespace_, name_='axis2', pretty_print=pretty_print) if self.axis_rotation is not None: self.axis_rotation.export(outfile, level, namespace_, name_='axis_rotation', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'axis1': class_obj_ = self.get_class_obj_(child_, axis_type) obj_ = class_obj_.factory() obj_.build(child_) self.axis1 = obj_ obj_.original_tagname_ = 'axis1' elif nodeName_ == 'axis2': obj_ = axis2Type.factory() obj_.build(child_) self.axis2 = obj_ obj_.original_tagname_ = 'axis2' elif nodeName_ == 'axis_rotation': obj_ = axis_rotationType.factory() obj_.build(child_) self.axis_rotation = obj_ obj_.original_tagname_ = 'axis_rotation' # end class tilt_series_type
[docs]class crystallography_microscopy_type(base_microscopy_type): member_data_items_ = [ MemberSpec_('camera_length', 'camera_lengthType', 0), MemberSpec_('tilt_list', 'tilt_listType', 0), MemberSpec_('tilt_series', 'tilt_series_type', 1), ] subclass = None superclass = base_microscopy_type def __init__(self, id=None, specimen_preparations=None, microscope=None, illumination_mode=None, imaging_mode=None, electron_source=None, acceleration_voltage=None, c2_aperture_diameter=None, nominal_cs=None, nominal_defocus_min=None, calibrated_defocus_min=None, nominal_defocus_max=None, calibrated_defocus_max=None, nominal_magnification=None, calibrated_magnification=None, specimen_holder_model=None, cooling_holder_cryogen=None, temperature=None, alignment_procedure=None, specialist_optics=None, software_list=None, details=None, date=None, image_recording_list=None, specimen_holder=None, tilt_angle_min=None, tilt_angle_max=None, camera_length=None, tilt_list=None, tilt_series=None): self.original_tagname_ = None super(crystallography_microscopy_type, self).__init__(id, specimen_preparations, microscope, illumination_mode, imaging_mode, electron_source, acceleration_voltage, c2_aperture_diameter, nominal_cs, nominal_defocus_min, calibrated_defocus_min, nominal_defocus_max, calibrated_defocus_max, nominal_magnification, calibrated_magnification, specimen_holder_model, cooling_holder_cryogen, temperature, alignment_procedure, specialist_optics, software_list, details, date, image_recording_list, specimen_holder, tilt_angle_min, tilt_angle_max, ) self.camera_length = camera_length self.tilt_list = tilt_list if tilt_series is None: self.tilt_series = [] else: self.tilt_series = tilt_series
[docs] def factory(*args_, **kwargs_): if crystallography_microscopy_type.subclass: return crystallography_microscopy_type.subclass(*args_, **kwargs_) else: return crystallography_microscopy_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_camera_length(self): return self.camera_length
[docs] def set_camera_length(self, camera_length): self.camera_length = camera_length
[docs] def get_tilt_list(self): return self.tilt_list
[docs] def set_tilt_list(self, tilt_list): self.tilt_list = tilt_list
[docs] def get_tilt_series(self): return self.tilt_series
[docs] def set_tilt_series(self, tilt_series): self.tilt_series = tilt_series
[docs] def add_tilt_series(self, value): self.tilt_series.append(value)
[docs] def insert_tilt_series_at(self, index, value): self.tilt_series.insert(index, value)
[docs] def replace_tilt_series_at(self, index, value): self.tilt_series[index] = value
[docs] def hasContent_(self): if ( self.camera_length is not None or self.tilt_list is not None or self.tilt_series or super(crystallography_microscopy_type, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='crystallography_microscopy_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='crystallography_microscopy_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='crystallography_microscopy_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='crystallography_microscopy_type'): super(crystallography_microscopy_type, self).exportAttributes(outfile, level, already_processed, namespace_, name_='crystallography_microscopy_type')
[docs] def exportChildren(self, outfile, level, namespace_='', name_='crystallography_microscopy_type', fromsubclass_=False, pretty_print=True): super(crystallography_microscopy_type, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print) if pretty_print: eol_ = '\n' else: eol_ = '' if self.camera_length is not None: self.camera_length.export(outfile, level, namespace_, name_='camera_length', pretty_print=pretty_print) if self.tilt_list is not None: self.tilt_list.export(outfile, level, namespace_, name_='tilt_list', pretty_print=pretty_print) for tilt_series_ in self.tilt_series: tilt_series_.export(outfile, level, namespace_, name_='tilt_series', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): super(crystallography_microscopy_type, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'camera_length': obj_ = camera_lengthType.factory() obj_.build(child_) self.camera_length = obj_ obj_.original_tagname_ = 'camera_length' elif nodeName_ == 'tilt_list': obj_ = tilt_listType.factory() obj_.build(child_) self.tilt_list = obj_ obj_.original_tagname_ = 'tilt_list' elif nodeName_ == 'tilt_series': obj_ = tilt_series_type.factory() obj_.build(child_) self.tilt_series.append(obj_) obj_.original_tagname_ = 'tilt_series' super(crystallography_microscopy_type, self).buildChildren(child_, node, nodeName_, True) # end class crystallography_microscopy_type
[docs]class crystallography_tilt_type(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if crystallography_tilt_type.subclass: return crystallography_tilt_type.subclass(*args_, **kwargs_) else: return crystallography_tilt_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='crystallography_tilt_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='crystallography_tilt_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='crystallography_tilt_type', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='crystallography_tilt_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='crystallography_tilt_type', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class crystallography_tilt_type
[docs]class image_recording_type(GeneratedsSuper): """Images may have been recorded on different detectors""" member_data_items_ = [ MemberSpec_('film', 'xs:string', 1), ] subclass = None superclass = None def __init__(self, film=None): self.original_tagname_ = None if film is None: self.film = [] else: self.film = film
[docs] def factory(*args_, **kwargs_): if image_recording_type.subclass: return image_recording_type.subclass(*args_, **kwargs_) else: return image_recording_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_film(self): return self.film
[docs] def set_film(self, film): self.film = film
[docs] def add_film(self, value): self.film.append(value)
[docs] def insert_film_at(self, index, value): self.film.insert(index, value)
[docs] def replace_film_at(self, index, value): self.film[index] = value
[docs] def hasContent_(self): if ( self.film ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='image_recording_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='image_recording_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='image_recording_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='image_recording_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='image_recording_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for film_ in self.film: showIndent(outfile, level, pretty_print) outfile.write('<%sfilm>%s</%sfilm>%s' % (namespace_, self.gds_format_string(quote_xml(film_).encode(ExternalEncoding), input_name='film'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'film': film_ = child_.text film_ = self.gds_validate_string(film_, node, 'film') self.film.append(film_) # end class image_recording_type
[docs]class film(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if film.subclass: return film.subclass(*args_, **kwargs_) else: return film(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='film', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='film') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='film', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='film'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='film', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class film
[docs]class reconstruction_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('number_images_used', 'xs:positiveInteger', 0), MemberSpec_('number_classes_used', 'xs:positiveInteger', 0), MemberSpec_('applied_symmetry', 'applied_symmetry_type', 0), MemberSpec_('algorithm', ['reconstruction_algorithm_type', 'xs:token'], 0), MemberSpec_('resolution', 'resolutionType', 0), MemberSpec_('resolution_method', ['resolution_methodType', 'xs:token'], 0), MemberSpec_('reconstruction_filtering', 'reconstruction_filtering_type', 0), MemberSpec_('software_list', 'software_list_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, number_images_used=None, number_classes_used=None, applied_symmetry=None, algorithm=None, resolution=None, resolution_method=None, reconstruction_filtering=None, software_list=None, details=None): self.original_tagname_ = None self.number_images_used = number_images_used self.number_classes_used = number_classes_used self.applied_symmetry = applied_symmetry self.algorithm = algorithm self.validate_reconstruction_algorithm_type(self.algorithm) self.resolution = resolution self.resolution_method = resolution_method self.validate_resolution_methodType(self.resolution_method) self.reconstruction_filtering = reconstruction_filtering self.software_list = software_list self.details = details
[docs] def factory(*args_, **kwargs_): if reconstruction_type.subclass: return reconstruction_type.subclass(*args_, **kwargs_) else: return reconstruction_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_number_images_used(self): return self.number_images_used
[docs] def set_number_images_used(self, number_images_used): self.number_images_used = number_images_used
[docs] def get_number_classes_used(self): return self.number_classes_used
[docs] def set_number_classes_used(self, number_classes_used): self.number_classes_used = number_classes_used
[docs] def get_applied_symmetry(self): return self.applied_symmetry
[docs] def set_applied_symmetry(self, applied_symmetry): self.applied_symmetry = applied_symmetry
[docs] def get_algorithm(self): return self.algorithm
[docs] def set_algorithm(self, algorithm): self.algorithm = algorithm
[docs] def get_resolution(self): return self.resolution
[docs] def set_resolution(self, resolution): self.resolution = resolution
[docs] def get_resolution_method(self): return self.resolution_method
[docs] def set_resolution_method(self, resolution_method): self.resolution_method = resolution_method
[docs] def get_reconstruction_filtering(self): return self.reconstruction_filtering
[docs] def set_reconstruction_filtering(self, reconstruction_filtering): self.reconstruction_filtering = reconstruction_filtering
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def validate_reconstruction_algorithm_type(self, value): # Validate type reconstruction_algorithm_type, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['ARTS', 'SIRT', 'BACK-PROJECTION RECONSTRUCTION', 'EXACT BACK-PROJECTION RECONSTRUCTION', 'FOURIER SPACE RECONSTRUCTION'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on reconstruction_algorithm_type' % {"value" : value.encode("utf-8")} )
[docs] def validate_resolution_methodType(self, value): # Validate type resolution_methodType, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['FSC 0.5 CUT-OFF', 'FSC 0.33 CUT-OFF', 'FSC 0.143 CUT-OFF', u'3\u03c3'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on resolution_methodType' % {"value" : value.encode("utf-8")} )
[docs] def hasContent_(self): if ( self.number_images_used is not None or self.number_classes_used is not None or self.applied_symmetry is not None or self.algorithm is not None or self.resolution is not None or self.resolution_method is not None or self.reconstruction_filtering is not None or self.software_list is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='reconstruction_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='reconstruction_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='reconstruction_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='reconstruction_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='reconstruction_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.number_images_used is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_images_used>%s</%snumber_images_used>%s' % (namespace_, self.gds_format_integer(self.number_images_used, input_name='number_images_used'), namespace_, eol_)) if self.number_classes_used is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_classes_used>%s</%snumber_classes_used>%s' % (namespace_, self.gds_format_integer(self.number_classes_used, input_name='number_classes_used'), namespace_, eol_)) if self.applied_symmetry is not None: self.applied_symmetry.export(outfile, level, namespace_, name_='applied_symmetry', pretty_print=pretty_print) if self.algorithm is not None: showIndent(outfile, level, pretty_print) outfile.write('<%salgorithm>%s</%salgorithm>%s' % (namespace_, self.gds_format_string(quote_xml(self.algorithm).encode(ExternalEncoding), input_name='algorithm'), namespace_, eol_)) if self.resolution is not None: self.resolution.export(outfile, level, namespace_, name_='resolution', pretty_print=pretty_print) if self.resolution_method is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sresolution_method>%s</%sresolution_method>%s' % (namespace_, self.gds_format_string(quote_xml(self.resolution_method).encode(ExternalEncoding), input_name='resolution_method'), namespace_, eol_)) if self.reconstruction_filtering is not None: self.reconstruction_filtering.export(outfile, level, namespace_, name_='reconstruction_filtering', pretty_print=pretty_print) if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'number_images_used': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'number_images_used') self.number_images_used = ival_ elif nodeName_ == 'number_classes_used': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'number_classes_used') self.number_classes_used = ival_ elif nodeName_ == 'applied_symmetry': obj_ = applied_symmetry_type.factory() obj_.build(child_) self.applied_symmetry = obj_ obj_.original_tagname_ = 'applied_symmetry' elif nodeName_ == 'algorithm': algorithm_ = child_.text algorithm_ = re_.sub(String_cleanup_pat_, " ", algorithm_).strip() algorithm_ = self.gds_validate_string(algorithm_, node, 'algorithm') self.algorithm = algorithm_ # validate type reconstruction_algorithm_type self.validate_reconstruction_algorithm_type(self.algorithm) elif nodeName_ == 'resolution': obj_ = resolutionType.factory() obj_.build(child_) self.resolution = obj_ obj_.original_tagname_ = 'resolution' elif nodeName_ == 'resolution_method': resolution_method_ = child_.text resolution_method_ = re_.sub(String_cleanup_pat_, " ", resolution_method_).strip() resolution_method_ = self.gds_validate_string(resolution_method_, node, 'resolution_method') self.resolution_method = resolution_method_ # validate type resolution_methodType self.validate_resolution_methodType(self.resolution_method) elif nodeName_ == 'reconstruction_filtering': obj_ = reconstruction_filtering_type.factory() obj_.build(child_) self.reconstruction_filtering = obj_ obj_.original_tagname_ = 'reconstruction_filtering' elif nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class reconstruction_type
[docs]class film_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('id', 'xs:positiveInteger', 0), MemberSpec_('film_material', 'xs:token', 0), MemberSpec_('film_topology', ['film_topologyType', 'xs:token'], 0), MemberSpec_('film_thickness', 'film_thicknessType', 0), ] subclass = None superclass = None def __init__(self, id=None, film_material=None, film_topology=None, film_thickness=None): self.original_tagname_ = None self.id = _cast(int, id) self.film_material = film_material self.film_topology = film_topology self.validate_film_topologyType(self.film_topology) self.film_thickness = film_thickness
[docs] def factory(*args_, **kwargs_): if film_type.subclass: return film_type.subclass(*args_, **kwargs_) else: return film_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_film_material(self): return self.film_material
[docs] def set_film_material(self, film_material): self.film_material = film_material
[docs] def get_film_topology(self): return self.film_topology
[docs] def set_film_topology(self, film_topology): self.film_topology = film_topology
[docs] def get_film_thickness(self): return self.film_thickness
[docs] def set_film_thickness(self, film_thickness): self.film_thickness = film_thickness
[docs] def get_id(self): return self.id
[docs] def set_id(self, id): self.id = id
[docs] def validate_film_topologyType(self, value): # Validate type film_topologyType, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['CONTINUOUS', 'LACEY', 'HOLEY', 'HOLEARRAY'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on film_topologyType' % {"value" : value.encode("utf-8")} )
[docs] def hasContent_(self): if ( self.film_material is not None or self.film_topology is not None or self.film_thickness is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='film_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='film_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='film_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='film_type'): if self.id is not None and 'id' not in already_processed: already_processed.add('id') outfile.write(' id="%s"' % self.gds_format_integer(self.id, input_name='id'))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='film_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.film_material is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sfilm_material>%s</%sfilm_material>%s' % (namespace_, self.gds_format_string(quote_xml(self.film_material).encode(ExternalEncoding), input_name='film_material'), namespace_, eol_)) if self.film_topology is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sfilm_topology>%s</%sfilm_topology>%s' % (namespace_, self.gds_format_string(quote_xml(self.film_topology).encode(ExternalEncoding), input_name='film_topology'), namespace_, eol_)) if self.film_thickness is not None: self.film_thickness.export(outfile, level, namespace_, name_='film_thickness', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('id', node) if value is not None and 'id' not in already_processed: already_processed.add('id') try: self.id = int(value) except ValueError as exp: raise_parse_error(node, 'Bad integer attribute: %s' % exp) if self.id <= 0: raise_parse_error(node, 'Invalid PositiveInteger')
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'film_material': film_material_ = child_.text film_material_ = re_.sub(String_cleanup_pat_, " ", film_material_).strip() film_material_ = self.gds_validate_string(film_material_, node, 'film_material') self.film_material = film_material_ elif nodeName_ == 'film_topology': film_topology_ = child_.text film_topology_ = re_.sub(String_cleanup_pat_, " ", film_topology_).strip() film_topology_ = self.gds_validate_string(film_topology_, node, 'film_topology') self.film_topology = film_topology_ # validate type film_topologyType self.validate_film_topologyType(self.film_topology) elif nodeName_ == 'film_thickness': obj_ = film_thicknessType.factory() obj_.build(child_) self.film_thickness = obj_ obj_.original_tagname_ = 'film_thickness' # end class film_type
[docs]class coordinate_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('spatial_frequency', 'spatial_frequencyType', 0), MemberSpec_('y', ['yType', 'xs:float'], 0), MemberSpec_('y_noise', ['y_noiseType', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, spatial_frequency=None, y=None, y_noise=None): self.original_tagname_ = None self.spatial_frequency = spatial_frequency self.y = y self.validate_yType(self.y) self.y_noise = y_noise self.validate_y_noiseType(self.y_noise)
[docs] def factory(*args_, **kwargs_): if coordinate_type.subclass: return coordinate_type.subclass(*args_, **kwargs_) else: return coordinate_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_spatial_frequency(self): return self.spatial_frequency
[docs] def set_spatial_frequency(self, spatial_frequency): self.spatial_frequency = spatial_frequency
[docs] def get_y(self): return self.y
[docs] def set_y(self, y): self.y = y
[docs] def get_y_noise(self): return self.y_noise
[docs] def set_y_noise(self, y_noise): self.y_noise = y_noise
[docs] def validate_yType(self, value): # Validate type yType, a restriction on xs:float. if value is not None and Validate_simpletypes_: if value < 0: warnings_.warn('Value "%(value)s" does not match xsd minInclusive restriction on yType' % {"value" : value} )
[docs] def validate_y_noiseType(self, value): # Validate type y_noiseType, a restriction on xs:float. if value is not None and Validate_simpletypes_: if value < 0: warnings_.warn('Value "%(value)s" does not match xsd minInclusive restriction on y_noiseType' % {"value" : value} )
[docs] def hasContent_(self): if ( self.spatial_frequency is not None or self.y is not None or self.y_noise is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='coordinate_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='coordinate_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='coordinate_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='coordinate_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='coordinate_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.spatial_frequency is not None: self.spatial_frequency.export(outfile, level, namespace_, name_='spatial_frequency', pretty_print=pretty_print) if self.y is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sy>%s</%sy>%s' % (namespace_, self.gds_format_float(self.y, input_name='y'), namespace_, eol_)) if self.y_noise is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sy_noise>%s</%sy_noise>%s' % (namespace_, self.gds_format_float(self.y_noise, input_name='y_noise'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'spatial_frequency': obj_ = spatial_frequencyType.factory() obj_.build(child_) self.spatial_frequency = obj_ obj_.original_tagname_ = 'spatial_frequency' elif nodeName_ == 'y': sval_ = child_.text try: fval_ = float(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires float or double: %s' % exp) fval_ = self.gds_validate_float(fval_, node, 'y') self.y = fval_ # validate type yType self.validate_yType(self.y) elif nodeName_ == 'y_noise': sval_ = child_.text try: fval_ = float(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires float or double: %s' % exp) fval_ = self.gds_validate_float(fval_, node, 'y_noise') self.y_noise = fval_ # validate type y_noiseType self.validate_y_noiseType(self.y_noise) # end class coordinate_type
[docs]class figure_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('file', ['fileType', 'xs:token'], 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, file=None, details=None): self.original_tagname_ = None self.file = file self.validate_fileType(self.file) self.details = details
[docs] def factory(*args_, **kwargs_): if figure_type.subclass: return figure_type.subclass(*args_, **kwargs_) else: return figure_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_file(self): return self.file
[docs] def set_file(self, file): self.file = file
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def validate_fileType(self, value): # Validate type fileType, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_fileType_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_fileType_patterns_, ))
validate_fileType_patterns_ = [['^emd_\\d{4,}.+$']]
[docs] def hasContent_(self): if ( self.file is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='figure_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='figure_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='figure_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='figure_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='figure_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.file is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sfile>%s</%sfile>%s' % (namespace_, self.gds_format_string(quote_xml(self.file).encode(ExternalEncoding), input_name='file'), namespace_, eol_)) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'file': file_ = child_.text file_ = re_.sub(String_cleanup_pat_, " ", file_).strip() file_ = self.gds_validate_string(file_, node, 'file') self.file = file_ # validate type fileType self.validate_fileType(self.file) elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class figure_type
[docs]class ctf_correction_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('phase_reversal', 'phase_reversalType', 0), MemberSpec_('amplitude_correction', 'amplitude_correctionType', 0), MemberSpec_('correction_operation', ['correction_operationType', 'xs:string'], 0), MemberSpec_('software_list', 'software_list_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, phase_reversal=None, amplitude_correction=None, correction_operation=None, software_list=None, details=None): self.original_tagname_ = None self.phase_reversal = phase_reversal self.amplitude_correction = amplitude_correction self.correction_operation = correction_operation self.validate_correction_operationType(self.correction_operation) self.software_list = software_list self.details = details
[docs] def factory(*args_, **kwargs_): if ctf_correction_type.subclass: return ctf_correction_type.subclass(*args_, **kwargs_) else: return ctf_correction_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_phase_reversal(self): return self.phase_reversal
[docs] def set_phase_reversal(self, phase_reversal): self.phase_reversal = phase_reversal
[docs] def get_amplitude_correction(self): return self.amplitude_correction
[docs] def set_amplitude_correction(self, amplitude_correction): self.amplitude_correction = amplitude_correction
[docs] def get_correction_operation(self): return self.correction_operation
[docs] def set_correction_operation(self, correction_operation): self.correction_operation = correction_operation
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def validate_correction_operationType(self, value): # Validate type correction_operationType, a restriction on xs:string. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['MULTIPLICATION', 'DIVISION'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on correction_operationType' % {"value" : value.encode("utf-8")} )
[docs] def hasContent_(self): if ( self.phase_reversal is not None or self.amplitude_correction is not None or self.correction_operation is not None or self.software_list is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='ctf_correction_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='ctf_correction_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='ctf_correction_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='ctf_correction_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='ctf_correction_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.phase_reversal is not None: self.phase_reversal.export(outfile, level, namespace_, name_='phase_reversal', pretty_print=pretty_print) if self.amplitude_correction is not None: self.amplitude_correction.export(outfile, level, namespace_, name_='amplitude_correction', pretty_print=pretty_print) if self.correction_operation is not None: showIndent(outfile, level, pretty_print) outfile.write('<%scorrection_operation>%s</%scorrection_operation>%s' % (namespace_, self.gds_format_string(quote_xml(self.correction_operation).encode(ExternalEncoding), input_name='correction_operation'), namespace_, eol_)) if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'phase_reversal': obj_ = phase_reversalType.factory() obj_.build(child_) self.phase_reversal = obj_ obj_.original_tagname_ = 'phase_reversal' elif nodeName_ == 'amplitude_correction': obj_ = amplitude_correctionType.factory() obj_.build(child_) self.amplitude_correction = obj_ obj_.original_tagname_ = 'amplitude_correction' elif nodeName_ == 'correction_operation': correction_operation_ = child_.text correction_operation_ = self.gds_validate_string(correction_operation_, node, 'correction_operation') self.correction_operation = correction_operation_ # validate type correction_operationType self.validate_correction_operationType(self.correction_operation) elif nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class ctf_correction_type
[docs]class angle_assignment_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('type_', ['typeType8', 'xs:token'], 0), MemberSpec_('projection_matching_processing', 'projection_matching_processingType', 0), MemberSpec_('software_list', 'software_list_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, type_=None, projection_matching_processing=None, software_list=None, details=None): self.original_tagname_ = None self.type_ = type_ self.validate_typeType8(self.type_) self.projection_matching_processing = projection_matching_processing self.software_list = software_list self.details = details
[docs] def factory(*args_, **kwargs_): if angle_assignment_type.subclass: return angle_assignment_type.subclass(*args_, **kwargs_) else: return angle_assignment_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_type(self): return self.type_
[docs] def set_type(self, type_): self.type_ = type_
[docs] def get_projection_matching_processing(self): return self.projection_matching_processing
[docs] def set_projection_matching_processing(self, projection_matching_processing): self.projection_matching_processing = projection_matching_processing
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def validate_typeType8(self, value): # Validate type typeType8, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['ANGULAR RECONSTITUTION', 'COMMON LINES', 'PROJECTION MATCHING', 'RANDOM ASSIGNMENT'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on typeType8' % {"value" : value.encode("utf-8")} )
[docs] def hasContent_(self): if ( self.type_ is not None or self.projection_matching_processing is not None or self.software_list is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='angle_assignment_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='angle_assignment_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='angle_assignment_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='angle_assignment_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='angle_assignment_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.type_ is not None: showIndent(outfile, level, pretty_print) outfile.write('<%stype>%s</%stype>%s' % (namespace_, self.gds_format_string(quote_xml(self.type_).encode(ExternalEncoding), input_name='type'), namespace_, eol_)) if self.projection_matching_processing is not None: self.projection_matching_processing.export(outfile, level, namespace_, name_='projection_matching_processing', pretty_print=pretty_print) if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'type': type_ = child_.text type_ = re_.sub(String_cleanup_pat_, " ", type_).strip() type_ = self.gds_validate_string(type_, node, 'type') self.type_ = type_ # validate type typeType8 self.validate_typeType8(self.type_) elif nodeName_ == 'projection_matching_processing': obj_ = projection_matching_processingType.factory() obj_.build(child_) self.projection_matching_processing = obj_ obj_.original_tagname_ = 'projection_matching_processing' elif nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class angle_assignment_type
[docs]class modelling_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('initial_model', 'initial_modelType', 1), MemberSpec_('final_model', 'final_modelType', 0), MemberSpec_('refinement_protocol', ['refinement_protocolType', 'xs:string'], 0), MemberSpec_('software_list', 'software_list_type', 0), MemberSpec_('details', 'xs:string', 0), MemberSpec_('target_criteria', 'xs:token', 0), MemberSpec_('refinement_space', 'xs:token', 0), MemberSpec_('overall_bvalue', 'xs:float', 0), ] subclass = None superclass = None def __init__(self, initial_model=None, final_model=None, refinement_protocol=None, software_list=None, details=None, target_criteria=None, refinement_space=None, overall_bvalue=None): self.original_tagname_ = None if initial_model is None: self.initial_model = [] else: self.initial_model = initial_model self.final_model = final_model self.refinement_protocol = refinement_protocol self.validate_refinement_protocolType(self.refinement_protocol) self.software_list = software_list self.details = details self.target_criteria = target_criteria self.refinement_space = refinement_space self.overall_bvalue = overall_bvalue
[docs] def factory(*args_, **kwargs_): if modelling_type.subclass: return modelling_type.subclass(*args_, **kwargs_) else: return modelling_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_initial_model(self): return self.initial_model
[docs] def set_initial_model(self, initial_model): self.initial_model = initial_model
[docs] def add_initial_model(self, value): self.initial_model.append(value)
[docs] def insert_initial_model_at(self, index, value): self.initial_model.insert(index, value)
[docs] def replace_initial_model_at(self, index, value): self.initial_model[index] = value
[docs] def get_final_model(self): return self.final_model
[docs] def set_final_model(self, final_model): self.final_model = final_model
[docs] def get_refinement_protocol(self): return self.refinement_protocol
[docs] def set_refinement_protocol(self, refinement_protocol): self.refinement_protocol = refinement_protocol
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def get_target_criteria(self): return self.target_criteria
[docs] def set_target_criteria(self, target_criteria): self.target_criteria = target_criteria
[docs] def get_refinement_space(self): return self.refinement_space
[docs] def set_refinement_space(self, refinement_space): self.refinement_space = refinement_space
[docs] def get_overall_bvalue(self): return self.overall_bvalue
[docs] def set_overall_bvalue(self, overall_bvalue): self.overall_bvalue = overall_bvalue
[docs] def validate_refinement_protocolType(self, value): # Validate type refinement_protocolType, a restriction on xs:string. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['RIGID BODY FITTING', 'RIGID BODY DOCKING', 'FLEXIBLE FITTING', 'FLEXIBLE DOCKING'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on refinement_protocolType' % {"value" : value.encode("utf-8")} )
[docs] def hasContent_(self): if ( self.initial_model or self.final_model is not None or self.refinement_protocol is not None or self.software_list is not None or self.details is not None or self.target_criteria is not None or self.refinement_space is not None or self.overall_bvalue is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='modelling_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='modelling_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='modelling_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='modelling_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='modelling_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for initial_model_ in self.initial_model: initial_model_.export(outfile, level, namespace_, name_='initial_model', pretty_print=pretty_print) if self.final_model is not None: self.final_model.export(outfile, level, namespace_, name_='final_model', pretty_print=pretty_print) if self.refinement_protocol is not None: showIndent(outfile, level, pretty_print) outfile.write('<%srefinement_protocol>%s</%srefinement_protocol>%s' % (namespace_, self.gds_format_string(quote_xml(self.refinement_protocol).encode(ExternalEncoding), input_name='refinement_protocol'), namespace_, eol_)) if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_)) if self.target_criteria is not None: showIndent(outfile, level, pretty_print) outfile.write('<%starget_criteria>%s</%starget_criteria>%s' % (namespace_, self.gds_format_string(quote_xml(self.target_criteria).encode(ExternalEncoding), input_name='target_criteria'), namespace_, eol_)) if self.refinement_space is not None: showIndent(outfile, level, pretty_print) outfile.write('<%srefinement_space>%s</%srefinement_space>%s' % (namespace_, self.gds_format_string(quote_xml(self.refinement_space).encode(ExternalEncoding), input_name='refinement_space'), namespace_, eol_)) if self.overall_bvalue is not None: showIndent(outfile, level, pretty_print) outfile.write('<%soverall_bvalue>%s</%soverall_bvalue>%s' % (namespace_, self.gds_format_float(self.overall_bvalue, input_name='overall_bvalue'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'initial_model': obj_ = initial_modelType.factory() obj_.build(child_) self.initial_model.append(obj_) obj_.original_tagname_ = 'initial_model' elif nodeName_ == 'final_model': obj_ = final_modelType.factory() obj_.build(child_) self.final_model = obj_ obj_.original_tagname_ = 'final_model' elif nodeName_ == 'refinement_protocol': refinement_protocol_ = child_.text refinement_protocol_ = self.gds_validate_string(refinement_protocol_, node, 'refinement_protocol') self.refinement_protocol = refinement_protocol_ # validate type refinement_protocolType self.validate_refinement_protocolType(self.refinement_protocol) elif nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ elif nodeName_ == 'target_criteria': target_criteria_ = child_.text target_criteria_ = re_.sub(String_cleanup_pat_, " ", target_criteria_).strip() target_criteria_ = self.gds_validate_string(target_criteria_, node, 'target_criteria') self.target_criteria = target_criteria_ elif nodeName_ == 'refinement_space': refinement_space_ = child_.text refinement_space_ = re_.sub(String_cleanup_pat_, " ", refinement_space_).strip() refinement_space_ = self.gds_validate_string(refinement_space_, node, 'refinement_space') self.refinement_space = refinement_space_ elif nodeName_ == 'overall_bvalue': sval_ = child_.text try: fval_ = float(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires float or double: %s' % exp) fval_ = self.gds_validate_float(fval_, node, 'overall_bvalue') self.overall_bvalue = fval_ # end class modelling_type
[docs]class maximum_likelihood_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('parameters', 'parametersType', 0), MemberSpec_('noise_model', 'noise_modelType', 0), MemberSpec_('software_list', 'software_list_type', 0), ] subclass = None superclass = None def __init__(self, parameters=None, noise_model=None, software_list=None): self.original_tagname_ = None self.parameters = parameters self.noise_model = noise_model self.software_list = software_list
[docs] def factory(*args_, **kwargs_): if maximum_likelihood_type.subclass: return maximum_likelihood_type.subclass(*args_, **kwargs_) else: return maximum_likelihood_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_parameters(self): return self.parameters
[docs] def set_parameters(self, parameters): self.parameters = parameters
[docs] def get_noise_model(self): return self.noise_model
[docs] def set_noise_model(self, noise_model): self.noise_model = noise_model
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def hasContent_(self): if ( self.parameters is not None or self.noise_model is not None or self.software_list is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='maximum_likelihood_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='maximum_likelihood_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='maximum_likelihood_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='maximum_likelihood_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='maximum_likelihood_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.parameters is not None: self.parameters.export(outfile, level, namespace_, name_='parameters', pretty_print=pretty_print) if self.noise_model is not None: self.noise_model.export(outfile, level, namespace_, name_='noise_model', pretty_print=pretty_print) if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'parameters': obj_ = parametersType.factory() obj_.build(child_) self.parameters = obj_ obj_.original_tagname_ = 'parameters' elif nodeName_ == 'noise_model': obj_ = noise_modelType.factory() obj_.build(child_) self.noise_model = obj_ obj_.original_tagname_ = 'noise_model' elif nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' # end class maximum_likelihood_type
[docs]class base_processing_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('id', 'xs:positiveInteger', 0), MemberSpec_('image_recording_id', 'xs:positiveInteger', 0), MemberSpec_('details', 'xs:token', 0), ] subclass = None superclass = None def __init__(self, id=None, image_recording_id=None, details=None, extensiontype_=None): self.original_tagname_ = None self.id = _cast(int, id) self.image_recording_id = image_recording_id self.details = details self.extensiontype_ = extensiontype_
[docs] def factory(*args_, **kwargs_): if base_processing_type.subclass: return base_processing_type.subclass(*args_, **kwargs_) else: return base_processing_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_image_recording_id(self): return self.image_recording_id
[docs] def set_image_recording_id(self, image_recording_id): self.image_recording_id = image_recording_id
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def get_id(self): return self.id
[docs] def set_id(self, id): self.id = id
[docs] def get_extensiontype_(self): return self.extensiontype_
[docs] def set_extensiontype_(self, extensiontype_): self.extensiontype_ = extensiontype_
[docs] def hasContent_(self): if ( self.image_recording_id is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='base_processing_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='base_processing_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='base_processing_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='base_processing_type'): if self.id is not None and 'id' not in already_processed: already_processed.add('id') outfile.write(' id="%s"' % self.gds_format_integer(self.id, input_name='id')) if self.extensiontype_ is not None and 'xsi:type' not in already_processed: already_processed.add('xsi:type') outfile.write(' xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"') outfile.write(' xsi:type="%s"' % self.extensiontype_)
[docs] def exportChildren(self, outfile, level, namespace_='', name_='base_processing_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.image_recording_id is not None: showIndent(outfile, level, pretty_print) outfile.write('<%simage_recording_id>%s</%simage_recording_id>%s' % (namespace_, self.gds_format_integer(self.image_recording_id, input_name='image_recording_id'), namespace_, eol_)) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('id', node) if value is not None and 'id' not in already_processed: already_processed.add('id') try: self.id = int(value) except ValueError as exp: raise_parse_error(node, 'Bad integer attribute: %s' % exp) if self.id <= 0: raise_parse_error(node, 'Invalid PositiveInteger') value = find_attr_value_('xsi:type', node) if value is not None and 'xsi:type' not in already_processed: already_processed.add('xsi:type') self.extensiontype_ = value
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'image_recording_id': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'image_recording_id') self.image_recording_id = ival_ elif nodeName_ == 'details': details_ = child_.text details_ = re_.sub(String_cleanup_pat_, " ", details_).strip() details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class base_processing_type
[docs]class singleparticle_processing_type(base_processing_type): member_data_items_ = [ MemberSpec_('particle_selection', 'particle_selection_type', 1), MemberSpec_('ctf_correction', 'ctf_correction_type', 0), MemberSpec_('startup_model', 'starting_map_type', 0), MemberSpec_('initial_angle_assignment', 'angle_assignment_type', 0), MemberSpec_('final_reconstruction', 'reconstruction_type', 0), MemberSpec_('final_angle_assignment', 'angle_assignment_type', 0), MemberSpec_('final_multi_reference_alignment', 'final_multi_reference_alignmentType11', 0), MemberSpec_('final_two_d_classification', 'classification_type', 0), MemberSpec_('final_three_d_classification', 'classification_type', 0), ] subclass = None superclass = base_processing_type def __init__(self, id=None, image_recording_id=None, details=None, particle_selection=None, ctf_correction=None, startup_model=None, initial_angle_assignment=None, final_reconstruction=None, final_angle_assignment=None, final_multi_reference_alignment=None, final_two_d_classification=None, final_three_d_classification=None): self.original_tagname_ = None super(singleparticle_processing_type, self).__init__(id, image_recording_id, details, ) if particle_selection is None: self.particle_selection = [] else: self.particle_selection = particle_selection self.ctf_correction = ctf_correction self.startup_model = startup_model self.initial_angle_assignment = initial_angle_assignment self.final_reconstruction = final_reconstruction self.final_angle_assignment = final_angle_assignment self.final_multi_reference_alignment = final_multi_reference_alignment self.final_two_d_classification = final_two_d_classification self.final_three_d_classification = final_three_d_classification
[docs] def factory(*args_, **kwargs_): if singleparticle_processing_type.subclass: return singleparticle_processing_type.subclass(*args_, **kwargs_) else: return singleparticle_processing_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_particle_selection(self): return self.particle_selection
[docs] def set_particle_selection(self, particle_selection): self.particle_selection = particle_selection
[docs] def add_particle_selection(self, value): self.particle_selection.append(value)
[docs] def insert_particle_selection_at(self, index, value): self.particle_selection.insert(index, value)
[docs] def replace_particle_selection_at(self, index, value): self.particle_selection[index] = value
[docs] def get_ctf_correction(self): return self.ctf_correction
[docs] def set_ctf_correction(self, ctf_correction): self.ctf_correction = ctf_correction
[docs] def get_startup_model(self): return self.startup_model
[docs] def set_startup_model(self, startup_model): self.startup_model = startup_model
[docs] def get_initial_angle_assignment(self): return self.initial_angle_assignment
[docs] def set_initial_angle_assignment(self, initial_angle_assignment): self.initial_angle_assignment = initial_angle_assignment
[docs] def get_final_reconstruction(self): return self.final_reconstruction
[docs] def set_final_reconstruction(self, final_reconstruction): self.final_reconstruction = final_reconstruction
[docs] def get_final_angle_assignment(self): return self.final_angle_assignment
[docs] def set_final_angle_assignment(self, final_angle_assignment): self.final_angle_assignment = final_angle_assignment
[docs] def get_final_multi_reference_alignment(self): return self.final_multi_reference_alignment
[docs] def set_final_multi_reference_alignment(self, final_multi_reference_alignment): self.final_multi_reference_alignment = final_multi_reference_alignment
[docs] def get_final_two_d_classification(self): return self.final_two_d_classification
[docs] def set_final_two_d_classification(self, final_two_d_classification): self.final_two_d_classification = final_two_d_classification
[docs] def get_final_three_d_classification(self): return self.final_three_d_classification
[docs] def set_final_three_d_classification(self, final_three_d_classification): self.final_three_d_classification = final_three_d_classification
[docs] def hasContent_(self): if ( self.particle_selection or self.ctf_correction is not None or self.startup_model is not None or self.initial_angle_assignment is not None or self.final_reconstruction is not None or self.final_angle_assignment is not None or self.final_multi_reference_alignment is not None or self.final_two_d_classification is not None or self.final_three_d_classification is not None or super(singleparticle_processing_type, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='singleparticle_processing_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='singleparticle_processing_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='singleparticle_processing_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='singleparticle_processing_type'): super(singleparticle_processing_type, self).exportAttributes(outfile, level, already_processed, namespace_, name_='singleparticle_processing_type')
[docs] def exportChildren(self, outfile, level, namespace_='', name_='singleparticle_processing_type', fromsubclass_=False, pretty_print=True): super(singleparticle_processing_type, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print) if pretty_print: eol_ = '\n' else: eol_ = '' for particle_selection_ in self.particle_selection: particle_selection_.export(outfile, level, namespace_, name_='particle_selection', pretty_print=pretty_print) if self.ctf_correction is not None: self.ctf_correction.export(outfile, level, namespace_, name_='ctf_correction', pretty_print=pretty_print) if self.startup_model is not None: self.startup_model.export(outfile, level, namespace_, name_='startup_model', pretty_print=pretty_print) if self.initial_angle_assignment is not None: self.initial_angle_assignment.export(outfile, level, namespace_, name_='initial_angle_assignment', pretty_print=pretty_print) if self.final_reconstruction is not None: self.final_reconstruction.export(outfile, level, namespace_, name_='final_reconstruction', pretty_print=pretty_print) if self.final_angle_assignment is not None: self.final_angle_assignment.export(outfile, level, namespace_, name_='final_angle_assignment', pretty_print=pretty_print) if self.final_multi_reference_alignment is not None: self.final_multi_reference_alignment.export(outfile, level, namespace_, name_='final_multi_reference_alignment', pretty_print=pretty_print) if self.final_two_d_classification is not None: self.final_two_d_classification.export(outfile, level, namespace_, name_='final_two_d_classification', pretty_print=pretty_print) if self.final_three_d_classification is not None: self.final_three_d_classification.export(outfile, level, namespace_, name_='final_three_d_classification', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): super(singleparticle_processing_type, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'particle_selection': obj_ = particle_selection_type.factory() obj_.build(child_) self.particle_selection.append(obj_) obj_.original_tagname_ = 'particle_selection' elif nodeName_ == 'ctf_correction': obj_ = ctf_correction_type.factory() obj_.build(child_) self.ctf_correction = obj_ obj_.original_tagname_ = 'ctf_correction' elif nodeName_ == 'startup_model': obj_ = starting_map_type.factory() obj_.build(child_) self.startup_model = obj_ obj_.original_tagname_ = 'startup_model' elif nodeName_ == 'initial_angle_assignment': obj_ = angle_assignment_type.factory() obj_.build(child_) self.initial_angle_assignment = obj_ obj_.original_tagname_ = 'initial_angle_assignment' elif nodeName_ == 'final_reconstruction': obj_ = reconstruction_type.factory() obj_.build(child_) self.final_reconstruction = obj_ obj_.original_tagname_ = 'final_reconstruction' elif nodeName_ == 'final_angle_assignment': obj_ = angle_assignment_type.factory() obj_.build(child_) self.final_angle_assignment = obj_ obj_.original_tagname_ = 'final_angle_assignment' elif nodeName_ == 'final_multi_reference_alignment': obj_ = final_multi_reference_alignmentType11.factory() obj_.build(child_) self.final_multi_reference_alignment = obj_ obj_.original_tagname_ = 'final_multi_reference_alignment' elif nodeName_ == 'final_two_d_classification': obj_ = classification_type.factory() obj_.build(child_) self.final_two_d_classification = obj_ obj_.original_tagname_ = 'final_two_d_classification' elif nodeName_ == 'final_three_d_classification': obj_ = classification_type.factory() obj_.build(child_) self.final_three_d_classification = obj_ obj_.original_tagname_ = 'final_three_d_classification' super(singleparticle_processing_type, self).buildChildren(child_, node, nodeName_, True) # end class singleparticle_processing_type
[docs]class subtomogram_averaging_processing_type(base_processing_type): member_data_items_ = [ MemberSpec_('final_reconstruction', 'subtomogram_reconstruction_type', 0), MemberSpec_('extraction', 'extractionType13', 0), MemberSpec_('ctf_correction', 'ctf_correction_type', 0), MemberSpec_('final_multi_reference_alignment', 'final_multi_reference_alignmentType14', 0), MemberSpec_('final_three_d_classification', 'classification_type', 0), MemberSpec_('final_angle_assignment', 'angle_assignment_type', 0), MemberSpec_('crystal_parameters', 'crystal_parameters_type', 0), ] subclass = None superclass = base_processing_type def __init__(self, id=None, image_recording_id=None, details=None, final_reconstruction=None, extraction=None, ctf_correction=None, final_multi_reference_alignment=None, final_three_d_classification=None, final_angle_assignment=None, crystal_parameters=None): self.original_tagname_ = None super(subtomogram_averaging_processing_type, self).__init__(id, image_recording_id, details, ) self.final_reconstruction = final_reconstruction self.extraction = extraction self.ctf_correction = ctf_correction self.final_multi_reference_alignment = final_multi_reference_alignment self.final_three_d_classification = final_three_d_classification self.final_angle_assignment = final_angle_assignment self.crystal_parameters = crystal_parameters
[docs] def factory(*args_, **kwargs_): if subtomogram_averaging_processing_type.subclass: return subtomogram_averaging_processing_type.subclass(*args_, **kwargs_) else: return subtomogram_averaging_processing_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_final_reconstruction(self): return self.final_reconstruction
[docs] def set_final_reconstruction(self, final_reconstruction): self.final_reconstruction = final_reconstruction
[docs] def get_extraction(self): return self.extraction
[docs] def set_extraction(self, extraction): self.extraction = extraction
[docs] def get_ctf_correction(self): return self.ctf_correction
[docs] def set_ctf_correction(self, ctf_correction): self.ctf_correction = ctf_correction
[docs] def get_final_multi_reference_alignment(self): return self.final_multi_reference_alignment
[docs] def set_final_multi_reference_alignment(self, final_multi_reference_alignment): self.final_multi_reference_alignment = final_multi_reference_alignment
[docs] def get_final_three_d_classification(self): return self.final_three_d_classification
[docs] def set_final_three_d_classification(self, final_three_d_classification): self.final_three_d_classification = final_three_d_classification
[docs] def get_final_angle_assignment(self): return self.final_angle_assignment
[docs] def set_final_angle_assignment(self, final_angle_assignment): self.final_angle_assignment = final_angle_assignment
[docs] def get_crystal_parameters(self): return self.crystal_parameters
[docs] def set_crystal_parameters(self, crystal_parameters): self.crystal_parameters = crystal_parameters
[docs] def hasContent_(self): if ( self.final_reconstruction is not None or self.extraction is not None or self.ctf_correction is not None or self.final_multi_reference_alignment is not None or self.final_three_d_classification is not None or self.final_angle_assignment is not None or self.crystal_parameters is not None or super(subtomogram_averaging_processing_type, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='subtomogram_averaging_processing_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='subtomogram_averaging_processing_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='subtomogram_averaging_processing_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='subtomogram_averaging_processing_type'): super(subtomogram_averaging_processing_type, self).exportAttributes(outfile, level, already_processed, namespace_, name_='subtomogram_averaging_processing_type')
[docs] def exportChildren(self, outfile, level, namespace_='', name_='subtomogram_averaging_processing_type', fromsubclass_=False, pretty_print=True): super(subtomogram_averaging_processing_type, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print) if pretty_print: eol_ = '\n' else: eol_ = '' if self.final_reconstruction is not None: self.final_reconstruction.export(outfile, level, namespace_, name_='final_reconstruction', pretty_print=pretty_print) if self.extraction is not None: self.extraction.export(outfile, level, namespace_, name_='extraction', pretty_print=pretty_print) if self.ctf_correction is not None: self.ctf_correction.export(outfile, level, namespace_, name_='ctf_correction', pretty_print=pretty_print) if self.final_multi_reference_alignment is not None: self.final_multi_reference_alignment.export(outfile, level, namespace_, name_='final_multi_reference_alignment', pretty_print=pretty_print) if self.final_three_d_classification is not None: self.final_three_d_classification.export(outfile, level, namespace_, name_='final_three_d_classification', pretty_print=pretty_print) if self.final_angle_assignment is not None: self.final_angle_assignment.export(outfile, level, namespace_, name_='final_angle_assignment', pretty_print=pretty_print) if self.crystal_parameters is not None: self.crystal_parameters.export(outfile, level, namespace_, name_='crystal_parameters', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): super(subtomogram_averaging_processing_type, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'final_reconstruction': obj_ = subtomogram_reconstruction_type.factory() obj_.build(child_) self.final_reconstruction = obj_ obj_.original_tagname_ = 'final_reconstruction' elif nodeName_ == 'extraction': obj_ = extractionType13.factory() obj_.build(child_) self.extraction = obj_ obj_.original_tagname_ = 'extraction' elif nodeName_ == 'ctf_correction': obj_ = ctf_correction_type.factory() obj_.build(child_) self.ctf_correction = obj_ obj_.original_tagname_ = 'ctf_correction' elif nodeName_ == 'final_multi_reference_alignment': obj_ = final_multi_reference_alignmentType14.factory() obj_.build(child_) self.final_multi_reference_alignment = obj_ obj_.original_tagname_ = 'final_multi_reference_alignment' elif nodeName_ == 'final_three_d_classification': obj_ = classification_type.factory() obj_.build(child_) self.final_three_d_classification = obj_ obj_.original_tagname_ = 'final_three_d_classification' elif nodeName_ == 'final_angle_assignment': obj_ = angle_assignment_type.factory() obj_.build(child_) self.final_angle_assignment = obj_ obj_.original_tagname_ = 'final_angle_assignment' elif nodeName_ == 'crystal_parameters': obj_ = crystal_parameters_type.factory() obj_.build(child_) self.crystal_parameters = obj_ obj_.original_tagname_ = 'crystal_parameters' super(subtomogram_averaging_processing_type, self).buildChildren(child_, node, nodeName_, True) # end class subtomogram_averaging_processing_type
[docs]class tomography_processing_type(base_processing_type): member_data_items_ = [ MemberSpec_('final_reconstruction', 'reconstruction_type', 0), MemberSpec_('series_aligment_software_list', 'software_list_type', 0), MemberSpec_('ctf_correction', 'ctf_correction_type', 0), MemberSpec_('crystal_parameters', 'crystal_parameters_type', 0), ] subclass = None superclass = base_processing_type def __init__(self, id=None, image_recording_id=None, details=None, final_reconstruction=None, series_aligment_software_list=None, ctf_correction=None, crystal_parameters=None): self.original_tagname_ = None super(tomography_processing_type, self).__init__(id, image_recording_id, details, ) self.final_reconstruction = final_reconstruction self.series_aligment_software_list = series_aligment_software_list self.ctf_correction = ctf_correction self.crystal_parameters = crystal_parameters
[docs] def factory(*args_, **kwargs_): if tomography_processing_type.subclass: return tomography_processing_type.subclass(*args_, **kwargs_) else: return tomography_processing_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_final_reconstruction(self): return self.final_reconstruction
[docs] def set_final_reconstruction(self, final_reconstruction): self.final_reconstruction = final_reconstruction
[docs] def get_series_aligment_software_list(self): return self.series_aligment_software_list
[docs] def set_series_aligment_software_list(self, series_aligment_software_list): self.series_aligment_software_list = series_aligment_software_list
[docs] def get_ctf_correction(self): return self.ctf_correction
[docs] def set_ctf_correction(self, ctf_correction): self.ctf_correction = ctf_correction
[docs] def get_crystal_parameters(self): return self.crystal_parameters
[docs] def set_crystal_parameters(self, crystal_parameters): self.crystal_parameters = crystal_parameters
[docs] def hasContent_(self): if ( self.final_reconstruction is not None or self.series_aligment_software_list is not None or self.ctf_correction is not None or self.crystal_parameters is not None or super(tomography_processing_type, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='tomography_processing_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='tomography_processing_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='tomography_processing_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='tomography_processing_type'): super(tomography_processing_type, self).exportAttributes(outfile, level, already_processed, namespace_, name_='tomography_processing_type')
[docs] def exportChildren(self, outfile, level, namespace_='', name_='tomography_processing_type', fromsubclass_=False, pretty_print=True): super(tomography_processing_type, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print) if pretty_print: eol_ = '\n' else: eol_ = '' if self.final_reconstruction is not None: self.final_reconstruction.export(outfile, level, namespace_, name_='final_reconstruction', pretty_print=pretty_print) if self.series_aligment_software_list is not None: self.series_aligment_software_list.export(outfile, level, namespace_, name_='series_aligment_software_list', pretty_print=pretty_print) if self.ctf_correction is not None: self.ctf_correction.export(outfile, level, namespace_, name_='ctf_correction', pretty_print=pretty_print) if self.crystal_parameters is not None: self.crystal_parameters.export(outfile, level, namespace_, name_='crystal_parameters', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): super(tomography_processing_type, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'final_reconstruction': obj_ = reconstruction_type.factory() obj_.build(child_) self.final_reconstruction = obj_ obj_.original_tagname_ = 'final_reconstruction' elif nodeName_ == 'series_aligment_software_list': obj_ = software_list_type.factory() obj_.build(child_) self.series_aligment_software_list = obj_ obj_.original_tagname_ = 'series_aligment_software_list' elif nodeName_ == 'ctf_correction': obj_ = ctf_correction_type.factory() obj_.build(child_) self.ctf_correction = obj_ obj_.original_tagname_ = 'ctf_correction' elif nodeName_ == 'crystal_parameters': obj_ = crystal_parameters_type.factory() obj_.build(child_) self.crystal_parameters = obj_ obj_.original_tagname_ = 'crystal_parameters' super(tomography_processing_type, self).buildChildren(child_, node, nodeName_, True) # end class tomography_processing_type
[docs]class crystallography_processing_type(base_processing_type): member_data_items_ = [ MemberSpec_('final_reconstruction', 'reconstruction_type', 0), MemberSpec_('crystal_parameters', 'crystal_parameters_type', 0), MemberSpec_('startup_model', 'starting_map_type', 1), MemberSpec_('ctf_correction', 'ctf_correction_type', 0), MemberSpec_('molecular_replacement', 'molecular_replacementType15', 0), MemberSpec_('lattice_distortion_correction', 'lattice_distortion_correctionType20', 0), MemberSpec_('symmetry_determination', 'symmetry_determinationType21', 0), MemberSpec_('merging', 'mergingType22', 0), MemberSpec_('crystallography_statistics', 'crystallography_statistics_type', 0), ] subclass = None superclass = base_processing_type def __init__(self, id=None, image_recording_id=None, details=None, final_reconstruction=None, crystal_parameters=None, startup_model=None, ctf_correction=None, molecular_replacement=None, lattice_distortion_correction=None, symmetry_determination=None, merging=None, crystallography_statistics=None): self.original_tagname_ = None super(crystallography_processing_type, self).__init__(id, image_recording_id, details, ) self.final_reconstruction = final_reconstruction self.crystal_parameters = crystal_parameters if startup_model is None: self.startup_model = [] else: self.startup_model = startup_model self.ctf_correction = ctf_correction self.molecular_replacement = molecular_replacement self.lattice_distortion_correction = lattice_distortion_correction self.symmetry_determination = symmetry_determination self.merging = merging self.crystallography_statistics = crystallography_statistics
[docs] def factory(*args_, **kwargs_): if crystallography_processing_type.subclass: return crystallography_processing_type.subclass(*args_, **kwargs_) else: return crystallography_processing_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_final_reconstruction(self): return self.final_reconstruction
[docs] def set_final_reconstruction(self, final_reconstruction): self.final_reconstruction = final_reconstruction
[docs] def get_crystal_parameters(self): return self.crystal_parameters
[docs] def set_crystal_parameters(self, crystal_parameters): self.crystal_parameters = crystal_parameters
[docs] def get_startup_model(self): return self.startup_model
[docs] def set_startup_model(self, startup_model): self.startup_model = startup_model
[docs] def add_startup_model(self, value): self.startup_model.append(value)
[docs] def insert_startup_model_at(self, index, value): self.startup_model.insert(index, value)
[docs] def replace_startup_model_at(self, index, value): self.startup_model[index] = value
[docs] def get_ctf_correction(self): return self.ctf_correction
[docs] def set_ctf_correction(self, ctf_correction): self.ctf_correction = ctf_correction
[docs] def get_molecular_replacement(self): return self.molecular_replacement
[docs] def set_molecular_replacement(self, molecular_replacement): self.molecular_replacement = molecular_replacement
[docs] def get_lattice_distortion_correction(self): return self.lattice_distortion_correction
[docs] def set_lattice_distortion_correction(self, lattice_distortion_correction): self.lattice_distortion_correction = lattice_distortion_correction
[docs] def get_symmetry_determination(self): return self.symmetry_determination
[docs] def set_symmetry_determination(self, symmetry_determination): self.symmetry_determination = symmetry_determination
[docs] def get_merging(self): return self.merging
[docs] def set_merging(self, merging): self.merging = merging
[docs] def get_crystallography_statistics(self): return self.crystallography_statistics
[docs] def set_crystallography_statistics(self, crystallography_statistics): self.crystallography_statistics = crystallography_statistics
[docs] def hasContent_(self): if ( self.final_reconstruction is not None or self.crystal_parameters is not None or self.startup_model or self.ctf_correction is not None or self.molecular_replacement is not None or self.lattice_distortion_correction is not None or self.symmetry_determination is not None or self.merging is not None or self.crystallography_statistics is not None or super(crystallography_processing_type, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='crystallography_processing_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='crystallography_processing_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='crystallography_processing_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='crystallography_processing_type'): super(crystallography_processing_type, self).exportAttributes(outfile, level, already_processed, namespace_, name_='crystallography_processing_type')
[docs] def exportChildren(self, outfile, level, namespace_='', name_='crystallography_processing_type', fromsubclass_=False, pretty_print=True): super(crystallography_processing_type, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print) if pretty_print: eol_ = '\n' else: eol_ = '' if self.final_reconstruction is not None: self.final_reconstruction.export(outfile, level, namespace_, name_='final_reconstruction', pretty_print=pretty_print) if self.crystal_parameters is not None: self.crystal_parameters.export(outfile, level, namespace_, name_='crystal_parameters', pretty_print=pretty_print) for startup_model_ in self.startup_model: startup_model_.export(outfile, level, namespace_, name_='startup_model', pretty_print=pretty_print) if self.ctf_correction is not None: self.ctf_correction.export(outfile, level, namespace_, name_='ctf_correction', pretty_print=pretty_print) if self.molecular_replacement is not None: self.molecular_replacement.export(outfile, level, namespace_, name_='molecular_replacement', pretty_print=pretty_print) if self.lattice_distortion_correction is not None: self.lattice_distortion_correction.export(outfile, level, namespace_, name_='lattice_distortion_correction', pretty_print=pretty_print) if self.symmetry_determination is not None: self.symmetry_determination.export(outfile, level, namespace_, name_='symmetry_determination', pretty_print=pretty_print) if self.merging is not None: self.merging.export(outfile, level, namespace_, name_='merging', pretty_print=pretty_print) if self.crystallography_statistics is not None: self.crystallography_statistics.export(outfile, level, namespace_, name_='crystallography_statistics', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): super(crystallography_processing_type, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'final_reconstruction': obj_ = reconstruction_type.factory() obj_.build(child_) self.final_reconstruction = obj_ obj_.original_tagname_ = 'final_reconstruction' elif nodeName_ == 'crystal_parameters': obj_ = crystal_parameters_type.factory() obj_.build(child_) self.crystal_parameters = obj_ obj_.original_tagname_ = 'crystal_parameters' elif nodeName_ == 'startup_model': obj_ = starting_map_type.factory() obj_.build(child_) self.startup_model.append(obj_) obj_.original_tagname_ = 'startup_model' elif nodeName_ == 'ctf_correction': obj_ = ctf_correction_type.factory() obj_.build(child_) self.ctf_correction = obj_ obj_.original_tagname_ = 'ctf_correction' elif nodeName_ == 'molecular_replacement': obj_ = molecular_replacementType15.factory() obj_.build(child_) self.molecular_replacement = obj_ obj_.original_tagname_ = 'molecular_replacement' elif nodeName_ == 'lattice_distortion_correction': obj_ = lattice_distortion_correctionType20.factory() obj_.build(child_) self.lattice_distortion_correction = obj_ obj_.original_tagname_ = 'lattice_distortion_correction' elif nodeName_ == 'symmetry_determination': obj_ = symmetry_determinationType21.factory() obj_.build(child_) self.symmetry_determination = obj_ obj_.original_tagname_ = 'symmetry_determination' elif nodeName_ == 'merging': obj_ = mergingType22.factory() obj_.build(child_) self.merging = obj_ obj_.original_tagname_ = 'merging' elif nodeName_ == 'crystallography_statistics': obj_ = crystallography_statistics_type.factory() obj_.build(child_) self.crystallography_statistics = obj_ obj_.original_tagname_ = 'crystallography_statistics' super(crystallography_processing_type, self).buildChildren(child_, node, nodeName_, True) # end class crystallography_processing_type
[docs]class helical_processing_type(base_processing_type): member_data_items_ = [ MemberSpec_('final_reconstruction', 'reconstruction_type', 0), MemberSpec_('ctf_correction', 'ctf_correction_type', 0), MemberSpec_('segment_selection', 'segment_selectionType23', 1), MemberSpec_('refinement', 'refinementType27', 0), MemberSpec_('startup_model', 'starting_map_type', 1), MemberSpec_('layer_lines', 'layer_lines', 0), MemberSpec_('initial_angle_assignment', 'angle_assignment_type', 0), MemberSpec_('final_angle_assignment', 'angle_assignment_type', 0), MemberSpec_('crystal_parameters', 'crystal_parameters_type', 0), ] subclass = None superclass = base_processing_type def __init__(self, id=None, image_recording_id=None, details=None, final_reconstruction=None, ctf_correction=None, segment_selection=None, refinement=None, startup_model=None, layer_lines=None, initial_angle_assignment=None, final_angle_assignment=None, crystal_parameters=None): self.original_tagname_ = None super(helical_processing_type, self).__init__(id, image_recording_id, details, ) self.final_reconstruction = final_reconstruction self.ctf_correction = ctf_correction if segment_selection is None: self.segment_selection = [] else: self.segment_selection = segment_selection self.refinement = refinement if startup_model is None: self.startup_model = [] else: self.startup_model = startup_model self.layer_lines = layer_lines self.initial_angle_assignment = initial_angle_assignment self.final_angle_assignment = final_angle_assignment self.crystal_parameters = crystal_parameters
[docs] def factory(*args_, **kwargs_): if helical_processing_type.subclass: return helical_processing_type.subclass(*args_, **kwargs_) else: return helical_processing_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_final_reconstruction(self): return self.final_reconstruction
[docs] def set_final_reconstruction(self, final_reconstruction): self.final_reconstruction = final_reconstruction
[docs] def get_ctf_correction(self): return self.ctf_correction
[docs] def set_ctf_correction(self, ctf_correction): self.ctf_correction = ctf_correction
[docs] def get_segment_selection(self): return self.segment_selection
[docs] def set_segment_selection(self, segment_selection): self.segment_selection = segment_selection
[docs] def add_segment_selection(self, value): self.segment_selection.append(value)
[docs] def insert_segment_selection_at(self, index, value): self.segment_selection.insert(index, value)
[docs] def replace_segment_selection_at(self, index, value): self.segment_selection[index] = value
[docs] def get_refinement(self): return self.refinement
[docs] def set_refinement(self, refinement): self.refinement = refinement
[docs] def get_startup_model(self): return self.startup_model
[docs] def set_startup_model(self, startup_model): self.startup_model = startup_model
[docs] def add_startup_model(self, value): self.startup_model.append(value)
[docs] def insert_startup_model_at(self, index, value): self.startup_model.insert(index, value)
[docs] def replace_startup_model_at(self, index, value): self.startup_model[index] = value
[docs] def get_layer_lines(self): return self.layer_lines
[docs] def set_layer_lines(self, layer_lines): self.layer_lines = layer_lines
[docs] def get_initial_angle_assignment(self): return self.initial_angle_assignment
[docs] def set_initial_angle_assignment(self, initial_angle_assignment): self.initial_angle_assignment = initial_angle_assignment
[docs] def get_final_angle_assignment(self): return self.final_angle_assignment
[docs] def set_final_angle_assignment(self, final_angle_assignment): self.final_angle_assignment = final_angle_assignment
[docs] def get_crystal_parameters(self): return self.crystal_parameters
[docs] def set_crystal_parameters(self, crystal_parameters): self.crystal_parameters = crystal_parameters
[docs] def hasContent_(self): if ( self.final_reconstruction is not None or self.ctf_correction is not None or self.segment_selection or self.refinement is not None or self.startup_model or self.layer_lines is not None or self.initial_angle_assignment is not None or self.final_angle_assignment is not None or self.crystal_parameters is not None or super(helical_processing_type, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='helical_processing_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='helical_processing_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='helical_processing_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='helical_processing_type'): super(helical_processing_type, self).exportAttributes(outfile, level, already_processed, namespace_, name_='helical_processing_type')
[docs] def exportChildren(self, outfile, level, namespace_='', name_='helical_processing_type', fromsubclass_=False, pretty_print=True): super(helical_processing_type, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print) if pretty_print: eol_ = '\n' else: eol_ = '' if self.final_reconstruction is not None: self.final_reconstruction.export(outfile, level, namespace_, name_='final_reconstruction', pretty_print=pretty_print) if self.ctf_correction is not None: self.ctf_correction.export(outfile, level, namespace_, name_='ctf_correction', pretty_print=pretty_print) for segment_selection_ in self.segment_selection: segment_selection_.export(outfile, level, namespace_, name_='segment_selection', pretty_print=pretty_print) if self.refinement is not None: self.refinement.export(outfile, level, namespace_, name_='refinement', pretty_print=pretty_print) for startup_model_ in self.startup_model: startup_model_.export(outfile, level, namespace_, name_='startup_model', pretty_print=pretty_print) if self.layer_lines is not None: self.layer_lines.export(outfile, level, namespace_, name_='layer_lines', pretty_print=pretty_print) if self.initial_angle_assignment is not None: self.initial_angle_assignment.export(outfile, level, namespace_, name_='initial_angle_assignment', pretty_print=pretty_print) if self.final_angle_assignment is not None: self.final_angle_assignment.export(outfile, level, namespace_, name_='final_angle_assignment', pretty_print=pretty_print) if self.crystal_parameters is not None: self.crystal_parameters.export(outfile, level, namespace_, name_='crystal_parameters', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): super(helical_processing_type, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'final_reconstruction': obj_ = reconstruction_type.factory() obj_.build(child_) self.final_reconstruction = obj_ obj_.original_tagname_ = 'final_reconstruction' elif nodeName_ == 'ctf_correction': obj_ = ctf_correction_type.factory() obj_.build(child_) self.ctf_correction = obj_ obj_.original_tagname_ = 'ctf_correction' elif nodeName_ == 'segment_selection': obj_ = segment_selectionType23.factory() obj_.build(child_) self.segment_selection.append(obj_) obj_.original_tagname_ = 'segment_selection' elif nodeName_ == 'refinement': obj_ = refinementType27.factory() obj_.build(child_) self.refinement = obj_ obj_.original_tagname_ = 'refinement' elif nodeName_ == 'startup_model': obj_ = starting_map_type.factory() obj_.build(child_) self.startup_model.append(obj_) obj_.original_tagname_ = 'startup_model' elif nodeName_ == 'layer_lines': obj_ = layer_linesType29.factory() obj_.build(child_) self.layer_lines = obj_ obj_.original_tagname_ = 'layer_lines' elif nodeName_ == 'initial_angle_assignment': obj_ = angle_assignment_type.factory() obj_.build(child_) self.initial_angle_assignment = obj_ obj_.original_tagname_ = 'initial_angle_assignment' elif nodeName_ == 'final_angle_assignment': obj_ = angle_assignment_type.factory() obj_.build(child_) self.final_angle_assignment = obj_ obj_.original_tagname_ = 'final_angle_assignment' elif nodeName_ == 'crystal_parameters': obj_ = crystal_parameters_type.factory() obj_.build(child_) self.crystal_parameters = obj_ obj_.original_tagname_ = 'crystal_parameters' super(helical_processing_type, self).buildChildren(child_, node, nodeName_, True) # end class helical_processing_type
[docs]class applied_symmetry_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('space_group', ['plane_and_space_group_type', 'xs:token'], 0), MemberSpec_('point_group', ['point_groupType', 'point_group_symmetry_type', 'xs:token'], 0), MemberSpec_('helical_parameters', 'helical_parameters_type', 0), ] subclass = None superclass = None def __init__(self, space_group=None, point_group=None, helical_parameters=None): self.original_tagname_ = None self.space_group = space_group self.validate_plane_and_space_group_type(self.space_group) self.point_group = point_group self.validate_point_groupType(self.point_group) self.helical_parameters = helical_parameters
[docs] def factory(*args_, **kwargs_): if applied_symmetry_type.subclass: return applied_symmetry_type.subclass(*args_, **kwargs_) else: return applied_symmetry_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_space_group(self): return self.space_group
[docs] def set_space_group(self, space_group): self.space_group = space_group
[docs] def get_point_group(self): return self.point_group
[docs] def set_point_group(self, point_group): self.point_group = point_group
[docs] def get_helical_parameters(self): return self.helical_parameters
[docs] def set_helical_parameters(self, helical_parameters): self.helical_parameters = helical_parameters
[docs] def validate_plane_and_space_group_type(self, value): # Validate type plane_and_space_group_type, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['1', 'P 1', 'P 1 2', 'P 1 21', 'P 2', 'P 2 2 2', 'P 2 2 21', 'P 2 21 21', 'P 3', 'P 3 1 2', 'P 3 2 1', 'P 4', 'P 4 2 2', 'P 4 21 2', 'P 6', 'P 6 2 2', 'C 1 2', 'C 2 2'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on plane_and_space_group_type' % {"value" : value.encode("utf-8")} )
[docs] def validate_point_groupType(self, value): # Validate type point_groupType, a restriction on point_group_symmetry_type. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_point_groupType_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_point_groupType_patterns_, ))
validate_point_groupType_patterns_ = [['^C\\d+|D\\d+|O|T|I$'], ['^C\\d+|D\\d+|O|T|I$']]
[docs] def hasContent_(self): if ( self.space_group is not None or self.point_group is not None or self.helical_parameters is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='applied_symmetry_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='applied_symmetry_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='applied_symmetry_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='applied_symmetry_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='applied_symmetry_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.space_group is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sspace_group>%s</%sspace_group>%s' % (namespace_, self.gds_format_string(quote_xml(self.space_group).encode(ExternalEncoding), input_name='space_group'), namespace_, eol_)) if self.point_group is not None: showIndent(outfile, level, pretty_print) outfile.write('<%spoint_group>%s</%spoint_group>%s' % (namespace_, self.gds_format_string(quote_xml(self.point_group).encode(ExternalEncoding), input_name='point_group'), namespace_, eol_)) if self.helical_parameters is not None: self.helical_parameters.export(outfile, level, namespace_, name_='helical_parameters', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'space_group': space_group_ = child_.text space_group_ = re_.sub(String_cleanup_pat_, " ", space_group_).strip() space_group_ = self.gds_validate_string(space_group_, node, 'space_group') self.space_group = space_group_ # validate type plane_and_space_group_type self.validate_plane_and_space_group_type(self.space_group) elif nodeName_ == 'point_group': point_group_ = child_.text point_group_ = re_.sub(String_cleanup_pat_, " ", point_group_).strip() point_group_ = self.gds_validate_string(point_group_, node, 'point_group') self.point_group = point_group_ # validate type point_groupType self.validate_point_groupType(self.point_group) elif nodeName_ == 'helical_parameters': obj_ = helical_parameters_type.factory() obj_.build(child_) self.helical_parameters = obj_ obj_.original_tagname_ = 'helical_parameters' # end class applied_symmetry_type
[docs]class starting_map_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('random_conical_tilt', 'random_conical_tiltType', 0), MemberSpec_('orthogonal_tilt', 'orthogonal_tiltType', 0), MemberSpec_('emdb_id', ['emdb_id_type', 'xs:token'], 0), MemberSpec_('pdb_model', 'pdb_model_type', 1), MemberSpec_('insilico_model', 'xs:token', 0), MemberSpec_('other', 'xs:string', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, random_conical_tilt=None, orthogonal_tilt=None, emdb_id=None, pdb_model=None, insilico_model=None, other=None, details=None): self.original_tagname_ = None self.random_conical_tilt = random_conical_tilt self.orthogonal_tilt = orthogonal_tilt self.emdb_id = emdb_id self.validate_emdb_id_type(self.emdb_id) if pdb_model is None: self.pdb_model = [] else: self.pdb_model = pdb_model self.insilico_model = insilico_model self.other = other self.details = details
[docs] def factory(*args_, **kwargs_): if starting_map_type.subclass: return starting_map_type.subclass(*args_, **kwargs_) else: return starting_map_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_random_conical_tilt(self): return self.random_conical_tilt
[docs] def set_random_conical_tilt(self, random_conical_tilt): self.random_conical_tilt = random_conical_tilt
[docs] def get_orthogonal_tilt(self): return self.orthogonal_tilt
[docs] def set_orthogonal_tilt(self, orthogonal_tilt): self.orthogonal_tilt = orthogonal_tilt
[docs] def get_emdb_id(self): return self.emdb_id
[docs] def set_emdb_id(self, emdb_id): self.emdb_id = emdb_id
[docs] def get_pdb_model(self): return self.pdb_model
[docs] def set_pdb_model(self, pdb_model): self.pdb_model = pdb_model
[docs] def add_pdb_model(self, value): self.pdb_model.append(value)
[docs] def insert_pdb_model_at(self, index, value): self.pdb_model.insert(index, value)
[docs] def replace_pdb_model_at(self, index, value): self.pdb_model[index] = value
[docs] def get_insilico_model(self): return self.insilico_model
[docs] def set_insilico_model(self, insilico_model): self.insilico_model = insilico_model
[docs] def get_other(self): return self.other
[docs] def set_other(self, other): self.other = other
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def validate_emdb_id_type(self, value): # Validate type emdb_id_type, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_emdb_id_type_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_emdb_id_type_patterns_, ))
validate_emdb_id_type_patterns_ = [['^EMD-\\d{4,}$']]
[docs] def hasContent_(self): if ( self.random_conical_tilt is not None or self.orthogonal_tilt is not None or self.emdb_id is not None or self.pdb_model or self.insilico_model is not None or self.other is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='starting_map_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='starting_map_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='starting_map_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='starting_map_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='starting_map_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.random_conical_tilt is not None: self.random_conical_tilt.export(outfile, level, namespace_, name_='random_conical_tilt', pretty_print=pretty_print) if self.orthogonal_tilt is not None: self.orthogonal_tilt.export(outfile, level, namespace_, name_='orthogonal_tilt', pretty_print=pretty_print) if self.emdb_id is not None: showIndent(outfile, level, pretty_print) outfile.write('<%semdb_id>%s</%semdb_id>%s' % (namespace_, self.gds_format_string(quote_xml(self.emdb_id).encode(ExternalEncoding), input_name='emdb_id'), namespace_, eol_)) for pdb_model_ in self.pdb_model: pdb_model_.export(outfile, level, namespace_, name_='pdb_model', pretty_print=pretty_print) if self.insilico_model is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sinsilico_model>%s</%sinsilico_model>%s' % (namespace_, self.gds_format_string(quote_xml(self.insilico_model).encode(ExternalEncoding), input_name='insilico_model'), namespace_, eol_)) if self.other is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sother>%s</%sother>%s' % (namespace_, self.gds_format_string(quote_xml(self.other).encode(ExternalEncoding), input_name='other'), namespace_, eol_)) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'random_conical_tilt': obj_ = random_conical_tiltType.factory() obj_.build(child_) self.random_conical_tilt = obj_ obj_.original_tagname_ = 'random_conical_tilt' elif nodeName_ == 'orthogonal_tilt': obj_ = orthogonal_tiltType.factory() obj_.build(child_) self.orthogonal_tilt = obj_ obj_.original_tagname_ = 'orthogonal_tilt' elif nodeName_ == 'emdb_id': emdb_id_ = child_.text emdb_id_ = re_.sub(String_cleanup_pat_, " ", emdb_id_).strip() emdb_id_ = self.gds_validate_string(emdb_id_, node, 'emdb_id') self.emdb_id = emdb_id_ # validate type emdb_id_type self.validate_emdb_id_type(self.emdb_id) elif nodeName_ == 'pdb_model': obj_ = pdb_model_type.factory() obj_.build(child_) self.pdb_model.append(obj_) obj_.original_tagname_ = 'pdb_model' elif nodeName_ == 'insilico_model': insilico_model_ = child_.text insilico_model_ = re_.sub(String_cleanup_pat_, " ", insilico_model_).strip() insilico_model_ = self.gds_validate_string(insilico_model_, node, 'insilico_model') self.insilico_model = insilico_model_ elif nodeName_ == 'other': other_ = child_.text other_ = self.gds_validate_string(other_, node, 'other') self.other = other_ elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class starting_map_type
[docs]class map_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('size_kbytes', 'xs:positiveInteger', 0), MemberSpec_('format', 'xs:string', 0), MemberSpec_('file', ['fileType32', 'xs:token'], 0), MemberSpec_('symmetry', 'applied_symmetry_type', 0), MemberSpec_('data_type', ['map_data_type', 'xs:string'], 0), MemberSpec_('dimensions', 'integer_vector_map_type', 0), MemberSpec_('origin', 'originType', 0), MemberSpec_('spacing', 'spacingType', 0), MemberSpec_('cell', 'cell', 0), MemberSpec_('axis_order', 'axis_orderType', 0), MemberSpec_('statistics', 'map_statistics_type', 0), MemberSpec_('pixel_spacing', 'pixel_spacingType', 0), MemberSpec_('contour_list', 'contour_listType', 0), MemberSpec_('label', 'xs:token', 0), MemberSpec_('annotation_details', 'xs:string', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, size_kbytes=None, format=None, file=None, symmetry=None, data_type=None, dimensions=None, origin=None, spacing=None, cell=None, axis_order=None, statistics=None, pixel_spacing=None, contour_list=None, label=None, annotation_details=None, details=None): self.original_tagname_ = None self.size_kbytes = _cast(int, size_kbytes) self.format = _cast(None, format) self.file = file self.validate_fileType32(self.file) self.symmetry = symmetry self.data_type = data_type self.validate_map_data_type(self.data_type) self.dimensions = dimensions self.origin = origin self.spacing = spacing self.cell = cell self.axis_order = axis_order self.statistics = statistics self.pixel_spacing = pixel_spacing self.contour_list = contour_list self.label = label self.annotation_details = annotation_details self.details = details
[docs] def factory(*args_, **kwargs_): if map_type.subclass: return map_type.subclass(*args_, **kwargs_) else: return map_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_file(self): return self.file
[docs] def set_file(self, file): self.file = file
[docs] def get_symmetry(self): return self.symmetry
[docs] def set_symmetry(self, symmetry): self.symmetry = symmetry
[docs] def get_data_type(self): return self.data_type
[docs] def set_data_type(self, data_type): self.data_type = data_type
[docs] def get_dimensions(self): return self.dimensions
[docs] def set_dimensions(self, dimensions): self.dimensions = dimensions
[docs] def get_origin(self): return self.origin
[docs] def set_origin(self, origin): self.origin = origin
[docs] def get_spacing(self): return self.spacing
[docs] def set_spacing(self, spacing): self.spacing = spacing
[docs] def get_cell(self): return self.cell
[docs] def set_cell(self, cell): self.cell = cell
[docs] def get_axis_order(self): return self.axis_order
[docs] def set_axis_order(self, axis_order): self.axis_order = axis_order
[docs] def get_statistics(self): return self.statistics
[docs] def set_statistics(self, statistics): self.statistics = statistics
[docs] def get_pixel_spacing(self): return self.pixel_spacing
[docs] def set_pixel_spacing(self, pixel_spacing): self.pixel_spacing = pixel_spacing
[docs] def get_contour_list(self): return self.contour_list
[docs] def set_contour_list(self, contour_list): self.contour_list = contour_list
[docs] def get_label(self): return self.label
[docs] def set_label(self, label): self.label = label
[docs] def get_annotation_details(self): return self.annotation_details
[docs] def set_annotation_details(self, annotation_details): self.annotation_details = annotation_details
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def get_size_kbytes(self): return self.size_kbytes
[docs] def set_size_kbytes(self, size_kbytes): self.size_kbytes = size_kbytes
[docs] def get_format(self): return self.format
[docs] def set_format(self, format): self.format = format
[docs] def validate_fileType32(self, value): # Validate type fileType32, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_fileType32_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_fileType32_patterns_, ))
validate_fileType32_patterns_ = [['^emd_\\d{4,}([A-Za-z0-9_]*).map(.gz|)$']]
[docs] def validate_map_data_type(self, value): # Validate type map_data_type, a restriction on xs:string. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['IMAGE STORED AS SIGNED BYTE', 'IMAGE STORED AS SIGNED INTEGER (2 BYTES)', 'IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on map_data_type' % {"value" : value.encode("utf-8")} )
[docs] def hasContent_(self): if ( self.file is not None or self.symmetry is not None or self.data_type is not None or self.dimensions is not None or self.origin is not None or self.spacing is not None or self.cell is not None or self.axis_order is not None or self.statistics is not None or self.pixel_spacing is not None or self.contour_list is not None or self.label is not None or self.annotation_details is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='map_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='map_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='map_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='map_type'): if self.size_kbytes is not None and 'size_kbytes' not in already_processed: already_processed.add('size_kbytes') outfile.write(' size_kbytes="%s"' % self.gds_format_integer(self.size_kbytes, input_name='size_kbytes')) if self.format is not None and 'format' not in already_processed: already_processed.add('format') outfile.write(' format=%s' % (self.gds_format_string(quote_attrib(self.format).encode(ExternalEncoding), input_name='format'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='map_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.file is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sfile>%s</%sfile>%s' % (namespace_, self.gds_format_string(quote_xml(self.file).encode(ExternalEncoding), input_name='file'), namespace_, eol_)) if self.symmetry is not None: self.symmetry.export(outfile, level, namespace_, name_='symmetry', pretty_print=pretty_print) if self.data_type is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdata_type>%s</%sdata_type>%s' % (namespace_, self.gds_format_string(quote_xml(self.data_type).encode(ExternalEncoding), input_name='data_type'), namespace_, eol_)) if self.dimensions is not None: self.dimensions.export(outfile, level, namespace_, name_='dimensions', pretty_print=pretty_print) if self.origin is not None: self.origin.export(outfile, level, namespace_, name_='origin', pretty_print=pretty_print) if self.spacing is not None: self.spacing.export(outfile, level, namespace_, name_='spacing', pretty_print=pretty_print) if self.cell is not None: self.cell.export(outfile, level, namespace_, name_='cell', pretty_print=pretty_print) if self.axis_order is not None: self.axis_order.export(outfile, level, namespace_, name_='axis_order', pretty_print=pretty_print) if self.statistics is not None: self.statistics.export(outfile, level, namespace_, name_='statistics', pretty_print=pretty_print) if self.pixel_spacing is not None: self.pixel_spacing.export(outfile, level, namespace_, name_='pixel_spacing', pretty_print=pretty_print) if self.contour_list is not None: self.contour_list.export(outfile, level, namespace_, name_='contour_list', pretty_print=pretty_print) if self.label is not None: showIndent(outfile, level, pretty_print) outfile.write('<%slabel>%s</%slabel>%s' % (namespace_, self.gds_format_string(quote_xml(self.label).encode(ExternalEncoding), input_name='label'), namespace_, eol_)) if self.annotation_details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sannotation_details>%s</%sannotation_details>%s' % (namespace_, self.gds_format_string(quote_xml(self.annotation_details).encode(ExternalEncoding), input_name='annotation_details'), namespace_, eol_)) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('size_kbytes', node) if value is not None and 'size_kbytes' not in already_processed: already_processed.add('size_kbytes') try: self.size_kbytes = int(value) except ValueError as exp: raise_parse_error(node, 'Bad integer attribute: %s' % exp) if self.size_kbytes <= 0: raise_parse_error(node, 'Invalid PositiveInteger') value = find_attr_value_('format', node) if value is not None and 'format' not in already_processed: already_processed.add('format') self.format = value
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'file': file_ = child_.text file_ = re_.sub(String_cleanup_pat_, " ", file_).strip() file_ = self.gds_validate_string(file_, node, 'file') self.file = file_ # validate type fileType32 self.validate_fileType32(self.file) elif nodeName_ == 'symmetry': obj_ = applied_symmetry_type.factory() obj_.build(child_) self.symmetry = obj_ obj_.original_tagname_ = 'symmetry' elif nodeName_ == 'data_type': data_type_ = child_.text data_type_ = self.gds_validate_string(data_type_, node, 'data_type') self.data_type = data_type_ # validate type map_data_type self.validate_map_data_type(self.data_type) elif nodeName_ == 'dimensions': obj_ = integer_vector_map_type.factory() obj_.build(child_) self.dimensions = obj_ obj_.original_tagname_ = 'dimensions' elif nodeName_ == 'origin': obj_ = originType.factory() obj_.build(child_) self.origin = obj_ obj_.original_tagname_ = 'origin' elif nodeName_ == 'spacing': obj_ = spacingType.factory() obj_.build(child_) self.spacing = obj_ obj_.original_tagname_ = 'spacing' elif nodeName_ == 'cell': obj_ = cellType.factory() obj_.build(child_) self.cell = obj_ obj_.original_tagname_ = 'cell' elif nodeName_ == 'axis_order': obj_ = axis_orderType.factory() obj_.build(child_) self.axis_order = obj_ obj_.original_tagname_ = 'axis_order' elif nodeName_ == 'statistics': obj_ = map_statistics_type.factory() obj_.build(child_) self.statistics = obj_ obj_.original_tagname_ = 'statistics' elif nodeName_ == 'pixel_spacing': obj_ = pixel_spacingType.factory() obj_.build(child_) self.pixel_spacing = obj_ obj_.original_tagname_ = 'pixel_spacing' elif nodeName_ == 'contour_list': obj_ = contour_listType.factory() obj_.build(child_) self.contour_list = obj_ obj_.original_tagname_ = 'contour_list' elif nodeName_ == 'label': label_ = child_.text label_ = re_.sub(String_cleanup_pat_, " ", label_).strip() label_ = self.gds_validate_string(label_, node, 'label') self.label = label_ elif nodeName_ == 'annotation_details': annotation_details_ = child_.text annotation_details_ = self.gds_validate_string(annotation_details_, node, 'annotation_details') self.annotation_details = annotation_details_ elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class map_type
[docs]class validation_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('fsc_curve', 'fsc_curve', 0), MemberSpec_('crystallography_validation', 'crystallography_validation', 0), ] subclass = None superclass = None def __init__(self, fsc_curve=None, crystallography_validation=None): self.original_tagname_ = None self.fsc_curve = fsc_curve self.crystallography_validation = crystallography_validation
[docs] def factory(*args_, **kwargs_): if validation_type.subclass: return validation_type.subclass(*args_, **kwargs_) else: return validation_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_fsc_curve(self): return self.fsc_curve
