def add_ITD(self):
# ItemDef 1
ttd1 = ODM.TranslatedText(_content="Date of measurements", lang="en")
ttq1 = ODM.TranslatedText(_content="Date", lang="en")
desc1 = ODM.Description()
desc1.TranslatedText = [ttd1]
q1 = ODM.Question()
q1.TranslatedText = [ttq1]
a1 = ODM.Alias(Context="CDASH", Name="VSDAT")
itd1 = ODM.ItemDef(OID="ODM.IT.VS.VSDAT",
Name="Date",
DataType="partialDate")
itd1.Description = desc1
itd1.Question = q1
itd1.Alias = [a1]
# ItemDef 2
ttd2 = ODM.TranslatedText(
_content=
"Result of the vital signs measurement as originally received or collected.",
lang="en")
ttq2 = ODM.TranslatedText(_content="Diastolic", lang="en")
desc2 = ODM.Description()
desc2.TranslatedText = [ttd2]
q2 = ODM.Question()
q2.TranslatedText = [ttq2]
a2a = ODM.Alias(Context="CDASH", Name="BP.DIABP.VSORRES")
a2b = ODM.Alias(Context="CDASH/SDTM", Name="VSORRES+VSORRESU")
itd2 = ODM.ItemDef(OID="ODM.IT.VS.BP.VSORRESU",
Name="BP Units",
DataType="text")
itd2.Description = desc2
itd2.Question = q2
itd2.Alias = [a2a, a2b]
return [itd1, itd2]
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 test_add_description(self):
tt1 = ODM.TranslatedText(_content="this is the first test description", lang="en")
tt2 = ODM.TranslatedText(_content="this is the second test description", lang="en")
self.formdef.Description = ODM.Description()
self.formdef.Description.TranslatedText = [tt1, tt2]
self.assertEqual(len(self.formdef.Description.TranslatedText), 2)
self.assertEqual(self.formdef.Description.TranslatedText[1]._content, 'this is the second test description')
def test_Protocol(self):
p = ODM.Protocol()
tt = ODM.TranslatedText(_content="Trace-XML Test CDASH File",
lang="en")
p.Description = ODM.Description()
p.Description.TranslatedText = [tt]
ser1 = ODM.StudyEventRef(StudyEventOID="BASELINE",
OrderNumber="1",
Mandatory="Yes")
ser2 = ODM.StudyEventRef(StudyEventOID="FOLLOW-UP",
OrderNumber="2",
Mandatory="Yes")
p.StudyEventRef = [ser1, ser2]
p.Alias = [
ODM.Alias(Context="ClinicalTrials.gov", Name="trace-protocol")
]
description_dict = p.Description.to_dict()
print(description_dict)
is_valid = self.validator.verify_conformance(description_dict,
"Description")
self.assertTrue(is_valid)
protocol_dict = p.to_dict()
print(protocol_dict)
is_valid = self.validator.verify_conformance(protocol_dict, "Protocol")
self.assertTrue(is_valid)
def test_ItemGroupDef(self):
attrs = {
"OID": "IG.VS",
"Name": "VS",
"Repeating": "Yes",
"Domain": "VS",
"Name": "VS",
"SASDatasetName": "VS",
"IsReferenceData": "No",
"Purpose": "Tabulation"
}
igd = ODM.ItemGroupDef(**attrs)
tt = ODM.TranslatedText(_content="this is the first test description",
lang="en")
igd.Description = ODM.Description()
igd.Description.TranslatedText = [tt]
ir1 = ODM.ItemRef(ItemOID="IT.STUDYID",
Mandatory="Yes",
OrderNumber="1")
ir2 = ODM.ItemRef(ItemOID="IT.VS.VSTEST",
Mandatory="No",
OrderNumber="2")
igd.ItemRef = [ir1, ir2]
igd_dict = igd.to_dict()
print(igd_dict)
is_valid = self.validator.verify_conformance(igd_dict, "ItemGroupDef")
self.assertTrue(is_valid)
def test_FormDef(self):
formdef = ODM.FormDef(OID="ODM.F.VS",
Name="Vital Signs Form",
Repeating="Yes")
tt1 = ODM.TranslatedText(_content="this is the first test description",
lang="en")
formdef.Description = ODM.Description()
formdef.Description.TranslatedText = [tt1]
igr = ODM.ItemGroupRef(ItemGroupOID="ODM.IG.COMMON",
Mandatory="Yes",
OrderNumber="1")
formdef.ItemGroupRef.append(igr)
igr = ODM.ItemGroupRef(ItemGroupOID="ODM.IG.VS_GENERAL",
Mandatory="Yes",
OrderNumber="2")
formdef.ItemGroupRef.append(igr)
igr = ODM.ItemGroupRef(ItemGroupOID="ODM.IG.VS",
Mandatory="Yes",
OrderNumber="3")
formdef.ItemGroupRef.append(igr)
formdef.Alias.append(ODM.Alias(Context="SDTMIG", Name="VS"))
fd_dict = formdef.to_dict()
print(fd_dict)
is_valid = self.validator.verify_conformance(fd_dict, "FormDef")
self.assertTrue(is_valid)
def test_add_description(self):
tt1 = ODM.TranslatedText(_content="Age at Screening Date (Screening Date - Birth date)", lang="en")
tt2 = ODM.TranslatedText(_content="For the complete algorithm see the referenced external document.", lang="fr")
self.methoddef.Description = ODM.Description()
self.methoddef.Description.TranslatedText = [tt1, tt2]
self.assertEqual(len(self.methoddef.Description.TranslatedText), 2)
self.assertEqual(self.methoddef.Description.TranslatedText[1]._content,
'For the complete algorithm see the referenced external document.')
