def test_HpdsQuery_func_getCount_handles_connection_error(
self, mock_picsure_connection, mock_http_request):
test_uuid = "my-test-uuid"
test_url = "http://my-test.url/"
test_token = "this.is.my.test.token"
test_connection_error = '{"results":{}, "error":"true"}'
conn = mock_picsure_connection()
API = PicSureHpds.BypassConnectionAPI(test_url, test_token)
def ret_API():
return API
conn._api_obj = ret_API
resource = PicSureHpds.HpdsResourceConnection(conn, test_uuid)
query = resource.query()
resp_headers = {"status": "200"}
mock_http_request.return_value = (
resp_headers, test_connection_error.encode("utf-8"))
req_body = json.dumps(query.buildQuery("COUNT"))
# micro test to confirm warning is printed on error
with patch('sys.stdout', new=io.StringIO()) as fake_stdout:
test = query.getCount()
sys.stdout = sys.__stdout__ # Reset redirect. Needed for it to work!
captured = fake_stdout.getvalue()
print("Message on parameter useage:\n" + captured)
self.assertTrue(len(captured) > 0)
self.assertEqual(test, test_connection_error)
def test_HpdsResourceConnection_func_query(self, MockPicSureConnection):
conn = MockPicSureConnection()
test_uuid = "my-test-uuid"
resource = PicSureHpds.HpdsResourceConnection(conn, test_uuid)
query = resource.query()
self.assertIsInstance(query, PicSureHpdsQuery.Query)
def test_HpdsQuery_func_getResultsDataFrame(self, mock_picsure_connection,
mock_http_request):
test_uuid = "my-test-uuid"
test_url = "http://my-test.url/"
test_token = "this.is.my.test.token"
test_return_CSV = "ROW\tVALUE\n" + "1\tTrue\n" + "2\tFalse\n" + "3\tUnknown\n"
conn = mock_picsure_connection()
API = PicSureHpds.BypassConnectionAPI(test_url, test_token)
def ret_API():
return API
conn._api_obj = ret_API
resource = PicSureHpds.HpdsResourceConnection(conn, test_uuid)
query = resource.query()
resp_headers = {"status": "200"}
mock_http_request.return_value = (resp_headers,
test_return_CSV.encode("utf-8"))
req_body = json.dumps(query.buildQuery("DATAFRAME"))
query.getResultsDataFrame()
mock_http_request.assert_called_with(
uri=test_url + "query/sync",
method="POST",
body=req_body,
headers={'Content-Type': 'application/json'})
def test_HpdsQuery_list_anyof(self, mock_picsure_connection):
conn = mock_picsure_connection()
test_uuid = "my-test-uuid"
test_key = "my-test-key"
resource = PicSureHpds.HpdsResourceConnection(conn, test_uuid)
query = resource.query()
self.assertIsInstance(query.anyof, types.MethodType)
my_list = query.anyof()
self.assertIsInstance(my_list.add, types.MethodType)
self.assertIsInstance(my_list.delete, types.MethodType)
self.assertIsInstance(my_list, PicSureHpdsLib.AttrListKeys)
# micro test to confirm warning is printed if parameters are passed
with patch('sys.stdout', new=io.StringIO()) as fake_stdout:
query.anyof("some_attempted_key")
sys.stdout = sys.__stdout__ # Reset redirect. Needed for it to work!
captured = fake_stdout.getvalue()
print("Message on parameter useage:\n" + captured)
self.assertTrue(len(captured) > 0)
# MagicMock the API's search function
query._apiObj.search.return_value = '{"results": {"phenotypes": {' \
'"somekey": {"name": "term1", "categorical": false, "min":0, "max":100}' \
'}}}'
my_list.add("somekey")
self.assertEqual(1, len(my_list.data))
output = query.save()
print(output)
def test_HpdsQuery_func_getCount(self, mock_picsure_connection,
mock_http_request):
test_uuid = "my-test-uuid"
test_url = "http://my-test.url/"
test_token = "this.is.my.test.token"
conn = mock_picsure_connection()
API = PicSureHpds.BypassConnectionAPI(test_url, test_token)
def ret_API():
return API
conn._api_obj = ret_API
resource = PicSureHpds.HpdsResourceConnection(conn, test_uuid)
query = resource.query()
resp_headers = {"status": "200"}
mock_http_request.return_value = (resp_headers, "1000".encode("utf-8"))
req_body = json.dumps(query.buildQuery("COUNT"))
query.getCount()
mock_http_request.assert_called_with(
uri=test_url + "query/sync",
method="POST",
body=req_body,
headers={'Content-Type': 'application/json'})
def test_HpdsResourceConnection_create(self, MockPicSureConnection):
conn = MockPicSureConnection()
test_uuid = "my-test-uuid"
resource = PicSureHpds.HpdsResourceConnection(conn, test_uuid)
self.assertIsInstance(resource, PicSureHpds.HpdsResourceConnection)
self.assertIs(test_uuid, resource.resource_uuid)
self.assertIs(conn, resource.connection_reference)
def test_HpdsQuery_create(self, mock_picsure_connection):
conn = mock_picsure_connection()
test_uuid = "my-test-uuid"
resource = PicSureHpds.HpdsResourceConnection(conn, test_uuid)
query = resource.query()
# test that it was created correctly
self.assertIsInstance(query, PicSureHpdsQuery.Query)
self.assertEqual(query._resourceUUID, test_uuid)
self.assertIs(query._refHpdsResourceConnection, resource)
def test_HpdsResourceConnection_func_help(self, MockPicSureConnection):
conn = MockPicSureConnection()
test_uuid = "my-test-uuid"
resource = PicSureHpds.HpdsResourceConnection(conn, test_uuid)
with patch('sys.stdout', new=io.StringIO()) as fake_stdout:
resource.help()
sys.stdout = sys.__stdout__ # Reset redirect. Needed for it to work!
