def test_prefix_without_url(self):
expected_ns = self.get_ns_defaults()
expected_ns.update({'odm': 'http://www.cdisc.org/ns/odm/v1.3'})
nsr = NS.NamespaceRegistry(prefix="def")
self.assertDictEqual(expected_ns, nsr.namespaces)
nsr = NS.NamespaceRegistry(uri='http://www.cdisc.org/ns/def/v2.0')
self.assertDictEqual(expected_ns, nsr.namespaces)
def test_odm_ns_entries(self):
NS.NamespaceRegistry(prefix="def",
uri="http://www.cdisc.org/ns/def/v2.0")
nsr = NS.NamespaceRegistry(
prefix="nciodm", uri="http://ncicb.nci.nih.gov/xml/odm/EVS/CDISC")
expected_ns = self.get_ns_defaults()
expected_ns.update({
'odm':
'http://www.cdisc.org/ns/odm/v1.3',
'def':
'http://www.cdisc.org/ns/def/v2.0',
'nciodm':
'http://ncicb.nci.nih.gov/xml/odm/EVS/CDISC'
})
self.assertDictEqual(expected_ns, nsr.namespaces)
odm_ns = nsr.get_odm_namespace_entries()
expected_list = [
'xmlns=http://www.cdisc.org/ns/odm/v1.3',
'xmlns:xs=http://www.w3.org/2001/XMLSchema-instance',
'xmlns:xml=http://www.w3.org/XML/1998/namespace',
'xmlns:xlink=http://www.w3.org/1999/xlink',
'xmlns:def=http://www.cdisc.org/ns/def/v2.0',
'xmlns:nciodm=http://ncicb.nci.nih.gov/xml/odm/EVS/CDISC'
]
self.assertListEqual(expected_list, odm_ns)
def test_remove_registry_entry(self):
# tests a singleton so each test builds on the previous one
NS.NamespaceRegistry(prefix="def",
uri="http://www.cdisc.org/ns/def/v2.0")
nsr = NS.NamespaceRegistry(
prefix="nciodm", uri="http://ncicb.nci.nih.gov/xml/odm/EVS/CDISC")
expected_ns = self.get_ns_defaults()
expected_ns.update({
'odm':
'http://www.cdisc.org/ns/odm/v1.3',
'def':
'http://www.cdisc.org/ns/def/v2.0',
'nciodm':
'http://ncicb.nci.nih.gov/xml/odm/EVS/CDISC'
})
self.assertDictEqual(expected_ns, nsr.namespaces)
nsr.remove_registry_entry("def")
expected_ns = self.get_ns_defaults()
expected_ns.update({
'odm':
'http://www.cdisc.org/ns/odm/v1.3',
'nciodm':
'http://ncicb.nci.nih.gov/xml/odm/EVS/CDISC'
})
self.assertDictEqual(expected_ns, nsr.namespaces)
def _set_registry(self, namespace_registry):
if namespace_registry:
self.nsr = namespace_registry
else:
NS.NamespaceRegistry(prefix="odm",
uri="http://www.cdisc.org/ns/odm/v1.3",
is_default=True)
self.nsr = NS.NamespaceRegistry(prefix="def", uri=self.ns_uri)
def test_write_dataset_xml(self):
self.root.write_xml(ODM_XML_FILE)
loader = OL.XMLODMLoader(model_package="dataset_1_0_1", ns_uri="http://www.cdisc.org/ns/Dataset-XML/v1.0")
NS.NamespaceRegistry(prefix="odm", uri="http://www.cdisc.org/ns/odm/v1.3", is_default=True)
ns = NS.NamespaceRegistry(prefix="data", uri="http://www.cdisc.org/ns/Dataset-XML/v1.0")
loader.create_document(ODM_XML_FILE, ns)
odm = loader.load_odm()
self.assertEqual(odm.FileOID, "ODM.DATASET.001")
self.assertEqual(odm.ClinicalData.ItemGroupData[0].ItemGroupOID, "IG.AE")
self.assertEqual(odm.ClinicalData.ItemGroupData[0].ItemData[2].Value, "CDISC01.100008")
self.assertEqual(odm.ClinicalData.ItemGroupData[1].ItemData[4].Value, "ANXIETY")
def setUp(self) -> None:
attrs = self.set_itemgroupdef_attributes()
self.igd = DEFINE.ItemGroupDef(**attrs)
self.test_file = os.path.join(
os.path.dirname(os.path.realpath(__file__)), 'data',
'define2-0-0-sdtm-test.xml')
self.nsr = NS.NamespaceRegistry(prefix="odm",
uri="http://www.cdisc.org/ns/odm/v1.3",
is_default=True)
self.nsr = NS.NamespaceRegistry(prefix="def",
