def setUp(self) -> None:
self.odm_file_1 = os.path.join(
os.path.dirname(os.path.realpath(__file__)), 'data',
'cdash-odm-test.xml')
self.parser = P.ODMParser(self.odm_file_1)
self.root = self.parser.parse()
self.mdv = self.parser.MetaDataVersion()
def test_clinical_data_from_xml(self):
parser = ODM_PARSER.ODMParser(self.odm_test_file)
parser.parse()
rd = parser.ReferenceData()
igd_list = parser.ItemGroupData(parent=rd[0])
item_data = parser.ItemData(parent=igd_list[1]["elem"])
self.assertEqual(item_data[0]["Value"], "2")
def test_clinical_data_from_xml(self):
parser = ODM_PARSER.ODMParser(self.odm_test_file)
parser.parse()
cd = parser.ClinicalData()
subj_list = parser.SubjectData(parent=cd[1])
sed = parser.StudyEventData(parent=subj_list[0]["elem"])
fd = parser.FormData(parent=sed[0]["elem"])
igd = parser.ItemGroupData(parent=fd[0]["elem"])
item_data = parser.ItemData(parent=igd[0]["elem"])
self.assertEqual(item_data[0]["Value"], "Fever")
def test_itemgroupdef_parse_xml(self):
parser = ODM_PARSER.ODMParser(self.input_file, self.nsr)
parser.parse()
mdv = parser.MetaDataVersion()
igd_list = parser.ItemGroupDef(parent=mdv[0])
igd_dict = igd_list[0]
self.assertEqual(igd_dict["OID"], "IG.TS")
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), 6)
igd_class = parser.Class(parent=igd_dict["elem"], ns_prefix="def")
self.assertEqual(igd_class[0]["Name"], "TRIAL DESIGN")
def test_itemgroupdef_iterator(self):
""" test the ability to reference a specific or slice of ItemRefs """
attrs = self.set_itemgroupdef_attributes()
igd = DEFINE.ItemGroupDef(**attrs)
tt = DEFINE.TranslatedText(_content="Vital Signs", lang="en")
igd.Description = DEFINE.Description()
igd.Description.TranslatedText = [tt]
item_refs = self.set_itemrefs()
igd.ItemRef = item_refs
parser = ODM_PARSER.ODMParser(self.test_file, self.nsr)
parser.parse()
parser.MetaDataVersion()
irs = [ir.ItemOID for ir in igd]
self.assertEqual(len(irs), 10)
def setUp(self) -> None:
self.odm_file_1 = os.path.join(
os.path.dirname(os.path.realpath(__file__)), 'data',
'define2-0-0-sdtm-test.xml')
NS.NamespaceRegistry(prefix="odm",
uri="http://www.cdisc.org/ns/odm/v1.3",
is_default=True)
NS.NamespaceRegistry(prefix="def",
uri="http://www.cdisc.org/ns/def/v2.0")
self.nsr = NS.NamespaceRegistry(
prefix="nciodm", uri="http://ncicb.nci.nih.gov/xml/odm/EVS/CDISC")
self.parser = P.ODMParser(self.odm_file_1, self.nsr)
self.root = self.parser.parse()
self.mdv = self.parser.MetaDataVersion()
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_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 setUp(self) -> None:
self.odm_file_1 = os.path.join(
os.path.dirname(os.path.realpath(__file__)), 'data',
'defineV21-SDTM-metadata.xml')
NS.NamespaceRegistry(prefix="odm",
uri="http://www.cdisc.org/ns/odm/v1.3",
is_default=True)
NS.NamespaceRegistry(prefix="def",
uri="http://www.cdisc.org/ns/def/v2.1")
self.nsr = NS.NamespaceRegistry(
prefix="nciodm", uri="http://ncicb.nci.nih.gov/xml/odm/EVS/CDISC")
self.parser = P.ODMParser(self.odm_file_1, self.nsr)
self.loader = LD.ODMLoader(
OL.XMLDefineLoader(model_package="define_2_1",
ns_uri="http://www.cdisc.org/ns/def/v2.1"))
self.root = self.loader.create_document(self.odm_file_1)
self.odm = self.loader.load_odm()
self.parser.parse()
self.mdv = self.parser.MetaDataVersion()
def create_document(self, filename, namespace_registry=None):
self.filename = filename
self._set_namespace(namespace_registry)
self.parser = P.ODMParser(self.filename, self.nsr)
root = self.parser.parse()
return root
def test_validate_tree_invalid(self):
odm_file = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'data', 'cdash-odm-test-invalid.xml')
self.parser = P.ODMParser(odm_file)
tree = self.parser.parse_tree()
is_valid = self.validator.validate_tree(tree)
self.assertFalse(is_valid)
def test_validate_tree_valid(self):
self.parser = P.ODMParser(self.odm_file)
tree = self.parser.parse_tree()
is_valid = self.validator.validate_tree(tree)
self.assertTrue(is_valid)