captured = fake_stdout.getvalue()
print("Captured:\n" + captured)
self.assertTrue(len(captured) > 0)
def test_HpdsResourceConnection_func_dictionary(self,
MockPicSureConnection):
conn = MockPicSureConnection()
test_uuid = "my-test-uuid"
resource = PicSureHpds.HpdsResourceConnection(conn, test_uuid)
self.assertIsInstance(resource, PicSureHpds.HpdsResourceConnection)
self.assertIs(resource.resource_uuid, test_uuid)
dictionary = resource.dictionary()
self.assertIsInstance(dictionary, PicSureHpdsDictionary.Dictionary)
def test_HpdsQuery_func_show(self, mock_picsure_connection):
conn = mock_picsure_connection()
test_uuid = "my-test-uuid"
resource = PicSureHpds.HpdsResourceConnection(conn, test_uuid)
query = resource.query()
with patch('sys.stdout', new=io.StringIO()) as fake_stdout:
query.show()
sys.stdout = sys.__stdout__ # Reset redirect. Needed for it to work!
captured = fake_stdout.getvalue()
print("Captured:\n" + captured)
self.assertTrue(len(captured) > 0)
def test_HpdsQuery_list_require(self, mock_picsure_connection):
conn = mock_picsure_connection()
test_uuid = "my-test-uuid"
test_key = "my-test-key"
resource = PicSureHpds.HpdsResourceConnection(conn, test_uuid)
query = resource.query()
self.assertIsInstance(query.require, types.MethodType)
my_list = query.require()
self.assertIsInstance(my_list.add, types.MethodType)
self.assertIsInstance(my_list.delete, types.MethodType)
self.assertIsInstance(my_list, PicSureHpdsLib.AttrListKeys)
# micro test to confirm warning is printed if parameters are passed
with patch('sys.stdout', new=io.StringIO()) as fake_stdout:
query.require("some_attempted_key")
sys.stdout = sys.__stdout__ # Reset redirect. Needed for it to work!
captured = fake_stdout.getvalue()
print("Message on parameter useage:\n" + captured)
self.assertTrue(len(captured) > 0)
def test_HpdsQuery_list_filter_input_a_list(self, mock_picsure_connection):
test_uuid = "my-test-uuid"
test_key1 = "my-test-key1"
test_key2 = "my-test-key2"
test_value = 1000
test_class = "my-test-class"
conn = mock_picsure_connection()
API = PicSureHpds.BypassConnectionAPI("", "")
API.search = MagicMock(return_value='{"results": {"' + test_class +
'": {"' + test_key1 + '": "foo", "' +
test_key2 + '": "bar"}}}')
def ret_API():
return API
conn._api_obj = ret_API
resource = PicSureHpds.HpdsResourceConnection(conn, test_uuid)
query = resource.query()
# micro test to confirm warning is printed if parameters are passed
with patch('sys.stdout', new=io.StringIO()) as fake_stdout:
query.filter().add([test_key1, test_key2], test_value)
self.assertEqual(len(query.filter().data), 2)
self.assertDictEqual(
query.filter().data[test_key1], {
'type': 'minmax',
'min': test_value,
'max': test_value,
'HpdsDataType': test_class
})
self.assertDictEqual(
query.filter().data[test_key2], {
'type': 'minmax',
'min': test_value,
'max': test_value,
'HpdsDataType': test_class
})
sys.stdout = sys.__stdout__ # Reset redirect. Needed for it to work!