uri="http://www.cdisc.org/ns/def/v2.0")
def setUp(self) -> None:
self.odm_file = os.path.join(
os.path.dirname(os.path.realpath(__file__)), 'data', 'ae_test.xml')
self.loader = OL.XMLODMLoader(
model_package="dataset_1_0_1",
ns_uri="http://www.cdisc.org/ns/Dataset-XML/v1.0")
NS.NamespaceRegistry(prefix="odm",
uri="http://www.cdisc.org/ns/odm/v1.3",
is_default=True)
self.ns = NS.NamespaceRegistry(
prefix="data", uri="http://www.cdisc.org/ns/Dataset-XML/v1.0")
def setUp(self) -> None:
NS.NamespaceRegistry(prefix="odm",
uri="http://www.cdisc.org/ns/odm/v1.3",
is_default=True,
is_reset=True)
NS.NamespaceRegistry(prefix="xs",
uri="http://www.w3.org/2001/XMLSchema-instance")
NS.NamespaceRegistry(prefix="xml",
uri="http://www.w3.org/XML/1998/namespace")
NS.NamespaceRegistry(prefix="xlink",
uri="http://www.w3.org/1999/xlink")
def setUp(self) -> None:
self.odm_file_1 = os.path.join(
os.path.dirname(os.path.realpath(__file__)), 'data',
'define2-0-0-sdtm-test.xml')
NS.NamespaceRegistry(prefix="odm",
uri="http://www.cdisc.org/ns/odm/v1.3",
is_default=True)
NS.NamespaceRegistry(prefix="def",
uri="http://www.cdisc.org/ns/def/v2.0")
self.nsr = NS.NamespaceRegistry(
prefix="nciodm", uri="http://ncicb.nci.nih.gov/xml/odm/EVS/CDISC")
self.parser = P.ODMParser(self.odm_file_1, self.nsr)
self.root = self.parser.parse()
self.mdv = self.parser.MetaDataVersion()
def __init__(self, ns_registry):
if ns_registry:
self.nsr = ns_registry
else:
self.nsr = NS.NamespaceRegistry(
prefix="odm",
uri="http://www.cdisc.org/ns/odm/v1.3",
is_default=True)
def test_default_ns(self):
NS.NamespaceRegistry(prefix="def",
uri="http://www.cdisc.org/ns/def/v2.0")
nsr = NS.NamespaceRegistry(
prefix="nciodm", uri="http://ncicb.nci.nih.gov/xml/odm/EVS/CDISC")
expected_ns = self.get_ns_defaults()
expected_ns.update({
'odm':
'http://www.cdisc.org/ns/odm/v1.3',
'def':
'http://www.cdisc.org/ns/def/v2.0',
'nciodm':
'http://ncicb.nci.nih.gov/xml/odm/EVS/CDISC'
})
self.assertDictEqual(expected_ns, nsr.namespaces)
self.assertDictEqual({'odm': 'http://www.cdisc.org/ns/odm/v1.3'},
nsr.default_namespace)
def setUp(self) -> None:
self.odm_file_1 = os.path.join(
os.path.dirname(os.path.realpath(__file__)), 'data',
'defineV21-SDTM-metadata.xml')
NS.NamespaceRegistry(prefix="odm",
uri="http://www.cdisc.org/ns/odm/v1.3",
is_default=True)
NS.NamespaceRegistry(prefix="def",
uri="http://www.cdisc.org/ns/def/v2.1")
self.nsr = NS.NamespaceRegistry(
prefix="nciodm", uri="http://ncicb.nci.nih.gov/xml/odm/EVS/CDISC")
self.parser = P.ODMParser(self.odm_file_1, self.nsr)
self.loader = LD.ODMLoader(
OL.XMLDefineLoader(model_package="define_2_1",
ns_uri="http://www.cdisc.org/ns/def/v2.1"))
self.root = self.loader.create_document(self.odm_file_1)
self.odm = self.loader.load_odm()
self.parser.parse()
self.mdv = self.parser.MetaDataVersion()
def __init__(self,
model_package="odm_1_3_2",
ns_uri="http://www.cdisc.org/ns/odm/v1.3",
local_model=False):
self.filename = None
self.parser = None
if local_model:
self.ODM = importlib.import_module(f"{model_package}.model")
else:
self.ODM = importlib.import_module(f"odmlib.{model_package}.model")
self.nsr = NS.NamespaceRegistry()
def __init__(self,
model_package="define_2_0",
ns_uri="http://www.cdisc.org/ns/def/v2.0",
local_model=False):
self.filename = None
self.parser = None
if local_model:
