def test_positive_type(self):
# testing Length as a positive integer
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)
self.assertEqual(item.Length, 1)
# testing Length = 0 as a positive integer
attrs["Length"] = 0
with self.assertRaises(TypeError):
item = ODM.ItemDef(**attrs)
# testing Length = -1 as a positive integer
attrs["Length"] = -1
with self.assertRaises(TypeError):
item = ODM.ItemDef(**attrs)
# testing Length = float as a positive integer
attrs["Length"] = 1.0
with self.assertRaises(TypeError):
item = ODM.ItemDef(**attrs)
def test_non_negative_type(self):
# testing SignificantDigits as a non-negative integer
attrs = {
"OID": "ODM.IT.AE.AEYN",
"Name": "Any AEs?",
"DataType": "text",
"Length": 1,
"SASFieldName": "AEYN",
"SDSVarName": "AEYN",
"Origin": "CRF",
"Comment": "Data management field",
"SignificantDigits": 1
}
item = ODM.ItemDef(**attrs)
self.assertEqual(item.SignificantDigits, 1)
# testing SignificantDigits = 0 as a non-negative integer
attrs["SignificantDigits"] = 0
item = ODM.ItemDef(**attrs)
self.assertEqual(item.SignificantDigits, 0)
# testing SignificantDigits = -1 as a non-negative integer
attrs["SignificantDigits"] = -1
with self.assertRaises(TypeError):
item = ODM.ItemDef(**attrs)
# testing SignificantDigits = float as a non-negative integer
attrs["SignificantDigits"] = 1.0
with self.assertRaises(TypeError):
item = ODM.ItemDef(**attrs)
def test_sasname_type(self):
# valid test
attrs = {
"OID": "ODM.IT.AE.AEYN",
"Name": "Any AEs?",
"DataType": "text",
"Length": 1,
"SASFieldName": "AEYN",
"SDSVarName": "AEYN",
"Origin": "CRF",
"Comment": "Data management field",
"SignificantDigits": 1
}
item = ODM.ItemDef(**attrs)
self.assertEqual(item.SASFieldName, "AEYN")
# start with an underscore
attrs["SASFieldName"] = "_AETERM"
item = ODM.ItemDef(**attrs)
self.assertEqual(item.SASFieldName, "_AETERM")
# start with a number
attrs["SASFieldName"] = "9AETERM"
with self.assertRaises(ValueError):
item = ODM.ItemDef(**attrs)
# end with a symbol
attrs["SASFieldName"] = "AETERM%"
with self.assertRaises(ValueError):
item = ODM.ItemDef(**attrs)
# test with none - does not throw an error when value is None
attrs["SASFieldName"] = None
item = ODM.ItemDef(**attrs)
self.assertIsNone(item.SASFieldName)
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_not_alias(self):
item = ODM.ItemDef(OID="ODM.IT.VSPOS", Name="VS Position", DataType="text")
with self.assertRaises(TypeError):
self.formdef.Alias = [item]
self.formdef.Alias.append(ODM.Alias(Context="SDTMIG", Name="VS"))
# list accepts invalid objects
self.formdef.Alias.append(ODM.ItemDef(OID="ODM.IT.VSDT", Name="VS Date", DataType="text"))
self.assertEqual(len(self.formdef.Alias), 2)
self.assertEqual(self.formdef.Alias[0].Context, "SDTMIG")
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_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 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 test_required_attributes_only(self):
attrs = {
"OID": "ODM.IT.AE.AEYN",
"Name": "Any AEs?",
"DataType": "text"
}
self.item = ODM.ItemDef(**attrs)
self.assertEqual(self.item.OID, "ODM.IT.AE.AEYN")
def test_invalid_attribute_data_type(self):
attrs = {
"OID": "ODM.IT.AE.AEYN",
"Name": "Any AEs?",
"DataType": "text",
"SignificantDigits": "A"
}
with self.assertRaises(TypeError):
self.item = ODM.ItemDef(**attrs)
def test_codelist_ref_exists_check(self):
attrs = self.set_item_attributes()
item = ODM.ItemDef(**attrs)
codelistref_check_succeeds = False
if not item.CodeListRef:
codelistref_check_succeeds = True
if item.CodeListRef:
codelistref_check_succeeds = False
