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-rw-r--r--tests/integration/test_gemma.py133
1 files changed, 71 insertions, 62 deletions
diff --git a/tests/integration/test_gemma.py b/tests/integration/test_gemma.py
index 6d2116b..822f088 100644
--- a/tests/integration/test_gemma.py
+++ b/tests/integration/test_gemma.py
@@ -21,19 +21,21 @@ class GemmaAPITest(unittest.TestCase):
"""Test cases for the Gemma API"""
def setUp(self):
self.app = create_app({
- "GENODIR": os.path.abspath(
- os.path.join(os.path.dirname(__file__),
- "test_data/")),
- "REDIS_JOB_QUEUE": "GN3::job-queue",
- "GEMMA_WRAPPER_CMD": "gemma-wrapper"}).test_client()
+ "GENODIR":
+ os.path.abspath(
+ os.path.join(os.path.dirname(__file__), "test_data/")),
+ "REDIS_JOB_QUEUE":
+ "GN3::job-queue",
+ "GEMMA_WRAPPER_CMD":
+ "gemma-wrapper"
+ }).test_client()
@mock.patch("gn3.api.gemma.run_cmd")
def test_get_version(self, mock_run_cmd):
"""Test that the correct response is returned"""
mock_run_cmd.return_value = {"status": 0, "output": "v1.9"}
response = self.app.get("/api/gemma/version", follow_redirects=True)
- self.assertEqual(response.get_json(),
- {"status": 0, "output": "v1.9"})
+ self.assertEqual(response.get_json(), {"status": 0, "output": "v1.9"})
self.assertEqual(response.status_code, 200)
@mock.patch("gn3.api.gemma.redis.Redis")
@@ -59,60 +61,69 @@ class GemmaAPITest(unittest.TestCase):
"bxd_GWA_gUFhGu4rLG7k+CXLPk1OUg.txt")
]
mock_queue_cmd.return_value = "my-unique-id"
- response = self.app.post("/api/gemma/k-gwa-computation", json={
- "trait_filename": "BXD.txt",
- "geno_filename": "BXD_geno",
- "values": ["X", "N/A", "X"],
- "dataset_groupname": "BXD",
- "trait_name": "Height",
- "email": "me@me.com",
- "dataset_name": "BXD"
- })
- mock_queue_cmd.assert_has_calls(
- [mock.call(conn=_redis_conn,
- email="me@me.com",
- job_queue="GN3::job-queue",
- cmd=("gemma-wrapper --json -- -g "
- "genofile.txt -p test.txt "
- "-a genofile_snps.txt -gk > "
- "/tmp/gn2/bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt "
- "&& gemma-wrapper --json --input "
- "/tmp/gn2/bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt"
- " -- -a genofile_snps.txt -lmm 9 -g "
- "genofile.txt -p test.txt "
- "-a genofile_snps.txt "
- "-gk > "
- "/tmp/gn2/"
- "bxd_GWA_gUFhGu4rLG7k+CXLPk1OUg.txt"))]
- )
+ response = self.app.post("/api/gemma/k-gwa-computation",
+ json={
+ "trait_filename": "BXD.txt",
+ "geno_filename": "BXD_geno",
+ "values": ["X", "N/A", "X"],
+ "dataset_groupname": "BXD",
+ "trait_name": "Height",
+ "email": "me@me.com",
+ "dataset_name": "BXD"
+ })
+ mock_queue_cmd.assert_has_calls([
+ mock.call(conn=_redis_conn,
+ email="me@me.com",
+ job_queue="GN3::job-queue",
+ cmd=("gemma-wrapper --json -- -g "
+ "genofile.txt -p test.txt "
+ "-a genofile_snps.txt -gk > "
+ "/tmp/gn2/bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt "
+ "&& gemma-wrapper --json --input "
+ "/tmp/gn2/bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt"
+ " -- -a genofile_snps.txt -lmm 9 -g "
+ "genofile.txt -p test.txt "
+ "-a genofile_snps.txt "
+ "-gk > "
+ "/tmp/gn2/"
+ "bxd_GWA_gUFhGu4rLG7k+CXLPk1OUg.txt"))
+ ])
