def test_add_form_ref(self): 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) self.sed.FormRef = [fr1, fr2, fr3] self.assertEqual(self.sed.FormRef[0].FormOID, "ODM.F.VS") self.assertEqual(self.sed.FormRef[2].OrderNumber, 3)
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 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 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_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 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")