diff options
| -rw-r--r-- | gn3/db/case_attributes.py | 56 | ||||
| -rw-r--r-- | tests/unit/db/test_case_attributes.py | 8 |
2 files changed, 48 insertions, 16 deletions
diff --git a/gn3/db/case_attributes.py b/gn3/db/case_attributes.py index 356b745..9f34ed5 100644 --- a/gn3/db/case_attributes.py +++ b/gn3/db/case_attributes.py @@ -11,6 +11,17 @@ import lmdb import MySQLdb +class EditStatus(Enum): + """Enumeration for the status of the edits.""" + review = auto() # pylint: disable=[invalid-name] + approved = auto() # pylint: disable=[invalid-name] + rejected = auto() # pylint: disable=[invalid-name] + + def __str__(self): + """Print out human-readable form.""" + return self.name + + @dataclass class CaseAttributeEdit: """Represents an edit operation for case attributes in the database. @@ -24,21 +35,11 @@ class CaseAttributeEdit: """ inbredset_id: int + status: EditStatus user_id: str changes: dict -class EditStatus(Enum): - """Enumeration for the status of the edits.""" - review = auto() # pylint: disable=[invalid-name] - approved = auto() # pylint: disable=[invalid-name] - rejected = auto() # pylint: disable=[invalid-name] - - def __str__(self): - """Print out human-readable form.""" - return self.name - - def queue_edit(cursor, directory: Path, edit: CaseAttributeEdit) -> Optional[int]: """Queues a case attribute edit for review by inserting it into the audit table and storing its review ID in an LMDB database. @@ -47,7 +48,7 @@ def queue_edit(cursor, directory: Path, edit: CaseAttributeEdit) -> Optional[int cursor: A database cursor for executing SQL queries. directory (Path): The base directory path for the LMDB database. edit (CaseAttributeEdit): A dataclass containing the edit details, including - inbredset_id, user_id, and changes. + inbredset_id, status, user_id, and changes. Returns: int: An id the particular case-attribute that was updated. @@ -64,8 +65,8 @@ def queue_edit(cursor, directory: Path, edit: CaseAttributeEdit) -> Optional[int "caseattributes_audit(status, editor, json_diff_data) " "VALUES (%s, %s, %s) " "ON DUPLICATE KEY UPDATE status=%s", - (str(EditStatus.review), - edit.user_id, json.dumps(edit.changes), str(EditStatus.review),)) + (str(edit.status), edit.user_id, + json.dumps(edit.changes), str(EditStatus.review),)) directory = f"{directory}/case-attributes/{edit.inbredset_id}" if not os.path.exists(directory): os.makedirs(directory) @@ -78,3 +79,30 @@ def queue_edit(cursor, directory: Path, edit: CaseAttributeEdit) -> Optional[int review_ids.add(_id) txn.put(b"review", pickle.dumps(review_ids)) return _id + + + +def update_case_attribute_table(cursor, edit: CaseAttributeEdit) -> int: + # Check for ID in LMDB. If it exists: + # 1. Update the case_attributes in mysql + # 2. Update the review list, remove from lmdb, and create a new approved set. + # 3. + for strain, changes in modifications.items(): + for case_attribute, value in changes.items(): + value = 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", + (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)", + (inbredset_id, strain_id, case_attr_id, value,)) diff --git a/tests/unit/db/test_case_attributes.py b/tests/unit/db/test_case_attributes.py index 097a96f..18de4d3 100644 --- a/tests/unit/db/test_case_attributes.py +++ b/tests/unit/db/test_case_attributes.py @@ -5,7 +5,10 @@ import tempfile import os from pytest_mock import MockFixture from gn3.db.case_attributes import queue_edit -from gn3.db.case_attributes import CaseAttributeEdit +from gn3.db.case_attributes import ( + CaseAttributeEdit, + EditStatus +) @pytest.mark.unit_test @@ -14,8 +17,9 @@ def test_queue_edit(mocker: MockFixture) -> None: with mock_conn.cursor() as cursor: type(cursor).lastrowid = 28 TMPDIR = os.environ.get("TMPDIR", tempfile.gettempdir()) - review_ids = queue_edit( + caseattr_id = queue_edit( cursor, + status=EditStatus.review directory=TMPDIR, edit=CaseAttributeEdit(inbredset_id=1, user_id="xxxx", changes={"a": 1, "b": 2})) cursor.execute.assert_called_once_with( |