From 24b3f7bdfad6d8ac0702076612318456bccee539 Mon Sep 17 00:00:00 2001 From: Alex VanTol Date: Fri, 14 Apr 2023 13:46:22 -0500 Subject: [PATCH 01/11] fix(google_update): don't fail early with Google errors (try to continue), improve logging --- fence/resources/google/access_utils.py | 32 +++++++++++++++++++++++--- fence/resources/user/__init__.py | 4 ++-- 2 files changed, 31 insertions(+), 5 deletions(-) diff --git a/fence/resources/google/access_utils.py b/fence/resources/google/access_utils.py index c3bf1efc3..5969c6d06 100644 --- a/fence/resources/google/access_utils.py +++ b/fence/resources/google/access_utils.py @@ -5,6 +5,7 @@ import time import flask from urllib.parse import unquote +import traceback from cirrus.google_cloud.iam import GooglePolicyMember @@ -47,6 +48,7 @@ def bulk_update_google_groups(google_bulk_mapping): google_project_id = ( config["STORAGE_CREDENTIALS"].get("google", {}).get("google_project_id") ) + google_update_failures = False with GoogleCloudManager(google_project_id) as gcm: for group, expected_members in google_bulk_mapping.items(): expected_members = set(expected_members) @@ -69,12 +71,37 @@ def bulk_update_google_groups(google_bulk_mapping): # do add for member_email in to_add: logger.info(f"Adding to group {group}: {member_email}") - gcm.add_member_to_group(member_email, group) + try: + gcm.add_member_to_group(member_email, group) + except Exception as exc: + logging.error( + f"ERROR: FAILED TO ADD MEMBER TO GOOGLE GROUP! This sync will SKIP " + f"the above user to try and update other authorization " + f"(rather than failing early). The error will be re-raised " + f"after attempting to update all other users. Exc: " + f"{traceback.format_exc()}" + ) + google_update_failures = True # do remove for member_email in to_delete: logger.info(f"Removing from group {group}: {member_email}") - gcm.remove_member_from_group(member_email, group) + try: + gcm.remove_member_from_group(member_email, group) + except Exception as exc: + logging.error( + f"ERROR: FAILED TO REMOVE MEMBER TO GOOGLE GROUP! This sync will SKIP " + f"the above user to try and update other authorization " + f"(rather than failing early). The error will be re-raised " + f"after attempting to update all other users. Exc: " + f"{traceback.format_exc()}" + ) + google_update_failures = True + + if google_update_failures: + raise Exception( + f"FAILED TO UPDATE GOOGLE GROUPS (see previous errors)." + ) def get_google_project_number(google_project_id, google_cloud_manager): @@ -716,7 +743,6 @@ def _revoke_user_service_account_from_google( if not g_manager.remove_member_from_group( member_email=service_account.email, group_id=access_group.email ): - logger.debug( "Removed {} from google group {}".format( service_account.email, access_group.email diff --git a/fence/resources/user/__init__.py b/fence/resources/user/__init__.py index b856cd952..c4c1647aa 100644 --- a/fence/resources/user/__init__.py +++ b/fence/resources/user/__init__.py @@ -118,9 +118,9 @@ def get_user_info(current_session, username): user.username ) auth_mapping = flask.current_app.arborist.auth_mapping(user.username) - except ArboristError: + except ArboristError as exc: logger.error( - "request to arborist for user's resources failed; going to list empty" + f"request to arborist for user's resources failed; going to list empty. Error: {exc}" ) resources = [] auth_mapping = {} From 551cad673f080799a55939b050bec9fa85c94797 Mon Sep 17 00:00:00 2001 From: Alex VanTol Date: Tue, 18 Apr 2023 12:48:47 -0500 Subject: [PATCH 02/11] feat(prometheus): start removing prometheus logic, metrics should be gathered by external tools by logs and not embedded into services --- fence/__init__.py | 13 ----- fence/blueprints/data/indexd.py | 5 -- tests/data/test_data.py | 99 --------------------------------- 3 files changed, 117 deletions(-) diff --git a/fence/__init__.py b/fence/__init__.py index 3e4942958..faa55cec7 100755 --- a/fence/__init__.py +++ b/fence/__init__.py @@ -509,28 +509,15 @@ def _setup_prometheus(app): multiprocess, make_wsgi_app, ) - from prometheus_flask_exporter import Counter - from prometheus_flask_exporter.multiprocess import ( - UWsgiPrometheusMetrics, - ) app.prometheus_registry = CollectorRegistry() multiprocess.MultiProcessCollector(app.prometheus_registry) - UWsgiPrometheusMetrics(app) - # Add prometheus wsgi middleware to route /metrics requests app.wsgi_app = DispatcherMiddleware( app.wsgi_app, {"/metrics": make_wsgi_app(registry=app.prometheus_registry)} ) - # set up counters - app.prometheus_counters["pre_signed_url_req"] = Counter( - "pre_signed_url_req", - "tracking presigned url requests", - ["requested_protocol"], - ) - @app.errorhandler(Exception) def handle_error(error): diff --git a/fence/blueprints/data/indexd.py b/fence/blueprints/data/indexd.py index c969bb162..83f4b115b 100755 --- a/fence/blueprints/data/indexd.py +++ b/fence/blueprints/data/indexd.py @@ -156,11 +156,6 @@ def get_signed_url_for_file( "sub": authorized_user_from_passport.id, } - # increment counter for gen3-metrics - counter = flask.current_app.prometheus_counters.get("pre_signed_url_req") - if counter: - counter.labels(requested_protocol).inc() - return {"url": signed_url} diff --git a/tests/data/test_data.py b/tests/data/test_data.py index 5e4ab361e..bea09c9bd 100755 --- a/tests/data/test_data.py +++ b/tests/data/test_data.py @@ -107,105 +107,6 @@ def test_indexd_download_file( ) -@pytest.mark.parametrize("indexd_client", ["s3"], indirect=True) -def test_indexd_prometheus_presigned_url_counter( - app, - client, - oauth_client, - user_client, - indexd_client, - kid, - rsa_private_key, - google_proxy_group, - primary_google_service_account, - cloud_manager, - google_signed_url, -): - """ - Test that when a user requests a presigned URL, the prometheus counter is increased. - """ - before = ( - app.prometheus_registry.get_sample_value( - "pre_signed_url_req_total", - { - "requested_protocol": indexd_client["indexed_file_location"], - }, - ) - or 0 - ) - - # make a presigned URL request - indexed_file_location = indexd_client["indexed_file_location"] - path = "/data/download/1" - query_string = {"protocol": indexed_file_location} - headers = { - "Authorization": "Bearer " - + jwt.encode( - utils.authorized_download_context_claims( - user_client.username, user_client.user_id - ), - key=rsa_private_key, - headers={"kid": kid}, - algorithm="RS256", - ) - } - response = client.get(path, headers=headers, query_string=query_string) - assert response.status_code == 200 - - # assert metrics have been processed successfully - after = app.prometheus_registry.get_sample_value( - "pre_signed_url_req_total", - { - "requested_protocol": indexd_client["indexed_file_location"], - }, - ) - assert after, "Presigned URL requests should have been counted" - assert 1 == (after - before), "1 presigned URL request should have been counted" - - # defaults to signing url, check that it's not just raw url - assert urllib.parse.urlparse(response.json["url"]).query != "" - - -@pytest.mark.parametrize( - "indexd_client", - ["gs", "s3", "gs_acl", "s3_acl", "s3_external", "no_urls", "az", "https"], - indirect=True, -) -def test_indexd_upload_file( - client, - oauth_client, - user_client, - indexd_client, - kid, - rsa_private_key, - google_proxy_group, - primary_google_service_account, - cloud_manager, - google_signed_url, -): - """ - Test ``GET /data/download/1``. - """ - file_id = "1" - indexed_file_location = indexd_client["indexed_file_location"] - path = f"/data/upload/{file_id}?protocol=" + indexed_file_location - headers = { - "Authorization": "Bearer " - + jwt.encode( - utils.authorized_upload_context_claims( - user_client.username, user_client.user_id - ), - key=rsa_private_key, - headers={"kid": kid}, - algorithm="RS256", - ) - } - response = client.get(path, headers=headers) - assert response.status_code == 200 - assert "url" in list(response.json.keys()) - assert file_id in response.json.get("url") - - @pytest.mark.parametrize( "indexd_client", ["gs", "s3", "gs_acl", "s3_acl", "s3_external", "az", "https"], From 8bb3937d22df1c73752aed731f78f1d3a151d0f4 Mon Sep 17 00:00:00 2001 From: Alex VanTol Date: Tue, 18 Apr 2023 12:52:31 -0500 Subject: [PATCH 03/11] feat(flask upgrade): upgrade many deps, replace deprecated session management library with recommended session strategies, fix other deprecated/removed features --- fence/__init__.py | 32 +- fence/auth.py | 34 +- fence/blueprints/admin.py | 94 +- fence/blueprints/data/indexd.py | 7 +- fence/blueprints/ga4gh.py | 3 +- fence/blueprints/google.py | 27 +- fence/blueprints/link.py | 32 +- fence/blueprints/login/ras.py | 4 +- fence/blueprints/login/synapse.py | 6 +- fence/blueprints/register.py | 6 +- fence/blueprints/storage_creds/__init__.py | 6 +- fence/blueprints/storage_creds/google.py | 12 +- fence/blueprints/user.py | 18 +- fence/blueprints/well_known.py | 2 +- fence/oidc/jwt_generator.py | 16 +- fence/resources/ga4gh/passports.py | 12 +- fence/resources/google/utils.py | 67 +- fence/resources/google/validity.py | 2 - fence/resources/openid/idp_oauth2.py | 7 +- fence/resources/openid/ras_oauth2.py | 8 +- fence/resources/user/user_session.py | 6 +- fence/scripting/fence_create.py | 9 +- fence/sync/sync_users.py | 30 +- fence/user.py | 4 +- poetry.lock | 1070 ++++++++++---------- pyproject.toml | 20 +- tests/conftest.py | 20 +- tests/google/conftest.py | 6 - tests/login/test_login_user.py | 1 - tests/test_app_config.py | 4 + tests/test_drs.py | 6 + 31 files changed, 809 insertions(+), 762 deletions(-) diff --git a/fence/__init__.py b/fence/__init__.py index faa55cec7..d42d91cdc 100755 --- a/fence/__init__.py +++ b/fence/__init__.py @@ -4,7 +4,9 @@ from urllib.parse import urljoin import flask from flask_cors import CORS -from flask_sqlalchemy_session import flask_scoped_session, current_session +from sqlalchemy.orm import scoped_session +from flask import _app_ctx_stack, current_app +from werkzeug.local import LocalProxy from authutils.oauth2.client import OAuthClient from cdislogging import get_logger @@ -112,7 +114,24 @@ def app_sessions(app): SQLAlchemyDriver.setup_db = lambda _: None app.db = SQLAlchemyDriver(config["DB"]) - session = flask_scoped_session(app.db.Session, app) # noqa + # app.db.Session is from SQLAlchemyDriver and uses + # SQLAlchemy's sessionmaker. Using scoped_session here ensures + # a thread-local db session is created. Effectively the below is expanded to: + # app.scoped_session = scoped_session( + # sessionmaker( + # bind=sqlalchemy.create_engine(config["DB"]), + # expire_on_commit=False, + # ) + # ) + # + # From the sqlalchemy docs: "The scoped_session object by default uses + # [Python's threading.local() construct] as + # storage, so that a single Session is maintained for all who call upon the + # scoped_session registry, but only within the scope of a single thread. + # Callers who call upon the registry in a different thread get a Session + # instance that is local to that other thread." + app.scoped_session = scoped_session(app.db.Session) + app.session_interface = UserSessionInterface() @@ -556,3 +575,12 @@ def check_csrf(): logger.debug("HTTP REFERER " + str(referer)) except Exception as e: raise UserError("CSRF verification failed: {}. Request aborted".format(e)) + + +@app.teardown_appcontext +def remove_scoped_session(*args, **kwargs): + if hasattr(app, "scoped_session"): + try: + app.scoped_session.remove() + except Exception as exc: + logger.warning(f"could not remove app.scoped_session. Error: {exc}") diff --git a/fence/auth.py b/fence/auth.py index a3049e0e1..3bc1873f3 100644 --- a/fence/auth.py +++ b/fence/auth.py @@ -1,5 +1,5 @@ import flask -from flask_sqlalchemy_session import current_session +from flask import current_app from datetime import datetime from functools import wraps import urllib.request, urllib.parse, urllib.error @@ -95,7 +95,7 @@ def set_flask_session_values(user): flask.g.scopes = ["_all"] flask.g.token = None - user = query_for_user(session=current_session, username=username) + user = query_for_user(session=current_app.scoped_session(), username=username) if user: _update_users_email(user, email) _update_users_id_from_idp(user, id_from_idp) @@ -120,7 +120,8 @@ def set_flask_session_values(user): # setup idp connection for new user (or existing user w/o it setup) idp = ( - current_session.query(IdentityProvider) + current_app.scoped_session() + .query(IdentityProvider) .filter(IdentityProvider.name == provider) .first() ) @@ -128,8 +129,8 @@ def set_flask_session_values(user): idp = IdentityProvider(name=provider) user.identity_provider = idp - current_session.add(user) - current_session.commit() + current_app.scoped_session().add(user) + current_app.scoped_session().commit() set_flask_session_values(user) @@ -238,7 +239,9 @@ def has_oauth(scope=None): raise Unauthorized("failed to validate token: {}".format(e)) if "sub" in access_token_claims: user_id = access_token_claims["sub"] - user = current_session.query(User).filter_by(id=int(user_id)).first() + user = ( + current_app.scoped_session().query(User).filter_by(id=int(user_id)).first() + ) if not user: raise Unauthorized("no user found with id: {}".format(user_id)) # set some application context for current user @@ -250,7 +253,12 @@ def has_oauth(scope=None): def get_user_from_claims(claims): - return current_session.query(User).filter(User.id == claims["sub"]).first() + return ( + current_app.scoped_session() + .query(User) + .filter(User.id == claims["sub"]) + .first() + ) def admin_required(f): @@ -284,8 +292,8 @@ def _update_users_email(user, email): ) user.email = email - current_session.add(user) - current_session.commit() + current_app.scoped_session().add(user) + current_app.scoped_session().commit() def _update_users_id_from_idp(user, id_from_idp): @@ -298,8 +306,8 @@ def _update_users_id_from_idp(user, id_from_idp): ) user.id_from_idp = id_from_idp - current_session.add(user) - current_session.commit() + current_app.scoped_session().add(user) + current_app.scoped_session().commit() def _update_users_last_auth(user): @@ -309,5 +317,5 @@ def _update_users_last_auth(user): logger.info(f"Updating username {user.username}'s _last_auth.") user._last_auth = datetime.now() - current_session.add(user) - current_session.commit() + current_app.scoped_session().add(user) + current_app.scoped_session().commit() diff --git a/fence/blueprints/admin.py b/fence/blueprints/admin.py index 206206774..509a68f93 100644 --- a/fence/blueprints/admin.py +++ b/fence/blueprints/admin.py @@ -7,7 +7,7 @@ import functools from flask import request, jsonify, Blueprint, current_app -from flask_sqlalchemy_session import current_session +from flask import current_app from cdislogging import get_logger @@ -52,7 +52,7 @@ def get_user(username): Returns a json object """ - return jsonify(admin.get_user_info(current_session, username)) + return jsonify(admin.get_user_info(current_app.scoped_session(), username)) @blueprint.route("/users", methods=["GET"]) @@ -65,7 +65,7 @@ def get_all_users(): Returns a json object. """ - return jsonify(admin.get_all_users(current_session)) + return jsonify(admin.get_all_users(current_app.scoped_session())) @blueprint.route("/users", methods=["POST"]) @@ -81,7 +81,9 @@ def create_user(): username = request.get_json().get("name", None) role = request.get_json().get("role", None) email = request.get_json().get("email", None) - return jsonify(admin.create_user(current_session, username, role, email)) + return jsonify( + admin.create_user(current_app.scoped_session(), username, role, email) + ) @blueprint.route("/users/", methods=["PUT"]) @@ -97,7 +99,9 @@ def update_user(username): name = request.get_json().get("name", None) role = request.get_json().get("role", None) email = request.get_json().get("email", None) - return jsonify(admin.update_user(current_session, username, role, email, name)) + return jsonify( + admin.update_user(current_app.scoped_session(), username, role, email, name) + ) @blueprint.route("/users/", methods=["DELETE"]) @@ -111,7 +115,7 @@ def delete_user(username): Returns json object """ - response = jsonify(admin.delete_user(current_session, username)) + response = jsonify(admin.delete_user(current_app.scoped_session(), username)) return response @@ -125,7 +129,7 @@ def get_user_groups(username): Returns a json object """ - return jsonify(admin.get_user_groups(current_session, username)) + return jsonify(admin.get_user_groups(current_app.scoped_session(), username)) @blueprint.route("/users//groups", methods=["PUT"]) @@ -139,7 +143,9 @@ def add_user_to_groups(username): Returns a json object """ groups = request.get_json().get("groups", []) - return jsonify(admin.add_user_to_groups(current_session, username, groups=groups)) + return jsonify( + admin.add_user_to_groups(current_app.scoped_session(), username, groups=groups) + ) @blueprint.route("/users//groups", methods=["DELETE"]) @@ -154,7 +160,9 @@ def remove_user_from_groups(username): """ groups = request.get_json().get("groups", []) return jsonify( - admin.remove_user_from_groups(current_session, username, groups=groups) + admin.remove_user_from_groups( + current_app.scoped_session(), username, groups=groups + ) ) @@ -169,7 +177,11 @@ def remove_user_from_projects(username): Returns a json object """ projects = request.get_json().get("projects", []) - return jsonify(admin.remove_user_from_projects(current_session, username, projects)) + return jsonify( + admin.remove_user_from_projects( + current_app.scoped_session(), username, projects + ) + ) @blueprint.route("/users//projects", methods=["PUT"]) @@ -185,7 +197,9 @@ def add_user_to_projects(username): """ projects = request.get_json().get("projects", []) return