[docs] def set_fsc_curve(self, fsc_curve): self.fsc_curve = fsc_curve
[docs] def get_crystallography_validation(self): return self.crystallography_validation
[docs] def set_crystallography_validation(self, crystallography_validation): self.crystallography_validation = crystallography_validation
[docs] def hasContent_(self): if ( self.fsc_curve is not None or self.crystallography_validation is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='validation_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='validation_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='validation_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='validation_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='validation_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.fsc_curve is not None: self.fsc_curve.export(outfile, level, namespace_, name_='fsc_curve', pretty_print=pretty_print) if self.crystallography_validation is not None: self.crystallography_validation.export(outfile, level, namespace_, name_='crystallography_validation', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'fsc_curve': obj_ = fsc_curve.factory() obj_.build(child_) self.fsc_curve = obj_ obj_.original_tagname_ = 'fsc_curve' elif nodeName_ == 'crystallography_validation': obj_ = crystallography_validation.factory() obj_.build(child_) self.crystallography_validation = obj_ obj_.original_tagname_ = 'crystallography_validation' # end class validation_type
[docs]class fsc_curve(GeneratedsSuper): member_data_items_ = [ MemberSpec_('file', ['fileType33', 'xs:token'], 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, file=None, details=None): self.original_tagname_ = None self.file = file self.validate_fileType33(self.file) self.details = details
[docs] def factory(*args_, **kwargs_): if fsc_curve.subclass: return fsc_curve.subclass(*args_, **kwargs_) else: return fsc_curve(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_file(self): return self.file
[docs] def set_file(self, file): self.file = file
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def validate_fileType33(self, value): # Validate type fileType33, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_fileType33_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_fileType33_patterns_, ))
validate_fileType33_patterns_ = [['^emd_\\d{4,}_fsc.xml$']]
[docs] def hasContent_(self): if ( self.file is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='fsc_curve', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='fsc_curve') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='fsc_curve', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='fsc_curve'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='fsc_curve', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.file is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sfile>%s</%sfile>%s' % (namespace_, self.gds_format_string(quote_xml(self.file).encode(ExternalEncoding), input_name='file'), namespace_, eol_)) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'file': file_ = child_.text file_ = re_.sub(String_cleanup_pat_, " ", file_).strip() file_ = self.gds_validate_string(file_, node, 'file') self.file = file_ # validate type fileType33 self.validate_fileType33(self.file) elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class fsc_curve
[docs]class layer_lines(GeneratedsSuper): member_data_items_ = [ MemberSpec_('file', ['fileType34', 'xs:token'], 0), ] subclass = None superclass = None def __init__(self, file=None): self.original_tagname_ = None self.file = file self.validate_fileType34(self.file)
[docs] def factory(*args_, **kwargs_): if layer_lines.subclass: return layer_lines.subclass(*args_, **kwargs_) else: return layer_lines(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_file(self): return self.file
[docs] def set_file(self, file): self.file = file
[docs] def validate_fileType34(self, value): # Validate type fileType34, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_fileType34_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_fileType34_patterns_, ))
validate_fileType34_patterns_ = [['^emd_\\d{4,}_fsc.xml$']]
[docs] def hasContent_(self): if ( self.file is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='layer_lines', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='layer_lines') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='layer_lines', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='layer_lines'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='layer_lines', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.file is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sfile>%s</%sfile>%s' % (namespace_, self.gds_format_string(quote_xml(self.file).encode(ExternalEncoding), input_name='file'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'file': file_ = child_.text file_ = re_.sub(String_cleanup_pat_, " ", file_).strip() file_ = self.gds_validate_string(file_, node, 'file') self.file = file_ # validate type fileType34 self.validate_fileType34(self.file) # end class layer_lines
[docs]class structure_factors(GeneratedsSuper): member_data_items_ = [ MemberSpec_('file', ['fileType35', 'xs:token'], 0), ] subclass = None superclass = None def __init__(self, file=None): self.original_tagname_ = None self.file = file self.validate_fileType35(self.file)
[docs] def factory(*args_, **kwargs_): if structure_factors.subclass: return structure_factors.subclass(*args_, **kwargs_) else: return structure_factors(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_file(self): return self.file
[docs] def set_file(self, file): self.file = file
[docs] def validate_fileType35(self, value): # Validate type fileType35, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_fileType35_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_fileType35_patterns_, ))
validate_fileType35_patterns_ = [['^emd_\\d{4,}_fsc.xml$']]
[docs] def hasContent_(self): if ( self.file is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='structure_factors', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='structure_factors') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='structure_factors', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='structure_factors'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='structure_factors', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.file is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sfile>%s</%sfile>%s' % (namespace_, self.gds_format_string(quote_xml(self.file).encode(ExternalEncoding), input_name='file'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'file': file_ = child_.text file_ = re_.sub(String_cleanup_pat_, " ", file_).strip() file_ = self.gds_validate_string(file_, node, 'file') self.file = file_ # validate type fileType35 self.validate_fileType35(self.file) # end class structure_factors
[docs]class crystallography_validation(GeneratedsSuper): member_data_items_ = [ MemberSpec_('parallel_resolution', 'xs:string', 0), MemberSpec_('perpendicular_resolution', 'xs:string', 0), MemberSpec_('number_observed_reflections', 'xs:string', 0), MemberSpec_('number_unique_reflections', 'xs:string', 0), MemberSpec_('weighted_phase_residual', 'xs:string', 0), MemberSpec_('weighted_r_factor', 'xs:string', 0), MemberSpec_('data_completeness', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, parallel_resolution=None, perpendicular_resolution=None, number_observed_reflections=None, number_unique_reflections=None, weighted_phase_residual=None, weighted_r_factor=None, data_completeness=None): self.original_tagname_ = None self.parallel_resolution = parallel_resolution self.perpendicular_resolution = perpendicular_resolution self.number_observed_reflections = number_observed_reflections self.number_unique_reflections = number_unique_reflections self.weighted_phase_residual = weighted_phase_residual self.weighted_r_factor = weighted_r_factor self.data_completeness = data_completeness
[docs] def factory(*args_, **kwargs_): if crystallography_validation.subclass: return crystallography_validation.subclass(*args_, **kwargs_) else: return crystallography_validation(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_parallel_resolution(self): return self.parallel_resolution
[docs] def set_parallel_resolution(self, parallel_resolution): self.parallel_resolution = parallel_resolution
[docs] def get_perpendicular_resolution(self): return self.perpendicular_resolution
[docs] def set_perpendicular_resolution(self, perpendicular_resolution): self.perpendicular_resolution = perpendicular_resolution
[docs] def get_number_observed_reflections(self): return self.number_observed_reflections
[docs] def set_number_observed_reflections(self, number_observed_reflections): self.number_observed_reflections = number_observed_reflections
[docs] def get_number_unique_reflections(self): return self.number_unique_reflections
[docs] def set_number_unique_reflections(self, number_unique_reflections): self.number_unique_reflections = number_unique_reflections
[docs] def get_weighted_phase_residual(self): return self.weighted_phase_residual
[docs] def set_weighted_phase_residual(self, weighted_phase_residual): self.weighted_phase_residual = weighted_phase_residual
[docs] def get_weighted_r_factor(self): return self.weighted_r_factor
[docs] def set_weighted_r_factor(self, weighted_r_factor): self.weighted_r_factor = weighted_r_factor
[docs] def get_data_completeness(self): return self.data_completeness
[docs] def set_data_completeness(self, data_completeness): self.data_completeness = data_completeness
[docs] def hasContent_(self): if ( self.parallel_resolution is not None or self.perpendicular_resolution is not None or self.number_observed_reflections is not None or self.number_unique_reflections is not None or self.weighted_phase_residual is not None or self.weighted_r_factor is not None or self.data_completeness is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='crystallography_validation', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='crystallography_validation') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='crystallography_validation', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='crystallography_validation'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='crystallography_validation', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.parallel_resolution is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sparallel_resolution>%s</%sparallel_resolution>%s' % (namespace_, self.gds_format_string(quote_xml(self.parallel_resolution).encode(ExternalEncoding), input_name='parallel_resolution'), namespace_, eol_)) if self.perpendicular_resolution is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sperpendicular_resolution>%s</%sperpendicular_resolution>%s' % (namespace_, self.gds_format_string(quote_xml(self.perpendicular_resolution).encode(ExternalEncoding), input_name='perpendicular_resolution'), namespace_, eol_)) if self.number_observed_reflections is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_observed_reflections>%s</%snumber_observed_reflections>%s' % (namespace_, self.gds_format_string(quote_xml(self.number_observed_reflections).encode(ExternalEncoding), input_name='number_observed_reflections'), namespace_, eol_)) if self.number_unique_reflections is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_unique_reflections>%s</%snumber_unique_reflections>%s' % (namespace_, self.gds_format_string(quote_xml(self.number_unique_reflections).encode(ExternalEncoding), input_name='number_unique_reflections'), namespace_, eol_)) if self.weighted_phase_residual is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sweighted_phase_residual>%s</%sweighted_phase_residual>%s' % (namespace_, self.gds_format_string(quote_xml(self.weighted_phase_residual).encode(ExternalEncoding), input_name='weighted_phase_residual'), namespace_, eol_)) if self.weighted_r_factor is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sweighted_r_factor>%s</%sweighted_r_factor>%s' % (namespace_, self.gds_format_string(quote_xml(self.weighted_r_factor).encode(ExternalEncoding), input_name='weighted_r_factor'), namespace_, eol_)) if self.data_completeness is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdata_completeness>%s</%sdata_completeness>%s' % (namespace_, self.gds_format_string(quote_xml(self.data_completeness).encode(ExternalEncoding), input_name='data_completeness'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'parallel_resolution': parallel_resolution_ = child_.text parallel_resolution_ = self.gds_validate_string(parallel_resolution_, node, 'parallel_resolution') self.parallel_resolution = parallel_resolution_ elif nodeName_ == 'perpendicular_resolution': perpendicular_resolution_ = child_.text perpendicular_resolution_ = self.gds_validate_string(perpendicular_resolution_, node, 'perpendicular_resolution') self.perpendicular_resolution = perpendicular_resolution_ elif nodeName_ == 'number_observed_reflections': number_observed_reflections_ = child_.text number_observed_reflections_ = self.gds_validate_string(number_observed_reflections_, node, 'number_observed_reflections') self.number_observed_reflections = number_observed_reflections_ elif nodeName_ == 'number_unique_reflections': number_unique_reflections_ = child_.text number_unique_reflections_ = self.gds_validate_string(number_unique_reflections_, node, 'number_unique_reflections') self.number_unique_reflections = number_unique_reflections_ elif nodeName_ == 'weighted_phase_residual': weighted_phase_residual_ = child_.text weighted_phase_residual_ = self.gds_validate_string(weighted_phase_residual_, node, 'weighted_phase_residual') self.weighted_phase_residual = weighted_phase_residual_ elif nodeName_ == 'weighted_r_factor': weighted_r_factor_ = child_.text weighted_r_factor_ = self.gds_validate_string(weighted_r_factor_, node, 'weighted_r_factor') self.weighted_r_factor = weighted_r_factor_ elif nodeName_ == 'data_completeness': data_completeness_ = child_.text data_completeness_ = self.gds_validate_string(data_completeness_, node, 'data_completeness') self.data_completeness = data_completeness_ # end class crystallography_validation
[docs]class parallel_resolution(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if parallel_resolution.subclass: return parallel_resolution.subclass(*args_, **kwargs_) else: return parallel_resolution(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='parallel_resolution', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='parallel_resolution') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='parallel_resolution', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='parallel_resolution'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='parallel_resolution', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class parallel_resolution
[docs]class perpendicular_resolution(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if perpendicular_resolution.subclass: return perpendicular_resolution.subclass(*args_, **kwargs_) else: return perpendicular_resolution(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='perpendicular_resolution', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='perpendicular_resolution') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='perpendicular_resolution', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='perpendicular_resolution'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='perpendicular_resolution', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class perpendicular_resolution
[docs]class number_observed_reflections(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if number_observed_reflections.subclass: return number_observed_reflections.subclass(*args_, **kwargs_) else: return number_observed_reflections(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='number_observed_reflections', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='number_observed_reflections') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='number_observed_reflections', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='number_observed_reflections'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='number_observed_reflections', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class number_observed_reflections
[docs]class number_unique_reflections(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if number_unique_reflections.subclass: return number_unique_reflections.subclass(*args_, **kwargs_) else: return number_unique_reflections(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='number_unique_reflections', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='number_unique_reflections') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='number_unique_reflections', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='number_unique_reflections'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='number_unique_reflections', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class number_unique_reflections
[docs]class weighted_phase_residual(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if weighted_phase_residual.subclass: return weighted_phase_residual.subclass(*args_, **kwargs_) else: return weighted_phase_residual(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='weighted_phase_residual', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='weighted_phase_residual') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='weighted_phase_residual', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='weighted_phase_residual'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='weighted_phase_residual', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class weighted_phase_residual
[docs]class weighted_r_factor(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if weighted_r_factor.subclass: return weighted_r_factor.subclass(*args_, **kwargs_) else: return weighted_r_factor(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='weighted_r_factor', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='weighted_r_factor') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='weighted_r_factor', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='weighted_r_factor'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='weighted_r_factor', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class weighted_r_factor
[docs]class data_completeness(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if data_completeness.subclass: return data_completeness.subclass(*args_, **kwargs_) else: return data_completeness(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='data_completeness', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='data_completeness') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='data_completeness', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='data_completeness'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='data_completeness', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class data_completeness
[docs]class grant_reference_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('funding_body', 'xs:token', 0), MemberSpec_('code', 'xs:token', 0), MemberSpec_('country', 'xs:token', 0), ] subclass = None superclass = None def __init__(self, funding_body=None, code=None, country=None): self.original_tagname_ = None self.funding_body = funding_body self.code = code self.country = country
[docs] def factory(*args_, **kwargs_): if grant_reference_type.subclass: return grant_reference_type.subclass(*args_, **kwargs_) else: return grant_reference_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_funding_body(self): return self.funding_body
[docs] def set_funding_body(self, funding_body): self.funding_body = funding_body
[docs] def get_code(self): return self.code
[docs] def set_code(self, code): self.code = code
[docs] def get_country(self): return self.country
[docs] def set_country(self, country): self.country = country
[docs] def hasContent_(self): if ( self.funding_body is not None or self.code is not None or self.country is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='grant_reference_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='grant_reference_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='grant_reference_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='grant_reference_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='grant_reference_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.funding_body is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sfunding_body>%s</%sfunding_body>%s' % (namespace_, self.gds_format_string(quote_xml(self.funding_body).encode(ExternalEncoding), input_name='funding_body'), namespace_, eol_)) if self.code is not None: showIndent(outfile, level, pretty_print) outfile.write('<%scode>%s</%scode>%s' % (namespace_, self.gds_format_string(quote_xml(self.code).encode(ExternalEncoding), input_name='code'), namespace_, eol_)) if self.country is not None: showIndent(outfile, level, pretty_print) outfile.write('<%scountry>%s</%scountry>%s' % (namespace_, self.gds_format_string(quote_xml(self.country).encode(ExternalEncoding), input_name='country'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'funding_body': funding_body_ = child_.text funding_body_ = re_.sub(String_cleanup_pat_, " ", funding_body_).strip() funding_body_ = self.gds_validate_string(funding_body_, node, 'funding_body') self.funding_body = funding_body_ elif nodeName_ == 'code': code_ = child_.text code_ = re_.sub(String_cleanup_pat_, " ", code_).strip() code_ = self.gds_validate_string(code_, node, 'code') self.code = code_ elif nodeName_ == 'country': country_ = child_.text country_ = re_.sub(String_cleanup_pat_, " ", country_).strip() country_ = self.gds_validate_string(country_, node, 'country') self.country = country_ # end class grant_reference_type
[docs]class chain_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('id', ['chain_pdb_id', 'xs:token'], 0), MemberSpec_('residue_range', ['residue_rangeType', 'xs:token'], 1), ] subclass = None superclass = None def __init__(self, id=None, residue_range=None, extensiontype_=None): self.original_tagname_ = None self.id = id self.validate_chain_pdb_id(self.id) if residue_range is None: self.residue_range = [] else: self.residue_range = residue_range self.extensiontype_ = extensiontype_
[docs] def factory(*args_, **kwargs_): if chain_type.subclass: return chain_type.subclass(*args_, **kwargs_) else: return chain_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_id(self): return self.id
[docs] def set_id(self, id): self.id = id
[docs] def get_residue_range(self): return self.residue_range
[docs] def set_residue_range(self, residue_range): self.residue_range = residue_range
[docs] def add_residue_range(self, value): self.residue_range.append(value)
[docs] def insert_residue_range_at(self, index, value): self.residue_range.insert(index, value)
[docs] def replace_residue_range_at(self, index, value): self.residue_range[index] = value
[docs] def get_extensiontype_(self): return self.extensiontype_
[docs] def set_extensiontype_(self, extensiontype_): self.extensiontype_ = extensiontype_
[docs] def validate_chain_pdb_id(self, value): # Validate type chain_pdb_id, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_chain_pdb_id_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_chain_pdb_id_patterns_, ))
validate_chain_pdb_id_patterns_ = [['^\\d|[A-Za-z]$']]
[docs] def validate_residue_rangeType(self, value): # Validate type residue_rangeType, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_residue_rangeType_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_residue_rangeType_patterns_, ))
validate_residue_rangeType_patterns_ = [['^\\d+-\\d+$']]
[docs] def hasContent_(self): if ( self.id is not None or self.residue_range ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='chain_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='chain_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='chain_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='chain_type'): if self.extensiontype_ is not None and 'xsi:type' not in already_processed: already_processed.add('xsi:type') outfile.write(' xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"') outfile.write(' xsi:type="%s"' % self.extensiontype_) pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='chain_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.id is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sid>%s</%sid>%s' % (namespace_, self.gds_format_string(quote_xml(self.id).encode(ExternalEncoding), input_name='id'), namespace_, eol_)) for residue_range_ in self.residue_range: showIndent(outfile, level, pretty_print) outfile.write('<%sresidue_range>%s</%sresidue_range>%s' % (namespace_, self.gds_format_string(quote_xml(residue_range_).encode(ExternalEncoding), input_name='residue_range'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('xsi:type', node) if value is not None and 'xsi:type' not in already_processed: already_processed.add('xsi:type') self.extensiontype_ = value
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'id': id_ = child_.text id_ = re_.sub(String_cleanup_pat_, " ", id_).strip() id_ = self.gds_validate_string(id_, node, 'id') self.id = id_ # validate type chain_pdb_id self.validate_chain_pdb_id(self.id) elif nodeName_ == 'residue_range': residue_range_ = child_.text residue_range_ = re_.sub(String_cleanup_pat_, " ", residue_range_).strip() residue_range_ = self.gds_validate_string(residue_range_, node, 'residue_range') self.residue_range.append(residue_range_) # validate type residue_rangeType self.validate_residue_rangeType(self.residue_range[-1]) # end class chain_type
[docs]class pdb_model_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('pdb_id', ['pdb_code_type', 'xs:token'], 0), MemberSpec_('chain_id_list', 'chain_id_list', 0), ] subclass = None superclass = None def __init__(self, pdb_id=None, chain_id_list=None): self.original_tagname_ = None self.pdb_id = pdb_id self.validate_pdb_code_type(self.pdb_id) self.chain_id_list = chain_id_list
[docs] def factory(*args_, **kwargs_): if pdb_model_type.subclass: return pdb_model_type.subclass(*args_, **kwargs_) else: return pdb_model_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_pdb_id(self): return self.pdb_id
[docs] def set_pdb_id(self, pdb_id): self.pdb_id = pdb_id
[docs] def get_chain_id_list(self): return self.chain_id_list
[docs] def set_chain_id_list(self, chain_id_list): self.chain_id_list = chain_id_list
[docs] def validate_pdb_code_type(self, value): # Validate type pdb_code_type, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_pdb_code_type_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_pdb_code_type_patterns_, ))
validate_pdb_code_type_patterns_ = [['^\\d[\\dA-Za-z]{3}$']]
[docs] def hasContent_(self): if ( self.pdb_id is not None or self.chain_id_list is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='pdb_model_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='pdb_model_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='pdb_model_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='pdb_model_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='pdb_model_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.pdb_id is not None: showIndent(outfile, level, pretty_print) outfile.write('<%spdb_id>%s</%spdb_id>%s' % (namespace_, self.gds_format_string(quote_xml(self.pdb_id).encode(ExternalEncoding), input_name='pdb_id'), namespace_, eol_)) if self.chain_id_list is not None: self.chain_id_list.export(outfile, level, namespace_, name_='chain_id_list', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'pdb_id': pdb_id_ = child_.text pdb_id_ = re_.sub(String_cleanup_pat_, " ", pdb_id_).strip() pdb_id_ = self.gds_validate_string(pdb_id_, node, 'pdb_id') self.pdb_id = pdb_id_ # validate type pdb_code_type self.validate_pdb_code_type(self.pdb_id) elif nodeName_ == 'chain_id_list': class_obj_ = self.get_class_obj_(child_, chain_type) obj_ = class_obj_.factory() obj_.build(child_) self.chain_id_list = obj_ obj_.original_tagname_ = 'chain_id_list' # end class pdb_model_type
[docs]class macromolecules_and_complexes_type(GeneratedsSuper): """Depending on the problem, one can either reference the sample on the macromolecule level or the complex level.""" member_data_items_ = [ MemberSpec_('macromolecule_id', 'xs:positiveInteger', 1), MemberSpec_('complex_id', 'xs:nonNegativeInteger', 1), ] subclass = None superclass = None def __init__(self, macromolecule_id=None, complex_id=None): self.original_tagname_ = None if macromolecule_id is None: self.macromolecule_id = [] else: self.macromolecule_id = macromolecule_id if complex_id is None: self.complex_id = [] else: self.complex_id = complex_id
[docs] def factory(*args_, **kwargs_): if macromolecules_and_complexes_type.subclass: return macromolecules_and_complexes_type.subclass(*args_, **kwargs_) else: return macromolecules_and_complexes_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_macromolecule_id(self): return self.macromolecule_id
[docs] def set_macromolecule_id(self, macromolecule_id): self.macromolecule_id = macromolecule_id
[docs] def add_macromolecule_id(self, value): self.macromolecule_id.append(value)
[docs] def insert_macromolecule_id_at(self, index, value): self.macromolecule_id.insert(index, value)
[docs] def replace_macromolecule_id_at(self, index, value): self.macromolecule_id[index] = value
[docs] def get_complex_id(self): return self.complex_id
[docs] def set_complex_id(self, complex_id): self.complex_id = complex_id
[docs] def add_complex_id(self, value): self.complex_id.append(value)
[docs] def insert_complex_id_at(self, index, value): self.complex_id.insert(index, value)
[docs] def replace_complex_id_at(self, index, value): self.complex_id[index] = value
[docs] def hasContent_(self): if ( self.macromolecule_id or self.complex_id ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='macromolecules_and_complexes_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='macromolecules_and_complexes_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='macromolecules_and_complexes_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='macromolecules_and_complexes_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='macromolecules_and_complexes_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for macromolecule_id_ in self.macromolecule_id: showIndent(outfile, level, pretty_print) outfile.write('<%smacromolecule_id>%s</%smacromolecule_id>%s' % (namespace_, self.gds_format_integer(macromolecule_id_, input_name='macromolecule_id'), namespace_, eol_)) for complex_id_ in self.complex_id: showIndent(outfile, level, pretty_print) outfile.write('<%scomplex_id>%s</%scomplex_id>%s' % (namespace_, self.gds_format_integer(complex_id_, input_name='complex_id'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'macromolecule_id': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'macromolecule_id') self.macromolecule_id.append(ival_) elif nodeName_ == 'complex_id': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ < 0: raise_parse_error(child_, 'requires nonNegativeInteger') ival_ = self.gds_validate_integer(ival_, node, 'complex_id') self.complex_id.append(ival_) # end class macromolecules_and_complexes_type
[docs]class base_supramolecule_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('id', 'xs:positiveInteger', 0), MemberSpec_('name', 'sci_name_type', 0), MemberSpec_('category', 'categoryType', 0), MemberSpec_('parent', 'xs:nonNegativeInteger', 0), MemberSpec_('macromolecule_list', 'macromolecule_listType', 0), MemberSpec_('details', 'xs:string', 0), MemberSpec_('number_of_copies', 'pos_int_or_string_type', 0), MemberSpec_('oligomeric_state', 'pos_int_or_string_type', 0), MemberSpec_('external_references', 'external_referencesType', 1), MemberSpec_('recombinant_exp_flag', 'xs:boolean', 0), ] subclass = None superclass = None def __init__(self, id=None, name=None, category=None, parent=None, macromolecule_list=None, details=None, number_of_copies=None, oligomeric_state=None, external_references=None, recombinant_exp_flag=None, extensiontype_=None): self.original_tagname_ = None self.id = _cast(int, id) self.name = name self.category = category self.parent = parent self.macromolecule_list = macromolecule_list self.details = details self.number_of_copies = number_of_copies self.validate_pos_int_or_string_type(self.number_of_copies) self.oligomeric_state = oligomeric_state self.validate_pos_int_or_string_type(self.oligomeric_state) if external_references is None: self.external_references = [] else: self.external_references = external_references self.recombinant_exp_flag = recombinant_exp_flag self.extensiontype_ = extensiontype_
[docs] def factory(*args_, **kwargs_): if base_supramolecule_type.subclass: return base_supramolecule_type.subclass(*args_, **kwargs_) else: return base_supramolecule_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_name(self): return self.name
[docs] def set_name(self, name): self.name = name
[docs] def get_category(self): return self.category
[docs] def set_category(self, category): self.category = category
[docs] def get_parent(self): return self.parent
[docs] def set_parent(self, parent): self.parent = parent
[docs] def get_macromolecule_list(self): return self.macromolecule_list
[docs] def set_macromolecule_list(self, macromolecule_list): self.macromolecule_list = macromolecule_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def get_number_of_copies(self): return self.number_of_copies
[docs] def set_number_of_copies(self, number_of_copies): self.number_of_copies = number_of_copies
[docs] def get_oligomeric_state(self): return self.oligomeric_state
[docs] def set_oligomeric_state(self, oligomeric_state): self.oligomeric_state = oligomeric_state
[docs] def get_external_references(self): return self.external_references
[docs] def set_external_references(self, external_references): self.external_references = external_references
[docs] def add_external_references(self, value): self.external_references.append(value)
[docs] def insert_external_references_at(self, index, value): self.external_references.insert(index, value)
[docs] def replace_external_references_at(self, index, value): self.external_references[index] = value
[docs] def get_recombinant_exp_flag(self): return self.recombinant_exp_flag
[docs] def set_recombinant_exp_flag(self, recombinant_exp_flag): self.recombinant_exp_flag = recombinant_exp_flag
[docs] def get_id(self): return self.id
[docs] def set_id(self, id): self.id = id
[docs] def get_extensiontype_(self): return self.extensiontype_
[docs] def set_extensiontype_(self, extensiontype_): self.extensiontype_ = extensiontype_
[docs] def validate_pos_int_or_string_type(self, value): # Validate type pos_int_or_string_type, a restriction on None. pass
[docs] def hasContent_(self): if ( self.name is not None or self.category is not None or self.parent is not None or self.macromolecule_list is not None or self.details is not None or self.number_of_copies is not None or self.oligomeric_state is not None or self.external_references or self.recombinant_exp_flag is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='base_supramolecule_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='base_supramolecule_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='base_supramolecule_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='base_supramolecule_type'): if self.id is not None and 'id' not in already_processed: already_processed.add('id') outfile.write(' id="%s"' % self.gds_format_integer(self.id, input_name='id')) if self.extensiontype_ is not None and 'xsi:type' not in already_processed: already_processed.add('xsi:type') outfile.write(' xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"') outfile.write(' xsi:type="%s"' % self.extensiontype_)
[docs] def exportChildren(self, outfile, level, namespace_='', name_='base_supramolecule_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.name is not None: self.name.export(outfile, level, namespace_, name_='name', pretty_print=pretty_print) if self.category is not None: self.category.export(outfile, level, namespace_, name_='category', pretty_print=pretty_print) if self.parent is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sparent>%s</%sparent>%s' % (namespace_, self.gds_format_integer(self.parent, input_name='parent'), namespace_, eol_)) if self.macromolecule_list is not None: self.macromolecule_list.export(outfile, level, namespace_, name_='macromolecule_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_)) if self.number_of_copies is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_of_copies>%s</%snumber_of_copies>%s' % (namespace_, self.gds_format_string(quote_xml(self.number_of_copies).encode(ExternalEncoding), input_name='number_of_copies'), namespace_, eol_)) if self.oligomeric_state is not None: showIndent(outfile, level, pretty_print) outfile.write('<%soligomeric_state>%s</%soligomeric_state>%s' % (namespace_, self.gds_format_string(quote_xml(self.oligomeric_state).encode(ExternalEncoding), input_name='oligomeric_state'), namespace_, eol_)) for external_references_ in self.external_references: external_references_.export(outfile, level, namespace_, name_='external_references', pretty_print=pretty_print) if self.recombinant_exp_flag is not None: showIndent(outfile, level, pretty_print) outfile.write('<%srecombinant_exp_flag>%s</%srecombinant_exp_flag>%s' % (namespace_, self.gds_format_boolean(self.recombinant_exp_flag, input_name='recombinant_exp_flag'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('id', node) if value is not None and 'id' not in already_processed: already_processed.add('id') try: self.id = int(value) except ValueError as exp: raise_parse_error(node, 'Bad integer attribute: %s' % exp) if self.id <= 0: raise_parse_error(node, 'Invalid PositiveInteger') value = find_attr_value_('xsi:type', node) if value is not None and 'xsi:type' not in already_processed: already_processed.add('xsi:type') self.extensiontype_ = value
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'name': obj_ = sci_name_type.factory() obj_.build(child_) self.name = obj_ obj_.original_tagname_ = 'name' elif nodeName_ == 'category': obj_ = categoryType.factory() obj_.build(child_) self.category = obj_ obj_.original_tagname_ = 'category' elif nodeName_ == 'parent': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ < 0: raise_parse_error(child_, 'requires nonNegativeInteger') ival_ = self.gds_validate_integer(ival_, node, 'parent') self.parent = ival_ elif nodeName_ == 'macromolecule_list': obj_ = macromolecule_listType.factory() obj_.build(child_) self.macromolecule_list = obj_ obj_.original_tagname_ = 'macromolecule_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ elif nodeName_ == 'number_of_copies': number_of_copies_ = child_.text number_of_copies_ = self.gds_validate_string(number_of_copies_, node, 'number_of_copies') self.number_of_copies = number_of_copies_ # validate type pos_int_or_string_type self.validate_pos_int_or_string_type(self.number_of_copies) elif nodeName_ == 'oligomeric_state': oligomeric_state_ = child_.text oligomeric_state_ = self.gds_validate_string(oligomeric_state_, node, 'oligomeric_state') self.oligomeric_state = oligomeric_state_ # validate type pos_int_or_string_type self.validate_pos_int_or_string_type(self.oligomeric_state) elif nodeName_ == 'external_references': obj_ = external_referencesType.factory() obj_.build(child_) self.external_references.append(obj_) obj_.original_tagname_ = 'external_references' elif nodeName_ == 'recombinant_exp_flag': sval_ = child_.text if sval_ in ('true', '1'): ival_ = True elif sval_ in ('false', '0'): ival_ = False else: raise_parse_error(child_, 'requires boolean') ival_ = self.gds_validate_boolean(ival_, node, 'recombinant_exp_flag') self.recombinant_exp_flag = ival_ # end class base_supramolecule_type
[docs]class complex_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('chimera', 'xs:boolean', 0), MemberSpec_('id', 'xs:positiveInteger', 0), MemberSpec_('name', 'xs:token', 0), MemberSpec_('category', 'categoryType39', 0), MemberSpec_('parent', 'xs:nonNegativeInteger', 0), MemberSpec_('macromolecule_list', 'macromolecule_listType40', 0), MemberSpec_('natural_source', 'natural_source_type', 1), MemberSpec_('recombinant_expression', 'recombinant_source_type', 1), MemberSpec_('molecular_weight', 'molecular_weightType', 0), MemberSpec_('virus_shell', 'virus_shellType41', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, chimera=None, id=None, name=None, category=None, parent=None, macromolecule_list=None, natural_source=None, recombinant_expression=None, molecular_weight=None, virus_shell=None, details=None): self.original_tagname_ = None self.chimera = _cast(bool, chimera) self.id = _cast(int, id) self.name = name self.category = category self.parent = parent self.macromolecule_list = macromolecule_list if natural_source is None: self.natural_source = [] else: self.natural_source = natural_source if recombinant_expression is None: self.recombinant_expression = [] else: self.recombinant_expression = recombinant_expression self.molecular_weight = molecular_weight self.virus_shell = virus_shell self.details = details
[docs] def factory(*args_, **kwargs_): if complex_type.subclass: return complex_type.subclass(*args_, **kwargs_) else: return complex_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_name(self): return self.name
[docs] def set_name(self, name): self.name = name
[docs] def get_category(self): return self.category
[docs] def set_category(self, category): self.category = category
[docs] def get_parent(self): return self.parent
[docs] def set_parent(self, parent): self.parent = parent
[docs] def get_macromolecule_list(self): return self.macromolecule_list
[docs] def set_macromolecule_list(self, macromolecule_list): self.macromolecule_list = macromolecule_list
[docs] def get_natural_source(self): return self.natural_source
[docs] def set_natural_source(self, natural_source): self.natural_source = natural_source
[docs] def add_natural_source(self, value): self.natural_source.append(value)
[docs] def insert_natural_source_at(self, index, value): self.natural_source.insert(index, value)
[docs] def replace_natural_source_at(self, index, value): self.natural_source[index] = value
[docs] def get_recombinant_expression(self): return self.recombinant_expression
[docs] def set_recombinant_expression(self, recombinant_expression): self.recombinant_expression = recombinant_expression
[docs] def add_recombinant_expression(self, value): self.recombinant_expression.append(value)
[docs] def insert_recombinant_expression_at(self, index, value): self.recombinant_expression.insert(index, value)
[docs] def replace_recombinant_expression_at(self, index, value): self.recombinant_expression[index] = value
[docs] def get_molecular_weight(self): return self.molecular_weight
[docs] def set_molecular_weight(self, molecular_weight): self.molecular_weight = molecular_weight
[docs] def get_virus_shell(self): return self.virus_shell
[docs] def set_virus_shell(self, virus_shell): self.virus_shell = virus_shell
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def get_chimera(self): return self.chimera
[docs] def set_chimera(self, chimera): self.chimera = chimera
[docs] def get_id(self): return self.id
[docs] def set_id(self, id): self.id = id
[docs] def hasContent_(self): if ( self.name is not None or self.category is not None or self.parent is not None or self.macromolecule_list is not None or self.natural_source or self.recombinant_expression or self.molecular_weight is not None or self.virus_shell is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='complex_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='complex_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='complex_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='complex_type'): if self.chimera is not None and 'chimera' not in already_processed: already_processed.add('chimera') outfile.write(' chimera="%s"' % self.gds_format_boolean(self.chimera, input_name='chimera')) if self.id is not None and 'id' not in already_processed: already_processed.add('id') outfile.write(' id="%s"' % self.gds_format_integer(self.id, input_name='id'))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='complex_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.name is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sname>%s</%sname>%s' % (namespace_, self.gds_format_string(quote_xml(self.name).encode(ExternalEncoding), input_name='name'), namespace_, eol_)) if self.category is not None: self.category.export(outfile, level, namespace_, name_='category', pretty_print=pretty_print) if self.parent is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sparent>%s</%sparent>%s' % (namespace_, self.gds_format_integer(self.parent, input_name='parent'), namespace_, eol_)) if self.macromolecule_list is not None: self.macromolecule_list.export(outfile, level, namespace_, name_='macromolecule_list', pretty_print=pretty_print) for natural_source_ in self.natural_source: natural_source_.export(outfile, level, namespace_, name_='natural_source', pretty_print=pretty_print) for recombinant_expression_ in self.recombinant_expression: recombinant_expression_.export(outfile, level, namespace_, name_='recombinant_expression', pretty_print=pretty_print) if self.molecular_weight is not None: self.molecular_weight.export(outfile, level, namespace_, name_='molecular_weight', pretty_print=pretty_print) if self.virus_shell is not None: self.virus_shell.export(outfile, level, namespace_, name_='virus_shell', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('chimera', node) if value is not None and 'chimera' not in already_processed: already_processed.add('chimera') if value in ('true', '1'): self.chimera = True elif value in ('false', '0'): self.chimera = False else: raise_parse_error(node, 'Bad boolean attribute') value = find_attr_value_('id', node) if value is not None and 'id' not in already_processed: already_processed.add('id') try: self.id = int(value) except ValueError as exp: raise_parse_error(node, 'Bad integer attribute: %s' % exp) if self.id <= 0: raise_parse_error(node, 'Invalid PositiveInteger')
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'name': name_ = child_.text name_ = re_.sub(String_cleanup_pat_, " ", name_).strip() name_ = self.gds_validate_string(name_, node, 'name') self.name = name_ elif nodeName_ == 'category': obj_ = categoryType39.factory() obj_.build(child_) self.category = obj_ obj_.original_tagname_ = 'category' elif nodeName_ == 'parent': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ < 0: raise_parse_error(child_, 'requires nonNegativeInteger') ival_ = self.gds_validate_integer(ival_, node, 'parent') self.parent = ival_ elif nodeName_ == 'macromolecule_list': obj_ = macromolecule_listType40.factory() obj_.build(child_) self.macromolecule_list = obj_ obj_.original_tagname_ = 'macromolecule_list' elif nodeName_ == 'natural_source': obj_ = natural_source_type.factory() obj_.build(child_) self.natural_source.append(obj_) obj_.original_tagname_ = 'natural_source' elif nodeName_ == 'recombinant_expression': obj_ = recombinant_source_type.factory() obj_.build(child_) self.recombinant_expression.append(obj_) obj_.original_tagname_ = 'recombinant_expression' elif nodeName_ == 'molecular_weight': obj_ = molecular_weightType.factory() obj_.build(child_) self.molecular_weight = obj_ obj_.original_tagname_ = 'molecular_weight' elif nodeName_ == 'virus_shell': obj_ = virus_shellType41.factory() obj_.build(child_) self.virus_shell = obj_ obj_.original_tagname_ = 'virus_shell' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class complex_type
[docs]class interpretation_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('modelling_list', 'modelling_listType', 0), MemberSpec_('figure_list', 'figure_listType', 0), MemberSpec_('segmentation_list', 'segmentation_listType', 0), MemberSpec_('slices_list', 'slices_listType', 0), MemberSpec_('additional_map_list', 'additional_map_listType', 0), MemberSpec_('half_map_list', 'half_map_listType', 0), ] subclass = None superclass = None def __init__(self, modelling_list=None, figure_list=None, segmentation_list=None, slices_list=None, additional_map_list=None, half_map_list=None): self.original_tagname_ = None self.modelling_list = modelling_list self.figure_list = figure_list self.segmentation_list = segmentation_list self.slices_list = slices_list self.additional_map_list = additional_map_list self.half_map_list = half_map_list
[docs] def factory(*args_, **kwargs_): if interpretation_type.subclass: return interpretation_type.subclass(*args_, **kwargs_) else: return interpretation_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_modelling_list(self): return self.modelling_list
[docs] def set_modelling_list(self, modelling_list): self.modelling_list = modelling_list
[docs] def get_figure_list(self): return self.figure_list
[docs] def set_figure_list(self, figure_list): self.figure_list = figure_list
[docs] def get_segmentation_list(self): return self.segmentation_list
[docs] def set_segmentation_list(self, segmentation_list): self.segmentation_list = segmentation_list
[docs] def get_slices_list(self): return self.slices_list
[docs] def set_slices_list(self, slices_list): self.slices_list = slices_list
[docs] def get_additional_map_list(self): return self.additional_map_list
[docs] def set_additional_map_list(self, additional_map_list): self.additional_map_list = additional_map_list
[docs] def get_half_map_list(self): return self.half_map_list
[docs] def set_half_map_list(self, half_map_list): self.half_map_list = half_map_list
[docs] def hasContent_(self): if ( self.modelling_list is not None or self.figure_list is not None or self.segmentation_list is not None or self.slices_list is not None or self.additional_map_list is not None or self.half_map_list is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='interpretation_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='interpretation_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='interpretation_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='interpretation_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='interpretation_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.modelling_list is not None: self.modelling_list.export(outfile, level, namespace_, name_='modelling_list', pretty_print=pretty_print) if self.figure_list is not None: self.figure_list.export(outfile, level, namespace_, name_='figure_list', pretty_print=pretty_print) if self.segmentation_list is not None: self.segmentation_list.export(outfile, level, namespace_, name_='segmentation_list', pretty_print=pretty_print) if self.slices_list is not None: self.slices_list.export(outfile, level, namespace_, name_='slices_list', pretty_print=pretty_print) if self.additional_map_list is not None: self.additional_map_list.export(outfile, level, namespace_, name_='additional_map_list', pretty_print=pretty_print) if self.half_map_list is not None: self.half_map_list.export(outfile, level, namespace_, name_='half_map_list', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'modelling_list': obj_ = modelling_listType.factory() obj_.build(child_) self.modelling_list = obj_ obj_.original_tagname_ = 'modelling_list' elif nodeName_ == 'figure_list': obj_ = figure_listType.factory() obj_.build(child_) self.figure_list = obj_ obj_.original_tagname_ = 'figure_list' elif nodeName_ == 'segmentation_list': obj_ = segmentation_listType.factory() obj_.build(child_) self.segmentation_list = obj_ obj_.original_tagname_ = 'segmentation_list' elif nodeName_ == 'slices_list': obj_ = slices_listType.factory() obj_.build(child_) self.slices_list = obj_ obj_.original_tagname_ = 'slices_list' elif nodeName_ == 'additional_map_list': obj_ = additional_map_listType.factory() obj_.build(child_) self.additional_map_list = obj_ obj_.original_tagname_ = 'additional_map_list' elif nodeName_ == 'half_map_list': obj_ = half_map_listType.factory() obj_.build(child_) self.half_map_list = obj_ obj_.original_tagname_ = 'half_map_list' # end class interpretation_type
[docs]class software_list_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('software', 'software_type', 1), ] subclass = None superclass = None def __init__(self, software=None): self.original_tagname_ = None if software is None: self.software = [] else: self.software = software
[docs] def factory(*args_, **kwargs_): if software_list_type.subclass: return software_list_type.subclass(*args_, **kwargs_) else: return software_list_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_software(self): return self.software
[docs] def set_software(self, software): self.software = software
[docs] def add_software(self, value): self.software.append(value)
[docs] def insert_software_at(self, index, value): self.software.insert(index, value)
[docs] def replace_software_at(self, index, value): self.software[index] = value
[docs] def hasContent_(self): if ( self.software ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='software_list_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='software_list_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='software_list_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='software_list_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='software_list_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for software_ in self.software: software_.export(outfile, level, namespace_, name_='software', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'software': obj_ = software_type.factory() obj_.build(child_) self.software.append(obj_) obj_.original_tagname_ = 'software' # end class software_list_type
[docs]class code_type(GeneratedsSuper): """It is true, if the current status is 'OBS' and the entry has been replaced by newer entries. This is true if the current status is 'REL' and there are older entries that have been made obsoleted because of this one.""" member_data_items_ = [ MemberSpec_('superseded', 'xs:boolean', 0), MemberSpec_('supersedes', 'xs:boolean', 0), MemberSpec_('valueOf_', ['status_code_type', 'xs:token'], 0), ] subclass = None superclass = None def __init__(self, superseded=None, supersedes=None, valueOf_=None): self.original_tagname_ = None self.superseded = _cast(bool, superseded) self.supersedes = _cast(bool, supersedes) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if code_type.subclass: return code_type.subclass(*args_, **kwargs_) else: return code_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_superseded(self): return self.superseded
[docs] def set_superseded(self, superseded): self.superseded = superseded
[docs] def get_supersedes(self): return self.supersedes
[docs] def set_supersedes(self, supersedes): self.supersedes = supersedes
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='code_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='code_type') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='code_type', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='code_type'): if self.superseded is not None and 'superseded' not in already_processed: already_processed.add('superseded') outfile.write(' superseded="%s"' % self.gds_format_boolean(self.superseded, input_name='superseded')) if self.supersedes is not None and 'supersedes' not in already_processed: already_processed.add('supersedes') outfile.write(' supersedes="%s"' % self.gds_format_boolean(self.supersedes, input_name='supersedes'))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='code_type', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('superseded', node) if value is not None and 'superseded' not in already_processed: already_processed.add('superseded') if value in ('true', '1'): self.superseded = True elif value in ('false', '0'): self.superseded = False else: raise_parse_error(node, 'Bad boolean attribute') value = find_attr_value_('supersedes', node) if value is not None and 'supersedes' not in already_processed: already_processed.add('supersedes') if value in ('true', '1'): self.supersedes = True elif value in ('false', '0'): self.supersedes = False else: raise_parse_error(node, 'Bad boolean attribute')
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class code_type
[docs]class author_order_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('order', 'xs:positiveInteger', 0), MemberSpec_('valueOf_', ['author_type', 'xs:token'], 0), ] subclass = None superclass = None def __init__(self, order=None, valueOf_=None): self.original_tagname_ = None self.order = _cast(int, order) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if author_order_type.subclass: return author_order_type.subclass(*args_, **kwargs_) else: return author_order_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_order(self): return self.order
[docs] def set_order(self, order): self.order = order
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='author_order_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='author_order_type') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='author_order_type', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='author_order_type'): if self.order is not None and 'order' not in already_processed: already_processed.add('order') outfile.write(' order="%s"' % self.gds_format_integer(self.order, input_name='order'))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='author_order_type', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('order', node) if value is not None and 'order' not in already_processed: already_processed.add('order') try: self.order = int(value) except ValueError as exp: raise_parse_error(node, 'Bad integer attribute: %s' % exp) if self.order <= 0: raise_parse_error(node, 'Invalid PositiveInteger')
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class author_order_type
[docs]class macromolecule_list_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('macromolecule', 'base_macromolecule_type', 1), ] subclass = None superclass = None def __init__(self, macromolecule=None): self.original_tagname_ = None if macromolecule is None: self.macromolecule = [] else: self.macromolecule = macromolecule
[docs] def factory(*args_, **kwargs_): if macromolecule_list_type.subclass: return macromolecule_list_type.subclass(*args_, **kwargs_) else: return macromolecule_list_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_macromolecule(self): return self.macromolecule
[docs] def set_macromolecule(self, macromolecule): self.macromolecule = macromolecule
[docs] def add_macromolecule(self, value): self.macromolecule.append(value)
[docs] def insert_macromolecule_at(self, index, value): self.macromolecule.insert(index, value)
[docs] def replace_macromolecule_at(self, index, value): self.macromolecule[index] = value
[docs] def hasContent_(self): if ( self.macromolecule ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='macromolecule_list_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='macromolecule_list_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='macromolecule_list_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='macromolecule_list_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='macromolecule_list_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for macromolecule_ in self.macromolecule: macromolecule_.export(outfile, level, namespace_, name_='macromolecule', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'macromolecule': class_obj_ = self.get_class_obj_(child_, base_macromolecule_type) obj_ = class_obj_.factory() obj_.build(child_) self.macromolecule.append(obj_) obj_.original_tagname_ = 'macromolecule' elif nodeName_ == 'protein_or_peptide': obj_ = protein_or_peptide.factory() obj_.build(child_) self.macromolecule.append(obj_) obj_.original_tagname_ = 'protein_or_peptide' elif nodeName_ == 'dna': obj_ = dna.factory() obj_.build(child_) self.macromolecule.append(obj_) obj_.original_tagname_ = 'dna' elif nodeName_ == 'rna': obj_ = rna.factory() obj_.build(child_) self.macromolecule.append(obj_) obj_.original_tagname_ = 'rna' elif nodeName_ == 'saccharide': obj_ = saccharide.factory() obj_.build(child_) self.macromolecule.append(obj_) obj_.original_tagname_ = 'saccharide' elif nodeName_ == 'lipid': obj_ = lipid.factory() obj_.build(child_) self.macromolecule.append(obj_) obj_.original_tagname_ = 'lipid' elif nodeName_ == 'ligand': obj_ = ligand.factory() obj_.build(child_) self.macromolecule.append(obj_) obj_.original_tagname_ = 'ligand' elif nodeName_ == 'em_label': obj_ = em_label.factory() obj_.build(child_) self.macromolecule.append(obj_) obj_.original_tagname_ = 'em_label' elif nodeName_ == 'other_macromolecule': obj_ = other_macromolecule.factory() obj_.build(child_) self.macromolecule.append(obj_) obj_.original_tagname_ = 'other_macromolecule' # end class macromolecule_list_type
[docs]class temperature_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_temperature', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if temperature_type.subclass: return temperature_type.subclass(*args_, **kwargs_) else: return temperature_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='temperature_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='temperature_type') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='temperature_type', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='temperature_type'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='temperature_type', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class temperature_type
[docs]class cell_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_cell_dim', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if cell_type.subclass: return cell_type.subclass(*args_, **kwargs_) else: return cell_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='cell_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='cell_type') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='cell_type', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='cell_type'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='cell_type', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class cell_type
[docs]class cell_angle_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_cell_angle', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if cell_angle_type.subclass: return cell_angle_type.subclass(*args_, **kwargs_) else: return cell_angle_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='cell_angle_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='cell_angle_type') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='cell_angle_type', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='cell_angle_type'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='cell_angle_type', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class cell_angle_type
[docs]class integer_vector_map_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('col', 'xs:positiveInteger', 0), MemberSpec_('row', 'xs:positiveInteger', 0), MemberSpec_('sec', 'xs:positiveInteger', 0), ] subclass = None superclass = None def __init__(self, col=None, row=None, sec=None): self.original_tagname_ = None self.col = col self.row = row self.sec = sec
[docs] def factory(*args_, **kwargs_): if integer_vector_map_type.subclass: return integer_vector_map_type.subclass(*args_, **kwargs_) else: return integer_vector_map_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_col(self): return self.col
[docs] def set_col(self, col): self.col = col
[docs] def get_row(self): return self.row
[docs] def set_row(self, row): self.row = row
[docs] def get_sec(self): return self.sec
[docs] def set_sec(self, sec): self.sec = sec
[docs] def hasContent_(self): if ( self.col is not None or self.row is not None or self.sec is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='integer_vector_map_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='integer_vector_map_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='integer_vector_map_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='integer_vector_map_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='integer_vector_map_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.col is not None: showIndent(outfile, level, pretty_print) outfile.write('<%scol>%s</%scol>%s' % (namespace_, self.gds_format_integer(self.col, input_name='col'), namespace_, eol_)) if self.row is not None: showIndent(outfile, level, pretty_print) outfile.write('<%srow>%s</%srow>%s' % (namespace_, self.gds_format_integer(self.row, input_name='row'), namespace_, eol_)) if self.sec is not None: showIndent(outfile, level, pretty_print) outfile.write('<%ssec>%s</%ssec>%s' % (namespace_, self.gds_format_integer(self.sec, input_name='sec'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'col': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'col') self.col = ival_ elif nodeName_ == 'row': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'row') self.row = ival_ elif nodeName_ == 'sec': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'sec') self.sec = ival_ # end class integer_vector_map_type
[docs]class citation_type(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if citation_type.subclass: return citation_type.subclass(*args_, **kwargs_) else: return citation_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='citation_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='citation_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='citation_type', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='citation_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='citation_type', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class citation_type
[docs]class non_journal_citation(GeneratedsSuper): member_data_items_ = [ MemberSpec_('published', 'xs:boolean', 0), MemberSpec_('author', 'author_order_type', 1), MemberSpec_('editor', 'author_order_type', 1), MemberSpec_('book_title', 'xs:token', 0), MemberSpec_('thesis_title', 'xs:token', 0), MemberSpec_('book_chapter_title', 'xs:token', 0), MemberSpec_('volume', 'xs:string', 0), MemberSpec_('publisher', 'xs:token', 0), MemberSpec_('publication_location', ['publication_locationType', 'xs:token'], 0), MemberSpec_('country', 'xs:token', 0), MemberSpec_('first_page', ['page_type', 'xs:string'], 0), MemberSpec_('last_page', ['page_type', 'xs:string'], 0), MemberSpec_('year', ['yearType', 'xs:gYear'], 0), MemberSpec_('language', 'xs:language', 0), MemberSpec_('external_references', 'external_referencesType45', 1), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, published=None, author=None, editor=None, book_title=None, thesis_title=None, book_chapter_title=None, volume=None, publisher=None, publication_location=None, country=None, first_page=None, last_page=None, year=None, language=None, external_references=None, details=None): self.original_tagname_ = None self.published = _cast(bool, published) if author is None: self.author = [] else: self.author = author if editor is None: self.editor = [] else: self.editor = editor self.book_title = book_title self.thesis_title = thesis_title self.book_chapter_title = book_chapter_title self.volume = volume self.publisher = publisher self.publication_location = publication_location self.validate_publication_locationType(self.publication_location) self.country = country self.first_page = first_page self.validate_page_type(self.first_page) self.last_page = last_page self.validate_page_type(self.last_page) self.year = year self.validate_yearType(self.year) self.language = language if external_references is None: self.external_references = [] else: self.external_references = external_references self.details = details
[docs] def factory(*args_, **kwargs_): if non_journal_citation.subclass: return non_journal_citation.subclass(*args_, **kwargs_) else: return non_journal_citation(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_author(self): return self.author
[docs] def set_author(self, author): self.author = author
[docs] def add_author(self, value): self.author.append(value)
[docs] def insert_author_at(self, index, value): self.author.insert(index, value)
[docs] def replace_author_at(self, index, value): self.author[index] = value
[docs] def get_editor(self): return self.editor
[docs] def set_editor(self, editor): self.editor = editor
[docs] def add_editor(self, value): self.editor.append(value)
[docs] def insert_editor_at(self, index, value): self.editor.insert(index, value)
[docs] def replace_editor_at(self, index, value): self.editor[index] = value
[docs] def get_book_title(self): return self.book_title
[docs] def set_book_title(self, book_title): self.book_title = book_title
[docs] def get_thesis_title(self): return self.thesis_title
[docs] def set_thesis_title(self, thesis_title): self.thesis_title = thesis_title
[docs] def get_book_chapter_title(self): return self.book_chapter_title
[docs] def set_book_chapter_title(self, book_chapter_title): self.book_chapter_title = book_chapter_title
[docs] def get_volume(self): return self.volume
[docs] def set_volume(self, volume): self.volume = volume
[docs] def get_publisher(self): return self.publisher
[docs] def set_publisher(self, publisher): self.publisher = publisher
[docs] def get_publication_location(self): return self.publication_location
[docs] def set_publication_location(self, publication_location): self.publication_location = publication_location
[docs] def get_country(self): return self.country
[docs] def set_country(self, country): self.country = country
[docs] def get_first_page(self): return self.first_page
[docs] def set_first_page(self, first_page): self.first_page = first_page
[docs] def get_last_page(self): return self.last_page
[docs] def set_last_page(self, last_page): self.last_page = last_page
[docs] def get_year(self): return self.year
[docs] def set_year(self, year): self.year = year
[docs] def get_language(self): return self.language
[docs] def set_language(self, language): self.language = language
[docs] def get_external_references(self): return self.external_references
[docs] def set_external_references(self, external_references): self.external_references = external_references
[docs] def add_external_references(self, value): self.external_references.append(value)
[docs] def insert_external_references_at(self, index, value): self.external_references.insert(index, value)
[docs] def replace_external_references_at(self, index, value): self.external_references[index] = value
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def get_published(self): return self.published
[docs] def set_published(self, published): self.published = published
[docs] def validate_publication_locationType(self, value): # Validate type publication_locationType, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_publication_locationType_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_publication_locationType_patterns_, ))
validate_publication_locationType_patterns_ = [['^[\\w -]+(, [\\w -]+)*$']]
[docs] def validate_page_type(self, value): # Validate type page_type, a restriction on xs:string. if value is not None and Validate_simpletypes_: pass
[docs] def validate_yearType(self, value): # Validate type yearType, a restriction on xs:gYear. if value is not None and Validate_simpletypes_: if value < 1900: warnings_.warn('Value "%(value)s" does not match xsd minInclusive restriction on yearType' % {"value" : value} )
[docs] def hasContent_(self): if ( self.author or self.editor or self.book_title is not None or self.thesis_title is not None or self.book_chapter_title is not None or self.volume is not None or self.publisher is not None or self.publication_location is not None or self.country is not None or self.first_page is not None or self.last_page is not None or self.year is not None or self.language is not None or self.external_references or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='non_journal_citation', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='non_journal_citation') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='non_journal_citation', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='non_journal_citation'): if self.published is not None and 'published' not in already_processed: already_processed.add('published') outfile.write(' published="%s"' % self.gds_format_boolean(self.published, input_name='published'))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='non_journal_citation', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for author_ in self.author: author_.export(outfile, level, namespace_, name_='author', pretty_print=pretty_print) for editor_ in self.editor: editor_.export(outfile, level, namespace_, name_='editor', pretty_print=pretty_print) if self.book_title is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sbook_title>%s</%sbook_title>%s' % (namespace_, self.gds_format_string(quote_xml(self.book_title).encode(ExternalEncoding), input_name='book_title'), namespace_, eol_)) if self.thesis_title is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sthesis_title>%s</%sthesis_title>%s' % (namespace_, self.gds_format_string(quote_xml(self.thesis_title).encode(ExternalEncoding), input_name='thesis_title'), namespace_, eol_)) if self.book_chapter_title is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sbook_chapter_title>%s</%sbook_chapter_title>%s' % (namespace_, self.gds_format_string(quote_xml(self.book_chapter_title).encode(ExternalEncoding), input_name='book_chapter_title'), namespace_, eol_)) if self.volume is not None: showIndent(outfile, level, pretty_print) outfile.write('<%svolume>%s</%svolume>%s' % (namespace_, self.gds_format_string(quote_xml(self.volume).encode(ExternalEncoding), input_name='volume'), namespace_, eol_)) if self.publisher is not None: showIndent(outfile, level, pretty_print) outfile.write('<%spublisher>%s</%spublisher>%s' % (namespace_, self.gds_format_string(quote_xml(self.publisher).encode(ExternalEncoding), input_name='publisher'), namespace_, eol_)) if self.publication_location is not None: showIndent(outfile, level, pretty_print) outfile.write('<%spublication_location>%s</%spublication_location>%s' % (namespace_, self.gds_format_string(quote_xml(self.publication_location).encode(ExternalEncoding), input_name='publication_location'), namespace_, eol_)) if self.country is not None: showIndent(outfile, level, pretty_print) outfile.write('<%scountry>%s</%scountry>%s' % (namespace_, self.gds_format_string(quote_xml(self.country).encode(ExternalEncoding), input_name='country'), namespace_, eol_)) if self.first_page is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sfirst_page>%s</%sfirst_page>%s' % (namespace_, self.gds_format_string(quote_xml(self.first_page).encode(ExternalEncoding), input_name='first_page'), namespace_, eol_)) if self.last_page is not None: showIndent(outfile, level, pretty_print) outfile.write('<%slast_page>%s</%slast_page>%s' % (namespace_, self.gds_format_string(quote_xml(self.last_page).encode(ExternalEncoding), input_name='last_page'), namespace_, eol_)) if self.year is not None: showIndent(outfile, level, pretty_print) outfile.write('<%syear>%s</%syear>%s' % (namespace_, self.gds_format_string(quote_xml(self.year).encode(ExternalEncoding), input_name='year'), namespace_, eol_)) if self.language is not None: showIndent(outfile, level, pretty_print) outfile.write('<%slanguage>%s</%slanguage>%s' % (namespace_, self.gds_format_string(quote_xml(self.language).encode(ExternalEncoding), input_name='language'), namespace_, eol_)) for external_references_ in self.external_references: external_references_.export(outfile, level, namespace_, name_='external_references', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('published', node) if value is not None and 'published' not in already_processed: already_processed.add('published') if value in ('true', '1'): self.published = True elif value in ('false', '0'): self.published = False else: raise_parse_error(node, 'Bad boolean attribute')
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'author': obj_ = author_order_type.factory() obj_.build(child_) self.author.append(obj_) obj_.original_tagname_ = 'author' elif nodeName_ == 'editor': obj_ = author_order_type.factory() obj_.build(child_) self.editor.append(obj_) obj_.original_tagname_ = 'editor' elif nodeName_ == 'book_title': book_title_ = child_.text book_title_ = re_.sub(String_cleanup_pat_, " ", book_title_).strip() book_title_ = self.gds_validate_string(book_title_, node, 'book_title') self.book_title = book_title_ elif nodeName_ == 'thesis_title': thesis_title_ = child_.text thesis_title_ = re_.sub(String_cleanup_pat_, " ", thesis_title_).strip() thesis_title_ = self.gds_validate_string(thesis_title_, node, 'thesis_title') self.thesis_title = thesis_title_ elif nodeName_ == 'book_chapter_title': book_chapter_title_ = child_.text book_chapter_title_ = re_.sub(String_cleanup_pat_, " ", book_chapter_title_).strip() book_chapter_title_ = self.gds_validate_string(book_chapter_title_, node, 'book_chapter_title') self.book_chapter_title = book_chapter_title_ elif nodeName_ == 'volume': volume_ = child_.text volume_ = self.gds_validate_string(volume_, node, 'volume') self.volume = volume_ elif nodeName_ == 'publisher': publisher_ = child_.text publisher_ = re_.sub(String_cleanup_pat_, " ", publisher_).strip() publisher_ = self.gds_validate_string(publisher_, node, 'publisher') self.publisher = publisher_ elif nodeName_ == 'publication_location': publication_location_ = child_.text publication_location_ = re_.sub(String_cleanup_pat_, " ", publication_location_).strip() publication_location_ = self.gds_validate_string(publication_location_, node, 'publication_location') self.publication_location = publication_location_ # validate type publication_locationType self.validate_publication_locationType(self.publication_location) elif nodeName_ == 'country': country_ = child_.text country_ = re_.sub(String_cleanup_pat_, " ", country_).strip() country_ = self.gds_validate_string(country_, node, 'country') self.country = country_ elif nodeName_ == 'first_page': first_page_ = child_.text first_page_ = self.gds_validate_string(first_page_, node, 'first_page') self.first_page = first_page_ # validate type page_type self.validate_page_type(self.first_page) elif nodeName_ == 'last_page': last_page_ = child_.text last_page_ = self.gds_validate_string(last_page_, node, 'last_page') self.last_page = last_page_ # validate type page_type self.validate_page_type(self.last_page) elif nodeName_ == 'year': year_ = child_.text year_ = self.gds_validate_string(year_, node, 'year') self.year = year_ # validate type yearType self.validate_yearType(self.year) elif nodeName_ == 'language': language_ = child_.text language_ = self.gds_validate_string(language_, node, 'language') self.language = language_ elif nodeName_ == 'external_references': obj_ = external_referencesType45.factory() obj_.build(child_) self.external_references.append(obj_) obj_.original_tagname_ = 'external_references' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class non_journal_citation
[docs]class journal_citation(GeneratedsSuper): member_data_items_ = [ MemberSpec_('published', 'xs:boolean', 0), MemberSpec_('author', 'author_order_type', 1), MemberSpec_('editor', 'author_order_type', 1), MemberSpec_('title', 'xs:token', 0), MemberSpec_('journal', 'xs:token', 0), MemberSpec_('journal_abbreviation', ['journal_abbreviationType', 'xs:token'], 0), MemberSpec_('country', 'xs:token', 0), MemberSpec_('issue', 'xs:positiveInteger', 0), MemberSpec_('volume', 'xs:string', 0), MemberSpec_('first_page', ['page_type', 'xs:string'], 0), MemberSpec_('last_page', ['page_type', 'xs:string'], 0), MemberSpec_('year', ['yearType46', 'xs:gYear'], 0), MemberSpec_('language', 'xs:language', 0), MemberSpec_('external_references', 'external_referencesType47', 1), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, published=None, author=None, editor=None, title=None, journal=None, journal_abbreviation=None, country=None, issue=None, volume=None, first_page=None, last_page=None, year=None, language=None, external_references=None, details=None): self.original_tagname_ = None self.published = _cast(bool, published) if author is None: self.author = [] else: self.author = author if editor is None: self.editor = [] else: self.editor = editor self.title = title self.journal = journal self.journal_abbreviation = journal_abbreviation self.validate_journal_abbreviationType(self.journal_abbreviation) self.country = country self.issue = issue self.volume = volume self.first_page = first_page self.validate_page_type(self.first_page) self.last_page = last_page self.validate_page_type(self.last_page) self.year = year self.validate_yearType46(self.year) self.language = language if external_references is None: self.external_references = [] else: self.external_references = external_references self.details = details
[docs] def factory(*args_, **kwargs_): if journal_citation.subclass: return journal_citation.subclass(*args_, **kwargs_) else: return journal_citation(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_author(self): return self.author
[docs] def set_author(self, author): self.author = author
[docs] def add_author(self, value): self.author.append(value)
[docs] def insert_author_at(self, index, value): self.author.insert(index, value)
[docs] def replace_author_at(self, index, value): self.author[index] = value
[docs] def get_editor(self): return self.editor
[docs] def set_editor(self, editor): self.editor = editor
[docs] def add_editor(self, value): self.editor.append(value)
[docs] def insert_editor_at(self, index, value): self.editor.insert(index, value)
[docs] def replace_editor_at(self, index, value): self.editor[index] = value
[docs] def get_title(self): return self.title
[docs] def set_title(self, title): self.title = title
[docs] def get_journal(self): return self.journal
[docs] def set_journal(self, journal): self.journal = journal
[docs] def get_journal_abbreviation(self): return self.journal_abbreviation
[docs] def set_journal_abbreviation(self, journal_abbreviation): self.journal_abbreviation = journal_abbreviation
[docs] def get_country(self): return self.country
[docs] def set_country(self, country): self.country = country
[docs] def get_issue(self): return self.issue
[docs] def set_issue(self, issue): self.issue = issue
[docs] def get_volume(self): return self.volume
[docs] def set_volume(self, volume): self.volume = volume
[docs] def get_first_page(self): return self.first_page
[docs] def set_first_page(self, first_page): self.first_page = first_page
[docs] def get_last_page(self): return self.last_page
[docs] def set_last_page(self, last_page): self.last_page = last_page
[docs] def get_year(self): return self.year
[docs] def set_year(self, year): self.year = year
[docs] def get_language(self): return self.language
[docs] def set_language(self, language): self.language = language
[docs] def get_external_references(self): return self.external_references
[docs] def set_external_references(self, external_references): self.external_references = external_references
[docs] def add_external_references(self, value): self.external_references.append(value)
[docs] def insert_external_references_at(self, index, value): self.external_references.insert(index, value)
[docs] def replace_external_references_at(self, index, value): self.external_references[index] = value
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def get_published(self): return self.published
[docs] def set_published(self, published): self.published = published
[docs] def validate_journal_abbreviationType(self, value): # Validate type journal_abbreviationType, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_journal_abbreviationType_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_journal_abbreviationType_patterns_, ))
validate_journal_abbreviationType_patterns_ = [['^[A-Z][a-z]*\\.?( [A-Z][a-z]+\\.?)*$']]
[docs] def validate_page_type(self, value): # Validate type page_type, a restriction on xs:string. if value is not None and Validate_simpletypes_: pass
[docs] def validate_yearType46(self, value): # Validate type yearType46, a restriction on xs:gYear. if value is not None and Validate_simpletypes_: if value < 1900: warnings_.warn('Value "%(value)s" does not match xsd minInclusive restriction on yearType46' % {"value" : value} )
[docs] def hasContent_(self): if ( self.author or self.editor or self.title is not None or self.journal is not None or self.journal_abbreviation is not None or self.country is not None or self.issue is not None or self.volume is not None or self.first_page is not None or self.last_page is not None or self.year is not None or self.language is not None or self.external_references or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='journal_citation', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='journal_citation') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='journal_citation', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='journal_citation'): if self.published is not None and 'published' not in already_processed: already_processed.add('published') outfile.write(' published="%s"' % self.gds_format_boolean(self.published, input_name='published'))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='journal_citation', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for author_ in self.author: author_.export(outfile, level, namespace_, name_='author', pretty_print=pretty_print) for editor_ in self.editor: editor_.export(outfile, level, namespace_, name_='editor', pretty_print=pretty_print) if self.title is not None: showIndent(outfile, level, pretty_print) outfile.write('<%stitle>%s</%stitle>%s' % (namespace_, self.gds_format_string(quote_xml(self.title).encode(ExternalEncoding), input_name='title'), namespace_, eol_)) if self.journal is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sjournal>%s</%sjournal>%s' % (namespace_, self.gds_format_string(quote_xml(self.journal).encode(ExternalEncoding), input_name='journal'), namespace_, eol_)) if self.journal_abbreviation is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sjournal_abbreviation>%s</%sjournal_abbreviation>%s' % (namespace_, self.gds_format_string(quote_xml(self.journal_abbreviation).encode(ExternalEncoding), input_name='journal_abbreviation'), namespace_, eol_)) if self.country is not None: showIndent(outfile, level, pretty_print) outfile.write('<%scountry>%s</%scountry>%s' % (namespace_, self.gds_format_string(quote_xml(self.country).encode(ExternalEncoding), input_name='country'), namespace_, eol_)) if self.issue is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sissue>%s</%sissue>%s' % (namespace_, self.gds_format_integer(self.issue, input_name='issue'), namespace_, eol_)) if self.volume is not None: showIndent(outfile, level, pretty_print) outfile.write('<%svolume>%s</%svolume>%s' % (namespace_, self.gds_format_string(quote_xml(self.volume).encode(ExternalEncoding), input_name='volume'), namespace_, eol_)) if self.first_page is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sfirst_page>%s</%sfirst_page>%s' % (namespace_, self.gds_format_string(quote_xml(self.first_page).encode(ExternalEncoding), input_name='first_page'), namespace_, eol_)) if self.last_page is not None: showIndent(outfile, level, pretty_print) outfile.write('<%slast_page>%s</%slast_page>%s' % (namespace_, self.gds_format_string(quote_xml(self.last_page).encode(ExternalEncoding), input_name='last_page'), namespace_, eol_)) if self.year is not None: showIndent(outfile, level, pretty_print) outfile.write('<%syear>%s</%syear>%s' % (namespace_, self.gds_format_string(quote_xml(self.year).encode(ExternalEncoding), input_name='year'), namespace_, eol_)) if self.language is not None: showIndent(outfile, level, pretty_print) outfile.write('<%slanguage>%s</%slanguage>%s' % (namespace_, self.gds_format_string(quote_xml(self.language).encode(ExternalEncoding), input_name='language'), namespace_, eol_)) for external_references_ in self.external_references: external_references_.export(outfile, level, namespace_, name_='external_references', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('published', node) if value is not None and 'published' not in already_processed: already_processed.add('published') if value in ('true', '1'): self.published = True elif value in ('false', '0'): self.published = False else: raise_parse_error(node, 'Bad boolean attribute')
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'author': obj_ = author_order_type.factory() obj_.build(child_) self.author.append(obj_) obj_.original_tagname_ = 'author' elif nodeName_ == 'editor': obj_ = author_order_type.factory() obj_.build(child_) self.editor.append(obj_) obj_.original_tagname_ = 'editor' elif nodeName_ == 'title': title_ = child_.text title_ = re_.sub(String_cleanup_pat_, " ", title_).strip() title_ = self.gds_validate_string(title_, node, 'title') self.title = title_ elif nodeName_ == 'journal': journal_ = child_.text journal_ = re_.sub(String_cleanup_pat_, " ", journal_).strip() journal_ = self.gds_validate_string(journal_, node, 'journal') self.journal = journal_ elif nodeName_ == 'journal_abbreviation': journal_abbreviation_ = child_.text journal_abbreviation_ = re_.sub(String_cleanup_pat_, " ", journal_abbreviation_).strip() journal_abbreviation_ = self.gds_validate_string(journal_abbreviation_, node, 'journal_abbreviation') self.journal_abbreviation = journal_abbreviation_ # validate type journal_abbreviationType self.validate_journal_abbreviationType(self.journal_abbreviation) elif nodeName_ == 'country': country_ = child_.text country_ = re_.sub(String_cleanup_pat_, " ", country_).strip() country_ = self.gds_validate_string(country_, node, 'country') self.country = country_ elif nodeName_ == 'issue': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'issue') self.issue = ival_ elif nodeName_ == 'volume': volume_ = child_.text volume_ = self.gds_validate_string(volume_, node, 'volume') self.volume = volume_ elif nodeName_ == 'first_page': first_page_ = child_.text first_page_ = self.gds_validate_string(first_page_, node, 'first_page') self.first_page = first_page_ # validate type page_type self.validate_page_type(self.first_page) elif nodeName_ == 'last_page': last_page_ = child_.text last_page_ = self.gds_validate_string(last_page_, node, 'last_page') self.last_page = last_page_ # validate type page_type self.validate_page_type(self.last_page) elif nodeName_ == 'year': year_ = child_.text year_ = self.gds_validate_string(year_, node, 'year') self.year = year_ # validate type yearType46 self.validate_yearType46(self.year) elif nodeName_ == 'language': language_ = child_.text language_ = self.gds_validate_string(language_, node, 'language') self.language = language_ elif nodeName_ == 'external_references': obj_ = external_referencesType47.factory() obj_.build(child_) self.external_references.append(obj_) obj_.original_tagname_ = 'external_references' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class journal_citation
[docs]class software_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('name', 'xs:token', 0), MemberSpec_('version', 'xs:token', 0), MemberSpec_('processing_details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, name=None, version=None, processing_details=None): self.original_tagname_ = None self.name = name self.version = version self.processing_details = processing_details
[docs] def factory(*args_, **kwargs_): if software_type.subclass: return software_type.subclass(*args_, **kwargs_) else: return software_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_name(self): return self.name
[docs] def set_name(self, name): self.name = name
[docs] def get_version(self): return self.version
[docs] def set_version(self, version): self.version = version
[docs] def get_processing_details(self): return self.processing_details
[docs] def set_processing_details(self, processing_details): self.processing_details = processing_details
[docs] def hasContent_(self): if ( self.name is not None or self.version is not None or self.processing_details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='software_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='software_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='software_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='software_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='software_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.name is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sname>%s</%sname>%s' % (namespace_, self.gds_format_string(quote_xml(self.name).encode(ExternalEncoding), input_name='name'), namespace_, eol_)) if self.version is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sversion>%s</%sversion>%s' % (namespace_, self.gds_format_string(quote_xml(self.version).encode(ExternalEncoding), input_name='version'), namespace_, eol_)) if self.processing_details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sprocessing_details>%s</%sprocessing_details>%s' % (namespace_, self.gds_format_string(quote_xml(self.processing_details).encode(ExternalEncoding), input_name='processing_details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'name': name_ = child_.text name_ = re_.sub(String_cleanup_pat_, " ", name_).strip() name_ = self.gds_validate_string(name_, node, 'name') self.name = name_ elif nodeName_ == 'version': version_ = child_.text version_ = re_.sub(String_cleanup_pat_, " ", version_).strip() version_ = self.gds_validate_string(version_, node, 'version') self.version = version_ elif nodeName_ == 'processing_details': processing_details_ = child_.text processing_details_ = self.gds_validate_string(processing_details_, node, 'processing_details') self.processing_details = processing_details_ # end class software_type
[docs]class telephone_number_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('country', ['countryType', 'xs:token'], 0), MemberSpec_('area', ['areaType', 'xs:token'], 0), MemberSpec_('local', ['localType', 'xs:token'], 0), ] subclass = None superclass = None def __init__(self, country=None, area=None, local=None): self.original_tagname_ = None self.country = country self.validate_countryType(self.country) self.area = area self.validate_areaType(self.area) self.local = local self.validate_localType(self.local)
[docs] def factory(*args_, **kwargs_): if telephone_number_type.subclass: return telephone_number_type.subclass(*args_, **kwargs_) else: return telephone_number_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_country(self): return self.country
[docs] def set_country(self, country): self.country = country
[docs] def get_area(self): return self.area
[docs] def set_area(self, area): self.area = area
[docs] def get_local(self): return self.local
[docs] def set_local(self, local): self.local = local
[docs] def validate_countryType(self, value): # Validate type countryType, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_countryType_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_countryType_patterns_, ))
validate_countryType_patterns_ = [['^\\d{1,3}$']]
[docs] def validate_areaType(self, value): # Validate type areaType, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_areaType_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_areaType_patterns_, ))
validate_areaType_patterns_ = [['^\\d{2,5}$']]
[docs] def validate_localType(self, value): # Validate type localType, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_localType_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_localType_patterns_, ))
validate_localType_patterns_ = [['^\\d+( ext. \\d+)?$']]
[docs] def hasContent_(self): if ( self.country is not None or self.area is not None or self.local is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='telephone_number_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='telephone_number_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='telephone_number_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='telephone_number_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='telephone_number_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.country is not None: showIndent(outfile, level, pretty_print) outfile.write('<%scountry>%s</%scountry>%s' % (namespace_, self.gds_format_string(quote_xml(self.country).encode(ExternalEncoding), input_name='country'), namespace_, eol_)) if self.area is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sarea>%s</%sarea>%s' % (namespace_, self.gds_format_string(quote_xml(self.area).encode(ExternalEncoding), input_name='area'), namespace_, eol_)) if self.local is not None: showIndent(outfile, level, pretty_print) outfile.write('<%slocal>%s</%slocal>%s' % (namespace_, self.gds_format_string(quote_xml(self.local).encode(ExternalEncoding), input_name='local'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'country': country_ = child_.text country_ = re_.sub(String_cleanup_pat_, " ", country_).strip() country_ = self.gds_validate_string(country_, node, 'country') self.country = country_ # validate type countryType self.validate_countryType(self.country) elif nodeName_ == 'area': area_ = child_.text area_ = re_.sub(String_cleanup_pat_, " ", area_).strip() area_ = self.gds_validate_string(area_, node, 'area') self.area = area_ # validate type areaType self.validate_areaType(self.area) elif nodeName_ == 'local': local_ = child_.text local_ = re_.sub(String_cleanup_pat_, " ", local_).strip() local_ = self.gds_validate_string(local_, node, 'local') self.local = local_ # validate type localType self.validate_localType(self.local) # end class telephone_number_type
[docs]class crystallography_preparation_type(base_preparation_type): """TODO: add limits and units.""" member_data_items_ = [ MemberSpec_('crystal_formation', 'crystal_formationType', 0), ] subclass = None superclass = base_preparation_type def __init__(self, id=None, concentration=None, buffer=None, staining=None, sugar_embedding=None, shadowing=None, grid=None, vitrification=None, details=None, crystal_formation=None): self.original_tagname_ = None super(crystallography_preparation_type, self).__init__(id, concentration, buffer, staining, sugar_embedding, shadowing, grid, vitrification, details, ) self.crystal_formation = crystal_formation
[docs] def factory(*args_, **kwargs_): if crystallography_preparation_type.subclass: return crystallography_preparation_type.subclass(*args_, **kwargs_) else: return crystallography_preparation_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_crystal_formation(self): return self.crystal_formation
[docs] def set_crystal_formation(self, crystal_formation): self.crystal_formation = crystal_formation
[docs] def hasContent_(self): if ( self.crystal_formation is not None or super(crystallography_preparation_type, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='crystallography_preparation_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='crystallography_preparation_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='crystallography_preparation_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='crystallography_preparation_type'): super(crystallography_preparation_type, self).exportAttributes(outfile, level, already_processed, namespace_, name_='crystallography_preparation_type')
[docs] def exportChildren(self, outfile, level, namespace_='', name_='crystallography_preparation_type', fromsubclass_=False, pretty_print=True): super(crystallography_preparation_type, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print) if pretty_print: eol_ = '\n' else: eol_ = '' if self.crystal_formation is not None: self.crystal_formation.export(outfile, level, namespace_, name_='crystal_formation', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): super(crystallography_preparation_type, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'crystal_formation': obj_ = crystal_formationType.factory() obj_.build(child_) self.crystal_formation = obj_ obj_.original_tagname_ = 'crystal_formation' super(crystallography_preparation_type, self).buildChildren(child_, node, nodeName_, True) # end class crystallography_preparation_type
