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_item_group_ref(self):
igr = ODM.ItemGroupRef(ItemGroupOID="ODM.IG.COMMON", Mandatory="Yes", OrderNumber=1)
self.formdef.ItemGroupRef.append(igr)
igr = ODM.ItemGroupRef(ItemGroupOID="ODM.IG.VS_GENERAL", Mandatory="Yes", OrderNumber=2)
self.formdef.ItemGroupRef.append(igr)
igr = ODM.ItemGroupRef(ItemGroupOID="ODM.IG.VS", Mandatory="Yes", OrderNumber=3)
self.formdef.ItemGroupRef.append(igr)
self.assertEqual(self.formdef.ItemGroupRef[0].ItemGroupOID, "ODM.IG.COMMON")
self.assertEqual(self.formdef.ItemGroupRef[2].OrderNumber, 3)
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_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_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 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_FD(self):
igr1 = ODM.ItemGroupRef(ItemGroupOID="ODM.IG.Common",
Mandatory="Yes",
OrderNumber=1)
igr2 = ODM.ItemGroupRef(ItemGroupOID="ODM.IG.VS_GENERAL",
Mandatory="Yes",
OrderNumber=2)
igr3 = ODM.ItemGroupRef(ItemGroupOID="ODM.IG.VS",
Mandatory="Yes",
OrderNumber=3)
fd1 = ODM.FormDef(OID="ODM.F.VS", Name="Vital Signs", Repeating="No")
fd1.ItemGroupRef = [igr1, igr2, igr3]
igr4 = ODM.ItemGroupRef(ItemGroupOID="ODM.IG.Common",
Mandatory="Yes",
OrderNumber=1)
igr5 = ODM.ItemGroupRef(ItemGroupOID="ODM.IG.DM",
Mandatory="Yes",
OrderNumber=2)
fd2 = ODM.FormDef(OID="ODM.F.DM", Name="Demographics", Repeating="No")
fd2.ItemGroupRef = [igr4, igr5]
return [fd1, fd2]
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")