diff options
| -rw-r--r-- | gn3/api/correlation.py | 2 | ||||
| -rw-r--r-- | gn3/commands.py | 5 | ||||
| -rw-r--r-- | gn3/computations/diff.py | 2 | ||||
| -rw-r--r-- | tests/integration/conftest.py | 4 | ||||
| -rw-r--r-- | tests/integration/test_correlation.py | 4 | ||||
| -rw-r--r-- | tests/integration/test_partial_correlations.py | 61 | ||||
| -rw-r--r-- | tests/performance/perf_query.py | 14 | ||||
| -rw-r--r-- | tests/unit/test_commands.py | 13 | ||||
| -rw-r--r-- | tests/unit/test_db_utils.py | 2 |
9 files changed, 57 insertions, 50 deletions
diff --git a/gn3/api/correlation.py b/gn3/api/correlation.py index f2ac4d7..67897e8 100644 --- a/gn3/api/correlation.py +++ b/gn3/api/correlation.py @@ -112,7 +112,7 @@ def partial_correlation(): return reduce(__field_errors__(request_data), fields, errors) - args = json.loads(request.get_json()) + args = request.get_json() request_errors = __errors__( args, ("primary_trait", "control_traits", "target_db", "method")) if request_errors: diff --git a/gn3/commands.py b/gn3/commands.py index 29e3df2..0e0b53c 100644 --- a/gn3/commands.py +++ b/gn3/commands.py @@ -84,11 +84,12 @@ Returns the name of the specific redis hash for the specific task. f"{str(uuid4())}") conn.rpush(job_queue, unique_id) for key, value in { - "cmd": json.dumps(cmd), "result": "", "status": "queued", - "env": json.dumps(env)}.items(): + "cmd": json.dumps(cmd), "result": "", "status": "queued"}.items(): conn.hset(name=unique_id, key=key, value=value) if email: conn.hset(name=unique_id, key="email", value=email) + if env: + conn.hset(name=unique_id, key="env", value=json.dumps(env)) return unique_id diff --git a/gn3/computations/diff.py b/gn3/computations/diff.py index af02f7f..0b6edd6 100644 --- a/gn3/computations/diff.py +++ b/gn3/computations/diff.py @@ -6,7 +6,7 @@ from gn3.commands import run_cmd def generate_diff(data: str, edited_data: str) -> Optional[str]: """Generate the diff between 2 files""" - results = run_cmd(f"diff {data} {edited_data}", success_codes=(1, 2)) + results = run_cmd(f'"diff {data} {edited_data}"', success_codes=(1, 2)) if results.get("code", -1) > 0: return results.get("output") return None diff --git a/tests/integration/conftest.py b/tests/integration/conftest.py index e1d1c37..be927a4 100644 --- a/tests/integration/conftest.py +++ b/tests/integration/conftest.py @@ -19,4 +19,6 @@ def client(): def db_conn(): """Create a db connection fixture for tests""" ## Update this to use temp db once that is in place - return database_connector()[0] + conn = database_connector() + yield conn + conn.close() diff --git a/tests/integration/test_correlation.py b/tests/integration/test_correlation.py index cf63c17..d52ab01 100644 --- a/tests/integration/test_correlation.py +++ b/tests/integration/test_correlation.py @@ -71,7 +71,9 @@ class CorrelationIntegrationTest(TestCase): mock_compute_corr.return_value = [] - database_connector.return_value = (mock.Mock(), mock.Mock()) + database_connector.return_value = mock.Mock() + database_connector.return_value.__enter__ = mock.Mock() + database_connector.return_value.__exit__ = mock.Mock() post_data = {"1426678_at": "68031", "1426679_at": "68036", diff --git a/tests/integration/test_partial_correlations.py b/tests/integration/test_partial_correlations.py index 7f9ff30..d249b42 100644 --- a/tests/integration/test_partial_correlations.py +++ b/tests/integration/test_partial_correlations.py @@ -1,4 +1,6 @@ """Test partial correlations""" +from unittest import mock + import pytest from gn3.computations.partial_correlations import partial_correlations_entry @@ -97,43 +99,46 @@ def test_partial_correlation_api_with_missing_request_data(client, post_data): @pytest.mark.parametrize( "post_data", ({# ProbeSet - "primary_trait": {"dataset": "a_dataset", "name": "a_name"}, + "primary_trait": {"dataset": "a_dataset", "trait_name": "a_name"}, "control_traits": [ - {"dataset": "a_dataset", "name": "a_name"}, - {"dataset": "a_dataset2", "name": "a_name2"}], + {"dataset": "a_dataset", "trait_name": "a_name"}, + {"dataset": "a_dataset2", "trait_name": "a_name2"}], "method": "a_method", "target_db": "a_db" }, {# Publish - "primary_trait": {"dataset": "a_Publish_dataset", "name": "a_name"}, + "primary_trait": { + "dataset": "a_Publish_dataset", "trait_name": "a_name"}, "control_traits": [ - {"dataset": "a_dataset", "name": "a_name"}, - {"dataset": "a_dataset2", "name": "a_name2"}], + {"dataset": "a_dataset", "trait_name": "a_name"}, + {"dataset": "a_dataset2", "trait_name": "a_name2"}], "method": "a_method", "target_db": "a_db" }, {# Geno - "primary_trait": {"dataset": "a_Geno_dataset", "name": "a_name"}, + "primary_trait": {"dataset": "a_Geno_dataset", "trait_name": "a_name"}, "control_traits": [ - {"dataset": "a_dataset", "name": "a_name"}, - {"dataset": "a_dataset2", "name": "a_name2"}], + {"dataset": "a_dataset", "trait_name": "a_name"}, + {"dataset": "a_dataset2", "trait_name": "a_name2"}], "method": "a_method", "target_db": "a_db" }, {# Temp - "primary_trait": {"dataset": "a_Temp_dataset", "name": "a_name"}, + "primary_trait": {"dataset": "a_Temp_dataset", "trait_name": "a_name"}, "control_traits": [ - {"dataset": "a_dataset", "name": "a_name"}, - {"dataset": "a_dataset2", "name": "a_name2"}], + {"dataset": "a_dataset", "trait_name": "a_name"}, + {"dataset": "a_dataset2", "trait_name": "a_name2"}], "method": "a_method", "target_db": "a_db" })) -def test_partial_correlation_api_with_non_existent_primary_traits(client, post_data): +def test_partial_correlation_api_with_non_existent_primary_traits( + client, post_data, mocker): """ Check that the system responds appropriately in the case where the user makes a request with a non-existent primary trait. """ + mocker.patch("gn3.api.correlation.redis.Redis", mock.MagicMock()) response = client.post("/api/correlation/partial", json=post_data) assert ( - response.status_code == 404 and response.is_json and - response.json.get("status") != "error") + response.status_code == 200 and response.is_json and + response.json.get("status") == "success") @pytest.mark.integration_test @pytest.mark.slow @@ -141,41 +146,43 @@ def test_partial_correlation_api_with_non_existent_primary_traits(client, post_d "post_data", ({# ProbeSet "primary_trait": { - "dataset": "UCLA_BXDBXH_CARTILAGE_V2", "name": "ILM103710672"}, + "dataset": "UCLA_BXDBXH_CARTILAGE_V2", + "trait_name": "ILM103710672"}, "control_traits": [ - {"dataset": "a_dataset", "name": "a_name"}, - {"dataset": "a_dataset2", "name": "a_name2"}], + {"dataset": "a_dataset", "trait_name": "a_name"}, + {"dataset": "a_dataset2", "trait_name": "a_name2"}], "method": "a_method", "target_db": "a_db" }, {# Publish - "primary_trait": {"dataset": "BXDPublish", "name": "BXD_12557"}, + "primary_trait": {"dataset": "BXDPublish", "trait_name": "BXD_12557"}, "control_traits": [ - {"dataset": "a_dataset", "name": "a_name"}, - {"dataset": "a_dataset2", "name": "a_name2"}], + {"dataset": "a_dataset", "trait_name": "a_name"}, + {"dataset": "a_dataset2", "trait_name": "a_name2"}], "method": "a_method", "target_db": "a_db" }, {# Geno - "primary_trait": {"dataset": "AKXDGeno", "name": "D4Mit16"}, + "primary_trait": {"dataset": "AKXDGeno", "trait_name": "D4Mit16"}, "control_traits": [ - {"dataset": "a_dataset", "name": "a_name"}, - {"dataset": "a_dataset2", "name": "a_name2"}], + {"dataset": "a_dataset", "trait_name": "a_name"}, + {"dataset": "a_dataset2", "trait_name": "a_name2"}], "method": "a_method", "target_db": "a_db" } # Temp -- the data in the database for these is ephemeral, making it # difficult to test for this )) -def test_partial_correlation_api_with_non_existent_control_traits(client, post_data): +def test_partial_correlation_api_with_non_existent_control_traits(client, post_data, mocker): """ Check that the system responds appropriately in the case where the user makes a request with a non-existent control traits. The code repetition here is on purpose - valuing clarity over succinctness. """ + mocker.patch("gn3.api.correlation.redis.Redis", mock.MagicMock()) response = client.post("/api/correlation/partial", json=post_data) assert ( - response.status_code == 404 and response.is_json and - response.json.get("status") != "error") + response.status_code == 200 and response.is_json and + response.json.get("status") == "success") @pytest.mark.integration_test @pytest.mark.slow diff --git a/tests/performance/perf_query.py b/tests/performance/perf_query.py index c22dcf5..e534e9b 100644 --- a/tests/performance/perf_query.py +++ b/tests/performance/perf_query.py @@ -28,15 +28,13 @@ def timer(func): def query_executor(query: str, fetch_all: bool = True): """function to execute a query""" - conn, _ = database_connector() + with database_connector() as conn: + with conn.cursor() as cursor: + cursor.execute(query) - with conn: - cursor = conn.cursor() - cursor.execute(query) - - if fetch_all: - return cursor.fetchall() - return cursor.fetchone() + if fetch_all: + return cursor.fetchall() + return cursor.fetchone() def fetch_probeset_query(dataset_name: str): diff --git a/tests/unit/test_commands.py b/tests/unit/test_commands.py index e0efaf7..4dd8735 100644 --- a/tests/unit/test_commands.py +++ b/tests/unit/test_commands.py @@ -96,8 +96,7 @@ class TestCommands(unittest.TestCase): @pytest.mark.unit_test @mock.patch("gn3.commands.datetime") @mock.patch("gn3.commands.uuid4") - def test_queue_cmd_correct_calls_to_redis(self, mock_uuid4, - mock_datetime): + def test_queue_cmd_correct_calls_to_redis(self, mock_uuid4, mock_datetime): """Test that the cmd is queued properly""" mock_uuid4.return_value = 1234 mock_datetime.now.return_value = datetime.fromisoformat('2021-02-12 ' @@ -112,7 +111,7 @@ class TestCommands(unittest.TestCase): job_queue="GN2::job-queue"), actual_unique_id) mock_redis_conn.hset.assert_has_calls( - [mock.call(name=actual_unique_id, key="cmd", value="ls"), + [mock.call(name=actual_unique_id, key="cmd", value='"ls"'), mock.call(name=actual_unique_id, key="result", value=""), mock.call(name=actual_unique_id, key="status", value="queued")]) mock_redis_conn.rpush.assert_has_calls( @@ -139,23 +138,23 @@ class TestCommands(unittest.TestCase): email="me@me.com"), actual_unique_id) mock_redis_conn.hset.assert_has_calls( - [mock.call(name=actual_unique_id, key="cmd", value="ls"), + [mock.call(name=actual_unique_id, key="cmd", value='"ls"'), mock.call(name=actual_unique_id, key="result", value=""), mock.call(name=actual_unique_id, key="status", value="queued"), mock.call(name=actual_unique_id, key="email", value="me@me.com") - ]) + ], any_order=True) mock_redis_conn.rpush.assert_has_calls( [mock.call("GN2::job-queue", actual_unique_id)]) @pytest.mark.unit_test def test_run_cmd_correct_input(self): """Test that a correct cmd is processed correctly""" - self.assertEqual(run_cmd("echo test"), + self.assertEqual(run_cmd('"echo test"'), {"code": 0, "output": "test\n"}) @pytest.mark.unit_test def test_run_cmd_incorrect_input(self): """Test that an incorrect cmd is processed correctly""" - result = run_cmd("echoo test") + result = run_cmd('"echoo test"') self.assertEqual(127, result.get("code")) self.assertIn("not found", result.get("output")) diff --git a/tests/unit/test_db_utils.py b/tests/unit/test_db_utils.py index 96ee68f..44d6703 100644 --- a/tests/unit/test_db_utils.py +++ b/tests/unit/test_db_utils.py @@ -27,8 +27,6 @@ class TestDatabase(TestCase): mock_sql.connect.assert_called_with( "localhost", "guest", "4321", "users") - self.assertIsInstance( - results, tuple, "database not created successfully") @pytest.mark.unit_test @mock.patch("gn3.db_utils.SQL_URI", |