def test_refdef_orphans(self):
attrs = {
"OID": "MDV.TRACE-XML-ODM-01",
"Name": "TRACE-XML MDV",
"Description": "Trace-XML Example"
}
self.mdv = ODM.MetaDataVersion(**attrs)
self.mdv.Protocol = self.add_protocol()
self.mdv.StudyEventDef = self.add_SED()
self.mdv.FormDef = self.add_FD()
self.mdv.ItemGroupDef = self.add_IGD()
self.mdv.ItemDef = self.add_ITD()
self.mdv.CodeList = self.add_CL()
self.mdv.MethodDef = self.add_MD()
self.mdv.ConditionDef = self.add_CD()
# oid uniqueness check and ref/def init
self.mdv.verify_oids(self.oid_checker)
orphans = self.mdv.unreferenced_oids(self.oid_checker)
expected_orphans = {
'MDV.TRACE-XML-ODM-01': 'MetaDataVersionOID',
'ODM.IT.VS.BP.VSORRESU': 'ItemOID',
'ODM.CL.NY_SUB_Y_N': 'CodeListOID',
'ODM.MT.DOB': 'MethodOID',
'ODM.CD.BRTHMO': 'CollectionExceptionConditionOID'
}
self.assertDictEqual(orphans, expected_orphans)
def test_refdef_orphans_unitialized(self):
attrs = {
"OID": "MDV.TRACE-XML-ODM-01",
"Name": "TRACE-XML MDV",
"Description": "Trace-XML Example"
}
self.mdv = ODM.MetaDataVersion(**attrs)
self.mdv.Protocol = self.add_protocol()
self.mdv.StudyEventDef = self.add_SED()
self.mdv.FormDef = self.add_FD()
self.mdv.ItemGroupDef = self.add_IGD()
self.mdv.ItemDef = self.add_ITD()
self.mdv.CodeList = self.add_CL()
self.mdv.MethodDef = self.add_MD()
self.mdv.ConditionDef = self.add_CD()
oid_checker = OID.OIDRef()
# use unitialized oid_checker
orphans = self.mdv.unreferenced_oids(oid_checker)
# returns an empty dictionary since oid index has not been created
expected_orphans = {
'MDV.TRACE-XML-ODM-01': 'MetaDataVersionOID',
'ODM.IT.VS.BP.VSORRESU': 'ItemOID',
'ODM.CL.NY_SUB_Y_N': 'CodeListOID',
'ODM.MT.DOB': 'MethodOID',
'ODM.CD.BRTHMO': 'CollectionExceptionConditionOID'
}
self.assertDictEqual(orphans, expected_orphans)
def test_OID_creation_dirty(self):
attrs = {
"OID": "MDV.TRACE-XML-ODM-01",
"Description": "Trace-XML Example"
}
with self.assertRaises(ValueError):
# MDV creation should fail due to missing Name attribute
self.mdv = ODM.MetaDataVersion(**attrs)
def setUp(self) -> None:
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)
# save the new ODM document to an ODM XML file
root.write_xml(ODM_XML_FILE)
# save the same ODM document to a JSON file
root.write_json(ODM_JSON_FILE)
def add_mdv(self):
attrs = self.set_mdv_attributes()
mdv = ODM.MetaDataVersion(**attrs)
mdv.Protocol = self.add_protocol()
mdv.StudyEventDef = self.add_SED()
mdv.FormDef = self.add_FD()
mdv.ItemGroupDef = self.add_IGD()
mdv.ItemDef = self.add_ITD()
mdv.CodeList = self.add_CL()
mdv.ConditionDef = self.add_CD()
mdv.MethodDef = self.add_MD()
return mdv
def test_OID_unique(self):
attrs = {
"OID": "MDV.TRACE-XML-ODM-01",
"Name": "TRACE-XML MDV",
"Description": "Trace-XML Example"
}
self.mdv = ODM.MetaDataVersion(**attrs)
self.mdv.Protocol = self.add_protocol()
self.mdv.StudyEventDef = self.add_SED()
self.mdv.FormDef = self.add_FD()
self.mdv.ItemGroupDef = self.add_IGD()
self.mdv.ItemDef = self.add_ITD()
self.mdv.CodeList = self.add_CL()
self.mdv.MethodDef = self.add_MD()
self.mdv.ConditionDef = self.add_CD()
oid_checker = OID.OIDRef()
self.mdv.verify_oids(oid_checker)