[docs]class background_masked_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('geometrical_shape', ['geometrical_shapeType', 'xs:token'], 0), MemberSpec_('dimensions', 'dimensionsType49', 0), MemberSpec_('software_list', 'software_list_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, geometrical_shape=None, dimensions=None, software_list=None, details=None): self.original_tagname_ = None self.geometrical_shape = geometrical_shape self.validate_geometrical_shapeType(self.geometrical_shape) self.dimensions = dimensions self.software_list = software_list self.details = details
[docs] def factory(*args_, **kwargs_): if background_masked_type.subclass: return background_masked_type.subclass(*args_, **kwargs_) else: return background_masked_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_geometrical_shape(self): return self.geometrical_shape
[docs] def set_geometrical_shape(self, geometrical_shape): self.geometrical_shape = geometrical_shape
[docs] def get_dimensions(self): return self.dimensions
[docs] def set_dimensions(self, dimensions): self.dimensions = dimensions
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def validate_geometrical_shapeType(self, value): # Validate type geometrical_shapeType, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['SPHERE', 'SOFT SPHERE', 'GAUSSIAN', 'CIRCLE', 'RECTANGLE', 'CYLINDER', 'OTHER'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on geometrical_shapeType' % {"value" : value.encode("utf-8")} )
[docs] def hasContent_(self): if ( self.geometrical_shape is not None or self.dimensions is not None or self.software_list is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='background_masked_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='background_masked_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='background_masked_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='background_masked_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='background_masked_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.geometrical_shape is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sgeometrical_shape>%s</%sgeometrical_shape>%s' % (namespace_, self.gds_format_string(quote_xml(self.geometrical_shape).encode(ExternalEncoding), input_name='geometrical_shape'), namespace_, eol_)) if self.dimensions is not None: self.dimensions.export(outfile, level, namespace_, name_='dimensions', pretty_print=pretty_print) if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'geometrical_shape': geometrical_shape_ = child_.text geometrical_shape_ = re_.sub(String_cleanup_pat_, " ", geometrical_shape_).strip() geometrical_shape_ = self.gds_validate_string(geometrical_shape_, node, 'geometrical_shape') self.geometrical_shape = geometrical_shape_ # validate type geometrical_shapeType self.validate_geometrical_shapeType(self.geometrical_shape) elif nodeName_ == 'dimensions': obj_ = dimensionsType49.factory() obj_.build(child_) self.dimensions = obj_ obj_.original_tagname_ = 'dimensions' elif nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class background_masked_type
[docs]class reconstruction_filtering_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('background_masked', 'background_masked_type', 0), MemberSpec_('spatial_filtering', 'spatial_filteringType', 0), MemberSpec_('sharpening', 'sharpeningType', 0), MemberSpec_('b_factorSharpening', 'b-factorSharpeningType', 0), MemberSpec_('other', 'otherType52', 0), ] subclass = None superclass = None def __init__(self, background_masked=None, spatial_filtering=None, sharpening=None, b_factorSharpening=None, other=None): self.original_tagname_ = None self.background_masked = background_masked self.spatial_filtering = spatial_filtering self.sharpening = sharpening self.b_factorSharpening = b_factorSharpening self.other = other
[docs] def factory(*args_, **kwargs_): if reconstruction_filtering_type.subclass: return reconstruction_filtering_type.subclass(*args_, **kwargs_) else: return reconstruction_filtering_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_background_masked(self): return self.background_masked
[docs] def set_background_masked(self, background_masked): self.background_masked = background_masked
[docs] def get_spatial_filtering(self): return self.spatial_filtering
[docs] def set_spatial_filtering(self, spatial_filtering): self.spatial_filtering = spatial_filtering
[docs] def get_sharpening(self): return self.sharpening
[docs] def set_sharpening(self, sharpening): self.sharpening = sharpening
[docs] def get_b_factorSharpening(self): return self.b_factorSharpening
[docs] def set_b_factorSharpening(self, b_factorSharpening): self.b_factorSharpening = b_factorSharpening
[docs] def get_other(self): return self.other
[docs] def set_other(self, other): self.other = other
[docs] def hasContent_(self): if ( self.background_masked is not None or self.spatial_filtering is not None or self.sharpening is not None or self.b_factorSharpening is not None or self.other is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='reconstruction_filtering_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='reconstruction_filtering_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='reconstruction_filtering_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='reconstruction_filtering_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='reconstruction_filtering_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.background_masked is not None: self.background_masked.export(outfile, level, namespace_, name_='background_masked', pretty_print=pretty_print) if self.spatial_filtering is not None: self.spatial_filtering.export(outfile, level, namespace_, name_='spatial_filtering', pretty_print=pretty_print) if self.sharpening is not None: self.sharpening.export(outfile, level, namespace_, name_='sharpening', pretty_print=pretty_print) if self.b_factorSharpening is not None: self.b_factorSharpening.export(outfile, level, namespace_, name_='b-factorSharpening', pretty_print=pretty_print) if self.other is not None: self.other.export(outfile, level, namespace_, name_='other', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'background_masked': obj_ = background_masked_type.factory() obj_.build(child_) self.background_masked = obj_ obj_.original_tagname_ = 'background_masked' elif nodeName_ == 'spatial_filtering': obj_ = spatial_filteringType.factory() obj_.build(child_) self.spatial_filtering = obj_ obj_.original_tagname_ = 'spatial_filtering' elif nodeName_ == 'sharpening': obj_ = sharpeningType.factory() obj_.build(child_) self.sharpening = obj_ obj_.original_tagname_ = 'sharpening' elif nodeName_ == 'b-factorSharpening': obj_ = b_factorSharpeningType.factory() obj_.build(child_) self.b_factorSharpening = obj_ obj_.original_tagname_ = 'b-factorSharpening' elif nodeName_ == 'other': obj_ = otherType52.factory() obj_.build(child_) self.other = obj_ obj_.original_tagname_ = 'other' # end class reconstruction_filtering_type
[docs]class chain_id_list(chain_type): member_data_items_ = [ ] subclass = None superclass = chain_type def __init__(self, id=None, residue_range=None): self.original_tagname_ = None super(chain_id_list, self).__init__(id, residue_range, )
[docs] def factory(*args_, **kwargs_): if chain_id_list.subclass: return chain_id_list.subclass(*args_, **kwargs_) else: return chain_id_list(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( super(chain_id_list, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='chain_id_list', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='chain_id_list') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='chain_id_list', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='chain_id_list'): super(chain_id_list, self).exportAttributes(outfile, level, already_processed, namespace_, name_='chain_id_list')
[docs] def exportChildren(self, outfile, level, namespace_='', name_='chain_id_list', fromsubclass_=False, pretty_print=True): super(chain_id_list, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): super(chain_id_list, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): super(chain_id_list, self).buildChildren(child_, node, nodeName_, True) pass # end class chain_id_list
[docs]class recombinant_source_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('database', 'xs:token', 0), MemberSpec_('organism', 'organism_type', 0), MemberSpec_('strain', 'xs:token', 0), MemberSpec_('cell', 'cell', 0), MemberSpec_('plasmid', 'xs:token', 0), MemberSpec_('synonym_organism', 'xs:token', 0), ] subclass = None superclass = None def __init__(self, database=None, organism=None, strain=None, cell=None, plasmid=None, synonym_organism=None): self.original_tagname_ = None self.database = _cast(None, database) self.organism = organism self.strain = strain self.cell = cell self.plasmid = plasmid self.synonym_organism = synonym_organism
[docs] def factory(*args_, **kwargs_): if recombinant_source_type.subclass: return recombinant_source_type.subclass(*args_, **kwargs_) else: return recombinant_source_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_organism(self): return self.organism
[docs] def set_organism(self, organism): self.organism = organism
[docs] def get_strain(self): return self.strain
[docs] def set_strain(self, strain): self.strain = strain
[docs] def get_cell(self): return self.cell
[docs] def set_cell(self, cell): self.cell = cell
[docs] def get_plasmid(self): return self.plasmid
[docs] def set_plasmid(self, plasmid): self.plasmid = plasmid
[docs] def get_synonym_organism(self): return self.synonym_organism
[docs] def set_synonym_organism(self, synonym_organism): self.synonym_organism = synonym_organism
[docs] def get_database(self): return self.database
[docs] def set_database(self, database): self.database = database
[docs] def hasContent_(self): if ( self.organism is not None or self.strain is not None or self.cell is not None or self.plasmid is not None or self.synonym_organism is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='recombinant_source_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='recombinant_source_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='recombinant_source_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='recombinant_source_type'): if self.database is not None and 'database' not in already_processed: already_processed.add('database') outfile.write(' database=%s' % (self.gds_format_string(quote_attrib(self.database).encode(ExternalEncoding), input_name='database'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='recombinant_source_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.organism is not None: self.organism.export(outfile, level, namespace_, name_='organism', pretty_print=pretty_print) if self.strain is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sstrain>%s</%sstrain>%s' % (namespace_, self.gds_format_string(quote_xml(self.strain).encode(ExternalEncoding), input_name='strain'), namespace_, eol_)) if self.cell is not None: showIndent(outfile, level, pretty_print) outfile.write('<%scell>%s</%scell>%s' % (namespace_, self.gds_format_string(quote_xml(self.cell).encode(ExternalEncoding), input_name='cell'), namespace_, eol_)) if self.plasmid is not None: showIndent(outfile, level, pretty_print) outfile.write('<%splasmid>%s</%splasmid>%s' % (namespace_, self.gds_format_string(quote_xml(self.plasmid).encode(ExternalEncoding), input_name='plasmid'), namespace_, eol_)) if self.synonym_organism is not None: showIndent(outfile, level, pretty_print) outfile.write('<%ssynonym_organism>%s</%ssynonym_organism>%s' % (namespace_, self.gds_format_string(quote_xml(self.synonym_organism).encode(ExternalEncoding), input_name='synonym_organism'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('database', node) if value is not None and 'database' not in already_processed: already_processed.add('database') self.database = value self.database = ' '.join(self.database.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'organism': obj_ = organism_type.factory() obj_.build(child_) self.organism = obj_ obj_.original_tagname_ = 'organism' elif nodeName_ == 'strain': strain_ = child_.text strain_ = re_.sub(String_cleanup_pat_, " ", strain_).strip() strain_ = self.gds_validate_string(strain_, node, 'strain') self.strain = strain_ elif nodeName_ == 'cell': cell_ = child_.text cell_ = re_.sub(String_cleanup_pat_, " ", cell_).strip() cell_ = self.gds_validate_string(cell_, node, 'cell') self.cell = cell_ elif nodeName_ == 'plasmid': plasmid_ = child_.text plasmid_ = re_.sub(String_cleanup_pat_, " ", plasmid_).strip() plasmid_ = self.gds_validate_string(plasmid_, node, 'plasmid') self.plasmid = plasmid_ elif nodeName_ == 'synonym_organism': synonym_organism_ = child_.text synonym_organism_ = re_.sub(String_cleanup_pat_, " ", synonym_organism_).strip() synonym_organism_ = self.gds_validate_string(synonym_organism_, node, 'synonym_organism') self.synonym_organism = synonym_organism_ # end class recombinant_source_type
[docs]class organism_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('ncbi', 'xs:positiveInteger', 0), MemberSpec_('valueOf_', 'xs:token', 0), ] subclass = None superclass = None def __init__(self, ncbi=None, valueOf_=None): self.original_tagname_ = None self.ncbi = _cast(int, ncbi) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if organism_type.subclass: return organism_type.subclass(*args_, **kwargs_) else: return organism_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_ncbi(self): return self.ncbi
[docs] def set_ncbi(self, ncbi): self.ncbi = ncbi
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='organism_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='organism_type') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='organism_type', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='organism_type'): if self.ncbi is not None and 'ncbi' not in already_processed: already_processed.add('ncbi') outfile.write(' ncbi="%s"' % self.gds_format_integer(self.ncbi, input_name='ncbi'))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='organism_type', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('ncbi', node) if value is not None and 'ncbi' not in already_processed: already_processed.add('ncbi') try: self.ncbi = int(value) except ValueError as exp: raise_parse_error(node, 'Bad integer attribute: %s' % exp) if self.ncbi <= 0: raise_parse_error(node, 'Invalid PositiveInteger')
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class organism_type
[docs]class base_natural_source_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('database', 'xs:token', 0), MemberSpec_('organism', 'organism_type', 0), MemberSpec_('strain', 'organism_type', 0), MemberSpec_('synonym_organism', 'xs:token', 0), ] subclass = None superclass = None def __init__(self, database=None, organism=None, strain=None, synonym_organism=None, extensiontype_=None): self.original_tagname_ = None self.database = _cast(None, database) self.organism = organism self.strain = strain self.synonym_organism = synonym_organism self.extensiontype_ = extensiontype_
[docs] def factory(*args_, **kwargs_): if base_natural_source_type.subclass: return base_natural_source_type.subclass(*args_, **kwargs_) else: return base_natural_source_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_organism(self): return self.organism
[docs] def set_organism(self, organism): self.organism = organism
[docs] def get_strain(self): return self.strain
[docs] def set_strain(self, strain): self.strain = strain
[docs] def get_synonym_organism(self): return self.synonym_organism
[docs] def set_synonym_organism(self, synonym_organism): self.synonym_organism = synonym_organism
[docs] def get_database(self): return self.database
[docs] def set_database(self, database): self.database = database
[docs] def get_extensiontype_(self): return self.extensiontype_
[docs] def set_extensiontype_(self, extensiontype_): self.extensiontype_ = extensiontype_
[docs] def hasContent_(self): if ( self.organism is not None or self.strain is not None or self.synonym_organism is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='base_natural_source_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='base_natural_source_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='base_natural_source_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='base_natural_source_type'): if self.database is not None and 'database' not in already_processed: already_processed.add('database') outfile.write(' database=%s' % (self.gds_format_string(quote_attrib(self.database).encode(ExternalEncoding), input_name='database'), )) if self.extensiontype_ is not None and 'xsi:type' not in already_processed: already_processed.add('xsi:type') outfile.write(' xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"') outfile.write(' xsi:type="%s"' % self.extensiontype_)
[docs] def exportChildren(self, outfile, level, namespace_='', name_='base_natural_source_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.organism is not None: self.organism.export(outfile, level, namespace_, name_='organism', pretty_print=pretty_print) if self.strain is not None: self.strain.export(outfile, level, namespace_, name_='strain', pretty_print=pretty_print) if self.synonym_organism is not None: showIndent(outfile, level, pretty_print) outfile.write('<%ssynonym_organism>%s</%ssynonym_organism>%s' % (namespace_, self.gds_format_string(quote_xml(self.synonym_organism).encode(ExternalEncoding), input_name='synonym_organism'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('database', node) if value is not None and 'database' not in already_processed: already_processed.add('database') self.database = value self.database = ' '.join(self.database.split()) value = find_attr_value_('xsi:type', node) if value is not None and 'xsi:type' not in already_processed: already_processed.add('xsi:type') self.extensiontype_ = value
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'organism': obj_ = organism_type.factory() obj_.build(child_) self.organism = obj_ obj_.original_tagname_ = 'organism' elif nodeName_ == 'strain': obj_ = organism_type.factory() obj_.build(child_) self.strain = obj_ obj_.original_tagname_ = 'strain' elif nodeName_ == 'synonym_organism': synonym_organism_ = child_.text synonym_organism_ = re_.sub(String_cleanup_pat_, " ", synonym_organism_).strip() synonym_organism_ = self.gds_validate_string(synonym_organism_, node, 'synonym_organism') self.synonym_organism = synonym_organism_ # end class base_natural_source_type
[docs]class natural_source_type(base_natural_source_type): member_data_items_ = [ MemberSpec_('organ', 'xs:token', 0), MemberSpec_('tissue', 'tissue', 0), MemberSpec_('cell', 'cell', 0), MemberSpec_('organelle', 'xs:token', 0), MemberSpec_('cellular_location', 'xs:token', 0), ] subclass = None superclass = base_natural_source_type def __init__(self, database=None, organism=None, strain=None, synonym_organism=None, organ=None, tissue=None, cell=None, organelle=None, cellular_location=None): self.original_tagname_ = None super(natural_source_type, self).__init__(database, organism, strain, synonym_organism, ) self.organ = organ self.tissue = tissue self.cell = cell self.organelle = organelle self.cellular_location = cellular_location
[docs] def factory(*args_, **kwargs_): if natural_source_type.subclass: return natural_source_type.subclass(*args_, **kwargs_) else: return natural_source_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_organ(self): return self.organ
[docs] def set_organ(self, organ): self.organ = organ
[docs] def get_tissue(self): return self.tissue
[docs] def set_tissue(self, tissue): self.tissue = tissue
[docs] def get_cell(self): return self.cell
[docs] def set_cell(self, cell): self.cell = cell
[docs] def get_organelle(self): return self.organelle
[docs] def set_organelle(self, organelle): self.organelle = organelle
[docs] def get_cellular_location(self): return self.cellular_location
[docs] def set_cellular_location(self, cellular_location): self.cellular_location = cellular_location
[docs] def hasContent_(self): if ( self.organ is not None or self.tissue is not None or self.cell is not None or self.organelle is not None or self.cellular_location is not None or super(natural_source_type, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='natural_source_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='natural_source_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='natural_source_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='natural_source_type'): super(natural_source_type, self).exportAttributes(outfile, level, already_processed, namespace_, name_='natural_source_type')
[docs] def exportChildren(self, outfile, level, namespace_='', name_='natural_source_type', fromsubclass_=False, pretty_print=True): super(natural_source_type, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print) if pretty_print: eol_ = '\n' else: eol_ = '' if self.organ is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sorgan>%s</%sorgan>%s' % (namespace_, self.gds_format_string(quote_xml(self.organ).encode(ExternalEncoding), input_name='organ'), namespace_, eol_)) if self.tissue is not None: showIndent(outfile, level, pretty_print) outfile.write('<%stissue>%s</%stissue>%s' % (namespace_, self.gds_format_string(quote_xml(self.tissue).encode(ExternalEncoding), input_name='tissue'), namespace_, eol_)) if self.cell is not None: showIndent(outfile, level, pretty_print) outfile.write('<%scell>%s</%scell>%s' % (namespace_, self.gds_format_string(quote_xml(self.cell).encode(ExternalEncoding), input_name='cell'), namespace_, eol_)) if self.organelle is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sorganelle>%s</%sorganelle>%s' % (namespace_, self.gds_format_string(quote_xml(self.organelle).encode(ExternalEncoding), input_name='organelle'), namespace_, eol_)) if self.cellular_location is not None: showIndent(outfile, level, pretty_print) outfile.write('<%scellular_location>%s</%scellular_location>%s' % (namespace_, self.gds_format_string(quote_xml(self.cellular_location).encode(ExternalEncoding), input_name='cellular_location'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): super(natural_source_type, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'organ': organ_ = child_.text organ_ = re_.sub(String_cleanup_pat_, " ", organ_).strip() organ_ = self.gds_validate_string(organ_, node, 'organ') self.organ = organ_ elif nodeName_ == 'tissue': tissue_ = child_.text tissue_ = re_.sub(String_cleanup_pat_, " ", tissue_).strip() tissue_ = self.gds_validate_string(tissue_, node, 'tissue') self.tissue = tissue_ elif nodeName_ == 'cell': cell_ = child_.text cell_ = re_.sub(String_cleanup_pat_, " ", cell_).strip() cell_ = self.gds_validate_string(cell_, node, 'cell') self.cell = cell_ elif nodeName_ == 'organelle': organelle_ = child_.text organelle_ = re_.sub(String_cleanup_pat_, " ", organelle_).strip() organelle_ = self.gds_validate_string(organelle_, node, 'organelle') self.organelle = organelle_ elif nodeName_ == 'cellular_location': cellular_location_ = child_.text cellular_location_ = re_.sub(String_cleanup_pat_, " ", cellular_location_).strip() cellular_location_ = self.gds_validate_string(cellular_location_, node, 'cellular_location') self.cellular_location = cellular_location_ super(natural_source_type, self).buildChildren(child_, node, nodeName_, True) # end class natural_source_type
[docs]class model_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('access_code', ['pdb_code_type', 'xs:token'], 0), MemberSpec_('chain', 'chainType53', 1), ] subclass = None superclass = None def __init__(self, access_code=None, chain=None): self.original_tagname_ = None self.access_code = access_code self.validate_pdb_code_type(self.access_code) if chain is None: self.chain = [] else: self.chain = chain
[docs] def factory(*args_, **kwargs_): if model_type.subclass: return model_type.subclass(*args_, **kwargs_) else: return model_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_access_code(self): return self.access_code
[docs] def set_access_code(self, access_code): self.access_code = access_code
[docs] def get_chain(self): return self.chain
[docs] def set_chain(self, chain): self.chain = chain
[docs] def add_chain(self, value): self.chain.append(value)
[docs] def insert_chain_at(self, index, value): self.chain.insert(index, value)
[docs] def replace_chain_at(self, index, value): self.chain[index] = value
[docs] def validate_pdb_code_type(self, value): # Validate type pdb_code_type, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_pdb_code_type_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_pdb_code_type_patterns_, ))
validate_pdb_code_type_patterns_ = [['^\\d[\\dA-Za-z]{3}$']]
[docs] def hasContent_(self): if ( self.access_code is not None or self.chain ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='model_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='model_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='model_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='model_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='model_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.access_code is not None: showIndent(outfile, level, pretty_print) outfile.write('<%saccess_code>%s</%saccess_code>%s' % (namespace_, self.gds_format_string(quote_xml(self.access_code).encode(ExternalEncoding), input_name='access_code'), namespace_, eol_)) for chain_ in self.chain: chain_.export(outfile, level, namespace_, name_='chain', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'access_code': access_code_ = child_.text access_code_ = re_.sub(String_cleanup_pat_, " ", access_code_).strip() access_code_ = self.gds_validate_string(access_code_, node, 'access_code') self.access_code = access_code_ # validate type pdb_code_type self.validate_pdb_code_type(self.access_code) elif nodeName_ == 'chain': obj_ = chainType53.factory() obj_.build(child_) self.chain.append(obj_) obj_.original_tagname_ = 'chain' # end class model_type
[docs]class chain_model_type(chain_type): member_data_items_ = [ ] subclass = None superclass = chain_type def __init__(self, id=None, residue_range=None, extensiontype_=None): self.original_tagname_ = None super(chain_model_type, self).__init__(id, residue_range, extensiontype_, ) self.extensiontype_ = extensiontype_
[docs] def factory(*args_, **kwargs_): if chain_model_type.subclass: return chain_model_type.subclass(*args_, **kwargs_) else: return chain_model_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_extensiontype_(self): return self.extensiontype_
[docs] def set_extensiontype_(self, extensiontype_): self.extensiontype_ = extensiontype_
[docs] def hasContent_(self): if ( super(chain_model_type, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='chain_model_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='chain_model_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='chain_model_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='chain_model_type'): super(chain_model_type, self).exportAttributes(outfile, level, already_processed, namespace_, name_='chain_model_type') if self.extensiontype_ is not None and 'xsi:type' not in already_processed: already_processed.add('xsi:type') outfile.write(' xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"') outfile.write(' xsi:type="%s"' % self.extensiontype_)
[docs] def exportChildren(self, outfile, level, namespace_='', name_='chain_model_type', fromsubclass_=False, pretty_print=True): super(chain_model_type, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('xsi:type', node) if value is not None and 'xsi:type' not in already_processed: already_processed.add('xsi:type') self.extensiontype_ = value super(chain_model_type, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): super(chain_model_type, self).buildChildren(child_, node, nodeName_, True) pass # end class chain_model_type
[docs]class helical_parameters_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('delta_z', 'delta_zType', 0), MemberSpec_('delta_phi', 'delta_phiType', 0), MemberSpec_('axial_symmetry', ['axial_symmetryType', 'xs:token'], 0), MemberSpec_('hand', ['handType', 'xs:token'], 0), ] subclass = None superclass = None def __init__(self, delta_z=None, delta_phi=None, axial_symmetry=None, hand=None): self.original_tagname_ = None self.delta_z = delta_z self.delta_phi = delta_phi self.axial_symmetry = axial_symmetry self.validate_axial_symmetryType(self.axial_symmetry) self.hand = hand self.validate_handType(self.hand)
[docs] def factory(*args_, **kwargs_): if helical_parameters_type.subclass: return helical_parameters_type.subclass(*args_, **kwargs_) else: return helical_parameters_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_delta_z(self): return self.delta_z
[docs] def set_delta_z(self, delta_z): self.delta_z = delta_z
[docs] def get_delta_phi(self): return self.delta_phi
[docs] def set_delta_phi(self, delta_phi): self.delta_phi = delta_phi
[docs] def get_axial_symmetry(self): return self.axial_symmetry
[docs] def set_axial_symmetry(self, axial_symmetry): self.axial_symmetry = axial_symmetry
[docs] def get_hand(self): return self.hand
[docs] def set_hand(self, hand): self.hand = hand
[docs] def validate_axial_symmetryType(self, value): # Validate type axial_symmetryType, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_axial_symmetryType_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_axial_symmetryType_patterns_, ))
validate_axial_symmetryType_patterns_ = [['^[C|D][1-9][0-9]*$']]
[docs] def validate_handType(self, value): # Validate type handType, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['LEFT HANDED', 'RIGHT HANDED'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on handType' % {"value" : value.encode("utf-8")} )
[docs] def hasContent_(self): if ( self.delta_z is not None or self.delta_phi is not None or self.axial_symmetry is not None or self.hand is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='helical_parameters_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='helical_parameters_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='helical_parameters_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='helical_parameters_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='helical_parameters_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.delta_z is not None: self.delta_z.export(outfile, level, namespace_, name_='delta_z', pretty_print=pretty_print) if self.delta_phi is not None: self.delta_phi.export(outfile, level, namespace_, name_='delta_phi', pretty_print=pretty_print) if self.axial_symmetry is not None: showIndent(outfile, level, pretty_print) outfile.write('<%saxial_symmetry>%s</%saxial_symmetry>%s' % (namespace_, self.gds_format_string(quote_xml(self.axial_symmetry).encode(ExternalEncoding), input_name='axial_symmetry'), namespace_, eol_)) if self.hand is not None: showIndent(outfile, level, pretty_print) outfile.write('<%shand>%s</%shand>%s' % (namespace_, self.gds_format_string(quote_xml(self.hand).encode(ExternalEncoding), input_name='hand'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'delta_z': obj_ = delta_zType.factory() obj_.build(child_) self.delta_z = obj_ obj_.original_tagname_ = 'delta_z' elif nodeName_ == 'delta_phi': obj_ = delta_phiType.factory() obj_.build(child_) self.delta_phi = obj_ obj_.original_tagname_ = 'delta_phi' elif nodeName_ == 'axial_symmetry': axial_symmetry_ = child_.text axial_symmetry_ = re_.sub(String_cleanup_pat_, " ", axial_symmetry_).strip() axial_symmetry_ = self.gds_validate_string(axial_symmetry_, node, 'axial_symmetry') self.axial_symmetry = axial_symmetry_ # validate type axial_symmetryType self.validate_axial_symmetryType(self.axial_symmetry) elif nodeName_ == 'hand': hand_ = child_.text hand_ = re_.sub(String_cleanup_pat_, " ", hand_).strip() hand_ = self.gds_validate_string(hand_, node, 'hand') self.hand = hand_ # validate type handType self.validate_handType(self.hand) # end class helical_parameters_type
[docs]class sci_name_type(GeneratedsSuper): """Deprecated (2014/11/12)""" member_data_items_ = [ MemberSpec_('synonym', 'xs:token', 0), MemberSpec_('valueOf_', 'xs:token', 0), ] subclass = None superclass = None def __init__(self, synonym=None, valueOf_=None): self.original_tagname_ = None self.synonym = _cast(None, synonym) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if sci_name_type.subclass: return sci_name_type.subclass(*args_, **kwargs_) else: return sci_name_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_synonym(self): return self.synonym
[docs] def set_synonym(self, synonym): self.synonym = synonym
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='sci_name_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='sci_name_type') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='sci_name_type', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='sci_name_type'): if self.synonym is not None and 'synonym' not in already_processed: already_processed.add('synonym') outfile.write(' synonym=%s' % (self.gds_format_string(quote_attrib(self.synonym).encode(ExternalEncoding), input_name='synonym'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='sci_name_type', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('synonym', node) if value is not None and 'synonym' not in already_processed: already_processed.add('synonym') self.synonym = value self.synonym = ' '.join(self.synonym.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class sci_name_type
[docs]class molecular_weight_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('experimental', 'experimentalType', 0), MemberSpec_('theoretical', 'theoreticalType', 0), MemberSpec_('method', 'xs:token', 0), ] subclass = None superclass = None def __init__(self, experimental=None, theoretical=None, method=None): self.original_tagname_ = None self.experimental = experimental self.theoretical = theoretical self.method = method
[docs] def factory(*args_, **kwargs_): if molecular_weight_type.subclass: return molecular_weight_type.subclass(*args_, **kwargs_) else: return molecular_weight_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_experimental(self): return self.experimental
[docs] def set_experimental(self, experimental): self.experimental = experimental
[docs] def get_theoretical(self): return self.theoretical
[docs] def set_theoretical(self, theoretical): self.theoretical = theoretical
[docs] def get_method(self): return self.method
[docs] def set_method(self, method): self.method = method
[docs] def hasContent_(self): if ( self.experimental is not None or self.theoretical is not None or self.method is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='molecular_weight_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='molecular_weight_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='molecular_weight_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='molecular_weight_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='molecular_weight_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.experimental is not None: self.experimental.export(outfile, level, namespace_, name_='experimental', pretty_print=pretty_print) if self.theoretical is not None: self.theoretical.export(outfile, level, namespace_, name_='theoretical', pretty_print=pretty_print) if self.method is not None: showIndent(outfile, level, pretty_print) outfile.write('<%smethod>%s</%smethod>%s' % (namespace_, self.gds_format_string(quote_xml(self.method).encode(ExternalEncoding), input_name='method'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'experimental': obj_ = experimentalType.factory() obj_.build(child_) self.experimental = obj_ obj_.original_tagname_ = 'experimental' elif nodeName_ == 'theoretical': obj_ = theoreticalType.factory() obj_.build(child_) self.theoretical = obj_ obj_.original_tagname_ = 'theoretical' elif nodeName_ == 'method': method_ = child_.text method_ = re_.sub(String_cleanup_pat_, " ", method_).strip() method_ = self.gds_validate_string(method_, node, 'method') self.method = method_ # end class molecular_weight_type
[docs]class virus_species_name_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('ncbi', 'xs:positiveInteger', 0), MemberSpec_('valueOf_', 'xs:token', 0), ] subclass = None superclass = None def __init__(self, ncbi=None, valueOf_=None): self.original_tagname_ = None self.ncbi = _cast(int, ncbi) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if virus_species_name_type.subclass: return virus_species_name_type.subclass(*args_, **kwargs_) else: return virus_species_name_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_ncbi(self): return self.ncbi
[docs] def set_ncbi(self, ncbi): self.ncbi = ncbi
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='virus_species_name_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='virus_species_name_type') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='virus_species_name_type', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='virus_species_name_type'): if self.ncbi is not None and 'ncbi' not in already_processed: already_processed.add('ncbi') outfile.write(' ncbi="%s"' % self.gds_format_integer(self.ncbi, input_name='ncbi'))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='virus_species_name_type', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('ncbi', node) if value is not None and 'ncbi' not in already_processed: already_processed.add('ncbi') try: self.ncbi = int(value) except ValueError as exp: raise_parse_error(node, 'Bad integer attribute: %s' % exp) if self.ncbi <= 0: raise_parse_error(node, 'Invalid PositiveInteger')
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class virus_species_name_type
[docs]class base_macromolecule_type(GeneratedsSuper): """Autogenerated unique identifier.""" member_data_items_ = [ MemberSpec_('mutant', 'xs:boolean', 0), MemberSpec_('chimera', 'xs:boolean', 0), MemberSpec_('id', 'xs:positiveInteger', 0), MemberSpec_('name', 'sci_name_type', 0), MemberSpec_('natural_source', 'natural_source_type', 0), MemberSpec_('molecular_weight', 'molecular_weight_type', 0), MemberSpec_('details', 'xs:string', 0), MemberSpec_('number_of_copies', 'pos_int_or_string_type', 0), MemberSpec_('oligomeric_state', 'pos_int_or_string_type', 0), MemberSpec_('recombinant_exp_flag', 'xs:boolean', 0), ] subclass = None superclass = None def __init__(self, mutant=None, chimera=None, id=None, name=None, natural_source=None, molecular_weight=None, details=None, number_of_copies=None, oligomeric_state=None, recombinant_exp_flag=None, extensiontype_=None): self.original_tagname_ = None self.mutant = _cast(bool, mutant) self.chimera = _cast(bool, chimera) self.id = _cast(int, id) self.name = name self.natural_source = natural_source self.molecular_weight = molecular_weight self.details = details self.number_of_copies = number_of_copies self.validate_pos_int_or_string_type(self.number_of_copies) self.oligomeric_state = oligomeric_state self.validate_pos_int_or_string_type(self.oligomeric_state) self.recombinant_exp_flag = recombinant_exp_flag self.extensiontype_ = extensiontype_
[docs] def factory(*args_, **kwargs_): if base_macromolecule_type.subclass: return base_macromolecule_type.subclass(*args_, **kwargs_) else: return base_macromolecule_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_name(self): return self.name
[docs] def set_name(self, name): self.name = name
[docs] def get_natural_source(self): return self.natural_source
[docs] def set_natural_source(self, natural_source): self.natural_source = natural_source
[docs] def get_molecular_weight(self): return self.molecular_weight
[docs] def set_molecular_weight(self, molecular_weight): self.molecular_weight = molecular_weight
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def get_number_of_copies(self): return self.number_of_copies
[docs] def set_number_of_copies(self, number_of_copies): self.number_of_copies = number_of_copies
[docs] def get_oligomeric_state(self): return self.oligomeric_state
[docs] def set_oligomeric_state(self, oligomeric_state): self.oligomeric_state = oligomeric_state
[docs] def get_recombinant_exp_flag(self): return self.recombinant_exp_flag
[docs] def set_recombinant_exp_flag(self, recombinant_exp_flag): self.recombinant_exp_flag = recombinant_exp_flag
[docs] def get_mutant(self): return self.mutant
[docs] def set_mutant(self, mutant): self.mutant = mutant
[docs] def get_chimera(self): return self.chimera
[docs] def set_chimera(self, chimera): self.chimera = chimera
[docs] def get_id(self): return self.id
[docs] def set_id(self, id): self.id = id
[docs] def get_extensiontype_(self): return self.extensiontype_
[docs] def set_extensiontype_(self, extensiontype_): self.extensiontype_ = extensiontype_
[docs] def validate_pos_int_or_string_type(self, value): # Validate type pos_int_or_string_type, a restriction on None. pass
[docs] def hasContent_(self): if ( self.name is not None or self.natural_source is not None or self.molecular_weight is not None or self.details is not None or self.number_of_copies is not None or self.oligomeric_state is not None or self.recombinant_exp_flag is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='base_macromolecule_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='base_macromolecule_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='base_macromolecule_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='base_macromolecule_type'): if self.mutant is not None and 'mutant' not in already_processed: already_processed.add('mutant') outfile.write(' mutant="%s"' % self.gds_format_boolean(self.mutant, input_name='mutant')) if self.chimera is not None and 'chimera' not in already_processed: already_processed.add('chimera') outfile.write(' chimera="%s"' % self.gds_format_boolean(self.chimera, input_name='chimera')) if self.id is not None and 'id' not in already_processed: already_processed.add('id') outfile.write(' id="%s"' % self.gds_format_integer(self.id, input_name='id')) if self.extensiontype_ is not None and 'xsi:type' not in already_processed: already_processed.add('xsi:type') outfile.write(' xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"') outfile.write(' xsi:type="%s"' % self.extensiontype_)
[docs] def exportChildren(self, outfile, level, namespace_='', name_='base_macromolecule_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.name is not None: self.name.export(outfile, level, namespace_, name_='name', pretty_print=pretty_print) if self.natural_source is not None: self.natural_source.export(outfile, level, namespace_, name_='natural_source', pretty_print=pretty_print) if self.molecular_weight is not None: self.molecular_weight.export(outfile, level, namespace_, name_='molecular_weight', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_)) if self.number_of_copies is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_of_copies>%s</%snumber_of_copies>%s' % (namespace_, self.gds_format_string(quote_xml(self.number_of_copies).encode(ExternalEncoding), input_name='number_of_copies'), namespace_, eol_)) if self.oligomeric_state is not None: showIndent(outfile, level, pretty_print) outfile.write('<%soligomeric_state>%s</%soligomeric_state>%s' % (namespace_, self.gds_format_string(quote_xml(self.oligomeric_state).encode(ExternalEncoding), input_name='oligomeric_state'), namespace_, eol_)) if self.recombinant_exp_flag is not None: showIndent(outfile, level, pretty_print) outfile.write('<%srecombinant_exp_flag>%s</%srecombinant_exp_flag>%s' % (namespace_, self.gds_format_boolean(self.recombinant_exp_flag, input_name='recombinant_exp_flag'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('mutant', node) if value is not None and 'mutant' not in already_processed: already_processed.add('mutant') if value in ('true', '1'): self.mutant = True elif value in ('false', '0'): self.mutant = False else: raise_parse_error(node, 'Bad boolean attribute') value = find_attr_value_('chimera', node) if value is not None and 'chimera' not in already_processed: already_processed.add('chimera') if value in ('true', '1'): self.chimera = True elif value in ('false', '0'): self.chimera = False else: raise_parse_error(node, 'Bad boolean attribute') value = find_attr_value_('id', node) if value is not None and 'id' not in already_processed: already_processed.add('id') try: self.id = int(value) except ValueError as exp: raise_parse_error(node, 'Bad integer attribute: %s' % exp) if self.id <= 0: raise_parse_error(node, 'Invalid PositiveInteger') value = find_attr_value_('xsi:type', node) if value is not None and 'xsi:type' not in already_processed: already_processed.add('xsi:type') self.extensiontype_ = value
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'name': obj_ = sci_name_type.factory() obj_.build(child_) self.name = obj_ obj_.original_tagname_ = 'name' elif nodeName_ == 'natural_source': obj_ = natural_source_type.factory() obj_.build(child_) self.natural_source = obj_ obj_.original_tagname_ = 'natural_source' elif nodeName_ == 'molecular_weight': obj_ = molecular_weight_type.factory() obj_.build(child_) self.molecular_weight = obj_ obj_.original_tagname_ = 'molecular_weight' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ elif nodeName_ == 'number_of_copies': number_of_copies_ = child_.text number_of_copies_ = self.gds_validate_string(number_of_copies_, node, 'number_of_copies') self.number_of_copies = number_of_copies_ # validate type pos_int_or_string_type self.validate_pos_int_or_string_type(self.number_of_copies) elif nodeName_ == 'oligomeric_state': oligomeric_state_ = child_.text oligomeric_state_ = self.gds_validate_string(oligomeric_state_, node, 'oligomeric_state') self.oligomeric_state = oligomeric_state_ # validate type pos_int_or_string_type self.validate_pos_int_or_string_type(self.oligomeric_state) elif nodeName_ == 'recombinant_exp_flag': sval_ = child_.text if sval_ in ('true', '1'): ival_ = True elif sval_ in ('false', '0'): ival_ = False else: raise_parse_error(child_, 'requires boolean') ival_ = self.gds_validate_boolean(ival_, node, 'recombinant_exp_flag') self.recombinant_exp_flag = ival_ # end class base_macromolecule_type
[docs]class protein_or_peptide(base_macromolecule_type): member_data_items_ = [ MemberSpec_('recombinant_expression', 'recombinant_source_type', 0), MemberSpec_('enantiomer', ['enantiomerType', 'xs:token'], 0), MemberSpec_('sequence', 'sequenceType', 0), MemberSpec_('ec_number', ['ec_numberType', 'xs:token'], 1), ] subclass = None superclass = base_macromolecule_type def __init__(self, mutant=None, chimera=None, id=None, name=None, natural_source=None, molecular_weight=None, details=None, number_of_copies=None, oligomeric_state=None, recombinant_exp_flag=None, recombinant_expression=None, enantiomer=None, sequence=None, ec_number=None): self.original_tagname_ = None super(protein_or_peptide, self).__init__(mutant, chimera, id, name, natural_source, molecular_weight, details, number_of_copies, oligomeric_state, recombinant_exp_flag, ) self.recombinant_expression = recombinant_expression self.enantiomer = enantiomer self.validate_enantiomerType(self.enantiomer) self.sequence = sequence if ec_number is None: self.ec_number = [] else: self.ec_number = ec_number
[docs] def factory(*args_, **kwargs_): if protein_or_peptide.subclass: return protein_or_peptide.subclass(*args_, **kwargs_) else: return protein_or_peptide(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_recombinant_expression(self): return self.recombinant_expression
[docs] def set_recombinant_expression(self, recombinant_expression): self.recombinant_expression = recombinant_expression
[docs] def get_enantiomer(self): return self.enantiomer
[docs] def set_enantiomer(self, enantiomer): self.enantiomer = enantiomer
[docs] def get_sequence(self): return self.sequence
[docs] def set_sequence(self, sequence): self.sequence = sequence
[docs] def get_ec_number(self): return self.ec_number
[docs] def set_ec_number(self, ec_number): self.ec_number = ec_number
[docs] def add_ec_number(self, value): self.ec_number.append(value)
[docs] def insert_ec_number_at(self, index, value): self.ec_number.insert(index, value)
[docs] def replace_ec_number_at(self, index, value): self.ec_number[index] = value
[docs] def validate_enantiomerType(self, value): # Validate type enantiomerType, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['LEVO', 'DEXTRO'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on enantiomerType' % {"value" : value.encode("utf-8")} )
[docs] def validate_ec_numberType(self, value): # Validate type ec_numberType, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_ec_numberType_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_ec_numberType_patterns_, ))
validate_ec_numberType_patterns_ = [['^EC \\d+(\\.\\d+){3}$']]
[docs] def hasContent_(self): if ( self.recombinant_expression is not None or self.enantiomer is not None or self.sequence is not None or self.ec_number or super(protein_or_peptide, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='protein_or_peptide', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='protein_or_peptide') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='protein_or_peptide', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='protein_or_peptide'): super(protein_or_peptide, self).exportAttributes(outfile, level, already_processed, namespace_, name_='protein_or_peptide')
[docs] def exportChildren(self, outfile, level, namespace_='', name_='protein_or_peptide', fromsubclass_=False, pretty_print=True): super(protein_or_peptide, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print) if pretty_print: eol_ = '\n' else: eol_ = '' if self.recombinant_expression is not None: self.recombinant_expression.export(outfile, level, namespace_, name_='recombinant_expression', pretty_print=pretty_print) if self.enantiomer is not None: showIndent(outfile, level, pretty_print) outfile.write('<%senantiomer>%s</%senantiomer>%s' % (namespace_, self.gds_format_string(quote_xml(self.enantiomer).encode(ExternalEncoding), input_name='enantiomer'), namespace_, eol_)) if self.sequence is not None: self.sequence.export(outfile, level, namespace_, name_='sequence', pretty_print=pretty_print) for ec_number_ in self.ec_number: showIndent(outfile, level, pretty_print) outfile.write('<%sec_number>%s</%sec_number>%s' % (namespace_, self.gds_format_string(quote_xml(ec_number_).encode(ExternalEncoding), input_name='ec_number'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): super(protein_or_peptide, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'recombinant_expression': obj_ = recombinant_source_type.factory() obj_.build(child_) self.recombinant_expression = obj_ obj_.original_tagname_ = 'recombinant_expression' elif nodeName_ == 'enantiomer': enantiomer_ = child_.text enantiomer_ = re_.sub(String_cleanup_pat_, " ", enantiomer_).strip() enantiomer_ = self.gds_validate_string(enantiomer_, node, 'enantiomer') self.enantiomer = enantiomer_ # validate type enantiomerType self.validate_enantiomerType(self.enantiomer) elif nodeName_ == 'sequence': obj_ = sequenceType.factory() obj_.build(child_) self.sequence = obj_ obj_.original_tagname_ = 'sequence' elif nodeName_ == 'ec_number': ec_number_ = child_.text ec_number_ = re_.sub(String_cleanup_pat_, " ", ec_number_).strip() ec_number_ = self.gds_validate_string(ec_number_, node, 'ec_number') self.ec_number.append(ec_number_) # validate type ec_numberType self.validate_ec_numberType(self.ec_number[-1]) super(protein_or_peptide, self).buildChildren(child_, node, nodeName_, True) # end class protein_or_peptide
[docs]class dna(base_macromolecule_type): """Is naturalExpression and recombinantExpression suitable for this component?""" member_data_items_ = [ MemberSpec_('sequence', 'sequenceType55', 0), MemberSpec_('classification', ['classificationType', 'xs:token'], 0), MemberSpec_('structure', 'xs:token', 0), MemberSpec_('synthetic_flag', 'xs:boolean', 0), ] subclass = None superclass = base_macromolecule_type def __init__(self, mutant=None, chimera=None, id=None, name=None, natural_source=None, molecular_weight=None, details=None, number_of_copies=None, oligomeric_state=None, recombinant_exp_flag=None, sequence=None, classification=None, structure=None, synthetic_flag=None): self.original_tagname_ = None super(dna, self).__init__(mutant, chimera, id, name, natural_source, molecular_weight, details, number_of_copies, oligomeric_state, recombinant_exp_flag, ) self.sequence = sequence self.classification = classification self.validate_classificationType(self.classification) self.structure = structure self.synthetic_flag = synthetic_flag
[docs] def factory(*args_, **kwargs_): if dna.subclass: return dna.subclass(*args_, **kwargs_) else: return dna(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_sequence(self): return self.sequence
[docs] def set_sequence(self, sequence): self.sequence = sequence
[docs] def get_classification(self): return self.classification
[docs] def set_classification(self, classification): self.classification = classification
[docs] def get_structure(self): return self.structure
[docs] def set_structure(self, structure): self.structure = structure
[docs] def get_synthetic_flag(self): return self.synthetic_flag
[docs] def set_synthetic_flag(self, synthetic_flag): self.synthetic_flag = synthetic_flag
[docs] def validate_classificationType(self, value): # Validate type classificationType, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['DNA'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on classificationType' % {"value" : value.encode("utf-8")} )
[docs] def hasContent_(self): if ( self.sequence is not None or self.classification is not None or self.structure is not None or self.synthetic_flag is not None or super(dna, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='dna', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='dna') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='dna', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='dna'): super(dna, self).exportAttributes(outfile, level, already_processed, namespace_, name_='dna')
[docs] def exportChildren(self, outfile, level, namespace_='', name_='dna', fromsubclass_=False, pretty_print=True): super(dna, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print) if pretty_print: eol_ = '\n' else: eol_ = '' if self.sequence is not None: self.sequence.export(outfile, level, namespace_, name_='sequence', pretty_print=pretty_print) if self.classification is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sclassification>%s</%sclassification>%s' % (namespace_, self.gds_format_string(quote_xml(self.classification).encode(ExternalEncoding), input_name='classification'), namespace_, eol_)) if self.structure is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sstructure>%s</%sstructure>%s' % (namespace_, self.gds_format_string(quote_xml(self.structure).encode(ExternalEncoding), input_name='structure'), namespace_, eol_)) if self.synthetic_flag is not None: showIndent(outfile, level, pretty_print) outfile.write('<%ssynthetic_flag>%s</%ssynthetic_flag>%s' % (namespace_, self.gds_format_boolean(self.synthetic_flag, input_name='synthetic_flag'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): super(dna, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'sequence': obj_ = sequenceType55.factory() obj_.build(child_) self.sequence = obj_ obj_.original_tagname_ = 'sequence' elif nodeName_ == 'classification': classification_ = child_.text classification_ = re_.sub(String_cleanup_pat_, " ", classification_).strip() classification_ = self.gds_validate_string(classification_, node, 'classification') self.classification = classification_ # validate type classificationType self.validate_classificationType(self.classification) elif nodeName_ == 'structure': structure_ = child_.text structure_ = re_.sub(String_cleanup_pat_, " ", structure_).strip() structure_ = self.gds_validate_string(structure_, node, 'structure') self.structure = structure_ elif nodeName_ == 'synthetic_flag': sval_ = child_.text if sval_ in ('true', '1'): ival_ = True elif sval_ in ('false', '0'): ival_ = False else: raise_parse_error(child_, 'requires boolean') ival_ = self.gds_validate_boolean(ival_, node, 'synthetic_flag') self.synthetic_flag = ival_ super(dna, self).buildChildren(child_, node, nodeName_, True) # end class dna
[docs]class rna(base_macromolecule_type): """Is naturalExpression and recombinantExpression suitable for this component?""" member_data_items_ = [ MemberSpec_('sequence', 'sequenceType60', 0), MemberSpec_('classification', ['classificationType65', 'xs:token'], 0), MemberSpec_('structure', 'xs:token', 0), MemberSpec_('synthetic_flag', 'xs:boolean', 0), ] subclass = None superclass = base_macromolecule_type def __init__(self, mutant=None, chimera=None, id=None, name=None, natural_source=None, molecular_weight=None, details=None, number_of_copies=None, oligomeric_state=None, recombinant_exp_flag=None, sequence=None, classification=None, structure=None, synthetic_flag=None): self.original_tagname_ = None super(rna, self).__init__(mutant, chimera, id, name, natural_source, molecular_weight, details, number_of_copies, oligomeric_state, recombinant_exp_flag, ) self.sequence = sequence self.classification = classification self.validate_classificationType65(self.classification) self.structure = structure self.synthetic_flag = synthetic_flag
[docs] def factory(*args_, **kwargs_): if rna.subclass: return rna.subclass(*args_, **kwargs_) else: return rna(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_sequence(self): return self.sequence
[docs] def set_sequence(self, sequence): self.sequence = sequence
[docs] def get_classification(self): return self.classification
[docs] def set_classification(self, classification): self.classification = classification
[docs] def get_structure(self): return self.structure
[docs] def set_structure(self, structure): self.structure = structure
[docs] def get_synthetic_flag(self): return self.synthetic_flag
[docs] def set_synthetic_flag(self, synthetic_flag): self.synthetic_flag = synthetic_flag
[docs] def validate_classificationType65(self, value): # Validate type classificationType65, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['MESSENGER', 'TRANSFER', 'RIBOSOMAL', 'NON-CODING', 'INTERFERENCE', 'SMALL INTERFERENCE', 'GENOMIC', 'PRE-MESSENGER', 'SMALL NUCLEOLAR', 'TRANSFER-MESSENGER', 'OTHER'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on classificationType65' % {"value" : value.encode("utf-8")} )
[docs] def hasContent_(self): if ( self.sequence is not None or self.classification is not None or self.structure is not None or self.synthetic_flag is not None or super(rna, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='rna', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='rna') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='rna', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='rna'): super(rna, self).exportAttributes(outfile, level, already_processed, namespace_, name_='rna')
[docs] def exportChildren(self, outfile, level, namespace_='', name_='rna', fromsubclass_=False, pretty_print=True): super(rna, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print) if pretty_print: eol_ = '\n' else: eol_ = '' if self.sequence is not None: self.sequence.export(outfile, level, namespace_, name_='sequence', pretty_print=pretty_print) if self.classification is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sclassification>%s</%sclassification>%s' % (namespace_, self.gds_format_string(quote_xml(self.classification).encode(ExternalEncoding), input_name='classification'), namespace_, eol_)) if self.structure is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sstructure>%s</%sstructure>%s' % (namespace_, self.gds_format_string(quote_xml(self.structure).encode(ExternalEncoding), input_name='structure'), namespace_, eol_)) if self.synthetic_flag is not None: showIndent(outfile, level, pretty_print) outfile.write('<%ssynthetic_flag>%s</%ssynthetic_flag>%s' % (namespace_, self.gds_format_boolean(self.synthetic_flag, input_name='synthetic_flag'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): super(rna, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'sequence': obj_ = sequenceType60.factory() obj_.build(child_) self.sequence = obj_ obj_.original_tagname_ = 'sequence' elif nodeName_ == 'classification': classification_ = child_.text classification_ = re_.sub(String_cleanup_pat_, " ", classification_).strip() classification_ = self.gds_validate_string(classification_, node, 'classification') self.classification = classification_ # validate type classificationType65 self.validate_classificationType65(self.classification) elif nodeName_ == 'structure': structure_ = child_.text structure_ = re_.sub(String_cleanup_pat_, " ", structure_).strip() structure_ = self.gds_validate_string(structure_, node, 'structure') self.structure = structure_ elif nodeName_ == 'synthetic_flag': sval_ = child_.text if sval_ in ('true', '1'): ival_ = True elif sval_ in ('false', '0'): ival_ = False else: raise_parse_error(child_, 'requires boolean') ival_ = self.gds_validate_boolean(ival_, node, 'synthetic_flag') self.synthetic_flag = ival_ super(rna, self).buildChildren(child_, node, nodeName_, True) # end class rna
[docs]class saccharide(base_macromolecule_type): """Is naturalExpression and recombinantExpression suitable for this component?""" member_data_items_ = [ MemberSpec_('enantiomer', ['enantiomerType66', 'xs:token'], 0), MemberSpec_('formula', ['formulaType67', 'xs:token'], 0), MemberSpec_('external_references', 'external_referencesType68', 1), ] subclass = None superclass = base_macromolecule_type def __init__(self, mutant=None, chimera=None, id=None, name=None, natural_source=None, molecular_weight=None, details=None, number_of_copies=None, oligomeric_state=None, recombinant_exp_flag=None, enantiomer=None, formula=None, external_references=None): self.original_tagname_ = None super(saccharide, self).__init__(mutant, chimera, id, name, natural_source, molecular_weight, details, number_of_copies, oligomeric_state, recombinant_exp_flag, ) self.enantiomer = enantiomer self.validate_enantiomerType66(self.enantiomer) self.formula = formula self.validate_formulaType67(self.formula) if external_references is None: self.external_references = [] else: self.external_references = external_references
[docs] def factory(*args_, **kwargs_): if saccharide.subclass: return saccharide.subclass(*args_, **kwargs_) else: return saccharide(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_enantiomer(self): return self.enantiomer
[docs] def set_enantiomer(self, enantiomer): self.enantiomer = enantiomer
[docs] def get_formula(self): return self.formula
[docs] def set_formula(self, formula): self.formula = formula
[docs] def get_external_references(self): return self.external_references
[docs] def set_external_references(self, external_references): self.external_references = external_references
[docs] def add_external_references(self, value): self.external_references.append(value)
[docs] def insert_external_references_at(self, index, value): self.external_references.insert(index, value)
[docs] def replace_external_references_at(self, index, value): self.external_references[index] = value
[docs] def validate_enantiomerType66(self, value): # Validate type enantiomerType66, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['LEVO', 'DEXTRO'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on enantiomerType66' % {"value" : value.encode("utf-8")} )
[docs] def validate_formulaType67(self, value): # Validate type formulaType67, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_formulaType67_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_formulaType67_patterns_, ))
validate_formulaType67_patterns_ = [['^([\\[\\]\\(\\)]*[A-Z][a-z]?[\\+\\-\\d/\\[\\]\\(\\)]*)+$']]
[docs] def hasContent_(self): if ( self.enantiomer is not None or self.formula is not None or self.external_references or super(saccharide, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='saccharide', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='saccharide') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='saccharide', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='saccharide'): super(saccharide, self).exportAttributes(outfile, level, already_processed, namespace_, name_='saccharide')
[docs] def exportChildren(self, outfile, level, namespace_='', name_='saccharide', fromsubclass_=False, pretty_print=True): super(saccharide, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print) if pretty_print: eol_ = '\n' else: eol_ = '' if self.enantiomer is not None: showIndent(outfile, level, pretty_print) outfile.write('<%senantiomer>%s</%senantiomer>%s' % (namespace_, self.gds_format_string(quote_xml(self.enantiomer).encode(ExternalEncoding), input_name='enantiomer'), namespace_, eol_)) if self.formula is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sformula>%s</%sformula>%s' % (namespace_, self.gds_format_string(quote_xml(self.formula).encode(ExternalEncoding), input_name='formula'), namespace_, eol_)) for external_references_ in self.external_references: external_references_.export(outfile, level, namespace_, name_='external_references', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): super(saccharide, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'enantiomer': enantiomer_ = child_.text enantiomer_ = re_.sub(String_cleanup_pat_, " ", enantiomer_).strip() enantiomer_ = self.gds_validate_string(enantiomer_, node, 'enantiomer') self.enantiomer = enantiomer_ # validate type enantiomerType66 self.validate_enantiomerType66(self.enantiomer) elif nodeName_ == 'formula': formula_ = child_.text formula_ = re_.sub(String_cleanup_pat_, " ", formula_).strip() formula_ = self.gds_validate_string(formula_, node, 'formula') self.formula = formula_ # validate type formulaType67 self.validate_formulaType67(self.formula) elif nodeName_ == 'external_references': obj_ = external_referencesType68.factory() obj_.build(child_) self.external_references.append(obj_) obj_.original_tagname_ = 'external_references' super(saccharide, self).buildChildren(child_, node, nodeName_, True) # end class saccharide
[docs]class lipid(base_macromolecule_type): """Is naturalExpression and recombinantExpression suitable for this component?""" member_data_items_ = [ MemberSpec_('formula', ['formulaType69', 'xs:token'], 0), MemberSpec_('external_references', 'external_referencesType70', 1), ] subclass = None superclass = base_macromolecule_type def __init__(self, mutant=None, chimera=None, id=None, name=None, natural_source=None, molecular_weight=None, details=None, number_of_copies=None, oligomeric_state=None, recombinant_exp_flag=None, formula=None, external_references=None): self.original_tagname_ = None super(lipid, self).__init__(mutant, chimera, id, name, natural_source, molecular_weight, details, number_of_copies, oligomeric_state, recombinant_exp_flag, ) self.formula = formula self.validate_formulaType69(self.formula) if external_references is None: self.external_references = [] else: self.external_references = external_references
[docs] def factory(*args_, **kwargs_): if lipid.subclass: return lipid.subclass(*args_, **kwargs_) else: return lipid(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_formula(self): return self.formula
[docs] def set_formula(self, formula): self.formula = formula
[docs] def get_external_references(self): return self.external_references
[docs] def set_external_references(self, external_references): self.external_references = external_references
[docs] def add_external_references(self, value): self.external_references.append(value)
[docs] def insert_external_references_at(self, index, value): self.external_references.insert(index, value)
[docs] def replace_external_references_at(self, index, value): self.external_references[index] = value
[docs] def validate_formulaType69(self, value): # Validate type formulaType69, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_formulaType69_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_formulaType69_patterns_, ))
validate_formulaType69_patterns_ = [['^([\\[\\]\\(\\)]*[A-Z][a-z]?[\\+\\-\\d/\\[\\]\\(\\)]*)+$']]
[docs] def hasContent_(self): if ( self.formula is not None or self.external_references or super(lipid, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='lipid', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='lipid') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='lipid', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='lipid'): super(lipid, self).exportAttributes(outfile, level, already_processed, namespace_, name_='lipid')
[docs] def exportChildren(self, outfile, level, namespace_='', name_='lipid', fromsubclass_=False, pretty_print=True): super(lipid, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print) if pretty_print: eol_ = '\n' else: eol_ = '' if self.formula is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sformula>%s</%sformula>%s' % (namespace_, self.gds_format_string(quote_xml(self.formula).encode(ExternalEncoding), input_name='formula'), namespace_, eol_)) for external_references_ in self.external_references: external_references_.export(outfile, level, namespace_, name_='external_references', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): super(lipid, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'formula': formula_ = child_.text formula_ = re_.sub(String_cleanup_pat_, " ", formula_).strip() formula_ = self.gds_validate_string(formula_, node, 'formula') self.formula = formula_ # validate type formulaType69 self.validate_formulaType69(self.formula) elif nodeName_ == 'external_references': obj_ = external_referencesType70.factory() obj_.build(child_) self.external_references.append(obj_) obj_.original_tagname_ = 'external_references' super(lipid, self).buildChildren(child_, node, nodeName_, True) # end class lipid
[docs]class ligand(base_macromolecule_type): """Is naturalExpression and recombinantExpression suitable for this component?""" member_data_items_ = [ MemberSpec_('formula', ['formulaType71', 'xs:token'], 0), MemberSpec_('external_references', 'external_referencesType72', 1), MemberSpec_('natural_source', 'natural_source_type', 0), MemberSpec_('recombinant_expression', 'recombinant_source_type', 0), ] subclass = None superclass = base_macromolecule_type def __init__(self, mutant=None, chimera=None, id=None, name=None, natural_source=None, molecular_weight=None, details=None, number_of_copies=None, oligomeric_state=None, recombinant_exp_flag=None, formula=None, external_references=None, recombinant_expression=None): self.original_tagname_ = None super(ligand, self).__init__(mutant, chimera, id, name, natural_source, molecular_weight, details, number_of_copies, oligomeric_state, recombinant_exp_flag, ) self.formula = formula self.validate_formulaType71(self.formula) if external_references is None: self.external_references = [] else: self.external_references = external_references self.natural_source = natural_source self.recombinant_expression = recombinant_expression
[docs] def factory(*args_, **kwargs_): if ligand.subclass: return ligand.subclass(*args_, **kwargs_) else: return ligand(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_formula(self): return self.formula
[docs] def set_formula(self, formula): self.formula = formula
[docs] def get_external_references(self): return self.external_references
[docs] def set_external_references(self, external_references): self.external_references = external_references
[docs] def add_external_references(self, value): self.external_references.append(value)
[docs] def insert_external_references_at(self, index, value): self.external_references.insert(index, value)
[docs] def replace_external_references_at(self, index, value): self.external_references[index] = value
[docs] def get_natural_source(self): return self.natural_source
[docs] def set_natural_source(self, natural_source): self.natural_source = natural_source
[docs] def get_recombinant_expression(self): return self.recombinant_expression
[docs] def set_recombinant_expression(self, recombinant_expression): self.recombinant_expression = recombinant_expression
[docs] def validate_formulaType71(self, value): # Validate type formulaType71, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_formulaType71_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_formulaType71_patterns_, ))
validate_formulaType71_patterns_ = [['^([\\[\\]\\(\\)]*[A-Z][a-z]?[\\+\\-\\d/\\[\\]\\(\\)]*)+$']]
[docs] def hasContent_(self): if ( self.formula is not None or self.external_references or self.natural_source is not None or self.recombinant_expression is not None or super(ligand, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='ligand', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='ligand') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='ligand', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='ligand'): super(ligand, self).exportAttributes(outfile, level, already_processed, namespace_, name_='ligand')
[docs] def exportChildren(self, outfile, level, namespace_='', name_='ligand', fromsubclass_=False, pretty_print=True): super(ligand, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print) if pretty_print: eol_ = '\n' else: eol_ = '' if self.formula is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sformula>%s</%sformula>%s' % (namespace_, self.gds_format_string(quote_xml(self.formula).encode(ExternalEncoding), input_name='formula'), namespace_, eol_)) for external_references_ in self.external_references: external_references_.export(outfile, level, namespace_, name_='external_references', pretty_print=pretty_print) if self.natural_source is not None: self.natural_source.export(outfile, level, namespace_, name_='natural_source', pretty_print=pretty_print) if self.recombinant_expression is not None: self.recombinant_expression.export(outfile, level, namespace_, name_='recombinant_expression', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): super(ligand, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'formula': formula_ = child_.text formula_ = re_.sub(String_cleanup_pat_, " ", formula_).strip() formula_ = self.gds_validate_string(formula_, node, 'formula') self.formula = formula_ # validate type formulaType71 self.validate_formulaType71(self.formula) elif nodeName_ == 'external_references': obj_ = external_referencesType72.factory() obj_.build(child_) self.external_references.append(obj_) obj_.original_tagname_ = 'external_references' elif nodeName_ == 'natural_source': obj_ = natural_source_type.factory() obj_.build(child_) self.natural_source = obj_ obj_.original_tagname_ = 'natural_source' elif nodeName_ == 'recombinant_expression': obj_ = recombinant_source_type.factory() obj_.build(child_) self.recombinant_expression = obj_ obj_.original_tagname_ = 'recombinant_expression' super(ligand, self).buildChildren(child_, node, nodeName_, True) # end class ligand
[docs]class em_label(base_macromolecule_type): member_data_items_ = [ MemberSpec_('formula', ['formulaType73', 'xs:token'], 0), ] subclass = None superclass = base_macromolecule_type def __init__(self, mutant=None, chimera=None, id=None, name=None, natural_source=None, molecular_weight=None, details=None, number_of_copies=None, oligomeric_state=None, recombinant_exp_flag=None, formula=None): self.original_tagname_ = None super(em_label, self).__init__(mutant, chimera, id, name, natural_source, molecular_weight, details, number_of_copies, oligomeric_state, recombinant_exp_flag, ) self.formula = formula self.validate_formulaType73(self.formula)
[docs] def factory(*args_, **kwargs_): if em_label.subclass: return em_label.subclass(*args_, **kwargs_) else: return em_label(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_formula(self): return self.formula
[docs] def set_formula(self, formula): self.formula = formula
[docs] def validate_formulaType73(self, value): # Validate type formulaType73, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_formulaType73_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_formulaType73_patterns_, ))
validate_formulaType73_patterns_ = [['^([\\[\\]\\(\\)]*[A-Z][a-z]?[\\+\\-\\d/\\[\\]\\(\\)]*)+$']]
[docs] def hasContent_(self): if ( self.formula is not None or super(em_label, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='em_label', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='em_label') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='em_label', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='em_label'): super(em_label, self).exportAttributes(outfile, level, already_processed, namespace_, name_='em_label')
[docs] def exportChildren(self, outfile, level, namespace_='', name_='em_label', fromsubclass_=False, pretty_print=True): super(em_label, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print) if pretty_print: eol_ = '\n' else: eol_ = '' if self.formula is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sformula>%s</%sformula>%s' % (namespace_, self.gds_format_string(quote_xml(self.formula).encode(ExternalEncoding), input_name='formula'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): super(em_label, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'formula': formula_ = child_.text formula_ = re_.sub(String_cleanup_pat_, " ", formula_).strip() formula_ = self.gds_validate_string(formula_, node, 'formula') self.formula = formula_ # validate type formulaType73 self.validate_formulaType73(self.formula) super(em_label, self).buildChildren(child_, node, nodeName_, True) # end class em_label
[docs]class map_statistics_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('minimum', 'xs:float', 0), MemberSpec_('maximum', 'xs:float', 0), MemberSpec_('average', 'xs:float', 0), MemberSpec_('std', 'xs:float', 0), ] subclass = None superclass = None def __init__(self, minimum=None, maximum=None, average=None, std=None): self.original_tagname_ = None self.minimum = minimum self.maximum = maximum self.average = average self.std = std
[docs] def factory(*args_, **kwargs_): if map_statistics_type.subclass: return map_statistics_type.subclass(*args_, **kwargs_) else: return map_statistics_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_minimum(self): return self.minimum
[docs] def set_minimum(self, minimum): self.minimum = minimum
[docs] def get_maximum(self): return self.maximum
[docs] def set_maximum(self, maximum): self.maximum = maximum
[docs] def get_average(self): return self.average
[docs] def set_average(self, average): self.average = average
[docs] def get_std(self): return self.std
[docs] def set_std(self, std): self.std = std
[docs] def hasContent_(self): if ( self.minimum is not None or self.maximum is not None or self.average is not None or self.std is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='map_statistics_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='map_statistics_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='map_statistics_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='map_statistics_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='map_statistics_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.minimum is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sminimum>%s</%sminimum>%s' % (namespace_, self.gds_format_float(self.minimum, input_name='minimum'), namespace_, eol_)) if self.maximum is not None: showIndent(outfile, level, pretty_print) outfile.write('<%smaximum>%s</%smaximum>%s' % (namespace_, self.gds_format_float(self.maximum, input_name='maximum'), namespace_, eol_)) if self.average is not None: showIndent(outfile, level, pretty_print) outfile.write('<%saverage>%s</%saverage>%s' % (namespace_, self.gds_format_float(self.average, input_name='average'), namespace_, eol_)) if self.std is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sstd>%s</%sstd>%s' % (namespace_, self.gds_format_float(self.std, input_name='std'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'minimum': sval_ = child_.text try: fval_ = float(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires float or double: %s' % exp) fval_ = self.gds_validate_float(fval_, node, 'minimum') self.minimum = fval_ elif nodeName_ == 'maximum': sval_ = child_.text try: fval_ = float(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires float or double: %s' % exp) fval_ = self.gds_validate_float(fval_, node, 'maximum') self.maximum = fval_ elif nodeName_ == 'average': sval_ = child_.text try: fval_ = float(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires float or double: %s' % exp) fval_ = self.gds_validate_float(fval_, node, 'average') self.average = fval_ elif nodeName_ == 'std': sval_ = child_.text try: fval_ = float(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires float or double: %s' % exp) fval_ = self.gds_validate_float(fval_, node, 'std') self.std = fval_ # end class map_statistics_type
[docs]class pixel_spacing_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_pixel_sampling', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if pixel_spacing_type.subclass: return pixel_spacing_type.subclass(*args_, **kwargs_) else: return pixel_spacing_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='pixel_spacing_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='pixel_spacing_type') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='pixel_spacing_type', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='pixel_spacing_type'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='pixel_spacing_type', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class pixel_spacing_type
[docs]class fiducial_marker_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('fiducial_type', 'xs:token', 0), MemberSpec_('manufacturer', 'xs:token', 0), MemberSpec_('diameter', 'diameterType74', 0), ] subclass = None superclass = None def __init__(self, fiducial_type=None, manufacturer=None, diameter=None): self.original_tagname_ = None self.fiducial_type = fiducial_type self.manufacturer = manufacturer self.diameter = diameter
[docs] def factory(*args_, **kwargs_): if fiducial_marker_type.subclass: return fiducial_marker_type.subclass(*args_, **kwargs_) else: return fiducial_marker_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_fiducial_type(self): return self.fiducial_type
[docs] def set_fiducial_type(self, fiducial_type): self.fiducial_type = fiducial_type
[docs] def get_manufacturer(self): return self.manufacturer
[docs] def set_manufacturer(self, manufacturer): self.manufacturer = manufacturer
[docs] def get_diameter(self): return self.diameter
[docs] def set_diameter(self, diameter): self.diameter = diameter
[docs] def hasContent_(self): if ( self.fiducial_type is not None or self.manufacturer is not None or self.diameter is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='fiducial_marker_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='fiducial_marker_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='fiducial_marker_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='fiducial_marker_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='fiducial_marker_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.fiducial_type is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sfiducial_type>%s</%sfiducial_type>%s' % (namespace_, self.gds_format_string(quote_xml(self.fiducial_type).encode(ExternalEncoding), input_name='fiducial_type'), namespace_, eol_)) if self.manufacturer is not None: showIndent(outfile, level, pretty_print) outfile.write('<%smanufacturer>%s</%smanufacturer>%s' % (namespace_, self.gds_format_string(quote_xml(self.manufacturer).encode(ExternalEncoding), input_name='manufacturer'), namespace_, eol_)) if self.diameter is not None: self.diameter.export(outfile, level, namespace_, name_='diameter', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'fiducial_type': fiducial_type_ = child_.text fiducial_type_ = re_.sub(String_cleanup_pat_, " ", fiducial_type_).strip() fiducial_type_ = self.gds_validate_string(fiducial_type_, node, 'fiducial_type') self.fiducial_type = fiducial_type_ elif nodeName_ == 'manufacturer': manufacturer_ = child_.text manufacturer_ = re_.sub(String_cleanup_pat_, " ", manufacturer_).strip() manufacturer_ = self.gds_validate_string(manufacturer_, node, 'manufacturer') self.manufacturer = manufacturer_ elif nodeName_ == 'diameter': obj_ = diameterType74.factory() obj_.build(child_) self.diameter = obj_ obj_.original_tagname_ = 'diameter' # end class fiducial_marker_type
[docs]class ultramicrotomy_final_thickness_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_microtome_thickness', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units='nm', valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if ultramicrotomy_final_thickness_type.subclass: return ultramicrotomy_final_thickness_type.subclass(*args_, **kwargs_) else: return ultramicrotomy_final_thickness_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='ultramicrotomy_final_thickness_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='ultramicrotomy_final_thickness_type') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='ultramicrotomy_final_thickness_type', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='ultramicrotomy_final_thickness_type'): if self.units != "nm" and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='ultramicrotomy_final_thickness_type', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class ultramicrotomy_final_thickness_type
[docs]class fib_voltage_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:string', 0), MemberSpec_('valueOf_', ['allowed_focus_ion_voltage', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if fib_voltage_type.subclass: return fib_voltage_type.subclass(*args_, **kwargs_) else: return fib_voltage_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='fib_voltage_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='fib_voltage_type') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='fib_voltage_type', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='fib_voltage_type'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='fib_voltage_type', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class fib_voltage_type
[docs]class fib_current_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:string', 0), MemberSpec_('valueOf_', ['allowed_focus_ion_current', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if fib_current_type.subclass: return fib_current_type.subclass(*args_, **kwargs_) else: return fib_current_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='fib_current_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='fib_current_type') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='fib_current_type', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='fib_current_type'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='fib_current_type', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class fib_current_type
[docs]class fib_dose_rate_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_focus_ion_dose_rate', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units='ions/nm^2/s', valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if fib_dose_rate_type.subclass: return fib_dose_rate_type.subclass(*args_, **kwargs_) else: return fib_dose_rate_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='fib_dose_rate_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='fib_dose_rate_type') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='fib_dose_rate_type', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='fib_dose_rate_type'): if self.units != "ions/nm^2/s" and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='fib_dose_rate_type', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class fib_dose_rate_type
[docs]class fib_duration_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', 'xs:positiveInteger', 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if fib_duration_type.subclass: return fib_duration_type.subclass(*args_, **kwargs_) else: return fib_duration_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='fib_duration_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='fib_duration_type') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='fib_duration_type', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='fib_duration_type'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='fib_duration_type', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class fib_duration_type
[docs]class fib_initial_thickness_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_focus_ion_initial_thickness', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units='nm', valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if fib_initial_thickness_type.subclass: return fib_initial_thickness_type.subclass(*args_, **kwargs_) else: return fib_initial_thickness_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='fib_initial_thickness_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='fib_initial_thickness_type') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='fib_initial_thickness_type', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='fib_initial_thickness_type'): if self.units != "nm" and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='fib_initial_thickness_type', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class fib_initial_thickness_type
[docs]class fib_final_thickness_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_focus_ion_final_thickness', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units='nm', valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if fib_final_thickness_type.subclass: return fib_final_thickness_type.subclass(*args_, **kwargs_) else: return fib_final_thickness_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='fib_final_thickness_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='fib_final_thickness_type') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='fib_final_thickness_type', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='fib_final_thickness_type'): if self.units != "nm" and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='fib_final_thickness_type', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class fib_final_thickness_type
[docs]class crystal_formation_temperature_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_crystal_formation_temperature_type', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if crystal_formation_temperature_type.subclass: return crystal_formation_temperature_type.subclass(*args_, **kwargs_) else: return crystal_formation_temperature_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='crystal_formation_temperature_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='crystal_formation_temperature_type') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='crystal_formation_temperature_type', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='crystal_formation_temperature_type'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='crystal_formation_temperature_type', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class crystal_formation_temperature_type
[docs]class crystal_formation_time_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['non_zero_float', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if crystal_formation_time_type.subclass: return crystal_formation_time_type.subclass(*args_, **kwargs_) else: return crystal_formation_time_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='crystal_formation_time_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='crystal_formation_time_type') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='crystal_formation_time_type', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='crystal_formation_time_type'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='crystal_formation_time_type', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class crystal_formation_time_type
[docs]class subtomogram_reconstruction_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('number_subtomograms_used', 'xs:positiveInteger', 0), MemberSpec_('applied_symmetry', 'applied_symmetry_type', 0), MemberSpec_('number_classes_used', 'xs:positiveInteger', 0), MemberSpec_('algorithm', ['reconstruction_algorithm_type', 'xs:token'], 0), MemberSpec_('resolution', 'resolutionType75', 0), MemberSpec_('resolution_method', ['resolution_methodType76', 'xs:token'], 0), MemberSpec_('reconstruction_filtering', 'reconstruction_filtering_type', 0), MemberSpec_('software_list', 'software_list_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, number_subtomograms_used=None, applied_symmetry=None, number_classes_used=None, algorithm=None, resolution=None, resolution_method=None, reconstruction_filtering=None, software_list=None, details=None): self.original_tagname_ = None self.number_subtomograms_used = number_subtomograms_used self.applied_symmetry = applied_symmetry self.number_classes_used = number_classes_used self.algorithm = algorithm self.validate_reconstruction_algorithm_type(self.algorithm) self.resolution = resolution self.resolution_method = resolution_method self.validate_resolution_methodType76(self.resolution_method) self.reconstruction_filtering = reconstruction_filtering self.software_list = software_list self.details = details
[docs] def factory(*args_, **kwargs_): if subtomogram_reconstruction_type.subclass: return subtomogram_reconstruction_type.subclass(*args_, **kwargs_) else: return subtomogram_reconstruction_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_number_subtomograms_used(self): return self.number_subtomograms_used
[docs] def set_number_subtomograms_used(self, number_subtomograms_used): self.number_subtomograms_used = number_subtomograms_used
[docs] def get_applied_symmetry(self): return self.applied_symmetry
[docs] def set_applied_symmetry(self, applied_symmetry): self.applied_symmetry = applied_symmetry
[docs] def get_number_classes_used(self): return self.number_classes_used
[docs] def set_number_classes_used(self, number_classes_used): self.number_classes_used = number_classes_used
[docs] def get_algorithm(self): return self.algorithm
[docs] def set_algorithm(self, algorithm): self.algorithm = algorithm
[docs] def get_resolution(self): return self.resolution
[docs] def set_resolution(self, resolution): self.resolution = resolution
[docs] def get_resolution_method(self): return self.resolution_method
[docs] def set_resolution_method(self, resolution_method): self.resolution_method = resolution_method
[docs] def get_reconstruction_filtering(self): return self.reconstruction_filtering
[docs] def set_reconstruction_filtering(self, reconstruction_filtering): self.reconstruction_filtering = reconstruction_filtering
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def validate_reconstruction_algorithm_type(self, value): # Validate type reconstruction_algorithm_type, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['ARTS', 'SIRT', 'BACK-PROJECTION RECONSTRUCTION', 'EXACT BACK-PROJECTION RECONSTRUCTION', 'FOURIER SPACE RECONSTRUCTION'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on reconstruction_algorithm_type' % {"value" : value.encode("utf-8")} )
[docs] def validate_resolution_methodType76(self, value): # Validate type resolution_methodType76, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['FSC 0.5 CUT-OFF', 'FSC 0.33 CUT-OFF', 'FSC 0.143 CUT-OFF', u'3\u03c3'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on resolution_methodType76' % {"value" : value.encode("utf-8")} )
[docs] def hasContent_(self): if ( self.number_subtomograms_used is not None or self.applied_symmetry is not None or self.number_classes_used is not None or self.algorithm is not None or self.resolution is not None or self.resolution_method is not None or self.reconstruction_filtering is not None or self.software_list is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='subtomogram_reconstruction_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='subtomogram_reconstruction_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='subtomogram_reconstruction_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='subtomogram_reconstruction_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='subtomogram_reconstruction_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.number_subtomograms_used is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_subtomograms_used>%s</%snumber_subtomograms_used>%s' % (namespace_, self.gds_format_integer(self.number_subtomograms_used, input_name='number_subtomograms_used'), namespace_, eol_)) if self.applied_symmetry is not None: self.applied_symmetry.export(outfile, level, namespace_, name_='applied_symmetry', pretty_print=pretty_print) if self.number_classes_used is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_classes_used>%s</%snumber_classes_used>%s' % (namespace_, self.gds_format_integer(self.number_classes_used, input_name='number_classes_used'), namespace_, eol_)) if self.algorithm is not None: showIndent(outfile, level, pretty_print) outfile.write('<%salgorithm>%s</%salgorithm>%s' % (namespace_, self.gds_format_string(quote_xml(self.algorithm).encode(ExternalEncoding), input_name='algorithm'), namespace_, eol_)) if self.resolution is not None: self.resolution.export(outfile, level, namespace_, name_='resolution', pretty_print=pretty_print) if self.resolution_method is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sresolution_method>%s</%sresolution_method>%s' % (namespace_, self.gds_format_string(quote_xml(self.resolution_method).encode(ExternalEncoding), input_name='resolution_method'), namespace_, eol_)) if self.reconstruction_filtering is not None: self.reconstruction_filtering.export(outfile, level, namespace_, name_='reconstruction_filtering', pretty_print=pretty_print) if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'number_subtomograms_used': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'number_subtomograms_used') self.number_subtomograms_used = ival_ elif nodeName_ == 'applied_symmetry': obj_ = applied_symmetry_type.factory() obj_.build(child_) self.applied_symmetry = obj_ obj_.original_tagname_ = 'applied_symmetry' elif nodeName_ == 'number_classes_used': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'number_classes_used') self.number_classes_used = ival_ elif nodeName_ == 'algorithm': algorithm_ = child_.text algorithm_ = re_.sub(String_cleanup_pat_, " ", algorithm_).strip() algorithm_ = self.gds_validate_string(algorithm_, node, 'algorithm') self.algorithm = algorithm_ # validate type reconstruction_algorithm_type self.validate_reconstruction_algorithm_type(self.algorithm) elif nodeName_ == 'resolution': obj_ = resolutionType75.factory() obj_.build(child_) self.resolution = obj_ obj_.original_tagname_ = 'resolution' elif nodeName_ == 'resolution_method': resolution_method_ = child_.text resolution_method_ = re_.sub(String_cleanup_pat_, " ", resolution_method_).strip() resolution_method_ = self.gds_validate_string(resolution_method_, node, 'resolution_method') self.resolution_method = resolution_method_ # validate type resolution_methodType76 self.validate_resolution_methodType76(self.resolution_method) elif nodeName_ == 'reconstruction_filtering': obj_ = reconstruction_filtering_type.factory() obj_.build(child_) self.reconstruction_filtering = obj_ obj_.original_tagname_ = 'reconstruction_filtering' elif nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class subtomogram_reconstruction_type
[docs]class other_macromolecule(base_macromolecule_type): """Use to cater for cyclic-pseudo-peptide, other, peptide nucleic acid and polydeoxyribonucleotide/polyribonucleotide hybrid categories. Most items are optional and there is no checking done""" member_data_items_ = [ MemberSpec_('sequence', 'sequenceType77', 0), MemberSpec_('classification', 'xs:token', 0), MemberSpec_('recombinant_expression', 'recombinant_source_type', 0), MemberSpec_('structure', 'xs:token', 0), MemberSpec_('synthetic_flag', 'xs:boolean', 0), ] subclass = None superclass = base_macromolecule_type def __init__(self, mutant=None, chimera=None, id=None, name=None, natural_source=None, molecular_weight=None, details=None, number_of_copies=None, oligomeric_state=None, recombinant_exp_flag=None, sequence=None, classification=None, recombinant_expression=None, structure=None, synthetic_flag=None): self.original_tagname_ = None super(other_macromolecule, self).__init__(mutant, chimera, id, name, natural_source, molecular_weight, details, number_of_copies, oligomeric_state, recombinant_exp_flag, ) self.sequence = sequence self.classification = classification self.recombinant_expression = recombinant_expression self.structure = structure self.synthetic_flag = synthetic_flag
