def add_SED(self):
fr1 = ODM.FormRef(FormOID="ODM.F.DM", Mandatory="Yes", OrderNumber=1)
fr2 = ODM.FormRef(FormOID="ODM.F.VS", Mandatory="Yes", OrderNumber=2)
fr3 = ODM.FormRef(FormOID="ODM.F.AE", Mandatory="Yes", OrderNumber=3)
ser1 = ODM.StudyEventDef(OID="BASELINE",
Name="Baseline Visit",
Repeating="No",
Type="Scheduled")
ser1.FormRef = [fr1, fr2, fr3]
ser2 = ODM.StudyEventDef(OID="FOLLOW-UP",
Name="Follow-up Visit",
Repeating="Yes",
Type="Scheduled")
ser2.FormRef = [fr1, fr2, fr3]
return [ser1, ser2]
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_dict(self):
attrs = self.set_attributes()
sed = ODM.StudyEventDef(**attrs)
tt1 = ODM.TranslatedText(_content="this is the first test description",
lang="en")
desc = ODM.Description()
desc.TranslatedText = [tt1]
sed.Description = desc
fr1 = ODM.FormRef(FormOID="ODM.F.VS", Mandatory="Yes", OrderNumber=1)
fr2 = ODM.FormRef(FormOID="ODM.F.DM", Mandatory="Yes", OrderNumber=2)
fr3 = ODM.FormRef(FormOID="ODM.F.MH", Mandatory="Yes", OrderNumber=3)
sed.FormRef = [fr1, fr2, fr3]
a1 = ODM.Alias(Context="SDTMIG", Name="VS")
sed.Alias = [a1]
sed_dict = sed.to_dict()
self.assertEqual(sed_dict["OID"], "ODM.SE.BASELINE")
self.assertDictEqual(sed_dict, self.expected_dict())
def test_studyeventdef_slice(self):
""" test the ability to reference a specific or slice of FormRefs """
attrs = self.set_attributes()
sed = ODM.StudyEventDef(**attrs)
tt1 = ODM.TranslatedText(_content="this is the first test description",
lang="en")
desc = ODM.Description()
desc.TranslatedText = [tt1]
sed.Description = desc
fr1 = ODM.FormRef(FormOID="ODM.F.VS", Mandatory="Yes", OrderNumber=1)
fr2 = ODM.FormRef(FormOID="ODM.F.DM", Mandatory="Yes", OrderNumber=2)
fr3 = ODM.FormRef(FormOID="ODM.F.MH", Mandatory="Yes", OrderNumber=3)
sed.FormRef = [fr1, fr2, fr3]
self.assertEqual(len(sed.FormRef), 3)
first_fr = sed[0]
self.assertEqual(first_fr.FormOID, "ODM.F.VS")
slice_fr = sed[1:3]
self.assertEqual(slice_fr[1].FormOID, "ODM.F.MH")
def test_to_xml(self):
attrs = self.set_attributes()
sed = ODM.StudyEventDef(**attrs)
tt1 = ODM.TranslatedText(_content="this is the first test description",
lang="en")
desc = ODM.Description()
desc.TranslatedText = [tt1]
sed.Description = desc
fr1 = ODM.FormRef(FormOID="ODM.F.VS", Mandatory="Yes", OrderNumber=1)
fr2 = ODM.FormRef(FormOID="ODM.F.DM", Mandatory="Yes", OrderNumber=2)
fr3 = ODM.FormRef(FormOID="ODM.F.MH", Mandatory="Yes", OrderNumber=3)
sed.FormRef = [fr1, fr2, fr3]
a1 = ODM.Alias(Context="SDTMIG", Name="VS")
sed.Alias = [a1]
sed_xml = sed.to_xml()
self.assertEqual(sed_xml.attrib["OID"], "ODM.SE.BASELINE")
fr = sed_xml.findall("FormRef")
self.assertEqual(len(fr), 3)
self.assertEqual(fr[0].attrib, {
"FormOID": "ODM.F.VS",
"Mandatory": "Yes",
"OrderNumber": "1"
})
def test_StudEventDef(self):
attrs = {
"OID": "ODM.SE.BASELINE",
"Name": "Baseline Visit",
"Repeating": "No",
"Type": "Scheduled",
"Category": "Pre-treatment"
}
sed = ODM.StudyEventDef(**attrs)
tt1 = ODM.TranslatedText(_content="this is the first test description",
lang="en")
sed.Description = ODM.Description()
sed.Description.TranslatedText = [tt1]
fr1 = ODM.FormRef(FormOID="ODM.F.VS", Mandatory="Yes", OrderNumber="1")
fr2 = ODM.FormRef(FormOID="ODM.F.DM", Mandatory="Yes", OrderNumber="2")
fr3 = ODM.FormRef(FormOID="ODM.F.MH", Mandatory="Yes", OrderNumber="3")
sed.FormRef = [fr1, fr2, fr3]
a1 = ODM.Alias(Context="SDTMIG", Name="VS")
a2 = ODM.Alias(Context="CDASHIG", Name="VS")
sed.Alias = [a1, a2]
sed_dict = sed.to_dict()
print(sed_dict)
is_valid = self.validator.verify_conformance(sed_dict, "StudyEventDef")
self.assertTrue(is_valid)
def setUp(self) -> None:
attrs = self.set_attributes()
self.sed = ODM.StudyEventDef(**attrs)
def test_add_bad_attribute(self):
attrs = self.set_attributes()
attrs["Type"] = "Rescheduled"
with self.assertRaises(ValueError):
self.sed = ODM.StudyEventDef(**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")