def test_add_description(self):
tt1 = ODM.TranslatedText(
_content="Skip the BRTHMO field when BRTHYR length NE 4",
lang="en")
self.cond_def.Description = ODM.Description()
self.cond_def.Description.TranslatedText = [tt1]
self.assertEqual(len(self.cond_def.Description.TranslatedText), 1)
self.assertEqual(self.cond_def.Description.TranslatedText[0]._content,
'Skip the BRTHMO field when BRTHYR length NE 4')
def add_CD(self):
tt1 = ODM.TranslatedText(
_content="Skip the BRTHMO field when BRTHYR length NE 4",
lang="en")
desc = ODM.Description()
desc.TranslatedText = [tt1]
cd = ODM.ConditionDef(OID="ODM.CD.BRTHMO",
Name="Skip BRTHMO when no BRTHYR")
cd.Description = desc
return [cd]
def test_to_xml_description(self):
tt1 = ODM.TranslatedText(_content="this is the first test description",
lang="en")
tt2 = ODM.TranslatedText(
_content="this is the second test description", lang="en")
desc = ODM.Description()
desc.TranslatedText = [tt1, tt2]
desc_xml = desc.to_xml()
tts = desc_xml.findall("TranslatedText")
self.assertEqual(tts[0].text, "this is the first test description")
def test_append_item_group_ref(self):
fd = ODM.FormDef(OID="ODM.F.VS", Name="Vital Signs Form", Repeating="Yes")
fd.Description = ODM.Description()
fd.Description.TranslatedText.append(ODM.TranslatedText(_content="this is the first test description", lang="en"))
fd.ItemGroupRef.append(ODM.ItemGroupRef(ItemGroupOID="ODM.IG.COMMON", Mandatory="Yes", OrderNumber=1))
fd.ItemGroupRef.append(ODM.ItemGroupRef(ItemGroupOID="ODM.IG.VS_GENERAL", Mandatory="Yes", OrderNumber=2))
fd.ItemGroupRef.append(ODM.ItemGroupRef(ItemGroupOID="ODM.IG.VS", Mandatory="Yes", OrderNumber=3))
self.assertEqual(fd.ItemGroupRef[0].ItemGroupOID, "ODM.IG.COMMON")
self.assertEqual(fd.ItemGroupRef[2].OrderNumber, 3)
self.assertEqual(fd.Description.TranslatedText[0]._content, "this is the first test description")
def test_to_dict(self):
attrs = self.set_attributes()
method = ODM.MethodDef(**attrs)
desc = ODM.Description()
tt1 = ODM.TranslatedText(_content="Age at Screening Date (Screening Date - Birth date)", lang="en")
desc.TranslatedText = [tt1]
method.Description = desc
fex = ODM.FormalExpression(Context="Python 3.7", _content="print('hello world')")
method.FormalExpression = [fex]
method_dict = method.to_dict()
self.assertEqual(method_dict["OID"], "ODM.MT.AGE")
self.assertDictEqual(method_dict, self.expected_dict())
def add_MD(self):
tt1 = ODM.TranslatedText(
_content=
"Concatenation of BRTHYR, BRTHMO, and BRTHDY in ISO 8601 format",
lang="en")
desc = ODM.Description()
desc.TranslatedText = [tt1]
md = ODM.MethodDef(OID="ODM.MT.DOB",
Name="Create BRTHDTC from date ELEMENTS",
Type="Computation")
md.Description = desc
return [md]
def test_to_dict(self):
attrs = self.set_formdef_attributes()
fd = ODM.FormDef(**attrs)
fd.Description = ODM.Description()
fd.Description.TranslatedText.append(ODM.TranslatedText(_content="this is the first test description", lang="en"))
fd.ItemGroupRef.append(ODM.ItemGroupRef(ItemGroupOID="ODM.IG.COMMON", Mandatory="Yes", OrderNumber=1))
fd.ItemGroupRef.append(ODM.ItemGroupRef(ItemGroupOID="ODM.IG.VS_GENERAL", Mandatory="Yes", OrderNumber=2))