self.DEF = importlib.import_module(f"{model_package}.model")
else:
self.DEF = importlib.import_module(f"odmlib.{model_package}.model")
self.ns_uri = ns_uri
self.nsr = NS.NamespaceRegistry()
def test_odm_ns_attributes(self):
odm_test_file = os.path.join(
os.path.dirname(os.path.realpath(__file__)), 'data',
'test_odm_namespace.xml')
NS.NamespaceRegistry(prefix="def",
uri="http://www.cdisc.org/ns/def/v2.0")
NS.NamespaceRegistry(prefix="nciodm",
uri="http://ncicb.nci.nih.gov/xml/odm/EVS/CDISC")
NS.NamespaceRegistry(prefix="xsi",
uri="http://www.w3.org/2001/XMLSchema-instance")
root = self.add_root()
odm_xml = root.to_xml()
nsr = NS.NamespaceRegistry()
nsr.set_odm_namespace_attributes(odm_xml)
tree = ET.ElementTree(odm_xml)
tree.write(odm_test_file,
xml_declaration=True,
encoding='utf-8',
method='xml',
short_empty_elements=True)
self.assertEqual("ODM.MDV.TEST.001", root.FileOID)
loader = LD.ODMLoader(DL.XMLDefineLoader())
odm_root = loader.open_odm_document(odm_test_file)
self.assertEqual("ODM.MDV.TEST.001", odm_root.attrib["FileOID"])
odm = loader.create_odmlib(odm_root)
self.assertEqual("ODM.MDV.TEST.001", odm.FileOID)
nsr2 = NS.NamespaceRegistry()
namespaces = nsr2.get_odm_namespace_entries()
expected_ns_list = [
'xmlns=http://www.cdisc.org/ns/odm/v1.3',
'xmlns:xs=http://www.w3.org/2001/XMLSchema-instance',
'xmlns:xml=http://www.w3.org/XML/1998/namespace',
'xmlns:xlink=http://www.w3.org/1999/xlink',
'xmlns:def=http://www.cdisc.org/ns/def/v2.0',
'xmlns:nciodm=http://ncicb.nci.nih.gov/xml/odm/EVS/CDISC',
'xmlns:xsi=http://www.w3.org/2001/XMLSchema-instance'
]
self.assertListEqual(namespaces, expected_ns_list)
def write_odm(odm_file, odm_elem):
"""
after converting ODMLIB to ElementTree, write the ElementTree to an ODM file
:param odm_file: path and file to write the ODM XML
:param odm_elem: Element object to write to ODM (presumably an ODM root)
"""
tree = ET.ElementTree(odm_elem)
root = tree.getroot()
# workaround for elementtree NS bug - NamespaceRegistry assumes at least 1 default NS has been set
nsr = NS.NamespaceRegistry()
nsr.set_odm_namespace_attributes(root)
tree.write(odm_file,
xml_declaration=True,
encoding='utf-8',
method='xml',
short_empty_elements=True)
import odmlib.odm_element as OE
import odmlib.typed as T
import odmlib.ns_registry as NS
NS.NamespaceRegistry(prefix="odm",
uri="http://www.cdisc.org/ns/odm/v1.3",
is_default=True)
NS.NamespaceRegistry(prefix="nciodm",
uri="http://ncicb.nci.nih.gov/xml/odm/EVS/CDISC")
NS.NamespaceRegistry(prefix="xs",
uri="http://www.w3.org/2001/XMLSchema-instance")
NS.NamespaceRegistry(prefix="xml", uri="http://www.w3.org/XML/1998/namespace")
NS.NamespaceRegistry(prefix="xlink", uri="http://www.w3.org/1999/xlink")
class TranslatedText(OE.ODMElement):
lang = T.String(namespace="xml")
_content = T.String(required=True)
class Alias(OE.ODMElement):
Context = T.String(required=True)
Name = T.String(required=True)
class StudyDescription(OE.ODMElement):
_content = T.String(required=True)
class ProtocolName(OE.ODMElement):
_content = T.String(required=True)
def test_xml_to_string(self):
current_datetime = datetime.datetime.utcnow().replace(tzinfo=datetime.timezone.utc).isoformat()
root = ODM.ODM(FileOID="ODM.DEMO.001", Granularity="Metadata", AsOfDateTime=current_datetime,
CreationDateTime=current_datetime, ODMVersion="1.3.2", FileType="Snapshot",
