def test_add_range_check(self):
rc = ODM.RangeCheck(Comparator="EQ", SoftHard="Soft")
tt1 = ODM.TranslatedText(_content="invalid test code", lang="en")
tt2 = ODM.TranslatedText(_content="code de test invalide", lang="fr")
rc.CheckValue = [ODM.CheckValue(_content="DIABP")]
rc.FormalExpression = [
ODM.FormalExpression(Context="Python 3.7",
_content="print('hello world')")
]
rc.MeasurementUnitRef = ODM.MeasurementUnitRef(
MeasurementUnitOID="ODM.MU.UNITS")
attrs = {"Comparator": "GT", "SoftHard": "Soft"}
rc1 = ODM.RangeCheck(**attrs)
tt1 = ODM.TranslatedText(_content="invalid test code", lang="en")
rc1.ErrorMessage.TranslatedText = [tt1]
rc1.CheckValue = [ODM.CheckValue(_content="SYSBP")]
rc1.FormalExpression = [
ODM.FormalExpression(Context="Python 3.7",
_content="print('hello world')")
]
rc1.MeasurementUnitRef = ODM.MeasurementUnitRef(
MeasurementUnitOID="ODM.MU.UNITS")
self.item.RangeCheck = [rc, rc1]
self.assertEqual(self.item.RangeCheck[0].Comparator, "EQ")
self.assertEqual(self.item.RangeCheck[1].Comparator, "GT")
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_ItemDef(self):
attrs = {
"OID": "ODM.IT.AE.AEYN",
"Name": "Any AEs?",
"DataType": "text",
"Length": "1",
"SASFieldName": "AEYN",
"SDSVarName": "AEYN",
"Origin": "CRF",
"Comment": "Data management field"
}
item = ODM.ItemDef(**attrs)
item.Description.TranslatedText = [
ODM.TranslatedText(_content="this is the first test description",
lang="en")
]
item.Question.TranslatedText = [
ODM.TranslatedText(_content="Any AEs?", lang="en")
]
item.CodeListRef = ODM.CodeListRef(
CodeListOID="CL.NY_SUB_Y_N_2011-10-24")
item_dict = item.to_dict()
print(item_dict)
is_valid = self.validator.verify_conformance(item_dict, "ItemDef")
self.assertTrue(is_valid)
def test_to_xml(self):
attrs = self.set_item_attributes()
item = ODM.ItemDef(**attrs)
item.Description.TranslatedText = [
ODM.TranslatedText(_content="this is the first test description",
lang="en")
]
item.Question.TranslatedText = [
ODM.TranslatedText(_content="Any AEs?", lang="en")
]
item.ExternalQuestion = ODM.ExternalQuestion(Dictionary="SF36",
Version="12",
Code="Walks 1-mile")
item.CodeListRef = ODM.CodeListRef(
CodeListOID="CL.NY_SUB_Y_N_2011-10-24")
item.RangeCheck = [ODM.RangeCheck(Comparator="EQ", SoftHard="Soft")]
item.RangeCheck[0].CheckValue = [ODM.CheckValue(_content="DIABP")]
item.RangeCheck[0].FormalExpression = [
ODM.FormalExpression(Context="Python 3.7",
_content="print('hello world')")
]
item.RangeCheck[0].MeasurementUnitRef = ODM.MeasurementUnitRef(
MeasurementUnitOID="ODM.MU.UNITS")
item.RangeCheck[0].ErrorMessage.TranslatedText = [
ODM.TranslatedText(_content="invalid test code", lang="en")
]
item_xml = item.to_xml()
self.assertEqual(item_xml.attrib["OID"], "ODM.IT.AE.AEYN")
cv = item_xml.find("*/CheckValue")
self.assertEqual(cv.text, "DIABP")
dt = item_xml.findall("Description/TranslatedText")
self.assertEqual(len(dt), 1)
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 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 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_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_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_json(self):
attrs = self.set_item_attributes()
item = ODM.ItemDef(**attrs)
item.Description.TranslatedText.append(
ODM.TranslatedText(_content="this is the first test description",
lang="en"))
item.Question.TranslatedText = [
ODM.TranslatedText(_content="Any AEs?", lang="en")
]
item.CodeListRef = ODM.CodeListRef(
CodeListOID="CL.NY_SUB_Y_N_2011-10-24")
item_json = item.to_json()
item_dict = json.loads(item_json)
self.assertEqual(item_dict["OID"], "ODM.IT.AE.AEYN")
def test_add_description(self):
attrs = {
"_content": "this is the first test description",
"lang": "en"
}
tt1 = ODM.TranslatedText(**attrs)
attrs = {
"_content": "this is the second test description",
"lang": "en"
}
tt2 = ODM.TranslatedText(**attrs)
self.item.Description.TranslatedText.append(tt1)
self.item.Description.TranslatedText.append(tt2)
self.assertEqual(self.item.Description.TranslatedText[1]._content,