fd.ItemGroupRef.append(ODM.ItemGroupRef(ItemGroupOID="ODM.IG.VS", Mandatory="Yes", OrderNumber=3))
fd.Alias.append(ODM.Alias(Context="SDTMIG", Name="VS"))
fd_dict = fd.to_dict()
self.assertEqual(fd_dict["OID"], "ODM.F.VS")
self.assertDictEqual(fd_dict, self.expected_dict())
def test_to_dict_description(self):
tt1 = ODM.TranslatedText(_content="this is the first test description",
lang="en")
tt2 = ODM.TranslatedText(
_content="this is the second test description", lang="en")
desc = ODM.Description()
desc.TranslatedText = [tt1, tt2]
desc_dict = desc.to_dict()
print(desc_dict)
self.assertDictEqual(desc_dict["TranslatedText"][1], {
'_content': 'this is the second test description',
'lang': 'en'
})
def test_to_xml(self):
attrs = self.set_formdef_attributes()
fd = ODM.FormDef(**attrs)
fd.Description = ODM.Description()
fd.Description.TranslatedText.append(ODM.TranslatedText(_content="this is the first test description", lang="en"))
fd.ItemGroupRef.append(ODM.ItemGroupRef(ItemGroupOID="ODM.IG.COMMON", Mandatory="Yes", OrderNumber=1))
fd.ItemGroupRef.append(ODM.ItemGroupRef(ItemGroupOID="ODM.IG.VS_GENERAL", Mandatory="Yes", OrderNumber=2))
fd.ItemGroupRef.append(ODM.ItemGroupRef(ItemGroupOID="ODM.IG.VS", Mandatory="Yes", OrderNumber=3))
fd.Alias.append(ODM.Alias(Context="SDTMIG", Name="VS"))
fd_xml = fd.to_xml()
self.assertEqual(fd_xml.attrib["OID"], "ODM.F.VS")
igr = fd_xml.findall("ItemGroupRef")
self.assertEqual(len(igr), 3)
self.assertEqual(igr[0].attrib, {"ItemGroupOID": "ODM.IG.COMMON", "Mandatory": "Yes", "OrderNumber": "1"})
def test_itemgroupdef_iterator(self):
""" test the ability to reference a specific or slice of ItemRefs """
attrs = self.set_itemgroupdef_attributes()
igd = ODM.ItemGroupDef(**attrs)
tt = ODM.TranslatedText(_content="Vital Signs", lang="en")
igd.Description = ODM.Description()
igd.Description.TranslatedText = [tt]
item_refs = self.set_itemrefs()
igd.ItemRef = item_refs
parser = ODM_PARSER.ODMParser(self.odm_test_file)
parser.parse()
parser.MetaDataVersion()
irs = [ir.ItemOID for ir in igd]
self.assertEqual(len(irs), 13)
self.assertEqual(len(igd), 13)
def test_to_dict(self):
attrs = self.set_attributes()
cd = ODM.ConditionDef(**attrs)
cd.Description = ODM.Description()
cd.Description.TranslatedText = [
ODM.TranslatedText(
_content="Skip the BRTHMO field when BRTHYR length NE 4",
lang="en")
]
cd.FormalExpression = [
ODM.FormalExpression(Context="Python 3.7", _content="BRTHYR != 4")
]
cd_dict = cd.to_dict()
print(cd_dict)
self.assertEqual(cd_dict["OID"], "ODM.CD.BRTHMO")
self.assertDictEqual(cd_dict, self.expected_dict())
def test_ConditionDef(self):
attrs = {"OID": "ODM.CD.BRTHMO", "Name": "Skip BRTHMO when no BRTHYR"}
cd = ODM.ConditionDef(**attrs)
cd.Description = ODM.Description()
cd.Description.TranslatedText = [
ODM.TranslatedText(
_content="Skip the BRTHMO field when BRTHYR length NE 4",
lang="en")
]
cd.FormalExpression = [
ODM.FormalExpression(Context="Python 3.7", _content="BRTHYR != 4")
]
cd_dict = cd.to_dict()
print(cd_dict)
is_valid = self.validator.verify_conformance(cd_dict, "ConditionDef")
self.assertTrue(is_valid)
def test_itemgroupdef_slice(self):
