diff options
| -rw-r--r-- | gn3/api/case_attributes.py | 3 | ||||
| -rw-r--r-- | gn3/db/case_attributes.py | 49 | ||||
| -rw-r--r-- | tests/unit/db/test_case_attributes.py | 94 |
3 files changed, 2 insertions, 144 deletions
diff --git a/gn3/api/case_attributes.py b/gn3/api/case_attributes.py index fa62942..0058bb9 100644 --- a/gn3/api/case_attributes.py +++ b/gn3/api/case_attributes.py @@ -231,8 +231,7 @@ def edit_case_attributes(inbredset_id: int, auth_token=None) -> Response: inbredset_id, ("system:inbredset:edit-case-attribute", "system:inbredset:apply-case-attribute-edit")) - edit.status = EditStatus.approved - match update_case_attributes(cursor=cursor, change_id=_id, edit=edit): + match apply_change(cursor, change_type=EditStatus.approved, directory=directory): case True: return jsonify({ "diff-status": "applied", diff --git a/gn3/db/case_attributes.py b/gn3/db/case_attributes.py index 0c3d115..b22d775 100644 --- a/gn3/db/case_attributes.py +++ b/gn3/db/case_attributes.py @@ -81,55 +81,6 @@ def queue_edit(cursor, directory: Path, edit: CaseAttributeEdit) -> Optional[int return _id -def update_case_attribute(cursor, directory: Path, - change_id: int, edit: CaseAttributeEdit) -> bool: - directory = f"{directory}/case-attributes/{edit.inbredset_id}" - if not os.path.exists(directory): - os.makedirs(directory) - env = lmdb.open(directory, map_size=8_000_000) # 1 MB - modifications = dict() - if edit.changes.get("Modifications") and \ - edit.changes.get("Modifications").get("Current"): - modifications = edit.changes.get("Modifications").get("Current") - if not modifications: - env.close() - return False - for strain, changes in modifications.items(): - for case_attribute, value in changes.items(): - value = str(value).strip() - cursor.execute("SELECT Id AS StrainId, Name AS StrainName FROM Strain " - "WHERE Name = %s", - (strain,)) - - strain_id, _ = cursor.fetchone() - cursor.execute("SELECT CaseAttributeId, Name AS CaseAttributeName " - "FROM CaseAttribute WHERE InbredSetId = %s " - "AND Name = %s", - (edit.inbredset_id, case_attribute,)) - case_attr_id, _ = cursor.fetchone() - cursor.execute( - "INSERT INTO CaseAttributeXRefNew" - "(InbredSetId, StrainId, CaseAttributeId, Value) " - "VALUES (%s, %s, %s, %s) " - "ON DUPLICATE KEY UPDATE Value=VALUES(value)", - (edit.inbredset_id, strain_id, case_attr_id, value,)) - cursor.execute( - "UPDATE caseattributes_audit SET " - "status = %s WHERE id = %s", - (str(edit.status), change_id,)) - with env.begin(write=True) as txn: - review_ids, approved_ids = set(), set() - if reviews := txn.get(b"review"): - review_ids = pickle.loads(reviews) - 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"approved", pickle.dumps(approved_ids)) - return True - - def __fetch_case_attrs_changes__(cursor, change_ids: tuple) -> list: placeholders = ','.join(['%s'] * len(change_ids)) cursor.execute( diff --git a/tests/unit/db/test_case_attributes.py b/tests/unit/db/test_case_attributes.py index 494461a..5d023f6 100644 --- a/tests/unit/db/test_case_attributes.py +++ b/tests/unit/db/test_case_attributes.py @@ -12,8 +12,7 @@ from gn3.db.case_attributes import ( CaseAttributeEdit, EditStatus, apply_change, - view_change, - update_case_attribute + view_change ) @@ -40,97 +39,6 @@ def test_queue_edit(mocker: MockFixture) -> None: @pytest.mark.unit_test -def test_update_case_attribute_success(mocker: MockFixture) -> None: - """Test successful case attribute update with valid modifications.""" - 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 - mock_txn.get.side_effect = [ - pickle.dumps({100}), # b"review" key - None, # b"approved" key - ] - - TMPDIR = Path(os.environ.get("TMPDIR", tempfile.gettempdir())) - edit = CaseAttributeEdit( - inbredset_id=1, - user_id="test_user", - status=EditStatus.approved, - changes={ - "Modifications": { - "Current": { - "Strain1": {"Attribute1": "Value1"} - } - } - } - ) - change_id = 100 - - # Mock cursor fetch results - mock_cursor.fetchone.side_effect = [ - (10, "Strain1"), # Strain query - (20, "Attribute1"), # CaseAttribute query - ] - - assert update_case_attribute(mock_cursor, TMPDIR, change_id, edit) - - # Assertions for lmdb interactions - mock_lmdb.open.assert_called_once_with( - f"{TMPDIR}/case-attributes/1", map_size=8_000_000) - mock_env.begin.assert_called_once_with(write=True) - mock_txn.get.assert_has_calls([ - mocker.call(b"review"), - mocker.call(b"approved") - ]) - mock_txn.put.assert_has_calls([ - mocker.call(b"review", pickle.dumps(set())), - mocker.call(b"approved", pickle.dumps({100})) - ]) - - # Assertions for SQL executions - mock_cursor.execute.assert_has_calls([ - mocker.call( - "SELECT Id AS StrainId, Name AS StrainName FROM Strain WHERE Name = %s", - ("Strain1",) - ), - mocker.call( - "SELECT CaseAttributeId, Name AS CaseAttributeName FROM CaseAttribute " - "WHERE InbredSetId = %s AND Name = %s", - (1, "Attribute1") - ), - mocker.call( - "INSERT INTO CaseAttributeXRefNew(InbredSetId, StrainId, CaseAttributeId, Value) " - "VALUES (%s, %s, %s, %s) ON DUPLICATE KEY UPDATE Value=VALUES(value)", - (1, 10, 20, "Value1") - ), - mocker.call( - "UPDATE caseattributes_audit SET status = %s WHERE id = %s", - ("approved", 100) - ) - ]) - - -@pytest.mark.unit_test -def test_update_case_attribute_no_modifications(mocker: MockFixture) -> None: - """Test update_case_attribute with no modifications in edit.changes.""" - 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() - TMPDIR = Path(os.environ.get("TMPDIR", tempfile.gettempdir())) - edit = CaseAttributeEdit( - inbredset_id=1, - user_id="test_user", - status=EditStatus.approved, - changes={} # No modifications - ) - change_id = 28 - assert not update_case_attribute(mock_cursor, TMPDIR, change_id, edit) - - -@pytest.mark.unit_test def test_view_change(mocker: MockFixture) -> None: """Test view_change function.""" sample_json_diff = { |