[docs] def factory(*args_, **kwargs_): if other_macromolecule.subclass: return other_macromolecule.subclass(*args_, **kwargs_) else: return other_macromolecule(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_sequence(self): return self.sequence
[docs] def set_sequence(self, sequence): self.sequence = sequence
[docs] def get_classification(self): return self.classification
[docs] def set_classification(self, classification): self.classification = classification
[docs] def get_recombinant_expression(self): return self.recombinant_expression
[docs] def set_recombinant_expression(self, recombinant_expression): self.recombinant_expression = recombinant_expression
[docs] def get_structure(self): return self.structure
[docs] def set_structure(self, structure): self.structure = structure
[docs] def get_synthetic_flag(self): return self.synthetic_flag
[docs] def set_synthetic_flag(self, synthetic_flag): self.synthetic_flag = synthetic_flag
[docs] def hasContent_(self): if ( self.sequence is not None or self.classification is not None or self.recombinant_expression is not None or self.structure is not None or self.synthetic_flag is not None or super(other_macromolecule, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='other_macromolecule', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='other_macromolecule') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='other_macromolecule', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='other_macromolecule'): super(other_macromolecule, self).exportAttributes(outfile, level, already_processed, namespace_, name_='other_macromolecule')
[docs] def exportChildren(self, outfile, level, namespace_='', name_='other_macromolecule', fromsubclass_=False, pretty_print=True): super(other_macromolecule, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print) if pretty_print: eol_ = '\n' else: eol_ = '' if self.sequence is not None: self.sequence.export(outfile, level, namespace_, name_='sequence', pretty_print=pretty_print) if self.classification is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sclassification>%s</%sclassification>%s' % (namespace_, self.gds_format_string(quote_xml(self.classification).encode(ExternalEncoding), input_name='classification'), namespace_, eol_)) if self.recombinant_expression is not None: self.recombinant_expression.export(outfile, level, namespace_, name_='recombinant_expression', pretty_print=pretty_print) if self.structure is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sstructure>%s</%sstructure>%s' % (namespace_, self.gds_format_string(quote_xml(self.structure).encode(ExternalEncoding), input_name='structure'), namespace_, eol_)) if self.synthetic_flag is not None: showIndent(outfile, level, pretty_print) outfile.write('<%ssynthetic_flag>%s</%ssynthetic_flag>%s' % (namespace_, self.gds_format_boolean(self.synthetic_flag, input_name='synthetic_flag'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): super(other_macromolecule, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'sequence': obj_ = sequenceType77.factory() obj_.build(child_) self.sequence = obj_ obj_.original_tagname_ = 'sequence' elif nodeName_ == 'classification': classification_ = child_.text classification_ = re_.sub(String_cleanup_pat_, " ", classification_).strip() classification_ = self.gds_validate_string(classification_, node, 'classification') self.classification = classification_ elif nodeName_ == 'recombinant_expression': obj_ = recombinant_source_type.factory() obj_.build(child_) self.recombinant_expression = obj_ obj_.original_tagname_ = 'recombinant_expression' elif nodeName_ == 'structure': structure_ = child_.text structure_ = re_.sub(String_cleanup_pat_, " ", structure_).strip() structure_ = self.gds_validate_string(structure_, node, 'structure') self.structure = structure_ elif nodeName_ == 'synthetic_flag': sval_ = child_.text if sval_ in ('true', '1'): ival_ = True elif sval_ in ('false', '0'): ival_ = False else: raise_parse_error(child_, 'requires boolean') ival_ = self.gds_validate_boolean(ival_, node, 'synthetic_flag') self.synthetic_flag = ival_ super(other_macromolecule, self).buildChildren(child_, node, nodeName_, True) # end class other_macromolecule
[docs]class unit_cell_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('a', 'cell_type', 0), MemberSpec_('b', 'cell_type', 0), MemberSpec_('c', 'cell_type', 0), MemberSpec_('c_sampling_length', 'cell_type', 0), MemberSpec_('gamma', 'cell_angle_type', 0), MemberSpec_('alpha', 'cell_angle_type', 0), MemberSpec_('beta', 'cell_angle_type', 0), ] subclass = None superclass = None def __init__(self, a=None, b=None, c=None, c_sampling_length=None, gamma=None, alpha=None, beta=None): self.original_tagname_ = None self.a = a self.b = b self.c = c self.c_sampling_length = c_sampling_length self.gamma = gamma self.alpha = alpha self.beta = beta
[docs] def factory(*args_, **kwargs_): if unit_cell_type.subclass: return unit_cell_type.subclass(*args_, **kwargs_) else: return unit_cell_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_a(self): return self.a
[docs] def set_a(self, a): self.a = a
[docs] def get_b(self): return self.b
[docs] def set_b(self, b): self.b = b
[docs] def get_c(self): return self.c
[docs] def set_c(self, c): self.c = c
[docs] def get_c_sampling_length(self): return self.c_sampling_length
[docs] def set_c_sampling_length(self, c_sampling_length): self.c_sampling_length = c_sampling_length
[docs] def get_gamma(self): return self.gamma
[docs] def set_gamma(self, gamma): self.gamma = gamma
[docs] def get_alpha(self): return self.alpha
[docs] def set_alpha(self, alpha): self.alpha = alpha
[docs] def get_beta(self): return self.beta
[docs] def set_beta(self, beta): self.beta = beta
[docs] def hasContent_(self): if ( self.a is not None or self.b is not None or self.c is not None or self.c_sampling_length is not None or self.gamma is not None or self.alpha is not None or self.beta is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='unit_cell_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='unit_cell_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='unit_cell_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='unit_cell_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='unit_cell_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.a is not None: self.a.export(outfile, level, namespace_, name_='a', pretty_print=pretty_print) if self.b is not None: self.b.export(outfile, level, namespace_, name_='b', pretty_print=pretty_print) if self.c is not None: self.c.export(outfile, level, namespace_, name_='c', pretty_print=pretty_print) if self.c_sampling_length is not None: self.c_sampling_length.export(outfile, level, namespace_, name_='c_sampling_length', pretty_print=pretty_print) if self.gamma is not None: self.gamma.export(outfile, level, namespace_, name_='gamma', pretty_print=pretty_print) if self.alpha is not None: self.alpha.export(outfile, level, namespace_, name_='alpha', pretty_print=pretty_print) if self.beta is not None: self.beta.export(outfile, level, namespace_, name_='beta', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'a': obj_ = cell_type.factory() obj_.build(child_) self.a = obj_ obj_.original_tagname_ = 'a' elif nodeName_ == 'b': obj_ = cell_type.factory() obj_.build(child_) self.b = obj_ obj_.original_tagname_ = 'b' elif nodeName_ == 'c': obj_ = cell_type.factory() obj_.build(child_) self.c = obj_ obj_.original_tagname_ = 'c' elif nodeName_ == 'c_sampling_length': obj_ = cell_type.factory() obj_.build(child_) self.c_sampling_length = obj_ obj_.original_tagname_ = 'c_sampling_length' elif nodeName_ == 'gamma': obj_ = cell_angle_type.factory() obj_.build(child_) self.gamma = obj_ obj_.original_tagname_ = 'gamma' elif nodeName_ == 'alpha': obj_ = cell_angle_type.factory() obj_.build(child_) self.alpha = obj_ obj_.original_tagname_ = 'alpha' elif nodeName_ == 'beta': obj_ = cell_angle_type.factory() obj_.build(child_) self.beta = obj_ obj_.original_tagname_ = 'beta' # end class unit_cell_type
[docs]class crystal_parameters_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('unit_cell', 'unit_cell_type', 0), MemberSpec_('plane_group', ['plane_groupType', 'xs:token'], 0), MemberSpec_('space_group', 'xs:token', 0), ] subclass = None superclass = None def __init__(self, unit_cell=None, plane_group=None, space_group=None): self.original_tagname_ = None self.unit_cell = unit_cell self.plane_group = plane_group self.validate_plane_groupType(self.plane_group) self.space_group = space_group
[docs] def factory(*args_, **kwargs_): if crystal_parameters_type.subclass: return crystal_parameters_type.subclass(*args_, **kwargs_) else: return crystal_parameters_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_unit_cell(self): return self.unit_cell
[docs] def set_unit_cell(self, unit_cell): self.unit_cell = unit_cell
[docs] def get_plane_group(self): return self.plane_group
[docs] def set_plane_group(self, plane_group): self.plane_group = plane_group
[docs] def get_space_group(self): return self.space_group
[docs] def set_space_group(self, space_group): self.space_group = space_group
[docs] def validate_plane_groupType(self, value): # Validate type plane_groupType, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['P 1', 'P 2', 'P 1 2', 'P 1 21', 'C 1 2', 'P 2 2 2', 'P 2 2 21', 'P2 21 21', 'C 2 2 2', 'P 4', 'P 4 2 2', 'P 4 21 2', 'P 3', 'P 3 1 2', 'P 3 2 1', 'P 6', 'P 6 2 2'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on plane_groupType' % {"value" : value.encode("utf-8")} )
[docs] def hasContent_(self): if ( self.unit_cell is not None or self.plane_group is not None or self.space_group is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='crystal_parameters_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='crystal_parameters_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='crystal_parameters_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='crystal_parameters_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='crystal_parameters_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.unit_cell is not None: self.unit_cell.export(outfile, level, namespace_, name_='unit_cell', pretty_print=pretty_print) if self.plane_group is not None: showIndent(outfile, level, pretty_print) outfile.write('<%splane_group>%s</%splane_group>%s' % (namespace_, self.gds_format_string(quote_xml(self.plane_group).encode(ExternalEncoding), input_name='plane_group'), namespace_, eol_)) if self.space_group is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sspace_group>%s</%sspace_group>%s' % (namespace_, self.gds_format_string(quote_xml(self.space_group).encode(ExternalEncoding), input_name='space_group'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'unit_cell': obj_ = unit_cell_type.factory() obj_.build(child_) self.unit_cell = obj_ obj_.original_tagname_ = 'unit_cell' elif nodeName_ == 'plane_group': plane_group_ = child_.text plane_group_ = re_.sub(String_cleanup_pat_, " ", plane_group_).strip() plane_group_ = self.gds_validate_string(plane_group_, node, 'plane_group') self.plane_group = plane_group_ # validate type plane_groupType self.validate_plane_groupType(self.plane_group) elif nodeName_ == 'space_group': space_group_ = child_.text space_group_ = re_.sub(String_cleanup_pat_, " ", space_group_).strip() space_group_ = self.gds_validate_string(space_group_, node, 'space_group') self.space_group = space_group_ # end class crystal_parameters_type
[docs]class crystallography_statistics_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('number_intensities_measured', 'xs:positiveInteger', 0), MemberSpec_('number_structure_factors', 'xs:positiveInteger', 0), MemberSpec_('fourier_space_coverage', 'xs:float', 0), MemberSpec_('r_sym', 'xs:float', 0), MemberSpec_('r_merge', 'xs:float', 0), MemberSpec_('overall_phase_error', 'xs:float', 0), MemberSpec_('overall_phase_residual', 'xs:float', 0), MemberSpec_('phase_error_rejection_criteria', 'xs:float', 0), MemberSpec_('high_resolution', 'high_resolutionType82', 0), MemberSpec_('shell_list', 'shell_listType', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, number_intensities_measured=None, number_structure_factors=None, fourier_space_coverage=None, r_sym=None, r_merge=None, overall_phase_error=None, overall_phase_residual=None, phase_error_rejection_criteria=None, high_resolution=None, shell_list=None, details=None): self.original_tagname_ = None self.number_intensities_measured = number_intensities_measured self.number_structure_factors = number_structure_factors self.fourier_space_coverage = fourier_space_coverage self.r_sym = r_sym self.r_merge = r_merge self.overall_phase_error = overall_phase_error self.overall_phase_residual = overall_phase_residual self.phase_error_rejection_criteria = phase_error_rejection_criteria self.high_resolution = high_resolution self.shell_list = shell_list self.details = details
[docs] def factory(*args_, **kwargs_): if crystallography_statistics_type.subclass: return crystallography_statistics_type.subclass(*args_, **kwargs_) else: return crystallography_statistics_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_number_intensities_measured(self): return self.number_intensities_measured
[docs] def set_number_intensities_measured(self, number_intensities_measured): self.number_intensities_measured = number_intensities_measured
[docs] def get_number_structure_factors(self): return self.number_structure_factors
[docs] def set_number_structure_factors(self, number_structure_factors): self.number_structure_factors = number_structure_factors
[docs] def get_fourier_space_coverage(self): return self.fourier_space_coverage
[docs] def set_fourier_space_coverage(self, fourier_space_coverage): self.fourier_space_coverage = fourier_space_coverage
[docs] def get_r_sym(self): return self.r_sym
[docs] def set_r_sym(self, r_sym): self.r_sym = r_sym
[docs] def get_r_merge(self): return self.r_merge
[docs] def set_r_merge(self, r_merge): self.r_merge = r_merge
[docs] def get_overall_phase_error(self): return self.overall_phase_error
[docs] def set_overall_phase_error(self, overall_phase_error): self.overall_phase_error = overall_phase_error
[docs] def get_overall_phase_residual(self): return self.overall_phase_residual
[docs] def set_overall_phase_residual(self, overall_phase_residual): self.overall_phase_residual = overall_phase_residual
[docs] def get_phase_error_rejection_criteria(self): return self.phase_error_rejection_criteria
[docs] def set_phase_error_rejection_criteria(self, phase_error_rejection_criteria): self.phase_error_rejection_criteria = phase_error_rejection_criteria
[docs] def get_high_resolution(self): return self.high_resolution
[docs] def set_high_resolution(self, high_resolution): self.high_resolution = high_resolution
[docs] def get_shell_list(self): return self.shell_list
[docs] def set_shell_list(self, shell_list): self.shell_list = shell_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def hasContent_(self): if ( self.number_intensities_measured is not None or self.number_structure_factors is not None or self.fourier_space_coverage is not None or self.r_sym is not None or self.r_merge is not None or self.overall_phase_error is not None or self.overall_phase_residual is not None or self.phase_error_rejection_criteria is not None or self.high_resolution is not None or self.shell_list is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='crystallography_statistics_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='crystallography_statistics_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='crystallography_statistics_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='crystallography_statistics_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='crystallography_statistics_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.number_intensities_measured is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_intensities_measured>%s</%snumber_intensities_measured>%s' % (namespace_, self.gds_format_integer(self.number_intensities_measured, input_name='number_intensities_measured'), namespace_, eol_)) if self.number_structure_factors is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_structure_factors>%s</%snumber_structure_factors>%s' % (namespace_, self.gds_format_integer(self.number_structure_factors, input_name='number_structure_factors'), namespace_, eol_)) if self.fourier_space_coverage is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sfourier_space_coverage>%s</%sfourier_space_coverage>%s' % (namespace_, self.gds_format_float(self.fourier_space_coverage, input_name='fourier_space_coverage'), namespace_, eol_)) if self.r_sym is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sr_sym>%s</%sr_sym>%s' % (namespace_, self.gds_format_float(self.r_sym, input_name='r_sym'), namespace_, eol_)) if self.r_merge is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sr_merge>%s</%sr_merge>%s' % (namespace_, self.gds_format_float(self.r_merge, input_name='r_merge'), namespace_, eol_)) if self.overall_phase_error is not None: showIndent(outfile, level, pretty_print) outfile.write('<%soverall_phase_error>%s</%soverall_phase_error>%s' % (namespace_, self.gds_format_float(self.overall_phase_error, input_name='overall_phase_error'), namespace_, eol_)) if self.overall_phase_residual is not None: showIndent(outfile, level, pretty_print) outfile.write('<%soverall_phase_residual>%s</%soverall_phase_residual>%s' % (namespace_, self.gds_format_float(self.overall_phase_residual, input_name='overall_phase_residual'), namespace_, eol_)) if self.phase_error_rejection_criteria is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sphase_error_rejection_criteria>%s</%sphase_error_rejection_criteria>%s' % (namespace_, self.gds_format_float(self.phase_error_rejection_criteria, input_name='phase_error_rejection_criteria'), namespace_, eol_)) if self.high_resolution is not None: self.high_resolution.export(outfile, level, namespace_, name_='high_resolution', pretty_print=pretty_print) if self.shell_list is not None: self.shell_list.export(outfile, level, namespace_, name_='shell_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'number_intensities_measured': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'number_intensities_measured') self.number_intensities_measured = ival_ elif nodeName_ == 'number_structure_factors': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'number_structure_factors') self.number_structure_factors = ival_ elif nodeName_ == 'fourier_space_coverage': sval_ = child_.text try: fval_ = float(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires float or double: %s' % exp) fval_ = self.gds_validate_float(fval_, node, 'fourier_space_coverage') self.fourier_space_coverage = fval_ elif nodeName_ == 'r_sym': sval_ = child_.text try: fval_ = float(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires float or double: %s' % exp) fval_ = self.gds_validate_float(fval_, node, 'r_sym') self.r_sym = fval_ elif nodeName_ == 'r_merge': sval_ = child_.text try: fval_ = float(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires float or double: %s' % exp) fval_ = self.gds_validate_float(fval_, node, 'r_merge') self.r_merge = fval_ elif nodeName_ == 'overall_phase_error': sval_ = child_.text try: fval_ = float(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires float or double: %s' % exp) fval_ = self.gds_validate_float(fval_, node, 'overall_phase_error') self.overall_phase_error = fval_ elif nodeName_ == 'overall_phase_residual': sval_ = child_.text try: fval_ = float(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires float or double: %s' % exp) fval_ = self.gds_validate_float(fval_, node, 'overall_phase_residual') self.overall_phase_residual = fval_ elif nodeName_ == 'phase_error_rejection_criteria': sval_ = child_.text try: fval_ = float(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires float or double: %s' % exp) fval_ = self.gds_validate_float(fval_, node, 'phase_error_rejection_criteria') self.phase_error_rejection_criteria = fval_ elif nodeName_ == 'high_resolution': obj_ = high_resolutionType82.factory() obj_.build(child_) self.high_resolution = obj_ obj_.original_tagname_ = 'high_resolution' elif nodeName_ == 'shell_list': obj_ = shell_listType.factory() obj_.build(child_) self.shell_list = obj_ obj_.original_tagname_ = 'shell_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class crystallography_statistics_type
[docs]class classification_type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('number_classes', 'xs:positiveInteger', 0), MemberSpec_('average_number_members_per_class', ['average_number_members_per_classType', 'xs:float'], 0), MemberSpec_('software_list', 'software_list_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, number_classes=None, average_number_members_per_class=None, software_list=None, details=None): self.original_tagname_ = None self.number_classes = number_classes self.average_number_members_per_class = average_number_members_per_class self.validate_average_number_members_per_classType(self.average_number_members_per_class) self.software_list = software_list self.details = details
[docs] def factory(*args_, **kwargs_): if classification_type.subclass: return classification_type.subclass(*args_, **kwargs_) else: return classification_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_number_classes(self): return self.number_classes
[docs] def set_number_classes(self, number_classes): self.number_classes = number_classes
[docs] def get_average_number_members_per_class(self): return self.average_number_members_per_class
[docs] def set_average_number_members_per_class(self, average_number_members_per_class): self.average_number_members_per_class = average_number_members_per_class
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def validate_average_number_members_per_classType(self, value): # Validate type average_number_members_per_classType, a restriction on xs:float. if value is not None and Validate_simpletypes_: if value <= 0: warnings_.warn('Value "%(value)s" does not match xsd minExclusive restriction on average_number_members_per_classType' % {"value" : value} )
[docs] def hasContent_(self): if ( self.number_classes is not None or self.average_number_members_per_class is not None or self.software_list is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='classification_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='classification_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='classification_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='classification_type'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='classification_type', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.number_classes is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_classes>%s</%snumber_classes>%s' % (namespace_, self.gds_format_integer(self.number_classes, input_name='number_classes'), namespace_, eol_)) if self.average_number_members_per_class is not None: showIndent(outfile, level, pretty_print) outfile.write('<%saverage_number_members_per_class>%s</%saverage_number_members_per_class>%s' % (namespace_, self.gds_format_float(self.average_number_members_per_class, input_name='average_number_members_per_class'), namespace_, eol_)) if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'number_classes': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'number_classes') self.number_classes = ival_ elif nodeName_ == 'average_number_members_per_class': sval_ = child_.text try: fval_ = float(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires float or double: %s' % exp) fval_ = self.gds_validate_float(fval_, node, 'average_number_members_per_class') self.average_number_members_per_class = fval_ # validate type average_number_members_per_classType self.validate_average_number_members_per_classType(self.average_number_members_per_class) elif nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class classification_type
[docs]class structure_determination_listType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('structure_determination', 'structure_determination_type', 1), ] subclass = None superclass = None def __init__(self, structure_determination=None): self.original_tagname_ = None if structure_determination is None: self.structure_determination = [] else: self.structure_determination = structure_determination
[docs] def factory(*args_, **kwargs_): if structure_determination_listType.subclass: return structure_determination_listType.subclass(*args_, **kwargs_) else: return structure_determination_listType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_structure_determination(self): return self.structure_determination
[docs] def set_structure_determination(self, structure_determination): self.structure_determination = structure_determination
[docs] def add_structure_determination(self, value): self.structure_determination.append(value)
[docs] def insert_structure_determination_at(self, index, value): self.structure_determination.insert(index, value)
[docs] def replace_structure_determination_at(self, index, value): self.structure_determination[index] = value
[docs] def hasContent_(self): if ( self.structure_determination ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='structure_determination_listType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='structure_determination_listType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='structure_determination_listType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='structure_determination_listType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='structure_determination_listType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for structure_determination_ in self.structure_determination: structure_determination_.export(outfile, level, namespace_, name_='structure_determination', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'structure_determination': obj_ = structure_determination_type.factory() obj_.build(child_) self.structure_determination.append(obj_) obj_.original_tagname_ = 'structure_determination' # end class structure_determination_listType
[docs]class validationType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('validation_type', 'validation_type', 1), ] subclass = None superclass = None def __init__(self, validation_type=None): self.original_tagname_ = None if validation_type is None: self.validation_type = [] else: self.validation_type = validation_type
[docs] def factory(*args_, **kwargs_): if validationType.subclass: return validationType.subclass(*args_, **kwargs_) else: return validationType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_validation_type(self): return self.validation_type
[docs] def set_validation_type(self, validation_type): self.validation_type = validation_type
[docs] def add_validation_type(self, value): self.validation_type.append(value)
[docs] def insert_validation_type_at(self, index, value): self.validation_type.insert(index, value)
[docs] def replace_validation_type_at(self, index, value): self.validation_type[index] = value
[docs] def hasContent_(self): if ( self.validation_type ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='validationType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='validationType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='validationType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='validationType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='validationType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for validation_type_ in self.validation_type: validation_type_.export(outfile, level, namespace_, name_='validation_type', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'validation_type': obj_ = validation_type.factory() obj_.build(child_) self.validation_type.append(obj_) obj_.original_tagname_ = 'validation_type' elif nodeName_ == 'fsc_curve': obj_ = fsc_curve.factory() obj_.build(child_) self.validation_type.append(obj_) obj_.original_tagname_ = 'fsc_curve' elif nodeName_ == 'layer_lines': obj_ = layer_lines.factory() obj_.build(child_) self.validation_type.append(obj_) obj_.original_tagname_ = 'layer_lines' elif nodeName_ == 'structure_factors': obj_ = structure_factors.factory() obj_.build(child_) self.validation_type.append(obj_) obj_.original_tagname_ = 'structure_factors' elif nodeName_ == 'crystallography_validation': obj_ = crystallography_validation.factory() obj_.build(child_) self.validation_type.append(obj_) obj_.original_tagname_ = 'crystallography_validation' # end class validationType
[docs]class sitesType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('deposition', ['depositionType', 'xs:token'], 0), MemberSpec_('last_processing', ['last_processingType', 'xs:token'], 0), ] subclass = None superclass = None def __init__(self, deposition=None, last_processing=None): self.original_tagname_ = None self.deposition = deposition self.validate_depositionType(self.deposition) self.last_processing = last_processing self.validate_last_processingType(self.last_processing)
[docs] def factory(*args_, **kwargs_): if sitesType.subclass: return sitesType.subclass(*args_, **kwargs_) else: return sitesType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_deposition(self): return self.deposition
[docs] def set_deposition(self, deposition): self.deposition = deposition
[docs] def get_last_processing(self): return self.last_processing
[docs] def set_last_processing(self, last_processing): self.last_processing = last_processing
[docs] def validate_depositionType(self, value): # Validate type depositionType, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['PDBe', 'PDBj', 'RCSB'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on depositionType' % {"value" : value.encode("utf-8")} )
[docs] def validate_last_processingType(self, value): # Validate type last_processingType, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['PDBe', 'PDBj', 'RCSB'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on last_processingType' % {"value" : value.encode("utf-8")} )
[docs] def hasContent_(self): if ( self.deposition is not None or self.last_processing is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='sitesType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='sitesType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='sitesType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='sitesType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='sitesType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.deposition is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdeposition>%s</%sdeposition>%s' % (namespace_, self.gds_format_string(quote_xml(self.deposition).encode(ExternalEncoding), input_name='deposition'), namespace_, eol_)) if self.last_processing is not None: showIndent(outfile, level, pretty_print) outfile.write('<%slast_processing>%s</%slast_processing>%s' % (namespace_, self.gds_format_string(quote_xml(self.last_processing).encode(ExternalEncoding), input_name='last_processing'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'deposition': deposition_ = child_.text deposition_ = re_.sub(String_cleanup_pat_, " ", deposition_).strip() deposition_ = self.gds_validate_string(deposition_, node, 'deposition') self.deposition = deposition_ # validate type depositionType self.validate_depositionType(self.deposition) elif nodeName_ == 'last_processing': last_processing_ = child_.text last_processing_ = re_.sub(String_cleanup_pat_, " ", last_processing_).strip() last_processing_ = self.gds_validate_string(last_processing_, node, 'last_processing') self.last_processing = last_processing_ # validate type last_processingType self.validate_last_processingType(self.last_processing) # end class sitesType
[docs]class key_datesType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('deposition', 'xs:date', 0), MemberSpec_('header_release', 'xs:date', 0), MemberSpec_('map_release', 'xs:date', 0), MemberSpec_('obsolete', 'xs:date', 0), MemberSpec_('update', 'xs:date', 0), ] subclass = None superclass = None def __init__(self, deposition=None, header_release=None, map_release=None, obsolete=None, update=None): self.original_tagname_ = None if isinstance(deposition, basestring): initvalue_ = datetime_.datetime.strptime(deposition, '%Y-%m-%d').date() else: initvalue_ = deposition self.deposition = initvalue_ if isinstance(header_release, basestring): initvalue_ = datetime_.datetime.strptime(header_release, '%Y-%m-%d').date() else: initvalue_ = header_release self.header_release = initvalue_ if isinstance(map_release, basestring): initvalue_ = datetime_.datetime.strptime(map_release, '%Y-%m-%d').date() else: initvalue_ = map_release self.map_release = initvalue_ if isinstance(obsolete, basestring): initvalue_ = datetime_.datetime.strptime(obsolete, '%Y-%m-%d').date() else: initvalue_ = obsolete self.obsolete = initvalue_ if isinstance(update, basestring): initvalue_ = datetime_.datetime.strptime(update, '%Y-%m-%d').date() else: initvalue_ = update self.update = initvalue_
[docs] def factory(*args_, **kwargs_): if key_datesType.subclass: return key_datesType.subclass(*args_, **kwargs_) else: return key_datesType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_deposition(self): return self.deposition
[docs] def set_deposition(self, deposition): self.deposition = deposition
[docs] def get_header_release(self): return self.header_release
[docs] def set_header_release(self, header_release): self.header_release = header_release
[docs] def get_map_release(self): return self.map_release
[docs] def set_map_release(self, map_release): self.map_release = map_release
[docs] def get_obsolete(self): return self.obsolete
[docs] def set_obsolete(self, obsolete): self.obsolete = obsolete
[docs] def get_update(self): return self.update
[docs] def set_update(self, update): self.update = update
[docs] def hasContent_(self): if ( self.deposition is not None or self.header_release is not None or self.map_release is not None or self.obsolete is not None or self.update is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='key_datesType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='key_datesType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='key_datesType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='key_datesType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='key_datesType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.deposition is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdeposition>%s</%sdeposition>%s' % (namespace_, self.gds_format_date(self.deposition, input_name='deposition'), namespace_, eol_)) if self.header_release is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sheader_release>%s</%sheader_release>%s' % (namespace_, self.gds_format_date(self.header_release, input_name='header_release'), namespace_, eol_)) if self.map_release is not None: showIndent(outfile, level, pretty_print) outfile.write('<%smap_release>%s</%smap_release>%s' % (namespace_, self.gds_format_date(self.map_release, input_name='map_release'), namespace_, eol_)) if self.obsolete is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sobsolete>%s</%sobsolete>%s' % (namespace_, self.gds_format_date(self.obsolete, input_name='obsolete'), namespace_, eol_)) if self.update is not None: showIndent(outfile, level, pretty_print) outfile.write('<%supdate>%s</%supdate>%s' % (namespace_, self.gds_format_date(self.update, input_name='update'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'deposition': sval_ = child_.text dval_ = self.gds_parse_date(sval_) self.deposition = dval_ elif nodeName_ == 'header_release': sval_ = child_.text dval_ = self.gds_parse_date(sval_) self.header_release = dval_ elif nodeName_ == 'map_release': sval_ = child_.text dval_ = self.gds_parse_date(sval_) self.map_release = dval_ elif nodeName_ == 'obsolete': sval_ = child_.text dval_ = self.gds_parse_date(sval_) self.obsolete = dval_ elif nodeName_ == 'update': sval_ = child_.text dval_ = self.gds_parse_date(sval_) self.update = dval_ # end class key_datesType
[docs]class obsolete_listType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('entry', 'supersedes_type', 1), ] subclass = None superclass = None def __init__(self, entry=None): self.original_tagname_ = None if entry is None: self.entry = [] else: self.entry = entry
[docs] def factory(*args_, **kwargs_): if obsolete_listType.subclass: return obsolete_listType.subclass(*args_, **kwargs_) else: return obsolete_listType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_entry(self): return self.entry
[docs] def set_entry(self, entry): self.entry = entry
[docs] def add_entry(self, value): self.entry.append(value)
[docs] def insert_entry_at(self, index, value): self.entry.insert(index, value)
[docs] def replace_entry_at(self, index, value): self.entry[index] = value
[docs] def hasContent_(self): if ( self.entry ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='obsolete_listType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='obsolete_listType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='obsolete_listType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='obsolete_listType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='obsolete_listType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for entry_ in self.entry: entry_.export(outfile, level, namespace_, name_='entry', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'entry': obj_ = supersedes_type.factory() obj_.build(child_) self.entry.append(obj_) obj_.original_tagname_ = 'entry' # end class obsolete_listType
[docs]class superseded_by_listType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('entry', 'supersedes_type', 1), ] subclass = None superclass = None def __init__(self, entry=None): self.original_tagname_ = None if entry is None: self.entry = [] else: self.entry = entry
[docs] def factory(*args_, **kwargs_): if superseded_by_listType.subclass: return superseded_by_listType.subclass(*args_, **kwargs_) else: return superseded_by_listType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_entry(self): return self.entry
[docs] def set_entry(self, entry): self.entry = entry
[docs] def add_entry(self, value): self.entry.append(value)
[docs] def insert_entry_at(self, index, value): self.entry.insert(index, value)
[docs] def replace_entry_at(self, index, value): self.entry[index] = value
[docs] def hasContent_(self): if ( self.entry ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='superseded_by_listType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='superseded_by_listType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='superseded_by_listType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='superseded_by_listType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='superseded_by_listType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for entry_ in self.entry: entry_.export(outfile, level, namespace_, name_='entry', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'entry': obj_ = supersedes_type.factory() obj_.build(child_) self.entry.append(obj_) obj_.original_tagname_ = 'entry' # end class superseded_by_listType
[docs]class grant_supportType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('grant_reference', 'grant_reference_type', 1), ] subclass = None superclass = None def __init__(self, grant_reference=None): self.original_tagname_ = None if grant_reference is None: self.grant_reference = [] else: self.grant_reference = grant_reference
[docs] def factory(*args_, **kwargs_): if grant_supportType.subclass: return grant_supportType.subclass(*args_, **kwargs_) else: return grant_supportType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_grant_reference(self): return self.grant_reference
[docs] def set_grant_reference(self, grant_reference): self.grant_reference = grant_reference
[docs] def add_grant_reference(self, value): self.grant_reference.append(value)
[docs] def insert_grant_reference_at(self, index, value): self.grant_reference.insert(index, value)
[docs] def replace_grant_reference_at(self, index, value): self.grant_reference[index] = value
[docs] def hasContent_(self): if ( self.grant_reference ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='grant_supportType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='grant_supportType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='grant_supportType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='grant_supportType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='grant_supportType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for grant_reference_ in self.grant_reference: grant_reference_.export(outfile, level, namespace_, name_='grant_reference', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'grant_reference': obj_ = grant_reference_type.factory() obj_.build(child_) self.grant_reference.append(obj_) obj_.original_tagname_ = 'grant_reference' # end class grant_supportType
[docs]class contact_authorType(contact_details_type): member_data_items_ = [ MemberSpec_('private', 'xs:string', 0), ] subclass = None superclass = contact_details_type def __init__(self, role=None, title=None, first_name=None, middle_name=None, last_name=None, organization=None, street=None, town_or_city=None, state_or_province=None, country=None, post_or_zip_code=None, email=None, telephone=None, fax=None, private=None): self.original_tagname_ = None super(contact_authorType, self).__init__(role, title, first_name, middle_name, last_name, organization, street, town_or_city, state_or_province, country, post_or_zip_code, email, telephone, fax, ) self.private = _cast(None, private)
[docs] def factory(*args_, **kwargs_): if contact_authorType.subclass: return contact_authorType.subclass(*args_, **kwargs_) else: return contact_authorType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_private(self): return self.private
[docs] def set_private(self, private): self.private = private
[docs] def hasContent_(self): if ( super(contact_authorType, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='contact_authorType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='contact_authorType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='contact_authorType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='contact_authorType'): super(contact_authorType, self).exportAttributes(outfile, level, already_processed, namespace_, name_='contact_authorType') if self.private is not None and 'private' not in already_processed: already_processed.add('private') outfile.write(' private=%s' % (self.gds_format_string(quote_attrib(self.private).encode(ExternalEncoding), input_name='private'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='contact_authorType', fromsubclass_=False, pretty_print=True): super(contact_authorType, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('private', node) if value is not None and 'private' not in already_processed: already_processed.add('private') self.private = value super(contact_authorType, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): super(contact_authorType, self).buildChildren(child_, node, nodeName_, True) pass # end class contact_authorType
[docs]class authors_listType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('author', ['author_type', 'xs:token'], 1), ] subclass = None superclass = None def __init__(self, author=None): self.original_tagname_ = None if author is None: self.author = [] else: self.author = author
[docs] def factory(*args_, **kwargs_): if authors_listType.subclass: return authors_listType.subclass(*args_, **kwargs_) else: return authors_listType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_author(self): return self.author
[docs] def set_author(self, author): self.author = author
[docs] def add_author(self, value): self.author.append(value)
[docs] def insert_author_at(self, index, value): self.author.insert(index, value)
[docs] def replace_author_at(self, index, value): self.author[index] = value
[docs] def validate_author_type(self, value): # Validate type author_type, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_author_type_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_author_type_patterns_, ))
validate_author_type_patterns_ = [["^[A-Za-z '\\-]+ [A-Z\\-]+$"]]
[docs] def hasContent_(self): if ( self.author ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='authors_listType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='authors_listType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='authors_listType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='authors_listType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='authors_listType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for author_ in self.author: showIndent(outfile, level, pretty_print) outfile.write('<%sauthor>%s</%sauthor>%s' % (namespace_, self.gds_format_string(quote_xml(author_).encode(ExternalEncoding), input_name='author'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'author': author_ = child_.text author_ = re_.sub(String_cleanup_pat_, " ", author_).strip() author_ = self.gds_validate_string(author_, node, 'author') self.author.append(author_) # validate type author_type self.validate_author_type(self.author[-1]) # end class authors_listType
[docs]class statusType(version_type): member_data_items_ = [ MemberSpec_('id', 'xs:positiveInteger', 0), ] subclass = None superclass = version_type def __init__(self, date=None, code=None, processing_site=None, annotator=None, details=None, id=None): self.original_tagname_ = None super(statusType, self).__init__(date, code, processing_site, annotator, details, ) self.id = _cast(int, id)
[docs] def factory(*args_, **kwargs_): if statusType.subclass: return statusType.subclass(*args_, **kwargs_) else: return statusType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_id(self): return self.id
[docs] def set_id(self, id): self.id = id
[docs] def hasContent_(self): if ( super(statusType, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='statusType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='statusType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='statusType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='statusType'): super(statusType, self).exportAttributes(outfile, level, already_processed, namespace_, name_='statusType') if self.id is not None and 'id' not in already_processed: already_processed.add('id') outfile.write(' id="%s"' % self.gds_format_integer(self.id, input_name='id'))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='statusType', fromsubclass_=False, pretty_print=True): super(statusType, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('id', node) if value is not None and 'id' not in already_processed: already_processed.add('id') try: self.id = int(value) except ValueError as exp: raise_parse_error(node, 'Bad integer attribute: %s' % exp) if self.id <= 0: raise_parse_error(node, 'Invalid PositiveInteger') super(statusType, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): super(statusType, self).buildChildren(child_, node, nodeName_, True) pass # end class statusType
[docs]class annotatorType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('private', 'xs:token', 0), MemberSpec_('valueOf_', 'xs:token', 0), ] subclass = None superclass = None def __init__(self, private=None, valueOf_=None): self.original_tagname_ = None self.private = _cast(None, private) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if annotatorType.subclass: return annotatorType.subclass(*args_, **kwargs_) else: return annotatorType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_private(self): return self.private
[docs] def set_private(self, private): self.private = private
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='annotatorType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='annotatorType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='annotatorType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='annotatorType'): if self.private is not None and 'private' not in already_processed: already_processed.add('private') outfile.write(' private=%s' % (self.gds_format_string(quote_attrib(self.private).encode(ExternalEncoding), input_name='private'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='annotatorType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('private', node) if value is not None and 'private' not in already_processed: already_processed.add('private') self.private = value self.private = ' '.join(self.private.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class annotatorType
[docs]class organizationType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('type', 'xs:token', 0), MemberSpec_('valueOf_', 'xs:token', 0), ] subclass = None superclass = None def __init__(self, type_=None, valueOf_=None): self.original_tagname_ = None self.type_ = _cast(None, type_) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if organizationType.subclass: return organizationType.subclass(*args_, **kwargs_) else: return organizationType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_type(self): return self.type_
[docs] def set_type(self, type_): self.type_ = type_
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='organizationType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='organizationType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='organizationType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='organizationType'): if self.type_ is not None and 'type_' not in already_processed: already_processed.add('type_') outfile.write(' type=%s' % (self.gds_format_string(quote_attrib(self.type_).encode(ExternalEncoding), input_name='type'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='organizationType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('type', node) if value is not None and 'type' not in already_processed: already_processed.add('type') self.type_ = value self.type_ = ' '.join(self.type_.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class organizationType
[docs]class citation_listType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('primary_citation', 'primary_citationType', 0), MemberSpec_('secondary_citation', 'secondary_citationType', 1), ] subclass = None superclass = None def __init__(self, primary_citation=None, secondary_citation=None): self.original_tagname_ = None self.primary_citation = primary_citation if secondary_citation is None: self.secondary_citation = [] else: self.secondary_citation = secondary_citation
[docs] def factory(*args_, **kwargs_): if citation_listType.subclass: return citation_listType.subclass(*args_, **kwargs_) else: return citation_listType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_primary_citation(self): return self.primary_citation
[docs] def set_primary_citation(self, primary_citation): self.primary_citation = primary_citation
[docs] def get_secondary_citation(self): return self.secondary_citation
[docs] def set_secondary_citation(self, secondary_citation): self.secondary_citation = secondary_citation
[docs] def add_secondary_citation(self, value): self.secondary_citation.append(value)
[docs] def insert_secondary_citation_at(self, index, value): self.secondary_citation.insert(index, value)
[docs] def replace_secondary_citation_at(self, index, value): self.secondary_citation[index] = value
[docs] def hasContent_(self): if ( self.primary_citation is not None or self.secondary_citation ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='citation_listType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='citation_listType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='citation_listType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='citation_listType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='citation_listType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.primary_citation is not None: self.primary_citation.export(outfile, level, namespace_, name_='primary_citation', pretty_print=pretty_print) for secondary_citation_ in self.secondary_citation: secondary_citation_.export(outfile, level, namespace_, name_='secondary_citation', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'primary_citation': obj_ = primary_citationType.factory() obj_.build(child_) self.primary_citation = obj_ obj_.original_tagname_ = 'primary_citation' elif nodeName_ == 'secondary_citation': obj_ = secondary_citationType.factory() obj_.build(child_) self.secondary_citation.append(obj_) obj_.original_tagname_ = 'secondary_citation' # end class citation_listType
[docs]class primary_citationType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('citation_type', 'citation_type', 0), ] subclass = None superclass = None def __init__(self, citation_type=None): self.original_tagname_ = None self.citation_type = citation_type
[docs] def factory(*args_, **kwargs_): if primary_citationType.subclass: return primary_citationType.subclass(*args_, **kwargs_) else: return primary_citationType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_citation_type(self): return self.citation_type
[docs] def set_citation_type(self, citation_type): self.citation_type = citation_type
[docs] def hasContent_(self): if ( self.citation_type is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='primary_citationType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='primary_citationType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='primary_citationType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='primary_citationType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='primary_citationType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.citation_type is not None: self.citation_type.export(outfile, level, namespace_, name_='citation_type', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'citation_type': obj_ = citation_type.factory() obj_.build(child_) self.citation_type = obj_ obj_.original_tagname_ = 'citation_type' elif nodeName_ == 'non_journal_citation': obj_ = non_journal_citation.factory() obj_.build(child_) self.citation_type = obj_ obj_.original_tagname_ = 'non_journal_citation' elif nodeName_ == 'journal_citation': obj_ = journal_citation.factory() obj_.build(child_) self.citation_type = obj_ obj_.original_tagname_ = 'journal_citation' # end class primary_citationType
[docs]class secondary_citationType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('citation_type', 'citation_type', 0), ] subclass = None superclass = None def __init__(self, citation_type=None): self.original_tagname_ = None self.citation_type = citation_type
[docs] def factory(*args_, **kwargs_): if secondary_citationType.subclass: return secondary_citationType.subclass(*args_, **kwargs_) else: return secondary_citationType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_citation_type(self): return self.citation_type
[docs] def set_citation_type(self, citation_type): self.citation_type = citation_type
[docs] def hasContent_(self): if ( self.citation_type is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='secondary_citationType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='secondary_citationType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='secondary_citationType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='secondary_citationType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='secondary_citationType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.citation_type is not None: self.citation_type.export(outfile, level, namespace_, name_='citation_type', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'citation_type': obj_ = citation_type.factory() obj_.build(child_) self.citation_type = obj_ obj_.original_tagname_ = 'citation_type' elif nodeName_ == 'non_journal_citation': obj_ = non_journal_citation.factory() obj_.build(child_) self.citation_type = obj_ obj_.original_tagname_ = 'non_journal_citation' elif nodeName_ == 'journal_citation': obj_ = journal_citation.factory() obj_.build(child_) self.citation_type = obj_ obj_.original_tagname_ = 'journal_citation' # end class secondary_citationType
[docs]class relationshipType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('in_frame', ['in_frameType', 'xs:token'], 0), MemberSpec_('other', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, in_frame=None, other=None): self.original_tagname_ = None self.in_frame = in_frame self.validate_in_frameType(self.in_frame) self.other = other
[docs] def factory(*args_, **kwargs_): if relationshipType.subclass: return relationshipType.subclass(*args_, **kwargs_) else: return relationshipType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_in_frame(self): return self.in_frame
[docs] def set_in_frame(self, in_frame): self.in_frame = in_frame
[docs] def get_other(self): return self.other
[docs] def set_other(self, other): self.other = other
[docs] def validate_in_frameType(self, value): # Validate type in_frameType, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['NOOVERLAP', 'PARTIALOVERLAP', 'FULLOVERLAP'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on in_frameType' % {"value" : value.encode("utf-8")} )
[docs] def hasContent_(self): if ( self.in_frame is not None or self.other is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='relationshipType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='relationshipType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='relationshipType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='relationshipType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='relationshipType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.in_frame is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sin_frame>%s</%sin_frame>%s' % (namespace_, self.gds_format_string(quote_xml(self.in_frame).encode(ExternalEncoding), input_name='in_frame'), namespace_, eol_)) if self.other is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sother>%s</%sother>%s' % (namespace_, self.gds_format_string(quote_xml(self.other).encode(ExternalEncoding), input_name='other'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'in_frame': in_frame_ = child_.text in_frame_ = re_.sub(String_cleanup_pat_, " ", in_frame_).strip() in_frame_ = self.gds_validate_string(in_frame_, node, 'in_frame') self.in_frame = in_frame_ # validate type in_frameType self.validate_in_frameType(self.in_frame) elif nodeName_ == 'other': other_ = child_.text other_ = self.gds_validate_string(other_, node, 'other') self.other = other_ # end class relationshipType
[docs]class relationshipType1(GeneratedsSuper): member_data_items_ = [ MemberSpec_('in_frame', ['in_frameType2', 'xs:token'], 0), MemberSpec_('other', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, in_frame=None, other=None): self.original_tagname_ = None self.in_frame = in_frame self.validate_in_frameType2(self.in_frame) self.other = other
[docs] def factory(*args_, **kwargs_): if relationshipType1.subclass: return relationshipType1.subclass(*args_, **kwargs_) else: return relationshipType1(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_in_frame(self): return self.in_frame
[docs] def set_in_frame(self, in_frame): self.in_frame = in_frame
[docs] def get_other(self): return self.other
[docs] def set_other(self, other): self.other = other
[docs] def validate_in_frameType2(self, value): # Validate type in_frameType2, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['NOOVERLAP', 'PARTIALOVERLAP', 'FULLOVERLAP'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on in_frameType2' % {"value" : value.encode("utf-8")} )
[docs] def hasContent_(self): if ( self.in_frame is not None or self.other is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='relationshipType1', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='relationshipType1') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='relationshipType1', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='relationshipType1'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='relationshipType1', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.in_frame is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sin_frame>%s</%sin_frame>%s' % (namespace_, self.gds_format_string(quote_xml(self.in_frame).encode(ExternalEncoding), input_name='in_frame'), namespace_, eol_)) if self.other is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sother>%s</%sother>%s' % (namespace_, self.gds_format_string(quote_xml(self.other).encode(ExternalEncoding), input_name='other'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'in_frame': in_frame_ = child_.text in_frame_ = re_.sub(String_cleanup_pat_, " ", in_frame_).strip() in_frame_ = self.gds_validate_string(in_frame_, node, 'in_frame') self.in_frame = in_frame_ # validate type in_frameType2 self.validate_in_frameType2(self.in_frame) elif nodeName_ == 'other': other_ = child_.text other_ = self.gds_validate_string(other_, node, 'other') self.other = other_ # end class relationshipType1
[docs]class specimen_preparation_listType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('specimen_preparation', 'base_preparation_type', 1), ] subclass = None superclass = None def __init__(self, specimen_preparation=None): self.original_tagname_ = None if specimen_preparation is None: self.specimen_preparation = [] else: self.specimen_preparation = specimen_preparation
[docs] def factory(*args_, **kwargs_): if specimen_preparation_listType.subclass: return specimen_preparation_listType.subclass(*args_, **kwargs_) else: return specimen_preparation_listType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_specimen_preparation(self): return self.specimen_preparation
[docs] def set_specimen_preparation(self, specimen_preparation): self.specimen_preparation = specimen_preparation
[docs] def add_specimen_preparation(self, value): self.specimen_preparation.append(value)
[docs] def insert_specimen_preparation_at(self, index, value): self.specimen_preparation.insert(index, value)
[docs] def replace_specimen_preparation_at(self, index, value): self.specimen_preparation[index] = value
[docs] def hasContent_(self): if ( self.specimen_preparation ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='specimen_preparation_listType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='specimen_preparation_listType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='specimen_preparation_listType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='specimen_preparation_listType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='specimen_preparation_listType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for specimen_preparation_ in self.specimen_preparation: specimen_preparation_.export(outfile, level, namespace_, name_='specimen_preparation', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'specimen_preparation': class_obj_ = self.get_class_obj_(child_, base_preparation_type) obj_ = class_obj_.factory() obj_.build(child_) self.specimen_preparation.append(obj_) obj_.original_tagname_ = 'specimen_preparation' elif nodeName_ == 'tomography_preparation': obj_ = tomography_preparation_type.factory() obj_.build(child_) self.specimen_preparation.append(obj_) obj_.original_tagname_ = 'tomography_preparation' elif nodeName_ == 'crystallography_preparation': obj_ = crystallography_preparation_type.factory() obj_.build(child_) self.specimen_preparation.append(obj_) obj_.original_tagname_ = 'crystallography_preparation' # end class specimen_preparation_listType
[docs]class microscopy_listType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('microscopy', 'base_microscopy_type', 1), ] subclass = None superclass = None def __init__(self, microscopy=None): self.original_tagname_ = None if microscopy is None: self.microscopy = [] else: self.microscopy = microscopy
[docs] def factory(*args_, **kwargs_): if microscopy_listType.subclass: return microscopy_listType.subclass(*args_, **kwargs_) else: return microscopy_listType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_microscopy(self): return self.microscopy
[docs] def set_microscopy(self, microscopy): self.microscopy = microscopy
[docs] def add_microscopy(self, value): self.microscopy.append(value)
[docs] def insert_microscopy_at(self, index, value): self.microscopy.insert(index, value)
[docs] def replace_microscopy_at(self, index, value): self.microscopy[index] = value
[docs] def hasContent_(self): if ( self.microscopy ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='microscopy_listType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='microscopy_listType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='microscopy_listType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='microscopy_listType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='microscopy_listType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for microscopy_ in self.microscopy: microscopy_.export(outfile, level, namespace_, name_='microscopy', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'microscopy': class_obj_ = self.get_class_obj_(child_, base_microscopy_type) obj_ = class_obj_.factory() obj_.build(child_) self.microscopy.append(obj_) obj_.original_tagname_ = 'microscopy' elif nodeName_ == 'tomography_microscopy': obj_ = tomography_microscopy_type.factory() obj_.build(child_) self.microscopy.append(obj_) obj_.original_tagname_ = 'tomography_microscopy' elif nodeName_ == 'crystallography_microscopy': obj_ = crystallography_microscopy_type.factory() obj_.build(child_) self.microscopy.append(obj_) obj_.original_tagname_ = 'crystallography_microscopy' # end class microscopy_listType
[docs]class supramolecule_listType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('supramolecule', 'base_supramolecule_type', 1), ] subclass = None superclass = None def __init__(self, supramolecule=None): self.original_tagname_ = None if supramolecule is None: self.supramolecule = [] else: self.supramolecule = supramolecule
[docs] def factory(*args_, **kwargs_): if supramolecule_listType.subclass: return supramolecule_listType.subclass(*args_, **kwargs_) else: return supramolecule_listType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_supramolecule(self): return self.supramolecule
[docs] def set_supramolecule(self, supramolecule): self.supramolecule = supramolecule
[docs] def add_supramolecule(self, value): self.supramolecule.append(value)
[docs] def insert_supramolecule_at(self, index, value): self.supramolecule.insert(index, value)
[docs] def replace_supramolecule_at(self, index, value): self.supramolecule[index] = value
[docs] def hasContent_(self): if ( self.supramolecule ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='supramolecule_listType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='supramolecule_listType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='supramolecule_listType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='supramolecule_listType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='supramolecule_listType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for supramolecule_ in self.supramolecule: supramolecule_.export(outfile, level, namespace_, name_='supramolecule', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'supramolecule': class_obj_ = self.get_class_obj_(child_, base_supramolecule_type) obj_ = class_obj_.factory() obj_.build(child_) self.supramolecule.append(obj_) obj_.original_tagname_ = 'supramolecule' elif nodeName_ == 'sample': obj_ = sample.factory() obj_.build(child_) self.supramolecule.append(obj_) obj_.original_tagname_ = 'sample' elif nodeName_ == 'cell': obj_ = cell.factory() obj_.build(child_) self.supramolecule.append(obj_) obj_.original_tagname_ = 'cell' elif nodeName_ == 'tissue': obj_ = tissue.factory() obj_.build(child_) self.supramolecule.append(obj_) obj_.original_tagname_ = 'tissue' elif nodeName_ == 'organelle_or_cellular_component': obj_ = organelle_or_cellular_component.factory() obj_.build(child_) self.supramolecule.append(obj_) obj_.original_tagname_ = 'organelle_or_cellular_component' elif nodeName_ == 'virus': obj_ = virus.factory() obj_.build(child_) self.supramolecule.append(obj_) obj_.original_tagname_ = 'virus' elif nodeName_ == 'complex': obj_ = complex.factory() obj_.build(child_) self.supramolecule.append(obj_) obj_.original_tagname_ = 'complex' # end class supramolecule_listType
[docs]class glow_dischargeType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('glow_discharge_params', 'glow_discharge_params_type', 0), ] subclass = None superclass = None def __init__(self, glow_discharge_params=None): self.original_tagname_ = None self.glow_discharge_params = glow_discharge_params
[docs] def factory(*args_, **kwargs_): if glow_dischargeType.subclass: return glow_dischargeType.subclass(*args_, **kwargs_) else: return glow_dischargeType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_glow_discharge_params(self): return self.glow_discharge_params
[docs] def set_glow_discharge_params(self, glow_discharge_params): self.glow_discharge_params = glow_discharge_params
[docs] def hasContent_(self): if ( self.glow_discharge_params is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='glow_dischargeType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='glow_dischargeType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='glow_dischargeType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='glow_dischargeType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='glow_dischargeType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.glow_discharge_params is not None: self.glow_discharge_params.export(outfile, level, namespace_, name_='glow_discharge_params', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'glow_discharge_params': obj_ = glow_discharge_params_type.factory() obj_.build(child_) self.glow_discharge_params = obj_ obj_.original_tagname_ = 'glow_discharge_params' # end class glow_dischargeType
[docs]class timeType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_time_glow_discharge', 'xs:positiveInteger'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if timeType.subclass: return timeType.subclass(*args_, **kwargs_) else: return timeType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='timeType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='timeType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='timeType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='timeType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='timeType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class timeType
[docs]class pressureType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_pressure_glow_discharge', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if pressureType.subclass: return pressureType.subclass(*args_, **kwargs_) else: return pressureType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='pressureType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='pressureType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='pressureType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='pressureType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='pressureType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class pressureType
[docs]class energy_filterType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('name', 'xs:token', 0), MemberSpec_('lower_energy_threshold', 'lower_energy_thresholdType', 0), MemberSpec_('upper_energy_threshold', 'upper_energy_thresholdType', 0), ] subclass = None superclass = None def __init__(self, name=None, lower_energy_threshold=None, upper_energy_threshold=None): self.original_tagname_ = None self.name = name self.lower_energy_threshold = lower_energy_threshold self.upper_energy_threshold = upper_energy_threshold
[docs] def factory(*args_, **kwargs_): if energy_filterType.subclass: return energy_filterType.subclass(*args_, **kwargs_) else: return energy_filterType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_name(self): return self.name
[docs] def set_name(self, name): self.name = name
[docs] def get_lower_energy_threshold(self): return self.lower_energy_threshold
[docs] def set_lower_energy_threshold(self, lower_energy_threshold): self.lower_energy_threshold = lower_energy_threshold
[docs] def get_upper_energy_threshold(self): return self.upper_energy_threshold
[docs] def set_upper_energy_threshold(self, upper_energy_threshold): self.upper_energy_threshold = upper_energy_threshold
[docs] def hasContent_(self): if ( self.name is not None or self.lower_energy_threshold is not None or self.upper_energy_threshold is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='energy_filterType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='energy_filterType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='energy_filterType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='energy_filterType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='energy_filterType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.name is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sname>%s</%sname>%s' % (namespace_, self.gds_format_string(quote_xml(self.name).encode(ExternalEncoding), input_name='name'), namespace_, eol_)) if self.lower_energy_threshold is not None: self.lower_energy_threshold.export(outfile, level, namespace_, name_='lower_energy_threshold', pretty_print=pretty_print) if self.upper_energy_threshold is not None: self.upper_energy_threshold.export(outfile, level, namespace_, name_='upper_energy_threshold', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'name': name_ = child_.text name_ = re_.sub(String_cleanup_pat_, " ", name_).strip() name_ = self.gds_validate_string(name_, node, 'name') self.name = name_ elif nodeName_ == 'lower_energy_threshold': obj_ = lower_energy_thresholdType.factory() obj_.build(child_) self.lower_energy_threshold = obj_ obj_.original_tagname_ = 'lower_energy_threshold' elif nodeName_ == 'upper_energy_threshold': obj_ = upper_energy_thresholdType.factory() obj_.build(child_) self.upper_energy_threshold = obj_ obj_.original_tagname_ = 'upper_energy_threshold' # end class energy_filterType
[docs]class lower_energy_thresholdType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_energy_window', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if lower_energy_thresholdType.subclass: return lower_energy_thresholdType.subclass(*args_, **kwargs_) else: return lower_energy_thresholdType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='lower_energy_thresholdType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='lower_energy_thresholdType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='lower_energy_thresholdType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='lower_energy_thresholdType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='lower_energy_thresholdType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class lower_energy_thresholdType
[docs]class upper_energy_thresholdType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_energy_window', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if upper_energy_thresholdType.subclass: return upper_energy_thresholdType.subclass(*args_, **kwargs_) else: return upper_energy_thresholdType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='upper_energy_thresholdType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='upper_energy_thresholdType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='upper_energy_thresholdType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='upper_energy_thresholdType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='upper_energy_thresholdType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class upper_energy_thresholdType
[docs]class validation_listType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('soft_validation_regexp', 'soft_validation_regexpType', 1), MemberSpec_('hard_validation_regexp', 'hard_validation_regexpType', 1), ] subclass = None superclass = None def __init__(self, soft_validation_regexp=None, hard_validation_regexp=None): self.original_tagname_ = None if soft_validation_regexp is None: self.soft_validation_regexp = [] else: self.soft_validation_regexp = soft_validation_regexp if hard_validation_regexp is None: self.hard_validation_regexp = [] else: self.hard_validation_regexp = hard_validation_regexp
[docs] def factory(*args_, **kwargs_): if validation_listType.subclass: return validation_listType.subclass(*args_, **kwargs_) else: return validation_listType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_soft_validation_regexp(self): return self.soft_validation_regexp
[docs] def set_soft_validation_regexp(self, soft_validation_regexp): self.soft_validation_regexp = soft_validation_regexp
[docs] def add_soft_validation_regexp(self, value): self.soft_validation_regexp.append(value)
[docs] def insert_soft_validation_regexp_at(self, index, value): self.soft_validation_regexp.insert(index, value)
[docs] def replace_soft_validation_regexp_at(self, index, value): self.soft_validation_regexp[index] = value
[docs] def get_hard_validation_regexp(self): return self.hard_validation_regexp
[docs] def set_hard_validation_regexp(self, hard_validation_regexp): self.hard_validation_regexp = hard_validation_regexp
[docs] def add_hard_validation_regexp(self, value): self.hard_validation_regexp.append(value)
[docs] def insert_hard_validation_regexp_at(self, index, value): self.hard_validation_regexp.insert(index, value)
[docs] def replace_hard_validation_regexp_at(self, index, value): self.hard_validation_regexp[index] = value
[docs] def hasContent_(self): if ( self.soft_validation_regexp or self.hard_validation_regexp ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='validation_listType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='validation_listType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='validation_listType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='validation_listType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='validation_listType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for soft_validation_regexp_ in self.soft_validation_regexp: soft_validation_regexp_.export(outfile, level, namespace_, name_='soft_validation_regexp', pretty_print=pretty_print) for hard_validation_regexp_ in self.hard_validation_regexp: hard_validation_regexp_.export(outfile, level, namespace_, name_='hard_validation_regexp', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'soft_validation_regexp': obj_ = soft_validation_regexpType.factory() obj_.build(child_) self.soft_validation_regexp.append(obj_) obj_.original_tagname_ = 'soft_validation_regexp' elif nodeName_ == 'hard_validation_regexp': obj_ = hard_validation_regexpType.factory() obj_.build(child_) self.hard_validation_regexp.append(obj_) obj_.original_tagname_ = 'hard_validation_regexp' # end class validation_listType
[docs]class soft_validation_regexpType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('warning_text', 'xs:string', 0), MemberSpec_('regexp', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, warning_text=None, regexp=None): self.original_tagname_ = None self.warning_text = warning_text self.regexp = regexp
[docs] def factory(*args_, **kwargs_): if soft_validation_regexpType.subclass: return soft_validation_regexpType.subclass(*args_, **kwargs_) else: return soft_validation_regexpType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_warning_text(self): return self.warning_text
[docs] def set_warning_text(self, warning_text): self.warning_text = warning_text
[docs] def get_regexp(self): return self.regexp
[docs] def set_regexp(self, regexp): self.regexp = regexp
[docs] def hasContent_(self): if ( self.warning_text is not None or self.regexp is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='soft_validation_regexpType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='soft_validation_regexpType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='soft_validation_regexpType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='soft_validation_regexpType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='soft_validation_regexpType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.warning_text is not None: showIndent(outfile, level, pretty_print) outfile.write('<%swarning_text>%s</%swarning_text>%s' % (namespace_, self.gds_format_string(quote_xml(self.warning_text).encode(ExternalEncoding), input_name='warning_text'), namespace_, eol_)) if self.regexp is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sregexp>%s</%sregexp>%s' % (namespace_, self.gds_format_string(quote_xml(self.regexp).encode(ExternalEncoding), input_name='regexp'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'warning_text': warning_text_ = child_.text warning_text_ = self.gds_validate_string(warning_text_, node, 'warning_text') self.warning_text = warning_text_ elif nodeName_ == 'regexp': regexp_ = child_.text regexp_ = self.gds_validate_string(regexp_, node, 'regexp') self.regexp = regexp_ # end class soft_validation_regexpType
[docs]class hard_validation_regexpType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('_error_text', 'xs:string', 0), MemberSpec_('regexp', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, _error_text=None, regexp=None): self.original_tagname_ = None self._error_text = _error_text self.regexp = regexp
[docs] def factory(*args_, **kwargs_): if hard_validation_regexpType.subclass: return hard_validation_regexpType.subclass(*args_, **kwargs_) else: return hard_validation_regexpType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get__error_text(self): return self._error_text
[docs] def set__error_text(self, _error_text): self._error_text = _error_text
[docs] def get_regexp(self): return self.regexp
[docs] def set_regexp(self, regexp): self.regexp = regexp
[docs] def hasContent_(self): if ( self._error_text is not None or self.regexp is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='hard_validation_regexpType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='hard_validation_regexpType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='hard_validation_regexpType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='hard_validation_regexpType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='hard_validation_regexpType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self._error_text is not None: showIndent(outfile, level, pretty_print) outfile.write('<%s_error_text>%s</%s_error_text>%s' % (namespace_, self.gds_format_string(quote_xml(self._error_text).encode(ExternalEncoding), input_name='_error_text'), namespace_, eol_)) if self.regexp is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sregexp>%s</%sregexp>%s' % (namespace_, self.gds_format_string(quote_xml(self.regexp).encode(ExternalEncoding), input_name='regexp'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == '_error_text': _error_text_ = child_.text _error_text_ = self.gds_validate_string(_error_text_, node, '_error_text') self._error_text = _error_text_ elif nodeName_ == 'regexp': regexp_ = child_.text regexp_ = self.gds_validate_string(regexp_, node, 'regexp') self.regexp = regexp_ # end class hard_validation_regexpType
[docs]class componentType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('concentration', 'concentrationType', 0), MemberSpec_('formula', ['formulaType', 'xs:token'], 0), MemberSpec_('name', 'xs:token', 0), ] subclass = None superclass = None def __init__(self, concentration=None, formula=None, name=None): self.original_tagname_ = None self.concentration = concentration self.formula = formula self.validate_formulaType(self.formula) self.name = name
[docs] def factory(*args_, **kwargs_): if componentType.subclass: return componentType.subclass(*args_, **kwargs_) else: return componentType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_concentration(self): return self.concentration
[docs] def set_concentration(self, concentration): self.concentration = concentration
[docs] def get_formula(self): return self.formula
[docs] def set_formula(self, formula): self.formula = formula
[docs] def get_name(self): return self.name
[docs] def set_name(self, name): self.name = name
[docs] def validate_formulaType(self, value): # Validate type formulaType, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_formulaType_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_formulaType_patterns_, ))
validate_formulaType_patterns_ = [['^([\\[\\]\\(\\)]*[A-Z][a-z]?[\\+\\-\\d/\\[\\]\\(\\)]*)+$']]
[docs] def hasContent_(self): if ( self.concentration is not None or self.formula is not None or self.name is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='componentType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='componentType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='componentType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='componentType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='componentType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.concentration is not None: self.concentration.export(outfile, level, namespace_, name_='concentration', pretty_print=pretty_print) if self.formula is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sformula>%s</%sformula>%s' % (namespace_, self.gds_format_string(quote_xml(self.formula).encode(ExternalEncoding), input_name='formula'), namespace_, eol_)) if self.name is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sname>%s</%sname>%s' % (namespace_, self.gds_format_string(quote_xml(self.name).encode(ExternalEncoding), input_name='name'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'concentration': obj_ = concentrationType.factory() obj_.build(child_) self.concentration = obj_ obj_.original_tagname_ = 'concentration' elif nodeName_ == 'formula': formula_ = child_.text formula_ = re_.sub(String_cleanup_pat_, " ", formula_).strip() formula_ = self.gds_validate_string(formula_, node, 'formula') self.formula = formula_ # validate type formulaType self.validate_formulaType(self.formula) elif nodeName_ == 'name': name_ = child_.text name_ = re_.sub(String_cleanup_pat_, " ", name_).strip() name_ = self.gds_validate_string(name_, node, 'name') self.name = name_ # end class componentType
[docs]class concentrationType(GeneratedsSuper): """_emd_buffer_component.concentration_units""" member_data_items_ = [ MemberSpec_('units', 'xs:string', 0), MemberSpec_('valueOf_', ['allowed_concentration', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if concentrationType.subclass: return concentrationType.subclass(*args_, **kwargs_) else: return concentrationType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='concentrationType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='concentrationType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='concentrationType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='concentrationType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='concentrationType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class concentrationType
[docs]class chamber_humidityType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_humidity_vitrification', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if chamber_humidityType.subclass: return chamber_humidityType.subclass(*args_, **kwargs_) else: return chamber_humidityType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='chamber_humidityType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='chamber_humidityType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='chamber_humidityType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='chamber_humidityType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='chamber_humidityType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass
[docs] def gds_format_float(self,input_data, input_name="" ): return ("%g" % input_data) # end class chamber_humidityType
[docs]class chamber_temperatureType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_temperature_vitrification', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if chamber_temperatureType.subclass: return chamber_temperatureType.subclass(*args_, **kwargs_) else: return chamber_temperatureType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='chamber_temperatureType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='chamber_temperatureType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='chamber_temperatureType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='chamber_temperatureType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='chamber_temperatureType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class chamber_temperatureType
[docs]class concentrationType3(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:string', 0), MemberSpec_('valueOf_', ['allowed_concentration', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if concentrationType3.subclass: return concentrationType3.subclass(*args_, **kwargs_) else: return concentrationType3(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='concentrationType3', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='concentrationType3') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='concentrationType3', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='concentrationType3'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='concentrationType3', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class concentrationType3
[docs]class stainingType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('type_', ['typeType', 'xs:token'], 0), MemberSpec_('material', 'xs:token', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, type_=None, material=None, details=None): self.original_tagname_ = None self.type_ = type_ self.validate_typeType(self.type_) self.material = material self.details = details
[docs] def factory(*args_, **kwargs_): if stainingType.subclass: return stainingType.subclass(*args_, **kwargs_) else: return stainingType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_type(self): return self.type_
[docs] def set_type(self, type_): self.type_ = type_
[docs] def get_material(self): return self.material
[docs] def set_material(self, material): self.material = material
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def validate_typeType(self, value): # Validate type typeType, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['NEGATIVE', 'POSITIVE'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on typeType' % {"value" : value.encode("utf-8")} )
[docs] def hasContent_(self): if ( self.type_ is not None or self.material is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='stainingType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='stainingType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='stainingType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='stainingType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='stainingType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.type_ is not None: showIndent(outfile, level, pretty_print) outfile.write('<%stype>%s</%stype>%s' % (namespace_, self.gds_format_string(quote_xml(self.type_).encode(ExternalEncoding), input_name='type'), namespace_, eol_)) if self.material is not None: showIndent(outfile, level, pretty_print) outfile.write('<%smaterial>%s</%smaterial>%s' % (namespace_, self.gds_format_string(quote_xml(self.material).encode(ExternalEncoding), input_name='material'), namespace_, eol_)) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'type': type_ = child_.text type_ = re_.sub(String_cleanup_pat_, " ", type_).strip() type_ = self.gds_validate_string(type_, node, 'type') self.type_ = type_ # validate type typeType self.validate_typeType(self.type_) elif nodeName_ == 'material': material_ = child_.text material_ = re_.sub(String_cleanup_pat_, " ", material_).strip() material_ = self.gds_validate_string(material_, node, 'material') self.material = material_ elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class stainingType
[docs]class sugar_embeddingType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('material', ['materialType4', 'xs:token'], 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, material=None, details=None): self.original_tagname_ = None self.material = material self.validate_materialType4(self.material) self.details = details
[docs] def factory(*args_, **kwargs_): if sugar_embeddingType.subclass: return sugar_embeddingType.subclass(*args_, **kwargs_) else: return sugar_embeddingType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_material(self): return self.material
[docs] def set_material(self, material): self.material = material
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def validate_materialType4(self, value): # Validate type materialType4, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['GLUCOSE', 'TREHALOSE', 'TANNIC ACID'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on materialType4' % {"value" : value.encode("utf-8")} )
[docs] def hasContent_(self): if ( self.material is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='sugar_embeddingType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='sugar_embeddingType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='sugar_embeddingType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='sugar_embeddingType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='sugar_embeddingType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.material is not None: showIndent(outfile, level, pretty_print) outfile.write('<%smaterial>%s</%smaterial>%s' % (namespace_, self.gds_format_string(quote_xml(self.material).encode(ExternalEncoding), input_name='material'), namespace_, eol_)) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'material': material_ = child_.text material_ = re_.sub(String_cleanup_pat_, " ", material_).strip() material_ = self.gds_validate_string(material_, node, 'material') self.material = material_ # validate type materialType4 self.validate_materialType4(self.material) elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class sugar_embeddingType
[docs]class shadowingType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('material', 'xs:token', 0), MemberSpec_('angle', 'angleType', 0), MemberSpec_('thickness', 'thicknessType', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, material=None, angle=None, thickness=None, details=None): self.original_tagname_ = None self.material = material self.angle = angle self.thickness = thickness self.details = details
[docs] def factory(*args_, **kwargs_): if shadowingType.subclass: return shadowingType.subclass(*args_, **kwargs_) else: return shadowingType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_material(self): return self.material
[docs] def set_material(self, material): self.material = material
[docs] def get_angle(self): return self.angle
[docs] def set_angle(self, angle): self.angle = angle
[docs] def get_thickness(self): return self.thickness
[docs] def set_thickness(self, thickness): self.thickness = thickness
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def hasContent_(self): if ( self.material is not None or self.angle is not None or self.thickness is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='shadowingType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='shadowingType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='shadowingType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='shadowingType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='shadowingType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.material is not None: showIndent(outfile, level, pretty_print) outfile.write('<%smaterial>%s</%smaterial>%s' % (namespace_, self.gds_format_string(quote_xml(self.material).encode(ExternalEncoding), input_name='material'), namespace_, eol_)) if self.angle is not None: self.angle.export(outfile, level, namespace_, name_='angle', pretty_print=pretty_print) if self.thickness is not None: self.thickness.export(outfile, level, namespace_, name_='thickness', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'material': material_ = child_.text material_ = re_.sub(String_cleanup_pat_, " ", material_).strip() material_ = self.gds_validate_string(material_, node, 'material') self.material = material_ elif nodeName_ == 'angle': obj_ = angleType.factory() obj_.build(child_) self.angle = obj_ obj_.original_tagname_ = 'angle' elif nodeName_ == 'thickness': obj_ = thicknessType.factory() obj_.build(child_) self.thickness = obj_ obj_.original_tagname_ = 'thickness' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class shadowingType
[docs]class angleType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_angle_shadowing', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if angleType.subclass: return angleType.subclass(*args_, **kwargs_) else: return angleType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='angleType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='angleType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='angleType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='angleType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='angleType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class angleType
[docs]class thicknessType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_thickness_shadowing', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if thicknessType.subclass: return thicknessType.subclass(*args_, **kwargs_) else: return thicknessType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='thicknessType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='thicknessType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='thicknessType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='thicknessType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='thicknessType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class thicknessType
[docs]class fiducial_markers_listType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('fiducial_marker', 'fiducial_marker_type', 1), ] subclass = None superclass = None def __init__(self, fiducial_marker=None): self.original_tagname_ = None if fiducial_marker is None: self.fiducial_marker = [] else: self.fiducial_marker = fiducial_marker
[docs] def factory(*args_, **kwargs_): if fiducial_markers_listType.subclass: return fiducial_markers_listType.subclass(*args_, **kwargs_) else: return fiducial_markers_listType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_fiducial_marker(self): return self.fiducial_marker
[docs] def set_fiducial_marker(self, fiducial_marker): self.fiducial_marker = fiducial_marker
[docs] def add_fiducial_marker(self, value): self.fiducial_marker.append(value)
[docs] def insert_fiducial_marker_at(self, index, value): self.fiducial_marker.insert(index, value)
[docs] def replace_fiducial_marker_at(self, index, value): self.fiducial_marker[index] = value
[docs] def hasContent_(self): if ( self.fiducial_marker ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='fiducial_markers_listType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='fiducial_markers_listType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='fiducial_markers_listType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='fiducial_markers_listType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='fiducial_markers_listType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for fiducial_marker_ in self.fiducial_marker: fiducial_marker_.export(outfile, level, namespace_, name_='fiducial_marker', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'fiducial_marker': obj_ = fiducial_marker_type.factory() obj_.build(child_) self.fiducial_marker.append(obj_) obj_.original_tagname_ = 'fiducial_marker' # end class fiducial_markers_listType
[docs]class high_pressure_freezingType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('instrument', ['instrumentType5', 'xs:token'], 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, instrument=None, details=None): self.original_tagname_ = None self.instrument = instrument self.validate_instrumentType5(self.instrument) self.details = details
