def test_ItemDef(self):
attrs = {
"OID": "ODM.IT.AE.AEYN",
"Name": "Any AEs?",
"DataType": "text",
"Length": "1",
"SASFieldName": "AEYN",
"SDSVarName": "AEYN",
"Origin": "CRF",
"Comment": "Data management field"
}
item = ODM.ItemDef(**attrs)
item.Description.TranslatedText = [
ODM.TranslatedText(_content="this is the first test description",
lang="en")
]
item.Question.TranslatedText = [
ODM.TranslatedText(_content="Any AEs?", lang="en")
]
item.CodeListRef = ODM.CodeListRef(
CodeListOID="CL.NY_SUB_Y_N_2011-10-24")
item_dict = item.to_dict()
print(item_dict)
is_valid = self.validator.verify_conformance(item_dict, "ItemDef")
self.assertTrue(is_valid)
def test_to_xml(self):
attrs = self.set_item_attributes()
item = ODM.ItemDef(**attrs)
item.Description.TranslatedText = [
ODM.TranslatedText(_content="this is the first test description",
lang="en")
]
item.Question.TranslatedText = [
ODM.TranslatedText(_content="Any AEs?", lang="en")
]
item.ExternalQuestion = ODM.ExternalQuestion(Dictionary="SF36",
Version="12",
Code="Walks 1-mile")
item.CodeListRef = ODM.CodeListRef(
CodeListOID="CL.NY_SUB_Y_N_2011-10-24")
item.RangeCheck = [ODM.RangeCheck(Comparator="EQ", SoftHard="Soft")]
item.RangeCheck[0].CheckValue = [ODM.CheckValue(_content="DIABP")]
item.RangeCheck[0].FormalExpression = [
ODM.FormalExpression(Context="Python 3.7",
_content="print('hello world')")
]
item.RangeCheck[0].MeasurementUnitRef = ODM.MeasurementUnitRef(
MeasurementUnitOID="ODM.MU.UNITS")
item.RangeCheck[0].ErrorMessage.TranslatedText = [
ODM.TranslatedText(_content="invalid test code", lang="en")
]
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_to_json(self):
attrs = self.set_item_attributes()
item = ODM.ItemDef(**attrs)
item.Description.TranslatedText.append(
ODM.TranslatedText(_content="this is the first test description",
lang="en"))
item.Question.TranslatedText = [
ODM.TranslatedText(_content="Any AEs?", lang="en")
]
item.CodeListRef = ODM.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_to_dict(self):
attrs = self.set_item_attributes()
item = ODM.ItemDef(**attrs)
item.Description.TranslatedText = [
ODM.TranslatedText(_content="this is the first test description",
lang="en")
]
item.Question.TranslatedText = [
ODM.TranslatedText(_content="Any AEs?", lang="en")
]
item.CodeListRef = ODM.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',
'SDSVarName': 'AEYN',
'Origin': 'CRF',
'Comment': 'Data management field',
'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_float_type(self):
# rank is a float - test as a float
attrs = {"CodedValue": "HGB", "Rank": 1.1}
cli = ODM.CodeListItem(**attrs)
self.assertEqual(cli.Rank, 1.1)
# test float as string
attrs = {"CodedValue": "HGB", "Rank": "1.1"}
cli = ODM.CodeListItem(**attrs)
self.assertEqual(cli.Rank, 1.1)
# test integer as float
attrs = {"CodedValue": "HGB", "Rank": 1}
cli = ODM.CodeListItem(**attrs)
self.assertEqual(cli.Rank, 1.0)
# test non-float as string
attrs = {"CodedValue": "HGB", "Rank": "a"}
with self.assertRaises(TypeError):
cli = ODM.CodeListItem(**attrs)
# test object as float
clr = ODM.CodeListRef(CodeListOID="CL.TEST")
attrs = {"CodedValue": "HGB", "Rank": clr}
with self.assertRaises(TypeError):
cli = ODM.CodeListItem(**attrs)
def test_codelist_ref(self):
self.item.CodeListRef = ODM.CodeListRef(
CodeListOID="CL.NY_SUB_Y_N_2011-10-24")
self.assertEqual(self.item.CodeListRef.CodeListOID,
"CL.NY_SUB_Y_N_2011-10-24")
def test_add_undefined_content(self):
# use conformance rules to check for unknown objects being added after creation
attrs = {
"OID": "ODM.IT.AE.AEYN",
"Name": "Any AEs?",
"DataType": "text",
"Length": 1,
"SASFieldName": "AEYN",
"SDSVarName": "AEYN",
"Origin": "CRF",
"Comment": "Data management field",
"SignificantDigits": 1
}
item = ODM.ItemDef(**attrs)
clr = ODM.CodeListRef(CodeListOID="CL.TEST")
with self.assertRaises(TypeError):
item.NewCodeList = clr
# cannot add unknown attributes or elements during creation, but can afterwards; catch with conformance checks
attrs = {
"OID": "ODM.IT.AE.AEYN",
"Name": "Any AEs?",
"DataType": "text",
"Length": 1,
"SASFieldName": "AEYN",
"SDSVarName": "AEYN",
"Origin": "CRF",
"Comment": "Data management field",
"SignificantDigits": 1
}
item = ODM.ItemDef(**attrs)
with self.assertRaises(TypeError):
item.InSignificantDigits = 1
# can add all objects during creation and they are validated
attrs = {
"OID": "ODM.IT.AE.AEYN",
"Name": "Any AEs?",
"DataType": "text",
"Length": 1,
"SASFieldName": "AEYN",
"SDSVarName": "AEYN",
"Origin": "CRF",
"Comment": "Data management field",
"CodeListRef": clr
}
item = ODM.ItemDef(**attrs)
self.assertEqual(item.CodeListRef, clr)
attrs["CodeListReference"] = clr
with self.assertRaises(TypeError):
# test shows that ItemDef fails the schema check because it has an unknown CodeListReference object
item = ODM.ItemDef(**attrs)
self.assertEqual(item.CodeListRef, clr)
# test adding the wrong type of object to a list
attrs = {
"OID": "ODM.IT.AE.AEYN",
"Name": "Any AEs?",
"DataType": "text",
"Length": 1,
"SASFieldName": "AEYN",
"SDSVarName": "AEYN",
"Origin": "CRF",
"Comment": "Data management field",
"Alias": [clr]
}
with self.assertRaises(TypeError):
item = ODM.ItemDef(**attrs)
# test adding the wrong type of object to a list
alias = ODM.Alias(Context="CDASH", Name="AEYN")
attrs = {
"OID": "ODM.IT.AE.AEYN",
"Name": "Any AEs?",
"DataType": "text",
"Length": 1,
"SASFieldName": "AEYN",
"SDSVarName": "AEYN",
"Origin": "CRF",
"Comment": "Data management field",
"Alias": alias
}
with self.assertRaises(TypeError):
item = ODM.ItemDef(**attrs)
# assign wrong type of object to an element
attrs = {
"OID": "ODM.IT.AE.AEYN",
"Name": "Any AEs?",
"DataType": "text",
"Length": 1,
"SASFieldName": "AEYN",
"SDSVarName": "AEYN",
"Origin": "CRF",
"Comment": "Data management field",
"CodeListRef": alias
}
with self.assertRaises(TypeError):
item = ODM.ItemDef(**attrs)