"this is the second test description")
def add_CL(self):
tt1 = ODM.TranslatedText(_content="No", lang="en")
dc1 = ODM.Decode()
dc1.TranslatedText = [tt1]
cli1 = ODM.CodeListItem(CodedValue="N")
cli1.Decode = dc1
tt2 = ODM.TranslatedText(_content="Yes", lang="en")
dc2 = ODM.Decode()
dc2.TranslatedText = [tt2]
cli2 = ODM.CodeListItem(CodedValue="Y")
cli2.Decode = dc2
cl = ODM.CodeList(OID="ODM.CL.NY_SUB_Y_N",
Name="No Yes Response",
DataType="text")
cl.CodeListItem = [cli1, cli2]
return [cl]
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_RangeCheck(self):
rc = ODM.RangeCheck(Comparator="EQ", SoftHard="Soft")
tt1 = ODM.TranslatedText(_content="invalid test code", lang="en")
tt2 = ODM.TranslatedText(_content="code de test invalide", lang="fr")
rc.ErrorMessage.TranslatedText = [tt1, tt2]
rc.CheckValue = [ODM.CheckValue(_content="DIABP")]
rc.FormalExpression = [
ODM.FormalExpression(Context="Python 3.7",
_content="print('hello world')")
]
rc.MeasurementUnitRef = ODM.MeasurementUnitRef(
MeasurementUnitOID="ODM.MU.UNITS")
rc_dict = rc.to_dict()
print(rc_dict)
is_valid = self.validator.verify_conformance(rc_dict, "RangeCheck")
self.assertTrue(is_valid)
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_set_invalid_description(self):
rc = ODM.RangeCheck(Comparator="EQ", SoftHard="Soft")
tt1 = ODM.TranslatedText(_content="invalid test code", lang="en")
tt2 = ODM.TranslatedText(_content="code de test invalide", lang="fr")
rc.ErrorMessage.TranslatedText.append(tt1)
rc.ErrorMessage.TranslatedText.append(tt2)
rc.CheckValue = [ODM.CheckValue(_content="DIABP")]
rc.FormalExpression = [
ODM.FormalExpression(Context="Python 3.7",
_content="print('hello world')")
]
rc.MeasurementUnitRef = [
ODM.MeasurementUnitRef(MeasurementUnitOID="ODM.MU.UNITS")
]
self.item.RangeCheck = [rc]
# Description requires a Description object, not a RangeCheck object
with self.assertRaises(TypeError):
self.item.Description = rc
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 test_no_description(self):
tt = ODM.TranslatedText(lang="en", _content="hello, world")
validator = METADATA.MetadataSchema()
results = tt.verify_conformance(validator)
self.methoddef.FormalExpression = [ODM.FormalExpression(Context="Python 3.7", _content="print('hello world')")]
self.assertEqual(self.methoddef.FormalExpression[0]._content, "print('hello world')")
with self.assertRaises(ValueError):
results = self.methoddef.verify_conformance(validator)
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_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_CodeListItem(self):
cli = ODM.CodeListItem(CodedValue="HGB", OrderNumber="1")
tt1 = ODM.TranslatedText(_content="Hemoglobin", lang="en")
decode = ODM.Decode()
decode.TranslatedText.append(tt1)
cli.Decode = decode
cli.Alias.append(ODM.Alias(Context="nci:ExtCodeID", Name="C64848"))
cli_dict = cli.to_dict()
print(cli_dict)
is_valid = self.validator.verify_conformance(cli_dict, "CodeListItem")
self.assertTrue(is_valid)
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(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_item_attributes()
item = ODM.ItemDef(**attrs)
item.Description.TranslatedText = [
ODM.TranslatedText(_content="this is the first test description",
lang="en")
]
item.Question.TranslatedText = [
ODM.TranslatedText(_content="Any AEs?", lang="en")
]
item.CodeListRef = ODM.CodeListRef(
CodeListOID="CL.NY_SUB_Y_N_2011-10-24")
item_dict = item.to_dict()
expected_dict = {
'OID': 'ODM.IT.AE.AEYN',
'Name': 'Any AEs?',
'DataType': 'text',
'Length': 1,
'SASFieldName': 'AEYN',
'SDSVarName': 'AEYN',
'Origin': 'CRF',
'Comment': 'Data management field',
'Description': {
'TranslatedText': [{
'_content': 'this is the first test description',
'lang': 'en'
}]
},
'Question': {
'TranslatedText': [{
'_content': 'Any AEs?',
'lang': 'en'
}]
},
'CodeListRef': {
'CodeListOID': 'CL.NY_SUB_Y_N_2011-10-24'
}
}
self.assertDictEqual(item_dict, expected_dict)
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_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")