self.assertTrue(codelistref_check_succeeds)
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_string_type(self):
attrs = {
"OID": "ODM.IT.AE.AEYN",
"Name": "Any AEs?",
"DataType": "text",
"Length": 1,
"SASFieldName": "AEYN",
"SDSVarName": "AEYN",
"Origin": "CRF",
"Comment": "Data management field",
"SignificantDigits": 1
}
item = ODM.ItemDef(**attrs)
self.assertEqual(item.Origin, "CRF")
# integer
attrs["Origin"] = 1
with self.assertRaises(TypeError):
item = ODM.ItemDef(**attrs)
attrs["Origin"] = None
item = ODM.ItemDef(**attrs)
self.assertIsNone(item.Origin)
def test_get_missing_undefined_attribute(self):
itd = ODM.ItemDef(OID="IT.VS.VSORRES",
Name="Vital Signs Results",
DataType="text")
self.assertEqual(itd.OID, "IT.VS.VSORRES")
self.assertListEqual(itd.MeasurementUnitRef, [])
result = itd.CodeListRef
self.assertIsNone(result)
itd.Alias.append(itd.CodeListRef)
self.assertListEqual(itd.Alias, [None])
with self.assertRaises(TypeError):
itd.new_thing = "hello"
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_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_get_missing_element_with_required(self):
itd = ODM.ItemDef(OID="IT.VS.VSORRES",
Name="Vital Signs Results",
DataType="text")
self.assertEqual(itd.OID, "IT.VS.VSORRES")
self.assertIsNone(itd.CodeListRef)
def test_add_undefined_content(self):
# use conformance rules to check for unknown objects being added after creation
attrs = {
"OID": "ODM.IT.AE.AEYN",
"Name": "Any AEs?",
"DataType": "text",
"Length": 1,
"SASFieldName": "AEYN",
"SDSVarName": "AEYN",
"Origin": "CRF",
"Comment": "Data management field",
"SignificantDigits": 1
}
item = ODM.ItemDef(**attrs)
clr = ODM.CodeListRef(CodeListOID="CL.TEST")
with self.assertRaises(TypeError):
item.NewCodeList = clr
# cannot add unknown attributes or elements during creation, but can afterwards; catch with conformance checks
attrs = {
"OID": "ODM.IT.AE.AEYN",
"Name": "Any AEs?",
"DataType": "text",
"Length": 1,
"SASFieldName": "AEYN",
"SDSVarName": "AEYN",
"Origin": "CRF",
"Comment": "Data management field",
"SignificantDigits": 1
}
item = ODM.ItemDef(**attrs)
with self.assertRaises(TypeError):
item.InSignificantDigits = 1
# can add all objects during creation and they are validated
attrs = {
"OID": "ODM.IT.AE.AEYN",
"Name": "Any AEs?",
"DataType": "text",
"Length": 1,
"SASFieldName": "AEYN",
"SDSVarName": "AEYN",
"Origin": "CRF",
"Comment": "Data management field",
"CodeListRef": clr
}
item = ODM.ItemDef(**attrs)
self.assertEqual(item.CodeListRef, clr)
attrs["CodeListReference"] = clr
with self.assertRaises(TypeError):
# test shows that ItemDef fails the schema check because it has an unknown CodeListReference object
item = ODM.ItemDef(**attrs)
self.assertEqual(item.CodeListRef, clr)
# test adding the wrong type of object to a list
attrs = {
"OID": "ODM.IT.AE.AEYN",
"Name": "Any AEs?",
"DataType": "text",
"Length": 1,
"SASFieldName": "AEYN",
"SDSVarName": "AEYN",
"Origin": "CRF",
"Comment": "Data management field",
"Alias": [clr]
}
with self.assertRaises(TypeError):
item = ODM.ItemDef(**attrs)
# test adding the wrong type of object to a list
alias = ODM.Alias(Context="CDASH", Name="AEYN")
attrs = {
"OID": "ODM.IT.AE.AEYN",
"Name": "Any AEs?",
"DataType": "text",
"Length": 1,
"SASFieldName": "AEYN",
"SDSVarName": "AEYN",
"Origin": "CRF",
"Comment": "Data management field",
"Alias": alias
}
with self.assertRaises(TypeError):
item = ODM.ItemDef(**attrs)
# assign wrong type of object to an element
attrs = {
"OID": "ODM.IT.AE.AEYN",
"Name": "Any AEs?",
"DataType": "text",
"Length": 1,
