diff options
| -rw-r--r-- | gn3/auth/authorisation/oauth2/__init__.py | 1 | ||||
| -rw-r--r-- | gn3/case_attributes.py | 39 | ||||
| -rw-r--r-- | gn3/errors.py | 1 |
3 files changed, 19 insertions, 22 deletions
diff --git a/gn3/auth/authorisation/oauth2/__init__.py b/gn3/auth/authorisation/oauth2/__init__.py new file mode 100644 index 0000000..d083773 --- /dev/null +++ b/gn3/auth/authorisation/oauth2/__init__.py @@ -0,0 +1 @@ +"""OAuth2 modules.""" diff --git a/gn3/case_attributes.py b/gn3/case_attributes.py index cec4850..c32e762 100644 --- a/gn3/case_attributes.py +++ b/gn3/case_attributes.py @@ -3,7 +3,6 @@ import os import csv import json import uuid -import requests import tempfile from enum import Enum, auto from pathlib import Path @@ -11,6 +10,7 @@ from functools import reduce from datetime import datetime from urllib.parse import urljoin +import requests from MySQLdb.cursors import DictCursor from authlib.integrations.flask_oauth2.errors import _HTTPException from flask import ( @@ -25,7 +25,6 @@ from gn3.commands import run_cmd from gn3.db_utils import Connection, database_connection -from gn3.auth.authorisation.users import User from gn3.auth.authorisation.errors import AuthorisationError from gn3.auth.authorisation.oauth2.resource_server import require_oauth @@ -42,9 +41,9 @@ class NoDiffError(ValueError): class EditStatus(Enum): """Enumeration for the status of the edits.""" - review = auto() - approved = auto() - rejected = auto() + 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.""" @@ -52,7 +51,7 @@ class EditStatus(Enum): class CAJSONEncoder(json.JSONEncoder): """Encoder for CaseAttribute-specific data""" - def default(self, obj): + def default(self, obj): # pylint: disable=[arguments-renamed] """Default encoder""" if isinstance(obj, datetime): return obj.isoformat() @@ -395,7 +394,7 @@ def __apply_deletions__( params) def __apply_diff__( - conn: Connection, inbredset_id: int, user: User, diff_filename, the_diff) -> None: + conn: Connection, inbredset_id: int, diff_filename, the_diff) -> None: """ Apply the changes in the diff at `diff_filename` to the data in the database if the user has appropriate privileges. @@ -417,7 +416,6 @@ def __apply_diff__( def __reject_diff__(conn: Connection, inbredset_id: int, - user: User, diff_filename: Path, diff: dict) -> Path: """ @@ -436,16 +434,16 @@ def __reject_diff__(conn: Connection, def add_case_attributes(inbredset_id: int) -> Response: """Add a new case attribute for `InbredSetId`.""" required_access(inbredset_id, ("system:inbredset:create-case-attribute",)) - with (require_oauth.acquire("profile resource") as the_token, - database_connection(current_app.config["SQL_URI"]) as conn): + with (require_oauth.acquire("profile resource") as the_token, # pylint: disable=[unused-variable] + database_connection(current_app.config["SQL_URI"]) as conn): # pylint: disable=[unused-variable] raise NotImplementedError @caseattr.route("/<int:inbredset_id>/delete", methods=["POST"]) def delete_case_attributes(inbredset_id: int) -> Response: """Delete a case attribute from `InbredSetId`.""" required_access(inbredset_id, ("system:inbredset:delete-case-attribute",)) - with (require_oauth.acquire("profile resource") as the_token, - database_connection(current_app.config["SQL_URI"]) as conn): + with (require_oauth.acquire("profile resource") as the_token, # pylint: disable=[unused-variable] + database_connection(current_app.config["SQL_URI"]) as conn): # pylint: disable=[unused-variable] raise NotImplementedError @caseattr.route("/<int:inbredset_id>/edit", methods=["POST"]) @@ -487,7 +485,7 @@ def edit_case_attributes(inbredset_id: int) -> Response: try: __apply_diff__( - conn, inbredset_id, user, diff_filename, __load_diff__(diff_filename)) + conn, inbredset_id, diff_filename, __load_diff__(diff_filename)) return jsonify({ "diff-status": "applied", "message": ("The changes to the case-attributes have been " @@ -558,9 +556,8 @@ def approve_case_attributes_diff(filename: str) -> Response: diff_dir = Path(current_app.config.get("TMPDIR"), CATTR_DIFFS_DIR) diff_filename = Path(diff_dir, filename) the_diff = __load_diff__(diff_filename) - with (require_oauth.acquire("profile resource") as the_token, - database_connection(current_app.config["SQL_URI"]) as conn): - __apply_diff__(conn, the_diff["inbredset_id"], the_token.user, diff_filename, the_diff) + with database_connection(current_app.config["SQL_URI"]) as conn: + __apply_diff__(conn, the_diff["inbredset_id"], diff_filename, the_diff) return jsonify({ "message": "Applied the diff successfully.", "diff_filename": diff_filename.name @@ -572,19 +569,17 @@ def reject_case_attributes_diff(filename: str) -> Response: diff_dir = Path(current_app.config.get("TMPDIR"), CATTR_DIFFS_DIR) diff_filename = Path(diff_dir, filename) the_diff = __load_diff__(diff_filename) - with (require_oauth.acquire("profile resource") as the_token, - database_connection(current_app.config["SQL_URI"]) as conn): - __reject_diff__(conn, the_diff["inbredset_id"], the_token.user, diff_filename, the_diff) + with database_connection(current_app.config["SQL_URI"]) as conn: + __reject_diff__(conn, the_diff["inbredset_id"], diff_filename, the_diff) return jsonify({ - "message": f"Rejected diff successfully", + "message": "Rejected diff successfully", "diff_filename": diff_filename.name }) @caseattr.route("/<int:inbredset_id>/diff/<int:diff_id>/view", methods=["GET"]) def view_diff(inbredset_id: int, diff_id: int) -> Response: """View a diff.""" - with (require_oauth.acquire("profile resource") as the_token, - database_connection(current_app.config["SQL_URI"]) as conn, + with (database_connection(current_app.config["SQL_URI"]) as conn, conn.cursor(cursorclass=DictCursor) as cursor): required_access(inbredset_id, ("system:inbredset:view-case-attribute",)) cursor.execute( diff --git a/gn3/errors.py b/gn3/errors.py index 121187c..cd707f3 100644 --- a/gn3/errors.py +++ b/gn3/errors.py @@ -6,6 +6,7 @@ from authlib.oauth2.rfc6749.errors import OAuth2Error from gn3.auth.authorisation.errors import AuthorisationError def page_not_found(pnf): + """Generic 404 handler.""" return jsonify({ "error": pnf.name, "error_description": pnf.description |