diff options
| -rw-r--r-- | gn3/api/case_attributes.py | 31 | ||||
| -rw-r--r-- | gn3/db/case_attributes.py | 5 | ||||
| -rw-r--r-- | tests/unit/db/test_case_attributes.py | 4 |
3 files changed, 23 insertions, 17 deletions
diff --git a/gn3/api/case_attributes.py b/gn3/api/case_attributes.py index 837d0d1..536d74d 100644 --- a/gn3/api/case_attributes.py +++ b/gn3/api/case_attributes.py @@ -6,13 +6,6 @@ from urllib.parse import urljoin import requests from MySQLdb.cursors import DictCursor -from gn3.db.case_attributes import ( - CaseAttributeEdit, - EditStatus, - view_change, - queue_edit, - apply_change, - get_changes) from authlib.integrations.flask_oauth2.errors import _HTTPException from flask import ( jsonify, @@ -20,6 +13,13 @@ from flask import ( Response, Blueprint, current_app) +from gn3.db.case_attributes import ( + CaseAttributeEdit, + EditStatus, + view_change, + queue_edit, + apply_change, + get_changes) from gn3.db_utils import Connection, database_connection @@ -246,7 +246,8 @@ def edit_case_attributes(inbredset_id: int, auth_token=None) -> Response: @caseattr.route("/<int:inbredset_id>/diff/list", methods=["GET"]) -def list_diffs(inbredset_id: int) -> Response: +@require_token +def list_diffs(inbredset_id: int, auth_token=None) -> Response: """List any changes that have not been approved/rejected.""" try: required_access(auth_token, @@ -267,9 +268,9 @@ def list_diffs(inbredset_id: int) -> Response: }), 401 -@caseattr.route("/approve/<int:change_id>", methods=["POST"]) +@caseattr.route("/<int:inbredset_id>/approve/<int:change_id>", methods=["POST"]) @require_token -def approve_case_attributes_diff(filename: str, auth_token=None) -> Response: +def approve_case_attributes_diff(inbredset_id: int, change_id: int, auth_token=None) -> Response: """Approve the changes to the case attributes in the diff.""" try: required_access(auth_token, @@ -278,6 +279,7 @@ def approve_case_attributes_diff(filename: str, auth_token=None) -> Response: with database_connection(current_app.config["SQL_URI"]) as conn, \ conn.cursor() as cursor: match apply_change(cursor, change_type=EditStatus.rejected, + change_id=change_id, directory=current_app.config["LMDB_DATA_PATH"]): case True: return jsonify({ @@ -296,9 +298,9 @@ def approve_case_attributes_diff(filename: str, auth_token=None) -> Response: }), 401 -@caseattr.route("/reject/<int:change_id>", methods=["POST"]) +@caseattr.route("/<int:inbredset_id>/reject/<int:change_id>", methods=["POST"]) @require_token -def reject_case_attributes_diff(filename: str, auth_token=None) -> Response: +def reject_case_attributes_diff(inbredset_id: int, change_id: int, auth_token=None) -> Response: """Reject the changes to the case attributes in the diff.""" try: required_access(auth_token, @@ -308,6 +310,7 @@ def reject_case_attributes_diff(filename: str, auth_token=None) -> Response: with database_connection(current_app.config["SQL_URI"]) as conn, \ conn.cursor() as cursor: match apply_change(cursor, change_type=EditStatus.rejected, + change_id=change_id, directory=current_app.config["LMDB_DATA_PATH"]): case True: return jsonify({ @@ -326,9 +329,9 @@ def reject_case_attributes_diff(filename: str, auth_token=None) -> Response: }), 401 -@caseattr.route("/<int:change_id>/diff/view", methods=["GET"]) +@caseattr.route("/<int:inbredset_id>/diff/<int:change_id>/view", methods=["GET"]) @require_token -def view_diff(inbredset_id: int, diff_id: int, auth_token=None) -> Response: +def view_diff(inbredset_id: int, change_id: int, auth_token=None) -> Response: """View a diff.""" try: required_access( diff --git a/gn3/db/case_attributes.py b/gn3/db/case_attributes.py index c164b06..b16bbdd 100644 --- a/gn3/db/case_attributes.py +++ b/gn3/db/case_attributes.py @@ -252,9 +252,10 @@ def get_changes(cursor, inbredset_id: int, directory: Path) -> dict: } -# pylint: disable[too-many-locals] +# pylint: disable=[too-many-locals] def apply_change(cursor, change_type: EditStatus, change_id: int, directory: Path) -> bool: - """Applies or rejects a case attribute change and updates its status in the audit table and LMDB. + """Applies or rejects a case attribute change and updates its + status in the audit table and LMDB. Processes a change identified by `change_id` based on the specified `change_type` (approved or rejected). For approved diff --git a/tests/unit/db/test_case_attributes.py b/tests/unit/db/test_case_attributes.py index f5f2058..d9da253 100644 --- a/tests/unit/db/test_case_attributes.py +++ b/tests/unit/db/test_case_attributes.py @@ -1,11 +1,11 @@ """Test cases for gn3.db.case_attributes.py""" -import pytest import pickle import tempfile import os import json from pathlib import Path +import pytest from pytest_mock import MockFixture from gn3.db.case_attributes import queue_edit from gn3.db.case_attributes import ( @@ -18,6 +18,7 @@ from gn3.db.case_attributes import ( @pytest.mark.unit_test def test_queue_edit(mocker: MockFixture) -> None: + """Test queueing an edit.""" mock_conn = mocker.MagicMock() with mock_conn.cursor() as cursor: type(cursor).lastrowid = 28 @@ -90,6 +91,7 @@ def test_view_change_no_data(mocker: MockFixture) -> None: "Test no result when view_change is called" change_id = 28 mock_cursor, mock_conn = mocker.MagicMock(), mocker.MagicMock() + mock_conn.cursor.return_value = mock_cursor mock_cursor.fetchone.return_value = (None, None) assert view_change(mock_cursor, change_id) == {} mock_cursor.execute.assert_called_once_with( |