def test_to_xml_description(self):
tt1 = DEFINE.TranslatedText(_content="this is the first test description", lang="en")
tt2 = DEFINE.TranslatedText(_content="this is the second test description", lang="en")
desc = DEFINE.Description()
desc.TranslatedText = [tt1, tt2]
desc_xml = desc.to_xml()
tts = desc_xml.findall("TranslatedText")
self.assertEqual(tts[0].text, "this is the first test description")
def test_add_description(self):
tt1 = DEFINE.TranslatedText(_content="Age at Screening Date (Screening Date - Birth date)", lang="en")
tt2 = DEFINE.TranslatedText(_content="For the complete algorithm see the referenced external document.", lang="fr")
self.methoddef.Description = DEFINE.Description()
self.methoddef.Description.TranslatedText = [tt1, tt2]
self.assertEqual(len(self.methoddef.Description.TranslatedText), 2)
self.assertEqual(self.methoddef.Description.TranslatedText[1]._content,
'For the complete algorithm see the referenced external document.')
def test_add_description(self):
attrs = {"_content": "this is the first test description", "lang": "en"}
tt1 = DEFINE.TranslatedText(**attrs)
attrs = {"_content": "this is the second test description", "lang": "en"}
tt2 = DEFINE.TranslatedText(**attrs)
self.item.Description.TranslatedText.append(tt1)
self.item.Description.TranslatedText.append(tt2)
self.assertEqual(self.item.Description.TranslatedText[1]._content, "this is the second test description")
def test_to_dict_description(self):
tt1 = DEFINE.TranslatedText(_content="this is the first test description", lang="en")
tt2 = DEFINE.TranslatedText(_content="this is the second test description", lang="en")
desc = DEFINE.Description()
desc.TranslatedText = [tt1, tt2]
desc_dict = desc.to_dict()
print(desc_dict)
self.assertDictEqual(desc_dict["TranslatedText"][1],
{'_content': 'this is the second test description', 'lang': 'en'})
def test_to_json(self):
attrs = self.set_item_attributes()
item = DEFINE.ItemDef(**attrs)
item.Description.TranslatedText.append(DEFINE.TranslatedText(_content="this is the first test description", lang="en"))
item.Question.TranslatedText = [DEFINE.TranslatedText(_content="Any AEs?", lang="en")]
item.CodeListRef = DEFINE.CodeListRef(CodeListOID="CL.NY_SUB_Y_N_2011-10-24")
item_json = item.to_json()
item_dict = json.loads(item_json)
self.assertEqual(item_dict["OID"], "ODM.IT.AE.AEYN")
def test_add_description(self):
tt1 = DEFINE.TranslatedText(
_content="this is the first test description", lang="en")
tt2 = DEFINE.TranslatedText(
_content="this is the second test description", lang="en")
self.igd.Description = DEFINE.Description()
self.igd.Description.TranslatedText = [tt1, tt2]
self.assertEqual(len(self.igd.Description.TranslatedText), 2)
self.assertEqual(self.igd.Description.TranslatedText[1]._content,
'this is the second test description')
def test_to_dict(self):
attrs = self.set_item_attributes()
item = DEFINE.ItemDef(**attrs)
item.Description.TranslatedText = [DEFINE.TranslatedText(_content="this is the first test description", lang="en")]
item.Question.TranslatedText = [DEFINE.TranslatedText(_content="Any AEs?", lang="en")]
item.CodeListRef = DEFINE.CodeListRef(CodeListOID="CL.NY_SUB_Y_N_2011-10-24")
item_dict = item.to_dict()
expected_dict = {'OID': 'ODM.IT.AE.AEYN', 'Name': 'Any AEs?', 'DataType': 'text', 'Length': 1,
'SASFieldName': 'AEYN', "CommentOID": "ODM.CO.120",
'Description': {'TranslatedText': [{'_content': 'this is the first test description',
'lang': 'en'}]},
'Question': {'TranslatedText': [{'_content': 'Any AEs?', 'lang': 'en'}]},
'CodeListRef': {'CodeListOID': 'CL.NY_SUB_Y_N_2011-10-24'}}
self.assertDictEqual(item_dict, expected_dict)
def test_comment_def(self):
comment = DEFINE.CommentDef(OID="COM.VS.VISITNUM")
comment.Description.TranslatedText.append(
DEFINE.TranslatedText(
_content="Assigned from the TV domain based on the VISIT",
lang="en"))
self.assertEqual("COM.VS.VISITNUM", comment.OID)
def test_add_value_list_ref(self):