# mock_pheno_txt_file.return_value = "/tmp/gn2/BXD_6OBEPW."
self.assertEqual(
- response.get_json(),
- {"unique_id": 'my-unique-id',
- "status": "queued",
- "output_file": "BXD_GWA_WzxVcfhKAn4fJnSWpsBq0g.txt"})
+ response.get_json(), {
+ "unique_id": 'my-unique-id',
+ "status": "queued",
+ "output_file": "BXD_GWA_WzxVcfhKAn4fJnSWpsBq0g.txt"
+ })
@mock.patch("gn3.api.gemma.redis.Redis")
@mock.patch("gn3.api.gemma.queue_cmd")
- def test_run_gemma_with_loco(self,
- mock_queue_cmd, mock_redis):
+ def test_run_gemma_with_loco(self, mock_queue_cmd, mock_redis):
"""Test that gemma composes the command correctly with loco"""
_redis_conn = MockRedis(redis=mock.MagicMock(), hget=mock.MagicMock())
mock_redis.return_value = _redis_conn
mock_queue_cmd.return_value = "my-unique-id"
- response = self.app.post("/api/gemma/k-gwa-computation", json={
- "trait_filename": os.path.abspath(os.path.join(
- os.path.dirname(__file__),
- "test_data/"
- )),
- "geno_filename": "BXD_geno.txt.gz",
- "values": ["X", "N/A", "X"],
- "dataset_groupname": "BXD",
- "trait_name": "Height",
- "email": "me@me.com",
- "dataset_name": "BXD",
- "loco": "1,2,3,4,5,6"
- })
+ response = self.app.post("/api/gemma/k-gwa-computation",
+ json={
+ "trait_filename":
+ os.path.abspath(
+ os.path.join(
+ os.path.dirname(__file__),
+ "test_data/")),
+ "geno_filename":
+ "BXD_geno.txt.gz",
+ "values": ["X", "N/A", "X"],
+ "dataset_groupname":
+ "BXD",
+ "trait_name":
+ "Height",
+ "email":
+ "me@me.com",
+ "dataset_name":
+ "BXD",
+ "loco":
+ "1,2,3,4,5,6"
+ })
mock_queue_cmd.called_with(
conn=_redis_conn,
email="me@me.com",
@@ -130,10 +141,11 @@ class GemmaAPITest(unittest.TestCase):
"/tmp/gn2/"
"bxd_GWA_gUFhGu4rLG7k+CXLPk1OUg.txt"))
self.assertEqual(
- response.get_json(),
- {"unique_id": 'my-unique-id',
- "status": "queued",
- "output_file": "BXD_GWA_WzxVcfhKAn4fJnSWpsBq0g.txt"})
+ response.get_json(), {
+ "unique_id": 'my-unique-id',
+ "status": "queued",
+ "output_file": "BXD_GWA_WzxVcfhKAn4fJnSWpsBq0g.txt"
+ })
@mock.patch("gn3.api.gemma.redis.Redis")
def test_check_cmd_status(self, mock_redis):
@@ -146,18 +158,15 @@ class GemmaAPITest(unittest.TestCase):
"cmd%3A%3A2021-02-1217-3224-3224-1234"),
follow_redirects=True)
mock_hget.assert_called_once_with(
- name="cmd::2021-02-1217-3224-3224-1234",
- key="status")
- self.assertEqual(response.get_json(),
- {"status": "test"})
+ name="cmd::2021-02-1217-3224-3224-1234", key="status")
+ self.assertEqual(response.get_json(), {"status": "test"})
@mock.patch("gn3.api.gemma.queue_cmd")
@mock.patch("gn3.api.gemma.get_hash_of_files")
@mock.patch("gn3.api.gemma.jsonfile_to_dict")
@mock.patch("gn3.api.gemma.do_paths_exist")
@mock.patch("gn3.api.gemma.redis.Redis")
- def test_k_compute(self, mock_redis, mock_path_exist,
- mock_json, mock_hash,
+ def test_k_compute(self, mock_redis, mock_path_exist, mock_json, mock_hash,
mock_queue_cmd):
"""Test /gemma/k-compute/<token>"""
mock_path_exist.return_value, _redis_conn = True, mock.MagicMock()
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 20:24:45 +0000