diff options
| -rw-r--r-- | gn3/db/case_attributes.py | 99 | ||||
| -rw-r--r-- | tests/unit/db/test_case_attributes.py | 120 |
2 files changed, 218 insertions, 1 deletions
diff --git a/gn3/db/case_attributes.py b/gn3/db/case_attributes.py index 4bdb654..0c3d115 100644 --- a/gn3/db/case_attributes.py +++ b/gn3/db/case_attributes.py @@ -123,7 +123,7 @@ def update_case_attribute(cursor, directory: Path, review_ids = pickle.loads(reviews) if approvals := txn.get(b"approved"): approved_ids = pickle.loads(approvals) - review_ids.remove(change_id) + review_ids.discard(change_id) approved_ids.add(change_id) txn.put(b"review", pickle.dumps(review_ids)) txn.put(b"approved", pickle.dumps(approved_ids)) @@ -186,3 +186,100 @@ def get_changes(cursor, inbredset_id: int, directory: Path) -> dict: "approvals": approvals, "rejections": rejections } + + +def apply_change(cursor, change_type: EditStatus, change_id: int, directory: Path) -> bool: + review_ids, approved_ids, rejected_ids = set(), set(), set() + env = lmdb.open(directory, map_size=8_000_000) # 1 MB + with env.begin(write=True) as txn: + if reviews := txn.get(b"review"): + review_ids = pickle.loads(reviews) + if change_id not in review_ids: + return False + match change_type: + case EditStatus.rejected: + cursor.execute( + "UPDATE caseattributes_audit " + "SET status = %s " + "WHERE id = %s", + (str(change_type), change_id)) + review_ids.discard(change_id) + rejected_ids.add(change_id) + txn.put(b"review", pickle.dumps(review_ids)) + txn.put(b"rejected", pickle.dumps(rejected_ids)) + return True + case EditStatus.approved: + cursor.execute( + "SELECT json_diff_data " + "FROM caseattributes_audit WHERE " + "id = %s", + (change_id,) + ) + json_diff_data, _ = cursor.fetchone() + json_diff_data = json.loads(json_diff_data) + inbredset_id = json_diff_data.get("inbredset_id") + modifications = json_diff_data.get( + "Modifications", {}).get("Current", {}) + strains = tuple(modifications.keys()) + case_attrs = set() + for data in modifications.values(): + case_attrs.update(data.keys()) + + # Bulk fetch strain ids + strain_id_map = {} + if strains: + cursor.execute( + "SELECT Name, Id FROM Strain WHERE Name IN " + f"({', '.join(['%s'] * len(strains))})", + strains + ) + for name, strain_id in cursor.fetchall(): + strain_id_map[name] = strain_id + + # Bulk fetch case attr ids + caseattr_id_map = {} + if case_attrs: + cursor.execute( + "SELECT Name, CaseAttributeId FROM CaseAttribute " + "WHERE InbredSetId = %s AND Name IN " + f"({', '.join(['%s'] * len(case_attrs))})", + (inbredset_id, *case_attrs) + ) + for name, caseattr_id in cursor.fetchall(): + caseattr_id_map[name] = caseattr_id + + # Bulk insert data + insert_data = [] + for strain, data in modifications.items(): + strain_id = strain_id_map.get(strain) + for case_attr, value in data.items(): + insert_data.append({ + "inbredset_id": inbredset_id, + "strain_id": strain_id, + "caseattr_id": caseattr_id_map.get(case_attr), + "value": value, + }) + if insert_data: + cursor.executemany( + "INSERT INTO CaseAttributeXRefNew " + "(InbredSetId, StrainId, CaseAttributeId, Value) " + "VALUES (%(inbredset_id)s, %(strain_id)s, %(caseattr_id)s, %(value)s) " + "ON DUPLICATE KEY UPDATE Value = VALUES(Value)", + insert_data + ) + + # Update LMDB and audit table + cursor.execute( + "UPDATE caseattributes_audit " + "SET status = %s " + "WHERE id = %s", + (str(change_type), change_id)) + if approvals := txn.get(b"approved"): + approved_ids = pickle.loads(approvals) + review_ids.discard(change_id) + approved_ids.add(change_id) + txn.put(b"review", pickle.dumps(review_ids)) + txn.put(b"approvals", pickle.dumps(approved_ids)) + return True + case _: + raise ValueError diff --git a/tests/unit/db/test_case_attributes.py b/tests/unit/db/test_case_attributes.py index 3580f93..494461a 100644 --- a/tests/unit/db/test_case_attributes.py +++ b/tests/unit/db/test_case_attributes.py @@ -11,6 +11,7 @@ from gn3.db.case_attributes import queue_edit from gn3.db.case_attributes import ( CaseAttributeEdit, EditStatus, + apply_change, view_change, update_case_attribute ) @@ -186,3 +187,122 @@ def test_view_change_no_data(mocker: MockFixture) -> None: mock_cursor.execute.assert_called_once_with( "SELECT json_diff_data FROM caseattributes_audit WHERE id = %s", (CHANGE_ID,)) + + +@pytest.mark.unit_test +def test_apply_change_approved(mocker: MockFixture) -> None: + """Test approving a change""" + mock_cursor, mock_conn = mocker.MagicMock(), mocker.MagicMock() + mock_conn.cursor.return_value = mock_cursor + mock_lmdb = mocker.patch("gn3.db.case_attributes.lmdb") + mock_env, mock_txn = mocker.MagicMock(), mocker.MagicMock() + mock_lmdb.open.return_value = mock_env + mock_env.begin.return_value.