[docs] def factory(*args_, **kwargs_): if high_pressure_freezingType.subclass: return high_pressure_freezingType.subclass(*args_, **kwargs_) else: return high_pressure_freezingType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_instrument(self): return self.instrument
[docs] def set_instrument(self, instrument): self.instrument = instrument
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def validate_instrumentType5(self, value): # Validate type instrumentType5, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['BAL-TEC HPM 010', 'EMS-002 RAPID IMMERSION FREEZER', 'LEICA EM HPM100', 'LEICA EM PACT', 'LEICA EM PACT2'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on instrumentType5' % {"value" : value.encode("utf-8")} )
[docs] def hasContent_(self): if ( self.instrument is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='high_pressure_freezingType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='high_pressure_freezingType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='high_pressure_freezingType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='high_pressure_freezingType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='high_pressure_freezingType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.instrument is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sinstrument>%s</%sinstrument>%s' % (namespace_, self.gds_format_string(quote_xml(self.instrument).encode(ExternalEncoding), input_name='instrument'), namespace_, eol_)) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'instrument': instrument_ = child_.text instrument_ = re_.sub(String_cleanup_pat_, " ", instrument_).strip() instrument_ = self.gds_validate_string(instrument_, node, 'instrument') self.instrument = instrument_ # validate type instrumentType5 self.validate_instrumentType5(self.instrument) elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class high_pressure_freezingType
[docs]class sectioningType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('ultramicrotomy', 'ultramicrotomyType', 0), MemberSpec_('focused_ion_beam', 'focused_ion_beamType', 0), MemberSpec_('other_sectioning', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, ultramicrotomy=None, focused_ion_beam=None, other_sectioning=None): self.original_tagname_ = None self.ultramicrotomy = ultramicrotomy self.focused_ion_beam = focused_ion_beam self.other_sectioning = other_sectioning
[docs] def factory(*args_, **kwargs_): if sectioningType.subclass: return sectioningType.subclass(*args_, **kwargs_) else: return sectioningType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_ultramicrotomy(self): return self.ultramicrotomy
[docs] def set_ultramicrotomy(self, ultramicrotomy): self.ultramicrotomy = ultramicrotomy
[docs] def get_focused_ion_beam(self): return self.focused_ion_beam
[docs] def set_focused_ion_beam(self, focused_ion_beam): self.focused_ion_beam = focused_ion_beam
[docs] def get_other_sectioning(self): return self.other_sectioning
[docs] def set_other_sectioning(self, other_sectioning): self.other_sectioning = other_sectioning
[docs] def hasContent_(self): if ( self.ultramicrotomy is not None or self.focused_ion_beam is not None or self.other_sectioning is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='sectioningType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='sectioningType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='sectioningType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='sectioningType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='sectioningType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.ultramicrotomy is not None: self.ultramicrotomy.export(outfile, level, namespace_, name_='ultramicrotomy', pretty_print=pretty_print) if self.focused_ion_beam is not None: self.focused_ion_beam.export(outfile, level, namespace_, name_='focused_ion_beam', pretty_print=pretty_print) if self.other_sectioning is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sother_sectioning>%s</%sother_sectioning>%s' % (namespace_, self.gds_format_string(quote_xml(self.other_sectioning).encode(ExternalEncoding), input_name='other_sectioning'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'ultramicrotomy': obj_ = ultramicrotomyType.factory() obj_.build(child_) self.ultramicrotomy = obj_ obj_.original_tagname_ = 'ultramicrotomy' elif nodeName_ == 'focused_ion_beam': obj_ = focused_ion_beamType.factory() obj_.build(child_) self.focused_ion_beam = obj_ obj_.original_tagname_ = 'focused_ion_beam' elif nodeName_ == 'other_sectioning': other_sectioning_ = child_.text other_sectioning_ = self.gds_validate_string(other_sectioning_, node, 'other_sectioning') self.other_sectioning = other_sectioning_ # end class sectioningType
[docs]class ultramicrotomyType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('instrument', 'xs:token', 0), MemberSpec_('temperature', 'temperature_type', 0), MemberSpec_('final_thickness', 'ultramicrotomy_final_thickness_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, instrument=None, temperature=None, final_thickness=None, details=None): self.original_tagname_ = None self.instrument = instrument self.temperature = temperature self.final_thickness = final_thickness self.details = details
[docs] def factory(*args_, **kwargs_): if ultramicrotomyType.subclass: return ultramicrotomyType.subclass(*args_, **kwargs_) else: return ultramicrotomyType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_instrument(self): return self.instrument
[docs] def set_instrument(self, instrument): self.instrument = instrument
[docs] def get_temperature(self): return self.temperature
[docs] def set_temperature(self, temperature): self.temperature = temperature
[docs] def get_final_thickness(self): return self.final_thickness
[docs] def set_final_thickness(self, final_thickness): self.final_thickness = final_thickness
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def hasContent_(self): if ( self.instrument is not None or self.temperature is not None or self.final_thickness is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='ultramicrotomyType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='ultramicrotomyType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='ultramicrotomyType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='ultramicrotomyType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='ultramicrotomyType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.instrument is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sinstrument>%s</%sinstrument>%s' % (namespace_, self.gds_format_string(quote_xml(self.instrument).encode(ExternalEncoding), input_name='instrument'), namespace_, eol_)) if self.temperature is not None: self.temperature.export(outfile, level, namespace_, name_='temperature', pretty_print=pretty_print) if self.final_thickness is not None: self.final_thickness.export(outfile, level, namespace_, name_='final_thickness', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'instrument': instrument_ = child_.text instrument_ = re_.sub(String_cleanup_pat_, " ", instrument_).strip() instrument_ = self.gds_validate_string(instrument_, node, 'instrument') self.instrument = instrument_ elif nodeName_ == 'temperature': obj_ = temperature_type.factory() obj_.build(child_) self.temperature = obj_ obj_.original_tagname_ = 'temperature' elif nodeName_ == 'final_thickness': obj_ = ultramicrotomy_final_thickness_type.factory() obj_.build(child_) self.final_thickness = obj_ obj_.original_tagname_ = 'final_thickness' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class ultramicrotomyType
[docs]class focused_ion_beamType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('instrument', ['instrumentType6', 'xs:token'], 0), MemberSpec_('ion', ['ionType', 'xs:token'], 0), MemberSpec_('voltage', 'fib_voltage_type', 0), MemberSpec_('current', 'fib_current_type', 0), MemberSpec_('dose_rate', 'fib_dose_rate_type', 0), MemberSpec_('duration', 'fib_duration_type', 0), MemberSpec_('temperature', 'temperature_type', 0), MemberSpec_('initial_thickness', 'fib_initial_thickness_type', 0), MemberSpec_('final_thickness', 'fib_final_thickness_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, instrument=None, ion=None, voltage=None, current=None, dose_rate=None, duration=None, temperature=None, initial_thickness=None, final_thickness=None, details=None): self.original_tagname_ = None self.instrument = instrument self.validate_instrumentType6(self.instrument) self.ion = ion self.validate_ionType(self.ion) self.voltage = voltage self.current = current self.dose_rate = dose_rate self.duration = duration self.temperature = temperature self.initial_thickness = initial_thickness self.final_thickness = final_thickness self.details = details
[docs] def factory(*args_, **kwargs_): if focused_ion_beamType.subclass: return focused_ion_beamType.subclass(*args_, **kwargs_) else: return focused_ion_beamType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_instrument(self): return self.instrument
[docs] def set_instrument(self, instrument): self.instrument = instrument
[docs] def get_ion(self): return self.ion
[docs] def set_ion(self, ion): self.ion = ion
[docs] def get_voltage(self): return self.voltage
[docs] def set_voltage(self, voltage): self.voltage = voltage
[docs] def get_current(self): return self.current
[docs] def set_current(self, current): self.current = current
[docs] def get_dose_rate(self): return self.dose_rate
[docs] def set_dose_rate(self, dose_rate): self.dose_rate = dose_rate
[docs] def get_duration(self): return self.duration
[docs] def set_duration(self, duration): self.duration = duration
[docs] def get_temperature(self): return self.temperature
[docs] def set_temperature(self, temperature): self.temperature = temperature
[docs] def get_initial_thickness(self): return self.initial_thickness
[docs] def set_initial_thickness(self, initial_thickness): self.initial_thickness = initial_thickness
[docs] def get_final_thickness(self): return self.final_thickness
[docs] def set_final_thickness(self, final_thickness): self.final_thickness = final_thickness
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def validate_instrumentType6(self, value): # Validate type instrumentType6, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['DB235'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on instrumentType6' % {"value" : value.encode("utf-8")} )
[docs] def validate_ionType(self, value): # Validate type ionType, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['GALLIUM+'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on ionType' % {"value" : value.encode("utf-8")} )
[docs] def hasContent_(self): if ( self.instrument is not None or self.ion is not None or self.voltage is not None or self.current is not None or self.dose_rate is not None or self.duration is not None or self.temperature is not None or self.initial_thickness is not None or self.final_thickness is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='focused_ion_beamType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='focused_ion_beamType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='focused_ion_beamType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='focused_ion_beamType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='focused_ion_beamType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.instrument is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sinstrument>%s</%sinstrument>%s' % (namespace_, self.gds_format_string(quote_xml(self.instrument).encode(ExternalEncoding), input_name='instrument'), namespace_, eol_)) if self.ion is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sion>%s</%sion>%s' % (namespace_, self.gds_format_string(quote_xml(self.ion).encode(ExternalEncoding), input_name='ion'), namespace_, eol_)) if self.voltage is not None: self.voltage.export(outfile, level, namespace_, name_='voltage', pretty_print=pretty_print) if self.current is not None: self.current.export(outfile, level, namespace_, name_='current', pretty_print=pretty_print) if self.dose_rate is not None: self.dose_rate.export(outfile, level, namespace_, name_='dose_rate', pretty_print=pretty_print) if self.duration is not None: self.duration.export(outfile, level, namespace_, name_='duration', pretty_print=pretty_print) if self.temperature is not None: self.temperature.export(outfile, level, namespace_, name_='temperature', pretty_print=pretty_print) if self.initial_thickness is not None: self.initial_thickness.export(outfile, level, namespace_, name_='initial_thickness', pretty_print=pretty_print) if self.final_thickness is not None: self.final_thickness.export(outfile, level, namespace_, name_='final_thickness', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'instrument': instrument_ = child_.text instrument_ = re_.sub(String_cleanup_pat_, " ", instrument_).strip() instrument_ = self.gds_validate_string(instrument_, node, 'instrument') self.instrument = instrument_ # validate type instrumentType6 self.validate_instrumentType6(self.instrument) elif nodeName_ == 'ion': ion_ = child_.text ion_ = re_.sub(String_cleanup_pat_, " ", ion_).strip() ion_ = self.gds_validate_string(ion_, node, 'ion') self.ion = ion_ # validate type ionType self.validate_ionType(self.ion) elif nodeName_ == 'voltage': obj_ = fib_voltage_type.factory() obj_.build(child_) self.voltage = obj_ obj_.original_tagname_ = 'voltage' elif nodeName_ == 'current': obj_ = fib_current_type.factory() obj_.build(child_) self.current = obj_ obj_.original_tagname_ = 'current' elif nodeName_ == 'dose_rate': obj_ = fib_dose_rate_type.factory() obj_.build(child_) self.dose_rate = obj_ obj_.original_tagname_ = 'dose_rate' elif nodeName_ == 'duration': obj_ = fib_duration_type.factory() obj_.build(child_) self.duration = obj_ obj_.original_tagname_ = 'duration' elif nodeName_ == 'temperature': obj_ = temperature_type.factory() obj_.build(child_) self.temperature = obj_ obj_.original_tagname_ = 'temperature' elif nodeName_ == 'initial_thickness': obj_ = fib_initial_thickness_type.factory() obj_.build(child_) self.initial_thickness = obj_ obj_.original_tagname_ = 'initial_thickness' elif nodeName_ == 'final_thickness': obj_ = fib_final_thickness_type.factory() obj_.build(child_) self.final_thickness = obj_ obj_.original_tagname_ = 'final_thickness' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class focused_ion_beamType
[docs]class specimen_preparationsType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('specimen_preparation_id', 'xs:positiveInteger', 1), ] subclass = None superclass = None def __init__(self, specimen_preparation_id=None): self.original_tagname_ = None if specimen_preparation_id is None: self.specimen_preparation_id = [] else: self.specimen_preparation_id = specimen_preparation_id
[docs] def factory(*args_, **kwargs_): if specimen_preparationsType.subclass: return specimen_preparationsType.subclass(*args_, **kwargs_) else: return specimen_preparationsType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_specimen_preparation_id(self): return self.specimen_preparation_id
[docs] def set_specimen_preparation_id(self, specimen_preparation_id): self.specimen_preparation_id = specimen_preparation_id
[docs] def add_specimen_preparation_id(self, value): self.specimen_preparation_id.append(value)
[docs] def insert_specimen_preparation_id_at(self, index, value): self.specimen_preparation_id.insert(index, value)
[docs] def replace_specimen_preparation_id_at(self, index, value): self.specimen_preparation_id[index] = value
[docs] def hasContent_(self): if ( self.specimen_preparation_id ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='specimen_preparationsType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='specimen_preparationsType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='specimen_preparationsType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='specimen_preparationsType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='specimen_preparationsType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for specimen_preparation_id_ in self.specimen_preparation_id: showIndent(outfile, level, pretty_print) outfile.write('<%sspecimen_preparation_id>%s</%sspecimen_preparation_id>%s' % (namespace_, self.gds_format_integer(specimen_preparation_id_, input_name='specimen_preparation_id'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'specimen_preparation_id': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'specimen_preparation_id') self.specimen_preparation_id.append(ival_) # end class specimen_preparationsType
[docs]class acceleration_voltageType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_acceleration_voltage', 'xs:positiveInteger'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if acceleration_voltageType.subclass: return acceleration_voltageType.subclass(*args_, **kwargs_) else: return acceleration_voltageType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='acceleration_voltageType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='acceleration_voltageType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='acceleration_voltageType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='acceleration_voltageType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='acceleration_voltageType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class acceleration_voltageType
[docs]class c2_aperture_diameterType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_c2_aperture_diameter', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if c2_aperture_diameterType.subclass: return c2_aperture_diameterType.subclass(*args_, **kwargs_) else: return c2_aperture_diameterType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='c2_aperture_diameterType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='c2_aperture_diameterType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='c2_aperture_diameterType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='c2_aperture_diameterType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='c2_aperture_diameterType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class c2_aperture_diameterType
[docs]class nominal_csType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_nominal_cs', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if nominal_csType.subclass: return nominal_csType.subclass(*args_, **kwargs_) else: return nominal_csType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='nominal_csType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='nominal_csType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='nominal_csType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='nominal_csType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='nominal_csType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class nominal_csType
[docs]class nominal_defocus_minType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_defocus_min', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if nominal_defocus_minType.subclass: return nominal_defocus_minType.subclass(*args_, **kwargs_) else: return nominal_defocus_minType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='nominal_defocus_minType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='nominal_defocus_minType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='nominal_defocus_minType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='nominal_defocus_minType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='nominal_defocus_minType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class nominal_defocus_minType
[docs]class calibrated_defocus_minType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_defocus_min', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if calibrated_defocus_minType.subclass: return calibrated_defocus_minType.subclass(*args_, **kwargs_) else: return calibrated_defocus_minType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='calibrated_defocus_minType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='calibrated_defocus_minType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='calibrated_defocus_minType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='calibrated_defocus_minType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='calibrated_defocus_minType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class calibrated_defocus_minType
[docs]class nominal_defocus_maxType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_defocus_max', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if nominal_defocus_maxType.subclass: return nominal_defocus_maxType.subclass(*args_, **kwargs_) else: return nominal_defocus_maxType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='nominal_defocus_maxType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='nominal_defocus_maxType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='nominal_defocus_maxType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='nominal_defocus_maxType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='nominal_defocus_maxType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class nominal_defocus_maxType
[docs]class calibrated_defocus_maxType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_defocus_max', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if calibrated_defocus_maxType.subclass: return calibrated_defocus_maxType.subclass(*args_, **kwargs_) else: return calibrated_defocus_maxType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='calibrated_defocus_maxType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='calibrated_defocus_maxType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='calibrated_defocus_maxType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='calibrated_defocus_maxType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='calibrated_defocus_maxType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class calibrated_defocus_maxType
[docs]class temperatureType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('temperature_min', 'temperature_minType', 0), MemberSpec_('temperature_max', 'temperature_maxType', 0), MemberSpec_('temperature_average', 'temperature_averageType', 0), ] subclass = None superclass = None def __init__(self, temperature_min=None, temperature_max=None, temperature_average=None): self.original_tagname_ = None self.temperature_min = temperature_min self.temperature_max = temperature_max self.temperature_average = temperature_average
[docs] def factory(*args_, **kwargs_): if temperatureType.subclass: return temperatureType.subclass(*args_, **kwargs_) else: return temperatureType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_temperature_min(self): return self.temperature_min
[docs] def set_temperature_min(self, temperature_min): self.temperature_min = temperature_min
[docs] def get_temperature_max(self): return self.temperature_max
[docs] def set_temperature_max(self, temperature_max): self.temperature_max = temperature_max
[docs] def get_temperature_average(self): return self.temperature_average
[docs] def set_temperature_average(self, temperature_average): self.temperature_average = temperature_average
[docs] def hasContent_(self): if ( self.temperature_min is not None or self.temperature_max is not None or self.temperature_average is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='temperatureType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='temperatureType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='temperatureType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='temperatureType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='temperatureType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.temperature_min is not None: self.temperature_min.export(outfile, level, namespace_, name_='temperature_min', pretty_print=pretty_print) if self.temperature_max is not None: self.temperature_max.export(outfile, level, namespace_, name_='temperature_max', pretty_print=pretty_print) if self.temperature_average is not None: self.temperature_average.export(outfile, level, namespace_, name_='temperature_average', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'temperature_min': obj_ = temperature_minType.factory() obj_.build(child_) self.temperature_min = obj_ obj_.original_tagname_ = 'temperature_min' elif nodeName_ == 'temperature_max': obj_ = temperature_maxType.factory() obj_.build(child_) self.temperature_max = obj_ obj_.original_tagname_ = 'temperature_max' elif nodeName_ == 'temperature_average': obj_ = temperature_averageType.factory() obj_.build(child_) self.temperature_average = obj_ obj_.original_tagname_ = 'temperature_average' # end class temperatureType
[docs]class temperature_minType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['complex_category_type', 'xs:token'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if temperature_minType.subclass: return temperature_minType.subclass(*args_, **kwargs_) else: return temperature_minType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='temperature_minType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='temperature_minType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='temperature_minType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='temperature_minType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='temperature_minType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class temperature_minType
[docs]class temperature_maxType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['complex_category_type', 'xs:token'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if temperature_maxType.subclass: return temperature_maxType.subclass(*args_, **kwargs_) else: return temperature_maxType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='temperature_maxType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='temperature_maxType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='temperature_maxType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='temperature_maxType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='temperature_maxType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class temperature_maxType
[docs]class temperature_averageType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['complex_category_type', 'xs:token'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if temperature_averageType.subclass: return temperature_averageType.subclass(*args_, **kwargs_) else: return temperature_averageType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='temperature_averageType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='temperature_averageType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='temperature_averageType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='temperature_averageType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='temperature_averageType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class temperature_averageType
[docs]class alignment_procedureType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('none', 'noneType', 0), MemberSpec_('basic', 'basicType', 0), MemberSpec_('zemlin_tableau', 'zemlin_tableauType', 0), MemberSpec_('coma_free', 'coma_freeType', 0), MemberSpec_('other', 'otherType', 0), MemberSpec_('legacy', 'legacyType', 0), ] subclass = None superclass = None def __init__(self, none=None, basic=None, zemlin_tableau=None, coma_free=None, other=None, legacy=None): self.original_tagname_ = None self.none = none self.basic = basic self.zemlin_tableau = zemlin_tableau self.coma_free = coma_free self.other = other self.legacy = legacy
[docs] def factory(*args_, **kwargs_): if alignment_procedureType.subclass: return alignment_procedureType.subclass(*args_, **kwargs_) else: return alignment_procedureType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_none(self): return self.none
[docs] def set_none(self, none): self.none = none
[docs] def get_basic(self): return self.basic
[docs] def set_basic(self, basic): self.basic = basic
[docs] def get_zemlin_tableau(self): return self.zemlin_tableau
[docs] def set_zemlin_tableau(self, zemlin_tableau): self.zemlin_tableau = zemlin_tableau
[docs] def get_coma_free(self): return self.coma_free
[docs] def set_coma_free(self, coma_free): self.coma_free = coma_free
[docs] def get_other(self): return self.other
[docs] def set_other(self, other): self.other = other
[docs] def get_legacy(self): return self.legacy
[docs] def set_legacy(self, legacy): self.legacy = legacy
[docs] def hasContent_(self): if ( self.none is not None or self.basic is not None or self.zemlin_tableau is not None or self.coma_free is not None or self.other is not None or self.legacy is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='alignment_procedureType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='alignment_procedureType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='alignment_procedureType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='alignment_procedureType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='alignment_procedureType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.none is not None: self.none.export(outfile, level, namespace_, name_='none', pretty_print=pretty_print) if self.basic is not None: self.basic.export(outfile, level, namespace_, name_='basic', pretty_print=pretty_print) if self.zemlin_tableau is not None: self.zemlin_tableau.export(outfile, level, namespace_, name_='zemlin_tableau', pretty_print=pretty_print) if self.coma_free is not None: self.coma_free.export(outfile, level, namespace_, name_='coma_free', pretty_print=pretty_print) if self.other is not None: self.other.export(outfile, level, namespace_, name_='other', pretty_print=pretty_print) if self.legacy is not None: self.legacy.export(outfile, level, namespace_, name_='legacy', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'none': obj_ = noneType.factory() obj_.build(child_) self.none = obj_ obj_.original_tagname_ = 'none' elif nodeName_ == 'basic': obj_ = basicType.factory() obj_.build(child_) self.basic = obj_ obj_.original_tagname_ = 'basic' elif nodeName_ == 'zemlin_tableau': obj_ = zemlin_tableauType.factory() obj_.build(child_) self.zemlin_tableau = obj_ obj_.original_tagname_ = 'zemlin_tableau' elif nodeName_ == 'coma_free': obj_ = coma_freeType.factory() obj_.build(child_) self.coma_free = obj_ obj_.original_tagname_ = 'coma_free' elif nodeName_ == 'other': obj_ = otherType.factory() obj_.build(child_) self.other = obj_ obj_.original_tagname_ = 'other' elif nodeName_ == 'legacy': obj_ = legacyType.factory() obj_.build(child_) self.legacy = obj_ obj_.original_tagname_ = 'legacy' # end class alignment_procedureType
[docs]class noneType(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if noneType.subclass: return noneType.subclass(*args_, **kwargs_) else: return noneType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='noneType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='noneType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='noneType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='noneType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='noneType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class noneType
[docs]class basicType(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if basicType.subclass: return basicType.subclass(*args_, **kwargs_) else: return basicType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='basicType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='basicType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='basicType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='basicType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='basicType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class basicType
[docs]class zemlin_tableauType(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if zemlin_tableauType.subclass: return zemlin_tableauType.subclass(*args_, **kwargs_) else: return zemlin_tableauType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='zemlin_tableauType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='zemlin_tableauType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='zemlin_tableauType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='zemlin_tableauType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='zemlin_tableauType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class zemlin_tableauType
[docs]class coma_freeType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('residual_tilt', 'xs:float', 0), ] subclass = None superclass = None def __init__(self, residual_tilt=None): self.original_tagname_ = None self.residual_tilt = residual_tilt
[docs] def factory(*args_, **kwargs_): if coma_freeType.subclass: return coma_freeType.subclass(*args_, **kwargs_) else: return coma_freeType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_residual_tilt(self): return self.residual_tilt
[docs] def set_residual_tilt(self, residual_tilt): self.residual_tilt = residual_tilt
[docs] def hasContent_(self): if ( self.residual_tilt is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='coma_freeType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='coma_freeType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='coma_freeType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='coma_freeType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='coma_freeType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.residual_tilt is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sresidual_tilt>%s</%sresidual_tilt>%s' % (namespace_, self.gds_format_float(self.residual_tilt, input_name='residual_tilt'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'residual_tilt': sval_ = child_.text try: fval_ = float(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires float or double: %s' % exp) fval_ = self.gds_validate_float(fval_, node, 'residual_tilt') self.residual_tilt = fval_ # end class coma_freeType
[docs]class otherType(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if otherType.subclass: return otherType.subclass(*args_, **kwargs_) else: return otherType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='otherType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='otherType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='otherType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='otherType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='otherType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class otherType
[docs]class legacyType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('astigmatism', 'xs:string', 0), MemberSpec_('electron_beam_tilt_params', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, astigmatism=None, electron_beam_tilt_params=None): self.original_tagname_ = None self.astigmatism = astigmatism self.electron_beam_tilt_params = electron_beam_tilt_params
[docs] def factory(*args_, **kwargs_): if legacyType.subclass: return legacyType.subclass(*args_, **kwargs_) else: return legacyType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_astigmatism(self): return self.astigmatism
[docs] def set_astigmatism(self, astigmatism): self.astigmatism = astigmatism
[docs] def get_electron_beam_tilt_params(self): return self.electron_beam_tilt_params
[docs] def set_electron_beam_tilt_params(self, electron_beam_tilt_params): self.electron_beam_tilt_params = electron_beam_tilt_params
[docs] def hasContent_(self): if ( self.astigmatism is not None or self.electron_beam_tilt_params is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='legacyType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='legacyType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='legacyType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='legacyType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='legacyType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.astigmatism is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sastigmatism>%s</%sastigmatism>%s' % (namespace_, self.gds_format_string(quote_xml(self.astigmatism).encode(ExternalEncoding), input_name='astigmatism'), namespace_, eol_)) if self.electron_beam_tilt_params is not None: showIndent(outfile, level, pretty_print) outfile.write('<%selectron_beam_tilt_params>%s</%selectron_beam_tilt_params>%s' % (namespace_, self.gds_format_string(quote_xml(self.electron_beam_tilt_params).encode(ExternalEncoding), input_name='electron_beam_tilt_params'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'astigmatism': astigmatism_ = child_.text astigmatism_ = self.gds_validate_string(astigmatism_, node, 'astigmatism') self.astigmatism = astigmatism_ elif nodeName_ == 'electron_beam_tilt_params': electron_beam_tilt_params_ = child_.text electron_beam_tilt_params_ = self.gds_validate_string(electron_beam_tilt_params_, node, 'electron_beam_tilt_params') self.electron_beam_tilt_params = electron_beam_tilt_params_ # end class legacyType
[docs]class image_recording_listType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('image_recording', 'image_recordingType', 1), ] subclass = None superclass = None def __init__(self, image_recording=None): self.original_tagname_ = None if image_recording is None: self.image_recording = [] else: self.image_recording = image_recording
[docs] def factory(*args_, **kwargs_): if image_recording_listType.subclass: return image_recording_listType.subclass(*args_, **kwargs_) else: return image_recording_listType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_image_recording(self): return self.image_recording
[docs] def set_image_recording(self, image_recording): self.image_recording = image_recording
[docs] def add_image_recording(self, value): self.image_recording.append(value)
[docs] def insert_image_recording_at(self, index, value): self.image_recording.insert(index, value)
[docs] def replace_image_recording_at(self, index, value): self.image_recording[index] = value
[docs] def hasContent_(self): if ( self.image_recording ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='image_recording_listType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='image_recording_listType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='image_recording_listType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='image_recording_listType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='image_recording_listType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for image_recording_ in self.image_recording: image_recording_.export(outfile, level, namespace_, name_='image_recording', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'image_recording': obj_ = image_recordingType.factory() obj_.build(child_) self.image_recording.append(obj_) obj_.original_tagname_ = 'image_recording' # end class image_recording_listType
[docs]class image_recordingType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('id', 'xs:positiveInteger', 0), MemberSpec_('film_or_detector_model', 'film_or_detector_modelType', 0), MemberSpec_('detector_mode', ['detector_modeType', 'xs:token'], 0), MemberSpec_('digitization_details', 'digitization_detailsType', 0), MemberSpec_('number_grids_imaged', 'xs:positiveInteger', 0), MemberSpec_('number_real_images', 'xs:positiveInteger', 0), MemberSpec_('number_diffraction_images', 'xs:positiveInteger', 0), MemberSpec_('average_exposure_time', 'average_exposure_timeType', 0), MemberSpec_('average_electron_dose_per_image', 'average_electron_dose_per_imageType', 0), MemberSpec_('detector_distance', 'xs:string', 0), MemberSpec_('details', 'xs:string', 0), MemberSpec_('od_range', 'xs:float', 0), MemberSpec_('bits_per_pixel', 'xs:float', 0), ] subclass = None superclass = None def __init__(self, id=None, film_or_detector_model=None, detector_mode=None, digitization_details=None, number_grids_imaged=None, number_real_images=None, number_diffraction_images=None, average_exposure_time=None, average_electron_dose_per_image=None, detector_distance=None, details=None, od_range=None, bits_per_pixel=None): self.original_tagname_ = None self.id = _cast(int, id) self.film_or_detector_model = film_or_detector_model self.detector_mode = detector_mode self.validate_detector_modeType(self.detector_mode) self.digitization_details = digitization_details self.number_grids_imaged = number_grids_imaged self.number_real_images = number_real_images self.number_diffraction_images = number_diffraction_images self.average_exposure_time = average_exposure_time self.average_electron_dose_per_image = average_electron_dose_per_image self.detector_distance = detector_distance self.details = details self.od_range = od_range self.bits_per_pixel = bits_per_pixel
[docs] def factory(*args_, **kwargs_): if image_recordingType.subclass: return image_recordingType.subclass(*args_, **kwargs_) else: return image_recordingType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_film_or_detector_model(self): return self.film_or_detector_model
[docs] def set_film_or_detector_model(self, film_or_detector_model): self.film_or_detector_model = film_or_detector_model
[docs] def get_detector_mode(self): return self.detector_mode
[docs] def set_detector_mode(self, detector_mode): self.detector_mode = detector_mode
[docs] def get_digitization_details(self): return self.digitization_details
[docs] def set_digitization_details(self, digitization_details): self.digitization_details = digitization_details
[docs] def get_number_grids_imaged(self): return self.number_grids_imaged
[docs] def set_number_grids_imaged(self, number_grids_imaged): self.number_grids_imaged = number_grids_imaged
[docs] def get_number_real_images(self): return self.number_real_images
[docs] def set_number_real_images(self, number_real_images): self.number_real_images = number_real_images
[docs] def get_number_diffraction_images(self): return self.number_diffraction_images
[docs] def set_number_diffraction_images(self, number_diffraction_images): self.number_diffraction_images = number_diffraction_images
[docs] def get_average_exposure_time(self): return self.average_exposure_time
[docs] def set_average_exposure_time(self, average_exposure_time): self.average_exposure_time = average_exposure_time
[docs] def get_average_electron_dose_per_image(self): return self.average_electron_dose_per_image
[docs] def set_average_electron_dose_per_image(self, average_electron_dose_per_image): self.average_electron_dose_per_image = average_electron_dose_per_image
[docs] def get_detector_distance(self): return self.detector_distance
[docs] def set_detector_distance(self, detector_distance): self.detector_distance = detector_distance
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def get_od_range(self): return self.od_range
[docs] def set_od_range(self, od_range): self.od_range = od_range
[docs] def get_bits_per_pixel(self): return self.bits_per_pixel
[docs] def set_bits_per_pixel(self, bits_per_pixel): self.bits_per_pixel = bits_per_pixel
[docs] def get_id(self): return self.id
[docs] def set_id(self, id): self.id = id
[docs] def validate_detector_modeType(self, value): # Validate type detector_modeType, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['COUNTING', 'INTEGRATING', 'SUPER-RESOLUTION'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on detector_modeType' % {"value" : value.encode("utf-8")} )
[docs] def hasContent_(self): if ( self.film_or_detector_model is not None or self.detector_mode is not None or self.digitization_details is not None or self.number_grids_imaged is not None or self.number_real_images is not None or self.number_diffraction_images is not None or self.average_exposure_time is not None or self.average_electron_dose_per_image is not None or self.detector_distance is not None or self.details is not None or self.od_range is not None or self.bits_per_pixel is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='image_recordingType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='image_recordingType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='image_recordingType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='image_recordingType'): if self.id is not None and 'id' not in already_processed: already_processed.add('id') outfile.write(' id="%s"' % self.gds_format_integer(self.id, input_name='id'))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='image_recordingType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.film_or_detector_model is not None: self.film_or_detector_model.export(outfile, level, namespace_, name_='film_or_detector_model', pretty_print=pretty_print) if self.detector_mode is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetector_mode>%s</%sdetector_mode>%s' % (namespace_, self.gds_format_string(quote_xml(self.detector_mode).encode(ExternalEncoding), input_name='detector_mode'), namespace_, eol_)) if self.digitization_details is not None: self.digitization_details.export(outfile, level, namespace_, name_='digitization_details', pretty_print=pretty_print) if self.number_grids_imaged is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_grids_imaged>%s</%snumber_grids_imaged>%s' % (namespace_, self.gds_format_integer(self.number_grids_imaged, input_name='number_grids_imaged'), namespace_, eol_)) if self.number_real_images is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_real_images>%s</%snumber_real_images>%s' % (namespace_, self.gds_format_integer(self.number_real_images, input_name='number_real_images'), namespace_, eol_)) if self.number_diffraction_images is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_diffraction_images>%s</%snumber_diffraction_images>%s' % (namespace_, self.gds_format_integer(self.number_diffraction_images, input_name='number_diffraction_images'), namespace_, eol_)) if self.average_exposure_time is not None: self.average_exposure_time.export(outfile, level, namespace_, name_='average_exposure_time', pretty_print=pretty_print) if self.average_electron_dose_per_image is not None: self.average_electron_dose_per_image.export(outfile, level, namespace_, name_='average_electron_dose_per_image', pretty_print=pretty_print) if self.detector_distance is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetector_distance>%s</%sdetector_distance>%s' % (namespace_, self.gds_format_string(quote_xml(self.detector_distance).encode(ExternalEncoding), input_name='detector_distance'), namespace_, eol_)) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_)) if self.od_range is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sod_range>%s</%sod_range>%s' % (namespace_, self.gds_format_float(self.od_range, input_name='od_range'), namespace_, eol_)) if self.bits_per_pixel is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sbits_per_pixel>%s</%sbits_per_pixel>%s' % (namespace_, self.gds_format_float(self.bits_per_pixel, input_name='bits_per_pixel'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('id', node) if value is not None and 'id' not in already_processed: already_processed.add('id') try: self.id = int(value) except ValueError as exp: raise_parse_error(node, 'Bad integer attribute: %s' % exp) if self.id <= 0: raise_parse_error(node, 'Invalid PositiveInteger')
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'film_or_detector_model': obj_ = film_or_detector_modelType.factory() obj_.build(child_) self.film_or_detector_model = obj_ obj_.original_tagname_ = 'film_or_detector_model' elif nodeName_ == 'detector_mode': detector_mode_ = child_.text detector_mode_ = re_.sub(String_cleanup_pat_, " ", detector_mode_).strip() detector_mode_ = self.gds_validate_string(detector_mode_, node, 'detector_mode') self.detector_mode = detector_mode_ # validate type detector_modeType self.validate_detector_modeType(self.detector_mode) elif nodeName_ == 'digitization_details': obj_ = digitization_detailsType.factory() obj_.build(child_) self.digitization_details = obj_ obj_.original_tagname_ = 'digitization_details' elif nodeName_ == 'number_grids_imaged': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'number_grids_imaged') self.number_grids_imaged = ival_ elif nodeName_ == 'number_real_images': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'number_real_images') self.number_real_images = ival_ elif nodeName_ == 'number_diffraction_images': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'number_diffraction_images') self.number_diffraction_images = ival_ elif nodeName_ == 'average_exposure_time': obj_ = average_exposure_timeType.factory() obj_.build(child_) self.average_exposure_time = obj_ obj_.original_tagname_ = 'average_exposure_time' elif nodeName_ == 'average_electron_dose_per_image': obj_ = average_electron_dose_per_imageType.factory() obj_.build(child_) self.average_electron_dose_per_image = obj_ obj_.original_tagname_ = 'average_electron_dose_per_image' elif nodeName_ == 'detector_distance': detector_distance_ = child_.text detector_distance_ = self.gds_validate_string(detector_distance_, node, 'detector_distance') self.detector_distance = detector_distance_ elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ elif nodeName_ == 'od_range': sval_ = child_.text try: fval_ = float(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires float or double: %s' % exp) fval_ = self.gds_validate_float(fval_, node, 'od_range') self.od_range = fval_ elif nodeName_ == 'bits_per_pixel': sval_ = child_.text try: fval_ = float(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires float or double: %s' % exp) fval_ = self.gds_validate_float(fval_, node, 'bits_per_pixel') self.bits_per_pixel = fval_ # end class image_recordingType
[docs]class film_or_detector_modelType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('category', 'xs:string', 0), MemberSpec_('valueOf_', ['allowed_film_or_detector_model', 'xs:token'], 0), ] subclass = None superclass = None def __init__(self, category=None, valueOf_=None): self.original_tagname_ = None self.category = _cast(None, category) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if film_or_detector_modelType.subclass: return film_or_detector_modelType.subclass(*args_, **kwargs_) else: return film_or_detector_modelType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_category(self): return self.category
[docs] def set_category(self, category): self.category = category
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='film_or_detector_modelType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='film_or_detector_modelType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='film_or_detector_modelType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='film_or_detector_modelType'): if self.category is not None and 'category' not in already_processed: already_processed.add('category') outfile.write(' category=%s' % (self.gds_format_string(quote_attrib(self.category).encode(ExternalEncoding), input_name='category'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='film_or_detector_modelType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('category', node) if value is not None and 'category' not in already_processed: already_processed.add('category') self.category = value
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class film_or_detector_modelType
[docs]class digitization_detailsType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('scanner', ['scannerType', 'xs:token'], 0), MemberSpec_('dimensions', 'dimensionsType', 0), MemberSpec_('sampling_interval', 'sampling_intervalType', 0), MemberSpec_('frames_per_image', 'xs:positiveInteger', 0), ] subclass = None superclass = None def __init__(self, scanner=None, dimensions=None, sampling_interval=None, frames_per_image=None): self.original_tagname_ = None self.scanner = scanner self.validate_scannerType(self.scanner) self.dimensions = dimensions self.sampling_interval = sampling_interval self.frames_per_image = frames_per_image
[docs] def factory(*args_, **kwargs_): if digitization_detailsType.subclass: return digitization_detailsType.subclass(*args_, **kwargs_) else: return digitization_detailsType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_scanner(self): return self.scanner
[docs] def set_scanner(self, scanner): self.scanner = scanner
[docs] def get_dimensions(self): return self.dimensions
[docs] def set_dimensions(self, dimensions): self.dimensions = dimensions
[docs] def get_sampling_interval(self): return self.sampling_interval
[docs] def set_sampling_interval(self, sampling_interval): self.sampling_interval = sampling_interval
[docs] def get_frames_per_image(self): return self.frames_per_image
[docs] def set_frames_per_image(self, frames_per_image): self.frames_per_image = frames_per_image
[docs] def validate_scannerType(self, value): # Validate type scannerType, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['EIKONIX IEEE 488', 'EMIL 10', 'NIKON COOLSCAN', 'NIKON SUPER COOLSCAN 9000', 'OPTRONICS', 'PATCHWORK DENSITOMETER', 'PERKIN ELMER', 'PRIMESCAN', 'TEMSCAN', 'ZEISS SCAI', 'OTHER'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on scannerType' % {"value" : value.encode("utf-8")} )
[docs] def hasContent_(self): if ( self.scanner is not None or self.dimensions is not None or self.sampling_interval is not None or self.frames_per_image is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='digitization_detailsType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='digitization_detailsType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='digitization_detailsType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='digitization_detailsType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='digitization_detailsType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.scanner is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sscanner>%s</%sscanner>%s' % (namespace_, self.gds_format_string(quote_xml(self.scanner).encode(ExternalEncoding), input_name='scanner'), namespace_, eol_)) if self.dimensions is not None: self.dimensions.export(outfile, level, namespace_, name_='dimensions', pretty_print=pretty_print) if self.sampling_interval is not None: self.sampling_interval.export(outfile, level, namespace_, name_='sampling_interval', pretty_print=pretty_print) if self.frames_per_image is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sframes_per_image>%s</%sframes_per_image>%s' % (namespace_, self.gds_format_integer(self.frames_per_image, input_name='frames_per_image'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'scanner': scanner_ = child_.text scanner_ = re_.sub(String_cleanup_pat_, " ", scanner_).strip() scanner_ = self.gds_validate_string(scanner_, node, 'scanner') self.scanner = scanner_ # validate type scannerType self.validate_scannerType(self.scanner) elif nodeName_ == 'dimensions': obj_ = dimensionsType.factory() obj_.build(child_) self.dimensions = obj_ obj_.original_tagname_ = 'dimensions' elif nodeName_ == 'sampling_interval': obj_ = sampling_intervalType.factory() obj_.build(child_) self.sampling_interval = obj_ obj_.original_tagname_ = 'sampling_interval' elif nodeName_ == 'frames_per_image': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'frames_per_image') self.frames_per_image = ival_ # end class digitization_detailsType
[docs]class dimensionsType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('width', 'widthType', 0), MemberSpec_('height', 'heightType', 0), ] subclass = None superclass = None def __init__(self, width=None, height=None): self.original_tagname_ = None self.width = width self.height = height
[docs] def factory(*args_, **kwargs_): if dimensionsType.subclass: return dimensionsType.subclass(*args_, **kwargs_) else: return dimensionsType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_width(self): return self.width
[docs] def set_width(self, width): self.width = width
[docs] def get_height(self): return self.height
[docs] def set_height(self, height): self.height = height
[docs] def hasContent_(self): if ( self.width is not None or self.height is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='dimensionsType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='dimensionsType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='dimensionsType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='dimensionsType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='dimensionsType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.width is not None: self.width.export(outfile, level, namespace_, name_='width', pretty_print=pretty_print) if self.height is not None: self.height.export(outfile, level, namespace_, name_='height', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'width': obj_ = widthType.factory() obj_.build(child_) self.width = obj_ obj_.original_tagname_ = 'width' elif nodeName_ == 'height': obj_ = heightType.factory() obj_.build(child_) self.height = obj_ obj_.original_tagname_ = 'height' # end class dimensionsType
[docs]class widthType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', 'xs:positiveInteger', 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if widthType.subclass: return widthType.subclass(*args_, **kwargs_) else: return widthType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='widthType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='widthType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='widthType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='widthType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='widthType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class widthType
[docs]class heightType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', 'xs:positiveInteger', 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if heightType.subclass: return heightType.subclass(*args_, **kwargs_) else: return heightType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='heightType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='heightType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='heightType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='heightType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='heightType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class heightType
[docs]class sampling_intervalType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_scaning_interval', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if sampling_intervalType.subclass: return sampling_intervalType.subclass(*args_, **kwargs_) else: return sampling_intervalType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='sampling_intervalType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='sampling_intervalType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='sampling_intervalType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='sampling_intervalType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='sampling_intervalType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class sampling_intervalType
[docs]class average_exposure_timeType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_average_exposure_time_type', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if average_exposure_timeType.subclass: return average_exposure_timeType.subclass(*args_, **kwargs_) else: return average_exposure_timeType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='average_exposure_timeType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='average_exposure_timeType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='average_exposure_timeType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='average_exposure_timeType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='average_exposure_timeType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class average_exposure_timeType
[docs]class average_electron_dose_per_imageType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_electron_dose', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if average_electron_dose_per_imageType.subclass: return average_electron_dose_per_imageType.subclass(*args_, **kwargs_) else: return average_electron_dose_per_imageType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='average_electron_dose_per_imageType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='average_electron_dose_per_imageType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='average_electron_dose_per_imageType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='average_electron_dose_per_imageType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='average_electron_dose_per_imageType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class average_electron_dose_per_imageType
[docs]class min_angleType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:string', 0), MemberSpec_('valueOf_', ['allowed_angle_tomography', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if min_angleType.subclass: return min_angleType.subclass(*args_, **kwargs_) else: return min_angleType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='min_angleType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='min_angleType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='min_angleType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='min_angleType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='min_angleType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class min_angleType
[docs]class max_angleType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:string', 0), MemberSpec_('valueOf_', ['allowed_angle_tomography', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if max_angleType.subclass: return max_angleType.subclass(*args_, **kwargs_) else: return max_angleType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='max_angleType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='max_angleType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='max_angleType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='max_angleType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='max_angleType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class max_angleType
[docs]class angle_incrementType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:string', 0), MemberSpec_('valueOf_', ['allowed_angle_increment', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if angle_incrementType.subclass: return angle_incrementType.subclass(*args_, **kwargs_) else: return angle_incrementType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='angle_incrementType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='angle_incrementType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='angle_incrementType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='angle_incrementType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='angle_incrementType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class angle_incrementType
[docs]class axis2Type(axis_type): member_data_items_ = [ MemberSpec_('axis_rotation', 'xs:string', 0), ] subclass = None superclass = axis_type def __init__(self, min_angle=None, max_angle=None, angle_increment=None, axis_rotation=None): self.original_tagname_ = None super(axis2Type, self).__init__(min_angle, max_angle, angle_increment, ) self.axis_rotation = axis_rotation
[docs] def factory(*args_, **kwargs_): if axis2Type.subclass: return axis2Type.subclass(*args_, **kwargs_) else: return axis2Type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_axis_rotation(self): return self.axis_rotation
[docs] def set_axis_rotation(self, axis_rotation): self.axis_rotation = axis_rotation
[docs] def hasContent_(self): if ( self.axis_rotation is not None or super(axis2Type, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='axis2Type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='axis2Type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='axis2Type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='axis2Type'): super(axis2Type, self).exportAttributes(outfile, level, already_processed, namespace_, name_='axis2Type')
[docs] def exportChildren(self, outfile, level, namespace_='', name_='axis2Type', fromsubclass_=False, pretty_print=True): super(axis2Type, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print) if pretty_print: eol_ = '\n' else: eol_ = '' if self.axis_rotation is not None: showIndent(outfile, level, pretty_print) outfile.write('<%saxis_rotation>%s</%saxis_rotation>%s' % (namespace_, self.gds_format_string(quote_xml(self.axis_rotation).encode(ExternalEncoding), input_name='axis_rotation'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): super(axis2Type, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'axis_rotation': axis_rotation_ = child_.text axis_rotation_ = self.gds_validate_string(axis_rotation_, node, 'axis_rotation') self.axis_rotation = axis_rotation_ super(axis2Type, self).buildChildren(child_, node, nodeName_, True) # end class axis2Type
[docs]class axis_rotation(GeneratedsSuper): """Rotation of axis relative to axis1""" member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if axis_rotation.subclass: return axis_rotation.subclass(*args_, **kwargs_) else: return axis_rotation(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='axis_rotation', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='axis_rotation') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='axis_rotation', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='axis_rotation'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='axis_rotation', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class axis_rotation
[docs]class axis_rotationType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', 'xs:float', 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if axis_rotationType.subclass: return axis_rotationType.subclass(*args_, **kwargs_) else: return axis_rotationType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='axis_rotationType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='axis_rotationType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='axis_rotationType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='axis_rotationType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='axis_rotationType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class axis_rotationType
[docs]class camera_lengthType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_camera_length', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if camera_lengthType.subclass: return camera_lengthType.subclass(*args_, **kwargs_) else: return camera_lengthType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='camera_lengthType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='camera_lengthType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='camera_lengthType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='camera_lengthType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='camera_lengthType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class camera_lengthType
[docs]class tilt_listType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('angle', ['angleType7', 'xs:float'], 1), ] subclass = None superclass = None def __init__(self, angle=None): self.original_tagname_ = None if angle is None: self.angle = [] else: self.angle = angle
[docs] def factory(*args_, **kwargs_): if tilt_listType.subclass: return tilt_listType.subclass(*args_, **kwargs_) else: return tilt_listType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_angle(self): return self.angle
[docs] def set_angle(self, angle): self.angle = angle
[docs] def add_angle(self, value): self.angle.append(value)
[docs] def insert_angle_at(self, index, value): self.angle.insert(index, value)
[docs] def replace_angle_at(self, index, value): self.angle[index] = value
[docs] def validate_angleType7(self, value): # Validate type angleType7, a restriction on xs:float. if value is not None and Validate_simpletypes_: if value < -70: warnings_.warn('Value "%(value)s" does not match xsd minInclusive restriction on angleType7' % {"value" : value} ) if value > 70: warnings_.warn('Value "%(value)s" does not match xsd maxInclusive restriction on angleType7' % {"value" : value} )
[docs] def hasContent_(self): if ( self.angle ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='tilt_listType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='tilt_listType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='tilt_listType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='tilt_listType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='tilt_listType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for angle_ in self.angle: showIndent(outfile, level, pretty_print) outfile.write('<%sangle>%s</%sangle>%s' % (namespace_, self.gds_format_float(angle_, input_name='angle'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'angle': sval_ = child_.text try: fval_ = float(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires float or double: %s' % exp) fval_ = self.gds_validate_float(fval_, node, 'angle') self.angle.append(fval_) # validate type angleType7 self.validate_angleType7(self.angle[-1]) # end class tilt_listType
[docs]class resolutionType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('type', 'xs:token', 0), MemberSpec_('valueOf_', ['resolution_type', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, type_=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.type_ = _cast(None, type_) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if resolutionType.subclass: return resolutionType.subclass(*args_, **kwargs_) else: return resolutionType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_type(self): return self.type_
[docs] def set_type(self, type_): self.type_ = type_
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='resolutionType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='resolutionType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='resolutionType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='resolutionType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), )) if self.type_ is not None and 'type_' not in already_processed: already_processed.add('type_') outfile.write(' type=%s' % (self.gds_format_string(quote_attrib(self.type_).encode(ExternalEncoding), input_name='type'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='resolutionType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split()) value = find_attr_value_('type', node) if value is not None and 'type' not in already_processed: already_processed.add('type') self.type_ = value self.type_ = ' '.join(self.type_.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass
[docs] def gds_format_float(self,input_data, input_name="" ): return ("%g" % input_data) # end class resolutionType
[docs]class film_thicknessType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_film_thickness', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if film_thicknessType.subclass: return film_thicknessType.subclass(*args_, **kwargs_) else: return film_thicknessType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='film_thicknessType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='film_thicknessType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='film_thicknessType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='film_thicknessType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='film_thicknessType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class film_thicknessType
[docs]class spatial_frequencyType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('valueOf_', 'xs:float', 0), ] subclass = None superclass = None def __init__(self, valueOf_=None): self.original_tagname_ = None self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if spatial_frequencyType.subclass: return spatial_frequencyType.subclass(*args_, **kwargs_) else: return spatial_frequencyType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='spatial_frequencyType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='spatial_frequencyType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='spatial_frequencyType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='spatial_frequencyType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='spatial_frequencyType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class spatial_frequencyType
[docs]class phase_reversalType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('anisotropic', 'xs:boolean', 0), MemberSpec_('correction_space', ['correction_space_type', 'xs:string'], 0), ] subclass = None superclass = None def __init__(self, anisotropic=None, correction_space=None): self.original_tagname_ = None self.anisotropic = anisotropic self.correction_space = correction_space self.validate_correction_space_type(self.correction_space)
[docs] def factory(*args_, **kwargs_): if phase_reversalType.subclass: return phase_reversalType.subclass(*args_, **kwargs_) else: return phase_reversalType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_anisotropic(self): return self.anisotropic
[docs] def set_anisotropic(self, anisotropic): self.anisotropic = anisotropic
[docs] def get_correction_space(self): return self.correction_space
[docs] def set_correction_space(self, correction_space): self.correction_space = correction_space
[docs] def validate_correction_space_type(self, value): # Validate type correction_space_type, a restriction on xs:string. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['2D', '3D'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on correction_space_type' % {"value" : value.encode("utf-8")} )
[docs] def hasContent_(self): if ( self.anisotropic is not None or self.correction_space is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='phase_reversalType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='phase_reversalType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='phase_reversalType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='phase_reversalType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='phase_reversalType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.anisotropic is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sanisotropic>%s</%sanisotropic>%s' % (namespace_, self.gds_format_boolean(self.anisotropic, input_name='anisotropic'), namespace_, eol_)) if self.correction_space is not None: showIndent(outfile, level, pretty_print) outfile.write('<%scorrection_space>%s</%scorrection_space>%s' % (namespace_, self.gds_format_string(quote_xml(self.correction_space).encode(ExternalEncoding), input_name='correction_space'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'anisotropic': sval_ = child_.text if sval_ in ('true', '1'): ival_ = True elif sval_ in ('false', '0'): ival_ = False else: raise_parse_error(child_, 'requires boolean') ival_ = self.gds_validate_boolean(ival_, node, 'anisotropic') self.anisotropic = ival_ elif nodeName_ == 'correction_space': correction_space_ = child_.text correction_space_ = self.gds_validate_string(correction_space_, node, 'correction_space') self.correction_space = correction_space_ # validate type correction_space_type self.validate_correction_space_type(self.correction_space) # end class phase_reversalType
[docs]class amplitude_correctionType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('factor', 'xs:float', 0), MemberSpec_('correction_space', ['correction_space_type', 'xs:string'], 0), ] subclass = None superclass = None def __init__(self, factor=None, correction_space=None): self.original_tagname_ = None self.factor = factor self.correction_space = correction_space self.validate_correction_space_type(self.correction_space)
[docs] def factory(*args_, **kwargs_): if amplitude_correctionType.subclass: return amplitude_correctionType.subclass(*args_, **kwargs_) else: return amplitude_correctionType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_factor(self): return self.factor
[docs] def set_factor(self, factor): self.factor = factor
[docs] def get_correction_space(self): return self.correction_space
[docs] def set_correction_space(self, correction_space): self.correction_space = correction_space
[docs] def validate_correction_space_type(self, value): # Validate type correction_space_type, a restriction on xs:string. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['2D', '3D'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on correction_space_type' % {"value" : value.encode("utf-8")} )
[docs] def hasContent_(self): if ( self.factor is not None or self.correction_space is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='amplitude_correctionType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='amplitude_correctionType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='amplitude_correctionType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='amplitude_correctionType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='amplitude_correctionType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.factor is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sfactor>%s</%sfactor>%s' % (namespace_, self.gds_format_float(self.factor, input_name='factor'), namespace_, eol_)) if self.correction_space is not None: showIndent(outfile, level, pretty_print) outfile.write('<%scorrection_space>%s</%scorrection_space>%s' % (namespace_, self.gds_format_string(quote_xml(self.correction_space).encode(ExternalEncoding), input_name='correction_space'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'factor': sval_ = child_.text try: fval_ = float(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires float or double: %s' % exp) fval_ = self.gds_validate_float(fval_, node, 'factor') self.factor = fval_ elif nodeName_ == 'correction_space': correction_space_ = child_.text correction_space_ = self.gds_validate_string(correction_space_, node, 'correction_space') self.correction_space = correction_space_ # validate type correction_space_type self.validate_correction_space_type(self.correction_space) # end class amplitude_correctionType
[docs]class projection_matching_processingType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('number_reference_projections', 'xs:positiveInteger', 0), MemberSpec_('merit_function', 'xs:token', 0), MemberSpec_('angular_sampling', 'angular_samplingType', 0), ] subclass = None superclass = None def __init__(self, number_reference_projections=None, merit_function=None, angular_sampling=None): self.original_tagname_ = None self.number_reference_projections = number_reference_projections self.merit_function = merit_function self.angular_sampling = angular_sampling
[docs] def factory(*args_, **kwargs_): if projection_matching_processingType.subclass: return projection_matching_processingType.subclass(*args_, **kwargs_) else: return projection_matching_processingType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_number_reference_projections(self): return self.number_reference_projections
[docs] def set_number_reference_projections(self, number_reference_projections): self.number_reference_projections = number_reference_projections
[docs] def get_merit_function(self): return self.merit_function
[docs] def set_merit_function(self, merit_function): self.merit_function = merit_function
[docs] def get_angular_sampling(self): return self.angular_sampling
[docs] def set_angular_sampling(self, angular_sampling): self.angular_sampling = angular_sampling
[docs] def hasContent_(self): if ( self.number_reference_projections is not None or self.merit_function is not None or self.angular_sampling is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='projection_matching_processingType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='projection_matching_processingType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='projection_matching_processingType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='projection_matching_processingType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='projection_matching_processingType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.number_reference_projections is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_reference_projections>%s</%snumber_reference_projections>%s' % (namespace_, self.gds_format_integer(self.number_reference_projections, input_name='number_reference_projections'), namespace_, eol_)) if self.merit_function is not None: showIndent(outfile, level, pretty_print) outfile.write('<%smerit_function>%s</%smerit_function>%s' % (namespace_, self.gds_format_string(quote_xml(self.merit_function).encode(ExternalEncoding), input_name='merit_function'), namespace_, eol_)) if self.angular_sampling is not None: self.angular_sampling.export(outfile, level, namespace_, name_='angular_sampling', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'number_reference_projections': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'number_reference_projections') self.number_reference_projections = ival_ elif nodeName_ == 'merit_function': merit_function_ = child_.text merit_function_ = re_.sub(String_cleanup_pat_, " ", merit_function_).strip() merit_function_ = self.gds_validate_string(merit_function_, node, 'merit_function') self.merit_function = merit_function_ elif nodeName_ == 'angular_sampling': obj_ = angular_samplingType.factory() obj_.build(child_) self.angular_sampling = obj_ obj_.original_tagname_ = 'angular_sampling' # end class projection_matching_processingType
[docs]class angular_samplingType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_angular_sampling', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if angular_samplingType.subclass: return angular_samplingType.subclass(*args_, **kwargs_) else: return angular_samplingType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='angular_samplingType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='angular_samplingType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='angular_samplingType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='angular_samplingType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='angular_samplingType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class angular_samplingType
[docs]class initial_modelType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('access_code', ['access_codeType', 'pdb_code_type', 'xs:token'], 0), MemberSpec_('chain', 'chainType', 1), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, access_code=None, chain=None, details=None): self.original_tagname_ = None self.access_code = access_code self.validate_access_codeType(self.access_code) if chain is None: self.chain = [] else: self.chain = chain self.details = details
[docs] def factory(*args_, **kwargs_): if initial_modelType.subclass: return initial_modelType.subclass(*args_, **kwargs_) else: return initial_modelType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_access_code(self): return self.access_code
[docs] def set_access_code(self, access_code): self.access_code = access_code
[docs] def get_chain(self): return self.chain
[docs] def set_chain(self, chain): self.chain = chain
[docs] def add_chain(self, value): self.chain.append(value)
[docs] def insert_chain_at(self, index, value): self.chain.insert(index, value)
[docs] def replace_chain_at(self, index, value): self.chain[index] = value
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def validate_access_codeType(self, value): # Validate type access_codeType, a restriction on pdb_code_type. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_access_codeType_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_access_codeType_patterns_, ))
validate_access_codeType_patterns_ = [['^\\d[\\dA-Za-z]{3}$'], ['^\\d[\\dA-Za-z]{3}$']]
[docs] def hasContent_(self): if ( self.access_code is not None or self.chain or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='initial_modelType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='initial_modelType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='initial_modelType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='initial_modelType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='initial_modelType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.access_code is not None: showIndent(outfile, level, pretty_print) outfile.write('<%saccess_code>%s</%saccess_code>%s' % (namespace_, self.gds_format_string(quote_xml(self.access_code).encode(ExternalEncoding), input_name='access_code'), namespace_, eol_)) for chain_ in self.chain: chain_.export(outfile, level, namespace_, name_='chain', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'access_code': access_code_ = child_.text access_code_ = re_.sub(String_cleanup_pat_, " ", access_code_).strip() access_code_ = self.gds_validate_string(access_code_, node, 'access_code') self.access_code = access_code_ # validate type access_codeType self.validate_access_codeType(self.access_code) elif nodeName_ == 'chain': obj_ = chainType.factory() obj_.build(child_) self.chain.append(obj_) obj_.original_tagname_ = 'chain' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class initial_modelType
[docs]class chainType(chain_model_type): member_data_items_ = [ MemberSpec_('number_of_copies_in_final_model', 'xs:positiveInteger', 0), ] subclass = None superclass = chain_model_type def __init__(self, id=None, residue_range=None, number_of_copies_in_final_model=None): self.original_tagname_ = None super(chainType, self).__init__(id, residue_range, ) self.number_of_copies_in_final_model = number_of_copies_in_final_model
[docs] def factory(*args_, **kwargs_): if chainType.subclass: return chainType.subclass(*args_, **kwargs_) else: return chainType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_number_of_copies_in_final_model(self): return self.number_of_copies_in_final_model
[docs] def set_number_of_copies_in_final_model(self, number_of_copies_in_final_model): self.number_of_copies_in_final_model = number_of_copies_in_final_model
[docs] def hasContent_(self): if ( self.number_of_copies_in_final_model is not None or super(chainType, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='chainType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='chainType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='chainType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='chainType'): super(chainType, self).exportAttributes(outfile, level, already_processed, namespace_, name_='chainType')
[docs] def exportChildren(self, outfile, level, namespace_='', name_='chainType', fromsubclass_=False, pretty_print=True): super(chainType, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print) if pretty_print: eol_ = '\n' else: eol_ = '' if self.number_of_copies_in_final_model is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_of_copies_in_final_model>%s</%snumber_of_copies_in_final_model>%s' % (namespace_, self.gds_format_integer(self.number_of_copies_in_final_model, input_name='number_of_copies_in_final_model'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): super(chainType, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'number_of_copies_in_final_model': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'number_of_copies_in_final_model') self.number_of_copies_in_final_model = ival_ super(chainType, self).buildChildren(child_, node, nodeName_, True) # end class chainType
[docs]class final_modelType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('access_code', ['pdb_code_type', 'xs:token'], 0), MemberSpec_('chain', 'chain_model_type', 1), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, access_code=None, chain=None, details=None): self.original_tagname_ = None self.access_code = access_code self.validate_pdb_code_type(self.access_code) if chain is None: self.chain = [] else: self.chain = chain self.details = details
[docs] def factory(*args_, **kwargs_): if final_modelType.subclass: return final_modelType.subclass(*args_, **kwargs_) else: return final_modelType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_access_code(self): return self.access_code
[docs] def set_access_code(self, access_code): self.access_code = access_code
[docs] def get_chain(self): return self.chain
[docs] def set_chain(self, chain): self.chain = chain
[docs] def add_chain(self, value): self.chain.append(value)
[docs] def insert_chain_at(self, index, value): self.chain.insert(index, value)
[docs] def replace_chain_at(self, index, value): self.chain[index] = value
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def validate_pdb_code_type(self, value): # Validate type pdb_code_type, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_pdb_code_type_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_pdb_code_type_patterns_, ))
validate_pdb_code_type_patterns_ = [['^\\d[\\dA-Za-z]{3}$']]
[docs] def hasContent_(self): if ( self.access_code is not None or self.chain or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='final_modelType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='final_modelType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='final_modelType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='final_modelType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='final_modelType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.access_code is not None: showIndent(outfile, level, pretty_print) outfile.write('<%saccess_code>%s</%saccess_code>%s' % (namespace_, self.gds_format_string(quote_xml(self.access_code).encode(ExternalEncoding), input_name='access_code'), namespace_, eol_)) for chain_ in self.chain: chain_.export(outfile, level, namespace_, name_='chain', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'access_code': access_code_ = child_.text access_code_ = re_.sub(String_cleanup_pat_, " ", access_code_).strip() access_code_ = self.gds_validate_string(access_code_, node, 'access_code') self.access_code = access_code_ # validate type pdb_code_type self.validate_pdb_code_type(self.access_code) elif nodeName_ == 'chain': class_obj_ = self.get_class_obj_(child_, chain_model_type) obj_ = class_obj_.factory() obj_.build(child_) self.chain.append(obj_) obj_.original_tagname_ = 'chain' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class final_modelType
[docs]class parametersType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('in_plane_translation', 'xs:string', 0), MemberSpec_('in_plane_rotation', 'xs:string', 0), MemberSpec_('out_of_plane_rotation', 'xs:string', 0), MemberSpec_('model_heterogeneity', 'model_heterogeneityType', 0), MemberSpec_('other', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, in_plane_translation=None, in_plane_rotation=None, out_of_plane_rotation=None, model_heterogeneity=None, other=None): self.original_tagname_ = None self.in_plane_translation = in_plane_translation self.in_plane_rotation = in_plane_rotation self.out_of_plane_rotation = out_of_plane_rotation self.model_heterogeneity = model_heterogeneity self.other = other
[docs] def factory(*args_, **kwargs_): if parametersType.subclass: return parametersType.subclass(*args_, **kwargs_) else: return parametersType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_in_plane_translation(self): return self.in_plane_translation
[docs] def set_in_plane_translation(self, in_plane_translation): self.in_plane_translation = in_plane_translation
[docs] def get_in_plane_rotation(self): return self.in_plane_rotation
[docs] def set_in_plane_rotation(self, in_plane_rotation): self.in_plane_rotation = in_plane_rotation
[docs] def get_out_of_plane_rotation(self): return self.out_of_plane_rotation
[docs] def set_out_of_plane_rotation(self, out_of_plane_rotation): self.out_of_plane_rotation = out_of_plane_rotation
[docs] def get_model_heterogeneity(self): return self.model_heterogeneity
[docs] def set_model_heterogeneity(self, model_heterogeneity): self.model_heterogeneity = model_heterogeneity
[docs] def get_other(self): return self.other
[docs] def set_other(self, other): self.other = other
[docs] def hasContent_(self): if ( self.in_plane_translation is not None or self.in_plane_rotation is not None or self.out_of_plane_rotation is not None or self.model_heterogeneity is not None or self.other is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='parametersType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='parametersType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='parametersType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='parametersType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='parametersType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.in_plane_translation is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sin_plane_translation>%s</%sin_plane_translation>%s' % (namespace_, self.gds_format_string(quote_xml(self.in_plane_translation).encode(ExternalEncoding), input_name='in_plane_translation'), namespace_, eol_)) if self.in_plane_rotation is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sin_plane_rotation>%s</%sin_plane_rotation>%s' % (namespace_, self.gds_format_string(quote_xml(self.in_plane_rotation).encode(ExternalEncoding), input_name='in_plane_rotation'), namespace_, eol_)) if self.out_of_plane_rotation is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sout_of_plane_rotation>%s</%sout_of_plane_rotation>%s' % (namespace_, self.gds_format_string(quote_xml(self.out_of_plane_rotation).encode(ExternalEncoding), input_name='out_of_plane_rotation'), namespace_, eol_)) if self.model_heterogeneity is not None: self.model_heterogeneity.export(outfile, level, namespace_, name_='model_heterogeneity', pretty_print=pretty_print) if self.other is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sother>%s</%sother>%s' % (namespace_, self.gds_format_string(quote_xml(self.other).encode(ExternalEncoding), input_name='other'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'in_plane_translation': in_plane_translation_ = child_.text in_plane_translation_ = self.gds_validate_string(in_plane_translation_, node, 'in_plane_translation') self.in_plane_translation = in_plane_translation_ elif nodeName_ == 'in_plane_rotation': in_plane_rotation_ = child_.text in_plane_rotation_ = self.gds_validate_string(in_plane_rotation_, node, 'in_plane_rotation') self.in_plane_rotation = in_plane_rotation_ elif nodeName_ == 'out_of_plane_rotation': out_of_plane_rotation_ = child_.text out_of_plane_rotation_ = self.gds_validate_string(out_of_plane_rotation_, node, 'out_of_plane_rotation') self.out_of_plane_rotation = out_of_plane_rotation_ elif nodeName_ == 'model_heterogeneity': obj_ = model_heterogeneityType.factory() obj_.build(child_) self.model_heterogeneity = obj_ obj_.original_tagname_ = 'model_heterogeneity' elif nodeName_ == 'other': other_ = child_.text other_ = self.gds_validate_string(other_, node, 'other') self.other = other_ # end class parametersType
[docs]class in_plane_translation(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if in_plane_translation.subclass: return in_plane_translation.subclass(*args_, **kwargs_) else: return in_plane_translation(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='in_plane_translation', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='in_plane_translation') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='in_plane_translation', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='in_plane_translation'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='in_plane_translation', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class in_plane_translation
[docs]class in_plane_rotation(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if in_plane_rotation.subclass: return in_plane_rotation.subclass(*args_, **kwargs_) else: return in_plane_rotation(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='in_plane_rotation', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='in_plane_rotation') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='in_plane_rotation', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='in_plane_rotation'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='in_plane_rotation', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class in_plane_rotation
[docs]class out_of_plane_rotation(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if out_of_plane_rotation.subclass: return out_of_plane_rotation.subclass(*args_, **kwargs_) else: return out_of_plane_rotation(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='out_of_plane_rotation', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='out_of_plane_rotation') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='out_of_plane_rotation', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='out_of_plane_rotation'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='out_of_plane_rotation', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class out_of_plane_rotation
[docs]class other(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if other.subclass: return other.subclass(*args_, **kwargs_) else: return other(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='other', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='other') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='other', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='other'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='other', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class other
[docs]class model_heterogeneityType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('number_classes', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, number_classes=None): self.original_tagname_ = None self.number_classes = number_classes
[docs] def factory(*args_, **kwargs_): if model_heterogeneityType.subclass: return model_heterogeneityType.subclass(*args_, **kwargs_) else: return model_heterogeneityType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_number_classes(self): return self.number_classes
[docs] def set_number_classes(self, number_classes): self.number_classes = number_classes
[docs] def hasContent_(self): if ( self.number_classes is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='model_heterogeneityType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='model_heterogeneityType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='model_heterogeneityType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='model_heterogeneityType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='model_heterogeneityType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.number_classes is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_classes>%s</%snumber_classes>%s' % (namespace_, self.gds_format_string(quote_xml(self.number_classes).encode(ExternalEncoding), input_name='number_classes'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'number_classes': number_classes_ = child_.text number_classes_ = self.gds_validate_string(number_classes_, node, 'number_classes') self.number_classes = number_classes_ # end class model_heterogeneityType
[docs]class number_classes(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if number_classes.subclass: return number_classes.subclass(*args_, **kwargs_) else: return number_classes(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='number_classes', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='number_classes') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='number_classes', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='number_classes'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='number_classes', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class number_classes
[docs]class noise_modelType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('white_gaussian', 'xs:string', 0), MemberSpec_('coloured_gaussian', 'xs:string', 0), MemberSpec_('other', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, white_gaussian=None, coloured_gaussian=None, other=None): self.original_tagname_ = None self.white_gaussian = white_gaussian self.coloured_gaussian = coloured_gaussian self.other = other
[docs] def factory(*args_, **kwargs_): if noise_modelType.subclass: return noise_modelType.subclass(*args_, **kwargs_) else: return noise_modelType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_white_gaussian(self): return self.white_gaussian
[docs] def set_white_gaussian(self, white_gaussian): self.white_gaussian = white_gaussian
[docs] def get_coloured_gaussian(self): return self.coloured_gaussian
[docs] def set_coloured_gaussian(self, coloured_gaussian): self.coloured_gaussian = coloured_gaussian
[docs] def get_other(self): return self.other
[docs] def set_other(self, other): self.other = other