vlr = DEFINE.ValueListRef(ValueListOID="VL.DA.DAORRES")
attrs = {"OID": "IT.DA.DAORRES", "Name": "DAORRES", "DataType": "text", "Length": "2", "SASFieldName": "DAORRES"}
itd = DEFINE.ItemDef(**attrs)
tt1 = DEFINE.TranslatedText(_content="Assessment Result in Original Units", lang="en")
desc = DEFINE.Description()
desc.TranslatedText.append(tt1)
itd.Description = desc
itd.ValueListRef = vlr
self.assertEqual(itd.ValueListRef.ValueListOID, "VL.DA.DAORRES")
self.assertEqual(itd.OID, "IT.DA.DAORRES")
def test_to_dict(self):
attrs = self.set_attributes()
method = DEFINE.MethodDef(**attrs)
desc = DEFINE.Description()
tt1 = DEFINE.TranslatedText(_content="Age at Screening Date (Screening Date - Birth date)", lang="en")
desc.TranslatedText = [tt1]
method.Description = desc
fex = DEFINE.FormalExpression(Context="Python 3.7", _content="print('hello world')")
method.FormalExpression = [fex]
method_dict = method.to_dict()
self.assertEqual(method_dict["OID"], "ODM.MT.AGE")
self.assertDictEqual(method_dict, self.expected_dict())
def test_to_xml(self):
attrs = self.set_item_attributes()
item = DEFINE.ItemDef(**attrs)
item.Description.TranslatedText = [DEFINE.TranslatedText(_content="this is the first test description", lang="en")]
item.CodeListRef = DEFINE.CodeListRef(CodeListOID="CL.NY_SUB_Y_N_2011-10-24")
item.RangeCheck = [DEFINE.RangeCheck(Comparator="EQ", SoftHard="Soft", ItemOID="IT.DA.DAORRES")]
item.RangeCheck[0].CheckValue = [DEFINE.CheckValue(_content="DIABP")]
item_xml = item.to_xml()
self.assertEqual(item_xml.attrib["OID"], "ODM.IT.AE.AEYN")
cv = item_xml.find("*/CheckValue")
self.assertEqual(cv.text, "DIABP")
dt = item_xml.findall("Description/TranslatedText")
self.assertEqual(len(dt), 1)
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 test_itemgroupdef_slice(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()
self.assertEqual(len(igd), 10)
self.assertEqual(igd.ItemRef[0].ItemOID, "IT.STUDYID")
slice_itr = igd.ItemRef[1:5]
self.assertEqual(slice_itr[1].ItemOID, "IT.TA.ARMCD")
def test_itemgroupdef_round_trip(self):
""" system test to create and serialize an ItemGroupDef object """
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()
mdv = parser.MetaDataVersion()
igd_list = parser.ItemGroupDef(parent=mdv[0])
igd_dict = igd_list[0]
self.assertEqual(igd_dict["OID"], "IG.TA")
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 test_to_xml(self):
attrs = self.set_itemgroupdef_attributes()
igd = DEFINE.ItemGroupDef(**attrs)
tt = DEFINE.TranslatedText(
_content="this is the first test description", lang="en")
desc = DEFINE.Description()
desc.TranslatedText = [tt]
igd.Description = desc
ir1 = DEFINE.ItemRef(ItemOID="IT.STUDYID",
Mandatory="Yes",
OrderNumber=1)
ir2 = DEFINE.ItemRef(ItemOID="IT.VS.VSTEST",
Mandatory="No",
OrderNumber=2)
igd.ItemRef = [ir1, ir2]
igd_xml = igd.to_xml()
self.assertEqual(igd_xml.attrib["OID"], "IG.VS")
self.assertListEqual(["Description", "ItemRef", "ItemRef"],
[e.tag for e in igd_xml.getchildren()])
def test_to_json(self):
attrs = self.set_itemgroupdef_attributes()
igd = DEFINE.ItemGroupDef(**attrs)
tt = DEFINE.TranslatedText(
_content="this is the first test description", lang="en")
igd.Description = DEFINE.Description()
igd.Description.TranslatedText = [tt]
ir1 = DEFINE.ItemRef(ItemOID="IT.STUDYID",
Mandatory="Yes",
OrderNumber=1)
ir2 = DEFINE.ItemRef(ItemOID="IT.VS.VSTEST",
Mandatory="No",
OrderNumber=2)
igd.ItemRef = [ir1, ir2]
igd_json = igd.to_json()
igd_dict = json.loads(igd_json)
print(igd_dict)
self.assertEqual(igd_dict["OID"], "IG.VS")
self.assertEqual(igd_dict["ItemRef"][1]["ItemOID"], "IT.VS.VSTEST")
def test_set_description(self):
attrs = {"_content": "Assessment Result in Original Units", "lang": "en"}
tt1 = DEFINE.TranslatedText(**attrs)
self.item.Description.TranslatedText.append(tt1)
self.assertEqual(self.item.Description.TranslatedText[0].lang, "en")
self.assertEqual(self.item.Description.TranslatedText[0]._content, "Assessment Result in Original Units")