Originator="swhume", SourceSystem="odmlib", SourceSystemVersion="0.1")
# create Study and add to ODM
root.Study.append(ODM.Study(OID="ODM.GET.STARTED"))
# create the global variables
root.Study[0].GlobalVariables = ODM.GlobalVariables()
root.Study[0].GlobalVariables.StudyName = ODM.StudyName(_content="Get Started with ODM XML")
root.Study[0].GlobalVariables.StudyDescription = ODM.StudyDescription(
_content="Demo to get started with odmlib")
root.Study[0].GlobalVariables.ProtocolName = ODM.ProtocolName(_content="ODM XML Get Started")
# create the MetaDataVersion
root.Study[0].MetaDataVersion.append(ODM.MetaDataVersion(OID="MDV.DEMO-ODM-01", Name="Get Started MDV",
Description="Get Started Demo"))
# create Protocol
p = ODM.Protocol()
p.Description = ODM.Description()
p.Description.TranslatedText.append(ODM.TranslatedText(_content="Get Started Protocol", lang="en"))
p.StudyEventRef.append(ODM.StudyEventRef(StudyEventOID="BASELINE", OrderNumber=1, Mandatory="Yes"))
root.Study[0].MetaDataVersion[0].Protocol = p
# create a StudyEventDef
sed = ODM.StudyEventDef(OID="BASELINE", Name="Baseline Visit", Repeating="No", Type="Scheduled")
sed.FormRef.append(ODM.FormRef(FormOID="ODM.F.DM", Mandatory="Yes", OrderNumber=1))
root.Study[0].MetaDataVersion[0].StudyEventDef.append(sed)
# create a FormDef
fd = ODM.FormDef(OID="ODM.F.DM", Name="Demographics", Repeating="No")
fd.ItemGroupRef.append(ODM.ItemGroupRef(ItemGroupOID="ODM.IG.DM", Mandatory="Yes", OrderNumber=2))
root.Study[0].MetaDataVersion[0].FormDef.append(fd)
# create an ItemGroupDef
igd = ODM.ItemGroupDef(OID="ODM.IG.DM", Name="Demographics", Repeating="No")
igd.ItemRef.append(ODM.ItemRef(ItemOID="ODM.IT.DM.BRTHYR", Mandatory="Yes"))
root.Study[0].MetaDataVersion[0].ItemGroupDef.append(igd)
# create an ItemDef
itd = ODM.ItemDef(OID="ODM.IT.DM.BRTHYR", Name="Birth Year", DataType="integer")
itd.Description = ODM.Description()
itd.Description.TranslatedText.append(ODM.TranslatedText(_content="Year of the subject's birth", lang="en"))
itd.Question = ODM.Question()
itd.Question.TranslatedText.append(ODM.TranslatedText(_content="Birth Year", lang="en"))
itd.Alias.append(ODM.Alias(Context="CDASH", Name="BRTHYR"))
itd.Alias.append(ODM.Alias(Context="SDTM", Name="BRTHDTC"))
root.Study[0].MetaDataVersion[0].ItemDef.append(itd)
odm_xml_string = root.to_xml_string()
# add namespaces
nsr = NS.NamespaceRegistry()
odm_str = nsr.set_odm_namespace_attributes_string(odm_xml_string)
with open("./data/simple_create_from_string.xml", "w") as xml_file:
xml_file.write(odm_str)
loader = LD.ODMLoader(OL.XMLODMLoader(model_package="odm_1_3_2", ns_uri="http://www.cdisc.org/ns/odm/v1.3"))
loader.open_odm_document("./data/simple_create_from_string.xml")
mdv = loader.MetaDataVersion()
item_list = mdv.ItemDef
item = item_list[0]
self.assertEqual(item.OID, "ODM.IT.DM.BRTHYR")
def test_use_existing_registry(self):
expected_ns = self.get_ns_defaults()
expected_ns.update({'odm': 'http://www.cdisc.org/ns/odm/v1.3'})
nsr = NS.NamespaceRegistry()
self.assertDictEqual(expected_ns, nsr.namespaces)
def test_get_ns_entry_dict_missing(self):
nsr = NS.NamespaceRegistry(prefix="def",
uri="http://www.cdisc.org/ns/def/v2.0")
missing_ns_dict = nsr.get_ns_entry_dict("ct")
expected_dict = {}
self.assertDictEqual(expected_dict, missing_ns_dict)