[docs] def hasContent_(self): if ( self.white_gaussian is not None or self.coloured_gaussian is not None or self.other is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='noise_modelType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='noise_modelType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='noise_modelType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='noise_modelType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='noise_modelType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.white_gaussian is not None: showIndent(outfile, level, pretty_print) outfile.write('<%swhite_gaussian>%s</%swhite_gaussian>%s' % (namespace_, self.gds_format_string(quote_xml(self.white_gaussian).encode(ExternalEncoding), input_name='white_gaussian'), namespace_, eol_)) if self.coloured_gaussian is not None: showIndent(outfile, level, pretty_print) outfile.write('<%scoloured_gaussian>%s</%scoloured_gaussian>%s' % (namespace_, self.gds_format_string(quote_xml(self.coloured_gaussian).encode(ExternalEncoding), input_name='coloured_gaussian'), namespace_, eol_)) if self.other is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sother>%s</%sother>%s' % (namespace_, self.gds_format_string(quote_xml(self.other).encode(ExternalEncoding), input_name='other'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'white_gaussian': white_gaussian_ = child_.text white_gaussian_ = self.gds_validate_string(white_gaussian_, node, 'white_gaussian') self.white_gaussian = white_gaussian_ elif nodeName_ == 'coloured_gaussian': coloured_gaussian_ = child_.text coloured_gaussian_ = self.gds_validate_string(coloured_gaussian_, node, 'coloured_gaussian') self.coloured_gaussian = coloured_gaussian_ elif nodeName_ == 'other': other_ = child_.text other_ = self.gds_validate_string(other_, node, 'other') self.other = other_ # end class noise_modelType
[docs]class white_gaussian(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if white_gaussian.subclass: return white_gaussian.subclass(*args_, **kwargs_) else: return white_gaussian(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='white_gaussian', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='white_gaussian') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='white_gaussian', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='white_gaussian'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='white_gaussian', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class white_gaussian
[docs]class coloured_gaussian(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if coloured_gaussian.subclass: return coloured_gaussian.subclass(*args_, **kwargs_) else: return coloured_gaussian(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='coloured_gaussian', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='coloured_gaussian') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='coloured_gaussian', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='coloured_gaussian'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='coloured_gaussian', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class coloured_gaussian
[docs]class final_multi_reference_alignmentType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('number_reference_projections', 'xs:positiveInteger', 0), MemberSpec_('merit_function', 'xs:string', 0), MemberSpec_('angular_sampling', 'angular_samplingType9', 0), MemberSpec_('software_list', 'software_list_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, number_reference_projections=None, merit_function=None, angular_sampling=None, software_list=None, details=None): self.original_tagname_ = None self.number_reference_projections = number_reference_projections self.merit_function = merit_function self.angular_sampling = angular_sampling self.software_list = software_list self.details = details
[docs] def factory(*args_, **kwargs_): if final_multi_reference_alignmentType.subclass: return final_multi_reference_alignmentType.subclass(*args_, **kwargs_) else: return final_multi_reference_alignmentType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_number_reference_projections(self): return self.number_reference_projections
[docs] def set_number_reference_projections(self, number_reference_projections): self.number_reference_projections = number_reference_projections
[docs] def get_merit_function(self): return self.merit_function
[docs] def set_merit_function(self, merit_function): self.merit_function = merit_function
[docs] def get_angular_sampling(self): return self.angular_sampling
[docs] def set_angular_sampling(self, angular_sampling): self.angular_sampling = angular_sampling
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def hasContent_(self): if ( self.number_reference_projections is not None or self.merit_function is not None or self.angular_sampling is not None or self.software_list is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='final_multi_reference_alignmentType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='final_multi_reference_alignmentType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='final_multi_reference_alignmentType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='final_multi_reference_alignmentType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='final_multi_reference_alignmentType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.number_reference_projections is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_reference_projections>%s</%snumber_reference_projections>%s' % (namespace_, self.gds_format_integer(self.number_reference_projections, input_name='number_reference_projections'), namespace_, eol_)) if self.merit_function is not None: showIndent(outfile, level, pretty_print) outfile.write('<%smerit_function>%s</%smerit_function>%s' % (namespace_, self.gds_format_string(quote_xml(self.merit_function).encode(ExternalEncoding), input_name='merit_function'), namespace_, eol_)) if self.angular_sampling is not None: self.angular_sampling.export(outfile, level, namespace_, name_='angular_sampling', pretty_print=pretty_print) if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'number_reference_projections': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'number_reference_projections') self.number_reference_projections = ival_ elif nodeName_ == 'merit_function': merit_function_ = child_.text merit_function_ = self.gds_validate_string(merit_function_, node, 'merit_function') self.merit_function = merit_function_ elif nodeName_ == 'angular_sampling': obj_ = angular_samplingType9.factory() obj_.build(child_) self.angular_sampling = obj_ obj_.original_tagname_ = 'angular_sampling' elif nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class final_multi_reference_alignmentType
[docs]class angular_samplingType9(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_angular_sampling', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if angular_samplingType9.subclass: return angular_samplingType9.subclass(*args_, **kwargs_) else: return angular_samplingType9(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='angular_samplingType9', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='angular_samplingType9') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='angular_samplingType9', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='angular_samplingType9'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='angular_samplingType9', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class angular_samplingType9
[docs]class extractionType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('number_tomograms', 'xs:positiveInteger', 0), MemberSpec_('number_subtomograms', 'xs:positiveInteger', 0), MemberSpec_('reference_model', 'xs:token', 0), MemberSpec_('method', 'xs:string', 0), MemberSpec_('software_list', 'software_list_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, number_tomograms=None, number_subtomograms=None, reference_model=None, method=None, software_list=None, details=None): self.original_tagname_ = None self.number_tomograms = number_tomograms self.number_subtomograms = number_subtomograms self.reference_model = reference_model self.method = method self.software_list = software_list self.details = details
[docs] def factory(*args_, **kwargs_): if extractionType.subclass: return extractionType.subclass(*args_, **kwargs_) else: return extractionType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_number_tomograms(self): return self.number_tomograms
[docs] def set_number_tomograms(self, number_tomograms): self.number_tomograms = number_tomograms
[docs] def get_number_subtomograms(self): return self.number_subtomograms
[docs] def set_number_subtomograms(self, number_subtomograms): self.number_subtomograms = number_subtomograms
[docs] def get_reference_model(self): return self.reference_model
[docs] def set_reference_model(self, reference_model): self.reference_model = reference_model
[docs] def get_method(self): return self.method
[docs] def set_method(self, method): self.method = method
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def hasContent_(self): if ( self.number_tomograms is not None or self.number_subtomograms is not None or self.reference_model is not None or self.method is not None or self.software_list is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='extractionType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='extractionType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='extractionType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='extractionType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='extractionType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.number_tomograms is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_tomograms>%s</%snumber_tomograms>%s' % (namespace_, self.gds_format_integer(self.number_tomograms, input_name='number_tomograms'), namespace_, eol_)) if self.number_subtomograms is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_subtomograms>%s</%snumber_subtomograms>%s' % (namespace_, self.gds_format_integer(self.number_subtomograms, input_name='number_subtomograms'), namespace_, eol_)) if self.reference_model is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sreference_model>%s</%sreference_model>%s' % (namespace_, self.gds_format_string(quote_xml(self.reference_model).encode(ExternalEncoding), input_name='reference_model'), namespace_, eol_)) if self.method is not None: showIndent(outfile, level, pretty_print) outfile.write('<%smethod>%s</%smethod>%s' % (namespace_, self.gds_format_string(quote_xml(self.method).encode(ExternalEncoding), input_name='method'), namespace_, eol_)) if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'number_tomograms': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'number_tomograms') self.number_tomograms = ival_ elif nodeName_ == 'number_subtomograms': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'number_subtomograms') self.number_subtomograms = ival_ elif nodeName_ == 'reference_model': reference_model_ = child_.text reference_model_ = re_.sub(String_cleanup_pat_, " ", reference_model_).strip() reference_model_ = self.gds_validate_string(reference_model_, node, 'reference_model') self.reference_model = reference_model_ elif nodeName_ == 'method': method_ = child_.text method_ = self.gds_validate_string(method_, node, 'method') self.method = method_ elif nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class extractionType
[docs]class final_multi_reference_alignmentType10(GeneratedsSuper): member_data_items_ = [ MemberSpec_('number_reference_projections', 'xs:positiveInteger', 0), MemberSpec_('merit_function', 'xs:string', 0), MemberSpec_('software_list', 'software_list_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, number_reference_projections=None, merit_function=None, software_list=None, details=None): self.original_tagname_ = None self.number_reference_projections = number_reference_projections self.merit_function = merit_function self.software_list = software_list self.details = details
[docs] def factory(*args_, **kwargs_): if final_multi_reference_alignmentType10.subclass: return final_multi_reference_alignmentType10.subclass(*args_, **kwargs_) else: return final_multi_reference_alignmentType10(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_number_reference_projections(self): return self.number_reference_projections
[docs] def set_number_reference_projections(self, number_reference_projections): self.number_reference_projections = number_reference_projections
[docs] def get_merit_function(self): return self.merit_function
[docs] def set_merit_function(self, merit_function): self.merit_function = merit_function
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def hasContent_(self): if ( self.number_reference_projections is not None or self.merit_function is not None or self.software_list is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='final_multi_reference_alignmentType10', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='final_multi_reference_alignmentType10') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='final_multi_reference_alignmentType10', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='final_multi_reference_alignmentType10'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='final_multi_reference_alignmentType10', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.number_reference_projections is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_reference_projections>%s</%snumber_reference_projections>%s' % (namespace_, self.gds_format_integer(self.number_reference_projections, input_name='number_reference_projections'), namespace_, eol_)) if self.merit_function is not None: showIndent(outfile, level, pretty_print) outfile.write('<%smerit_function>%s</%smerit_function>%s' % (namespace_, self.gds_format_string(quote_xml(self.merit_function).encode(ExternalEncoding), input_name='merit_function'), namespace_, eol_)) if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'number_reference_projections': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'number_reference_projections') self.number_reference_projections = ival_ elif nodeName_ == 'merit_function': merit_function_ = child_.text merit_function_ = self.gds_validate_string(merit_function_, node, 'merit_function') self.merit_function = merit_function_ elif nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class final_multi_reference_alignmentType10
[docs]class molecular_replacementType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('starting_model', 'starting_modelType', 1), MemberSpec_('resolution_range', 'resolution_rangeType', 0), MemberSpec_('software_list', 'software_list_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, starting_model=None, resolution_range=None, software_list=None, details=None): self.original_tagname_ = None if starting_model is None: self.starting_model = [] else: self.starting_model = starting_model self.resolution_range = resolution_range self.software_list = software_list self.details = details
[docs] def factory(*args_, **kwargs_): if molecular_replacementType.subclass: return molecular_replacementType.subclass(*args_, **kwargs_) else: return molecular_replacementType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_starting_model(self): return self.starting_model
[docs] def set_starting_model(self, starting_model): self.starting_model = starting_model
[docs] def add_starting_model(self, value): self.starting_model.append(value)
[docs] def insert_starting_model_at(self, index, value): self.starting_model.insert(index, value)
[docs] def replace_starting_model_at(self, index, value): self.starting_model[index] = value
[docs] def get_resolution_range(self): return self.resolution_range
[docs] def set_resolution_range(self, resolution_range): self.resolution_range = resolution_range
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def hasContent_(self): if ( self.starting_model or self.resolution_range is not None or self.software_list is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='molecular_replacementType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='molecular_replacementType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='molecular_replacementType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='molecular_replacementType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='molecular_replacementType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for starting_model_ in self.starting_model: starting_model_.export(outfile, level, namespace_, name_='starting_model', pretty_print=pretty_print) if self.resolution_range is not None: self.resolution_range.export(outfile, level, namespace_, name_='resolution_range', pretty_print=pretty_print) if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'starting_model': obj_ = starting_modelType.factory() obj_.build(child_) self.starting_model.append(obj_) obj_.original_tagname_ = 'starting_model' elif nodeName_ == 'resolution_range': obj_ = resolution_rangeType.factory() obj_.build(child_) self.resolution_range = obj_ obj_.original_tagname_ = 'resolution_range' elif nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class molecular_replacementType
[docs]class starting_modelType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('access_code', ['pdb_code_type', 'xs:token'], 0), MemberSpec_('chain', 'chain_type', 1), ] subclass = None superclass = None def __init__(self, access_code=None, chain=None): self.original_tagname_ = None self.access_code = access_code self.validate_pdb_code_type(self.access_code) if chain is None: self.chain = [] else: self.chain = chain
[docs] def factory(*args_, **kwargs_): if starting_modelType.subclass: return starting_modelType.subclass(*args_, **kwargs_) else: return starting_modelType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_access_code(self): return self.access_code
[docs] def set_access_code(self, access_code): self.access_code = access_code
[docs] def get_chain(self): return self.chain
[docs] def set_chain(self, chain): self.chain = chain
[docs] def add_chain(self, value): self.chain.append(value)
[docs] def insert_chain_at(self, index, value): self.chain.insert(index, value)
[docs] def replace_chain_at(self, index, value): self.chain[index] = value
[docs] def validate_pdb_code_type(self, value): # Validate type pdb_code_type, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_pdb_code_type_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_pdb_code_type_patterns_, ))
validate_pdb_code_type_patterns_ = [['^\\d[\\dA-Za-z]{3}$']]
[docs] def hasContent_(self): if ( self.access_code is not None or self.chain ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='starting_modelType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='starting_modelType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='starting_modelType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='starting_modelType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='starting_modelType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.access_code is not None: showIndent(outfile, level, pretty_print) outfile.write('<%saccess_code>%s</%saccess_code>%s' % (namespace_, self.gds_format_string(quote_xml(self.access_code).encode(ExternalEncoding), input_name='access_code'), namespace_, eol_)) for chain_ in self.chain: chain_.export(outfile, level, namespace_, name_='chain', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'access_code': access_code_ = child_.text access_code_ = re_.sub(String_cleanup_pat_, " ", access_code_).strip() access_code_ = self.gds_validate_string(access_code_, node, 'access_code') self.access_code = access_code_ # validate type pdb_code_type self.validate_pdb_code_type(self.access_code) elif nodeName_ == 'chain': class_obj_ = self.get_class_obj_(child_, chain_type) obj_ = class_obj_.factory() obj_.build(child_) self.chain.append(obj_) obj_.original_tagname_ = 'chain' # end class starting_modelType
[docs]class resolution_rangeType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('high_resolution', 'high_resolutionType', 0), MemberSpec_('low_resolution', 'low_resolutionType', 0), ] subclass = None superclass = None def __init__(self, high_resolution=None, low_resolution=None): self.original_tagname_ = None self.high_resolution = high_resolution self.low_resolution = low_resolution
[docs] def factory(*args_, **kwargs_): if resolution_rangeType.subclass: return resolution_rangeType.subclass(*args_, **kwargs_) else: return resolution_rangeType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_high_resolution(self): return self.high_resolution
[docs] def set_high_resolution(self, high_resolution): self.high_resolution = high_resolution
[docs] def get_low_resolution(self): return self.low_resolution
[docs] def set_low_resolution(self, low_resolution): self.low_resolution = low_resolution
[docs] def hasContent_(self): if ( self.high_resolution is not None or self.low_resolution is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='resolution_rangeType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='resolution_rangeType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='resolution_rangeType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='resolution_rangeType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='resolution_rangeType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.high_resolution is not None: self.high_resolution.export(outfile, level, namespace_, name_='high_resolution', pretty_print=pretty_print) if self.low_resolution is not None: self.low_resolution.export(outfile, level, namespace_, name_='low_resolution', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'high_resolution': obj_ = high_resolutionType.factory() obj_.build(child_) self.high_resolution = obj_ obj_.original_tagname_ = 'high_resolution' elif nodeName_ == 'low_resolution': obj_ = low_resolutionType.factory() obj_.build(child_) self.low_resolution = obj_ obj_.original_tagname_ = 'low_resolution' # end class resolution_rangeType
[docs]class high_resolutionType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['resolution_type', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if high_resolutionType.subclass: return high_resolutionType.subclass(*args_, **kwargs_) else: return high_resolutionType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='high_resolutionType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='high_resolutionType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='high_resolutionType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='high_resolutionType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='high_resolutionType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class high_resolutionType
[docs]class low_resolutionType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['resolution_type', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if low_resolutionType.subclass: return low_resolutionType.subclass(*args_, **kwargs_) else: return low_resolutionType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='low_resolutionType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='low_resolutionType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='low_resolutionType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='low_resolutionType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='low_resolutionType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class low_resolutionType
[docs]class lattice_distortion_correctionType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('software_list', 'software_list_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, software_list=None, details=None): self.original_tagname_ = None self.software_list = software_list self.details = details
[docs] def factory(*args_, **kwargs_): if lattice_distortion_correctionType.subclass: return lattice_distortion_correctionType.subclass(*args_, **kwargs_) else: return lattice_distortion_correctionType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def hasContent_(self): if ( self.software_list is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='lattice_distortion_correctionType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='lattice_distortion_correctionType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='lattice_distortion_correctionType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='lattice_distortion_correctionType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='lattice_distortion_correctionType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class lattice_distortion_correctionType
[docs]class symmetry_determinationType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('software_list', 'software_list_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, software_list=None, details=None): self.original_tagname_ = None self.software_list = software_list self.details = details
[docs] def factory(*args_, **kwargs_): if symmetry_determinationType.subclass: return symmetry_determinationType.subclass(*args_, **kwargs_) else: return symmetry_determinationType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def hasContent_(self): if ( self.software_list is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='symmetry_determinationType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='symmetry_determinationType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='symmetry_determinationType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='symmetry_determinationType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='symmetry_determinationType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class symmetry_determinationType
[docs]class mergingType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('software_list', 'software_list_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, software_list=None, details=None): self.original_tagname_ = None self.software_list = software_list self.details = details
[docs] def factory(*args_, **kwargs_): if mergingType.subclass: return mergingType.subclass(*args_, **kwargs_) else: return mergingType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def hasContent_(self): if ( self.software_list is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='mergingType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='mergingType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='mergingType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='mergingType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='mergingType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class mergingType
[docs]class segment_selectionType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('number_segments', 'xs:positiveInteger', 0), MemberSpec_('segment_length', 'segment_lengthType', 0), MemberSpec_('segment_overlap', 'segment_overlapType', 0), MemberSpec_('total_filament_length', 'total_filament_lengthType', 0), MemberSpec_('software_list', 'software_list_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, number_segments=None, segment_length=None, segment_overlap=None, total_filament_length=None, software_list=None, details=None): self.original_tagname_ = None self.number_segments = number_segments self.segment_length = segment_length self.segment_overlap = segment_overlap self.total_filament_length = total_filament_length self.software_list = software_list self.details = details
[docs] def factory(*args_, **kwargs_): if segment_selectionType.subclass: return segment_selectionType.subclass(*args_, **kwargs_) else: return segment_selectionType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_number_segments(self): return self.number_segments
[docs] def set_number_segments(self, number_segments): self.number_segments = number_segments
[docs] def get_segment_length(self): return self.segment_length
[docs] def set_segment_length(self, segment_length): self.segment_length = segment_length
[docs] def get_segment_overlap(self): return self.segment_overlap
[docs] def set_segment_overlap(self, segment_overlap): self.segment_overlap = segment_overlap
[docs] def get_total_filament_length(self): return self.total_filament_length
[docs] def set_total_filament_length(self, total_filament_length): self.total_filament_length = total_filament_length
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def hasContent_(self): if ( self.number_segments is not None or self.segment_length is not None or self.segment_overlap is not None or self.total_filament_length is not None or self.software_list is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='segment_selectionType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='segment_selectionType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='segment_selectionType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='segment_selectionType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='segment_selectionType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.number_segments is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_segments>%s</%snumber_segments>%s' % (namespace_, self.gds_format_integer(self.number_segments, input_name='number_segments'), namespace_, eol_)) if self.segment_length is not None: self.segment_length.export(outfile, level, namespace_, name_='segment_length', pretty_print=pretty_print) if self.segment_overlap is not None: self.segment_overlap.export(outfile, level, namespace_, name_='segment_overlap', pretty_print=pretty_print) if self.total_filament_length is not None: self.total_filament_length.export(outfile, level, namespace_, name_='total_filament_length', pretty_print=pretty_print) if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'number_segments': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'number_segments') self.number_segments = ival_ elif nodeName_ == 'segment_length': obj_ = segment_lengthType.factory() obj_.build(child_) self.segment_length = obj_ obj_.original_tagname_ = 'segment_length' elif nodeName_ == 'segment_overlap': obj_ = segment_overlapType.factory() obj_.build(child_) self.segment_overlap = obj_ obj_.original_tagname_ = 'segment_overlap' elif nodeName_ == 'total_filament_length': obj_ = total_filament_lengthType.factory() obj_.build(child_) self.total_filament_length = obj_ obj_.original_tagname_ = 'total_filament_length' elif nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class segment_selectionType
[docs]class segment_lengthType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['non_zero_float', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if segment_lengthType.subclass: return segment_lengthType.subclass(*args_, **kwargs_) else: return segment_lengthType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='segment_lengthType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='segment_lengthType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='segment_lengthType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='segment_lengthType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='segment_lengthType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class segment_lengthType
[docs]class segment_overlapType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['non_zero_float', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if segment_overlapType.subclass: return segment_overlapType.subclass(*args_, **kwargs_) else: return segment_overlapType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='segment_overlapType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='segment_overlapType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='segment_overlapType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='segment_overlapType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='segment_overlapType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class segment_overlapType
[docs]class total_filament_lengthType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['non_zero_float', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if total_filament_lengthType.subclass: return total_filament_lengthType.subclass(*args_, **kwargs_) else: return total_filament_lengthType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='total_filament_lengthType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='total_filament_lengthType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='total_filament_lengthType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='total_filament_lengthType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='total_filament_lengthType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class total_filament_lengthType
[docs]class refinementType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('startup_model', 'starting_map_type', 1), MemberSpec_('starting_symmetry', 'starting_symmetryType', 1), MemberSpec_('software_list', 'software_list_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, startup_model=None, starting_symmetry=None, software_list=None, details=None): self.original_tagname_ = None if startup_model is None: self.startup_model = [] else: self.startup_model = startup_model if starting_symmetry is None: self.starting_symmetry = [] else: self.starting_symmetry = starting_symmetry self.software_list = software_list self.details = details
[docs] def factory(*args_, **kwargs_): if refinementType.subclass: return refinementType.subclass(*args_, **kwargs_) else: return refinementType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_startup_model(self): return self.startup_model
[docs] def set_startup_model(self, startup_model): self.startup_model = startup_model
[docs] def add_startup_model(self, value): self.startup_model.append(value)
[docs] def insert_startup_model_at(self, index, value): self.startup_model.insert(index, value)
[docs] def replace_startup_model_at(self, index, value): self.startup_model[index] = value
[docs] def get_starting_symmetry(self): return self.starting_symmetry
[docs] def set_starting_symmetry(self, starting_symmetry): self.starting_symmetry = starting_symmetry
[docs] def add_starting_symmetry(self, value): self.starting_symmetry.append(value)
[docs] def insert_starting_symmetry_at(self, index, value): self.starting_symmetry.insert(index, value)
[docs] def replace_starting_symmetry_at(self, index, value): self.starting_symmetry[index] = value
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def hasContent_(self): if ( self.startup_model or self.starting_symmetry or self.software_list is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='refinementType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='refinementType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='refinementType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='refinementType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='refinementType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for startup_model_ in self.startup_model: startup_model_.export(outfile, level, namespace_, name_='startup_model', pretty_print=pretty_print) for starting_symmetry_ in self.starting_symmetry: starting_symmetry_.export(outfile, level, namespace_, name_='starting_symmetry', pretty_print=pretty_print) if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'startup_model': obj_ = starting_map_type.factory() obj_.build(child_) self.startup_model.append(obj_) obj_.original_tagname_ = 'startup_model' elif nodeName_ == 'starting_symmetry': obj_ = starting_symmetryType.factory() obj_.build(child_) self.starting_symmetry.append(obj_) obj_.original_tagname_ = 'starting_symmetry' elif nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class refinementType
[docs]class starting_symmetryType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('helical_parameters', 'helical_parameters_type', 0), ] subclass = None superclass = None def __init__(self, helical_parameters=None): self.original_tagname_ = None self.helical_parameters = helical_parameters
[docs] def factory(*args_, **kwargs_): if starting_symmetryType.subclass: return starting_symmetryType.subclass(*args_, **kwargs_) else: return starting_symmetryType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_helical_parameters(self): return self.helical_parameters
[docs] def set_helical_parameters(self, helical_parameters): self.helical_parameters = helical_parameters
[docs] def hasContent_(self): if ( self.helical_parameters is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='starting_symmetryType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='starting_symmetryType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='starting_symmetryType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='starting_symmetryType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='starting_symmetryType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.helical_parameters is not None: self.helical_parameters.export(outfile, level, namespace_, name_='helical_parameters', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'helical_parameters': obj_ = helical_parameters_type.factory() obj_.build(child_) self.helical_parameters = obj_ obj_.original_tagname_ = 'helical_parameters' # end class starting_symmetryType
[docs]class layer_linesType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('number_helices', 'xs:string', 0), MemberSpec_('helix_length', 'helix_lengthType', 0), MemberSpec_('straightening', 'xs:boolean', 0), MemberSpec_('indexing', 'indexingType', 0), ] subclass = None superclass = None def __init__(self, number_helices=None, helix_length=None, straightening=None, indexing=None): self.original_tagname_ = None self.number_helices = number_helices self.helix_length = helix_length self.straightening = straightening self.indexing = indexing
[docs] def factory(*args_, **kwargs_): if layer_linesType.subclass: return layer_linesType.subclass(*args_, **kwargs_) else: return layer_linesType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_number_helices(self): return self.number_helices
[docs] def set_number_helices(self, number_helices): self.number_helices = number_helices
[docs] def get_helix_length(self): return self.helix_length
[docs] def set_helix_length(self, helix_length): self.helix_length = helix_length
[docs] def get_straightening(self): return self.straightening
[docs] def set_straightening(self, straightening): self.straightening = straightening
[docs] def get_indexing(self): return self.indexing
[docs] def set_indexing(self, indexing): self.indexing = indexing
[docs] def hasContent_(self): if ( self.number_helices is not None or self.helix_length is not None or self.straightening is not None or self.indexing is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='layer_linesType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='layer_linesType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='layer_linesType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='layer_linesType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='layer_linesType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.number_helices is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_helices>%s</%snumber_helices>%s' % (namespace_, self.gds_format_string(quote_xml(self.number_helices).encode(ExternalEncoding), input_name='number_helices'), namespace_, eol_)) if self.helix_length is not None: self.helix_length.export(outfile, level, namespace_, name_='helix_length', pretty_print=pretty_print) if self.straightening is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sstraightening>%s</%sstraightening>%s' % (namespace_, self.gds_format_boolean(self.straightening, input_name='straightening'), namespace_, eol_)) if self.indexing is not None: self.indexing.export(outfile, level, namespace_, name_='indexing', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'number_helices': number_helices_ = child_.text number_helices_ = self.gds_validate_string(number_helices_, node, 'number_helices') self.number_helices = number_helices_ elif nodeName_ == 'helix_length': obj_ = helix_lengthType.factory() obj_.build(child_) self.helix_length = obj_ obj_.original_tagname_ = 'helix_length' elif nodeName_ == 'straightening': sval_ = child_.text if sval_ in ('true', '1'): ival_ = True elif sval_ in ('false', '0'): ival_ = False else: raise_parse_error(child_, 'requires boolean') ival_ = self.gds_validate_boolean(ival_, node, 'straightening') self.straightening = ival_ elif nodeName_ == 'indexing': obj_ = indexingType.factory() obj_.build(child_) self.indexing = obj_ obj_.original_tagname_ = 'indexing' # end class layer_linesType
[docs]class number_helices(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if number_helices.subclass: return number_helices.subclass(*args_, **kwargs_) else: return number_helices(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='number_helices', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='number_helices') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='number_helices', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='number_helices'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='number_helices', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class number_helices
[docs]class helix_lengthType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('min', 'xs:string', 0), MemberSpec_('max', 'xs:string', 0), MemberSpec_('average', 'xs:string', 0), MemberSpec_('software_list', 'software_list_type', 0), ] subclass = None superclass = None def __init__(self, min=None, max=None, average=None, software_list=None): self.original_tagname_ = None self.min = min self.max = max self.average = average self.software_list = software_list
[docs] def factory(*args_, **kwargs_): if helix_lengthType.subclass: return helix_lengthType.subclass(*args_, **kwargs_) else: return helix_lengthType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_min(self): return self.min
[docs] def set_min(self, min): self.min = min
[docs] def get_max(self): return self.max
[docs] def set_max(self, max): self.max = max
[docs] def get_average(self): return self.average
[docs] def set_average(self, average): self.average = average
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def hasContent_(self): if ( self.min is not None or self.max is not None or self.average is not None or self.software_list is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='helix_lengthType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='helix_lengthType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='helix_lengthType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='helix_lengthType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='helix_lengthType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.min is not None: showIndent(outfile, level, pretty_print) outfile.write('<%smin>%s</%smin>%s' % (namespace_, self.gds_format_string(quote_xml(self.min).encode(ExternalEncoding), input_name='min'), namespace_, eol_)) if self.max is not None: showIndent(outfile, level, pretty_print) outfile.write('<%smax>%s</%smax>%s' % (namespace_, self.gds_format_string(quote_xml(self.max).encode(ExternalEncoding), input_name='max'), namespace_, eol_)) if self.average is not None: showIndent(outfile, level, pretty_print) outfile.write('<%saverage>%s</%saverage>%s' % (namespace_, self.gds_format_string(quote_xml(self.average).encode(ExternalEncoding), input_name='average'), namespace_, eol_)) if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'min': min_ = child_.text min_ = self.gds_validate_string(min_, node, 'min') self.min = min_ elif nodeName_ == 'max': max_ = child_.text max_ = self.gds_validate_string(max_, node, 'max') self.max = max_ elif nodeName_ == 'average': average_ = child_.text average_ = self.gds_validate_string(average_, node, 'average') self.average = average_ elif nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' # end class helix_lengthType
[docs]class min(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if min.subclass: return min.subclass(*args_, **kwargs_) else: return min(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='min', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='min') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='min', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='min'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='min', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class min
[docs]class max(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if max.subclass: return max.subclass(*args_, **kwargs_) else: return max(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='max', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='max') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='max', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='max'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='max', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class max
[docs]class average(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if average.subclass: return average.subclass(*args_, **kwargs_) else: return average(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='average', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='average') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='average', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='average'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='average', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class average
[docs]class indexingType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('software_list', 'software_list_type', 0), ] subclass = None superclass = None def __init__(self, software_list=None): self.original_tagname_ = None self.software_list = software_list
[docs] def factory(*args_, **kwargs_): if indexingType.subclass: return indexingType.subclass(*args_, **kwargs_) else: return indexingType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def hasContent_(self): if ( self.software_list is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='indexingType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='indexingType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='indexingType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='indexingType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='indexingType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' # end class indexingType
[docs]class final_multi_reference_alignmentType11(GeneratedsSuper): member_data_items_ = [ MemberSpec_('number_reference_projections', 'xs:positiveInteger', 0), MemberSpec_('merit_function', 'xs:string', 0), MemberSpec_('angular_sampling', 'angular_samplingType12', 0), MemberSpec_('software_list', 'software_list_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, number_reference_projections=None, merit_function=None, angular_sampling=None, software_list=None, details=None): self.original_tagname_ = None self.number_reference_projections = number_reference_projections self.merit_function = merit_function self.angular_sampling = angular_sampling self.software_list = software_list self.details = details
[docs] def factory(*args_, **kwargs_): if final_multi_reference_alignmentType11.subclass: return final_multi_reference_alignmentType11.subclass(*args_, **kwargs_) else: return final_multi_reference_alignmentType11(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_number_reference_projections(self): return self.number_reference_projections
[docs] def set_number_reference_projections(self, number_reference_projections): self.number_reference_projections = number_reference_projections
[docs] def get_merit_function(self): return self.merit_function
[docs] def set_merit_function(self, merit_function): self.merit_function = merit_function
[docs] def get_angular_sampling(self): return self.angular_sampling
[docs] def set_angular_sampling(self, angular_sampling): self.angular_sampling = angular_sampling
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def hasContent_(self): if ( self.number_reference_projections is not None or self.merit_function is not None or self.angular_sampling is not None or self.software_list is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='final_multi_reference_alignmentType11', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='final_multi_reference_alignmentType11') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='final_multi_reference_alignmentType11', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='final_multi_reference_alignmentType11'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='final_multi_reference_alignmentType11', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.number_reference_projections is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_reference_projections>%s</%snumber_reference_projections>%s' % (namespace_, self.gds_format_integer(self.number_reference_projections, input_name='number_reference_projections'), namespace_, eol_)) if self.merit_function is not None: showIndent(outfile, level, pretty_print) outfile.write('<%smerit_function>%s</%smerit_function>%s' % (namespace_, self.gds_format_string(quote_xml(self.merit_function).encode(ExternalEncoding), input_name='merit_function'), namespace_, eol_)) if self.angular_sampling is not None: self.angular_sampling.export(outfile, level, namespace_, name_='angular_sampling', pretty_print=pretty_print) if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'number_reference_projections': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'number_reference_projections') self.number_reference_projections = ival_ elif nodeName_ == 'merit_function': merit_function_ = child_.text merit_function_ = self.gds_validate_string(merit_function_, node, 'merit_function') self.merit_function = merit_function_ elif nodeName_ == 'angular_sampling': obj_ = angular_samplingType12.factory() obj_.build(child_) self.angular_sampling = obj_ obj_.original_tagname_ = 'angular_sampling' elif nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class final_multi_reference_alignmentType11
[docs]class angular_samplingType12(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_angular_sampling', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if angular_samplingType12.subclass: return angular_samplingType12.subclass(*args_, **kwargs_) else: return angular_samplingType12(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='angular_samplingType12', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='angular_samplingType12') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='angular_samplingType12', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='angular_samplingType12'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='angular_samplingType12', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class angular_samplingType12
[docs]class extractionType13(GeneratedsSuper): member_data_items_ = [ MemberSpec_('number_tomograms', 'xs:positiveInteger', 0), MemberSpec_('number_subtomograms', 'xs:positiveInteger', 0), MemberSpec_('reference_model', 'xs:token', 0), MemberSpec_('method', 'xs:string', 0), MemberSpec_('software_list', 'software_list_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, number_tomograms=None, number_subtomograms=None, reference_model=None, method=None, software_list=None, details=None): self.original_tagname_ = None self.number_tomograms = number_tomograms self.number_subtomograms = number_subtomograms self.reference_model = reference_model self.method = method self.software_list = software_list self.details = details
[docs] def factory(*args_, **kwargs_): if extractionType13.subclass: return extractionType13.subclass(*args_, **kwargs_) else: return extractionType13(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_number_tomograms(self): return self.number_tomograms
[docs] def set_number_tomograms(self, number_tomograms): self.number_tomograms = number_tomograms
[docs] def get_number_subtomograms(self): return self.number_subtomograms
[docs] def set_number_subtomograms(self, number_subtomograms): self.number_subtomograms = number_subtomograms
[docs] def get_reference_model(self): return self.reference_model
[docs] def set_reference_model(self, reference_model): self.reference_model = reference_model
[docs] def get_method(self): return self.method
[docs] def set_method(self, method): self.method = method
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def hasContent_(self): if ( self.number_tomograms is not None or self.number_subtomograms is not None or self.reference_model is not None or self.method is not None or self.software_list is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='extractionType13', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='extractionType13') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='extractionType13', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='extractionType13'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='extractionType13', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.number_tomograms is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_tomograms>%s</%snumber_tomograms>%s' % (namespace_, self.gds_format_integer(self.number_tomograms, input_name='number_tomograms'), namespace_, eol_)) if self.number_subtomograms is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_subtomograms>%s</%snumber_subtomograms>%s' % (namespace_, self.gds_format_integer(self.number_subtomograms, input_name='number_subtomograms'), namespace_, eol_)) if self.reference_model is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sreference_model>%s</%sreference_model>%s' % (namespace_, self.gds_format_string(quote_xml(self.reference_model).encode(ExternalEncoding), input_name='reference_model'), namespace_, eol_)) if self.method is not None: showIndent(outfile, level, pretty_print) outfile.write('<%smethod>%s</%smethod>%s' % (namespace_, self.gds_format_string(quote_xml(self.method).encode(ExternalEncoding), input_name='method'), namespace_, eol_)) if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'number_tomograms': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'number_tomograms') self.number_tomograms = ival_ elif nodeName_ == 'number_subtomograms': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'number_subtomograms') self.number_subtomograms = ival_ elif nodeName_ == 'reference_model': reference_model_ = child_.text reference_model_ = re_.sub(String_cleanup_pat_, " ", reference_model_).strip() reference_model_ = self.gds_validate_string(reference_model_, node, 'reference_model') self.reference_model = reference_model_ elif nodeName_ == 'method': method_ = child_.text method_ = self.gds_validate_string(method_, node, 'method') self.method = method_ elif nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class extractionType13
[docs]class final_multi_reference_alignmentType14(GeneratedsSuper): member_data_items_ = [ MemberSpec_('number_reference_projections', 'xs:positiveInteger', 0), MemberSpec_('merit_function', 'xs:string', 0), MemberSpec_('software_list', 'software_list_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, number_reference_projections=None, merit_function=None, software_list=None, details=None): self.original_tagname_ = None self.number_reference_projections = number_reference_projections self.merit_function = merit_function self.software_list = software_list self.details = details
[docs] def factory(*args_, **kwargs_): if final_multi_reference_alignmentType14.subclass: return final_multi_reference_alignmentType14.subclass(*args_, **kwargs_) else: return final_multi_reference_alignmentType14(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_number_reference_projections(self): return self.number_reference_projections
[docs] def set_number_reference_projections(self, number_reference_projections): self.number_reference_projections = number_reference_projections
[docs] def get_merit_function(self): return self.merit_function
[docs] def set_merit_function(self, merit_function): self.merit_function = merit_function
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def hasContent_(self): if ( self.number_reference_projections is not None or self.merit_function is not None or self.software_list is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='final_multi_reference_alignmentType14', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='final_multi_reference_alignmentType14') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='final_multi_reference_alignmentType14', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='final_multi_reference_alignmentType14'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='final_multi_reference_alignmentType14', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.number_reference_projections is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_reference_projections>%s</%snumber_reference_projections>%s' % (namespace_, self.gds_format_integer(self.number_reference_projections, input_name='number_reference_projections'), namespace_, eol_)) if self.merit_function is not None: showIndent(outfile, level, pretty_print) outfile.write('<%smerit_function>%s</%smerit_function>%s' % (namespace_, self.gds_format_string(quote_xml(self.merit_function).encode(ExternalEncoding), input_name='merit_function'), namespace_, eol_)) if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'number_reference_projections': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'number_reference_projections') self.number_reference_projections = ival_ elif nodeName_ == 'merit_function': merit_function_ = child_.text merit_function_ = self.gds_validate_string(merit_function_, node, 'merit_function') self.merit_function = merit_function_ elif nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class final_multi_reference_alignmentType14
[docs]class molecular_replacementType15(GeneratedsSuper): member_data_items_ = [ MemberSpec_('starting_model', 'starting_modelType16', 1), MemberSpec_('resolution_range', 'resolution_rangeType17', 0), MemberSpec_('software_list', 'software_list_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, starting_model=None, resolution_range=None, software_list=None, details=None): self.original_tagname_ = None if starting_model is None: self.starting_model = [] else: self.starting_model = starting_model self.resolution_range = resolution_range self.software_list = software_list self.details = details
[docs] def factory(*args_, **kwargs_): if molecular_replacementType15.subclass: return molecular_replacementType15.subclass(*args_, **kwargs_) else: return molecular_replacementType15(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_starting_model(self): return self.starting_model
[docs] def set_starting_model(self, starting_model): self.starting_model = starting_model
[docs] def add_starting_model(self, value): self.starting_model.append(value)
[docs] def insert_starting_model_at(self, index, value): self.starting_model.insert(index, value)
[docs] def replace_starting_model_at(self, index, value): self.starting_model[index] = value
[docs] def get_resolution_range(self): return self.resolution_range
[docs] def set_resolution_range(self, resolution_range): self.resolution_range = resolution_range
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def hasContent_(self): if ( self.starting_model or self.resolution_range is not None or self.software_list is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='molecular_replacementType15', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='molecular_replacementType15') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='molecular_replacementType15', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='molecular_replacementType15'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='molecular_replacementType15', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for starting_model_ in self.starting_model: starting_model_.export(outfile, level, namespace_, name_='starting_model', pretty_print=pretty_print) if self.resolution_range is not None: self.resolution_range.export(outfile, level, namespace_, name_='resolution_range', pretty_print=pretty_print) if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'starting_model': obj_ = starting_modelType16.factory() obj_.build(child_) self.starting_model.append(obj_) obj_.original_tagname_ = 'starting_model' elif nodeName_ == 'resolution_range': obj_ = resolution_rangeType17.factory() obj_.build(child_) self.resolution_range = obj_ obj_.original_tagname_ = 'resolution_range' elif nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class molecular_replacementType15
[docs]class starting_modelType16(GeneratedsSuper): member_data_items_ = [ MemberSpec_('access_code', ['pdb_code_type', 'xs:token'], 0), MemberSpec_('chain', 'chain_type', 1), ] subclass = None superclass = None def __init__(self, access_code=None, chain=None): self.original_tagname_ = None self.access_code = access_code self.validate_pdb_code_type(self.access_code) if chain is None: self.chain = [] else: self.chain = chain
[docs] def factory(*args_, **kwargs_): if starting_modelType16.subclass: return starting_modelType16.subclass(*args_, **kwargs_) else: return starting_modelType16(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_access_code(self): return self.access_code
[docs] def set_access_code(self, access_code): self.access_code = access_code
[docs] def get_chain(self): return self.chain
[docs] def set_chain(self, chain): self.chain = chain
[docs] def add_chain(self, value): self.chain.append(value)
[docs] def insert_chain_at(self, index, value): self.chain.insert(index, value)
[docs] def replace_chain_at(self, index, value): self.chain[index] = value
[docs] def validate_pdb_code_type(self, value): # Validate type pdb_code_type, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_pdb_code_type_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_pdb_code_type_patterns_, ))
validate_pdb_code_type_patterns_ = [['^\\d[\\dA-Za-z]{3}$']]
[docs] def hasContent_(self): if ( self.access_code is not None or self.chain ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='starting_modelType16', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='starting_modelType16') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='starting_modelType16', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='starting_modelType16'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='starting_modelType16', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.access_code is not None: showIndent(outfile, level, pretty_print) outfile.write('<%saccess_code>%s</%saccess_code>%s' % (namespace_, self.gds_format_string(quote_xml(self.access_code).encode(ExternalEncoding), input_name='access_code'), namespace_, eol_)) for chain_ in self.chain: chain_.export(outfile, level, namespace_, name_='chain', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'access_code': access_code_ = child_.text access_code_ = re_.sub(String_cleanup_pat_, " ", access_code_).strip() access_code_ = self.gds_validate_string(access_code_, node, 'access_code') self.access_code = access_code_ # validate type pdb_code_type self.validate_pdb_code_type(self.access_code) elif nodeName_ == 'chain': class_obj_ = self.get_class_obj_(child_, chain_type) obj_ = class_obj_.factory() obj_.build(child_) self.chain.append(obj_) obj_.original_tagname_ = 'chain' # end class starting_modelType16
[docs]class resolution_rangeType17(GeneratedsSuper): member_data_items_ = [ MemberSpec_('high_resolution', 'high_resolutionType18', 0), MemberSpec_('low_resolution', 'low_resolutionType19', 0), ] subclass = None superclass = None def __init__(self, high_resolution=None, low_resolution=None): self.original_tagname_ = None self.high_resolution = high_resolution self.low_resolution = low_resolution
[docs] def factory(*args_, **kwargs_): if resolution_rangeType17.subclass: return resolution_rangeType17.subclass(*args_, **kwargs_) else: return resolution_rangeType17(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_high_resolution(self): return self.high_resolution
[docs] def set_high_resolution(self, high_resolution): self.high_resolution = high_resolution
[docs] def get_low_resolution(self): return self.low_resolution
[docs] def set_low_resolution(self, low_resolution): self.low_resolution = low_resolution
[docs] def hasContent_(self): if ( self.high_resolution is not None or self.low_resolution is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='resolution_rangeType17', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='resolution_rangeType17') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='resolution_rangeType17', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='resolution_rangeType17'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='resolution_rangeType17', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.high_resolution is not None: self.high_resolution.export(outfile, level, namespace_, name_='high_resolution', pretty_print=pretty_print) if self.low_resolution is not None: self.low_resolution.export(outfile, level, namespace_, name_='low_resolution', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'high_resolution': obj_ = high_resolutionType18.factory() obj_.build(child_) self.high_resolution = obj_ obj_.original_tagname_ = 'high_resolution' elif nodeName_ == 'low_resolution': obj_ = low_resolutionType19.factory() obj_.build(child_) self.low_resolution = obj_ obj_.original_tagname_ = 'low_resolution' # end class resolution_rangeType17
[docs]class high_resolutionType18(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['resolution_type', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if high_resolutionType18.subclass: return high_resolutionType18.subclass(*args_, **kwargs_) else: return high_resolutionType18(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='high_resolutionType18', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='high_resolutionType18') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='high_resolutionType18', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='high_resolutionType18'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='high_resolutionType18', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class high_resolutionType18
[docs]class low_resolutionType19(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['resolution_type', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if low_resolutionType19.subclass: return low_resolutionType19.subclass(*args_, **kwargs_) else: return low_resolutionType19(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='low_resolutionType19', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='low_resolutionType19') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='low_resolutionType19', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='low_resolutionType19'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='low_resolutionType19', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class low_resolutionType19
[docs]class lattice_distortion_correctionType20(GeneratedsSuper): member_data_items_ = [ MemberSpec_('software_list', 'software_list_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, software_list=None, details=None): self.original_tagname_ = None self.software_list = software_list self.details = details
[docs] def factory(*args_, **kwargs_): if lattice_distortion_correctionType20.subclass: return lattice_distortion_correctionType20.subclass(*args_, **kwargs_) else: return lattice_distortion_correctionType20(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def hasContent_(self): if ( self.software_list is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='lattice_distortion_correctionType20', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='lattice_distortion_correctionType20') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='lattice_distortion_correctionType20', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='lattice_distortion_correctionType20'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='lattice_distortion_correctionType20', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class lattice_distortion_correctionType20
[docs]class symmetry_determinationType21(GeneratedsSuper): member_data_items_ = [ MemberSpec_('software_list', 'software_list_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, software_list=None, details=None): self.original_tagname_ = None self.software_list = software_list self.details = details
[docs] def factory(*args_, **kwargs_): if symmetry_determinationType21.subclass: return symmetry_determinationType21.subclass(*args_, **kwargs_) else: return symmetry_determinationType21(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def hasContent_(self): if ( self.software_list is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='symmetry_determinationType21', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='symmetry_determinationType21') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='symmetry_determinationType21', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='symmetry_determinationType21'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='symmetry_determinationType21', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class symmetry_determinationType21
[docs]class mergingType22(GeneratedsSuper): member_data_items_ = [ MemberSpec_('software_list', 'software_list_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, software_list=None, details=None): self.original_tagname_ = None self.software_list = software_list self.details = details
[docs] def factory(*args_, **kwargs_): if mergingType22.subclass: return mergingType22.subclass(*args_, **kwargs_) else: return mergingType22(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def hasContent_(self): if ( self.software_list is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='mergingType22', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='mergingType22') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='mergingType22', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='mergingType22'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='mergingType22', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class mergingType22
[docs]class segment_selectionType23(GeneratedsSuper): member_data_items_ = [ MemberSpec_('number_segments', 'xs:positiveInteger', 0), MemberSpec_('segment_length', 'segment_lengthType24', 0), MemberSpec_('segment_overlap', 'segment_overlapType25', 0), MemberSpec_('total_filament_length', 'total_filament_lengthType26', 0), MemberSpec_('software_list', 'software_list_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, number_segments=None, segment_length=None, segment_overlap=None, total_filament_length=None, software_list=None, details=None): self.original_tagname_ = None self.number_segments = number_segments self.segment_length = segment_length self.segment_overlap = segment_overlap self.total_filament_length = total_filament_length self.software_list = software_list self.details = details
[docs] def factory(*args_, **kwargs_): if segment_selectionType23.subclass: return segment_selectionType23.subclass(*args_, **kwargs_) else: return segment_selectionType23(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_number_segments(self): return self.number_segments
[docs] def set_number_segments(self, number_segments): self.number_segments = number_segments
[docs] def get_segment_length(self): return self.segment_length
[docs] def set_segment_length(self, segment_length): self.segment_length = segment_length
[docs] def get_segment_overlap(self): return self.segment_overlap
[docs] def set_segment_overlap(self, segment_overlap): self.segment_overlap = segment_overlap
[docs] def get_total_filament_length(self): return self.total_filament_length
[docs] def set_total_filament_length(self, total_filament_length): self.total_filament_length = total_filament_length
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def hasContent_(self): if ( self.number_segments is not None or self.segment_length is not None or self.segment_overlap is not None or self.total_filament_length is not None or self.software_list is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='segment_selectionType23', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='segment_selectionType23') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='segment_selectionType23', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='segment_selectionType23'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='segment_selectionType23', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.number_segments is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_segments>%s</%snumber_segments>%s' % (namespace_, self.gds_format_integer(self.number_segments, input_name='number_segments'), namespace_, eol_)) if self.segment_length is not None: self.segment_length.export(outfile, level, namespace_, name_='segment_length', pretty_print=pretty_print) if self.segment_overlap is not None: self.segment_overlap.export(outfile, level, namespace_, name_='segment_overlap', pretty_print=pretty_print) if self.total_filament_length is not None: self.total_filament_length.export(outfile, level, namespace_, name_='total_filament_length', pretty_print=pretty_print) if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'number_segments': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'number_segments') self.number_segments = ival_ elif nodeName_ == 'segment_length': obj_ = segment_lengthType24.factory() obj_.build(child_) self.segment_length = obj_ obj_.original_tagname_ = 'segment_length' elif nodeName_ == 'segment_overlap': obj_ = segment_overlapType25.factory() obj_.build(child_) self.segment_overlap = obj_ obj_.original_tagname_ = 'segment_overlap' elif nodeName_ == 'total_filament_length': obj_ = total_filament_lengthType26.factory() obj_.build(child_) self.total_filament_length = obj_ obj_.original_tagname_ = 'total_filament_length' elif nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class segment_selectionType23
[docs]class segment_lengthType24(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['non_zero_float', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if segment_lengthType24.subclass: return segment_lengthType24.subclass(*args_, **kwargs_) else: return segment_lengthType24(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='segment_lengthType24', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='segment_lengthType24') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='segment_lengthType24', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='segment_lengthType24'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='segment_lengthType24', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class segment_lengthType24
[docs]class segment_overlapType25(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['non_zero_float', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if segment_overlapType25.subclass: return segment_overlapType25.subclass(*args_, **kwargs_) else: return segment_overlapType25(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='segment_overlapType25', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='segment_overlapType25') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='segment_overlapType25', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='segment_overlapType25'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='segment_overlapType25', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class segment_overlapType25
[docs]class total_filament_lengthType26(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['non_zero_float', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if total_filament_lengthType26.subclass: return total_filament_lengthType26.subclass(*args_, **kwargs_) else: return total_filament_lengthType26(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='total_filament_lengthType26', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='total_filament_lengthType26') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='total_filament_lengthType26', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='total_filament_lengthType26'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='total_filament_lengthType26', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class total_filament_lengthType26
[docs]class refinementType27(GeneratedsSuper): member_data_items_ = [ MemberSpec_('startup_model', 'starting_map_type', 1), MemberSpec_('starting_symmetry', 'starting_symmetryType28', 1), MemberSpec_('software_list', 'software_list_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, startup_model=None, starting_symmetry=None, software_list=None, details=None): self.original_tagname_ = None if startup_model is None: self.startup_model = [] else: self.startup_model = startup_model if starting_symmetry is None: self.starting_symmetry = [] else: self.starting_symmetry = starting_symmetry self.software_list = software_list self.details = details
[docs] def factory(*args_, **kwargs_): if refinementType27.subclass: return refinementType27.subclass(*args_, **kwargs_) else: return refinementType27(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_startup_model(self): return self.startup_model
[docs] def set_startup_model(self, startup_model): self.startup_model = startup_model
[docs] def add_startup_model(self, value): self.startup_model.append(value)
[docs] def insert_startup_model_at(self, index, value): self.startup_model.insert(index, value)
[docs] def replace_startup_model_at(self, index, value): self.startup_model[index] = value
[docs] def get_starting_symmetry(self): return self.starting_symmetry
[docs] def set_starting_symmetry(self, starting_symmetry): self.starting_symmetry = starting_symmetry
[docs] def add_starting_symmetry(self, value): self.starting_symmetry.append(value)
[docs] def insert_starting_symmetry_at(self, index, value): self.starting_symmetry.insert(index, value)
[docs] def replace_starting_symmetry_at(self, index, value): self.starting_symmetry[index] = value
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def hasContent_(self): if ( self.startup_model or self.starting_symmetry or self.software_list is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='refinementType27', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='refinementType27') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='refinementType27', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='refinementType27'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='refinementType27', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for startup_model_ in self.startup_model: startup_model_.export(outfile, level, namespace_, name_='startup_model', pretty_print=pretty_print) for starting_symmetry_ in self.starting_symmetry: starting_symmetry_.export(outfile, level, namespace_, name_='starting_symmetry', pretty_print=pretty_print) if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'startup_model': obj_ = starting_map_type.factory() obj_.build(child_) self.startup_model.append(obj_) obj_.original_tagname_ = 'startup_model' elif nodeName_ == 'starting_symmetry': obj_ = starting_symmetryType28.factory() obj_.build(child_) self.starting_symmetry.append(obj_) obj_.original_tagname_ = 'starting_symmetry' elif nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class refinementType27
[docs]class starting_symmetryType28(GeneratedsSuper): member_data_items_ = [ MemberSpec_('helical_parameters', 'helical_parameters_type', 0), ] subclass = None superclass = None def __init__(self, helical_parameters=None): self.original_tagname_ = None self.helical_parameters = helical_parameters
[docs] def factory(*args_, **kwargs_): if starting_symmetryType28.subclass: return starting_symmetryType28.subclass(*args_, **kwargs_) else: return starting_symmetryType28(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_helical_parameters(self): return self.helical_parameters
[docs] def set_helical_parameters(self, helical_parameters): self.helical_parameters = helical_parameters
[docs] def hasContent_(self): if ( self.helical_parameters is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='starting_symmetryType28', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='starting_symmetryType28') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='starting_symmetryType28', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='starting_symmetryType28'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='starting_symmetryType28', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.helical_parameters is not None: self.helical_parameters.export(outfile, level, namespace_, name_='helical_parameters', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'helical_parameters': obj_ = helical_parameters_type.factory() obj_.build(child_) self.helical_parameters = obj_ obj_.original_tagname_ = 'helical_parameters' # end class starting_symmetryType28
[docs]class layer_linesType29(GeneratedsSuper): member_data_items_ = [ MemberSpec_('number_helices', 'xs:string', 0), MemberSpec_('helix_length', 'helix_lengthType30', 0), MemberSpec_('straightening', 'xs:boolean', 0), MemberSpec_('indexing', 'indexingType31', 0), ] subclass = None superclass = None def __init__(self, number_helices=None, helix_length=None, straightening=None, indexing=None): self.original_tagname_ = None self.number_helices = number_helices self.helix_length = helix_length self.straightening = straightening self.indexing = indexing
[docs] def factory(*args_, **kwargs_): if layer_linesType29.subclass: return layer_linesType29.subclass(*args_, **kwargs_) else: return layer_linesType29(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_number_helices(self): return self.number_helices
[docs] def set_number_helices(self, number_helices): self.number_helices = number_helices
[docs] def get_helix_length(self): return self.helix_length
[docs] def set_helix_length(self, helix_length): self.helix_length = helix_length
[docs] def get_straightening(self): return self.straightening
[docs] def set_straightening(self, straightening): self.straightening = straightening
[docs] def get_indexing(self): return self.indexing
[docs] def set_indexing(self, indexing): self.indexing = indexing
[docs] def hasContent_(self): if ( self.number_helices is not None or self.helix_length is not None or self.straightening is not None or self.indexing is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='layer_linesType29', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='layer_linesType29') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='layer_linesType29', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='layer_linesType29'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='layer_linesType29', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.number_helices is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_helices>%s</%snumber_helices>%s' % (namespace_, self.gds_format_string(quote_xml(self.number_helices).encode(ExternalEncoding), input_name='number_helices'), namespace_, eol_)) if self.helix_length is not None: self.helix_length.export(outfile, level, namespace_, name_='helix_length', pretty_print=pretty_print) if self.straightening is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sstraightening>%s</%sstraightening>%s' % (namespace_, self.gds_format_boolean(self.straightening, input_name='straightening'), namespace_, eol_)) if self.indexing is not None: self.indexing.export(outfile, level, namespace_, name_='indexing', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'number_helices': number_helices_ = child_.text number_helices_ = self.gds_validate_string(number_helices_, node, 'number_helices') self.number_helices = number_helices_ elif nodeName_ == 'helix_length': obj_ = helix_lengthType30.factory() obj_.build(child_) self.helix_length = obj_ obj_.original_tagname_ = 'helix_length' elif nodeName_ == 'straightening': sval_ = child_.text if sval_ in ('true', '1'): ival_ = True elif sval_ in ('false', '0'): ival_ = False else: raise_parse_error(child_, 'requires boolean') ival_ = self.gds_validate_boolean(ival_, node, 'straightening') self.straightening = ival_ elif nodeName_ == 'indexing': obj_ = indexingType31.factory() obj_.build(child_) self.indexing = obj_ obj_.original_tagname_ = 'indexing' # end class layer_linesType29
[docs]class helix_lengthType30(GeneratedsSuper): member_data_items_ = [ MemberSpec_('min', 'xs:string', 0), MemberSpec_('max', 'xs:string', 0), MemberSpec_('average', 'xs:string', 0), MemberSpec_('software_list', 'software_list_type', 0), ] subclass = None superclass = None def __init__(self, min=None, max=None, average=None, software_list=None): self.original_tagname_ = None self.min = min self.max = max self.average = average self.software_list = software_list
[docs] def factory(*args_, **kwargs_): if helix_lengthType30.subclass: return helix_lengthType30.subclass(*args_, **kwargs_) else: return helix_lengthType30(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_min(self): return self.min
[docs] def set_min(self, min): self.min = min
[docs] def get_max(self): return self.max
[docs] def set_max(self, max): self.max = max
[docs] def get_average(self): return self.average
[docs] def set_average(self, average): self.average = average
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def hasContent_(self): if ( self.min is not None or self.max is not None or self.average is not None or self.software_list is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='helix_lengthType30', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='helix_lengthType30') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='helix_lengthType30', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='helix_lengthType30'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='helix_lengthType30', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.min is not None: showIndent(outfile, level, pretty_print) outfile.write('<%smin>%s</%smin>%s' % (namespace_, self.gds_format_string(quote_xml(self.min).encode(ExternalEncoding), input_name='min'), namespace_, eol_)) if self.max is not None: showIndent(outfile, level, pretty_print) outfile.write('<%smax>%s</%smax>%s' % (namespace_, self.gds_format_string(quote_xml(self.max).encode(ExternalEncoding), input_name='max'), namespace_, eol_)) if self.average is not None: showIndent(outfile, level, pretty_print) outfile.write('<%saverage>%s</%saverage>%s' % (namespace_, self.gds_format_string(quote_xml(self.average).encode(ExternalEncoding), input_name='average'), namespace_, eol_)) if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'min': min_ = child_.text min_ = self.gds_validate_string(min_, node, 'min') self.min = min_ elif nodeName_ == 'max': max_ = child_.text max_ = self.gds_validate_string(max_, node, 'max') self.max = max_ elif nodeName_ == 'average': average_ = child_.text average_ = self.gds_validate_string(average_, node, 'average') self.average = average_ elif nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' # end class helix_lengthType30
[docs]class indexingType31(GeneratedsSuper): member_data_items_ = [ MemberSpec_('software_list', 'software_list_type', 0), ] subclass = None superclass = None def __init__(self, software_list=None): self.original_tagname_ = None self.software_list = software_list
[docs] def factory(*args_, **kwargs_): if indexingType31.subclass: return indexingType31.subclass(*args_, **kwargs_) else: return indexingType31(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def hasContent_(self): if ( self.software_list is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='indexingType31', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='indexingType31') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='indexingType31', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='indexingType31'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='indexingType31', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' # end class indexingType31
[docs]class random_conical_tiltType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('number_images', 'xs:positiveInteger', 0), MemberSpec_('tilt_angle', 'tilt_angleType', 0), MemberSpec_('software_list', 'software_list_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, number_images=None, tilt_angle=None, software_list=None, details=None): self.original_tagname_ = None self.number_images = number_images self.tilt_angle = tilt_angle self.software_list = software_list self.details = details
[docs] def factory(*args_, **kwargs_): if random_conical_tiltType.subclass: return random_conical_tiltType.subclass(*args_, **kwargs_) else: return random_conical_tiltType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_number_images(self): return self.number_images
[docs] def set_number_images(self, number_images): self.number_images = number_images
[docs] def get_tilt_angle(self): return self.tilt_angle
[docs] def set_tilt_angle(self, tilt_angle): self.tilt_angle = tilt_angle
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def hasContent_(self): if ( self.number_images is not None or self.tilt_angle is not None or self.software_list is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='random_conical_tiltType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='random_conical_tiltType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='random_conical_tiltType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='random_conical_tiltType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='random_conical_tiltType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.number_images is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_images>%s</%snumber_images>%s' % (namespace_, self.gds_format_integer(self.number_images, input_name='number_images'), namespace_, eol_)) if self.tilt_angle is not None: self.tilt_angle.export(outfile, level, namespace_, name_='tilt_angle', pretty_print=pretty_print) if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'number_images': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'number_images') self.number_images = ival_ elif nodeName_ == 'tilt_angle': obj_ = tilt_angleType.factory() obj_.build(child_) self.tilt_angle = obj_ obj_.original_tagname_ = 'tilt_angle' elif nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class random_conical_tiltType
[docs]class tilt_angleType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_tilt_angle_random_conical', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if tilt_angleType.subclass: return tilt_angleType.subclass(*args_, **kwargs_) else: return tilt_angleType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='tilt_angleType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='tilt_angleType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='tilt_angleType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='tilt_angleType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='tilt_angleType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class tilt_angleType
[docs]class orthogonal_tiltType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('software_list', 'software_list_type', 0), MemberSpec_('number_images', 'xs:positiveInteger', 0), MemberSpec_('tilt_angle1', 'tilt_angle1Type', 0), MemberSpec_('tilt_angle2', 'tilt_angle2Type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, software_list=None, number_images=None, tilt_angle1=None, tilt_angle2=None, details=None): self.original_tagname_ = None self.software_list = software_list self.number_images = number_images self.tilt_angle1 = tilt_angle1 self.tilt_angle2 = tilt_angle2 self.details = details
[docs] def factory(*args_, **kwargs_): if orthogonal_tiltType.subclass: return orthogonal_tiltType.subclass(*args_, **kwargs_) else: return orthogonal_tiltType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def get_number_images(self): return self.number_images
[docs] def set_number_images(self, number_images): self.number_images = number_images
[docs] def get_tilt_angle1(self): return self.tilt_angle1
[docs] def set_tilt_angle1(self, tilt_angle1): self.tilt_angle1 = tilt_angle1
[docs] def get_tilt_angle2(self): return self.tilt_angle2
[docs] def set_tilt_angle2(self, tilt_angle2): self.tilt_angle2 = tilt_angle2
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def hasContent_(self): if ( self.software_list is not None or self.number_images is not None or self.tilt_angle1 is not None or self.tilt_angle2 is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='orthogonal_tiltType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='orthogonal_tiltType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='orthogonal_tiltType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='orthogonal_tiltType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='orthogonal_tiltType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print) if self.number_images is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_images>%s</%snumber_images>%s' % (namespace_, self.gds_format_integer(self.number_images, input_name='number_images'), namespace_, eol_)) if self.tilt_angle1 is not None: self.tilt_angle1.export(outfile, level, namespace_, name_='tilt_angle1', pretty_print=pretty_print) if self.tilt_angle2 is not None: self.tilt_angle2.export(outfile, level, namespace_, name_='tilt_angle2', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' elif nodeName_ == 'number_images': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'number_images') self.number_images = ival_ elif nodeName_ == 'tilt_angle1': obj_ = tilt_angle1Type.factory() obj_.build(child_) self.tilt_angle1 = obj_ obj_.original_tagname_ = 'tilt_angle1' elif nodeName_ == 'tilt_angle2': obj_ = tilt_angle2Type.factory() obj_.build(child_) self.tilt_angle2 = obj_ obj_.original_tagname_ = 'tilt_angle2' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class orthogonal_tiltType
[docs]class tilt_angle1Type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_tilt_angle1Orthogonal', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if tilt_angle1Type.subclass: return tilt_angle1Type.subclass(*args_, **kwargs_) else: return tilt_angle1Type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='tilt_angle1Type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='tilt_angle1Type') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='tilt_angle1Type', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='tilt_angle1Type'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='tilt_angle1Type', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class tilt_angle1Type
[docs]class tilt_angle2Type(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_tilt_angle2Orthogonal', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if tilt_angle2Type.subclass: return tilt_angle2Type.subclass(*args_, **kwargs_) else: return tilt_angle2Type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='tilt_angle2Type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='tilt_angle2Type') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='tilt_angle2Type', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='tilt_angle2Type'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='tilt_angle2Type', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class tilt_angle2Type
[docs]class originType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('col', 'xs:integer', 0), MemberSpec_('row', 'xs:integer', 0), MemberSpec_('sec', 'xs:integer', 0), ] subclass = None superclass = None def __init__(self, col=None, row=None, sec=None): self.original_tagname_ = None self.col = col self.row = row self.sec = sec
[docs] def factory(*args_, **kwargs_): if originType.subclass: return originType.subclass(*args_, **kwargs_) else: return originType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_col(self): return self.col
[docs] def set_col(self, col): self.col = col
[docs] def get_row(self): return self.row
[docs] def set_row(self, row): self.row = row
[docs] def get_sec(self): return self.sec
[docs] def set_sec(self, sec): self.sec = sec
[docs] def hasContent_(self): if ( self.col is not None or self.row is not None or self.sec is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='originType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='originType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='originType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='originType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='originType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.col is not None: showIndent(outfile, level, pretty_print) outfile.write('<%scol>%s</%scol>%s' % (namespace_, self.gds_format_integer(self.col, input_name='col'), namespace_, eol_)) if self.row is not None: showIndent(outfile, level, pretty_print) outfile.write('<%srow>%s</%srow>%s' % (namespace_, self.gds_format_integer(self.row, input_name='row'), namespace_, eol_)) if self.sec is not None: showIndent(outfile, level, pretty_print) outfile.write('<%ssec>%s</%ssec>%s' % (namespace_, self.gds_format_integer(self.sec, input_name='sec'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'col': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) ival_ = self.gds_validate_integer(ival_, node, 'col') self.col = ival_ elif nodeName_ == 'row': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) ival_ = self.gds_validate_integer(ival_, node, 'row') self.row = ival_ elif nodeName_ == 'sec': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) ival_ = self.gds_validate_integer(ival_, node, 'sec') self.sec = ival_ # end class originType
[docs]class spacingType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('x', 'xs:positiveInteger', 0), MemberSpec_('y', 'xs:nonNegativeInteger', 0), MemberSpec_('z', 'xs:nonNegativeInteger', 0), ] subclass = None superclass = None def __init__(self, x=None, y=None, z=None): self.original_tagname_ = None self.x = x self.y = y self.z = z
[docs] def factory(*args_, **kwargs_): if spacingType.subclass: return spacingType.subclass(*args_, **kwargs_) else: return spacingType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_x(self): return self.x
[docs] def set_x(self, x): self.x = x
[docs] def get_y(self): return self.y
[docs] def set_y(self, y): self.y = y
[docs] def get_z(self): return self.z
[docs] def set_z(self, z): self.z = z
[docs] def hasContent_(self): if ( self.x is not None or self.y is not None or self.z is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='spacingType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='spacingType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='spacingType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='spacingType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='spacingType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.x is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sx>%s</%sx>%s' % (namespace_, self.gds_format_integer(self.x, input_name='x'), namespace_, eol_)) if self.y is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sy>%s</%sy>%s' % (namespace_, self.gds_format_integer(self.y, input_name='y'), namespace_, eol_)) if self.z is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sz>%s</%sz>%s' % (namespace_, self.gds_format_integer(self.z, input_name='z'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'x': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'x') self.x = ival_ elif nodeName_ == 'y': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ < 0: raise_parse_error(child_, 'requires nonNegativeInteger') ival_ = self.gds_validate_integer(ival_, node, 'y') self.y = ival_ elif nodeName_ == 'z': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ < 0: raise_parse_error(child_, 'requires nonNegativeInteger') ival_ = self.gds_validate_integer(ival_, node, 'z') self.z = ival_ # end class spacingType
[docs]class cellType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('a', 'cell_type', 0), MemberSpec_('b', 'cell_type', 0), MemberSpec_('c', 'cell_type', 0), MemberSpec_('alpha', 'cell_angle_type', 0), MemberSpec_('beta', 'cell_angle_type', 0), MemberSpec_('gamma', 'cell_angle_type', 0), ] subclass = None superclass = None def __init__(self, a=None, b=None, c=None, alpha=None, beta=None, gamma=None): self.original_tagname_ = None self.a = a self.b = b self.c = c self.alpha = alpha self.beta = beta self.gamma = gamma