self.assertTrue(oid_checker.check_oid_refs())
def test_OID_unique_dirty(self):
attrs = {
"OID": "MDV.TRACE-XML-ODM-01",
"Name": "TRACE-XML MDV",
"Description": "Trace-XML Example"
}
self.mdv = ODM.MetaDataVersion(**attrs)
self.mdv.Protocol = self.add_protocol()
self.mdv.StudyEventDef = self.add_SED()
self.mdv.FormDef = self.add_FD()
self.mdv.ItemGroupDef = self.add_IGD()
self.mdv.ItemDef = self.add_ITD_nonunique()
self.mdv.CodeList = self.add_CL()
self.mdv.MethodDef = self.add_MD()
self.mdv.ConditionDef = self.add_CD()
oid_checker = OID.OIDRef()
with self.assertRaises(ValueError):
# checks for non-unique OIDs and runs the ref/def check
self.mdv.verify_oids(oid_checker)
def test_MetaDataVersion(self):
attrs = {
"OID": "MDV.TRACE-XML-ODM-01",
"Name": "TRACE-XML MDV",
"Description": "Trace-XML Example"
}
self.mdv = ODM.MetaDataVersion(**attrs)
self.mdv.Protocol = self.add_protocol()
self.mdv.StudyEventDef = self.add_SED()
self.mdv.FormDef = self.add_FD()
self.mdv.ItemGroupDef = self.add_IGD()
self.mdv.ItemDef = self.add_ITD()
self.mdv.CodeList = self.add_CL()
self.mdv.MethodDef = self.add_MD()
self.mdv.ConditionDef = self.add_CD()
mdv_dict = self.mdv.to_dict()
print(mdv_dict)
is_valid = self.validator.verify_conformance(mdv_dict,
"MetaDataVersion")
self.assertTrue(is_valid)
def test_MethodDef_missing_Description(self):
attrs = {
"OID": "MDV.TRACE-XML-ODM-01",
"Name": "TRACE-XML MDV",
"Description": "Trace-XML Example"
}
self.mdv = ODM.MetaDataVersion(**attrs)
tt1 = ODM.TranslatedText(
_content="Age at Screening Date (Screening Date - Birth date)",
lang="en")
desc1 = ODM.Description()
desc1.TranslatedText.append(tt1)
# MethodDef creation that includes the Description object
md1 = ODM.MethodDef(OID="ODM.MT.AGE",
Name="Algorithm to dervive AGE",
Type="Computation",
Description=desc1)
self.mdv.MethodDef.append(md1)
# MethodDef creation succeeds without Description object
md2 = ODM.MethodDef(OID="ODM.MT.DOB",
Name="Create BRTHDTC from date ELEMENTS",
Type="Computation")
self.mdv.MethodDef.append(md2)
# test that both MethodDefs were added to MDV
self.assertEqual(len(self.mdv.MethodDef), 2)
# test that the content of Description exists for the first MethodDef
self.assertEqual(
self.mdv.MethodDef[0].Description.TranslatedText[0]._content,
"Age at Screening Date (Screening Date - Birth date)")
validator = METADATA.MetadataSchema()
# this is how you check conformance that includes required elements, not just attributes
is_valid = self.mdv.MethodDef[0].verify_conformance(validator)
# Test shows that MethodDef conforms to schema
self.assertTrue(is_valid)
print(self.mdv.MethodDef[0].to_dict())
print(self.mdv.MethodDef[1].to_dict())
with self.assertRaises(ValueError):
# test shows that MethodDef two fails the schema check because it is missing the required Description object
self.mdv.MethodDef[1].verify_conformance(validator)
def setUp(self) -> None:
attrs = self.set_attributes()
self.mdv = ODM.MetaDataVersion(**attrs)
self.odm_test_file = os.path.join(
os.path.dirname(os.path.realpath(__file__)), 'data',
'test_mdv_001.xml')
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")
