def test_insert_item_with_none_element(self):
attrs = self.set_item_attributes()
item = ODM.ItemDef(**attrs)
# to support the test a null version of CodeListRef is created, but should be ignored on output
if item.CodeListRef:
self.assertIsNotNone(item.CodeListRef)
if item.SignificantDigits:
self.assertIsNotNone(item.SignificantDigits)
self.loader.open_odm_document(self.odm_file)
mdv = self.loader.MetaDataVersion()
mdv.ItemDef.append(item)
attrs = self.get_root_attributes()
root = ODM.ODM(**attrs)
study = self.add_study(mdv)
root.Study = [study]
root.write_xml(self.odm_file_out)
loader = LD.ODMLoader(OL.XMLODMLoader())
loader.open_odm_document(self.odm_file_out)
mdv = loader.MetaDataVersion()
# is_found_inserted_item = False
# for it in mdv.ItemDef:
# if it.OID == "ODM.IT.AE.TEST":
# is_found_inserted_item = True
# self.assertTrue(is_found_inserted_item)
itd = mdv.find("ItemDef", "OID", "ODM.IT.AE.TEST")
self.assertEqual(itd.OID, "ODM.IT.AE.TEST")
# comment was created as None and should not be part of the object
self.assertIsNone(itd.Comment)
itd_json = itd.to_json()
self.assertNotIn("Comment", itd_json)
odm_json = root.to_json()
def setUp(self) -> None:
self.odm_file = os.path.join(
os.path.dirname(os.path.realpath(__file__)), 'data',
'cdash-odm-test.xml')
self.loader = LD.ODMLoader(OL.XMLODMLoader())
self.loader.open_odm_document(self.odm_file)
self.odm = self.loader.root()
def setUp(self) -> None:
self.odm_file = os.path.join(
os.path.dirname(os.path.realpath(__file__)), 'data',
'define2-0-0-sdtm-test.xml')
with open(self.odm_file, "r", encoding="utf-8") as f:
self.odm_string = f.read()
self.loader = LD.ODMLoader(OL.XMLDefineLoader())
def setUp(self):
self.odm_file = os.path.join(
os.path.dirname(os.path.realpath(__file__)), 'data',
'cdash-odm-test.xml')
self.odm_file_out = os.path.join(
os.path.dirname(os.path.realpath(__file__)), 'data',
'cdash-odm-test-insert.xml')
self.loader = LD.ODMLoader(OL.XMLODMLoader())
def test_read_odm_xml(self):
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(ODM_XML_FILE)
mdv = loader.MetaDataVersion()
item_list = mdv.ItemDef
item = item_list[0]
self.assertEqual(item.OID, "ODM.IT.DM.BRTHYR")
# tests the __len__ in ItemGroupDef
self.assertEqual(len(item_list), 1)
def setUp(self) -> None:
self.odm = self.add_root()
self.odm_test_file = os.path.join(
os.path.dirname(os.path.realpath(__file__)), 'data',
'test_odm_001.xml')
self.odm_writer_test_file = os.path.join(
os.path.dirname(os.path.realpath(__file__)), 'data',
'test_odm_002.xml')
self.loader = LD.ODMLoader(OL.XMLODMLoader())
def test_find_record(self):
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(self.odm_test_file)
odm = loader.load_odm()
subject = odm.ClinicalData[0].find("SubjectData", "SubjectKey", "1000")
self.assertEqual(subject.TransactionType, "Insert")
self.assertEqual(subject.SubjectKey, "1000")
def test_read_odm_json(self):
loader = LD.ODMLoader(OL.JSONODMLoader(model_package="odm_1_3_2"))
loader.open_odm_document(ODM_JSON_FILE)
mdv = loader.MetaDataVersion()
igd_list = mdv.ItemGroupDef
igd = igd_list[0]
self.assertEqual(igd.OID, "ODM.IG.DM")
# tests the __len__ in ItemGroupDef
self.assertEqual(len(igd_list), 1)
def test_load_odm_xml_data(self):
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(self.odm_test_file2)
odm = loader.load_odm()
self.assertEqual(odm.FileOID, "Study-MetaD20220210213634")
self.assertEqual(odm.ClinicalData[0].StudyOID, "1001_corona")
igd_0 = odm.ClinicalData[0].SubjectData[0].StudyEventData[0].FormData[
0].ItemGroupData[0]
self.assertEqual(igd_0.ItemGroupOID, "IG.DM")
self.assertEqual(igd_0.ItemData[2].ItemOID, "IT.BRTHDAT")
self.assertEqual(igd_0.ItemData[2].Value, "1966-02-10")
def test_odm_round_trip(self):
root = self.loader.load_odm_string(self.odm_string)
odm = self.loader.create_odmlib(root)
odm_json = odm.to_json()
odm_json_file = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'data', 'cdash_odm_test.json')
with open(odm_json_file, "w") as odm_in:
odm_in.write(odm_json)
json_loader = LD.ODMLoader(OL.JSONODMLoader())