def test_get_ns_entry_dict(self):
nsr = NS.NamespaceRegistry(prefix="def",
uri="http://www.cdisc.org/ns/def/v2.0")
def_ns_dict = nsr.get_ns_entry_dict("def")
expected_dict = {"def": "http://www.cdisc.org/ns/def/v2.0"}
self.assertDictEqual(expected_dict, def_ns_dict)
def test_get_ns_prefix_missing(self):
nsr = NS.NamespaceRegistry(prefix="def",
uri="http://www.cdisc.org/ns/def/v2.0")
with self.assertRaises(ValueError):
def_prefix = nsr.get_prefix_ns_from_uri(
"http://www.cdisc.org/ns/def/v3.0")
def test_get_ns_prefix(self):
nsr = NS.NamespaceRegistry(prefix="def",
uri="http://www.cdisc.org/ns/def/v2.0")
def_prefix = nsr.get_prefix_ns_from_uri(
"http://www.cdisc.org/ns/def/v2.0")
self.assertEqual("def", def_prefix)
def test_bad_ns_url(self):
with self.assertRaises(ValueError):
nsr = NS.NamespaceRegistry(prefix="def",
uri="www.cdisc.org/ns/def/v2.0")
import odmlib.odm_element as OE
import odmlib.typed as T
import odmlib.ns_registry as NS
NS.NamespaceRegistry(prefix="odm",
uri="http://www.cdisc.org/ns/odm/v2.0",
is_default=True)
NS.NamespaceRegistry(prefix="xs",
uri="http://www.w3.org/2001/XMLSchema-instance")
NS.NamespaceRegistry(prefix="xml", uri="http://www.w3.org/XML/1998/namespace")
NS.NamespaceRegistry(prefix="xlink", uri="http://www.w3.org/1999/xlink")
class TranslatedText(OE.ODMElement):
lang = T.String(namespace="xml")
Type = T.String()
_content = T.String(required=True)
class Description(OE.ODMElement):
TranslatedText = T.ODMListObject(required=True,
element_class=TranslatedText)
class Alias(OE.ODMElement):
Context = T.String(required=True)
Name = T.String(required=True)
class StudyDescription(OE.ODMElement):
Description = T.ODMObject(element_class=Description, required=True)
import odmlib.odm_1_3_2.model as ODM
import odmlib.odm_element as OE
import odmlib.typed as T
import odmlib.ns_registry as NS
NS.NamespaceRegistry(prefix="odm", uri="http://www.cdisc.org/ns/odm/v1.3", is_default=True)
NS.NamespaceRegistry(prefix="xs", uri="http://www.w3.org/2001/XMLSchema-instance")
NS.NamespaceRegistry(prefix="xml", uri="http://www.w3.org/XML/1998/namespace")
NS.NamespaceRegistry(prefix="data", uri="http://www.cdisc.org/ns/Dataset-XML/v1.0")
class ItemData(OE.ODMElement):
ItemOID = T.OIDRef(required=True)
Value = T.String(required=False)
class ItemGroupData(OE.ODMElement):
ItemGroupOID = T.OIDRef(required=True)
ItemGroupDataSeq = T.PositiveInteger(required=True, namespace="data")
ItemData = T.ODMListObject(required=False, element_class=ItemData)
def __len__(self):
return len(self.ItemData)
def __getitem__(self, position):
return self.ItemData[position]
def __iter__(self):
return iter(self.ItemData)
import odmlib.odm_1_3_2.model as ODM
import odmlib.odm_element as OE
import odmlib.typed as T
import odmlib.ns_registry as NS
NS.NamespaceRegistry(prefix="def", uri="http://www.cdisc.org/ns/def/v2.1")
class TranslatedText(ODM.TranslatedText):
lang = ODM.TranslatedText.lang
_content = ODM.TranslatedText._content
class Alias(ODM.Alias):
Context = ODM.Alias.Context
Name = ODM.Alias.Name
class StudyDescription(ODM.StudyDescription):
_content = ODM.StudyDescription._content
class ProtocolName(ODM.ProtocolName):
_content = ODM.ProtocolName._content
class StudyName(ODM.StudyName):
_content = ODM.StudyName._content
class GlobalVariables(ODM.GlobalVariables):