[docs] def factory(*args_, **kwargs_): if cellType.subclass: return cellType.subclass(*args_, **kwargs_) else: return cellType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_a(self): return self.a
[docs] def set_a(self, a): self.a = a
[docs] def get_b(self): return self.b
[docs] def set_b(self, b): self.b = b
[docs] def get_c(self): return self.c
[docs] def set_c(self, c): self.c = c
[docs] def get_alpha(self): return self.alpha
[docs] def set_alpha(self, alpha): self.alpha = alpha
[docs] def get_beta(self): return self.beta
[docs] def set_beta(self, beta): self.beta = beta
[docs] def get_gamma(self): return self.gamma
[docs] def set_gamma(self, gamma): self.gamma = gamma
[docs] def hasContent_(self): if ( self.a is not None or self.b is not None or self.c is not None or self.alpha is not None or self.beta is not None or self.gamma is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='cellType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='cellType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='cellType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='cellType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='cellType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.a is not None: self.a.export(outfile, level, namespace_, name_='a', pretty_print=pretty_print) if self.b is not None: self.b.export(outfile, level, namespace_, name_='b', pretty_print=pretty_print) if self.c is not None: self.c.export(outfile, level, namespace_, name_='c', pretty_print=pretty_print) if self.alpha is not None: self.alpha.export(outfile, level, namespace_, name_='alpha', pretty_print=pretty_print) if self.beta is not None: self.beta.export(outfile, level, namespace_, name_='beta', pretty_print=pretty_print) if self.gamma is not None: self.gamma.export(outfile, level, namespace_, name_='gamma', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'a': obj_ = cell_type.factory() obj_.build(child_) self.a = obj_ obj_.original_tagname_ = 'a' elif nodeName_ == 'b': obj_ = cell_type.factory() obj_.build(child_) self.b = obj_ obj_.original_tagname_ = 'b' elif nodeName_ == 'c': obj_ = cell_type.factory() obj_.build(child_) self.c = obj_ obj_.original_tagname_ = 'c' elif nodeName_ == 'alpha': obj_ = cell_angle_type.factory() obj_.build(child_) self.alpha = obj_ obj_.original_tagname_ = 'alpha' elif nodeName_ == 'beta': obj_ = cell_angle_type.factory() obj_.build(child_) self.beta = obj_ obj_.original_tagname_ = 'beta' elif nodeName_ == 'gamma': obj_ = cell_angle_type.factory() obj_.build(child_) self.gamma = obj_ obj_.original_tagname_ = 'gamma' # end class cellType
[docs]class axis_orderType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('fast', ['fastType', 'xs:token'], 0), MemberSpec_('medium', ['mediumType', 'xs:token'], 0), MemberSpec_('slow', ['slowType', 'xs:token'], 0), ] subclass = None superclass = None def __init__(self, fast=None, medium=None, slow=None): self.original_tagname_ = None self.fast = fast self.validate_fastType(self.fast) self.medium = medium self.validate_mediumType(self.medium) self.slow = slow self.validate_slowType(self.slow)
[docs] def factory(*args_, **kwargs_): if axis_orderType.subclass: return axis_orderType.subclass(*args_, **kwargs_) else: return axis_orderType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_fast(self): return self.fast
[docs] def set_fast(self, fast): self.fast = fast
[docs] def get_medium(self): return self.medium
[docs] def set_medium(self, medium): self.medium = medium
[docs] def get_slow(self): return self.slow
[docs] def set_slow(self, slow): self.slow = slow
[docs] def validate_fastType(self, value): # Validate type fastType, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_fastType_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_fastType_patterns_, ))
validate_fastType_patterns_ = [['^X|Y|Z$']]
[docs] def validate_mediumType(self, value): # Validate type mediumType, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_mediumType_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_mediumType_patterns_, ))
validate_mediumType_patterns_ = [['^X|Y|Z$']]
[docs] def validate_slowType(self, value): # Validate type slowType, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_slowType_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_slowType_patterns_, ))
validate_slowType_patterns_ = [['^X|Y|Z$']]
[docs] def hasContent_(self): if ( self.fast is not None or self.medium is not None or self.slow is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='axis_orderType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='axis_orderType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='axis_orderType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='axis_orderType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='axis_orderType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.fast is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sfast>%s</%sfast>%s' % (namespace_, self.gds_format_string(quote_xml(self.fast).encode(ExternalEncoding), input_name='fast'), namespace_, eol_)) if self.medium is not None: showIndent(outfile, level, pretty_print) outfile.write('<%smedium>%s</%smedium>%s' % (namespace_, self.gds_format_string(quote_xml(self.medium).encode(ExternalEncoding), input_name='medium'), namespace_, eol_)) if self.slow is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sslow>%s</%sslow>%s' % (namespace_, self.gds_format_string(quote_xml(self.slow).encode(ExternalEncoding), input_name='slow'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'fast': fast_ = child_.text fast_ = re_.sub(String_cleanup_pat_, " ", fast_).strip() fast_ = self.gds_validate_string(fast_, node, 'fast') self.fast = fast_ # validate type fastType self.validate_fastType(self.fast) elif nodeName_ == 'medium': medium_ = child_.text medium_ = re_.sub(String_cleanup_pat_, " ", medium_).strip() medium_ = self.gds_validate_string(medium_, node, 'medium') self.medium = medium_ # validate type mediumType self.validate_mediumType(self.medium) elif nodeName_ == 'slow': slow_ = child_.text slow_ = re_.sub(String_cleanup_pat_, " ", slow_).strip() slow_ = self.gds_validate_string(slow_, node, 'slow') self.slow = slow_ # validate type slowType self.validate_slowType(self.slow) # end class axis_orderType
[docs]class pixel_spacingType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('x', 'pixel_spacing_type', 0), MemberSpec_('y', 'pixel_spacing_type', 0), MemberSpec_('z', 'pixel_spacing_type', 0), ] subclass = None superclass = None def __init__(self, x=None, y=None, z=None): self.original_tagname_ = None self.x = x self.y = y self.z = z
[docs] def factory(*args_, **kwargs_): if pixel_spacingType.subclass: return pixel_spacingType.subclass(*args_, **kwargs_) else: return pixel_spacingType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_x(self): return self.x
[docs] def set_x(self, x): self.x = x
[docs] def get_y(self): return self.y
[docs] def set_y(self, y): self.y = y
[docs] def get_z(self): return self.z
[docs] def set_z(self, z): self.z = z
[docs] def hasContent_(self): if ( self.x is not None or self.y is not None or self.z is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='pixel_spacingType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='pixel_spacingType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='pixel_spacingType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='pixel_spacingType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='pixel_spacingType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.x is not None: self.x.export(outfile, level, namespace_, name_='x', pretty_print=pretty_print) if self.y is not None: self.y.export(outfile, level, namespace_, name_='y', pretty_print=pretty_print) if self.z is not None: self.z.export(outfile, level, namespace_, name_='z', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'x': obj_ = pixel_spacing_type.factory() obj_.build(child_) self.x = obj_ obj_.original_tagname_ = 'x' elif nodeName_ == 'y': obj_ = pixel_spacing_type.factory() obj_.build(child_) self.y = obj_ obj_.original_tagname_ = 'y' elif nodeName_ == 'z': obj_ = pixel_spacing_type.factory() obj_.build(child_) self.z = obj_ obj_.original_tagname_ = 'z' # end class pixel_spacingType
[docs]class contour_listType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('contour', 'contourType', 1), ] subclass = None superclass = None def __init__(self, contour=None): self.original_tagname_ = None if contour is None: self.contour = [] else: self.contour = contour
[docs] def factory(*args_, **kwargs_): if contour_listType.subclass: return contour_listType.subclass(*args_, **kwargs_) else: return contour_listType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_contour(self): return self.contour
[docs] def set_contour(self, contour): self.contour = contour
[docs] def add_contour(self, value): self.contour.append(value)
[docs] def insert_contour_at(self, index, value): self.contour.insert(index, value)
[docs] def replace_contour_at(self, index, value): self.contour[index] = value
[docs] def hasContent_(self): if ( self.contour ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='contour_listType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='contour_listType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='contour_listType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='contour_listType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='contour_listType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for contour_ in self.contour: contour_.export(outfile, level, namespace_, name_='contour', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'contour': obj_ = contourType.factory() obj_.build(child_) self.contour.append(obj_) obj_.original_tagname_ = 'contour' # end class contour_listType
[docs]class contourType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('primary', 'xs:boolean', 0), MemberSpec_('level', 'xs:float', 0), MemberSpec_('source', ['sourceType', 'xs:token'], 0), ] subclass = None superclass = None def __init__(self, primary=None, level=None, source=None): self.original_tagname_ = None self.primary = _cast(bool, primary) self.level = level self.source = source self.validate_sourceType(self.source)
[docs] def factory(*args_, **kwargs_): if contourType.subclass: return contourType.subclass(*args_, **kwargs_) else: return contourType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_level(self): return self.level
[docs] def set_level(self, level): self.level = level
[docs] def get_source(self): return self.source
[docs] def set_source(self, source): self.source = source
[docs] def get_primary(self): return self.primary
[docs] def set_primary(self, primary): self.primary = primary
[docs] def validate_sourceType(self, value): # Validate type sourceType, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['EMDB', 'AUTHOR'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on sourceType' % {"value" : value.encode("utf-8")} )
[docs] def hasContent_(self): if ( self.level is not None or self.source is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='contourType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='contourType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='contourType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='contourType'): if self.primary is not None and 'primary' not in already_processed: already_processed.add('primary') outfile.write(' primary="%s"' % self.gds_format_boolean(self.primary, input_name='primary'))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='contourType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.level is not None: showIndent(outfile, level, pretty_print) outfile.write('<%slevel>%s</%slevel>%s' % (namespace_, self.gds_format_float(self.level, input_name='level'), namespace_, eol_)) if self.source is not None: showIndent(outfile, level, pretty_print) outfile.write('<%ssource>%s</%ssource>%s' % (namespace_, self.gds_format_string(quote_xml(self.source).encode(ExternalEncoding), input_name='source'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('primary', node) if value is not None and 'primary' not in already_processed: already_processed.add('primary') if value in ('true', '1'): self.primary = True elif value in ('false', '0'): self.primary = False else: raise_parse_error(node, 'Bad boolean attribute')
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'level': sval_ = child_.text try: fval_ = float(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires float or double: %s' % exp) fval_ = self.gds_validate_float(fval_, node, 'level') self.level = fval_ elif nodeName_ == 'source': source_ = child_.text source_ = re_.sub(String_cleanup_pat_, " ", source_).strip() source_ = self.gds_validate_string(source_, node, 'source') self.source = source_ # validate type sourceType self.validate_sourceType(self.source)
[docs] def gds_format_float(self,input_data, input_name="" ): return ("%g" % input_data) # end class contourType
[docs]class natural_sourceType(base_natural_source_type): member_data_items_ = [ MemberSpec_('organ', 'xs:token', 0), MemberSpec_('tissue', 'tissue', 0), MemberSpec_('cell', 'cell', 0), ] subclass = None superclass = base_natural_source_type def __init__(self, database=None, organism=None, strain=None, synonym_organism=None, organ=None, tissue=None, cell=None): self.original_tagname_ = None super(natural_sourceType, self).__init__(database, organism, strain, synonym_organism, ) self.organ = organ self.tissue = tissue self.cell = cell
[docs] def factory(*args_, **kwargs_): if natural_sourceType.subclass: return natural_sourceType.subclass(*args_, **kwargs_) else: return natural_sourceType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_organ(self): return self.organ
[docs] def set_organ(self, organ): self.organ = organ
[docs] def get_tissue(self): return self.tissue
[docs] def set_tissue(self, tissue): self.tissue = tissue
[docs] def get_cell(self): return self.cell
[docs] def set_cell(self, cell): self.cell = cell
[docs] def hasContent_(self): if ( self.organ is not None or self.tissue is not None or self.cell is not None or super(natural_sourceType, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='natural_sourceType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='natural_sourceType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='natural_sourceType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='natural_sourceType'): super(natural_sourceType, self).exportAttributes(outfile, level, already_processed, namespace_, name_='natural_sourceType')
[docs] def exportChildren(self, outfile, level, namespace_='', name_='natural_sourceType', fromsubclass_=False, pretty_print=True): super(natural_sourceType, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print) if pretty_print: eol_ = '\n' else: eol_ = '' if self.organ is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sorgan>%s</%sorgan>%s' % (namespace_, self.gds_format_string(quote_xml(self.organ).encode(ExternalEncoding), input_name='organ'), namespace_, eol_)) if self.tissue is not None: showIndent(outfile, level, pretty_print) outfile.write('<%stissue>%s</%stissue>%s' % (namespace_, self.gds_format_string(quote_xml(self.tissue).encode(ExternalEncoding), input_name='tissue'), namespace_, eol_)) if self.cell is not None: showIndent(outfile, level, pretty_print) outfile.write('<%scell>%s</%scell>%s' % (namespace_, self.gds_format_string(quote_xml(self.cell).encode(ExternalEncoding), input_name='cell'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): super(natural_sourceType, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'organ': organ_ = child_.text organ_ = re_.sub(String_cleanup_pat_, " ", organ_).strip() organ_ = self.gds_validate_string(organ_, node, 'organ') self.organ = organ_ elif nodeName_ == 'tissue': tissue_ = child_.text tissue_ = re_.sub(String_cleanup_pat_, " ", tissue_).strip() tissue_ = self.gds_validate_string(tissue_, node, 'tissue') self.tissue = tissue_ elif nodeName_ == 'cell': cell_ = child_.text cell_ = re_.sub(String_cleanup_pat_, " ", cell_).strip() cell_ = self.gds_validate_string(cell_, node, 'cell') self.cell = cell_ super(natural_sourceType, self).buildChildren(child_, node, nodeName_, True) # end class natural_sourceType
[docs]class natural_sourceType36(base_natural_source_type): member_data_items_ = [ MemberSpec_('organ', 'xs:token', 0), MemberSpec_('tissue', 'tissue', 0), MemberSpec_('cell', 'cell', 0), ] subclass = None superclass = base_natural_source_type def __init__(self, database=None, organism=None, strain=None, synonym_organism=None, organ=None, tissue=None, cell=None): self.original_tagname_ = None super(natural_sourceType36, self).__init__(database, organism, strain, synonym_organism, ) self.organ = organ self.tissue = tissue self.cell = cell
[docs] def factory(*args_, **kwargs_): if natural_sourceType36.subclass: return natural_sourceType36.subclass(*args_, **kwargs_) else: return natural_sourceType36(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_organ(self): return self.organ
[docs] def set_organ(self, organ): self.organ = organ
[docs] def get_tissue(self): return self.tissue
[docs] def set_tissue(self, tissue): self.tissue = tissue
[docs] def get_cell(self): return self.cell
[docs] def set_cell(self, cell): self.cell = cell
[docs] def hasContent_(self): if ( self.organ is not None or self.tissue is not None or self.cell is not None or super(natural_sourceType36, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='natural_sourceType36', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='natural_sourceType36') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='natural_sourceType36', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='natural_sourceType36'): super(natural_sourceType36, self).exportAttributes(outfile, level, already_processed, namespace_, name_='natural_sourceType36')
[docs] def exportChildren(self, outfile, level, namespace_='', name_='natural_sourceType36', fromsubclass_=False, pretty_print=True): super(natural_sourceType36, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print) if pretty_print: eol_ = '\n' else: eol_ = '' if self.organ is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sorgan>%s</%sorgan>%s' % (namespace_, self.gds_format_string(quote_xml(self.organ).encode(ExternalEncoding), input_name='organ'), namespace_, eol_)) if self.tissue is not None: showIndent(outfile, level, pretty_print) outfile.write('<%stissue>%s</%stissue>%s' % (namespace_, self.gds_format_string(quote_xml(self.tissue).encode(ExternalEncoding), input_name='tissue'), namespace_, eol_)) if self.cell is not None: showIndent(outfile, level, pretty_print) outfile.write('<%scell>%s</%scell>%s' % (namespace_, self.gds_format_string(quote_xml(self.cell).encode(ExternalEncoding), input_name='cell'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): super(natural_sourceType36, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'organ': organ_ = child_.text organ_ = re_.sub(String_cleanup_pat_, " ", organ_).strip() organ_ = self.gds_validate_string(organ_, node, 'organ') self.organ = organ_ elif nodeName_ == 'tissue': tissue_ = child_.text tissue_ = re_.sub(String_cleanup_pat_, " ", tissue_).strip() tissue_ = self.gds_validate_string(tissue_, node, 'tissue') self.tissue = tissue_ elif nodeName_ == 'cell': cell_ = child_.text cell_ = re_.sub(String_cleanup_pat_, " ", cell_).strip() cell_ = self.gds_validate_string(cell_, node, 'cell') self.cell = cell_ super(natural_sourceType36, self).buildChildren(child_, node, nodeName_, True) # end class natural_sourceType36
[docs]class natural_sourceType37(base_natural_source_type): member_data_items_ = [ MemberSpec_('organ', 'xs:token', 0), MemberSpec_('tissue', 'tissue', 0), ] subclass = None superclass = base_natural_source_type def __init__(self, database=None, organism=None, strain=None, synonym_organism=None, organ=None, tissue=None): self.original_tagname_ = None super(natural_sourceType37, self).__init__(database, organism, strain, synonym_organism, ) self.organ = organ self.tissue = tissue
[docs] def factory(*args_, **kwargs_): if natural_sourceType37.subclass: return natural_sourceType37.subclass(*args_, **kwargs_) else: return natural_sourceType37(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_organ(self): return self.organ
[docs] def set_organ(self, organ): self.organ = organ
[docs] def get_tissue(self): return self.tissue
[docs] def set_tissue(self, tissue): self.tissue = tissue
[docs] def hasContent_(self): if ( self.organ is not None or self.tissue is not None or super(natural_sourceType37, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='natural_sourceType37', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='natural_sourceType37') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='natural_sourceType37', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='natural_sourceType37'): super(natural_sourceType37, self).exportAttributes(outfile, level, already_processed, namespace_, name_='natural_sourceType37')
[docs] def exportChildren(self, outfile, level, namespace_='', name_='natural_sourceType37', fromsubclass_=False, pretty_print=True): super(natural_sourceType37, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print) if pretty_print: eol_ = '\n' else: eol_ = '' if self.organ is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sorgan>%s</%sorgan>%s' % (namespace_, self.gds_format_string(quote_xml(self.organ).encode(ExternalEncoding), input_name='organ'), namespace_, eol_)) if self.tissue is not None: showIndent(outfile, level, pretty_print) outfile.write('<%stissue>%s</%stissue>%s' % (namespace_, self.gds_format_string(quote_xml(self.tissue).encode(ExternalEncoding), input_name='tissue'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): super(natural_sourceType37, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'organ': organ_ = child_.text organ_ = re_.sub(String_cleanup_pat_, " ", organ_).strip() organ_ = self.gds_validate_string(organ_, node, 'organ') self.organ = organ_ elif nodeName_ == 'tissue': tissue_ = child_.text tissue_ = re_.sub(String_cleanup_pat_, " ", tissue_).strip() tissue_ = self.gds_validate_string(tissue_, node, 'tissue') self.tissue = tissue_ super(natural_sourceType37, self).buildChildren(child_, node, nodeName_, True) # end class natural_sourceType37
[docs]class natural_sourceType38(base_natural_source_type): member_data_items_ = [ MemberSpec_('organ', 'xs:token', 0), MemberSpec_('tissue', 'tissue', 0), MemberSpec_('cell', 'cell', 0), MemberSpec_('organelle', 'xs:token', 0), MemberSpec_('cellular_location', 'xs:token', 0), ] subclass = None superclass = base_natural_source_type def __init__(self, database=None, organism=None, strain=None, synonym_organism=None, organ=None, tissue=None, cell=None, organelle=None, cellular_location=None): self.original_tagname_ = None super(natural_sourceType38, self).__init__(database, organism, strain, synonym_organism, ) self.organ = organ self.tissue = tissue self.cell = cell self.organelle = organelle self.cellular_location = cellular_location
[docs] def factory(*args_, **kwargs_): if natural_sourceType38.subclass: return natural_sourceType38.subclass(*args_, **kwargs_) else: return natural_sourceType38(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_organ(self): return self.organ
[docs] def set_organ(self, organ): self.organ = organ
[docs] def get_tissue(self): return self.tissue
[docs] def set_tissue(self, tissue): self.tissue = tissue
[docs] def get_cell(self): return self.cell
[docs] def set_cell(self, cell): self.cell = cell
[docs] def get_organelle(self): return self.organelle
[docs] def set_organelle(self, organelle): self.organelle = organelle
[docs] def get_cellular_location(self): return self.cellular_location
[docs] def set_cellular_location(self, cellular_location): self.cellular_location = cellular_location
[docs] def hasContent_(self): if ( self.organ is not None or self.tissue is not None or self.cell is not None or self.organelle is not None or self.cellular_location is not None or super(natural_sourceType38, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='natural_sourceType38', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='natural_sourceType38') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='natural_sourceType38', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='natural_sourceType38'): super(natural_sourceType38, self).exportAttributes(outfile, level, already_processed, namespace_, name_='natural_sourceType38')
[docs] def exportChildren(self, outfile, level, namespace_='', name_='natural_sourceType38', fromsubclass_=False, pretty_print=True): super(natural_sourceType38, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print) if pretty_print: eol_ = '\n' else: eol_ = '' if self.organ is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sorgan>%s</%sorgan>%s' % (namespace_, self.gds_format_string(quote_xml(self.organ).encode(ExternalEncoding), input_name='organ'), namespace_, eol_)) if self.tissue is not None: showIndent(outfile, level, pretty_print) outfile.write('<%stissue>%s</%stissue>%s' % (namespace_, self.gds_format_string(quote_xml(self.tissue).encode(ExternalEncoding), input_name='tissue'), namespace_, eol_)) if self.cell is not None: showIndent(outfile, level, pretty_print) outfile.write('<%scell>%s</%scell>%s' % (namespace_, self.gds_format_string(quote_xml(self.cell).encode(ExternalEncoding), input_name='cell'), namespace_, eol_)) if self.organelle is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sorganelle>%s</%sorganelle>%s' % (namespace_, self.gds_format_string(quote_xml(self.organelle).encode(ExternalEncoding), input_name='organelle'), namespace_, eol_)) if self.cellular_location is not None: showIndent(outfile, level, pretty_print) outfile.write('<%scellular_location>%s</%scellular_location>%s' % (namespace_, self.gds_format_string(quote_xml(self.cellular_location).encode(ExternalEncoding), input_name='cellular_location'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): super(natural_sourceType38, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'organ': organ_ = child_.text organ_ = re_.sub(String_cleanup_pat_, " ", organ_).strip() organ_ = self.gds_validate_string(organ_, node, 'organ') self.organ = organ_ elif nodeName_ == 'tissue': tissue_ = child_.text tissue_ = re_.sub(String_cleanup_pat_, " ", tissue_).strip() tissue_ = self.gds_validate_string(tissue_, node, 'tissue') self.tissue = tissue_ elif nodeName_ == 'cell': cell_ = child_.text cell_ = re_.sub(String_cleanup_pat_, " ", cell_).strip() cell_ = self.gds_validate_string(cell_, node, 'cell') self.cell = cell_ elif nodeName_ == 'organelle': organelle_ = child_.text organelle_ = re_.sub(String_cleanup_pat_, " ", organelle_).strip() organelle_ = self.gds_validate_string(organelle_, node, 'organelle') self.organelle = organelle_ elif nodeName_ == 'cellular_location': cellular_location_ = child_.text cellular_location_ = re_.sub(String_cleanup_pat_, " ", cellular_location_).strip() cellular_location_ = self.gds_validate_string(cellular_location_, node, 'cellular_location') self.cellular_location = cellular_location_ super(natural_sourceType38, self).buildChildren(child_, node, nodeName_, True) # end class natural_sourceType38
[docs]class natural_hostType(base_natural_source_type): member_data_items_ = [ ] subclass = None superclass = base_natural_source_type def __init__(self, database=None, organism=None, strain=None, synonym_organism=None): self.original_tagname_ = None super(natural_hostType, self).__init__(database, organism, strain, synonym_organism, )
[docs] def factory(*args_, **kwargs_): if natural_hostType.subclass: return natural_hostType.subclass(*args_, **kwargs_) else: return natural_hostType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( super(natural_hostType, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='natural_hostType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='natural_hostType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='natural_hostType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='natural_hostType'): super(natural_hostType, self).exportAttributes(outfile, level, already_processed, namespace_, name_='natural_hostType')
[docs] def exportChildren(self, outfile, level, namespace_='', name_='natural_hostType', fromsubclass_=False, pretty_print=True): super(natural_hostType, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): super(natural_hostType, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): super(natural_hostType, self).buildChildren(child_, node, nodeName_, True) pass # end class natural_hostType
[docs]class virus_shellType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('id', 'xs:positiveInteger', 0), MemberSpec_('name', 'xs:token', 0), MemberSpec_('diameter', 'diameterType', 0), MemberSpec_('triangulation', 'xs:positiveInteger', 0), ] subclass = None superclass = None def __init__(self, id=None, name=None, diameter=None, triangulation=None): self.original_tagname_ = None self.id = _cast(int, id) self.name = name self.diameter = diameter self.triangulation = triangulation
[docs] def factory(*args_, **kwargs_): if virus_shellType.subclass: return virus_shellType.subclass(*args_, **kwargs_) else: return virus_shellType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_name(self): return self.name
[docs] def set_name(self, name): self.name = name
[docs] def get_diameter(self): return self.diameter
[docs] def set_diameter(self, diameter): self.diameter = diameter
[docs] def get_triangulation(self): return self.triangulation
[docs] def set_triangulation(self, triangulation): self.triangulation = triangulation
[docs] def get_id(self): return self.id
[docs] def set_id(self, id): self.id = id
[docs] def hasContent_(self): if ( self.name is not None or self.diameter is not None or self.triangulation is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='virus_shellType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='virus_shellType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='virus_shellType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='virus_shellType'): if self.id is not None and 'id' not in already_processed: already_processed.add('id') outfile.write(' id="%s"' % self.gds_format_integer(self.id, input_name='id'))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='virus_shellType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.name is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sname>%s</%sname>%s' % (namespace_, self.gds_format_string(quote_xml(self.name).encode(ExternalEncoding), input_name='name'), namespace_, eol_)) if self.diameter is not None: self.diameter.export(outfile, level, namespace_, name_='diameter', pretty_print=pretty_print) if self.triangulation is not None: showIndent(outfile, level, pretty_print) outfile.write('<%striangulation>%s</%striangulation>%s' % (namespace_, self.gds_format_integer(self.triangulation, input_name='triangulation'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('id', node) if value is not None and 'id' not in already_processed: already_processed.add('id') try: self.id = int(value) except ValueError as exp: raise_parse_error(node, 'Bad integer attribute: %s' % exp) if self.id <= 0: raise_parse_error(node, 'Invalid PositiveInteger')
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'name': name_ = child_.text name_ = re_.sub(String_cleanup_pat_, " ", name_).strip() name_ = self.gds_validate_string(name_, node, 'name') self.name = name_ elif nodeName_ == 'diameter': obj_ = diameterType.factory() obj_.build(child_) self.diameter = obj_ obj_.original_tagname_ = 'diameter' elif nodeName_ == 'triangulation': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'triangulation') self.triangulation = ival_ # end class virus_shellType
[docs]class diameterType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:string', 0), MemberSpec_('valueOf_', ['allowed_shell_diameter', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if diameterType.subclass: return diameterType.subclass(*args_, **kwargs_) else: return diameterType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='diameterType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='diameterType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='diameterType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='diameterType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='diameterType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class diameterType
[docs]class categoryType(GeneratedsSuper): """Currently we only support Gene Ontology.""" member_data_items_ = [ MemberSpec_('type', 'xs:token', 0), MemberSpec_('valueOf_', ['complex_category_type', 'xs:token'], 0), ] subclass = None superclass = None def __init__(self, type_=None, valueOf_=None): self.original_tagname_ = None self.type_ = _cast(None, type_) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if categoryType.subclass: return categoryType.subclass(*args_, **kwargs_) else: return categoryType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_type(self): return self.type_
[docs] def set_type(self, type_): self.type_ = type_
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='categoryType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='categoryType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='categoryType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='categoryType'): if self.type_ is not None and 'type_' not in already_processed: already_processed.add('type_') outfile.write(' type=%s' % (self.gds_format_string(quote_attrib(self.type_).encode(ExternalEncoding), input_name='type'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='categoryType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('type', node) if value is not None and 'type' not in already_processed: already_processed.add('type') self.type_ = value self.type_ = ' '.join(self.type_.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class categoryType
[docs]class macromolecule_listType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('macromolecule', 'base_macromolecule_type', 1), ] subclass = None superclass = None def __init__(self, macromolecule=None): self.original_tagname_ = None if macromolecule is None: self.macromolecule = [] else: self.macromolecule = macromolecule
[docs] def factory(*args_, **kwargs_): if macromolecule_listType.subclass: return macromolecule_listType.subclass(*args_, **kwargs_) else: return macromolecule_listType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_macromolecule(self): return self.macromolecule
[docs] def set_macromolecule(self, macromolecule): self.macromolecule = macromolecule
[docs] def add_macromolecule(self, value): self.macromolecule.append(value)
[docs] def insert_macromolecule_at(self, index, value): self.macromolecule.insert(index, value)
[docs] def replace_macromolecule_at(self, index, value): self.macromolecule[index] = value
[docs] def hasContent_(self): if ( self.macromolecule ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='macromolecule_listType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='macromolecule_listType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='macromolecule_listType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='macromolecule_listType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='macromolecule_listType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for macromolecule_ in self.macromolecule: macromolecule_.export(outfile, level, namespace_, name_='macromolecule', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'macromolecule': obj_ = macromoleculeType.factory() obj_.build(child_) self.macromolecule.append(obj_) obj_.original_tagname_ = 'macromolecule' elif nodeName_ == 'protein_or_peptide': obj_ = protein_or_peptide.factory() obj_.build(child_) self.macromolecule.append(obj_) obj_.original_tagname_ = 'protein_or_peptide' elif nodeName_ == 'dna': obj_ = dna.factory() obj_.build(child_) self.macromolecule.append(obj_) obj_.original_tagname_ = 'dna' elif nodeName_ == 'rna': obj_ = rna.factory() obj_.build(child_) self.macromolecule.append(obj_) obj_.original_tagname_ = 'rna' elif nodeName_ == 'saccharide': obj_ = saccharide.factory() obj_.build(child_) self.macromolecule.append(obj_) obj_.original_tagname_ = 'saccharide' elif nodeName_ == 'lipid': obj_ = lipid.factory() obj_.build(child_) self.macromolecule.append(obj_) obj_.original_tagname_ = 'lipid' elif nodeName_ == 'ligand': obj_ = ligand.factory() obj_.build(child_) self.macromolecule.append(obj_) obj_.original_tagname_ = 'ligand' elif nodeName_ == 'em_label': obj_ = em_label.factory() obj_.build(child_) self.macromolecule.append(obj_) obj_.original_tagname_ = 'em_label' elif nodeName_ == 'other_macromolecule': obj_ = other_macromolecule.factory() obj_.build(child_) self.macromolecule.append(obj_) obj_.original_tagname_ = 'other_macromolecule' # end class macromolecule_listType
[docs]class macromoleculeType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('id', 'xs:positiveInteger', 0), MemberSpec_('number_of_copies', 'xs:positiveInteger', 0), MemberSpec_('oligomeric_state', 'xs:token', 0), ] subclass = None superclass = None def __init__(self, id=None, number_of_copies=None, oligomeric_state=None): self.original_tagname_ = None self.id = id self.number_of_copies = number_of_copies self.oligomeric_state = oligomeric_state
[docs] def factory(*args_, **kwargs_): if macromoleculeType.subclass: return macromoleculeType.subclass(*args_, **kwargs_) else: return macromoleculeType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_id(self): return self.id
[docs] def set_id(self, id): self.id = id
[docs] def get_number_of_copies(self): return self.number_of_copies
[docs] def set_number_of_copies(self, number_of_copies): self.number_of_copies = number_of_copies
[docs] def get_oligomeric_state(self): return self.oligomeric_state
[docs] def set_oligomeric_state(self, oligomeric_state): self.oligomeric_state = oligomeric_state
[docs] def hasContent_(self): if ( self.id is not None or self.number_of_copies is not None or self.oligomeric_state is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='macromoleculeType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='macromoleculeType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='macromoleculeType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='macromoleculeType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='macromoleculeType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.id is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sid>%s</%sid>%s' % (namespace_, self.gds_format_integer(self.id, input_name='id'), namespace_, eol_)) if self.number_of_copies is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_of_copies>%s</%snumber_of_copies>%s' % (namespace_, self.gds_format_integer(self.number_of_copies, input_name='number_of_copies'), namespace_, eol_)) if self.oligomeric_state is not None: showIndent(outfile, level, pretty_print) outfile.write('<%soligomeric_state>%s</%soligomeric_state>%s' % (namespace_, self.gds_format_string(quote_xml(self.oligomeric_state).encode(ExternalEncoding), input_name='oligomeric_state'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'id': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'id') self.id = ival_ elif nodeName_ == 'number_of_copies': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'number_of_copies') self.number_of_copies = ival_ elif nodeName_ == 'oligomeric_state': oligomeric_state_ = child_.text oligomeric_state_ = re_.sub(String_cleanup_pat_, " ", oligomeric_state_).strip() oligomeric_state_ = self.gds_validate_string(oligomeric_state_, node, 'oligomeric_state') self.oligomeric_state = oligomeric_state_ # end class macromoleculeType
[docs]class external_referencesType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('type', 'xs:token', 0), MemberSpec_('valueOf_', 'xs:token', 0), ] subclass = None superclass = None def __init__(self, type_=None, valueOf_=None): self.original_tagname_ = None self.type_ = _cast(None, type_) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if external_referencesType.subclass: return external_referencesType.subclass(*args_, **kwargs_) else: return external_referencesType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_type(self): return self.type_
[docs] def set_type(self, type_): self.type_ = type_
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='external_referencesType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='external_referencesType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='external_referencesType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='external_referencesType'): if self.type_ is not None and 'type_' not in already_processed: already_processed.add('type_') outfile.write(' type=%s' % (self.gds_format_string(quote_attrib(self.type_).encode(ExternalEncoding), input_name='type'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='external_referencesType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('type', node) if value is not None and 'type' not in already_processed: already_processed.add('type') self.type_ = value self.type_ = ' '.join(self.type_.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class external_referencesType
[docs]class categoryType39(GeneratedsSuper): """Currently we only support Gene Ontology.""" member_data_items_ = [ MemberSpec_('type', 'xs:token', 0), MemberSpec_('valueOf_', ['complex_category_type', 'xs:token'], 0), ] subclass = None superclass = None def __init__(self, type_=None, valueOf_=None): self.original_tagname_ = None self.type_ = _cast(None, type_) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if categoryType39.subclass: return categoryType39.subclass(*args_, **kwargs_) else: return categoryType39(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_type(self): return self.type_
[docs] def set_type(self, type_): self.type_ = type_
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='categoryType39', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='categoryType39') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='categoryType39', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='categoryType39'): if self.type_ is not None and 'type_' not in already_processed: already_processed.add('type_') outfile.write(' type=%s' % (self.gds_format_string(quote_attrib(self.type_).encode(ExternalEncoding), input_name='type'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='categoryType39', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('type', node) if value is not None and 'type' not in already_processed: already_processed.add('type') self.type_ = value self.type_ = ' '.join(self.type_.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class categoryType39
[docs]class macromolecule_listType40(GeneratedsSuper): member_data_items_ = [ MemberSpec_('macromolecule_id', 'xs:positiveInteger', 1), ] subclass = None superclass = None def __init__(self, macromolecule_id=None): self.original_tagname_ = None if macromolecule_id is None: self.macromolecule_id = [] else: self.macromolecule_id = macromolecule_id
[docs] def factory(*args_, **kwargs_): if macromolecule_listType40.subclass: return macromolecule_listType40.subclass(*args_, **kwargs_) else: return macromolecule_listType40(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_macromolecule_id(self): return self.macromolecule_id
[docs] def set_macromolecule_id(self, macromolecule_id): self.macromolecule_id = macromolecule_id
[docs] def add_macromolecule_id(self, value): self.macromolecule_id.append(value)
[docs] def insert_macromolecule_id_at(self, index, value): self.macromolecule_id.insert(index, value)
[docs] def replace_macromolecule_id_at(self, index, value): self.macromolecule_id[index] = value
[docs] def hasContent_(self): if ( self.macromolecule_id ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='macromolecule_listType40', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='macromolecule_listType40') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='macromolecule_listType40', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='macromolecule_listType40'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='macromolecule_listType40', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for macromolecule_id_ in self.macromolecule_id: showIndent(outfile, level, pretty_print) outfile.write('<%smacromolecule_id>%s</%smacromolecule_id>%s' % (namespace_, self.gds_format_integer(macromolecule_id_, input_name='macromolecule_id'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'macromolecule_id': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'macromolecule_id') self.macromolecule_id.append(ival_) # end class macromolecule_listType40
[docs]class molecular_weightType(GeneratedsSuper): """kDa/nm is for helices.""" member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('theoretical', 'xs:boolean', 0), MemberSpec_('valueOf_', ['allowed_assembly_weights', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, theoretical=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.theoretical = _cast(bool, theoretical) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if molecular_weightType.subclass: return molecular_weightType.subclass(*args_, **kwargs_) else: return molecular_weightType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_theoretical(self): return self.theoretical
[docs] def set_theoretical(self, theoretical): self.theoretical = theoretical
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='molecular_weightType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='molecular_weightType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='molecular_weightType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='molecular_weightType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), )) if self.theoretical is not None and 'theoretical' not in already_processed: already_processed.add('theoretical') outfile.write(' theoretical="%s"' % self.gds_format_boolean(self.theoretical, input_name='theoretical'))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='molecular_weightType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split()) value = find_attr_value_('theoretical', node) if value is not None and 'theoretical' not in already_processed: already_processed.add('theoretical') if value in ('true', '1'): self.theoretical = True elif value in ('false', '0'): self.theoretical = False else: raise_parse_error(node, 'Bad boolean attribute')
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class molecular_weightType
[docs]class virus_shellType41(GeneratedsSuper): member_data_items_ = [ MemberSpec_('name', 'xs:token', 0), MemberSpec_('diameter', 'diameterType42', 0), MemberSpec_('triangulation', 'xs:positiveInteger', 0), ] subclass = None superclass = None def __init__(self, name=None, diameter=None, triangulation=None): self.original_tagname_ = None self.name = name self.diameter = diameter self.triangulation = triangulation
[docs] def factory(*args_, **kwargs_): if virus_shellType41.subclass: return virus_shellType41.subclass(*args_, **kwargs_) else: return virus_shellType41(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_name(self): return self.name
[docs] def set_name(self, name): self.name = name
[docs] def get_diameter(self): return self.diameter
[docs] def set_diameter(self, diameter): self.diameter = diameter
[docs] def get_triangulation(self): return self.triangulation
[docs] def set_triangulation(self, triangulation): self.triangulation = triangulation
[docs] def hasContent_(self): if ( self.name is not None or self.diameter is not None or self.triangulation is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='virus_shellType41', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='virus_shellType41') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='virus_shellType41', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='virus_shellType41'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='virus_shellType41', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.name is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sname>%s</%sname>%s' % (namespace_, self.gds_format_string(quote_xml(self.name).encode(ExternalEncoding), input_name='name'), namespace_, eol_)) if self.diameter is not None: self.diameter.export(outfile, level, namespace_, name_='diameter', pretty_print=pretty_print) if self.triangulation is not None: showIndent(outfile, level, pretty_print) outfile.write('<%striangulation>%s</%striangulation>%s' % (namespace_, self.gds_format_integer(self.triangulation, input_name='triangulation'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'name': name_ = child_.text name_ = re_.sub(String_cleanup_pat_, " ", name_).strip() name_ = self.gds_validate_string(name_, node, 'name') self.name = name_ elif nodeName_ == 'diameter': obj_ = diameterType42.factory() obj_.build(child_) self.diameter = obj_ obj_.original_tagname_ = 'diameter' elif nodeName_ == 'triangulation': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'triangulation') self.triangulation = ival_ # end class virus_shellType41
[docs]class diameterType42(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:string', 0), MemberSpec_('valueOf_', ['allowed_shell_diameter', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if diameterType42.subclass: return diameterType42.subclass(*args_, **kwargs_) else: return diameterType42(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='diameterType42', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='diameterType42') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='diameterType42', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='diameterType42'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='diameterType42', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class diameterType42
[docs]class modelling_listType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('modelling', 'modelling_type', 1), ] subclass = None superclass = None def __init__(self, modelling=None): self.original_tagname_ = None if modelling is None: self.modelling = [] else: self.modelling = modelling
[docs] def factory(*args_, **kwargs_): if modelling_listType.subclass: return modelling_listType.subclass(*args_, **kwargs_) else: return modelling_listType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_modelling(self): return self.modelling
[docs] def set_modelling(self, modelling): self.modelling = modelling
[docs] def add_modelling(self, value): self.modelling.append(value)
[docs] def insert_modelling_at(self, index, value): self.modelling.insert(index, value)
[docs] def replace_modelling_at(self, index, value): self.modelling[index] = value
[docs] def hasContent_(self): if ( self.modelling ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='modelling_listType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='modelling_listType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='modelling_listType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='modelling_listType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='modelling_listType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for modelling_ in self.modelling: modelling_.export(outfile, level, namespace_, name_='modelling', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'modelling': obj_ = modelling_type.factory() obj_.build(child_) self.modelling.append(obj_) obj_.original_tagname_ = 'modelling' # end class modelling_listType
[docs]class figure_listType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('figure', 'figure_type', 1), ] subclass = None superclass = None def __init__(self, figure=None): self.original_tagname_ = None if figure is None: self.figure = [] else: self.figure = figure
[docs] def factory(*args_, **kwargs_): if figure_listType.subclass: return figure_listType.subclass(*args_, **kwargs_) else: return figure_listType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_figure(self): return self.figure
[docs] def set_figure(self, figure): self.figure = figure
[docs] def add_figure(self, value): self.figure.append(value)
[docs] def insert_figure_at(self, index, value): self.figure.insert(index, value)
[docs] def replace_figure_at(self, index, value): self.figure[index] = value
[docs] def hasContent_(self): if ( self.figure ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='figure_listType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='figure_listType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='figure_listType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='figure_listType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='figure_listType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for figure_ in self.figure: figure_.export(outfile, level, namespace_, name_='figure', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'figure': obj_ = figure_type.factory() obj_.build(child_) self.figure.append(obj_) obj_.original_tagname_ = 'figure' # end class figure_listType
[docs]class segmentation_listType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('segmentation', 'segmentationType', 1), ] subclass = None superclass = None def __init__(self, segmentation=None): self.original_tagname_ = None if segmentation is None: self.segmentation = [] else: self.segmentation = segmentation
[docs] def factory(*args_, **kwargs_): if segmentation_listType.subclass: return segmentation_listType.subclass(*args_, **kwargs_) else: return segmentation_listType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_segmentation(self): return self.segmentation
[docs] def set_segmentation(self, segmentation): self.segmentation = segmentation
[docs] def add_segmentation(self, value): self.segmentation.append(value)
[docs] def insert_segmentation_at(self, index, value): self.segmentation.insert(index, value)
[docs] def replace_segmentation_at(self, index, value): self.segmentation[index] = value
[docs] def hasContent_(self): if ( self.segmentation ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='segmentation_listType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='segmentation_listType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='segmentation_listType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='segmentation_listType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='segmentation_listType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for segmentation_ in self.segmentation: segmentation_.export(outfile, level, namespace_, name_='segmentation', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'segmentation': obj_ = segmentationType.factory() obj_.build(child_) self.segmentation.append(obj_) obj_.original_tagname_ = 'segmentation' # end class segmentation_listType
[docs]class segmentationType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('file', ['fileType43', 'xs:token'], 0), MemberSpec_('details', 'xs:string', 0), MemberSpec_('mask_details', 'map_type', 0), ] subclass = None superclass = None def __init__(self, file=None, details=None, mask_details=None): self.original_tagname_ = None self.file = file self.validate_fileType43(self.file) self.details = details self.mask_details = mask_details
[docs] def factory(*args_, **kwargs_): if segmentationType.subclass: return segmentationType.subclass(*args_, **kwargs_) else: return segmentationType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_file(self): return self.file
[docs] def set_file(self, file): self.file = file
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def get_mask_details(self): return self.mask_details
[docs] def set_mask_details(self, mask_details): self.mask_details = mask_details
[docs] def validate_fileType43(self, value): # Validate type fileType43, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_fileType43_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_fileType43_patterns_, ))
validate_fileType43_patterns_ = [['^emd_\\d{4,}_seg.xml$']]
[docs] def hasContent_(self): if ( self.file is not None or self.details is not None or self.mask_details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='segmentationType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='segmentationType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='segmentationType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='segmentationType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='segmentationType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.file is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sfile>%s</%sfile>%s' % (namespace_, self.gds_format_string(quote_xml(self.file).encode(ExternalEncoding), input_name='file'), namespace_, eol_)) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_)) if self.mask_details is not None: self.mask_details.export(outfile, level, namespace_, name_='mask_details', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'file': file_ = child_.text file_ = re_.sub(String_cleanup_pat_, " ", file_).strip() file_ = self.gds_validate_string(file_, node, 'file') self.file = file_ # validate type fileType43 self.validate_fileType43(self.file) elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ elif nodeName_ == 'mask_details': obj_ = map_type.factory() obj_.build(child_) self.mask_details = obj_ obj_.original_tagname_ = 'mask_details' # end class segmentationType
[docs]class slices_listType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('slice', 'map_type', 1), ] subclass = None superclass = None def __init__(self, slice=None): self.original_tagname_ = None if slice is None: self.slice = [] else: self.slice = slice
[docs] def factory(*args_, **kwargs_): if slices_listType.subclass: return slices_listType.subclass(*args_, **kwargs_) else: return slices_listType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_slice(self): return self.slice
[docs] def set_slice(self, slice): self.slice = slice
[docs] def add_slice(self, value): self.slice.append(value)
[docs] def insert_slice_at(self, index, value): self.slice.insert(index, value)
[docs] def replace_slice_at(self, index, value): self.slice[index] = value
[docs] def hasContent_(self): if ( self.slice ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='slices_listType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='slices_listType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='slices_listType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='slices_listType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='slices_listType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for slice_ in self.slice: slice_.export(outfile, level, namespace_, name_='slice', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'slice': obj_ = map_type.factory() obj_.build(child_) self.slice.append(obj_) obj_.original_tagname_ = 'slice' # end class slices_listType
[docs]class additional_map_listType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('additional_map', 'map_type', 1), ] subclass = None superclass = None def __init__(self, additional_map=None): self.original_tagname_ = None if additional_map is None: self.additional_map = [] else: self.additional_map = additional_map
[docs] def factory(*args_, **kwargs_): if additional_map_listType.subclass: return additional_map_listType.subclass(*args_, **kwargs_) else: return additional_map_listType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_additional_map(self): return self.additional_map
[docs] def set_additional_map(self, additional_map): self.additional_map = additional_map
[docs] def add_additional_map(self, value): self.additional_map.append(value)
[docs] def insert_additional_map_at(self, index, value): self.additional_map.insert(index, value)
[docs] def replace_additional_map_at(self, index, value): self.additional_map[index] = value
[docs] def hasContent_(self): if ( self.additional_map ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='additional_map_listType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='additional_map_listType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='additional_map_listType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='additional_map_listType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='additional_map_listType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for additional_map_ in self.additional_map: additional_map_.export(outfile, level, namespace_, name_='additional_map', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'additional_map': obj_ = map_type.factory() obj_.build(child_) self.additional_map.append(obj_) obj_.original_tagname_ = 'additional_map' # end class additional_map_listType
[docs]class half_map_listType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('half_map', 'map_type', 1), ] subclass = None superclass = None def __init__(self, half_map=None): self.original_tagname_ = None if half_map is None: self.half_map = [] else: self.half_map = half_map
[docs] def factory(*args_, **kwargs_): if half_map_listType.subclass: return half_map_listType.subclass(*args_, **kwargs_) else: return half_map_listType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_half_map(self): return self.half_map
[docs] def set_half_map(self, half_map): self.half_map = half_map
[docs] def add_half_map(self, value): self.half_map.append(value)
[docs] def insert_half_map_at(self, index, value): self.half_map.insert(index, value)
[docs] def replace_half_map_at(self, index, value): self.half_map[index] = value
[docs] def hasContent_(self): if ( self.half_map ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='half_map_listType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='half_map_listType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='half_map_listType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='half_map_listType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='half_map_listType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for half_map_ in self.half_map: half_map_.export(outfile, level, namespace_, name_='half_map', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'half_map': obj_ = map_type.factory() obj_.build(child_) self.half_map.append(obj_) obj_.original_tagname_ = 'half_map' # end class half_map_listType
[docs]class external_referencesType45(GeneratedsSuper): member_data_items_ = [ MemberSpec_('type', 'xs:token', 0), MemberSpec_('valueOf_', 'xs:token', 0), ] subclass = None superclass = None def __init__(self, type_=None, valueOf_=None): self.original_tagname_ = None self.type_ = _cast(None, type_) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if external_referencesType45.subclass: return external_referencesType45.subclass(*args_, **kwargs_) else: return external_referencesType45(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_type(self): return self.type_
[docs] def set_type(self, type_): self.type_ = type_
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='external_referencesType45', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='external_referencesType45') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='external_referencesType45', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='external_referencesType45'): if self.type_ is not None and 'type_' not in already_processed: already_processed.add('type_') outfile.write(' type=%s' % (self.gds_format_string(quote_attrib(self.type_).encode(ExternalEncoding), input_name='type'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='external_referencesType45', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('type', node) if value is not None and 'type' not in already_processed: already_processed.add('type') self.type_ = value self.type_ = ' '.join(self.type_.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class external_referencesType45
[docs]class external_referencesType47(GeneratedsSuper): member_data_items_ = [ MemberSpec_('type', 'xs:token', 0), MemberSpec_('valueOf_', 'xs:token', 0), ] subclass = None superclass = None def __init__(self, type_=None, valueOf_=None): self.original_tagname_ = None self.type_ = _cast(None, type_) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if external_referencesType47.subclass: return external_referencesType47.subclass(*args_, **kwargs_) else: return external_referencesType47(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_type(self): return self.type_
[docs] def set_type(self, type_): self.type_ = type_
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='external_referencesType47', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='external_referencesType47') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='external_referencesType47', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='external_referencesType47'): if self.type_ is not None and 'type_' not in already_processed: already_processed.add('type_') outfile.write(' type=%s' % (self.gds_format_string(quote_attrib(self.type_).encode(ExternalEncoding), input_name='type'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='external_referencesType47', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('type', node) if value is not None and 'type' not in already_processed: already_processed.add('type') self.type_ = value self.type_ = ' '.join(self.type_.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class external_referencesType47
[docs]class crystal_formationType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('lipid_protein_ratio', 'xs:float', 0), MemberSpec_('lipid_mixture', 'xs:token', 0), MemberSpec_('instrument', ['instrumentType48', 'xs:token'], 0), MemberSpec_('atmosphere', 'xs:token', 0), MemberSpec_('temperature', 'crystal_formation_temperature_type', 0), MemberSpec_('time', 'crystal_formation_time_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, lipid_protein_ratio=None, lipid_mixture=None, instrument=None, atmosphere=None, temperature=None, time=None, details=None): self.original_tagname_ = None self.lipid_protein_ratio = lipid_protein_ratio self.lipid_mixture = lipid_mixture self.instrument = instrument self.validate_instrumentType48(self.instrument) self.atmosphere = atmosphere self.temperature = temperature self.time = time self.details = details
[docs] def factory(*args_, **kwargs_): if crystal_formationType.subclass: return crystal_formationType.subclass(*args_, **kwargs_) else: return crystal_formationType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_lipid_protein_ratio(self): return self.lipid_protein_ratio
[docs] def set_lipid_protein_ratio(self, lipid_protein_ratio): self.lipid_protein_ratio = lipid_protein_ratio
[docs] def get_lipid_mixture(self): return self.lipid_mixture
[docs] def set_lipid_mixture(self, lipid_mixture): self.lipid_mixture = lipid_mixture
[docs] def get_instrument(self): return self.instrument
[docs] def set_instrument(self, instrument): self.instrument = instrument
[docs] def get_atmosphere(self): return self.atmosphere
[docs] def set_atmosphere(self, atmosphere): self.atmosphere = atmosphere
[docs] def get_temperature(self): return self.temperature
[docs] def set_temperature(self, temperature): self.temperature = temperature
[docs] def get_time(self): return self.time
[docs] def set_time(self, time): self.time = time
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def validate_instrumentType48(self, value): # Validate type instrumentType48, a restriction on xs:token. if value is not None and Validate_simpletypes_: pass
[docs] def hasContent_(self): if ( self.lipid_protein_ratio is not None or self.lipid_mixture is not None or self.instrument is not None or self.atmosphere is not None or self.temperature is not None or self.time is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='crystal_formationType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='crystal_formationType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='crystal_formationType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='crystal_formationType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='crystal_formationType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.lipid_protein_ratio is not None: showIndent(outfile, level, pretty_print) outfile.write('<%slipid_protein_ratio>%s</%slipid_protein_ratio>%s' % (namespace_, self.gds_format_float(self.lipid_protein_ratio, input_name='lipid_protein_ratio'), namespace_, eol_)) if self.lipid_mixture is not None: showIndent(outfile, level, pretty_print) outfile.write('<%slipid_mixture>%s</%slipid_mixture>%s' % (namespace_, self.gds_format_string(quote_xml(self.lipid_mixture).encode(ExternalEncoding), input_name='lipid_mixture'), namespace_, eol_)) if self.instrument is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sinstrument>%s</%sinstrument>%s' % (namespace_, self.gds_format_string(quote_xml(self.instrument).encode(ExternalEncoding), input_name='instrument'), namespace_, eol_)) if self.atmosphere is not None: showIndent(outfile, level, pretty_print) outfile.write('<%satmosphere>%s</%satmosphere>%s' % (namespace_, self.gds_format_string(quote_xml(self.atmosphere).encode(ExternalEncoding), input_name='atmosphere'), namespace_, eol_)) if self.temperature is not None: self.temperature.export(outfile, level, namespace_, name_='temperature', pretty_print=pretty_print) if self.time is not None: self.time.export(outfile, level, namespace_, name_='time', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'lipid_protein_ratio': sval_ = child_.text try: fval_ = float(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires float or double: %s' % exp) fval_ = self.gds_validate_float(fval_, node, 'lipid_protein_ratio') self.lipid_protein_ratio = fval_ elif nodeName_ == 'lipid_mixture': lipid_mixture_ = child_.text lipid_mixture_ = re_.sub(String_cleanup_pat_, " ", lipid_mixture_).strip() lipid_mixture_ = self.gds_validate_string(lipid_mixture_, node, 'lipid_mixture') self.lipid_mixture = lipid_mixture_ elif nodeName_ == 'instrument': instrument_ = child_.text instrument_ = re_.sub(String_cleanup_pat_, " ", instrument_).strip() instrument_ = self.gds_validate_string(instrument_, node, 'instrument') self.instrument = instrument_ # validate type instrumentType48 self.validate_instrumentType48(self.instrument) elif nodeName_ == 'atmosphere': atmosphere_ = child_.text atmosphere_ = re_.sub(String_cleanup_pat_, " ", atmosphere_).strip() atmosphere_ = self.gds_validate_string(atmosphere_, node, 'atmosphere') self.atmosphere = atmosphere_ elif nodeName_ == 'temperature': obj_ = crystal_formation_temperature_type.factory() obj_.build(child_) self.temperature = obj_ obj_.original_tagname_ = 'temperature' elif nodeName_ == 'time': obj_ = crystal_formation_time_type.factory() obj_.build(child_) self.time = obj_ obj_.original_tagname_ = 'time' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class crystal_formationType
[docs]class dimensionsType49(GeneratedsSuper): member_data_items_ = [ MemberSpec_('radius', 'radiusType', 0), MemberSpec_('width', 'widthType50', 0), MemberSpec_('height', 'heightType51', 0), MemberSpec_('depth', 'depthType', 0), ] subclass = None superclass = None def __init__(self, radius=None, width=None, height=None, depth=None): self.original_tagname_ = None self.radius = radius self.width = width self.height = height self.depth = depth
[docs] def factory(*args_, **kwargs_): if dimensionsType49.subclass: return dimensionsType49.subclass(*args_, **kwargs_) else: return dimensionsType49(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_radius(self): return self.radius
[docs] def set_radius(self, radius): self.radius = radius
[docs] def get_width(self): return self.width
[docs] def set_width(self, width): self.width = width
[docs] def get_height(self): return self.height
[docs] def set_height(self, height): self.height = height
[docs] def get_depth(self): return self.depth
[docs] def set_depth(self, depth): self.depth = depth
[docs] def hasContent_(self): if ( self.radius is not None or self.width is not None or self.height is not None or self.depth is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='dimensionsType49', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='dimensionsType49') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='dimensionsType49', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='dimensionsType49'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='dimensionsType49', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.radius is not None: self.radius.export(outfile, level, namespace_, name_='radius', pretty_print=pretty_print) if self.width is not None: self.width.export(outfile, level, namespace_, name_='width', pretty_print=pretty_print) if self.height is not None: self.height.export(outfile, level, namespace_, name_='height', pretty_print=pretty_print) if self.depth is not None: self.depth.export(outfile, level, namespace_, name_='depth', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'radius': obj_ = radiusType.factory() obj_.build(child_) self.radius = obj_ obj_.original_tagname_ = 'radius' elif nodeName_ == 'width': obj_ = widthType50.factory() obj_.build(child_) self.width = obj_ obj_.original_tagname_ = 'width' elif nodeName_ == 'height': obj_ = heightType51.factory() obj_.build(child_) self.height = obj_ obj_.original_tagname_ = 'height' elif nodeName_ == 'depth': obj_ = depthType.factory() obj_.build(child_) self.depth = obj_ obj_.original_tagname_ = 'depth' # end class dimensionsType49
[docs]class radiusType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', 'xs:float', 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if radiusType.subclass: return radiusType.subclass(*args_, **kwargs_) else: return radiusType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='radiusType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='radiusType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='radiusType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='radiusType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='radiusType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class radiusType
[docs]class widthType50(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', 'xs:float', 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if widthType50.subclass: return widthType50.subclass(*args_, **kwargs_) else: return widthType50(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='widthType50', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='widthType50') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='widthType50', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='widthType50'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='widthType50', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class widthType50
[docs]class heightType51(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', 'xs:float', 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if heightType51.subclass: return heightType51.subclass(*args_, **kwargs_) else: return heightType51(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='heightType51', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='heightType51') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='heightType51', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='heightType51'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='heightType51', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class heightType51
[docs]class depthType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', 'xs:float', 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if depthType.subclass: return depthType.subclass(*args_, **kwargs_) else: return depthType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='depthType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='depthType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='depthType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='depthType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='depthType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class depthType
[docs]class spatial_filteringType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('low_frequency_cutoff', 'low_frequency_cutoffType', 0), MemberSpec_('high_frequency_cutoff', 'high_frequency_cutoffType', 0), MemberSpec_('filter_function', 'xs:token', 0), MemberSpec_('software_list', 'software_list_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, low_frequency_cutoff=None, high_frequency_cutoff=None, filter_function=None, software_list=None, details=None): self.original_tagname_ = None self.low_frequency_cutoff = low_frequency_cutoff self.high_frequency_cutoff = high_frequency_cutoff self.filter_function = filter_function self.software_list = software_list self.details = details
[docs] def factory(*args_, **kwargs_): if spatial_filteringType.subclass: return spatial_filteringType.subclass(*args_, **kwargs_) else: return spatial_filteringType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_low_frequency_cutoff(self): return self.low_frequency_cutoff
[docs] def set_low_frequency_cutoff(self, low_frequency_cutoff): self.low_frequency_cutoff = low_frequency_cutoff
[docs] def get_high_frequency_cutoff(self): return self.high_frequency_cutoff
[docs] def set_high_frequency_cutoff(self, high_frequency_cutoff): self.high_frequency_cutoff = high_frequency_cutoff
[docs] def get_filter_function(self): return self.filter_function
[docs] def set_filter_function(self, filter_function): self.filter_function = filter_function
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def hasContent_(self): if ( self.low_frequency_cutoff is not None or self.high_frequency_cutoff is not None or self.filter_function is not None or self.software_list is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='spatial_filteringType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='spatial_filteringType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='spatial_filteringType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='spatial_filteringType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='spatial_filteringType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.low_frequency_cutoff is not None: self.low_frequency_cutoff.export(outfile, level, namespace_, name_='low_frequency_cutoff', pretty_print=pretty_print) if self.high_frequency_cutoff is not None: self.high_frequency_cutoff.export(outfile, level, namespace_, name_='high_frequency_cutoff', pretty_print=pretty_print) if self.filter_function is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sfilter_function>%s</%sfilter_function>%s' % (namespace_, self.gds_format_string(quote_xml(self.filter_function).encode(ExternalEncoding), input_name='filter_function'), namespace_, eol_)) if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'low_frequency_cutoff': obj_ = low_frequency_cutoffType.factory() obj_.build(child_) self.low_frequency_cutoff = obj_ obj_.original_tagname_ = 'low_frequency_cutoff' elif nodeName_ == 'high_frequency_cutoff': obj_ = high_frequency_cutoffType.factory() obj_.build(child_) self.high_frequency_cutoff = obj_ obj_.original_tagname_ = 'high_frequency_cutoff' elif nodeName_ == 'filter_function': filter_function_ = child_.text filter_function_ = re_.sub(String_cleanup_pat_, " ", filter_function_).strip() filter_function_ = self.gds_validate_string(filter_function_, node, 'filter_function') self.filter_function = filter_function_ elif nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class spatial_filteringType
[docs]class low_frequency_cutoffType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:string', 0), MemberSpec_('valueOf_', 'xs:float', 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if low_frequency_cutoffType.subclass: return low_frequency_cutoffType.subclass(*args_, **kwargs_) else: return low_frequency_cutoffType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='low_frequency_cutoffType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='low_frequency_cutoffType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='low_frequency_cutoffType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='low_frequency_cutoffType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='low_frequency_cutoffType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class low_frequency_cutoffType
[docs]class high_frequency_cutoffType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:string', 0), MemberSpec_('valueOf_', 'xs:float', 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if high_frequency_cutoffType.subclass: return high_frequency_cutoffType.subclass(*args_, **kwargs_) else: return high_frequency_cutoffType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='high_frequency_cutoffType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='high_frequency_cutoffType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='high_frequency_cutoffType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='high_frequency_cutoffType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='high_frequency_cutoffType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class high_frequency_cutoffType
[docs]class sharpeningType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('software_list', 'software_list_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, software_list=None, details=None): self.original_tagname_ = None self.software_list = software_list self.details = details
[docs] def factory(*args_, **kwargs_): if sharpeningType.subclass: return sharpeningType.subclass(*args_, **kwargs_) else: return sharpeningType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def hasContent_(self): if ( self.software_list is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='sharpeningType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='sharpeningType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='sharpeningType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='sharpeningType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='sharpeningType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class sharpeningType
[docs]class b_factorSharpeningType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('_brestore', '_brestoreType', 0), MemberSpec_('software_list', 'software_list_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, _brestore=None, software_list=None, details=None): self.original_tagname_ = None self._brestore = _brestore self.software_list = software_list self.details = details
[docs] def factory(*args_, **kwargs_): if b_factorSharpeningType.subclass: return b_factorSharpeningType.subclass(*args_, **kwargs_) else: return b_factorSharpeningType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get__brestore(self): return self._brestore
[docs] def set__brestore(self, _brestore): self._brestore = _brestore
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def hasContent_(self): if ( self._brestore is not None or self.software_list is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='b-factorSharpeningType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='b-factorSharpeningType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='b-factorSharpeningType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='b-factorSharpeningType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='b-factorSharpeningType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self._brestore is not None: self._brestore.export(outfile, level, namespace_, name_='_brestore', pretty_print=pretty_print) if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == '_brestore': obj_ = _brestoreType.factory() obj_.build(child_) self._brestore = obj_ obj_.original_tagname_ = '_brestore' elif nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class b_factorSharpeningType
class _brestoreType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_brestore_type', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_ def factory(*args_, **kwargs_): if _brestoreType.subclass: return _brestoreType.subclass(*args_, **kwargs_) else: return _brestoreType(*args_, **kwargs_) factory = staticmethod(factory) def get_units(self): return self.units def set_units(self, units): self.units = units def get_valueOf_(self): return self.valueOf_ def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_ def hasContent_(self): if ( self.valueOf_ ): return True else: return False def export(self, outfile, level, namespace_='', name_='_brestoreType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='_brestoreType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='_brestoreType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, )) def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='_brestoreType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), )) def exportChildren(self, outfile, level, namespace_='', name_='_brestoreType', fromsubclass_=False, pretty_print=True): pass def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split()) def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class _brestoreType
[docs]class otherType52(GeneratedsSuper): member_data_items_ = [ MemberSpec_('software_list', 'software_list_type', 0), MemberSpec_('details', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, software_list=None, details=None): self.original_tagname_ = None self.software_list = software_list self.details = details
[docs] def factory(*args_, **kwargs_): if otherType52.subclass: return otherType52.subclass(*args_, **kwargs_) else: return otherType52(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_software_list(self): return self.software_list
[docs] def set_software_list(self, software_list): self.software_list = software_list
[docs] def get_details(self): return self.details
[docs] def set_details(self, details): self.details = details
[docs] def hasContent_(self): if ( self.software_list is not None or self.details is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='otherType52', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='otherType52') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='otherType52', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='otherType52'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='otherType52', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.software_list is not None: self.software_list.export(outfile, level, namespace_, name_='software_list', pretty_print=pretty_print) if self.details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sdetails>%s</%sdetails>%s' % (namespace_, self.gds_format_string(quote_xml(self.details).encode(ExternalEncoding), input_name='details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'software_list': obj_ = software_list_type.factory() obj_.build(child_) self.software_list = obj_ obj_.original_tagname_ = 'software_list' elif nodeName_ == 'details': details_ = child_.text details_ = self.gds_validate_string(details_, node, 'details') self.details = details_ # end class otherType52
[docs]class chainType53(chain_model_type): member_data_items_ = [ MemberSpec_('number_of_copies_in_final_model', 'xs:positiveInteger', 0), ] subclass = None superclass = chain_model_type def __init__(self, id=None, residue_range=None, number_of_copies_in_final_model=None): self.original_tagname_ = None super(chainType53, self).__init__(id, residue_range, ) self.number_of_copies_in_final_model = number_of_copies_in_final_model
[docs] def factory(*args_, **kwargs_): if chainType53.subclass: return chainType53.subclass(*args_, **kwargs_) else: return chainType53(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_number_of_copies_in_final_model(self): return self.number_of_copies_in_final_model
[docs] def set_number_of_copies_in_final_model(self, number_of_copies_in_final_model): self.number_of_copies_in_final_model = number_of_copies_in_final_model
[docs] def hasContent_(self): if ( self.number_of_copies_in_final_model is not None or super(chainType53, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='chainType53', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='chainType53') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='chainType53', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='chainType53'): super(chainType53, self).exportAttributes(outfile, level, already_processed, namespace_, name_='chainType53')
[docs] def exportChildren(self, outfile, level, namespace_='', name_='chainType53', fromsubclass_=False, pretty_print=True): super(chainType53, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print) if pretty_print: eol_ = '\n' else: eol_ = '' if self.number_of_copies_in_final_model is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_of_copies_in_final_model>%s</%snumber_of_copies_in_final_model>%s' % (namespace_, self.gds_format_integer(self.number_of_copies_in_final_model, input_name='number_of_copies_in_final_model'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): super(chainType53, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'number_of_copies_in_final_model': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'number_of_copies_in_final_model') self.number_of_copies_in_final_model = ival_ super(chainType53, self).buildChildren(child_, node, nodeName_, True) # end class chainType53
[docs]class delta_zType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_rise_type', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if delta_zType.subclass: return delta_zType.subclass(*args_, **kwargs_) else: return delta_zType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='delta_zType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='delta_zType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='delta_zType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='delta_zType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='delta_zType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class delta_zType
[docs]class delta_phiType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_twist_type', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if delta_phiType.subclass: return delta_phiType.subclass(*args_, **kwargs_) else: return delta_phiType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='delta_phiType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='delta_phiType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='delta_phiType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='delta_phiType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='delta_phiType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class delta_phiType
[docs]class experimentalType(GeneratedsSuper): """kDa/nm is for helices.""" member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_assembly_weights', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if experimentalType.subclass: return experimentalType.subclass(*args_, **kwargs_) else: return experimentalType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='experimentalType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='experimentalType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='experimentalType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='experimentalType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='experimentalType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class experimentalType
[docs]class theoreticalType(GeneratedsSuper): """kDa/nm is for helices.""" member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_assembly_weights', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if theoreticalType.subclass: return theoreticalType.subclass(*args_, **kwargs_) else: return theoreticalType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='theoreticalType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='theoreticalType') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='theoreticalType', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='theoreticalType'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='theoreticalType', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class theoreticalType
[docs]class sequenceType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('string', ['stringType', 'xs:token'], 0), MemberSpec_('discrepancy_list', 'discrepancy_listType', 0), MemberSpec_('connectivity', 'connectivityType', 0), MemberSpec_('external_references', 'external_referencesType54', 1), ] subclass = None superclass = None def __init__(self, string=None, discrepancy_list=None, connectivity=None, external_references=None): self.original_tagname_ = None self.string = string self.validate_stringType(self.string) self.discrepancy_list = discrepancy_list self.connectivity = connectivity if external_references is None: self.external_references = [] else: self.external_references = external_references
[docs] def factory(*args_, **kwargs_): if sequenceType.subclass: return sequenceType.subclass(*args_, **kwargs_) else: return sequenceType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_string(self): return self.string
[docs] def set_string(self, string): self.string = string
[docs] def get_discrepancy_list(self): return self.discrepancy_list
[docs] def set_discrepancy_list(self, discrepancy_list): self.discrepancy_list = discrepancy_list
[docs] def get_connectivity(self): return self.connectivity
[docs] def set_connectivity(self, connectivity): self.connectivity = connectivity
[docs] def get_external_references(self): return self.external_references
[docs] def set_external_references(self, external_references): self.external_references = external_references
[docs] def add_external_references(self, value): self.external_references.append(value)
[docs] def insert_external_references_at(self, index, value): self.external_references.insert(index, value)
[docs] def replace_external_references_at(self, index, value): self.external_references[index] = value
[docs] def validate_stringType(self, value): # Validate type stringType, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_stringType_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_stringType_patterns_, ))
validate_stringType_patterns_ = [['^[ ARNDCEQGHILKMFPSTWYVUOBZJX]+$']]
[docs] def hasContent_(self): if ( self.string is not None or self.discrepancy_list is not None or self.connectivity is not None or self.external_references ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='sequenceType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='sequenceType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='sequenceType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='sequenceType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='sequenceType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.string is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sstring>%s</%sstring>%s' % (namespace_, self.gds_format_string(quote_xml(self.string).encode(ExternalEncoding), input_name='string'), namespace_, eol_)) if self.discrepancy_list is not None: self.discrepancy_list.export(outfile, level, namespace_, name_='discrepancy_list', pretty_print=pretty_print) if self.connectivity is not None: self.connectivity.export(outfile, level, namespace_, name_='connectivity', pretty_print=pretty_print) for external_references_ in self.external_references: external_references_.export(outfile, level, namespace_, name_='external_references', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'string': string_ = child_.text string_ = re_.sub(String_cleanup_pat_, " ", string_).strip() string_ = self.gds_validate_string(string_, node, 'string') self.string = string_ # validate type stringType self.validate_stringType(self.string) elif nodeName_ == 'discrepancy_list': obj_ = discrepancy_listType.factory() obj_.build(child_) self.discrepancy_list = obj_ obj_.original_tagname_ = 'discrepancy_list' elif nodeName_ == 'connectivity': obj_ = connectivityType.factory() obj_.build(child_) self.connectivity = obj_ obj_.original_tagname_ = 'connectivity' elif nodeName_ == 'external_references': obj_ = external_referencesType54.factory() obj_.build(child_) self.external_references.append(obj_) obj_.original_tagname_ = 'external_references' # end class sequenceType
[docs]class discrepancy_listType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('discrepancy', ['discrepancyType', 'xs:token'], 1), ] subclass = None superclass = None def __init__(self, discrepancy=None): self.original_tagname_ = None if discrepancy is None: self.discrepancy = [] else: self.discrepancy = discrepancy
[docs] def factory(*args_, **kwargs_): if discrepancy_listType.subclass: return discrepancy_listType.subclass(*args_, **kwargs_) else: return discrepancy_listType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_discrepancy(self): return self.discrepancy
[docs] def set_discrepancy(self, discrepancy): self.discrepancy = discrepancy
[docs] def add_discrepancy(self, value): self.discrepancy.append(value)
[docs] def insert_discrepancy_at(self, index, value): self.discrepancy.insert(index, value)
[docs] def replace_discrepancy_at(self, index, value): self.discrepancy[index] = value
[docs] def validate_discrepancyType(self, value): # Validate type discrepancyType, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_discrepancyType_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_discrepancyType_patterns_, ))
validate_discrepancyType_patterns_ = [['^[ARNDCEQGHILKMFPSTWYVUOBZJX]\\d+[ARNDCEQGHILKMFPSTWYVUOBZJX]$']]
[docs] def hasContent_(self): if ( self.discrepancy ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='discrepancy_listType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='discrepancy_listType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='discrepancy_listType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='discrepancy_listType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='discrepancy_listType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for discrepancy_ in self.discrepancy: showIndent(outfile, level, pretty_print) outfile.write('<%sdiscrepancy>%s</%sdiscrepancy>%s' % (namespace_, self.gds_format_string(quote_xml(discrepancy_).encode(ExternalEncoding), input_name='discrepancy'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'discrepancy': discrepancy_ = child_.text discrepancy_ = re_.sub(String_cleanup_pat_, " ", discrepancy_).strip() discrepancy_ = self.gds_validate_string(discrepancy_, node, 'discrepancy') self.discrepancy.append(discrepancy_) # validate type discrepancyType self.validate_discrepancyType(self.discrepancy[-1]) # end class discrepancy_listType
[docs]class connectivityType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('_n_link', '_n-linkType', 0), MemberSpec_('_c_link', '_c-linkType', 0), ] subclass = None superclass = None def __init__(self, _n_link=None, _c_link=None): self.original_tagname_ = None self._n_link = _n_link self._c_link = _c_link
[docs] def factory(*args_, **kwargs_): if connectivityType.subclass: return connectivityType.subclass(*args_, **kwargs_) else: return connectivityType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( self._n_link is not None or self._c_link is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='connectivityType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='connectivityType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='connectivityType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='connectivityType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='connectivityType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self._n_link is not None: self._n_link.export(outfile, level, namespace_, name_='_n-link', pretty_print=pretty_print) if self._c_link is not None: self._c_link.export(outfile, level, namespace_, name_='_c-link', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == '_n-link': obj_ = _n_linkType.factory() obj_.build(child_) self._n_link = obj_ obj_.original_tagname_ = '_n-link' elif nodeName_ == '_c-link': obj_ = _c_linkType.factory() obj_.build(child_) self._c_link = obj_ obj_.original_tagname_ = '_c-link' # end class connectivityType
