Skip to content

Commit

Permalink
test: search API tests + project list test
Browse files Browse the repository at this point in the history
  • Loading branch information
@davidlougheed
davidlougheed committed Dec 19, 2024
1 parent 3a319e8 commit a31966c
Show file tree
Hide file tree
Showing 2 changed files with 100 additions and 77 deletions.
9 changes: 9 additions & 0 deletions chord_metadata_service/chord/tests/test_api.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -57,6 +57,15 @@ def test_create_project_forbidden(self):
self.assertEqual(r.status_code, status.HTTP_403_FORBIDDEN)


class ListProjectAPITest(AuthzAPITestCaseWithProjectJSON):

def test_list_projects(self):
r = self.client.get("/api/projects")
self.assertEqual(r.status_code, status.HTTP_200_OK)
res = r.json()
self.assertEqual(len(res["results"]), 1)


class UpdateProjectTest(AuthzAPITestCaseWithProjectJSON):
def setUp(self) -> None:
super().setUp()
Expand Down
168 changes: 91 additions & 77 deletions chord_metadata_service/chord/tests/test_api_search.py
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
import json
import uuid

from django.urls import reverse
from rest_framework import status
Expand Down Expand Up @@ -40,6 +41,17 @@

POST_GET = ("POST", "GET")

SQ1_DATA = {
"data_type": DATA_TYPE_PHENOPACKET,
"query": TEST_SEARCH_QUERY_1
}

# Valid query to search for phenotypic feature type
SQ3_DATA = {
"query": TEST_SEARCH_QUERY_3,
"data_type": DATA_TYPE_PHENOPACKET,
}


class SearchTest(AuthzAPITestCase):
def setUp(self) -> None:
Expand Down Expand Up @@ -82,7 +94,7 @@ def setUp(self) -> None:
biosample=self.biosample_1, instrument=self.instrument, dataset=self.dataset))
self.experiment.experiment_results.set([self.experiment_result])

def _search_call(self, endpoint, args=None, data=None, method="GET"):
def _search_call(self, endpoint, args=None, data=None, method="GET", authz: bool = True):
args = args or []

if method == "POST":
Expand All @@ -93,122 +105,124 @@ def _search_call(self, endpoint, args=None, data=None, method="GET"):
"query": json.dumps(data["query"]),
}

return (self.one_authz_post if method == "POST" else self.one_authz_get)(
reverse(endpoint, args=args), data=data)
if authz:
fn = (self.one_authz_post if method == "POST" else self.one_authz_get)
else:
fn = (self.one_no_authz_post if method == "POST" else self.one_no_authz_get)

return fn(reverse(endpoint, args=args), data=data)

def test_common_search_1(self):
# No body
for method in POST_GET:
r = self._search_call("private-search", method=method)
self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST)
with self.subTest(params=(method,)):
r = self._search_call("private-search", method=method)
self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST)

def test_common_search_2(self):
# No data type
for method in POST_GET:
r = self._search_call("private-search", data={"query": TEST_SEARCH_QUERY_1}, method=method)
self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST)
with self.subTest(params=(method,)):
r = self._search_call("private-search", data={"query": TEST_SEARCH_QUERY_1}, method=method)
self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST)

def test_common_search_3(self):
# No query
for method in POST_GET:
r = self._search_call("private-search", data={"data_type": DATA_TYPE_PHENOPACKET}, method=method)
self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST)
with self.subTest(params=(method,)):
r = self._search_call("private-search", data={"data_type": DATA_TYPE_PHENOPACKET}, method=method)
self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST)

def test_common_search_4(self):
# Bad data type
for method in POST_GET:
r = self._search_call("private-search", data={
"data_type": "bad_data_type",
"query": TEST_SEARCH_QUERY_1,
}, method=method)
self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST)
with self.subTest(params=(method,)):
r = self._search_call("private-search", data={
"data_type": "bad_data_type",
"query": TEST_SEARCH_QUERY_1,
}, method=method)
self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST)

def test_common_search_5(self):
# Bad syntax for query
for method in POST_GET:
r = self._search_call("private-search", data={
"data_type": DATA_TYPE_PHENOPACKET,
"query": ["hello", "world"]
}, method=method)
self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST)
with self.subTest(params=(method,)):
r = self._search_call("private-search", data={
"data_type": DATA_TYPE_PHENOPACKET,
"query": ["hello", "world"]
}, method=method)
self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST)

def test_search_without_result(self):
# Valid search without result
for method in POST_GET:
r = self._search_call("private-search", data={
"data_type": DATA_TYPE_PHENOPACKET,
"query": TEST_SEARCH_QUERY_2
}, method=method)
self.assertEqual(r.status_code, status.HTTP_200_OK)
c = r.json()
self.assertEqual(len(c["results"]), 0)
with self.subTest(params=(method,)):
r = self._search_call("private-search", data={
"data_type": DATA_TYPE_PHENOPACKET,
"query": TEST_SEARCH_QUERY_2
}, method=method)
self.assertEqual(r.status_code, status.HTTP_200_OK)
c = r.json()
self.assertEqual(len(c["results"]), 0)