captured = fake_stdout.getvalue()
print("Message on parameter useage:\n" + captured)
self.assertTrue(len(captured) == 0)
def test_HpdsQuery_func_load(self, mock_picsure_connection):
test_uuid = "my-test-uuid"
query_obj = {
"query": {
"fields": ["\\select\\key"],
"crossCountFields":
["\\crosscounts\\key1", "\\crosscounts\\key2"],
"requiredFields": ["\\require\\key"],
"anyRecordOf": ["\\anyof\\key1", "\\anyof\\key2"],
"numericFilters": {
"\\filter_numeric\\range1": {
"min": 40,
"max": 60
},
"\\filter_numeric\\value1": {
"min": 50,
"max": 50
}
},
"categoryFilters": {
"\\filter_categorical\\set1": ["cat1"],
"\\filter_categorical\\set2": ["catA", "catC"]
},
"variantInfoFilters": [{
"categoryVariantInfoFilters": {
"Variant_severity": ["HIGH"]
},
"numericVariantInfoFilters": {
"AF": {
"min": 0.1,
"max": 0.9
}
}
}]
},
"resourceUUID": "my-test-uuid"
}
query_str = json.dumps(query_obj)
return_vals = {}
conn = mock_picsure_connection()
API = PicSureHpds.BypassConnectionAPI("", "")
API.search = MagicMock(return_value=json.dumps(return_vals))
def ret_API():
return API
conn._api_obj = ret_API
resource = PicSureHpds.HpdsResourceConnection(conn, test_uuid)
query = resource.query()
# micro test to confirm warning is printed if parameters are passed
with patch('sys.stdout', new=io.StringIO()) as fake_stdout:
query.load(query_str)
sys.stdout = sys.__stdout__ # Reset redirect. Needed for it to work!
captured = fake_stdout.getvalue()
print("Message on parameter useage:\n" + captured)
self.assertDictEqual(query_obj, json.loads(query.save()))
def test_HpdsQuery_func_save(self, mock_picsure_connection):
test_uuid = "my-test-uuid"
test_value = 50
return_vals = {
"results": {
"phenotypes": {
"\\select\\key": {},
"\\require\\key": {},
"\\crosscounts\\key1": {},
"\\crosscounts\\key2": {},
"\\anyof\\key1": {},
"\\anyof\\key2": {},
"\\filter_numeric\\key1": {
"name": "key1",
"categorical": False,
"min": 0,
"max": 100
},
"\\filter_numeric\\range1": {
"name": "term1",
"categorical": False,
"min": 0,
"max": 100
},
"\\filter_numeric\\value1": {
"name": "value1",
"categorical": False,
"min": 0,
"max": 100
},
"\\filter_categorical\\set1": {
"name": "set1",
"categorical": True,
"categoryValues": ["cat1"]
},
"\\filter_categorical\\set2": {
"name": "set2",
"categorical": True,
"categoryValues": ["catA", "catB", "catC"]
}
},
"info": {
"Variant_severity": {
"values": ["HIGH", "LOW"],
"continuous": False
},
"AF": {
"values": [],
"continuous": True
}
}
}
}
conn = mock_picsure_connection()
API = PicSureHpds.BypassConnectionAPI("", "")
API.search = MagicMock(return_value=json.dumps(return_vals))
def ret_API():
return API
conn._api_obj = ret_API
resource = PicSureHpds.HpdsResourceConnection(conn, test_uuid)
query = resource.query()
# micro test to confirm warning is printed if parameters are passed
with patch('sys.stdout', new=io.StringIO()) as fake_stdout:
query.select().add("\\select\\key")
query.crosscounts().add(
["\\crosscounts\\key1", "\\crosscounts\\key2"])
query.require().add("\\require\\key")
query.anyof().add(["\\anyof\\key1", "\\anyof\\key2"])
query.filter().add("\\filter_numeric\\range1", test_value - 10,
test_value + 10)
query.filter().add("\\filter_numeric\\value1", test_value)
query.filter().add("\\filter_categorical\\set1", "cat1")
query.filter().add("\\filter_categorical\\set2", ["catA", "catC"])
query.filter().add("Variant_severity", ["HIGH"])
query.filter().add("AF", min=0.1, max=0.9)
sys.stdout = sys.__stdout__ # Reset redirect. Needed for it to work!
captured = fake_stdout.getvalue()
print("Message on parameter useage:\n" + captured)
query_obj = {
"query": {
"fields": ["\\select\\key"],
"crossCountFields":
["\\crosscounts\\key1", "\\crosscounts\\key2"],
"requiredFields": ["\\require\\key"],
"anyRecordOf": ["\\anyof\\key1", "\\anyof\\key2"],
"numericFilters": {
"\\filter_numeric\\range1": {
"min": 40,
"max": 60
},
"\\filter_numeric\\value1": {
"min": 50,
"max": 50
}
},
"categoryFilters": {
"\\filter_categorical\\set1": ["cat1"],
"\\filter_categorical\\set2": ["catA", "catC"]
},
"variantInfoFilters": [{
"categoryVariantInfoFilters": {
"Variant_severity": ["HIGH"]
},
"numericVariantInfoFilters": {
"AF": {
"min": 0.1,
"max": 0.9
}
}
}]
},
"resourceUUID": "my-test-uuid"
}
self.assertDictEqual(query_obj, json.loads(query.save()))
