diff options
Diffstat (limited to 'tests/integration')
| -rw-r--r-- | tests/integration/test_gemma.py | 69 |
1 files changed, 62 insertions, 7 deletions
diff --git a/tests/integration/test_gemma.py b/tests/integration/test_gemma.py index 598c91f..1f59530 100644 --- a/tests/integration/test_gemma.py +++ b/tests/integration/test_gemma.py @@ -1,4 +1,5 @@ """Integration tests for gemma API endpoints""" +import os import unittest from dataclasses import dataclass @@ -17,7 +18,14 @@ class MockRedis: class GemmaAPITest(unittest.TestCase): """Test cases for the Gemma API""" def setUp(self): - self.app = create_app().test_client() + self.app = create_app({ + "APP_DEFAULTS": { + "GENODIR": os.path.abspath( + os.path.join(os.path.dirname(__file__), + "test_data/")), + "TMPDIR": "/tmp", + "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): @@ -31,9 +39,9 @@ class GemmaAPITest(unittest.TestCase): @mock.patch("gn3.api.gemma.redis.Redis") @mock.patch("gn3.api.gemma.queue_cmd") @mock.patch("gn3.api.gemma.generate_gemma_computation_cmd") - def test_run_gemma(self, mock_gemma_computation_cmd, - mock_queue_cmd, mock_redis): - """Test that gemma composes the command correctly""" + def test_run_gemma_no_loco(self, mock_gemma_computation_cmd, + mock_queue_cmd, mock_redis): + """Test that gemma composes the command correctly without loco""" _redis_conn = MockRedis(redis=mock.MagicMock(), hget=mock.MagicMock()) mock_redis.return_value = _redis_conn mock_gemma_computation_cmd.side_effect = [ @@ -42,7 +50,9 @@ class GemmaAPITest(unittest.TestCase): "test.txt -a genofile_snps.txt " "-gk > /tmp/gn2/" "bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt"), - ("gemma-wrapper --json -- " + ("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/" @@ -66,7 +76,9 @@ class GemmaAPITest(unittest.TestCase): "genofile.txt -p test.txt " "-a genofile_snps.txt -gk > " "/tmp/gn2/bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt " - "&& gemma-wrapper --json -- -g " + "&& 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 > " @@ -78,7 +90,50 @@ class GemmaAPITest(unittest.TestCase): response.get_json(), {"unique_id": 'my-unique-id', "status": "queued", - "output_file": "BXD_GWA_9lo8zwOOXbfB73EcyXxAYQ.txt"}) + "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): + """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("/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", + 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")) + self.assertEqual( + 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): |