class _n_linkType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('molecule_id', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, molecule_id=None): self.original_tagname_ = None self.molecule_id = molecule_id def factory(*args_, **kwargs_): if _n_linkType.subclass: return _n_linkType.subclass(*args_, **kwargs_) else: return _n_linkType(*args_, **kwargs_) factory = staticmethod(factory) def get_molecule_id(self): return self.molecule_id def set_molecule_id(self, molecule_id): self.molecule_id = molecule_id def hasContent_(self): if ( self.molecule_id is not None ): return True else: return False def export(self, outfile, level, namespace_='', name_='_n-linkType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='_n-linkType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='_n-linkType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, )) def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='_n-linkType'): pass def exportChildren(self, outfile, level, namespace_='', name_='_n-linkType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.molecule_id is not None: showIndent(outfile, level, pretty_print) outfile.write('<%smolecule_id>%s</%smolecule_id>%s' % (namespace_, self.gds_format_string(quote_xml(self.molecule_id).encode(ExternalEncoding), input_name='molecule_id'), namespace_, eol_)) def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self def buildAttributes(self, node, attrs, already_processed): pass def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'molecule_id': molecule_id_ = child_.text molecule_id_ = self.gds_validate_string(molecule_id_, node, 'molecule_id') self.molecule_id = molecule_id_ # end class _n_linkType
[docs]class molecule_id(GeneratedsSuper): member_data_items_ = [ ] subclass = None superclass = None def __init__(self): self.original_tagname_ = None
[docs] def factory(*args_, **kwargs_): if molecule_id.subclass: return molecule_id.subclass(*args_, **kwargs_) else: return molecule_id(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='molecule_id', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='molecule_id') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='molecule_id', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='molecule_id'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='molecule_id', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class molecule_id
class _c_linkType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('molecule_id', 'xs:string', 0), ] subclass = None superclass = None def __init__(self, molecule_id=None): self.original_tagname_ = None self.molecule_id = molecule_id def factory(*args_, **kwargs_): if _c_linkType.subclass: return _c_linkType.subclass(*args_, **kwargs_) else: return _c_linkType(*args_, **kwargs_) factory = staticmethod(factory) def get_molecule_id(self): return self.molecule_id def set_molecule_id(self, molecule_id): self.molecule_id = molecule_id def hasContent_(self): if ( self.molecule_id is not None ): return True else: return False def export(self, outfile, level, namespace_='', name_='_c-linkType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='_c-linkType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='_c-linkType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, )) def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='_c-linkType'): pass def exportChildren(self, outfile, level, namespace_='', name_='_c-linkType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.molecule_id is not None: showIndent(outfile, level, pretty_print) outfile.write('<%smolecule_id>%s</%smolecule_id>%s' % (namespace_, self.gds_format_string(quote_xml(self.molecule_id).encode(ExternalEncoding), input_name='molecule_id'), namespace_, eol_)) def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self def buildAttributes(self, node, attrs, already_processed): pass def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'molecule_id': molecule_id_ = child_.text molecule_id_ = self.gds_validate_string(molecule_id_, node, 'molecule_id') self.molecule_id = molecule_id_ # end class _c_linkType
[docs]class external_referencesType54(GeneratedsSuper): member_data_items_ = [ MemberSpec_('type', 'xs:token', 0), MemberSpec_('valueOf_', 'xs:token', 0), ] subclass = None superclass = None def __init__(self, type_=None, valueOf_=None): self.original_tagname_ = None self.type_ = _cast(None, type_) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if external_referencesType54.subclass: return external_referencesType54.subclass(*args_, **kwargs_) else: return external_referencesType54(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_type(self): return self.type_
[docs] def set_type(self, type_): self.type_ = type_
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='external_referencesType54', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='external_referencesType54') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='external_referencesType54', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='external_referencesType54'): if self.type_ is not None and 'type_' not in already_processed: already_processed.add('type_') outfile.write(' type=%s' % (self.gds_format_string(quote_attrib(self.type_).encode(ExternalEncoding), input_name='type'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='external_referencesType54', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('type', node) if value is not None and 'type' not in already_processed: already_processed.add('type') self.type_ = value self.type_ = ' '.join(self.type_.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class external_referencesType54
[docs]class sequenceType55(GeneratedsSuper): member_data_items_ = [ MemberSpec_('string', ['stringType56', 'xs:token'], 0), MemberSpec_('discrepancy_list', 'discrepancy_listType57', 0), MemberSpec_('external_references', 'external_referencesType59', 1), ] subclass = None superclass = None def __init__(self, string=None, discrepancy_list=None, external_references=None): self.original_tagname_ = None self.string = string self.validate_stringType56(self.string) self.discrepancy_list = discrepancy_list if external_references is None: self.external_references = [] else: self.external_references = external_references
[docs] def factory(*args_, **kwargs_): if sequenceType55.subclass: return sequenceType55.subclass(*args_, **kwargs_) else: return sequenceType55(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_string(self): return self.string
[docs] def set_string(self, string): self.string = string
[docs] def get_discrepancy_list(self): return self.discrepancy_list
[docs] def set_discrepancy_list(self, discrepancy_list): self.discrepancy_list = discrepancy_list
[docs] def get_external_references(self): return self.external_references
[docs] def set_external_references(self, external_references): self.external_references = external_references
[docs] def add_external_references(self, value): self.external_references.append(value)
[docs] def insert_external_references_at(self, index, value): self.external_references.insert(index, value)
[docs] def replace_external_references_at(self, index, value): self.external_references[index] = value
[docs] def validate_stringType56(self, value): # Validate type stringType56, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_stringType56_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_stringType56_patterns_, ))
validate_stringType56_patterns_ = [['^[ ACGTRYSWKMBDHVN\\.-]+$']]
[docs] def hasContent_(self): if ( self.string is not None or self.discrepancy_list is not None or self.external_references ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='sequenceType55', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='sequenceType55') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='sequenceType55', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='sequenceType55'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='sequenceType55', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.string is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sstring>%s</%sstring>%s' % (namespace_, self.gds_format_string(quote_xml(self.string).encode(ExternalEncoding), input_name='string'), namespace_, eol_)) if self.discrepancy_list is not None: self.discrepancy_list.export(outfile, level, namespace_, name_='discrepancy_list', pretty_print=pretty_print) for external_references_ in self.external_references: external_references_.export(outfile, level, namespace_, name_='external_references', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'string': string_ = child_.text string_ = re_.sub(String_cleanup_pat_, " ", string_).strip() string_ = self.gds_validate_string(string_, node, 'string') self.string = string_ # validate type stringType56 self.validate_stringType56(self.string) elif nodeName_ == 'discrepancy_list': obj_ = discrepancy_listType57.factory() obj_.build(child_) self.discrepancy_list = obj_ obj_.original_tagname_ = 'discrepancy_list' elif nodeName_ == 'external_references': obj_ = external_referencesType59.factory() obj_.build(child_) self.external_references.append(obj_) obj_.original_tagname_ = 'external_references' # end class sequenceType55
[docs]class discrepancy_listType57(GeneratedsSuper): member_data_items_ = [ MemberSpec_('discrepancy', ['discrepancyType58', 'xs:token'], 1), ] subclass = None superclass = None def __init__(self, discrepancy=None): self.original_tagname_ = None if discrepancy is None: self.discrepancy = [] else: self.discrepancy = discrepancy
[docs] def factory(*args_, **kwargs_): if discrepancy_listType57.subclass: return discrepancy_listType57.subclass(*args_, **kwargs_) else: return discrepancy_listType57(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_discrepancy(self): return self.discrepancy
[docs] def set_discrepancy(self, discrepancy): self.discrepancy = discrepancy
[docs] def add_discrepancy(self, value): self.discrepancy.append(value)
[docs] def insert_discrepancy_at(self, index, value): self.discrepancy.insert(index, value)
[docs] def replace_discrepancy_at(self, index, value): self.discrepancy[index] = value
[docs] def validate_discrepancyType58(self, value): # Validate type discrepancyType58, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_discrepancyType58_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_discrepancyType58_patterns_, ))
validate_discrepancyType58_patterns_ = [['^[AGCTRYSWKMBDHVN\\.-]\\d+[AGCTRYSWKMBDHVN\\.-]$']]
[docs] def hasContent_(self): if ( self.discrepancy ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='discrepancy_listType57', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='discrepancy_listType57') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='discrepancy_listType57', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='discrepancy_listType57'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='discrepancy_listType57', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for discrepancy_ in self.discrepancy: showIndent(outfile, level, pretty_print) outfile.write('<%sdiscrepancy>%s</%sdiscrepancy>%s' % (namespace_, self.gds_format_string(quote_xml(discrepancy_).encode(ExternalEncoding), input_name='discrepancy'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'discrepancy': discrepancy_ = child_.text discrepancy_ = re_.sub(String_cleanup_pat_, " ", discrepancy_).strip() discrepancy_ = self.gds_validate_string(discrepancy_, node, 'discrepancy') self.discrepancy.append(discrepancy_) # validate type discrepancyType58 self.validate_discrepancyType58(self.discrepancy[-1]) # end class discrepancy_listType57
[docs]class external_referencesType59(GeneratedsSuper): member_data_items_ = [ MemberSpec_('type', 'xs:token', 0), MemberSpec_('valueOf_', 'xs:token', 0), ] subclass = None superclass = None def __init__(self, type_=None, valueOf_=None): self.original_tagname_ = None self.type_ = _cast(None, type_) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if external_referencesType59.subclass: return external_referencesType59.subclass(*args_, **kwargs_) else: return external_referencesType59(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_type(self): return self.type_
[docs] def set_type(self, type_): self.type_ = type_
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='external_referencesType59', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='external_referencesType59') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='external_referencesType59', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='external_referencesType59'): if self.type_ is not None and 'type_' not in already_processed: already_processed.add('type_') outfile.write(' type=%s' % (self.gds_format_string(quote_attrib(self.type_).encode(ExternalEncoding), input_name='type'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='external_referencesType59', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('type', node) if value is not None and 'type' not in already_processed: already_processed.add('type') self.type_ = value self.type_ = ' '.join(self.type_.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class external_referencesType59
[docs]class sequenceType60(GeneratedsSuper): member_data_items_ = [ MemberSpec_('string', ['stringType61', 'xs:token'], 0), MemberSpec_('discrepancy_list', 'discrepancy_listType62', 0), MemberSpec_('external_references', 'external_referencesType64', 1), ] subclass = None superclass = None def __init__(self, string=None, discrepancy_list=None, external_references=None): self.original_tagname_ = None self.string = string self.validate_stringType61(self.string) self.discrepancy_list = discrepancy_list if external_references is None: self.external_references = [] else: self.external_references = external_references
[docs] def factory(*args_, **kwargs_): if sequenceType60.subclass: return sequenceType60.subclass(*args_, **kwargs_) else: return sequenceType60(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_string(self): return self.string
[docs] def set_string(self, string): self.string = string
[docs] def get_discrepancy_list(self): return self.discrepancy_list
[docs] def set_discrepancy_list(self, discrepancy_list): self.discrepancy_list = discrepancy_list
[docs] def get_external_references(self): return self.external_references
[docs] def set_external_references(self, external_references): self.external_references = external_references
[docs] def add_external_references(self, value): self.external_references.append(value)
[docs] def insert_external_references_at(self, index, value): self.external_references.insert(index, value)
[docs] def replace_external_references_at(self, index, value): self.external_references[index] = value
[docs] def validate_stringType61(self, value): # Validate type stringType61, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_stringType61_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_stringType61_patterns_, ))
validate_stringType61_patterns_ = [['^[ ACGURYSWKMBDHVN\\.-]+$']]
[docs] def hasContent_(self): if ( self.string is not None or self.discrepancy_list is not None or self.external_references ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='sequenceType60', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='sequenceType60') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='sequenceType60', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='sequenceType60'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='sequenceType60', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.string is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sstring>%s</%sstring>%s' % (namespace_, self.gds_format_string(quote_xml(self.string).encode(ExternalEncoding), input_name='string'), namespace_, eol_)) if self.discrepancy_list is not None: self.discrepancy_list.export(outfile, level, namespace_, name_='discrepancy_list', pretty_print=pretty_print) for external_references_ in self.external_references: external_references_.export(outfile, level, namespace_, name_='external_references', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'string': string_ = child_.text string_ = re_.sub(String_cleanup_pat_, " ", string_).strip() string_ = self.gds_validate_string(string_, node, 'string') self.string = string_ # validate type stringType61 self.validate_stringType61(self.string) elif nodeName_ == 'discrepancy_list': obj_ = discrepancy_listType62.factory() obj_.build(child_) self.discrepancy_list = obj_ obj_.original_tagname_ = 'discrepancy_list' elif nodeName_ == 'external_references': obj_ = external_referencesType64.factory() obj_.build(child_) self.external_references.append(obj_) obj_.original_tagname_ = 'external_references' # end class sequenceType60
[docs]class discrepancy_listType62(GeneratedsSuper): member_data_items_ = [ MemberSpec_('discrepancy', ['discrepancyType63', 'xs:token'], 1), ] subclass = None superclass = None def __init__(self, discrepancy=None): self.original_tagname_ = None if discrepancy is None: self.discrepancy = [] else: self.discrepancy = discrepancy
[docs] def factory(*args_, **kwargs_): if discrepancy_listType62.subclass: return discrepancy_listType62.subclass(*args_, **kwargs_) else: return discrepancy_listType62(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_discrepancy(self): return self.discrepancy
[docs] def set_discrepancy(self, discrepancy): self.discrepancy = discrepancy
[docs] def add_discrepancy(self, value): self.discrepancy.append(value)
[docs] def insert_discrepancy_at(self, index, value): self.discrepancy.insert(index, value)
[docs] def replace_discrepancy_at(self, index, value): self.discrepancy[index] = value
[docs] def validate_discrepancyType63(self, value): # Validate type discrepancyType63, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_discrepancyType63_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_discrepancyType63_patterns_, ))
validate_discrepancyType63_patterns_ = [['^[AGCURYSWKMBDHVN\\.-]\\d+[AGCURYSWKMBDHVN\\.-]$']]
[docs] def hasContent_(self): if ( self.discrepancy ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='discrepancy_listType62', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='discrepancy_listType62') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='discrepancy_listType62', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='discrepancy_listType62'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='discrepancy_listType62', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for discrepancy_ in self.discrepancy: showIndent(outfile, level, pretty_print) outfile.write('<%sdiscrepancy>%s</%sdiscrepancy>%s' % (namespace_, self.gds_format_string(quote_xml(discrepancy_).encode(ExternalEncoding), input_name='discrepancy'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'discrepancy': discrepancy_ = child_.text discrepancy_ = re_.sub(String_cleanup_pat_, " ", discrepancy_).strip() discrepancy_ = self.gds_validate_string(discrepancy_, node, 'discrepancy') self.discrepancy.append(discrepancy_) # validate type discrepancyType63 self.validate_discrepancyType63(self.discrepancy[-1]) # end class discrepancy_listType62
[docs]class external_referencesType64(GeneratedsSuper): member_data_items_ = [ MemberSpec_('type', 'xs:token', 0), MemberSpec_('valueOf_', 'xs:token', 0), ] subclass = None superclass = None def __init__(self, type_=None, valueOf_=None): self.original_tagname_ = None self.type_ = _cast(None, type_) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if external_referencesType64.subclass: return external_referencesType64.subclass(*args_, **kwargs_) else: return external_referencesType64(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_type(self): return self.type_
[docs] def set_type(self, type_): self.type_ = type_
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='external_referencesType64', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='external_referencesType64') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='external_referencesType64', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='external_referencesType64'): if self.type_ is not None and 'type_' not in already_processed: already_processed.add('type_') outfile.write(' type=%s' % (self.gds_format_string(quote_attrib(self.type_).encode(ExternalEncoding), input_name='type'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='external_referencesType64', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('type', node) if value is not None and 'type' not in already_processed: already_processed.add('type') self.type_ = value self.type_ = ' '.join(self.type_.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class external_referencesType64
[docs]class external_referencesType68(GeneratedsSuper): member_data_items_ = [ MemberSpec_('type', 'xs:token', 0), MemberSpec_('valueOf_', 'xs:token', 0), ] subclass = None superclass = None def __init__(self, type_=None, valueOf_=None): self.original_tagname_ = None self.type_ = _cast(None, type_) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if external_referencesType68.subclass: return external_referencesType68.subclass(*args_, **kwargs_) else: return external_referencesType68(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_type(self): return self.type_
[docs] def set_type(self, type_): self.type_ = type_
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='external_referencesType68', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='external_referencesType68') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='external_referencesType68', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='external_referencesType68'): if self.type_ is not None and 'type_' not in already_processed: already_processed.add('type_') outfile.write(' type=%s' % (self.gds_format_string(quote_attrib(self.type_).encode(ExternalEncoding), input_name='type'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='external_referencesType68', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('type', node) if value is not None and 'type' not in already_processed: already_processed.add('type') self.type_ = value self.type_ = ' '.join(self.type_.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class external_referencesType68
[docs]class external_referencesType70(GeneratedsSuper): member_data_items_ = [ MemberSpec_('type', 'xs:token', 0), MemberSpec_('valueOf_', 'xs:token', 0), ] subclass = None superclass = None def __init__(self, type_=None, valueOf_=None): self.original_tagname_ = None self.type_ = _cast(None, type_) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if external_referencesType70.subclass: return external_referencesType70.subclass(*args_, **kwargs_) else: return external_referencesType70(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_type(self): return self.type_
[docs] def set_type(self, type_): self.type_ = type_
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='external_referencesType70', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='external_referencesType70') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='external_referencesType70', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='external_referencesType70'): if self.type_ is not None and 'type_' not in already_processed: already_processed.add('type_') outfile.write(' type=%s' % (self.gds_format_string(quote_attrib(self.type_).encode(ExternalEncoding), input_name='type'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='external_referencesType70', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('type', node) if value is not None and 'type' not in already_processed: already_processed.add('type') self.type_ = value self.type_ = ' '.join(self.type_.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class external_referencesType70
[docs]class external_referencesType72(GeneratedsSuper): member_data_items_ = [ MemberSpec_('type', 'xs:token', 0), MemberSpec_('valueOf_', 'xs:token', 0), ] subclass = None superclass = None def __init__(self, type_=None, valueOf_=None): self.original_tagname_ = None self.type_ = _cast(None, type_) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if external_referencesType72.subclass: return external_referencesType72.subclass(*args_, **kwargs_) else: return external_referencesType72(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_type(self): return self.type_
[docs] def set_type(self, type_): self.type_ = type_
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='external_referencesType72', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='external_referencesType72') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='external_referencesType72', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='external_referencesType72'): if self.type_ is not None and 'type_' not in already_processed: already_processed.add('type_') outfile.write(' type=%s' % (self.gds_format_string(quote_attrib(self.type_).encode(ExternalEncoding), input_name='type'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='external_referencesType72', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('type', node) if value is not None and 'type' not in already_processed: already_processed.add('type') self.type_ = value self.type_ = ' '.join(self.type_.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class external_referencesType72
[docs]class diameterType74(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['allowed_diameter_colloidal_gold', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if diameterType74.subclass: return diameterType74.subclass(*args_, **kwargs_) else: return diameterType74(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='diameterType74', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='diameterType74') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='diameterType74', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='diameterType74'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='diameterType74', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class diameterType74
[docs]class resolutionType75(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('type', 'xs:token', 0), MemberSpec_('valueOf_', ['resolution_type', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, type_=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.type_ = _cast(None, type_) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if resolutionType75.subclass: return resolutionType75.subclass(*args_, **kwargs_) else: return resolutionType75(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_type(self): return self.type_
[docs] def set_type(self, type_): self.type_ = type_
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='resolutionType75', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='resolutionType75') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='resolutionType75', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='resolutionType75'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), )) if self.type_ is not None and 'type_' not in already_processed: already_processed.add('type_') outfile.write(' type=%s' % (self.gds_format_string(quote_attrib(self.type_).encode(ExternalEncoding), input_name='type'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='resolutionType75', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split()) value = find_attr_value_('type', node) if value is not None and 'type' not in already_processed: already_processed.add('type') self.type_ = value self.type_ = ' '.join(self.type_.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class resolutionType75
[docs]class sequenceType77(GeneratedsSuper): member_data_items_ = [ MemberSpec_('string', ['stringType78', 'xs:token'], 0), MemberSpec_('discrepancy_list', 'discrepancy_listType79', 0), MemberSpec_('external_references', 'external_referencesType81', 1), ] subclass = None superclass = None def __init__(self, string=None, discrepancy_list=None, external_references=None): self.original_tagname_ = None self.string = string self.validate_stringType78(self.string) self.discrepancy_list = discrepancy_list if external_references is None: self.external_references = [] else: self.external_references = external_references
[docs] def factory(*args_, **kwargs_): if sequenceType77.subclass: return sequenceType77.subclass(*args_, **kwargs_) else: return sequenceType77(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_string(self): return self.string
[docs] def set_string(self, string): self.string = string
[docs] def get_discrepancy_list(self): return self.discrepancy_list
[docs] def set_discrepancy_list(self, discrepancy_list): self.discrepancy_list = discrepancy_list
[docs] def get_external_references(self): return self.external_references
[docs] def set_external_references(self, external_references): self.external_references = external_references
[docs] def add_external_references(self, value): self.external_references.append(value)
[docs] def insert_external_references_at(self, index, value): self.external_references.insert(index, value)
[docs] def replace_external_references_at(self, index, value): self.external_references[index] = value
[docs] def validate_stringType78(self, value): # Validate type stringType78, a restriction on xs:token. if value is not None and Validate_simpletypes_: pass
[docs] def hasContent_(self): if ( self.string is not None or self.discrepancy_list is not None or self.external_references ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='sequenceType77', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='sequenceType77') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='sequenceType77', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='sequenceType77'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='sequenceType77', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.string is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sstring>%s</%sstring>%s' % (namespace_, self.gds_format_string(quote_xml(self.string).encode(ExternalEncoding), input_name='string'), namespace_, eol_)) if self.discrepancy_list is not None: self.discrepancy_list.export(outfile, level, namespace_, name_='discrepancy_list', pretty_print=pretty_print) for external_references_ in self.external_references: external_references_.export(outfile, level, namespace_, name_='external_references', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'string': string_ = child_.text string_ = re_.sub(String_cleanup_pat_, " ", string_).strip() string_ = self.gds_validate_string(string_, node, 'string') self.string = string_ # validate type stringType78 self.validate_stringType78(self.string) elif nodeName_ == 'discrepancy_list': obj_ = discrepancy_listType79.factory() obj_.build(child_) self.discrepancy_list = obj_ obj_.original_tagname_ = 'discrepancy_list' elif nodeName_ == 'external_references': obj_ = external_referencesType81.factory() obj_.build(child_) self.external_references.append(obj_) obj_.original_tagname_ = 'external_references' # end class sequenceType77
[docs]class discrepancy_listType79(GeneratedsSuper): member_data_items_ = [ MemberSpec_('discrepancy', ['discrepancyType80', 'xs:token'], 1), ] subclass = None superclass = None def __init__(self, discrepancy=None): self.original_tagname_ = None if discrepancy is None: self.discrepancy = [] else: self.discrepancy = discrepancy
[docs] def factory(*args_, **kwargs_): if discrepancy_listType79.subclass: return discrepancy_listType79.subclass(*args_, **kwargs_) else: return discrepancy_listType79(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_discrepancy(self): return self.discrepancy
[docs] def set_discrepancy(self, discrepancy): self.discrepancy = discrepancy
[docs] def add_discrepancy(self, value): self.discrepancy.append(value)
[docs] def insert_discrepancy_at(self, index, value): self.discrepancy.insert(index, value)
[docs] def replace_discrepancy_at(self, index, value): self.discrepancy[index] = value
[docs] def validate_discrepancyType80(self, value): # Validate type discrepancyType80, a restriction on xs:token. if value is not None and Validate_simpletypes_: if not self.gds_validate_simple_patterns( self.validate_discrepancyType80_patterns_, value): warnings_.warn('Value "%s" does not match xsd pattern restrictions: %s' % (value.encode('utf-8'), self.validate_discrepancyType80_patterns_, ))
validate_discrepancyType80_patterns_ = [['^[AGCTRYSWKMBDHVN\\.-]\\d+[AGCTRYSWKMBDHVN\\.-]$']]
[docs] def hasContent_(self): if ( self.discrepancy ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='discrepancy_listType79', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='discrepancy_listType79') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='discrepancy_listType79', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='discrepancy_listType79'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='discrepancy_listType79', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for discrepancy_ in self.discrepancy: showIndent(outfile, level, pretty_print) outfile.write('<%sdiscrepancy>%s</%sdiscrepancy>%s' % (namespace_, self.gds_format_string(quote_xml(discrepancy_).encode(ExternalEncoding), input_name='discrepancy'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'discrepancy': discrepancy_ = child_.text discrepancy_ = re_.sub(String_cleanup_pat_, " ", discrepancy_).strip() discrepancy_ = self.gds_validate_string(discrepancy_, node, 'discrepancy') self.discrepancy.append(discrepancy_) # validate type discrepancyType80 self.validate_discrepancyType80(self.discrepancy[-1]) # end class discrepancy_listType79
[docs]class external_referencesType81(GeneratedsSuper): member_data_items_ = [ MemberSpec_('type', 'xs:token', 0), MemberSpec_('valueOf_', 'xs:token', 0), ] subclass = None superclass = None def __init__(self, type_=None, valueOf_=None): self.original_tagname_ = None self.type_ = _cast(None, type_) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if external_referencesType81.subclass: return external_referencesType81.subclass(*args_, **kwargs_) else: return external_referencesType81(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_type(self): return self.type_
[docs] def set_type(self, type_): self.type_ = type_
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='external_referencesType81', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='external_referencesType81') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='external_referencesType81', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='external_referencesType81'): if self.type_ is not None and 'type_' not in already_processed: already_processed.add('type_') outfile.write(' type=%s' % (self.gds_format_string(quote_attrib(self.type_).encode(ExternalEncoding), input_name='type'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='external_referencesType81', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('type', node) if value is not None and 'type' not in already_processed: already_processed.add('type') self.type_ = value self.type_ = ' '.join(self.type_.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class external_referencesType81
[docs]class high_resolutionType82(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['resolution_type', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if high_resolutionType82.subclass: return high_resolutionType82.subclass(*args_, **kwargs_) else: return high_resolutionType82(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='high_resolutionType82', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='high_resolutionType82') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='high_resolutionType82', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='high_resolutionType82'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='high_resolutionType82', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class high_resolutionType82
[docs]class shell_listType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('shell', 'shellType', 1), ] subclass = None superclass = None def __init__(self, shell=None): self.original_tagname_ = None if shell is None: self.shell = [] else: self.shell = shell
[docs] def factory(*args_, **kwargs_): if shell_listType.subclass: return shell_listType.subclass(*args_, **kwargs_) else: return shell_listType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_shell(self): return self.shell
[docs] def set_shell(self, shell): self.shell = shell
[docs] def add_shell(self, value): self.shell.append(value)
[docs] def insert_shell_at(self, index, value): self.shell.insert(index, value)
[docs] def replace_shell_at(self, index, value): self.shell[index] = value
[docs] def hasContent_(self): if ( self.shell ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='shell_listType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='shell_listType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='shell_listType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='shell_listType'): pass
[docs] def exportChildren(self, outfile, level, namespace_='', name_='shell_listType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' for shell_ in self.shell: shell_.export(outfile, level, namespace_, name_='shell', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): pass
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'shell': obj_ = shellType.factory() obj_.build(child_) self.shell.append(obj_) obj_.original_tagname_ = 'shell' # end class shell_listType
[docs]class shellType(GeneratedsSuper): member_data_items_ = [ MemberSpec_('id', 'xs:positiveInteger', 0), MemberSpec_('high_resolution', 'high_resolutionType83', 0), MemberSpec_('low_resolution', 'low_resolutionType84', 0), MemberSpec_('number_structure_factors', 'xs:positiveInteger', 0), MemberSpec_('phase_residual', 'xs:float', 0), MemberSpec_('fourier_space_coverage', 'xs:float', 0), MemberSpec_('multiplicity', 'xs:float', 0), ] subclass = None superclass = None def __init__(self, id=None, high_resolution=None, low_resolution=None, number_structure_factors=None, phase_residual=None, fourier_space_coverage=None, multiplicity=None): self.original_tagname_ = None self.id = _cast(int, id) self.high_resolution = high_resolution self.low_resolution = low_resolution self.number_structure_factors = number_structure_factors self.phase_residual = phase_residual self.fourier_space_coverage = fourier_space_coverage self.multiplicity = multiplicity
[docs] def factory(*args_, **kwargs_): if shellType.subclass: return shellType.subclass(*args_, **kwargs_) else: return shellType(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_high_resolution(self): return self.high_resolution
[docs] def set_high_resolution(self, high_resolution): self.high_resolution = high_resolution
[docs] def get_low_resolution(self): return self.low_resolution
[docs] def set_low_resolution(self, low_resolution): self.low_resolution = low_resolution
[docs] def get_number_structure_factors(self): return self.number_structure_factors
[docs] def set_number_structure_factors(self, number_structure_factors): self.number_structure_factors = number_structure_factors
[docs] def get_phase_residual(self): return self.phase_residual
[docs] def set_phase_residual(self, phase_residual): self.phase_residual = phase_residual
[docs] def get_fourier_space_coverage(self): return self.fourier_space_coverage
[docs] def set_fourier_space_coverage(self, fourier_space_coverage): self.fourier_space_coverage = fourier_space_coverage
[docs] def get_multiplicity(self): return self.multiplicity
[docs] def set_multiplicity(self, multiplicity): self.multiplicity = multiplicity
[docs] def get_id(self): return self.id
[docs] def set_id(self, id): self.id = id
[docs] def hasContent_(self): if ( self.high_resolution is not None or self.low_resolution is not None or self.number_structure_factors is not None or self.phase_residual is not None or self.fourier_space_coverage is not None or self.multiplicity is not None ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='shellType', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='shellType') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='shellType', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='shellType'): if self.id is not None and 'id' not in already_processed: already_processed.add('id') outfile.write(' id="%s"' % self.gds_format_integer(self.id, input_name='id'))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='shellType', fromsubclass_=False, pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.high_resolution is not None: self.high_resolution.export(outfile, level, namespace_, name_='high_resolution', pretty_print=pretty_print) if self.low_resolution is not None: self.low_resolution.export(outfile, level, namespace_, name_='low_resolution', pretty_print=pretty_print) if self.number_structure_factors is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_structure_factors>%s</%snumber_structure_factors>%s' % (namespace_, self.gds_format_integer(self.number_structure_factors, input_name='number_structure_factors'), namespace_, eol_)) if self.phase_residual is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sphase_residual>%s</%sphase_residual>%s' % (namespace_, self.gds_format_float(self.phase_residual, input_name='phase_residual'), namespace_, eol_)) if self.fourier_space_coverage is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sfourier_space_coverage>%s</%sfourier_space_coverage>%s' % (namespace_, self.gds_format_float(self.fourier_space_coverage, input_name='fourier_space_coverage'), namespace_, eol_)) if self.multiplicity is not None: showIndent(outfile, level, pretty_print) outfile.write('<%smultiplicity>%s</%smultiplicity>%s' % (namespace_, self.gds_format_float(self.multiplicity, input_name='multiplicity'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('id', node) if value is not None and 'id' not in already_processed: already_processed.add('id') try: self.id = int(value) except ValueError as exp: raise_parse_error(node, 'Bad integer attribute: %s' % exp) if self.id <= 0: raise_parse_error(node, 'Invalid PositiveInteger')
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'high_resolution': obj_ = high_resolutionType83.factory() obj_.build(child_) self.high_resolution = obj_ obj_.original_tagname_ = 'high_resolution' elif nodeName_ == 'low_resolution': obj_ = low_resolutionType84.factory() obj_.build(child_) self.low_resolution = obj_ obj_.original_tagname_ = 'low_resolution' elif nodeName_ == 'number_structure_factors': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'number_structure_factors') self.number_structure_factors = ival_ elif nodeName_ == 'phase_residual': sval_ = child_.text try: fval_ = float(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires float or double: %s' % exp) fval_ = self.gds_validate_float(fval_, node, 'phase_residual') self.phase_residual = fval_ elif nodeName_ == 'fourier_space_coverage': sval_ = child_.text try: fval_ = float(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires float or double: %s' % exp) fval_ = self.gds_validate_float(fval_, node, 'fourier_space_coverage') self.fourier_space_coverage = fval_ elif nodeName_ == 'multiplicity': sval_ = child_.text try: fval_ = float(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires float or double: %s' % exp) fval_ = self.gds_validate_float(fval_, node, 'multiplicity') self.multiplicity = fval_ # end class shellType
[docs]class high_resolutionType83(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['resolution_type', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if high_resolutionType83.subclass: return high_resolutionType83.subclass(*args_, **kwargs_) else: return high_resolutionType83(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='high_resolutionType83', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='high_resolutionType83') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='high_resolutionType83', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='high_resolutionType83'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='high_resolutionType83', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class high_resolutionType83
[docs]class low_resolutionType84(GeneratedsSuper): member_data_items_ = [ MemberSpec_('units', 'xs:token', 0), MemberSpec_('valueOf_', ['resolution_type', 'xs:float'], 0), ] subclass = None superclass = None def __init__(self, units=None, valueOf_=None): self.original_tagname_ = None self.units = _cast(None, units) self.valueOf_ = valueOf_
[docs] def factory(*args_, **kwargs_): if low_resolutionType84.subclass: return low_resolutionType84.subclass(*args_, **kwargs_) else: return low_resolutionType84(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_units(self): return self.units
[docs] def set_units(self, units): self.units = units
[docs] def get_valueOf_(self): return self.valueOf_
[docs] def set_valueOf_(self, valueOf_): self.valueOf_ = valueOf_
[docs] def hasContent_(self): if ( self.valueOf_ ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='low_resolutionType84', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='low_resolutionType84') if self.hasContent_(): outfile.write('>') if type(self.valueOf_) is float: x_ = self.gds_format_float(self.valueOf_) elif type(self.valueOf_) is str: x_ = quote_xml(self.valueOf_) else: x_ = str(self.valueOf_) outfile.write(x_.encode(ExternalEncoding)) self.exportChildren(outfile, level + 1, namespace_='', name_='low_resolutionType84', pretty_print=pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='low_resolutionType84'): if self.units is not None and 'units' not in already_processed: already_processed.add('units') outfile.write(' units=%s' % (self.gds_format_string(quote_attrib(self.units).encode(ExternalEncoding), input_name='units'), ))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='low_resolutionType84', fromsubclass_=False, pretty_print=True): pass
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) self.valueOf_ = get_all_text_(node) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('units', node) if value is not None and 'units' not in already_processed: already_processed.add('units') self.units = value self.units = ' '.join(self.units.split())
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): pass # end class low_resolutionType84
[docs]class complex(base_supramolecule_type): member_data_items_ = [ MemberSpec_('chimera', 'xs:boolean', 0), MemberSpec_('natural_source', 'natural_source_type', 1), MemberSpec_('recombinant_expression', 'recombinant_source_type', 1), MemberSpec_('molecular_weight', 'molecular_weight_type', 0), MemberSpec_('ribosome_details', 'xs:string', 0), ] subclass = None superclass = base_supramolecule_type def __init__(self, id=None, name=None, category=None, parent=None, macromolecule_list=None, details=None, number_of_copies=None, oligomeric_state=None, external_references=None, recombinant_exp_flag=None, chimera=None, natural_source=None, recombinant_expression=None, molecular_weight=None, ribosome_details=None): self.original_tagname_ = None super(complex, self).__init__(id, name, category, parent, macromolecule_list, details, number_of_copies, oligomeric_state, external_references, recombinant_exp_flag, ) self.chimera = _cast(bool, chimera) if natural_source is None: self.natural_source = [] else: self.natural_source = natural_source if recombinant_expression is None: self.recombinant_expression = [] else: self.recombinant_expression = recombinant_expression self.molecular_weight = molecular_weight self.ribosome_details = ribosome_details
[docs] def factory(*args_, **kwargs_): if complex.subclass: return complex.subclass(*args_, **kwargs_) else: return complex(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_natural_source(self): return self.natural_source
[docs] def set_natural_source(self, natural_source): self.natural_source = natural_source
[docs] def add_natural_source(self, value): self.natural_source.append(value)
[docs] def insert_natural_source_at(self, index, value): self.natural_source.insert(index, value)
[docs] def replace_natural_source_at(self, index, value): self.natural_source[index] = value
[docs] def get_recombinant_expression(self): return self.recombinant_expression
[docs] def set_recombinant_expression(self, recombinant_expression): self.recombinant_expression = recombinant_expression
[docs] def add_recombinant_expression(self, value): self.recombinant_expression.append(value)
[docs] def insert_recombinant_expression_at(self, index, value): self.recombinant_expression.insert(index, value)
[docs] def replace_recombinant_expression_at(self, index, value): self.recombinant_expression[index] = value
[docs] def get_molecular_weight(self): return self.molecular_weight
[docs] def set_molecular_weight(self, molecular_weight): self.molecular_weight = molecular_weight
[docs] def get_ribosome_details(self): return self.ribosome_details
[docs] def set_ribosome_details(self, ribosome_details): self.ribosome_details = ribosome_details
[docs] def get_chimera(self): return self.chimera
[docs] def set_chimera(self, chimera): self.chimera = chimera
[docs] def hasContent_(self): if ( self.natural_source or self.recombinant_expression or self.molecular_weight is not None or self.ribosome_details is not None or super(complex, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='complex', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='complex') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='complex', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='complex'): super(complex, self).exportAttributes(outfile, level, already_processed, namespace_, name_='complex') if self.chimera is not None and 'chimera' not in already_processed: already_processed.add('chimera') outfile.write(' chimera="%s"' % self.gds_format_boolean(self.chimera, input_name='chimera'))
[docs] def exportChildren(self, outfile, level, namespace_='', name_='complex', fromsubclass_=False, pretty_print=True): super(complex, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print) if pretty_print: eol_ = '\n' else: eol_ = '' for natural_source_ in self.natural_source: natural_source_.export(outfile, level, namespace_, name_='natural_source', pretty_print=pretty_print) for recombinant_expression_ in self.recombinant_expression: recombinant_expression_.export(outfile, level, namespace_, name_='recombinant_expression', pretty_print=pretty_print) if self.molecular_weight is not None: self.molecular_weight.export(outfile, level, namespace_, name_='molecular_weight', pretty_print=pretty_print) if self.ribosome_details is not None: showIndent(outfile, level, pretty_print) outfile.write('<%sribosome-details>%s</%sribosome-details>%s' % (namespace_, self.gds_format_string(quote_xml(self.ribosome_details).encode(ExternalEncoding), input_name='ribosome-details'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): value = find_attr_value_('chimera', node) if value is not None and 'chimera' not in already_processed: already_processed.add('chimera') if value in ('true', '1'): self.chimera = True elif value in ('false', '0'): self.chimera = False else: raise_parse_error(node, 'Bad boolean attribute') super(complex, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'natural_source': obj_ = natural_source_type.factory() obj_.build(child_) self.natural_source.append(obj_) obj_.original_tagname_ = 'natural_source' elif nodeName_ == 'recombinant_expression': obj_ = recombinant_source_type.factory() obj_.build(child_) self.recombinant_expression.append(obj_) obj_.original_tagname_ = 'recombinant_expression' elif nodeName_ == 'molecular_weight': obj_ = molecular_weight_type.factory() obj_.build(child_) self.molecular_weight = obj_ obj_.original_tagname_ = 'molecular_weight' elif nodeName_ == 'ribosome-details': ribosome_details_ = child_.text ribosome_details_ = self.gds_validate_string(ribosome_details_, node, 'ribosome_details') self.ribosome_details = ribosome_details_ super(complex, self).buildChildren(child_, node, nodeName_, True) # end class complex
[docs]class virus(base_supramolecule_type): member_data_items_ = [ MemberSpec_('sci_species_name', 'virus_species_name_type', 0), MemberSpec_('sci_species_strain', 'xs:string', 0), MemberSpec_('natural_host', 'natural_hostType', 1), MemberSpec_('host_system', 'recombinant_source_type', 0), MemberSpec_('molecular_weight', 'molecular_weight_type', 0), MemberSpec_('virus_shell', 'virus_shellType', 1), MemberSpec_('virus_type', ['virus_typeType', 'xs:token'], 0), MemberSpec_('virus_isolate', ['virus_isolateType', 'xs:token'], 0), MemberSpec_('virus_enveloped', 'xs:boolean', 0), MemberSpec_('virus_empty', 'xs:boolean', 0), MemberSpec_('syn_species_name', 'xs:string', 0), MemberSpec_('sci_species_serotype', 'xs:string', 0), MemberSpec_('sci_species_serocomplex', 'xs:string', 0), MemberSpec_('sci_species_subspecies', 'xs:string', 0), ] subclass = None superclass = base_supramolecule_type def __init__(self, id=None, name=None, category=None, parent=None, macromolecule_list=None, details=None, number_of_copies=None, oligomeric_state=None, external_references=None, recombinant_exp_flag=None, sci_species_name=None, sci_species_strain=None, natural_host=None, host_system=None, molecular_weight=None, virus_shell=None, virus_type=None, virus_isolate=None, virus_enveloped=None, virus_empty=None, syn_species_name=None, sci_species_serotype=None, sci_species_serocomplex=None, sci_species_subspecies=None): self.original_tagname_ = None super(virus, self).__init__(id, name, category, parent, macromolecule_list, details, number_of_copies, oligomeric_state, external_references, recombinant_exp_flag, ) self.sci_species_name = sci_species_name self.sci_species_strain = sci_species_strain if natural_host is None: self.natural_host = [] else: self.natural_host = natural_host self.host_system = host_system self.molecular_weight = molecular_weight if virus_shell is None: self.virus_shell = [] else: self.virus_shell = virus_shell self.virus_type = virus_type self.validate_virus_typeType(self.virus_type) self.virus_isolate = virus_isolate self.validate_virus_isolateType(self.virus_isolate) self.virus_enveloped = virus_enveloped self.virus_empty = virus_empty self.syn_species_name = syn_species_name self.sci_species_serotype = sci_species_serotype self.sci_species_serocomplex = sci_species_serocomplex self.sci_species_subspecies = sci_species_subspecies
[docs] def factory(*args_, **kwargs_): if virus.subclass: return virus.subclass(*args_, **kwargs_) else: return virus(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_sci_species_name(self): return self.sci_species_name
[docs] def set_sci_species_name(self, sci_species_name): self.sci_species_name = sci_species_name
[docs] def get_sci_species_strain(self): return self.sci_species_strain
[docs] def set_sci_species_strain(self, sci_species_strain): self.sci_species_strain = sci_species_strain
[docs] def get_natural_host(self): return self.natural_host
[docs] def set_natural_host(self, natural_host): self.natural_host = natural_host
[docs] def add_natural_host(self, value): self.natural_host.append(value)
[docs] def insert_natural_host_at(self, index, value): self.natural_host.insert(index, value)
[docs] def replace_natural_host_at(self, index, value): self.natural_host[index] = value
[docs] def get_host_system(self): return self.host_system
[docs] def set_host_system(self, host_system): self.host_system = host_system
[docs] def get_molecular_weight(self): return self.molecular_weight
[docs] def set_molecular_weight(self, molecular_weight): self.molecular_weight = molecular_weight
[docs] def get_virus_shell(self): return self.virus_shell
[docs] def set_virus_shell(self, virus_shell): self.virus_shell = virus_shell
[docs] def add_virus_shell(self, value): self.virus_shell.append(value)
[docs] def insert_virus_shell_at(self, index, value): self.virus_shell.insert(index, value)
[docs] def replace_virus_shell_at(self, index, value): self.virus_shell[index] = value
[docs] def get_virus_type(self): return self.virus_type
[docs] def set_virus_type(self, virus_type): self.virus_type = virus_type
[docs] def get_virus_isolate(self): return self.virus_isolate
[docs] def set_virus_isolate(self, virus_isolate): self.virus_isolate = virus_isolate
[docs] def get_virus_enveloped(self): return self.virus_enveloped
[docs] def set_virus_enveloped(self, virus_enveloped): self.virus_enveloped = virus_enveloped
[docs] def get_virus_empty(self): return self.virus_empty
[docs] def set_virus_empty(self, virus_empty): self.virus_empty = virus_empty
[docs] def get_syn_species_name(self): return self.syn_species_name
[docs] def set_syn_species_name(self, syn_species_name): self.syn_species_name = syn_species_name
[docs] def get_sci_species_serotype(self): return self.sci_species_serotype
[docs] def set_sci_species_serotype(self, sci_species_serotype): self.sci_species_serotype = sci_species_serotype
[docs] def get_sci_species_serocomplex(self): return self.sci_species_serocomplex
[docs] def set_sci_species_serocomplex(self, sci_species_serocomplex): self.sci_species_serocomplex = sci_species_serocomplex
[docs] def get_sci_species_subspecies(self): return self.sci_species_subspecies
[docs] def set_sci_species_subspecies(self, sci_species_subspecies): self.sci_species_subspecies = sci_species_subspecies
[docs] def validate_virus_typeType(self, value): # Validate type virus_typeType, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['VIRION', 'SATELLITE', 'PRION', 'VIROID', 'VIRUS-LIKE PARTICLE', 'OTHER'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on virus_typeType' % {"value" : value.encode("utf-8")} )
[docs] def validate_virus_isolateType(self, value): # Validate type virus_isolateType, a restriction on xs:token. if value is not None and Validate_simpletypes_: value = str(value) enumerations = ['STRAIN', 'SEROTYPE', 'SEROCOMPLEX', 'SUBSPECIES', 'SPECIES', 'OTHER'] enumeration_respectee = False for enum in enumerations: if value == enum: enumeration_respectee = True break if not enumeration_respectee: warnings_.warn('Value "%(value)s" does not match xsd enumeration restriction on virus_isolateType' % {"value" : value.encode("utf-8")} )
[docs] def hasContent_(self): if ( self.sci_species_name is not None or self.sci_species_strain is not None or self.natural_host or self.host_system is not None or self.molecular_weight is not None or self.virus_shell or self.virus_type is not None or self.virus_isolate is not None or self.virus_enveloped is not None or self.virus_empty is not None or self.syn_species_name is not None or self.sci_species_serotype is not None or self.sci_species_serocomplex is not None or self.sci_species_subspecies is not None or super(virus, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='virus', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='virus') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='virus', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='virus'): super(virus, self).exportAttributes(outfile, level, already_processed, namespace_, name_='virus')
[docs] def exportChildren(self, outfile, level, namespace_='', name_='virus', fromsubclass_=False, pretty_print=True): super(virus, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print) if pretty_print: eol_ = '\n' else: eol_ = '' if self.sci_species_name is not None: self.sci_species_name.export(outfile, level, namespace_, name_='sci_species_name', pretty_print=pretty_print) if self.sci_species_strain is not None: showIndent(outfile, level, pretty_print) outfile.write('<%ssci_species_strain>%s</%ssci_species_strain>%s' % (namespace_, self.gds_format_string(quote_xml(self.sci_species_strain).encode(ExternalEncoding), input_name='sci_species_strain'), namespace_, eol_)) for natural_host_ in self.natural_host: natural_host_.export(outfile, level, namespace_, name_='natural_host', pretty_print=pretty_print) if self.host_system is not None: self.host_system.export(outfile, level, namespace_, name_='host_system', pretty_print=pretty_print) if self.molecular_weight is not None: self.molecular_weight.export(outfile, level, namespace_, name_='molecular_weight', pretty_print=pretty_print) for virus_shell_ in self.virus_shell: virus_shell_.export(outfile, level, namespace_, name_='virus_shell', pretty_print=pretty_print) if self.virus_type is not None: showIndent(outfile, level, pretty_print) outfile.write('<%svirus_type>%s</%svirus_type>%s' % (namespace_, self.gds_format_string(quote_xml(self.virus_type).encode(ExternalEncoding), input_name='virus_type'), namespace_, eol_)) if self.virus_isolate is not None: showIndent(outfile, level, pretty_print) outfile.write('<%svirus_isolate>%s</%svirus_isolate>%s' % (namespace_, self.gds_format_string(quote_xml(self.virus_isolate).encode(ExternalEncoding), input_name='virus_isolate'), namespace_, eol_)) if self.virus_enveloped is not None: showIndent(outfile, level, pretty_print) outfile.write('<%svirus_enveloped>%s</%svirus_enveloped>%s' % (namespace_, self.gds_format_boolean(self.virus_enveloped, input_name='virus_enveloped'), namespace_, eol_)) if self.virus_empty is not None: showIndent(outfile, level, pretty_print) outfile.write('<%svirus_empty>%s</%svirus_empty>%s' % (namespace_, self.gds_format_boolean(self.virus_empty, input_name='virus_empty'), namespace_, eol_)) if self.syn_species_name is not None: showIndent(outfile, level, pretty_print) outfile.write('<%ssyn_species_name>%s</%ssyn_species_name>%s' % (namespace_, self.gds_format_string(quote_xml(self.syn_species_name).encode(ExternalEncoding), input_name='syn_species_name'), namespace_, eol_)) if self.sci_species_serotype is not None: showIndent(outfile, level, pretty_print) outfile.write('<%ssci_species_serotype>%s</%ssci_species_serotype>%s' % (namespace_, self.gds_format_string(quote_xml(self.sci_species_serotype).encode(ExternalEncoding), input_name='sci_species_serotype'), namespace_, eol_)) if self.sci_species_serocomplex is not None: showIndent(outfile, level, pretty_print) outfile.write('<%ssci_species_serocomplex>%s</%ssci_species_serocomplex>%s' % (namespace_, self.gds_format_string(quote_xml(self.sci_species_serocomplex).encode(ExternalEncoding), input_name='sci_species_serocomplex'), namespace_, eol_)) if self.sci_species_subspecies is not None: showIndent(outfile, level, pretty_print) outfile.write('<%ssci_species_subspecies>%s</%ssci_species_subspecies>%s' % (namespace_, self.gds_format_string(quote_xml(self.sci_species_subspecies).encode(ExternalEncoding), input_name='sci_species_subspecies'), namespace_, eol_))
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): super(virus, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'sci_species_name': obj_ = virus_species_name_type.factory() obj_.build(child_) self.sci_species_name = obj_ obj_.original_tagname_ = 'sci_species_name' elif nodeName_ == 'sci_species_strain': sci_species_strain_ = child_.text sci_species_strain_ = self.gds_validate_string(sci_species_strain_, node, 'sci_species_strain') self.sci_species_strain = sci_species_strain_ elif nodeName_ == 'natural_host': obj_ = natural_hostType.factory() obj_.build(child_) self.natural_host.append(obj_) obj_.original_tagname_ = 'natural_host' elif nodeName_ == 'host_system': obj_ = recombinant_source_type.factory() obj_.build(child_) self.host_system = obj_ obj_.original_tagname_ = 'host_system' elif nodeName_ == 'molecular_weight': obj_ = molecular_weight_type.factory() obj_.build(child_) self.molecular_weight = obj_ obj_.original_tagname_ = 'molecular_weight' elif nodeName_ == 'virus_shell': obj_ = virus_shellType.factory() obj_.build(child_) self.virus_shell.append(obj_) obj_.original_tagname_ = 'virus_shell' elif nodeName_ == 'virus_type': virus_type_ = child_.text virus_type_ = re_.sub(String_cleanup_pat_, " ", virus_type_).strip() virus_type_ = self.gds_validate_string(virus_type_, node, 'virus_type') self.virus_type = virus_type_ # validate type virus_typeType self.validate_virus_typeType(self.virus_type) elif nodeName_ == 'virus_isolate': virus_isolate_ = child_.text virus_isolate_ = re_.sub(String_cleanup_pat_, " ", virus_isolate_).strip() virus_isolate_ = self.gds_validate_string(virus_isolate_, node, 'virus_isolate') self.virus_isolate = virus_isolate_ # validate type virus_isolateType self.validate_virus_isolateType(self.virus_isolate) elif nodeName_ == 'virus_enveloped': sval_ = child_.text if sval_ in ('true', '1'): ival_ = True elif sval_ in ('false', '0'): ival_ = False else: raise_parse_error(child_, 'requires boolean') ival_ = self.gds_validate_boolean(ival_, node, 'virus_enveloped') self.virus_enveloped = ival_ elif nodeName_ == 'virus_empty': sval_ = child_.text if sval_ in ('true', '1'): ival_ = True elif sval_ in ('false', '0'): ival_ = False else: raise_parse_error(child_, 'requires boolean') ival_ = self.gds_validate_boolean(ival_, node, 'virus_empty') self.virus_empty = ival_ elif nodeName_ == 'syn_species_name': syn_species_name_ = child_.text syn_species_name_ = self.gds_validate_string(syn_species_name_, node, 'syn_species_name') self.syn_species_name = syn_species_name_ elif nodeName_ == 'sci_species_serotype': sci_species_serotype_ = child_.text sci_species_serotype_ = self.gds_validate_string(sci_species_serotype_, node, 'sci_species_serotype') self.sci_species_serotype = sci_species_serotype_ elif nodeName_ == 'sci_species_serocomplex': sci_species_serocomplex_ = child_.text sci_species_serocomplex_ = self.gds_validate_string(sci_species_serocomplex_, node, 'sci_species_serocomplex') self.sci_species_serocomplex = sci_species_serocomplex_ elif nodeName_ == 'sci_species_subspecies': sci_species_subspecies_ = child_.text sci_species_subspecies_ = self.gds_validate_string(sci_species_subspecies_, node, 'sci_species_subspecies') self.sci_species_subspecies = sci_species_subspecies_ super(virus, self).buildChildren(child_, node, nodeName_, True) # end class virus
[docs]class organelle_or_cellular_component(base_supramolecule_type): member_data_items_ = [ MemberSpec_('natural_source', 'natural_sourceType38', 0), MemberSpec_('molecular_weight', 'molecular_weight_type', 0), MemberSpec_('recombinant_expression', 'recombinant_source_type', 0), ] subclass = None superclass = base_supramolecule_type def __init__(self, id=None, name=None, category=None, parent=None, macromolecule_list=None, details=None, number_of_copies=None, oligomeric_state=None, external_references=None, recombinant_exp_flag=None, natural_source=None, molecular_weight=None, recombinant_expression=None): self.original_tagname_ = None super(organelle_or_cellular_component, self).__init__(id, name, category, parent, macromolecule_list, details, number_of_copies, oligomeric_state, external_references, recombinant_exp_flag, ) self.natural_source = natural_source self.molecular_weight = molecular_weight self.recombinant_expression = recombinant_expression
[docs] def factory(*args_, **kwargs_): if organelle_or_cellular_component.subclass: return organelle_or_cellular_component.subclass(*args_, **kwargs_) else: return organelle_or_cellular_component(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_natural_source(self): return self.natural_source
[docs] def set_natural_source(self, natural_source): self.natural_source = natural_source
[docs] def get_molecular_weight(self): return self.molecular_weight
[docs] def set_molecular_weight(self, molecular_weight): self.molecular_weight = molecular_weight
[docs] def get_recombinant_expression(self): return self.recombinant_expression
[docs] def set_recombinant_expression(self, recombinant_expression): self.recombinant_expression = recombinant_expression
[docs] def hasContent_(self): if ( self.natural_source is not None or self.molecular_weight is not None or self.recombinant_expression is not None or super(organelle_or_cellular_component, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='organelle_or_cellular_component', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='organelle_or_cellular_component') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='organelle_or_cellular_component', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='organelle_or_cellular_component'): super(organelle_or_cellular_component, self).exportAttributes(outfile, level, already_processed, namespace_, name_='organelle_or_cellular_component')
[docs] def exportChildren(self, outfile, level, namespace_='', name_='organelle_or_cellular_component', fromsubclass_=False, pretty_print=True): super(organelle_or_cellular_component, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print) if pretty_print: eol_ = '\n' else: eol_ = '' if self.natural_source is not None: self.natural_source.export(outfile, level, namespace_, name_='natural_source', pretty_print=pretty_print) if self.molecular_weight is not None: self.molecular_weight.export(outfile, level, namespace_, name_='molecular_weight', pretty_print=pretty_print) if self.recombinant_expression is not None: self.recombinant_expression.export(outfile, level, namespace_, name_='recombinant_expression', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): super(organelle_or_cellular_component, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'natural_source': obj_ = natural_sourceType38.factory() obj_.build(child_) self.natural_source = obj_ obj_.original_tagname_ = 'natural_source' elif nodeName_ == 'molecular_weight': obj_ = molecular_weight_type.factory() obj_.build(child_) self.molecular_weight = obj_ obj_.original_tagname_ = 'molecular_weight' elif nodeName_ == 'recombinant_expression': obj_ = recombinant_source_type.factory() obj_.build(child_) self.recombinant_expression = obj_ obj_.original_tagname_ = 'recombinant_expression' super(organelle_or_cellular_component, self).buildChildren(child_, node, nodeName_, True) # end class organelle_or_cellular_component
[docs]class tissue(base_supramolecule_type): member_data_items_ = [ MemberSpec_('natural_source', 'natural_sourceType37', 0), ] subclass = None superclass = base_supramolecule_type def __init__(self, id=None, name=None, category=None, parent=None, macromolecule_list=None, details=None, number_of_copies=None, oligomeric_state=None, external_references=None, recombinant_exp_flag=None, natural_source=None): self.original_tagname_ = None super(tissue, self).__init__(id, name, category, parent, macromolecule_list, details, number_of_copies, oligomeric_state, external_references, recombinant_exp_flag, ) self.natural_source = natural_source
[docs] def factory(*args_, **kwargs_): if tissue.subclass: return tissue.subclass(*args_, **kwargs_) else: return tissue(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_natural_source(self): return self.natural_source
[docs] def set_natural_source(self, natural_source): self.natural_source = natural_source
[docs] def hasContent_(self): if ( self.natural_source is not None or super(tissue, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='tissue', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='tissue') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='tissue', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='tissue'): super(tissue, self).exportAttributes(outfile, level, already_processed, namespace_, name_='tissue')
[docs] def exportChildren(self, outfile, level, namespace_='', name_='tissue', fromsubclass_=False, pretty_print=True): super(tissue, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print) if pretty_print: eol_ = '\n' else: eol_ = '' if self.natural_source is not None: self.natural_source.export(outfile, level, namespace_, name_='natural_source', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): super(tissue, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'natural_source': obj_ = natural_sourceType37.factory() obj_.build(child_) self.natural_source = obj_ obj_.original_tagname_ = 'natural_source' super(tissue, self).buildChildren(child_, node, nodeName_, True) # end class tissue
[docs]class cell(base_supramolecule_type): member_data_items_ = [ MemberSpec_('natural_source', 'natural_sourceType36', 0), ] subclass = None superclass = base_supramolecule_type def __init__(self, id=None, name=None, category=None, parent=None, macromolecule_list=None, details=None, number_of_copies=None, oligomeric_state=None, external_references=None, recombinant_exp_flag=None, natural_source=None): self.original_tagname_ = None super(cell, self).__init__(id, name, category, parent, macromolecule_list, details, number_of_copies, oligomeric_state, external_references, recombinant_exp_flag, ) self.natural_source = natural_source
[docs] def factory(*args_, **kwargs_): if cell.subclass: return cell.subclass(*args_, **kwargs_) else: return cell(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_natural_source(self): return self.natural_source
[docs] def set_natural_source(self, natural_source): self.natural_source = natural_source
[docs] def hasContent_(self): if ( self.natural_source is not None or super(cell, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='cell', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='cell') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='cell', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='cell'): super(cell, self).exportAttributes(outfile, level, already_processed, namespace_, name_='cell')
[docs] def exportChildren(self, outfile, level, namespace_='', name_='cell', fromsubclass_=False, pretty_print=True): super(cell, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print) if pretty_print: eol_ = '\n' else: eol_ = '' if self.natural_source is not None: self.natural_source.export(outfile, level, namespace_, name_='natural_source', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): super(cell, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'natural_source': obj_ = natural_sourceType36.factory() obj_.build(child_) self.natural_source = obj_ obj_.original_tagname_ = 'natural_source' super(cell, self).buildChildren(child_, node, nodeName_, True) # end class cell
[docs]class sample(base_supramolecule_type): """Deprecated (2014-10-21)""" member_data_items_ = [ MemberSpec_('natural_source', 'natural_sourceType', 0), MemberSpec_('number_unique_components', 'xs:positiveInteger', 0), MemberSpec_('molecular_weight', 'molecular_weight_type', 0), ] subclass = None superclass = base_supramolecule_type def __init__(self, id=None, name=None, category=None, parent=None, macromolecule_list=None, details=None, number_of_copies=None, oligomeric_state=None, external_references=None, recombinant_exp_flag=None, natural_source=None, number_unique_components=None, molecular_weight=None): self.original_tagname_ = None super(sample, self).__init__(id, name, category, parent, macromolecule_list, details, number_of_copies, oligomeric_state, external_references, recombinant_exp_flag, ) self.natural_source = natural_source self.number_unique_components = number_unique_components self.molecular_weight = molecular_weight
[docs] def factory(*args_, **kwargs_): if sample.subclass: return sample.subclass(*args_, **kwargs_) else: return sample(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def get_natural_source(self): return self.natural_source
[docs] def set_natural_source(self, natural_source): self.natural_source = natural_source
[docs] def get_number_unique_components(self): return self.number_unique_components
[docs] def set_number_unique_components(self, number_unique_components): self.number_unique_components = number_unique_components
[docs] def get_molecular_weight(self): return self.molecular_weight
[docs] def set_molecular_weight(self, molecular_weight): self.molecular_weight = molecular_weight
[docs] def hasContent_(self): if ( self.natural_source is not None or self.number_unique_components is not None or self.molecular_weight is not None or super(sample, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='sample', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='sample') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='sample', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='sample'): super(sample, self).exportAttributes(outfile, level, already_processed, namespace_, name_='sample')
[docs] def exportChildren(self, outfile, level, namespace_='', name_='sample', fromsubclass_=False, pretty_print=True): super(sample, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print) if pretty_print: eol_ = '\n' else: eol_ = '' if self.natural_source is not None: self.natural_source.export(outfile, level, namespace_, name_='natural_source', pretty_print=pretty_print) if self.number_unique_components is not None: showIndent(outfile, level, pretty_print) outfile.write('<%snumber_unique_components>%s</%snumber_unique_components>%s' % (namespace_, self.gds_format_integer(self.number_unique_components, input_name='number_unique_components'), namespace_, eol_)) if self.molecular_weight is not None: self.molecular_weight.export(outfile, level, namespace_, name_='molecular_weight', pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): super(sample, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): if nodeName_ == 'natural_source': obj_ = natural_sourceType.factory() obj_.build(child_) self.natural_source = obj_ obj_.original_tagname_ = 'natural_source' elif nodeName_ == 'number_unique_components': sval_ = child_.text try: ival_ = int(sval_) except (TypeError, ValueError) as exp: raise_parse_error(child_, 'requires integer: %s' % exp) if ival_ <= 0: raise_parse_error(child_, 'requires positiveInteger') ival_ = self.gds_validate_integer(ival_, node, 'number_unique_components') self.number_unique_components = ival_ elif nodeName_ == 'molecular_weight': obj_ = molecular_weight_type.factory() obj_.build(child_) self.molecular_weight = obj_ obj_.original_tagname_ = 'molecular_weight' super(sample, self).buildChildren(child_, node, nodeName_, True) # end class sample
[docs]class string_type(base_type): member_data_items_ = [ ] subclass = None superclass = base_type def __init__(self, help_text=None, warning_text=None, error_text=None, validation_rules=None, label=None, value=None): self.original_tagname_ = None super(string_type, self).__init__(help_text, warning_text, error_text, validation_rules, label, value, )
[docs] def factory(*args_, **kwargs_): if string_type.subclass: return string_type.subclass(*args_, **kwargs_) else: return string_type(*args_, **kwargs_)
factory = staticmethod(factory)
[docs] def hasContent_(self): if ( super(string_type, self).hasContent_() ): return True else: return False
[docs] def export(self, outfile, level, namespace_='', name_='string_type', namespacedef_='', pretty_print=True): if pretty_print: eol_ = '\n' else: eol_ = '' if self.original_tagname_ is not None: name_ = self.original_tagname_ showIndent(outfile, level, pretty_print) outfile.write('<%s%s%s' % (namespace_, name_, namespacedef_ and ' ' + namespacedef_ or '', )) already_processed = set() self.exportAttributes(outfile, level, already_processed, namespace_, name_='string_type') if self.hasContent_(): outfile.write('>%s' % (eol_, )) self.exportChildren(outfile, level + 1, namespace_='', name_='string_type', pretty_print=pretty_print) showIndent(outfile, level, pretty_print) outfile.write('</%s%s>%s' % (namespace_, name_, eol_)) else: outfile.write('/>%s' % (eol_, ))
[docs] def exportAttributes(self, outfile, level, already_processed, namespace_='', name_='string_type'): super(string_type, self).exportAttributes(outfile, level, already_processed, namespace_, name_='string_type')
[docs] def exportChildren(self, outfile, level, namespace_='', name_='string_type', fromsubclass_=False, pretty_print=True): super(string_type, self).exportChildren(outfile, level, namespace_, name_, True, pretty_print=pretty_print)
[docs] def build(self, node): already_processed = set() self.buildAttributes(node, node.attrib, already_processed) for child in node: nodeName_ = Tag_pattern_.match(child.tag).groups()[-1] self.buildChildren(child, node, nodeName_) return self
[docs] def buildAttributes(self, node, attrs, already_processed): super(string_type, self).buildAttributes(node, attrs, already_processed)
[docs] def buildChildren(self, child_, node, nodeName_, fromsubclass_=False): super(string_type, self).buildChildren(child_, node, nodeName_, True) pass # end class string_type
GDSClassesMapping = { 'structure_determination_list': structure_determination_listType, 'code': code_type, 'interpretation': interpretation_type, 'temperature_average': temperature_averageType, 'chain': chain_type, 'microscopy_list': microscopy_listType, 'axis_order': axis_orderType, 'molecular_replacement': molecular_replacementType15, 'acceleration_voltage': acceleration_voltageType, 'segmentation_list': segmentation_listType, 'half_map': map_type, 'initial_angle_assignment': angle_assignment_type, 'voltage': fib_voltage_type, 'pdb_reference': pdb_cross_reference_type, 'staining': stainingType, 'thickness': thicknessType, 'random_conical_tilt': random_conical_tiltType, 'image_processing': base_processing_type, 'upper_energy_threshold': upper_energy_thresholdType, 'natural_source': natural_source_type, 'crystallography_processing': crystallography_processing_type, 'high_resolution': high_resolutionType83, 'parameters': parametersType, 'noise_model': noise_modelType, 'coma_free': coma_freeType, 'crystal_parameters': crystal_parameters_type, 'support_film': film_type, 'sampling_interval': sampling_intervalType, 'primary_citation': primary_citationType, 'contour_list': contour_listType, 'final_thickness': fib_final_thickness_type, 'focused_ion_beam': focused_ion_beamType, 'axis_rotation': axis_rotationType, 'subtomogram_averaging_processing': subtomogram_averaging_processing_type, 'fax': telephone_number_type, 'particle_selection': particle_selection_type, 'glow_discharge': glow_dischargeType, 'chamber_humidity': chamber_humidityType, 'supramolecule_list': supramolecule_listType, 'indexing': indexingType31, 'supramolecule': base_supramolecule_type, 'key_dates': key_datesType, 'final_three_d_classification': classification_type, 'helical_processing': helical_processing_type, 'helix_length': helix_lengthType30, 'grid': grid_type, 'sugar_embedding': sugar_embeddingType, 'crystallography_statistics': crystallography_statistics_type, 'validation_rules': string_validation_type, 'validation_list': validation_listType, 'zemlin_tableau': zemlin_tableauType, 'max_angle': max_angleType, 'symmetry_determination': symmetry_determinationType21, 'emd': entry_type, 'spatial_frequency': spatial_frequencyType, '_n-link': _n_linkType, 'name': sci_name_type, 'virus_shell': virus_shellType41, 'microscopy': base_microscopy_type, 'temperature_max': temperature_maxType, 'reconstruction_filtering': reconstruction_filtering_type, 'x': pixel_spacing_type, 'delta_phi': delta_phiType, 'temperature_min': temperature_minType, 'shell_list': shell_listType, 'status': statusType, 'starting_model': starting_modelType16, 'alignment_procedure': alignment_procedureType, 'sequence': sequenceType77, '_brestore': _brestoreType, 'final_two_d_classification': classification_type, 'lower_energy_threshold': lower_energy_thresholdType, 'modelling_list': modelling_listType, 'auxiliary_link': auxiliary_link_type, 'legacy': legacyType, 'c2_aperture_diameter': c2_aperture_diameterType, 'superseded_by_list': superseded_by_listType, 'phase_reversal': phase_reversalType, 'initial_thickness': fib_initial_thickness_type, 'category': categoryType39, 'tomography_processing': tomography_processing_type, 'startup_model': starting_map_type, 'tilt_angle1': tilt_angle1Type, 'tilt_angle2': tilt_angle2Type, 'slice': map_type, 'shadowing': shadowingType, 'contact_author': contact_authorType, 'recombinant_expression': recombinant_source_type, 'sites': sitesType, 'sci_species_name': virus_species_name_type, 'slices_list': slices_listType, 'cell': cellType, 'crystallography_microscopy': crystallography_microscopy_type, 'min_angle': min_angleType, 'citation_list': citation_listType, 'macromolecule_list': macromolecule_listType40, 'current_status': version_type, 'authors_list': authors_listType, 'segmentation': segmentationType, 'tilt_angle': tilt_angleType, 'tomography_microscopy': tomography_microscopy_type, 'pdb_list': pdb_cross_reference_list_type, 'delta_z': delta_zType, 'film_thickness': film_thicknessType, 'image_recording': image_recordingType, 'spacing': spacingType, 'component': componentType, 'initial_model': initial_modelType, 'pressure': pressureType, 'amplitude_correction': amplitude_correctionType, 'helical_parameters': helical_parameters_type, 'auxiliary_link_list': auxiliary_link_listType, 'macromolecules_and_complexes': macromolecules_and_complexes_type, 'structure_determination': structure_determination_type, 'c': cell_type, 'z': pixel_spacing_type, 'final_angle_assignment': angle_assignment_type, 'refinement': refinementType27, 'admin': admin_type, 'starting_symmetry': starting_symmetryType28, 'tomography_preparation': tomography_preparation_type, 'current': fib_current_type, 'additional_map': map_type, 'sharpening': sharpeningType, 'merging': mergingType22, 'dose_rate': fib_dose_rate_type, 'film_or_detector_model': film_or_detector_modelType, 'specimen_preparation': base_preparation_type, 'crossreferences': crossreferences_type, 'calibrated_defocus_max': calibrated_defocus_maxType, 'total_filament_length': total_filament_lengthType26, 'experimental': experimentalType, 'software': software_type, 'origin': originType, 'diameter': diameterType42, 'software_list': software_list_type, 'macromolecule': macromoleculeType, 'symmetry': applied_symmetry_type, 'low_resolution': low_resolutionType84, 'image_recording_list': image_recording_listType, 'height': heightType51, 'contour': contourType, 'chain_id_list': chain_type, 'segment_overlap': segment_overlapType25, 'high_frequency_cutoff': high_frequency_cutoffType, 'average_electron_dose_per_image': average_electron_dose_per_imageType, 'statistics': map_statistics_type, 'glow_discharge_params': glow_discharge_params_type, 'temperature': crystal_formation_temperature_type, 'width': widthType50, 'half_map_list': half_map_listType, 'projection_matching_processing': projection_matching_processingType, 'background_masked': background_masked_type, 'extraction': extractionType13, 'editor': author_order_type, 'basic': basicType, 'c_sampling_length': cell_type, 'discrepancy_list': discrepancy_listType79, 'energy_filter': energy_filterType, 'theoretical': theoreticalType, 'sectioning': sectioningType, 'chamber_temperature': chamber_temperatureType, 'shell': shellType, 'external_references': external_referencesType81, 'relationship': relationshipType1, 'nominal_cs': nominal_csType, 'duration': fib_duration_type, 'secondary_citation': secondary_citationType, 'pdb_model': pdb_model_type, 'modelling': modelling_type, 'average_exposure_time': average_exposure_timeType, 'resolution_range': resolution_rangeType17, 'unit_cell': unit_cell_type, 'digitization_details': digitization_detailsType, 'final_multi_reference_alignment': final_multi_reference_alignmentType14, 'none': noneType, 'b': cell_type, 'hard_validation_regexp': hard_validation_regexpType, 'segment_selection': segment_selectionType23, 'strain': organism_type, 'crystallography_preparation': crystallography_preparation_type, 'spatial_filtering': spatial_filteringType, 'specialist_optics': specialist_optics_type, 'series_aligment_software_list': software_list_type, 'fiducial_marker': fiducial_marker_type, 'camera_length': camera_lengthType, 'high_pressure_freezing': high_pressure_freezingType, 'tilt_series': tilt_series_type, 'angular_sampling': angular_samplingType12, 'final_model': final_modelType, 'radius': radiusType, 'figure': figure_type, 'model_heterogeneity': model_heterogeneityType, 'soft_validation_regexp': soft_validation_regexpType, 'singleparticle_processing': singleparticle_processing_type, 'telephone': telephone_number_type, 'sample': sample_type, 'natural_host': natural_hostType, 'specimen_preparation_list': specimen_preparation_listType, 'host_system': recombinant_source_type, 'concentration': concentrationType, 'lattice_distortion_correction': lattice_distortion_correctionType20, 'vitrification': vitrification_type, 'b-factorSharpening': b_factorSharpeningType, 'specimen_preparations': specimen_preparationsType, 'mask_details': map_type, 'angle': angleType, 'axis1': axis_type, 'axis2': axis2Type, 'author': author_order_type, 'figure_list': figure_listType, 'layer_lines': layer_linesType29, 'molecular_weight': molecular_weight_type, 'emdb_list': emdb_cross_reference_list_type, 'ultramicrotomy': ultramicrotomyType, 'other': otherType, 'obsolete_list': obsolete_listType, 'pixel_spacing': pixel_spacingType, 'status_history_list': version_list_type, 'grant_reference': grant_reference_type, 'nominal_defocus_min': nominal_defocus_minType, 'map': map_type, 'crystal_formation': crystal_formationType, 'buffer': buffer_type, 'tilt_list': tilt_listType, 'segment_length': segment_lengthType24, 'low_frequency_cutoff': low_frequency_cutoffType, 'annotator': annotatorType, 'nominal_defocus_max': nominal_defocus_maxType, 'additional_map_list': additional_map_listType, 'connectivity': connectivityType, 'beta': cell_angle_type, 'entry': supersedes_type, 'applied_symmetry': applied_symmetry_type, 'alpha': cell_angle_type, 'emdb_reference': emdb_cross_reference_type, 'ctf_correction': ctf_correction_type, 'dimensions': dimensionsType, 'a': cell_type, '_c-link': _c_linkType, 'organism': organism_type, 'orthogonal_tilt': orthogonal_tiltType, 'final_reconstruction': reconstruction_type, 'angle_increment': angle_incrementType, 'grant_support': grant_supportType, 'fiducial_markers_list': fiducial_markers_listType, 'depth': depthType, 'gamma': cell_angle_type, 'time': crystal_formation_time_type, 'y': pixel_spacing_type, 'organization': organizationType, 'validation': validationType, 'resolution': resolutionType75, 'calibrated_defocus_min': calibrated_defocus_minType, } USAGE_TEXT = """ Usage: python <Parser>.py [ -s ] <in_xml_file> """ def usage(): print(USAGE_TEXT) sys.exit(1) def get_root_tag(node): tag = Tag_pattern_.match(node.tag).groups()[-1] rootClass = GDSClassesMapping.get(tag) if rootClass is None: rootClass = globals().get(tag) return tag, rootClass def parse(inFileName, silence=False): parser = None doc = parsexml_(inFileName, parser) rootNode = doc.getroot() rootTag, rootClass = get_root_tag(rootNode) if rootClass is None: rootTag = 'entry_type' rootClass = entry_type rootObj = rootClass.factory() rootObj.build(rootNode) # Enable Python to collect the space used by the DOM. doc = None if not silence: sys.stdout.write('<?xml version="1.0" ?>\n') rootObj.export( sys.stdout, 0, name_=rootTag, namespacedef_='', pretty_print=True) return rootObj def parseEtree(inFileName, silence=False): parser = None doc = parsexml_(inFileName, parser) rootNode = doc.getroot() rootTag, rootClass = get_root_tag(rootNode) if rootClass is None: rootTag = 'entry_type' rootClass = entry_type rootObj = rootClass.factory() rootObj.build(rootNode) # Enable Python to collect the space used by the DOM. doc = None mapping = {} rootElement = rootObj.to_etree(None, name_=rootTag, mapping_=mapping) reverse_mapping = rootObj.gds_reverse_node_mapping(mapping) if not silence: content = etree_.tostring( rootElement, pretty_print=True, xml_declaration=True, encoding="utf-8") sys.stdout.write(content) sys.stdout.write('\n') return rootObj, rootElement, mapping, reverse_mapping def parseString(inString, silence=False): from StringIO import StringIO parser = None doc = parsexml_(StringIO(inString), parser) rootNode = doc.getroot() rootTag, rootClass = get_root_tag(rootNode) if rootClass is None: rootTag = 'entry_type' rootClass = entry_type rootObj = rootClass.factory() rootObj.build(rootNode) # Enable Python to collect the space used by the DOM. doc = None if not silence: sys.stdout.write('<?xml version="1.0" ?>\n') rootObj.export( sys.stdout, 0, name_=rootTag, namespacedef_='') return rootObj def parseLiteral(inFileName, silence=False): parser = None doc = parsexml_(inFileName, parser) rootNode = doc.getroot() rootTag, rootClass = get_root_tag(rootNode) if rootClass is None: rootTag = 'entry_type' rootClass = entry_type rootObj = rootClass.factory() rootObj.build(rootNode) # Enable Python to collect the space used by the DOM. doc = None if not silence: sys.stdout.write('#from emdb_da import *\n\n') sys.stdout.write('import emdb_da as model_\n\n') sys.stdout.write('rootObj = model_.rootClass(\n') rootObj.exportLiteral(sys.stdout, 0, name_=rootTag) sys.stdout.write(')\n') return rootObj def main(): args = sys.argv[1:] if len(args) == 1: parse(args[0]) else: usage() if __name__ == '__main__': #import pdb; pdb.set_trace() main() __all__ = [ "_brestoreType", "_c_linkType", "_n_linkType", "acceleration_voltageType", "additional_map_listType", "address_type", "admin_type", "alignment_procedureType", "ammonium_molybdate", "amplitude_correctionType", "angleType", "angle_assignment_type", "angle_incrementType", "angular_samplingType", "angular_samplingType12", "angular_samplingType9", "annotatorType", "applied_symmetry_type", "auro_glucothionate", "author_order_type", "authors_listType", "auxiliary_link_listType", "auxiliary_link_type", "average", "average_electron_dose_per_imageType", "average_exposure_timeType", "axis2Type", "axis_orderType", "axis_rotation", "axis_rotationType", "axis_type", "b_factorSharpeningType", "background_masked_type", "base_macromolecule_type", "base_microscopy_type", "base_natural_source_type", "base_preparation_type", "base_processing_type", "base_supramolecule_type", "base_type", "basicType", "buffer_type", "c2_aperture_diameterType", "calibrated_defocus_maxType", "calibrated_defocus_minType", "camera_lengthType", "categoryType", "categoryType39", "cell", "cellType", "cell_angle_type", "cell_type", "chainType", "chainType53", "chain_id_list", "chain_model_type", "chain_type", "chamber_humidityType", "chamber_temperatureType", "citation_listType", "citation_list_type", "citation_type", "classification_type", "code_type", "coloured_gaussian", "coma_freeType", "complex", "complex_type", "componentType", "concentrationType", "concentrationType3", "connectivityType", "contact_authorType", "contact_details_type", "contourType", "contour_listType", "coordinate_type", "crossreferences_type", "crystal_formationType", "crystal_formation_temperature_type", "crystal_formation_time_type", "crystal_parameters_type", "crystallography_microscopy_type", "crystallography_preparation_type", "crystallography_processing_type", "crystallography_statistics_type", "crystallography_tilt_type", "crystallography_validation", "ctf_correction_type", "data_completeness", "delta_phiType", "delta_zType", "depthType", "diameterType", "diameterType42", "diameterType74", "digitization_detailsType", "dimensionsType", "dimensionsType49", "discrepancy_listType", "discrepancy_listType57", "discrepancy_listType62", "discrepancy_listType79", "dna", "em_label", "emdb_cross_reference_list_type", "emdb_cross_reference_type", "energy_filterType", "entry_type", "experimentalType", "external_referencesType", "external_referencesType45", "external_referencesType47", "external_referencesType54", "external_referencesType59", "external_referencesType64", "external_referencesType68", "external_referencesType70", "external_referencesType72", "external_referencesType81", "extractionType", "extractionType13", "fib_current_type", "fib_dose_rate_type", "fib_duration_type", "fib_final_thickness_type", "fib_initial_thickness_type", "fib_voltage_type", "fiducial_marker_type", "fiducial_markers_listType", "figure_listType", "figure_type", "film", "film_or_detector_modelType", "film_thicknessType", "film_type", "final_modelType", "final_multi_reference_alignmentType", "final_multi_reference_alignmentType10", "final_multi_reference_alignmentType11", "final_multi_reference_alignmentType14", "focused_ion_beamType", "fsc_curve", "glow_dischargeType", "glow_discharge_params_type", "grant_reference_type", "grant_supportType", "grid_type", "half_map_listType", "hard_validation_regexpType", "heightType", "heightType51", "helical_parameters_type", "helical_processing_type", "helix_lengthType", "helix_lengthType30", "high_frequency_cutoffType", "high_pressure_freezingType", "high_resolutionType", "high_resolutionType18", "high_resolutionType82", "high_resolutionType83", "image_recordingType", "image_recording_listType", "image_recording_type", "in_plane_rotation", "in_plane_translation", "indexingType", "indexingType31", "initial_modelType", "integer_vector_map_type", "interpretation_type", "journal_citation", "key_datesType", "lattice_distortion_correctionType", "lattice_distortion_correctionType20", "layer_lines", "layer_linesType", "layer_linesType29", "legacyType", "ligand", "lipid", "low_frequency_cutoffType", "low_resolutionType", "low_resolutionType19", "low_resolutionType84", "lower_energy_thresholdType", "macromoleculeType", "macromolecule_listType", "macromolecule_listType40", "macromolecule_list_type", "macromolecules_and_complexes_type", "map_statistics_type", "map_type", "max", "max_angleType", "maximum_likelihood_type", "mergingType", "mergingType22", "microscopy_listType", "min", "min_angleType", "model_heterogeneityType", "model_type", "modelling_listType", "modelling_type", "molecular_replacementType", "molecular_replacementType15", "molecular_weightType", "molecular_weight_type", "molecule_id", "name_type", "natural_hostType", "natural_sourceType", "natural_sourceType36", "natural_sourceType37", "natural_sourceType38", "natural_source_type", "noise_modelType", "nominal_csType", "nominal_defocus_maxType", "nominal_defocus_minType", "non_journal_citation", "noneType", "number_classes", "number_helices", "number_observed_reflections", "number_unique_reflections", "obsolete_listType", "organelle_or_cellular_component", "organism_type", "organizationType", "originType", "orthogonal_tiltType", "osmium_ferricyanide", "osmium_tetroxide", "other", "otherType", "otherType52", "other_macromolecule", "out_of_plane_rotation", "parallel_resolution", "parametersType", "particle_selection_type", "pdb_cross_reference_list_type", "pdb_cross_reference_type", "pdb_model_type", "perpendicular_resolution", "phase_reversalType", "phophotungstic_acid", "pixel_spacingType", "pixel_spacing_type", "pressureType", "primary_citationType", "projection_matching_processingType", "protein_or_peptide", "radiusType", "random_conical_tiltType", "recombinant_source_type", "reconstruction_filtering_type", "reconstruction_type", "refinementType", "refinementType27", "regexp_string", "relationshipType", "relationshipType1", "resolutionType", "resolutionType75", "resolution_rangeType", "resolution_rangeType17", "results_type", "rna", "saccharide", "sample", "sample_type", "sampling_intervalType", "sci_name_type", "secondary_citationType", "sectioningType", "segment_lengthType", "segment_lengthType24", "segment_overlapType", "segment_overlapType25", "segment_selectionType", "segment_selectionType23", "segmentationType", "segmentation_listType", "sequenceType", "sequenceType55", "sequenceType60", "sequenceType77", "shadowingType", "sharpeningType", "shellType", "shell_listType", "singleparticle_processing_type", "sitesType", "slices_listType", "soft_validation_regexpType", "software_list_type", "software_type", "spacingType", "spatial_filteringType", "spatial_frequencyType", "specialist_optics_type", "specimen_preparation_listType", "specimen_preparationsType", "stain_type", "stainingType", "starting_map_type", "starting_modelType", "starting_modelType16", "starting_symmetryType", "starting_symmetryType28", "statusType", "status_type", "string_type", "string_validation_type", "structure_determination_listType", "structure_determination_type", "structure_factors", "subtomogram_averaging_processing_type", "subtomogram_reconstruction_type", "sugar_embeddingType", "superseded_by_listType", "supersedes_type", "supramolecule_listType", "symmetry_determinationType", "symmetry_determinationType21", "telephone_number_type", "temperatureType", "temperature_averageType", "temperature_maxType", "temperature_minType", "temperature_type", "theoreticalType", "thicknessType", "tilt_angle1Type", "tilt_angle2Type", "tilt_angleType", "tilt_angle_max", "tilt_angle_min", "tilt_listType", "tilt_series_type", "timeType", "tissue", "tomography_microscopy_type", "tomography_preparation_type", "tomography_processing_type", "total_filament_lengthType", "total_filament_lengthType26", "ultramicrotomyType", "ultramicrotomy_final_thickness_type", "unit_cell_type", "upper_energy_thresholdType", "uranyl_acetate", "uranyl_formate", "validationType", "validation_listType", "validation_type", "version_list_type", "version_type", "virus", "virus_shellType", "virus_shellType41", "virus_species_name_type", "vitrification_type", "weighted_phase_residual", "weighted_r_factor", "white_gaussian", "widthType", "widthType50", "zemlin_tableauType" ]