__enter__.return_value = mock_txn + CHANGE_ID, review_ids = 1, {1, 2, 3} + mock_txn.get.side_effect = ( + pickle.dumps(review_ids), # b"review" key + None, # b"approved" key + ) + TMPDIR = Path(os.environ.get("TMPDIR", tempfile.gettempdir())) + mock_cursor.fetchone.return_value = (json.dumps({ + "inbredset_id": 1, + "Modifications": { + "Current": { + "B6D2F1": {"Epoch": "10"}, + "BXD100": {"Epoch": "3"}, + "BXD101": {"SeqCvge": "2"}, + "BXD102": {"Epoch": "3"}, + "BXD108": {"SeqCvge": "oo"} + } + } + }), None) + mock_cursor.fetchall.side_effect = [ + [ # Strain query + ("B6D2F1", 1), ("BXD100", 2), + ("BXD101", 3), ("BXD102", 4), + ("BXD108", 5)], + [ # CaseAttribute query + ("Epoch", 101), ("SeqCvge", 102)] + ] + assert apply_change(mock_cursor, EditStatus.approved, + CHANGE_ID, TMPDIR) is True + assert mock_cursor.execute.call_count == 4 + mock_cursor.execute.assert_has_calls([ + mocker.call( + "SELECT json_diff_data FROM caseattributes_audit WHERE id = %s", + (CHANGE_ID,)), + mocker.call( + "SELECT Name, Id FROM Strain WHERE Name IN (%s, %s, %s, %s, %s)", + ("B6D2F1", "BXD100", "BXD101", "BXD102", "BXD108")), + mocker.call( + "SELECT Name, CaseAttributeId FROM CaseAttribute WHERE InbredSetId = %s AND Name IN (%s, %s)", + (1, "SeqCvge", "Epoch")), + mocker.call( + "UPDATE caseattributes_audit SET status = %s WHERE id = %s", + ("approved", CHANGE_ID)) + ]) + mock_cursor.executemany.assert_called_once_with( + "INSERT INTO CaseAttributeXRefNew (InbredSetId, StrainId, CaseAttributeId, Value) " + "VALUES (%(inbredset_id)s, %(strain_id)s, %(caseattr_id)s, %(value)s) " + "ON DUPLICATE KEY UPDATE Value = VALUES(Value)", + [ + {"inbredset_id": 1, "strain_id": 1, "caseattr_id": 101, "value": "10"}, + {"inbredset_id": 1, "strain_id": 2, "caseattr_id": 101, "value": "3"}, + {"inbredset_id": 1, "strain_id": 3, "caseattr_id": 102, "value": "2"}, + {"inbredset_id": 1, "strain_id": 4, "caseattr_id": 101, "value": "3"}, + {"inbredset_id": 1, "strain_id": 5, "caseattr_id": 102, "value": "oo"} + ] + ) + + +@pytest.mark.unit_test +def test_apply_change_rejected(mocker: MockFixture) -> None: + """Test rejecting a change""" + mock_cursor, mock_conn = mocker.MagicMock(), mocker.MagicMock() + mock_conn.cursor.return_value = mock_cursor + mock_lmdb = mocker.patch("gn3.db.case_attributes.lmdb") + mock_env, mock_txn = mocker.MagicMock(), mocker.MagicMock() + mock_lmdb.open.return_value = mock_env + mock_env.begin.return_value.__enter__.return_value = mock_txn + TMPDIR = Path(os.environ.get("TMPDIR", tempfile.gettempdir())) + CHANGE_ID, review_ids = 3, {1, 2, 3} + mock_txn.get.side_effect = [ + pickle.dumps(review_ids), # review_ids + None # rejected_ids (initially empty) + ] + + assert apply_change(mock_cursor, EditStatus.rejected, + CHANGE_ID, TMPDIR) is True + + # Verify SQL query call sequence + mock_cursor.execute.assert_called_once_with( + "UPDATE caseattributes_audit SET status = %s WHERE id = %s", + (str(EditStatus.rejected), CHANGE_ID)) + mock_cursor.executemany.assert_not_called() + + # Verify LMDB operations + mock_env.begin.assert_called_once_with(write=True) + expected_txn_calls = [ + mocker.call(b"review", pickle.dumps({1, 2})), + mocker.call(b"rejected", pickle.dumps({3})) + ] + mock_txn.put.assert_has_calls(expected_txn_calls, any_order=False) + + +@pytest.mark.unit_test +def test_apply_change_non_existent_change_id(mocker: MockFixture) -> None: + """Test that there's a missing change_id from the returned LMDB rejected set.""" + mock_env, mock_txn = mocker.MagicMock(), mocker.MagicMock() + mock_cursor, mock_conn = mocker.MagicMock(), mocker.MagicMock() + mock_lmdb = mocker.patch("gn3.db.case_attributes.lmdb") + mock_lmdb.open.return_value = mock_env + mock_conn.cursor.return_value = mock_cursor + mock_env.begin.return_value.__enter__.return_value = mock_txn + CHANGE_ID, review_ids = 28, {1, 2, 3} + mock_txn.get.side_effect = [ + pickle.dumps(review_ids), # b"review" key + None, # b"approved" key + ] + TMPDIR = Path(os.environ.get("TMPDIR", tempfile.gettempdir())) + assert apply_change(mock_cursor, EditStatus.approved, + CHANGE_ID, TMPDIR) is False |