""" test the ability to reference a specific or slice of ItemRefs """
attrs = self.set_itemgroupdef_attributes()
igd = ODM.ItemGroupDef(**attrs)
tt = ODM.TranslatedText(_content="Vital Signs", lang="en")
igd.Description = ODM.Description()
igd.Description.TranslatedText = [tt]
item_refs = self.set_itemrefs()
igd.ItemRef = item_refs
parser = ODM_PARSER.ODMParser(self.odm_test_file)
parser.parse()
parser.MetaDataVersion()
self.assertEqual(len(igd), 13)
self.assertEqual(igd.ItemRef[0].ItemOID, "IT.STUDYID")
slice_itr = igd.ItemRef[1:5]
self.assertEqual(slice_itr[1].ItemOID, "IT.VS.USUBJID")
def test_to_xml(self):
attrs = self.set_attributes()
cd = ODM.ConditionDef(**attrs)
cd.Description = ODM.Description()
cd.Description.TranslatedText = [
ODM.TranslatedText(
_content="Skip the BRTHMO field when BRTHYR length NE 4",
lang="en")
]
cd.FormalExpression = [
ODM.FormalExpression(Context="Python 3.7", _content="BRTHYR != 4")
]
cd_xml = cd.to_xml()
self.assertEqual(cd_xml.attrib["OID"], "ODM.CD.BRTHMO")
fex_xml = cd_xml.find("FormalExpression")
self.assertEqual(fex_xml.attrib["Context"], "Python 3.7")
def test_to_json(self):
attrs = self.set_itemgroupdef_attributes()
igd = ODM.ItemGroupDef(**attrs)
tt = ODM.TranslatedText(_content="this is the first test description",
lang="en")
igd.Description = ODM.Description()
igd.Description.TranslatedText = [tt]
ir1 = ODM.ItemRef(ItemOID="IT.STUDYID", Mandatory="Yes", OrderNumber=1)
ir2 = ODM.ItemRef(ItemOID="IT.VS.VSTEST",
Mandatory="No",
OrderNumber=2)
igd.ItemRef = [ir1, ir2]
igd_json = igd.to_json()
igd_dict = json.loads(igd_json)
print(igd_dict)
self.assertEqual(igd_dict["OID"], "IG.VS")
self.assertEqual(igd_dict["ItemRef"][1]["ItemOID"], "IT.VS.VSTEST")
def test_to_xml(self):
attrs = self.set_itemgroupdef_attributes()
igd = ODM.ItemGroupDef(**attrs)
tt = ODM.TranslatedText(_content="this is the first test description",
lang="en")
desc = ODM.Description()
desc.TranslatedText = [tt]
igd.Description = desc
ir1 = ODM.ItemRef(ItemOID="IT.STUDYID", Mandatory="Yes", OrderNumber=1)
ir2 = ODM.ItemRef(ItemOID="IT.VS.VSTEST",
Mandatory="No",
OrderNumber=2)
igd.ItemRef = [ir1, ir2]
igd_xml = igd.to_xml()
self.assertEqual(igd_xml.attrib["OID"], "IG.VS")
self.assertListEqual(["Description", "ItemRef", "ItemRef"],
[e.tag for e in igd_xml.getchildren()])
def add_protocol(self):
p = ODM.Protocol()
tt = ODM.TranslatedText(_content="Trace-XML Test CDASH File",
lang="en")
p.Description = ODM.Description()
p.Description.TranslatedText = [tt]
ser1 = ODM.StudyEventRef(StudyEventOID="BASELINE",
OrderNumber=1,
Mandatory="Yes")
ser2 = ODM.StudyEventRef(StudyEventOID="FOLLOW-UP",
OrderNumber=2,
Mandatory="Yes")
p.StudyEventRef = [ser1, ser2]
p.Alias = [
ODM.Alias(Context="ClinicalTrials.gov", Name="trace-protocol")
]
return p
def test_to_dict(self):
attrs = self.set_attributes()
sed = ODM.StudyEventDef(**attrs)
tt1 = ODM.TranslatedText(_content="this is the first test description",
lang="en")
desc = ODM.Description()
desc.TranslatedText = [tt1]
sed.Description = desc
fr1 = ODM.FormRef(FormOID="ODM.F.VS", Mandatory="Yes", OrderNumber=1)
fr2 = ODM.FormRef(FormOID="ODM.F.DM", Mandatory="Yes", OrderNumber=2)