jsonify( - admin.add_user_to_projects(current_session, username, projects=projects) + admin.add_user_to_projects( + current_app.scoped_session(), username, projects=projects + ) ) @@ -201,7 +215,7 @@ def get_project(projectname): from the userdatamodel database Returns a json object """ - return jsonify(admin.get_project_info(current_session, projectname)) + return jsonify(admin.get_project_info(current_app.scoped_session(), projectname)) @blueprint.route("/projects", methods=["GET"]) @@ -213,7 +227,7 @@ def get_all_projects(): from the userdatamodel database Returns a json object """ - return jsonify(admin.get_all_projects(current_session)) + return jsonify(admin.get_all_projects(current_app.scoped_session())) @blueprint.route("/projects/", methods=["POST"]) @@ -227,7 +241,9 @@ def create_project(projectname): auth_id = request.get_json().get("auth_id") storage_accesses = request.get_json().get("storage_accesses", []) response = jsonify( - admin.create_project(current_session, projectname, auth_id, storage_accesses) + admin.create_project( + current_app.scoped_session(), projectname, auth_id, storage_accesses + ) ) return response @@ -240,7 +256,7 @@ def delete_project(projectname): Remove project. No Buckets should be associated with it. Returns a json object. """ - response = jsonify(admin.delete_project(current_session, projectname)) + response = jsonify(admin.delete_project(current_app.scoped_session(), projectname)) return response @@ -254,7 +270,9 @@ def remove_projects_from_group(groupname): """ projects = request.get_json().get("projects", []) return jsonify( - admin.remove_projects_from_group(current_session, groupname, projects) + admin.remove_projects_from_group( + current_app.scoped_session(), groupname, projects + ) ) @@ -267,7 +285,9 @@ def add_project_to_groups(projectname): """ groups = request.get_json().get("groups", []) return jsonify( - admin.add_project_to_groups(current_session, username, groups=groups) + admin.add_project_to_groups( + current_app.scoped_session(), username, groups=groups + ) ) @@ -281,7 +301,7 @@ def create_bucket_in_project(projectname, bucketname): providername = request.get_json().get("provider") response = jsonify( admin.create_bucket_on_project( - current_session, projectname, bucketname, providername + current_app.scoped_session(), projectname, bucketname, providername ) ) return response @@ -297,7 +317,9 @@ def delete_bucket_from_project(projectname, bucketname): Returns a json object. """ return jsonify( - admin.delete_bucket_on_project(current_session, projectname, bucketname) + admin.delete_bucket_on_project( + current_app.scoped_session(), projectname, bucketname + ) ) @@ -310,7 +332,7 @@ def list_buckets_from_project(projectname): Returns a json object. """ response = jsonify( - admin.list_buckets_on_project_by_name(current_session, projectname) + admin.list_buckets_on_project_by_name(current_app.scoped_session(), projectname) ) return response @@ -326,7 +348,7 @@ def get_group_info(groupname): buckets created within a project. Returns a json object. """ - return jsonify(admin.get_group_info(current_session, groupname)) + return jsonify(admin.get_group_info(current_app.scoped_session(), groupname)) @blueprint.route("/groups", methods=["GET"]) @@ -337,7 +359,7 @@ def get_all_groups(): buckets created within a project. Returns a json object. """ - return jsonify(admin.get_all_groups(current_session)) + return jsonify(admin.get_all_groups(current_app.scoped_session())) @blueprint.route("/groups//users", methods=["GET"]) @@ -348,7 +370,7 @@ def get_group_users(groupname): buckets created within a project. Returns a json object. """ - return jsonify(admin.get_group_users(current_session, groupname)) + return jsonify(admin.get_group_users(current_app.scoped_session(), groupname)) @blueprint.route("/groups", methods=["POST"]) @@ -361,9 +383,9 @@ def create_group(): """ groupname = request.get_json().get("name") description = request.get_json().get("description") - grp = admin.create_group(current_session, groupname, description) + grp = admin.create_group(current_app.scoped_session(), groupname, description) if grp: - response = admin.get_group_info(current_session, groupname) + response = admin.get_group_info(current_app.scoped_session(), groupname) else: response = {"result": "group creation failed"} response = jsonify(response) @@ -381,7 +403,7 @@ def update_group(groupname): name = request.get_json().get("name", None) description = request.get_json().get("description", None) response = jsonify( - admin.update_group(current_session, groupname, description, name) + admin.update_group(current_app.scoped_session(), groupname, description, name) ) return response @@ -394,7 +416,7 @@ def delete_group(groupname): buckets created within a project. Returns a json object. """ - response = jsonify(admin.delete_group(current_session, groupname)) + response = jsonify(admin.delete_group(current_app.scoped_session(), groupname)) return response @@ -407,7 +429,7 @@ def add_projects_to_group(groupname): """ projects = request.get_json().get("projects", []) response = jsonify( - admin.add_projects_to_group(current_session, groupname, projects) + admin.add_projects_to_group(current_app.scoped_session(), groupname, projects) ) return response @@ -419,7 +441,7 @@ def get_group_projects(groupname): Create a user to group relationship in the database Returns a json object """ - values = admin.get_group_projects(current_session, groupname) + values = admin.get_group_projects(current_app.scoped_session(), groupname) return jsonify({"projects": values}) @@ -434,7 +456,7 @@ def get_cloud_provider(providername): Retriev the information related to a cloud provider Returns a json object. """ - return jsonify(admin.get_provider(current_session, providername)) + return jsonify(admin.get_provider(current_app.scoped_session(), providername)) @blueprint.route("/cloud_providers/", methods=["POST"]) @@ -449,7 +471,10 @@ def create_cloud_provider(providername): service_name = request.get_json().get("service") response = jsonify( admin.create_provider( - current_session, providername, backend=backend_name, service=service_name + current_app.scoped_session(), + providername, + backend=backend_name, + service=service_name, ) ) return response @@ -465,7 +490,9 @@ def delete_cloud_provider(providername): or removed. Returns a json object. """ - response = jsonify(admin.delete_provider(current_session, providername)) + response = jsonify( + admin.delete_provider(current_app.scoped_session(), providername) + ) return response @@ -478,7 +505,8 @@ def get_registered_users(): - Response json structure is provisional. """ registered_users = ( - current_session.query(User) + current_app.scoped_session() + .query(User) .filter(User.additional_info["registration_info"] != "{}") .all() ) diff --git a/fence/blueprints/data/indexd.py b/fence/blueprints/data/indexd.py index 83f4b115b..af67d2978 100755 --- a/fence/blueprints/data/indexd.py +++ b/fence/blueprints/data/indexd.py @@ -12,7 +12,7 @@ from cdispyutils.config import get_value from cdispyutils.hmac4 import generate_aws_presigned_url import flask -from flask_sqlalchemy_session import current_session +from flask import current_app import requests from azure.storage.blob import ( BlobServiceClient, @@ -77,7 +77,7 @@ def get_signed_url_for_file( ): requested_protocol = requested_protocol or flask.request.args.get("protocol", None) r_pays_project = flask.request.args.get("userProject", None) - db_session = db_session or current_session + db_session = db_session or current_app.scoped_session() # default to signing the url force_signed_url = True @@ -959,7 +959,6 @@ def get_signed_url( authorized_user=None, **kwargs, ): - aws_creds = get_value( config, "AWS_CREDENTIALS", InternalError("credentials not configured") ) @@ -1530,7 +1529,7 @@ def _get_auth_info_for_id_or_from_request( IT WILL ALWAYS GIVE YOU BACK ANONYMOUS USER INFO. Only use this after you've authorized the access to the data via other means. """ - db_session = db_session or current_session + db_session = db_session or current_app.scoped_session() # set default "anonymous" user_id and username # this is fine b/c it might be public data or a client token that is not diff --git a/fence/blueprints/ga4gh.py b/fence/blueprints/ga4gh.py index 4bb110bcc..e73a42465 100644 --- a/fence/blueprints/ga4gh.py +++ b/fence/blueprints/ga4gh.py @@ -11,7 +11,7 @@ @blueprint.route( - "/drs/v1/objects//access", + "/drs/v1/objects//access/", defaults={"access_id": None}, methods=["GET"], ) @@ -20,7 +20,6 @@ methods=["GET", "POST"], ) def get_ga4gh_signed_url(object_id, access_id): - if not access_id: raise UserError("Access ID/Protocol is required.") diff --git a/fence/blueprints/google.py b/fence/blueprints/google.py index e68cb6d30..a3c8b2348 100644 --- a/fence/blueprints/google.py +++ b/fence/blueprints/google.py @@ -39,7 +39,7 @@ ) from fence.models import UserServiceAccount from fence.utils