def add_IGD_refdef(self):
itr1 = ODM.ItemRef(ItemOID="ODM.IT.VS.VSDAT", Mandatory="Yes")
itr2 = ODM.ItemRef(ItemOID="ODM.IT.VS.BP.DIABP.VSORRES_BAD",
Mandatory="Yes")
itr3 = ODM.ItemRef(ItemOID="ODM.IT.VS.BP.SYSBP.VSORRES",
Mandatory="Yes")
igd1 = ODM.ItemGroupDef(OID="ODM.IG.VS",
Name="Vital Sign Measurement",
Repeating="Yes")
igd1.ItemRef = [itr1, itr2, itr3]
igr4 = ODM.ItemRef(ItemOID="ODM.IT.DM.BRTHYR", Mandatory="Yes")
igr5 = ODM.ItemRef(ItemOID="ODM.IT.DM.SEX", Mandatory="Yes")
igd2 = ODM.ItemGroupDef(OID="ODM.IG.DM",
Name="Demographics",
Repeating="No")
igd2.ItemRef = [igr4, igr5]
igr6 = ODM.ItemRef(ItemOID="ODM.IT.Common.SubjectID", Mandatory="Yes")
igr7 = ODM.ItemRef(ItemOID="ODM.IT.Common.Visit", Mandatory="Yes")
igd3 = ODM.ItemGroupDef(OID="ODM.IG.Common",
Name="Common",
Repeating="No")
igd3.ItemRef = [igr6, igr7]
igr8 = ODM.ItemRef(ItemOID="ODM.IT.AE.AETERM", Mandatory="Yes")
igr9 = ODM.ItemRef(ItemOID="ODM.IT.AE.AESEV", Mandatory="Yes")
igd4 = ODM.ItemGroupDef(OID="ODM.IG.AE",
Name="Adverse Events",
Repeating="Yes")
igd4.ItemRef = [igr8, igr9]
return [igd1, igd2, igd3, igd4]
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 add_IGD(self):
itr1 = ODM.ItemRef(ItemOID="ODM.IT.VS.VSDAT", Mandatory="Yes")
itr2 = ODM.ItemRef(ItemOID="ODM.IT.VS.BP.DIABP.VSORRES",
Mandatory="Yes")
itr3 = ODM.ItemRef(ItemOID="ODM.IT.VS.BP.SYSBP.VSORRES",
Mandatory="Yes")
igd1 = ODM.ItemGroupDef(OID="ODM.IG.VS",
Name="Vital Sign Measurement",
Repeating="Yes")
igd1.ItemRef = [itr1, itr2, itr3]
igr4 = ODM.ItemRef(ItemOID="ODM.IT.DM.BRTHYR", Mandatory="Yes")
igr5 = ODM.ItemRef(ItemOID="ODM.IT.DM.SEX", Mandatory="Yes")
igd2 = ODM.ItemGroupDef(OID="ODM.IG.DM",
Name="Demographics",
Repeating="No")
igd2.ItemRef = [igr4, igr5]
return [igd1, igd2]
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_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_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 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_item_group_valid_kwargs_only(self):
igd = ODM.ItemGroupDef(OID="IG.VS", Name="VS", Repeating="Yes")
self.assertEqual(igd.OID, "IG.VS")
def setUp(self) -> None:
attrs = self.set_itemgroupdef_attributes()
self.igd = ODM.ItemGroupDef(**attrs)
self.odm_test_file = os.path.join(
os.path.dirname(os.path.realpath(__file__)), 'data',
'test_igd_001.xml')
def test_get_missing_attribute(self):
igd = ODM.ItemGroupDef(OID="IG.VS",
Name="Vital Signs",
Repeating="Yes")
self.assertEqual(igd.OID, "IG.VS")
self.assertIsNone(igd.Comment)
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")