def test_bad_get_variant_request(self):
invalid_id = "Jijf30453hwbur-PWFvWIvwPRGrjnib"
request = self.factory.get("/data/ga4gh/variants/"+invalid_id)
response = views.get_variant(request, invalid_id)
# Useful error message for an id which is not supported
self.assertEqual(response.status_code, 404)
self.assertJSONEqual(response.content, views.ErrorMessages['notFoundId'])
invalid_id_2 = "hg37-999999999999"
request = self.factory.get("/data/ga4gh/variants/" + invalid_id_2)
response = views.get_variant(request, invalid_id_2)
# Useful error for elements non existent in data base"""
self.assertEqual(response.status_code, 404)
self.assertJSONEqual(response.content, views.ErrorMessages['notFoundId'])
def test_bad_get_variant_request(self):
invalid_id = "Jijf30453hwbur-PWFvWIvwPRGrjnib"
request = self.factory.get("/data/ga4gh/variants/"+invalid_id)
response = views.get_variant(request, invalid_id)
# Useful error message for an id which is not supported
self.assertEqual(response.status_code, 404)
self.assertJSONEqual(response.content, views.ErrorMessages['notFoundId'])
invalid_id_2 = "hg37-999999999999"
request = self.factory.get("/data/ga4gh/variants/" + invalid_id_2)
response = views.get_variant(request, invalid_id_2)
# Useful error for elements non existent in data base"""
self.assertEqual(response.status_code, 404)
self.assertJSONEqual(response.content, views.ErrorMessages['notFoundId'])
def test_get_variant_by_id(self):
"""Ensures the results found via search variants and get variant by ID are equal."""
search_request = self.factory.post("/data/ga4gh/variants/search",
json.dumps({"referenceName": "chr17",
"variantSetId": "brca-hg37",
"start" : 4124692, "end" : 41247086,
"pageSize": 1}),
content_type="application/json"
)
search_response = views.search_variants(search_request)
json_search_response = json.loads(search_response.content)["variants"][0]
self.assertIsNotNone(json_search_response["variantSetId"])
self.assertIsNotNone(json_search_response["referenceName"])
self.assertIsNotNone(json_search_response["id"])
search_based_id = str(json_search_response['id'])
get_request = self.factory.get("/data/ga4gh/variants/"+search_based_id)
response = views.get_variant(get_request, search_based_id)
json_get_response = json.loads(response.content)
"""Note, because we made a get_request based on the search above,
we should be able to confirm that the individual variant request is exactly the same one"""
self.assertEqual(json_get_response["referenceName"], json_search_response["referenceName"])
self.assertEqual(json_get_response["start"], json_search_response["start"])
self.assertEqual(json_get_response["end"], json_search_response["end"])
def test_get_variant_by_id(self):
"""Ensures the results found via search variants and get variant by ID are equal."""
search_request = self.factory.post("/data/ga4gh/variants/search",
json.dumps({
"referenceName": "chr17",
"variantSetId": "brca-hg37",
"start": 4124692,
"end": 41247086,
"pageSize": 1
}),
content_type="application/json")
search_response = views.search_variants(search_request)
json_search_response = json.loads(
search_response.content)["variants"][0]
self.assertIsNotNone(json_search_response["variantSetId"])
self.assertIsNotNone(json_search_response["referenceName"])
self.assertIsNotNone(json_search_response["id"])
search_based_id = str(json_search_response['id'])
get_request = self.factory.get("/data/ga4gh/variants/" +
search_based_id)
response = views.get_variant(get_request, search_based_id)
json_get_response = json.loads(response.content)
"""Note, because we made a get_request based on the search above,
we should be able to confirm that the individual variant request is exactly the same one"""
self.assertEqual(json_get_response["referenceName"],
json_search_response["referenceName"])
self.assertEqual(json_get_response["start"],
json_search_response["start"])
self.assertEqual(json_get_response["end"], json_search_response["end"])
def test_origin(self):
variant_id = "hg37-55"
request = self.factory.get("/data/ga4gh/variants/"+variant_id)
response = views.get_variant(request, variant_id)
json_response = json.loads(response.content)
hgvs_start = int(
json_response['info']["Genomic_Coordinate_hg37"][0].split(':')[1].replace('g.',''))
# Note that `Genomic Coordinate hg37` is 1 base offset from its determined 'start' position"""
self.assertEqual(int(json_response['start']), hgvs_start,
"`base_1_start`, obtained from 'Genomic Coordinate hg37' minus 1 should be equal to the `start` Variant parameter {} {}".format(
int(json_response['start']), hgvs_start - 1))
variant_id = "hg38-945"
request = self.factory.get("/data/ga4gh/variants/" + variant_id)
response = views.get_variant(request, variant_id)
json_response = json.loads(response.content)
# Note that `start` is 0 base offset from its determined 'Genomic Coordinate' field"""
hgvs_start = int(json_response['info']['Genomic_Coordinate_hg38'][0].split(':')[1].replace('g.',''))
self.assertEqual(int(json_response['start']), hgvs_start - 1)
def test_origin(self):
variant_id = "hg37-" + str(self.existing_variant_materialized_view.id)
request = self.factory.get("/data/ga4gh/variants/"+variant_id)
response = views.get_variant(request, variant_id)
json_response = json.loads(response.content)
hgvs_start = int(
json_response['info']["Genomic_Coordinate_hg37"][0].split(':')[1].replace('g.', ''))
# Note that `Genomic Coordinate hg37` is 1 base offset from its determined 'start' position"""
self.assertEqual(int(json_response['start']), hgvs_start,
"`base_1_start`, obtained from 'Genomic Coordinate hg37' minus 1 should be equal to the `start` Variant parameter {} {}".format(
int(json_response['start']), hgvs_start - 1))
variant_id = "hg38-" + str(self.existing_variant_materialized_view.id)
request = self.factory.get("/data/ga4gh/variants/" + variant_id)
response = views.get_variant(request, variant_id)
json_response = json.loads(response.content)
# Note that `start` is 0 base offset from its determined 'Genomic Coordinate' field"""
hgvs_start = int(json_response['info']['Genomic_Coordinate_hg38'][0].split(':')[1].replace('g.', ''))
self.assertEqual(int(json_response['start']), hgvs_start)
def test_origin(self):
variant_id = "hg37-55"
request = self.factory.get("/data/ga4gh/variants/" + variant_id)
response = views.get_variant(request, variant_id)
json_response = json.loads(response.content)
base_1_start = int(json_response['info']["Genomic_Coordinate_hg37"]
[0].split(':')[1]) - 1
# Note that `Genomic Coordinate hg37` is 1 base offset from its determined 'start' position"""
self.assertEqual(
int(json_response['start']), base_1_start,
"`base_1_start`, obtained from 'Genomic Coordinate hg37' minus 1 should be equal to the `start` Variant parameter"
)
variant_id_2 = "hg36-945"
request_2 = self.factory.get("/data/ga4gh/variants/" + variant_id_2)
response_2 = views.get_variant(request_2, variant_id_2)
json_response_2 = json.loads(response_2.content)
base_0_start = int(json_response_2['start']) + 1
# Note that `start` is 0 base offset from its determined 'Genomic Coordinate' field"""
genomic_coordinate_start = int(
json_response_2['info']['Genomic_Coordinate_hg36'][0].split(
':')[1])
self.assertEqual(genomic_coordinate_start, base_0_start)