fr3 = ODM.FormRef(FormOID="ODM.F.MH", Mandatory="Yes", OrderNumber=3)
sed.FormRef = [fr1, fr2, fr3]
a1 = ODM.Alias(Context="SDTMIG", Name="VS")
sed.Alias = [a1]
sed_dict = sed.to_dict()
self.assertEqual(sed_dict["OID"], "ODM.SE.BASELINE")
self.assertDictEqual(sed_dict, self.expected_dict())
def test_MethodDef(self):
attrs = {
"OID": "ODM.MT.AGE",
"Name": "Algorithm to derive AGE",
"Type": "Computation"
}
method = ODM.MethodDef(**attrs)
method.Description = ODM.Description()
method.Description.TranslatedText.append(
ODM.TranslatedText(
_content="Age at Screening Date (Screening Date - Birth date)",
lang="en"))
method.FormalExpression.append(
ODM.FormalExpression(Context="Python 3.7",
_content="print('hello world')"))
is_valid = self.validator.verify_conformance(method.to_dict(),
"MethodDef")
self.assertTrue(is_valid)
def test_studyeventdef_slice(self):
""" test the ability to reference a specific or slice of FormRefs """
attrs = self.set_attributes()
sed = ODM.StudyEventDef(**attrs)
tt1 = ODM.TranslatedText(_content="this is the first test description",
lang="en")
desc = ODM.Description()
desc.TranslatedText = [tt1]
sed.Description = desc
fr1 = ODM.FormRef(FormOID="ODM.F.VS", Mandatory="Yes", OrderNumber=1)
fr2 = ODM.FormRef(FormOID="ODM.F.DM", Mandatory="Yes", OrderNumber=2)
fr3 = ODM.FormRef(FormOID="ODM.F.MH", Mandatory="Yes", OrderNumber=3)
sed.FormRef = [fr1, fr2, fr3]
self.assertEqual(len(sed.FormRef), 3)
first_fr = sed[0]
self.assertEqual(first_fr.FormOID, "ODM.F.VS")
slice_fr = sed[1:3]
self.assertEqual(slice_fr[1].FormOID, "ODM.F.MH")
def test_itemgroupdef_round_trip(self):
""" system test to create and serialize an ItemGroupDef object """
attrs = self.set_itemgroupdef_attributes()
igd = ODM.ItemGroupDef(**attrs)
tt = ODM.TranslatedText(_content="Vital Signs", lang="en")
igd.Description = ODM.Description()
igd.Description.TranslatedText = [tt]
item_refs = self.set_itemrefs()
igd.ItemRef = item_refs
parser = ODM_PARSER.ODMParser(self.odm_test_file)
parser.parse()
mdv = parser.MetaDataVersion()
igd_list = parser.ItemGroupDef(parent=mdv[0])
igd_dict = igd_list[0]
self.assertEqual(igd_dict["OID"], "IG.VS")
ir_list = parser.ItemRef(parent=igd_dict["elem"])
# tests the __len__ in ItemGroupDef as well as the add_item_ref
self.assertEqual(len(ir_list), len(igd))
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 test_to_xml(self):
attrs = self.set_attributes()
sed = ODM.StudyEventDef(**attrs)
tt1 = ODM.TranslatedText(_content="this is the first test description",
lang="en")
desc = ODM.Description()
desc.TranslatedText = [tt1]
sed.Description = desc
fr1 = ODM.FormRef(FormOID="ODM.F.VS", Mandatory="Yes", OrderNumber=1)
fr2 = ODM.FormRef(FormOID="ODM.F.DM", Mandatory="Yes", OrderNumber=2)
fr3 = ODM.FormRef(FormOID="ODM.F.MH", Mandatory="Yes", OrderNumber=3)
sed.FormRef = [fr1, fr2, fr3]
a1 = ODM.Alias(Context="SDTMIG", Name="VS")
sed.Alias = [a1]
sed_xml = sed.to_xml()
self.assertEqual(sed_xml.attrib["OID"], "ODM.SE.BASELINE")
fr = sed_xml.findall("FormRef")
self.assertEqual(len(fr), 3)
self.assertEqual(fr[0].attrib, {
"FormOID": "ODM.F.VS",
"Mandatory": "Yes",
"OrderNumber": "1"
})