"SASFieldName": "AEYN",
"SDSVarName": "AEYN",
"Origin": "CRF",
"Comment": "Data management field",
"CodeListRef": alias
}
with self.assertRaises(TypeError):
item = ODM.ItemDef(**attrs)
def add_ITD_nonunique(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]
# ItemDef 3
ttd3 = ODM.TranslatedText(_content="Adverse Event Term", lang="en")
ttq3 = ODM.TranslatedText(_content="AE Term", lang="en")
desc3 = ODM.Description()
desc3.TranslatedText = [ttd3]
q3 = ODM.Question()
q3.TranslatedText = [ttq3]
itd3 = ODM.ItemDef(OID="ODM.IT.AE.AETERM",
Name="AE Term",
DataType="text")
itd3.Description = desc3
itd3.Question = q3
# ItemDef 4
ttd4 = ODM.TranslatedText(_content="Adverse Event Severity", lang="en")
ttq4 = ODM.TranslatedText(_content="AE Severity", lang="en")
desc4 = ODM.Description()
desc4.TranslatedText = [ttd4]
q4 = ODM.Question()
q4.TranslatedText = [ttq4]
itd4 = ODM.ItemDef(OID="ODM.IT.AE.AESEV",
Name="AE Severity",
DataType="text")
itd4.Description = desc4
itd4.Question = q4
# ItemDef 5
ttd5 = ODM.TranslatedText(_content="Subject ID", lang="en")
ttq5 = ODM.TranslatedText(_content="Subject ID", lang="en")
desc5 = ODM.Description()
desc5.TranslatedText = [ttd5]
q5 = ODM.Question()
q5.TranslatedText = [ttq5]
itd5 = ODM.ItemDef(OID="ODM.IT.Common.SubjectID",
Name="Subject ID",
DataType="text")
itd5.Description = desc5
itd5.Question = q5
# ItemDef 6
ttd6 = ODM.TranslatedText(_content="Diastolic Blood Pressure Result",
lang="en")
ttq6 = ODM.TranslatedText(_content="Diastolic BP", lang="en")
desc6 = ODM.Description()
desc6.TranslatedText = [ttd6]
q6 = ODM.Question()
q6.TranslatedText = [ttq6]
itd6 = ODM.ItemDef(OID="ODM.IT.VS.BP.SYSBP.VSORRES",
Name="DBP Result",
DataType="text")
itd6.Description = desc6
itd6.Question = q6
# ItemDef 7
ttd7 = ODM.TranslatedText(_content="Birth Year", lang="en")
ttq7 = ODM.TranslatedText(_content="DOB Year", lang="en")
desc7 = ODM.Description()
desc7.TranslatedText = [ttd7]
q7 = ODM.Question()
q7.TranslatedText = [ttq7]
itd7 = ODM.ItemDef(OID="ODM.IT.DM.BRTHYR",
Name="Birth Year",
DataType="text")
itd7.Description = desc7
itd7.Question = q7
# ItemDef 8
ttd8 = ODM.TranslatedText(_content="Visit", lang="en")
ttq8 = ODM.TranslatedText(_content="Visit", lang="en")
desc8 = ODM.Description()
desc8.TranslatedText = [ttd8]
q8 = ODM.Question()
q8.TranslatedText = [ttq8]
itd8 = ODM.ItemDef(OID="ODM.IT.Common.Visit",
Name="Visit",
DataType="text")
itd8.Description = desc8
itd8.Question = q8
# ItemDef 9
ttd9 = ODM.TranslatedText(_content="Sex", lang="en")
ttq9 = ODM.TranslatedText(_content="Sex", lang="en")
desc9 = ODM.Description()
desc9.TranslatedText = [ttd9]
q9 = ODM.Question()
q9.TranslatedText = [ttq9]
itd9 = ODM.ItemDef(OID="ODM.IT.DM.SEX", Name="Sex", DataType="text")
itd9.Description = desc9
itd9.Question = q9
# ItemDef 10
ttd10 = ODM.TranslatedText(_content="Systolic Blood Pressure Result",
lang="en")
ttq10 = ODM.TranslatedText(_content="Systolic BP", lang="en")
desc10 = ODM.Description()
desc10.TranslatedText = [ttd10]
q10 = ODM.Question()
q10.TranslatedText = [ttq10]
itd10 = ODM.ItemDef(OID="ODM.IT.VS.BP.SYSBP.VSORRES",
Name="Systolic BP Result",
DataType="text")
itd10.Description = desc10
itd10.Question = q10
return [itd1, itd2, itd3, itd4, itd5, itd6, itd7, itd8, itd9, itd10]
def setUp(self) -> None:
attrs = self.set_item_attributes()
self.item = ODM.ItemDef(**attrs)
def test_missing_itemdef_attributes(self):
attrs = {"OID": "ODM.IT.AE.AEYN", "Name": "Any AEs?"}
with self.assertRaises(ValueError):
ODM.ItemDef(**attrs)
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")