def test_private_search(self):
# Valid search with result
for method in POST_GET:
r = self._search_call("private-search", data={
"data_type": DATA_TYPE_PHENOPACKET,
"query": TEST_SEARCH_QUERY_1
}, method=method)
self.assertEqual(r.status_code, status.HTTP_200_OK)
c = r.json()
with self.subTest(params=(method,)):
r = self._search_call("private-search", data=SQ1_DATA, method=method)
self.assertEqual(r.status_code, status.HTTP_200_OK)
c = r.json()

self.assertIn(str(self.dataset.identifier), c["results"])
self.assertEqual(c["results"][str(self.dataset.identifier)]["data_type"], DATA_TYPE_PHENOPACKET)
self.assertEqual(self.phenopacket.id, c["results"][str(self.dataset.identifier)]["matches"][0]["id"])
self.assertIn(str(self.dataset.identifier), c["results"])
self.assertEqual(c["results"][str(self.dataset.identifier)]["data_type"], DATA_TYPE_PHENOPACKET)
self.assertEqual(self.phenopacket.id, c["results"][str(self.dataset.identifier)]["matches"][0]["id"])

# TODO: Check schema?

def test_private_dataset_search_2(self):
# No query
def test_private_search_forbidden(self):
for method in POST_GET:
r = self._search_call("private-dataset-search", args=[str(self.dataset.identifier)], data={}, method=method)
self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST)

def test_private_dataset_search_3(self):
# Bad syntax for query
d = {"query": ["hello", "world"]}
for method in POST_GET:
r = self._search_call("private-dataset-search", args=[str(self.dataset.identifier)], data=d, method=method)
self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST)

def test_private_dataset_search_4(self):
# Valid query with one result

d = {
"data_type": DATA_TYPE_PHENOPACKET,
"query": TEST_SEARCH_QUERY_1,
}

with self.subTest(params=(method,)):
r = self._search_call("private-search", data=SQ1_DATA, method=method, authz=False)
self.assertEqual(r.status_code, status.HTTP_403_FORBIDDEN)

def test_private_dataset_search_basic(self):
param_set = [
({}, status.HTTP_400_BAD_REQUEST), # No query
({"query": ["hello", "world"]}, status.HTTP_400_BAD_REQUEST), # Bad syntax for query
(SQ1_DATA, status.HTTP_200_OK), # Valid query with one result
({"query": True, "data_type": DATA_TYPE_PHENOPACKET}, status.HTTP_200_OK), # Valid query with one result
]
args = [str(self.dataset.identifier)]

for params in param_set:
for method in POST_GET:
with self.subTest(params=(*params, method)):
r = self._search_call("private-dataset-search", args=args, data=params[0], method=method)
self.assertEqual(r.status_code, params[1])
if params[1] == status.HTTP_200_OK:
c = r.json()
self.assertEqual(len(c["results"]), 1)
self.assertEqual(self.phenopacket.id, c["results"][0]["id"])

r_forbidden = self._search_call(
"private-dataset-search", args=args, data=params[0], method=method, authz=False)
self.assertEqual(r_forbidden.status_code, status.HTTP_403_FORBIDDEN)

def test_private_dataset_search_not_found(self):
for method in POST_GET:
r = self._search_call("private-dataset-search", args=[str(self.dataset.identifier)], data=d, method=method)
self.assertEqual(r.status_code, status.HTTP_200_OK)
c = r.json()
self.assertEqual(len(c["results"]), 1)
self.assertEqual(self.phenopacket.id, c["results"][0]["id"])
with self.subTest(params=(method,)):
r = self._search_call("private-dataset-search", args=["does-not-exist"], data=SQ3_DATA, method=method)
self.assertEqual(r.status_code, status.HTTP_404_NOT_FOUND)

def test_private_search_5(self):
d = {
"query": True,
"data_type": DATA_TYPE_PHENOPACKET
}
for method in POST_GET:
r = self._search_call("private-dataset-search", args=[str(self.dataset.identifier)], data=d, method=method)
self.assertEqual(r.status_code, status.HTTP_200_OK)
c = r.json()
self.assertEqual(len(c["results"]), 1)
self.assertEqual(self.phenopacket.id, c["results"][0]["id"])
r = self._search_call("private-dataset-search", args=[str(uuid.uuid4())], data=SQ3_DATA, method=method)
self.assertEqual(r.status_code, status.HTTP_404_NOT_FOUND)

def test_private_dataset_search_6(self):
# Valid query to search for phenotypic feature type

d = {
"query": TEST_SEARCH_QUERY_3,
"data_type": DATA_TYPE_PHENOPACKET,
}

for method in POST_GET:
r = self._search_call("private-dataset-search", args=[str(self.dataset.identifier)], data=d, method=method)
r = self._search_call(
"private-dataset-search", args=[str(self.dataset.identifier)], data=SQ3_DATA, method=method)
self.assertEqual(r.status_code, status.HTTP_200_OK)
c = r.json()
self.assertEqual(len(c["results"]), 1)
Expand Down

0 comments on commit a31966c

Please sign in to comment.