import get_valid_expiration_from_request -from flask_sqlalchemy_session import current_session +from flask import current_app class ValidationErrors(str, Enum): @@ -218,7 +218,10 @@ def _post_new_service_account(self, sa): return error_response, 400 sa_exists = ( - current_session.query(UserServiceAccount).filter_by(email=sa.email).all() + current_app.scoped_session() + .query(UserServiceAccount) + .filter_by(email=sa.email) + .all() ) if sa_exists: @@ -261,17 +264,22 @@ def _register_new_service_account(self, sa): google_project_id=sa.google_project_id, ) - current_session.add(db_service_account) - current_session.commit() + current_app.scoped_session().add(db_service_account) + current_app.scoped_session().commit() project_ids = get_project_ids_from_project_auth_ids( - current_session, sa.project_access + current_app.scoped_session(), sa.project_access ) - add_user_service_account_to_db(current_session, project_ids, db_service_account) + add_user_service_account_to_db( + current_app.scoped_session(), project_ids, db_service_account + ) add_user_service_account_to_google( - current_session, project_ids, sa.google_project_id, db_service_account + current_app.scoped_session(), + project_ids, + sa.google_project_id, + db_service_account, ) return { @@ -408,7 +416,10 @@ def post(self, id_): error_response = _get_service_account_error_status(sa) sa_exists = ( - current_session.query(UserServiceAccount).filter_by(email=sa.email).all() + current_app.scoped_session() + .query(UserServiceAccount) + .filter_by(email=sa.email) + .all() ) if sa_exists: diff --git a/fence/blueprints/link.py b/fence/blueprints/link.py index 9fda3cd30..944909e51 100644 --- a/fence/blueprints/link.py +++ b/fence/blueprints/link.py @@ -2,7 +2,7 @@ import flask from flask_restful import Resource -from flask_sqlalchemy_session import current_session +from flask import current_app from cdislogging import get_logger @@ -197,7 +197,8 @@ def _unlink_google_account(): user_id = current_token["sub"] g_account = ( - current_session.query(UserGoogleAccount) + current_app.scoped_session() + .query(UserGoogleAccount) .filter(UserGoogleAccount.user_id == user_id) .first() ) @@ -214,7 +215,8 @@ def _unlink_google_account(): return error_message, 404 g_account_access = ( - current_session.query(UserGoogleAccountToProxyGroup) + current_app.scoped_session() + .query(UserGoogleAccountToProxyGroup) .filter( UserGoogleAccountToProxyGroup.user_google_account_id == g_account.id ) @@ -239,11 +241,11 @@ def _unlink_google_account(): _clear_google_link_info_from_session() return error_message, 400 - current_session.delete(g_account_access) - current_session.commit() + current_app.scoped_session().delete(g_account_access) + current_app.scoped_session().commit() - current_session.delete(g_account) - current_session.commit() + current_app.scoped_session().delete(g_account) + current_app.scoped_session().commit() # clear session and cookies so access token and session don't have # outdated linkage info @@ -376,7 +378,8 @@ def get_errors_update_user_google_account_dry_run( error_description = None user_google_account = ( - current_session.query(UserGoogleAccount) + current_app.scoped_session() + .query(UserGoogleAccount) .filter(UserGoogleAccount.email == google_email) .first() ) @@ -449,7 +452,8 @@ def _force_update_user_google_account( Expiration time of the newly updated google account's access """ user_google_account = ( - current_session.query(UserGoogleAccount) + current_app.scoped_session() + .query(UserGoogleAccount) .filter(UserGoogleAccount.email == google_email) .first() ) @@ -458,7 +462,7 @@ def _force_update_user_google_account( if _allow_new: if user_id is not None: user_google_account = add_new_user_google_account( - user_id, google_email, current_session + user_id, google_email, current_app.scoped_session() ) logger.info( "Linking Google account {} to user with id {}.".format( @@ -483,7 +487,11 @@ def _force_update_user_google_account( expiration = min(requested_expiration, expiration) force_update_user_google_account_expiration( - user_google_account, proxy_group_id, google_email, expiration, current_session + user_google_account, + proxy_group_id, + google_email, + expiration, + current_app.scoped_session(), ) logger.info( @@ -493,7 +501,7 @@ def _force_update_user_google_account( ) ) - current_session.commit() + current_app.scoped_session().commit() return expiration diff --git a/fence/blueprints/login/ras.py b/fence/blueprints/login/ras.py index 9bdd0a788..9b6e01cdb 100644 --- a/fence/blueprints/login/ras.py +++ b/fence/blueprints/login/ras.py @@ -9,7 +9,7 @@ from authutils.errors import JWTError from cdislogging import get_logger -from flask_sqlalchemy_session import current_session +from flask import current_app from gen3authz.client.arborist.client import ArboristClient from fence.blueprints.login.base import DefaultOAuth2Login, DefaultOAuth2Callback @@ -73,7 +73,7 @@ def post_login(self, user=None, token_result=None, id_from_idp=None): users_from_passports = fence.resources.ga4gh.passports.sync_gen3_users_authz_from_ga4gh_passports( [passport], pkey_cache=PKEY_CACHE, - db_session=current_session, + db_session=current_app.scoped_session(), ) user_ids_from_passports = list(users_from_passports.keys()) diff --git a/fence/blueprints/login/synapse.py b/fence/blueprints/login/synapse.py index b6f3cbeb7..dee5ea5eb 100644 --- a/fence/blueprints/login/synapse.py +++ b/fence/blueprints/login/synapse.py @@ -1,7 +1,7 @@ from datetime import datetime, timezone, timedelta import flask -from flask_sqlalchemy_session import current_session +from flask import current_app from fence.config import config from fence.models import IdentityProvider @@ -35,8 +35,8 @@ def post_login(self, user=None, token_result=None, id_from_idp=None): info.pop("fence_username", None) info.pop("exp", None) user.additional_info = info - current_session.add(user) - current_session.commit() + current_app.scoped_session().add(user) + current_app.scoped_session().commit() with flask.current_app.arborist.context(authz_provider="synapse"): if config["DREAM_CHALLENGE_TEAM"] in token_result.get("team", []): diff --git a/fence/blueprints/register.py b/fence/blueprints/register.py index 50d51f18d..b15cb1a6e 100644 --- a/fence/blueprints/register.py +++ b/fence/blueprints/register.py @@ -5,7 +5,7 @@ """ import flask -from flask_sqlalchemy_session import current_session +from flask import current_app from flask_wtf import FlaskForm from wtforms import StringField from wtforms.validators import DataRequired, Email, StopValidation, ValidationError @@ -109,8 +109,8 @@ def register_user(): } combined_info.update(registration_info) flask.g.user.additional_info = combined_info - current_session.add(flask.g.user) - current_session.commit() + current_app.scoped_session().add(flask.g.user) + current_app.scoped_session().commit() with flask.current_app.arborist.context(): # make sure the user exists in Arborist diff --git a/fence/blueprints/storage_creds/__init__.py b/fence/blueprints/storage_creds/__init__.py index 869cc9942..057d1659a 100644 --- a/fence/blueprints/storage_creds/__init__.py +++ b/fence/blueprints/storage_creds/__init__.py @@ -1,5 +1,5 @@ import flask -from flask_sqlalchemy_session import current_session +from flask import current_app from fence.auth import require_auth_header from fence.blueprints.storage_creds.api import AccessKey, ApiKey, ApiKeyList @@ -76,6 +76,8 @@ def list_sources(): if info.get("backend") ] ) - return flask.jsonify(get_endpoints_descriptions(services, current_session)) + return flask.jsonify( + get_endpoints_descriptions(services, current_app.scoped_session()) + ) return blueprint diff --git a/fence/blueprints/storage_creds/google.py b/fence/blueprints/storage_creds/google.py index e3d623856..b9c67fee3 100644 --- a/fence/blueprints/storage_creds/google.py +++ b/fence/blueprints/storage_creds/google.py @@ -4,7 +4,7 @@ import time from distutils.util import strtobool from flask_restful import Resource -from flask_sqlalchemy_session import current_session +from flask import current_app from cirrus import GoogleCloudManager from cirrus.config import config as cirrus_config @@ -85,7 +85,8 @@ def get(self): for i, key in enumerate(keys): key_id = reg.findall(key["name"])[0] db_entry = ( - current_session.query(GoogleServiceAccountKey) + current_app.scoped_session() + .query(GoogleServiceAccountKey) .filter_by(service_account_id=service_account.id) .filter_by(key_id=key_id) .first() @@ -315,13 +316,14 @@ def _delete_service_account_key(g_cloud, service_account_id, access_key): ) db_entry = ( - current_session.query(GoogleServiceAccountKey) + current_app.scoped_session() + .query(GoogleServiceAccountKey) .filter_by(key_id=access_key) .first() ) if db_entry: - current_session.delete(db_entry) - current_session.commit() + current_app.scoped_session().delete(db_entry) + current_app.scoped_session().commit() logger.info( "Removed