diff options
| -rw-r--r-- | gn3/api/async_commands.py | 6 | ||||
| -rw-r--r-- | gn3/api/correlation.py | 6 | ||||
| -rw-r--r-- | gn3/commands.py | 1 | ||||
| -rw-r--r-- | gn3/db_utils.py | 5 | ||||
| -rw-r--r-- | gn3/fs_helpers.py | 5 | ||||
| -rw-r--r-- | tests/unit/test_db_utils.py | 2 | ||||
| -rw-r--r-- | tests/unit/test_file_utils.py | 2 |
7 files changed, 9 insertions, 18 deletions
diff --git a/gn3/api/async_commands.py b/gn3/api/async_commands.py index 81c3c44..c0cf4bb 100644 --- a/gn3/api/async_commands.py +++ b/gn3/api/async_commands.py @@ -1,6 +1,4 @@ """Endpoints and functions concerning commands run in external processes.""" -import json - import redis from flask import jsonify, Blueprint @@ -8,11 +6,11 @@ async_commands = Blueprint("async_commands", __name__) @async_commands.route("/state/<command_id>") def command_state(command_id): + """Respond with the current state of command identified by `command_id`.""" with redis.Redis(decode_responses=True) as rconn: state = rconn.hgetall(name=command_id) if not state: return jsonify( status=404, error="The command id provided does not exist.") - state = {key: val for key,val in state.items()} - return jsonify(state) + return jsonify(dict(state.items())) diff --git a/gn3/api/correlation.py b/gn3/api/correlation.py index 67897e8..7eb7cd6 100644 --- a/gn3/api/correlation.py +++ b/gn3/api/correlation.py @@ -1,6 +1,5 @@ """Endpoints for running correlations""" import sys -import json from functools import reduce import redis @@ -17,7 +16,6 @@ from gn3.computations.correlations import map_shared_keys_to_values from gn3.computations.correlations import compute_tissue_correlation from gn3.computations.correlations import compute_all_lit_correlation from gn3.computations.correlations import compute_all_sample_correlation -from gn3.computations.partial_correlations import partial_correlations_entry correlation = Blueprint("correlation", __name__) @@ -132,7 +130,3 @@ def partial_correlation(): int(args.get("criteria", 500))), job_queue=current_app.config.get("REDIS_JOB_QUEUE"), env = {"PYTHONPATH": ":".join(sys.path), "SQL_URI": SQL_URI})}) - -@correlation.route("/partial/<job_id>", methods=["GET"]) -def partial_correlation_results(): - raise Exception("Not implemented!!") diff --git a/gn3/commands.py b/gn3/commands.py index 0e0b53c..e622068 100644 --- a/gn3/commands.py +++ b/gn3/commands.py @@ -54,6 +54,7 @@ def compose_rqtl_cmd(rqtl_wrapper_cmd: str, def compose_pcorrs_command( primary_trait: str, control_traits: Tuple[str, ...], method: str, target_database: str, criteria: int = 500): + """Compose the command to run partias correlations""" rundir = os.path.abspath(".") return ( f"{sys.executable}", f"{rundir}/scripts/partial_correlations.py", diff --git a/gn3/db_utils.py b/gn3/db_utils.py index 3703cbb..3b72d28 100644 --- a/gn3/db_utils.py +++ b/gn3/db_utils.py @@ -17,7 +17,4 @@ def parse_db_url() -> Tuple: def database_connector() -> mdb.Connection: """function to create db connector""" host, user, passwd, db_name = parse_db_url() - conn = mdb.connect(host, user, passwd, db_name) - cursor = conn.cursor() - - return conn + return mdb.connect(host, user, passwd, db_name) diff --git a/gn3/fs_helpers.py b/gn3/fs_helpers.py index 578269b..f313086 100644 --- a/gn3/fs_helpers.py +++ b/gn3/fs_helpers.py @@ -71,9 +71,8 @@ contents to TARGET_DIR/<dir-hash>. os.mkdir(os.path.join(target_dir, token)) gzipped_file.save(tar_target_loc) # Extract to "tar_target_loc/token" - tar = tarfile.open(tar_target_loc) - tar.extractall(path=os.path.join(target_dir, token)) - tar.close() + with tarfile.open(tar_target_loc) as tar: + tar.extractall(path=os.path.join(target_dir, token)) # pylint: disable=W0703 except Exception: return {"status": 128, "error": "gzip failed to unpack file"} diff --git a/tests/unit/test_db_utils.py b/tests/unit/test_db_utils.py index 44d6703..7dc66c0 100644 --- a/tests/unit/test_db_utils.py +++ b/tests/unit/test_db_utils.py @@ -27,6 +27,8 @@ class TestDatabase(TestCase): mock_sql.connect.assert_called_with( "localhost", "guest", "4321", "users") + self.assertIsInstance( + results, SimpleNamespace, "database not created successfully") @pytest.mark.unit_test @mock.patch("gn3.db_utils.SQL_URI", diff --git a/tests/unit/test_file_utils.py b/tests/unit/test_file_utils.py index 7048d43..2c6f0b6 100644 --- a/tests/unit/test_file_utils.py +++ b/tests/unit/test_file_utils.py @@ -66,7 +66,7 @@ non-existent""" "upload-data.tar.gz") mock_tarfile.open.assert_called_once_with("/tmp/abcdef-abcdef/" "upload-data.tar.gz") - mock_tarfile.open.return_value.extractall.assert_called_once_with( + mock_tarfile.open.return_value.__enter__.return_value.extractall.assert_called_once_with( path='/tmp/abcdef-abcdef') mock_file.assert_called_once_with("upload-data.tar.gz") self.assertEqual(result, {"status": 0, "token": "abcdef-abcdef"}) |