def test_datetime_type(self):
attrs = {
"FileOID": "ODM.MDV.TEST.001",
"Granularity": "Metadata",
"AsOfDateTime": "2020-07-13T00:13:51.309617+00:00",
"CreationDateTime": "2020-07-13T00:13:51.309617+00:00",
"ODMVersion": "1.3.2",
"FileType": "Snapshot",
"Originator": "RDS",
"SourceSystem": "ODMLib"
}
odm = ODM.ODM(**attrs)
self.assertEqual(odm.AsOfDateTime, "2020-07-13T00:13:51.309617+00:00")
# derived current datetime in ISO formate from datetime library
attrs["AsOfDateTime"] = self.set_datetime()
odm = ODM.ODM(**attrs)
self.assertIsInstance(odm, ODM.ODM)
# date only
attrs["AsOfDateTime"] = "2020-07-13"
with self.assertRaises(ValueError):
odm = ODM.ODM(**attrs)
# basic time
attrs["AsOfDateTime"] = "2020-07-13T00:13:51"
odm = ODM.ODM(**attrs)
self.assertEqual(odm.AsOfDateTime, "2020-07-13T00:13:51")
# out of range time
attrs["AsOfDateTime"] = "2020-07-13T00:13:61"
with self.assertRaises(ValueError):
odm = ODM.ODM(**attrs)
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 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 create_root(self):
"""
create the ODM root element object with test data
:return: ODM root element object
"""
root = {
"FileOID": "ODM.TEST.CD.001",
"Granularity": "Metadata",
"AsOfDateTime": self.set_datetime(),
"CreationDateTime": self.set_datetime(),
"ODMVersion": "1.3.2",
"Originator": "ODMLIB",
"SourceSystem": "ODMLIB",
"SourceSystemVersion": "0.1",
"FileType": "Snapshot"
}
root = ODM.ODM(**root)
return root
def add_root(self):
attrs = self.get_root_attributes()
root = ODM.ODM(**attrs)
return root
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")