Google Service Account {} Key with ID: {} from Google and our DB.".format( diff --git a/fence/blueprints/user.py b/fence/blueprints/user.py index 59a6d27fc..1307e9ef6 100644 --- a/fence/blueprints/user.py +++ b/fence/blueprints/user.py @@ -1,5 +1,5 @@ import flask -from flask_sqlalchemy_session import current_session +from flask import current_app from fence.auth import login_required, current_token from fence.errors import Unauthorized, UserError, NotFound @@ -42,7 +42,7 @@ def any_access(): project = flask.request.args.get("project") projects = None if flask.g.token is None: - flask.g.user = current_session.merge(flask.g.user) + flask.g.user = current_app.scoped_session().merge(flask.g.user) projects = flask.g.user.project_access else: projects = flask.g.token["context"]["user"]["projects"] @@ -66,7 +66,7 @@ def any_access(): @blueprint.route("/cert", methods=["GET"]) @login_required({"user"}) def missing_certificate(): - flask.g.user = current_session.merge(flask.g.user) + flask.g.user = current_app.scoped_session().merge(flask.g.user) if not flask.g.user.application: return flask.jsonify(REQUIRED_CERTIFICATES) certificates = [c.name for c in flask.g.user.application.certificates_uploaded] @@ -88,9 +88,10 @@ def upload_certificate(certificate): if not flask.g.user.application: flask.g.user.application = Application() - current_session.merge(flask.g.user) + current_app.scoped_session().merge(flask.g.user) cert = ( - current_session.query(Certificate) + current_app.scoped_session() + .query(Certificate) .filter(Certificate.name == certificate) .filter(Certificate.application_id == flask.g.user.application.id) .first() @@ -100,7 +101,7 @@ def upload_certificate(certificate): cert.application_id = flask.g.user.application.id cert.extension = extension cert.data = flask.request.data - current_session.merge(cert) + current_app.scoped_session().merge(cert) certificates = flask.g.user.application.certificates_uploaded if set(REQUIRED_CERTIFICATES.keys()).issubset(set(c.name for c in certificates)): @@ -127,9 +128,10 @@ def upload_certificate(certificate): def download_certificate(certificate): if not flask.g.user.application: flask.g.user.application = Application() - current_session.merge(flask.g.user) + current_app.scoped_session().merge(flask.g.user) cert = ( - current_session.query(Certificate) + current_app.scoped_session() + .query(Certificate) .filter(Certificate.name == certificate) .filter(Certificate.application_id == flask.g.user.application.id) .first() diff --git a/fence/blueprints/well_known.py b/fence/blueprints/well_known.py index 0931eaf92..9cc1e91fc 100644 --- a/fence/blueprints/well_known.py +++ b/fence/blueprints/well_known.py @@ -10,7 +10,7 @@ from fence.config import config -blueprint = flask.Blueprint(".well-known", __name__) +blueprint = flask.Blueprint("well-known", __name__) @blueprint.route("/jwks", methods=["GET"]) diff --git a/fence/oidc/jwt_generator.py b/fence/oidc/jwt_generator.py index eb9073113..dfba556b6 100644 --- a/fence/oidc/jwt_generator.py +++ b/fence/oidc/jwt_generator.py @@ -1,5 +1,5 @@ import flask -from flask_sqlalchemy_session import current_session +from flask import current_app from fence.jwt.token import ( AuthFlowTypes, @@ -78,8 +78,8 @@ def generate_implicit_response( } """ # prevent those bothersome "not bound to session" errors - if user not in current_session: - user = current_session.query(User).filter_by(id=user.id).first() + if user not in current_app.scoped_session(): + user = current_app.scoped_session().query(User).filter_by(id=user.id).first() if not user: raise OIDCError("user not authenticated") @@ -169,8 +169,8 @@ def generate_token_response( } """ # prevent those bothersome "not bound to session" errors - if user not in current_session: - user = current_session.query(User).filter_by(id=user.id).first() + if user not in current_app.scoped_session(): + user = current_app.scoped_session().query(User).filter_by(id=user.id).first() if not user: # Find the ``User`` model. @@ -183,7 +183,8 @@ def generate_token_response( else: code = flask.request.form.get("code") user = ( - current_session.query(AuthorizationCode) + current_app.scoped_session() + .query(AuthorizationCode) .filter_by(code=code) .first() .user @@ -191,7 +192,8 @@ def generate_token_response( if grant_type == "refresh_token": # For refresh token, the user ID is the ``sub`` field in the token. user = ( - current_session.query(User) + current_app.scoped_session() + .query(User) .filter_by(id=int(refresh_token_claims["sub"])) .first() ) diff --git a/fence/resources/ga4gh/passports.py b/fence/resources/ga4gh/passports.py index e0e3c6539..9b8a84179 100644 --- a/fence/resources/ga4gh/passports.py +++ b/fence/resources/ga4gh/passports.py @@ -12,7 +12,7 @@ from authutils.errors import JWTError from authutils.token.core import get_iss, get_kid from cdislogging import get_logger -from flask_sqlalchemy_session import current_session +from flask import current_app from fence.jwt.validate import validate_jwt from fence.config import config @@ -54,7 +54,7 @@ def sync_gen3_users_authz_from_ga4gh_passports( list: a list of users, each corresponding to a valid visa identity embedded within the passports passed in """ - db_session = db_session or current_session + db_session = db_session or current_app.scoped_session() # {"username": user, "username2": user2} users_from_all_passports = {} @@ -321,7 +321,7 @@ def get_or_create_gen3_user_from_iss_sub(issuer, subject_id, db_session=None): Return: userdatamodel.user.User: the Fence user corresponding to issuer and subject_id """ - db_session = db_session or current_session + db_session = db_session or current_app.scoped_session() logger.debug( f"get_or_create_gen3_user_from_iss_sub: issuer: {issuer} & subject_id: {subject_id}" ) @@ -387,7 +387,7 @@ def _sync_validated_visa_authorization( Return: None """ - db_session = db_session or current_session + db_session = db_session or current_app.scoped_session() default_args = fence.scripting.fence_create.get_default_init_syncer_inputs( authz_provider="GA4GH" ) @@ -423,7 +423,7 @@ def get_gen3_usernames_for_passport_from_cache(passport, db_session=None): list[str]: list of usernames for users referred to by the previously validated and non-expired passport """ - db_session = db_session or current_session + db_session = db_session or current_app.scoped_session() user_ids_from_passports = None current_time = int(time.time()) @@ -486,7 +486,7 @@ def put_gen3_usernames_for_passport_into_cache( the previously validated and non-expired passport expires_at (int): expiration time in unix time """ - db_session = db_session or current_session + db_session = db_session or current_app.scoped_session() passport_hash = hashlib.sha256(passport.encode("utf-8")).hexdigest() diff --git a/fence/resources/google/utils.py b/fence/resources/google/utils.py index 1dd1090ab..ab1005b4b 100644 --- a/fence/resources/google/utils.py +++ b/fence/resources/google/utils.py @@ -3,7 +3,7 @@ import os from cryptography.fernet import Fernet import flask -from flask_sqlalchemy_session import current_session +from flask import current_app from sqlalchemy import desc, func from cdislogging import get_logger @@ -99,7 +99,8 @@ def _get_primary_service_account_key(user_id, username, proxy_group_id): if user_google_service_account: user_service_account_key = ( - current_session.query(GoogleServiceAccountKey) + current_app.scoped_session() + .query(GoogleServiceAccountKey) .filter( GoogleServiceAccountKey.service_account_id == user_google_service_account.id @@ -376,8 +377,8 @@ def add_custom_service_account_key_expiration( expires=expires, private_key=private_key, ) - current_session.add(sa_key) - current_session.commit() + current_app.scoped_session().add(sa_key) + current_app.scoped_session().commit() def get_service_account(client_id, user_id, username): @@ -394,7 +395,8 @@ def get_service_account(client_id, user_id, username): fence.models.GoogleServiceAccount: Client's service account """ service_accounts = ( - current_session.query(GoogleServiceAccount) + current_app.scoped_session() + .query(GoogleServiceAccount) .filter_by(client_id=client_id, user_id=user_id) .all() ) @@ -430,19 +432,20 @@ def get_service_account(client_id, user_id, username): ) old_service_account_keys_db_entries = ( - current_session.query(GoogleServiceAccountKey) + current_app.scoped_session() + .query(GoogleServiceAccountKey) .filter(GoogleServiceAccountKey.service_account_id == sa.id) .all() ) # remove the keys then the sa itself from db for old_key in old_service_account_keys_db_entries: - current_session.delete(old_key) + current_app.scoped_session().delete(old_key) # commit the deletion of keys first, then do SA deletion - current_session.commit() - current_session.delete(sa) - current_session.commit() + current_app.scoped_session().commit() + current_app.scoped_session().delete(sa) + current_app.scoped_session().commit() return