From 5c56425d51ab6a6b4ffd6ec8f86121bd91ff5e63 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Fri, 5 Mar 2021 12:06:22 +0300 Subject: Apply pep-8 formatting Began using elpy's format code fn --- tests/integration/test_gemma.py | 133 +++++++++++++++++++++------------------- 1 file changed, 71 insertions(+), 62 deletions(-) (limited to 'tests/integration') 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/""" mock_path_exist.return_value, _redis_conn = True, mock.MagicMock() -- cgit v1.2.3