odm_dict = json_loader.open_odm_document(odm_json_file)
rt_odm = json_loader.create_odmlib(odm_dict, "ODM")
odm_xml_file = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'data', 'cdash_odm_test_roundtrip.xml')
rt_odm.write_xml(odm_xml_file)
root2 = self.loader.open_odm_document(odm_xml_file)
odm2 = self.loader.create_odmlib(root2)
self.assertEqual(odm2.Study[0].MetaDataVersion[0].ItemDef[0].OID, "ODM.IT.Common.StudyID")
self.assertEqual(len(odm2.Study[0].MetaDataVersion[0].ItemGroupDef[1]), 7)
def test_oid_index_define_igd(self):
self.define_file = os.path.join(
os.path.dirname(os.path.realpath(__file__)), 'data',
'defineV21-SDTM.xml')
self.loader = LD.ODMLoader(
DL.XMLDefineLoader(model_package="define_2_1",
ns_uri="http://www.cdisc.org/ns/def/v2.1"))
self.loader.open_odm_document(self.define_file)
self.odm = self.loader.root()
idx = self.odm.build_oid_index()
found = idx.find_all("IG.VS")
self.assertEqual(len(found), 1)
self.assertEqual(found[0].ItemRef[2].ItemOID, "IT.USUBJID")
self.assertEqual(found[0].ItemRef[5].ItemOID, "IT.VS.VSTEST")
it_found = idx.find_all("IT.EX.EXSTDTC")
self.assertEqual(len(it_found), 2)
self.assertEqual(it_found[1].Name, "EXSTDTC")
def test_odm_round_trip(self):
root = self.loader.open_odm_document(self.odm_file)
odm = self.loader.create_odmlib(root)
odm_json = odm.to_json()
odm_json_file = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'data', 'sdtm_define2_test.json')
with open(odm_json_file, "w") as odm_in:
odm_in.write(odm_json)
json_loader = LD.ODMLoader(OL.JSONDefineLoader())
odm_dict = json_loader.open_odm_document(odm_json_file)
rt_odm = json_loader.create_odmlib(odm_dict, "ODM")
def_xml_file = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'data', 'sdtm_def_test_roundtrip.xml')
rt_odm.write_xml(def_xml_file)
root2 = self.loader.open_odm_document(def_xml_file)
odm2 = self.loader.create_odmlib(root2)
self.assertEqual(odm2.Study[0].MetaDataVersion.OID, "MDV.CDISC01.SDTMIG.3.1.2.SDTM.1.2")
print(f"ItemRefs = {len(odm2.Study[0].MetaDataVersion.ItemGroupDef[1])}")
self.assertEqual(len(odm2.Study[0].MetaDataVersion.ItemGroupDef[1]), 6)
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 test_load_odm_xml_data_iterator(self):
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(self.odm_test_file2)
odm = loader.load_odm()
self.assertEqual(odm.FileOID, "Study-MetaD20220210213634")
self.assertEqual(odm.ClinicalData[0].StudyOID, "1001_corona")
igd_0 = odm.ClinicalData[0].SubjectData[0].StudyEventData[0].FormData[
0].ItemGroupData[0]
values = []
for item in igd_0:
values.append(item.Value)
test_values = self._get_test_values()
self.assertListEqual(values, test_values)
subjects = []
for subject in odm.ClinicalData[0]:
subjects.append(subject.SubjectKey)
test_subjects = ["SS_0001", "SS_0002"]
self.assertListEqual(subjects, test_subjects)
def test_write_json(self):
attrs = self.set_itemgroupdef_attributes()
igd = DEFINE.ItemGroupDef(**attrs)
tt = DEFINE.TranslatedText(
_content="this is the first test description", lang="en")
desc = DEFINE.Description()
desc.TranslatedText = [tt]
igd.Description = desc
ir_list = self.set_itemrefs()
igd.ItemRef = ir_list
self.create_odm_document_json(igd)
loader = LD.ODMLoader(OL.JSONDefineLoader(model_package="define_2_1"))
loader.open_odm_document(self.test_file_json)
mdv = loader.MetaDataVersion()
igd_list = mdv.ItemGroupDef
igd = igd_list[0]
self.assertEqual(igd.OID, "IG.VS")
# tests the __len__ in ItemGroupDef
self.assertEqual(len(igd.ItemRef), 10)
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 test_unknown_loader(self):
with self.assertRaises(TypeError):
loader = LD.ODMLoader(self.test_mdv_find_by_OID())
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 setUp(self) -> None:
self.odm_file = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'data', 'define2-0-0-sdtm-test.xml')
self.odm_file_json = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'data', 'sdtm_define2_test.json')
self.loader = LD.ODMLoader(OL.XMLDefineLoader())
self.jloader = LD.ODMLoader(OL.JSONDefineLoader())