service_account @@ -507,7 +510,8 @@ def _update_service_account_db_entry( # clear out old SA and keys if there is one old_service_account_db_entry = ( - current_session.query(GoogleServiceAccount) + current_app.scoped_session() + .query(GoogleServiceAccount) .filter(GoogleServiceAccount.email == old_sa_email) .first() ) @@ -521,7 +525,8 @@ def _update_service_account_db_entry( ) old_service_account_keys_db_entries = ( - current_session.query(GoogleServiceAccountKey) + current_app.scoped_session() + .query(GoogleServiceAccountKey) .filter( GoogleServiceAccountKey.service_account_id == old_service_account_db_entry.id @@ -531,13 +536,14 @@ def _update_service_account_db_entry( # remove the keys then the sa itself from db for old_key in old_service_account_keys_db_entries: - current_session.delete(old_key) + current_app.scoped_session().delete(old_key) - current_session.commit() - current_session.delete(old_service_account_db_entry) + current_app.scoped_session().commit() + current_app.scoped_session().delete(old_service_account_db_entry) service_account_db_entry = ( - current_session.query(GoogleServiceAccount) + current_app.scoped_session() + .query(GoogleServiceAccount) .filter(GoogleServiceAccount.email == new_service_account["email"]) .first() ) @@ -550,13 +556,13 @@ def _update_service_account_db_entry( email=new_service_account["email"], google_project_id=new_service_account["projectId"], ) - current_session.add(service_account_db_entry) + current_app.scoped_session().add(service_account_db_entry) else: service_account_db_entry.google_unique_id = new_service_account["uniqueId"] service_account_db_entry.email = new_service_account["email"] service_account_db_entry.google_project_id = (new_service_account["projectId"],) - current_session.commit() + current_app.scoped_session().commit() logger.info( "Created service account {} for proxy group {}.".format( @@ -578,9 +584,9 @@ def get_or_create_proxy_group_id(expires=None, user_id=None, username=None): proxy_group_id = _get_proxy_group_id(user_id=user_id, username=username) if not proxy_group_id: try: - user_by_id = query_for_user_by_id(current_session, user_id) + user_by_id = query_for_user_by_id(current_app.scoped_session(), user_id) user_by_username = query_for_user( - session=current_session, username=username + session=current_app.scoped_session(), username=username ) except Exception: user_by_id = None @@ -603,8 +609,10 @@ def get_or_create_proxy_group_id(expires=None, user_id=None, username=None): proxy_group_id = _create_proxy_group(user_id, username).id - privileges = current_session.query(AccessPrivilege).filter( - AccessPrivilege.user_id == user_id + privileges = ( + current_app.scoped_session() + .query(AccessPrivilege) + .filter(AccessPrivilege.user_id == user_id) ) for p in privileges: @@ -612,7 +620,6 @@ def get_or_create_proxy_group_id(expires=None, user_id=None, username=None): for sa in storage_accesses: if sa.provider.name == STORAGE_ACCESS_PROVIDER_NAME: - flask.current_app.storage_manager.logger.info( "grant {} access {} to {} in {}".format( username, p.privilege, p.project_id, p.auth_provider @@ -624,7 +631,7 @@ def get_or_create_proxy_group_id(expires=None, user_id=None, username=None): username=username, project=p.project, access=p.privilege, - session=current_session, + session=current_app.scoped_session(), expires=expires, ) @@ -645,9 +652,9 @@ def _get_proxy_group_id(user_id=None, username=None): user_id = user_id or current_token["sub"] try: - user = query_for_user_by_id(current_session, user_id) + user = query_for_user_by_id(current_app.scoped_session(), user_id) if not user: - user = query_for_user(current_session, username) + user = query_for_user(current_app.scoped_session(), username) except Exception: user = None @@ -680,11 +687,11 @@ def _create_proxy_group(user_id, username): ) # link proxy group to user - user = current_session.query(User).filter_by(id=user_id).first() + user = current_app.scoped_session().query(User).filter_by(id=user_id).first() user.google_proxy_group_id = proxy_group.id - current_session.add(proxy_group) - current_session.commit() + current_app.scoped_session().add(proxy_group) + current_app.scoped_session().commit() logger.info( "Created proxy group {} for user {} with id {}.".format( @@ -962,4 +969,4 @@ def get_db_session(db=None): if db: return SQLAlchemyDriver(db).Session() else: - return current_session + return current_app.scoped_session() diff --git a/fence/resources/google/validity.py b/fence/resources/google/validity.py index b26c92e6c..0cf372032 100644 --- a/fence/resources/google/validity.py +++ b/fence/resources/google/validity.py @@ -755,7 +755,6 @@ def check_validity( self.set("policy_accessible", policy_accessible) if check_external_access: - if not policy_accessible: logger.warning( "Invalid function use. External Access check requires " @@ -781,7 +780,6 @@ def check_validity( # check if the SA is an allowed type if check_type: - if not policy_accessible: logger.warning( "Policy access was not checked. If the service account's " diff --git a/fence/resources/openid/idp_oauth2.py b/fence/resources/openid/idp_oauth2.py index 78e7a52d9..68e9a41b7 100644 --- a/fence/resources/openid/idp_oauth2.py +++ b/fence/resources/openid/idp_oauth2.py @@ -1,6 +1,6 @@ from authlib.client import OAuth2Session from cached_property import cached_property -from flask_sqlalchemy_session import current_session +from flask import current_app from jose import jwt import requests import time @@ -220,12 +220,11 @@ def get_access_token(self, user, token_endpoint, db_session=None): return token_response - def store_refresh_token( - self, user, refresh_token, expires, db_session=current_session - ): + def store_refresh_token(self, user, refresh_token, expires, db_session=None): """ Store refresh token in db. """ + db_session = db_session or current_app.scoped_session() user.upstream_refresh_tokens = [] upstream_refresh_token = UpstreamRefreshToken( user=user, diff --git a/fence/resources/openid/ras_oauth2.py b/fence/resources/openid/ras_oauth2.py index b836c4f71..c894e5d36 100644 --- a/fence/resources/openid/ras_oauth2.py +++ b/fence/resources/openid/ras_oauth2.py @@ -8,7 +8,7 @@ import fence.scripting.fence_create import fence.resources.ga4gh.passports -from flask_sqlalchemy_session import current_session +from flask import current_app from jose import jwt as jose_jwt from authutils.errors import JWTError @@ -118,7 +118,6 @@ def get_encoded_visas_v11_userinfo(self, userinfo, pkey_cache=None): ) def get_user_id(self, code): - err_msg = "Unable to parse UserID from RAS userinfo response" try: @@ -216,7 +215,7 @@ def map_iss_sub_pair_to_user( username that was passed in in all cases except for the exception noted above """ - db_session = db_session or current_session + db_session = db_session or current_app.scoped_session() iss_sub_pair_to_user = db_session.query(IssSubPairToUser).get( (issuer, subject_id) ) @@ -290,11 +289,12 @@ def map_iss_sub_pair_to_user( return iss_sub_pair_to_user.user.username @backoff.on_exception(backoff.expo, Exception, **DEFAULT_BACKOFF_SETTINGS) - def update_user_authorization(self, user, pkey_cache, db_session=current_session): + def update_user_authorization(self, user, pkey_cache, db_session=None): """ Updates user's RAS refresh token and uses the new access token to retrieve new visas from RAS's /userinfo endpoint and update access """ + db_session = db_session or current_app.scoped_session() try: token_endpoint = self.get_value_from_discovery_doc("token_endpoint", "") diff --git a/fence/resources/user/user_session.py b/fence/resources/user/user_session.py index 0c73c750f..b17ffb775 100644 --- a/fence/resources/user/user_session.py +++ b/fence/resources/user/user_session.py @@ -166,7 +166,7 @@ def __init__(self): super(UserSessionInterface, self).