diff options
| -rw-r--r-- | gn3/db/case_attributes.py | 22 | ||||
| -rw-r--r-- | tests/unit/db/test_case_attributes.py | 102 |
2 files changed, 112 insertions, 12 deletions
diff --git a/gn3/db/case_attributes.py b/gn3/db/case_attributes.py index afebb7f..e14d99b 100644 --- a/gn3/db/case_attributes.py +++ b/gn3/db/case_attributes.py @@ -82,14 +82,17 @@ def queue_edit(cursor, directory: Path, edit: CaseAttributeEdit) -> Optional[int def update_case_attribute(cursor, directory: Path, - change_id: int, edit: CaseAttributeEdit) -> int: + 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 = {} - if edit.changes.get("Modifications").get("Current"): - modifications = edit.get("Modifications").get("Current") + modifications = dict() + if edit.changes.get("Modifications") and \ + edit.changes.get("Modifications").get("Current"): + modifications = edit.changes.get("Modifications").get("Current") + if not modifications: + return False for strain, changes in modifications.items(): for case_attribute, value in changes.items(): value = str(value).strip() @@ -101,7 +104,7 @@ def update_case_attribute(cursor, directory: Path, cursor.execute("SELECT CaseAttributeId, Name AS CaseAttributeName " "FROM CaseAttribute WHERE InbredSetId = %s " "AND Name = %s", - (inbredset_id, edit.inbredset_id,)) + (edit.inbredset_id, case_attribute,)) case_attr_id, _ = cursor.fetchone() cursor.execute( "INSERT INTO CaseAttributeXRefNew" @@ -110,16 +113,17 @@ def update_case_attribute(cursor, directory: Path, "ON DUPLICATE KEY UPDATE Value=VALUES(value)", (edit.inbredset_id, strain_id, case_attr_id, value,)) cursor.execute( - "UPDATE caseattributes_audit SET ", + "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) - review_ids.remove(change_id) - if approvals := txn.get(b"review"): + if approvals := txn.get(b"approved"): approved_ids = pickle.loads(approvals) - approved_ids.add(change_id) + review_ids.remove(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 diff --git a/tests/unit/db/test_case_attributes.py b/tests/unit/db/test_case_attributes.py index 18de4d3..790dbe6 100644 --- a/tests/unit/db/test_case_attributes.py +++ b/tests/unit/db/test_case_attributes.py @@ -1,13 +1,16 @@ """Test cases for gn3.db.case_attributes.py""" import pytest +import pickle import tempfile import os +from pathlib import Path from pytest_mock import MockFixture from gn3.db.case_attributes import queue_edit from gn3.db.case_attributes import ( CaseAttributeEdit, - EditStatus + EditStatus, + update_case_attribute ) @@ -19,9 +22,11 @@ def test_queue_edit(mocker: MockFixture) -> None: TMPDIR = os.environ.get("TMPDIR", tempfile.gettempdir()) caseattr_id = queue_edit( cursor, - status=EditStatus.review directory=TMPDIR, - edit=CaseAttributeEdit(inbredset_id=1, user_id="xxxx", changes={"a": 1, "b": 2})) + edit=CaseAttributeEdit( + inbredset_id=1, status=EditStatus.review, + user_id="xxxx", changes={"a": 1, "b": 2} + )) cursor.execute.assert_called_once_with( "INSERT INTO " "caseattributes_audit(status, editor, json_diff_data) " @@ -29,3 +34,94 @@ def test_queue_edit(mocker: MockFixture) -> None: "ON DUPLICATE KEY UPDATE status=%s", ('review', 'xxxx', '{"a": 1, "b": 2}', 'review')) assert 28 == caseattr_id + + +@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) |