__init__() def open_session(self, app, request): - jwt = request.cookies.get(app.session_cookie_name) + jwt = request.cookies.get(app.config["SESSION_COOKIE_NAME"]) session = UserSession(jwt) # NOTE: If we did the expiration check in save_session @@ -190,7 +190,7 @@ def save_session(self, app, session, response): token = session.get_updated_token(app) if token: response.set_cookie( - app.session_cookie_name, + app.config["SESSION_COOKIE_NAME"], token, expires=self.get_expiration_time(app, session), httponly=True, @@ -250,7 +250,7 @@ def save_session(self, app, session, response): # expiration it just won't be stored in the cookie # anymore response.set_cookie( - app.session_cookie_name, + app.config["SESSION_COOKIE_NAME"], expires=0, httponly=True, domain=domain, diff --git a/fence/scripting/fence_create.py b/fence/scripting/fence_create.py index f069d6f24..56f5cba3c 100644 --- a/fence/scripting/fence_create.py +++ b/fence/scripting/fence_create.py @@ -1102,7 +1102,6 @@ def _verify_google_service_account_member(session, access_group, member): class JWTCreator(object): - required_kwargs = ["kid", "private_key", "username", "scopes"] all_kwargs = required_kwargs + ["expires_in"] @@ -1521,7 +1520,6 @@ def _setup_google_bucket_access_group( storage_creds_project_id, privileges, ): - access_group = _create_google_bucket_access_group( db_session, google_bucket_name, bucket_db_id, google_project_id, privileges ) @@ -1590,7 +1588,6 @@ def _get_or_create_google_provider(db_session): def link_external_bucket(db, name): - """ Link with bucket owned by an external party. This will create the bucket in fence database and create a google group to access the bucket in both @@ -1645,7 +1642,11 @@ def link_external_bucket(db, name): privileges = ["read"] access_group = _create_google_bucket_access_group( - current_session, name, bucket_db_entry.id, google_project_id, privileges + current_session, + name, + bucket_db_entry.id, + google_project_id, + privileges, ) logger.info("bucket access group email: {}".format(access_group.email)) diff --git a/fence/sync/sync_users.py b/fence/sync/sync_users.py index 0639a1679..477110be2 100644 --- a/fence/sync/sync_users.py +++ b/fence/sync/sync_users.py @@ -370,15 +370,15 @@ def _match_pattern(filepath, id_patterns, encrypted=True): Returns: bool: whether the pattern matches """ - id_patterns.append("authentication_file_phs(\d{6}).(csv|txt)") + id_patterns.append(r"authentication_file_phs(\d{6}).(csv|txt)") for pattern in id_patterns: - pattern = r"{}".format(pattern) if encrypted: - pattern += ".enc" - pattern += "$" - pattern = pattern.encode().decode( - "unicode_escape" - ) # when converting the YAML from fence-config, python reads it as Python string literal. So "\" turns into "\\" which messes with the regex match + pattern += r".enc" + pattern += r"$" + # when converting the YAML from fence-config, + # python reads it as Python string literal. So "\" turns into "\\" + # which messes with the regex match + pattern = pattern.encode().decode("unicode_escape") if re.match(pattern, os.path.basename(filepath)): return True return False @@ -499,7 +499,10 @@ def _parse_csv(self, file_dict, sess, dbgap_config={}, encrypted=True): dbgap_key = dbgap_config.get("decrypt_key", None) self.id_patterns += ( - dbgap_config.get("allowed_whitelist_patterns", []) + [ + r"{}".format(item) + for item in dbgap_config.get("allowed_whitelist_patterns", []) + ] if dbgap_config.get("allow_non_dbGaP_whitelist", False) else [] ) @@ -943,7 +946,7 @@ def _revoke_from_db(self, sess, to_delete): Return: None """ - for (username, project_auth_id) in to_delete: + for username, project_auth_id in to_delete: q = ( sess.query(AccessPrivilege) .filter(AccessPrivilege.project.has(auth_id=project_auth_id)) @@ -999,7 +1002,7 @@ def _update_from_db(self, sess, to_update, user_project): None """ - for (username, project_auth_id) in to_update: + for username, project_auth_id in to_update: q = ( sess.query(AccessPrivilege) .filter(AccessPrivilege.project.has(auth_id=project_auth_id)) @@ -1026,7 +1029,7 @@ def _grant_from_db(self, sess, to_add, user_info, user_project, auth_provider_li Return: None """ - for (username, project_auth_id) in to_add: + for username, project_auth_id in to_add: u = query_for_user(session=sess, username=username) auth_provider = auth_provider_list[0] @@ -1117,7 +1120,7 @@ def _revoke_from_storage(self, to_delete, sess, google_bulk_mapping=None): Return: None """ - for (username, project_auth_id) in to_delete: + for username, project_auth_id in to_delete: project = ( sess.query(Project).filter(Project.auth_id == project_auth_id).first() ) @@ -1161,7 +1164,7 @@ def _grant_from_storage( Return: None """ - for (username, project_auth_id) in to_add: + for username, project_auth_id in to_add: project = self._projects[project_auth_id] for sa in project.storage_access: access = list(user_project[username][project_auth_id]) @@ -1391,7 +1394,6 @@ def _process_user_projects( dbgap_config, sess, ): - for username in user_projects.keys(): for project in user_projects[username].keys(): phsid = project.split(".") diff --git a/fence/user.py b/fence/user.py index b240191d2..d02dd26e4 100644 --- a/fence/user.py +++ b/fence/user.py @@ -1,5 +1,5 @@ import flask -from flask_sqlalchemy_session import current_session +from flask import current_app from fence.errors import Unauthorized from fence.models import query_for_user @@ -13,4 +13,4 @@ def get_current_user(flask_session=None): username = "test" if not username: raise Unauthorized("User not logged in") - return query_for_user(session=current_session, username=username) + return query_for_user(session=current_app.scoped_session(), username=username) diff --git a/poetry.lock b/poetry.lock index e972a7001..33241d18f 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry and should not be changed by hand. +# This file is automatically @generated by Poetry 1.4.1 and should not be changed by hand. [[package]] name = "addict" @@ -14,19 +14,20 @@ files = [ [[package]] name = "alembic" -version = "1.9.3" +version = "1.10.3" description = "A database migration tool for SQLAlchemy." category = "main" optional = false python-versions = ">=3.7" files = [ - {file = "alembic-1.9.3-py3-none-any.whl", hash = "sha256:ed2f73ea9c986f43af8ad7502c5f60d6bb1400bcd6d29f230e760e08884cb476"}, - {file = "alembic-1.9.3.tar.gz", hash = "sha256:8fd6aaea56f5a703a190d25a705dfa91d7c313bb71de2f9c68f5abdcaf5df164"}, + {file = "alembic-1.10.3-py3-none-any.whl", hash = "sha256:b2e0a6cfd3a8ce936a1168320bcbe94aefa3f4463cd773a968a55071beb3cd37"}, + {file = "alembic-1.10.3.tar.gz", hash = "sha256:32a69b13a613aeb7e8093f242da60eff9daed13c0df02fff279c1b06c32965d2"}, ] [package.dependencies] Mako = "*" SQLAlchemy = ">=1.3.0" +typing-extensions = ">=4" [package.extras] tz = ["python-dateutil"] @@ -80,22 +81,22 @@ files = [ [[package]] name = "attrs" -version = "22.2.0" +version = "23.1.0" description = "Classes Without Boilerplate" category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" files = [ - {file = "attrs-22.2.0-py3-none-any.whl", hash = "sha256:29e95c7f6778868dbd49170f98f8818f78f3dc5e0e37c0b1f474e3561b240836"}, - {file = "attrs-22.2.0.tar.gz", hash = "sha256:c9227bfc2f01993c03f68db37d1d15c9690188323c067c641f1a35ca58185f99"}, + {file = "attrs-23.1.0-py3-none-any.whl", hash = "sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04"}, + {file = "attrs-23.1.0.tar.gz", hash = "sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015"}, ] [package.extras] -cov = ["attrs[tests]", "coverage-enable-subprocess", "coverage[toml] (>=5.3)"] -dev = ["attrs[docs,tests]"] -docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope.interface"] -tests = ["attrs[tests-no-zope]", "zope.interface"] -tests-no-zope = ["cloudpickle", "cloudpickle", "hypothesis", "hypothesis", "mypy (>=0.971,<0.990)", "mypy (>=0.971,<0.990)", "pympler", "pympler", "pytest (>=4.3.0)", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-mypy-plugins", "pytest-xdist[psutil]", "pytest-xdist[psutil]"] +cov = ["attrs[tests]", "coverage[toml] (>=5.3)"] +dev = ["attrs[docs,tests]", "pre-commit"] +docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"] +tests = ["attrs[tests-no-zope]", "zope-interface"] +tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] [[package]] name = "authlib" @@ -156,40 +157,44 @@ wrapt = "*" [[package]] name = "azure-core" -version = "1.26.3" +version = "1.26.4" description = "Microsoft Azure Core Library for Python" category = "main" optional = false python-versions = ">=3.7" files = [ - {file = "azure-core-1.26.3.zip", hash = "sha256:acbd0daa9675ce88623da35c80d819cdafa91731dee6b2695c64d7ca9da82db4"}, - {file = "azure_core-1.26.3-py3-none-any.whl", hash = "sha256:f7bad0a7b4d800d6e73733ea7e13a616016221ac111ff9a344fe4cba41e51bbe"}, + {file = "azure-core-1.26.4.zip", hash = "sha256:075fe06b74c3007950dd93d49440c2f3430fd9b4a5a2756ec8c79454afc989c6"}, + {file = "azure_core-1.26.4-py3-none-any.whl", hash = "sha256:d9664b4bc2675d72fba461a285ac43ae33abb2967014a955bf136d9703a2ab3c"}, ] [package.dependencies] requests = ">=2.18.4" six = ">=1.11.0" -typing-extensions = ">=4.0.1" +typing-extensions = ">=4.3.0" [package.extras] aio = ["aiohttp (>=3.0)"] [[package]] name = "azure-storage-blob" -version = "12.14.1" +version = "12.16.0" description = "Microsoft Azure Blob Storage Client Library for Python" category = "main" optional = false python-versions = ">=3.7" files = [ - {file = "azure-storage-blob-12.14.1.zip", hash = "sha256:860d4d82985a4bfc7d3271e71275af330f54f330a754355435a7ba749ccde997"}, - {file = "azure_storage_blob-12.14.1-py3-none-any.whl", hash = "sha256:52b84658e8df7853a3cf1c563814655b5028b979b2a87905b92aa6bb30be240e"}, + {file = "azure-storage-blob-12.16.0.zip", hash = "sha256:43b45f19a518a5c6895632f263b3825ebc23574f25cc84b66e1630a6160e466f"}, + {file = "azure_storage_blob-12.16.0-py3-none-any.whl", hash = "sha256:91bb192b2a97939c4259c72373bac0f41e30810bbc853d5184f0f45904eacafd"}, ] [package.dependencies] -azure-core = ">=1.24.2,<2.0.0" +azure-core = ">=1.26.0,<2.0.0" cryptography = ">=2.1.4" -msrest = ">=0.7.1" +isodate = ">=0.6.1" +typing-extensions = ">=4.0.1" + +[package.extras] +aio = ["azure-core[aio] (>=1.26.0,<2.0.0)"] [[package]] name = "backoff" @@ -469,114 +474,104 @@ pycparser = "*" [[package]] name = "charset-normalizer" -version = "3.0.1" +version = "3.1.0" description = "The Real First Universal Charset Detector. 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(>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<4.0.0" -content-hash = "b081b776f4359fabbfcef7131be1561bd37ede696a8c89dbc6a29d4cf6d002b4" +content-hash = "3d059cb739b1a4391378ba488a5c3bc9e33e11fda22737d1683ae7266e7cd3f5" diff --git a/pyproject.toml b/pyproject.toml index e409c5228..f70c7caa8 100755 --- a/pyproject.toml +++ b/pyproject.toml @@ -23,24 +23,22 @@ cdiserrors = "<2.0.0" cdislogging = "^1.0.0" cdispyutils = "^2.0.1" cryptography = ">=3.2" -flask = ">=1.1.1" -flask-cors = "^3.0.3" -flask-restful = "^0.3.6" -flask_sqlalchemy_session = "^1.1" +flask = ">=2.2.3" +flask-cors = ">=3.0.3" +flask-restful = ">=0.3.8" email_validator = "^1.1.1" gen3authz = "^1.5.1" gen3cirrus = "^2.0.0" -gen3config = "^0.1.7" +gen3config = {git = "https://github.com/uc-cdis/gen3config", rev = "feat/poetry"} gen3users = "^0.6.0" idna = "^2.10" # https://github.com/python-poetry/poetry/issues/3555 markdown = "^3.1.1" # this markupsafe pin is due to an error somewhere between Python 3.9.6 and 3.9.16 -markupsafe = "2.0.1" +markupsafe = "^2.0.1" paramiko = "^2.6.0" prometheus-client = "^0.9.0" -prometheus-flask-exporter = "^0.18.1" psycopg2 = "^2.8.3" PyJWT = "^2.4.0" python_dateutil = "^2.6.1" @@ -50,11 +48,11 @@ requests = ">=2.18.0" retry = "^0.9.2" sqlalchemy = "^1.3.3" storageclient = {git = "https://github.com/uc-cdis/storage-client", rev = "1.0.2"} -userdatamodel = "^2.4.0" -werkzeug = "^1.0.0" +userdatamodel = {git = "https://github.com/uc-cdis/userdatamodel", rev = "fix/deps"} +werkzeug = ">=2.2.3" cachelib = "^0.2.0" azure-storage-blob = "^12.6.0" -Flask-WTF = "^0.14.3" +Flask-WTF = "^1.0.0" [tool.poetry.dev-dependencies] @@ -66,7 +64,7 @@ mock = "^2.0.0" moto = "^1.1.24" pytest = "^3.2.3" pytest-cov = "^2.5.1" -pytest-flask = "^0.15.0" +pytest-flask = ">=0.15.0" [tool.poetry.scripts] fence-create = 'bin.fence_create:main' diff --git a/tests/conftest.py b/tests/conftest.py index 69661e6ad..5b9e6c7b0 100755 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1270,27 +1270,9 @@ def public_bucket_indexd_client(app, request): @pytest.fixture(scope="function") def patch_app_db_session(app, monkeypatch): - """ - TODO - """ - def do_patch(session): monkeypatch.setattr(app.db, "Session", lambda: session) - modules_to_patch = [ - "fence.auth", - "fence.resources.google.utils", - "fence.blueprints.admin", - "fence.blueprints.link", - "fence.blueprints.google", - "fence.oidc.jwt_generator", - "fence.user", - "fence.blueprints.login.synapse", - "fence.blueprints.login.ras", - "fence.blueprints.data.indexd", - "fence.resources.ga4gh.passports", - ] - for module in modules_to_patch: - monkeypatch.setattr("{}.current_session".format(module), session) + monkeypatch.setattr(app, "scoped_session", lambda: session) return do_patch diff --git a/tests/google/conftest.py b/tests/google/conftest.py index 4376c4f2b..778924694 100644 --- a/tests/google/conftest.py +++ b/tests/google/conftest.py @@ -22,8 +22,6 @@ from tests import utils -from flask_sqlalchemy_session import current_session - from userdatamodel.models import Project, Bucket, ProjectToBucket from fence.models import GoogleBucketAccessGroup @@ -788,7 +786,6 @@ def add_user_service_account_to_google_mock(): @pytest.fixture(scope="function") def test_project(db_session): - project = Project(id=1, name="test_project", auth_id="test_project") db_session.add(project) db_session.commit() @@ -798,7 +795,6 @@ def test_project(db_session): @pytest.fixture(scope="function") def test_user(db_session): - user = User(id=1, email="google_test_user@gmail.com") test_user = db_session.query(User).filter_by(id=1).first() if not test_user: @@ -810,7 +806,6 @@ def test_user(db_session): @pytest.fixture(scope="function") def test_linked_user(db_session, test_user): - user_google_account = UserGoogleAccount( id=1, email="google_test_linked_user@gmail.com", user_id=1 ) @@ -822,7 +817,6 @@ def test_linked_user(db_session, test_user): @pytest.fixture(scope="function") def test_linked_user_with_access(db_session, test_linked_user, test_project): - access_privilege = AccessPrivilege( user_id=test_linked_user.user_id, project_id=test_project.id ) diff --git a/tests/login/test_login_user.py b/tests/login/test_login_user.py index 76021065e..2afb7b5e0 100644 --- a/tests/login/test_login_user.py +++ b/tests/login/test_login_user.py @@ -1,5 +1,4 @@ import flask -from flask_sqlalchemy_session import current_session from fence.auth import login_user, logout from fence.models import User, IdentityProvider import time diff --git a/tests/test_app_config.py b/tests/test_app_config.py index 109c0ee86..283555f90 100755 --- a/tests/test_app_config.py +++ b/tests/test_app_config.py @@ -112,5 +112,9 @@ def test_app_config(): assert fence.app.config # nosec + # Clean up registered blueprints to avoid error when repeatedly + # registers blueprints with the same name in subsequent tests + fence.app.blueprints = {} + for patcher in patchers: patcher.stop() diff --git a/tests/test_drs.py b/tests/test_drs.py index 2bde43229..0cc8589c3 100644 --- a/tests/test_drs.py +++ b/tests/test_drs.py @@ -121,6 +121,12 @@ def test_get_presigned_url_no_access_id( ) assert res.status_code == 400 + res = client.get( + "/ga4gh/drs/v1/objects/" + test_guid + "/access", + headers=user, + ) + assert res.status_code == 400 + @pytest.mark.parametrize("indexd_client", ["s3", "gs"], indirect=True) def test_get_presigned_url_no_bearer_token( From 69fe261fed8a048c2a9f0198d562b709793d182f Mon Sep 17 00:00:00 2001 From: Alex VanTol Date: Tue, 18 Apr 2023 14:30:11 -0500 Subject: [PATCH 04/11] chore(deps): use pinned versions --- poetry.lock | 32 +++++++++++--------------------- pyproject.toml | 4 ++-- 2 files changed, 13 insertions(+), 23 deletions(-) diff --git a/poetry.lock b/poetry.lock index 33241d18f..928410313 100644 --- a/poetry.lock +++ b/poetry.lock @@ -979,8 +979,9 @@ description = "Gen3 Configuration Library" category = "main" optional = false python-versions = "^3.9" -files = [] -develop = false +files = [ + {file = "gen3config-1.1.0.tar.gz", hash = "sha256:a8f460d683131a4ad7d46f35e84c6f4f77cd8f1d87126642c37e248404aa0b16"}, +] [package.dependencies] cdiserrors = "*" @@ -989,12 +990,6 @@ jinja2 = "*" pyyaml = "*" six = "*" -[package.source] -type = "git" -url = "https://github.com/uc-cdis/gen3config" -reference = "feat/poetry" -resolved_reference = "845222a965340d9ea127cf7257eaef68c8fdf360" - [[package]] name = "gen3users" version = "0.6.0" @@ -1414,14 +1409,14 @@ files = [ [[package]] name = "importlib-metadata" -version = "6.4.1" +version = "6.5.0" description = "Read metadata from Python packages" category = "main" optional = false python-versions = ">=3.7" files = [ - {file = "importlib_metadata-6.4.1-py3-none-any.whl", hash = "sha256:63ace321e24167d12fbb176b6015f4dbe06868c54a2af4f15849586afb9027fd"}, - {file = "importlib_metadata-6.4.1.tar.gz", hash = "sha256:eb1a7933041f0f85c94cd130258df3fb0dec060ad8c1c9318892ef4192c47ce1"}, + {file = "importlib_metadata-6.5.0-py3-none-any.whl", hash = "sha256:03ba783c3a2c69d751b109fc0c94a62c51f581b3d6acf8ed1331b6d5729321ff"}, + {file = "importlib_metadata-6.5.0.tar.gz", hash = "sha256:7a8bdf1bc3a726297f5cfbc999e6e7ff6b4fa41b26bba4afc580448624460045"}, ] [package.dependencies] @@ -2453,24 +2448,19 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] [[package]] name = "userdatamodel" -version = "2.4.0" +version = "2.4.3" description = "" category = "main" optional = false python-versions = "*" -files = [] -develop = false +files = [ + {file = "userdatamodel-2.4.3.tar.gz", hash = "sha256:760e41bc7f29bc16b3a9964956b52a3386db971a64dc3c873d362e135adda5b9"}, +] [package.dependencies] cdislogging = "*" sqlalchemy = ">=1.3.3" -[package.source] -type = "git" -url = "https://github.com/uc-cdis/userdatamodel" -reference = "fix/deps" -resolved_reference = "593efb04ccff13bb37e7b3f404da8288adcc3425" - [[package]] name = "websocket-client" version = "1.5.1" @@ -2640,4 +2630,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more [metadata] lock-version = "2.0" python-versions = ">=3.9,<4.0.0" -content-hash = "3d059cb739b1a4391378ba488a5c3bc9e33e11fda22737d1683ae7266e7cd3f5" +content-hash = "d86ef8b74c0707b148ad9818a7dcb882d611e535b4f06052355686fc0eb84e42" diff --git a/pyproject.toml b/pyproject.toml index f70c7caa8..fd57ced3d 100755 --- a/pyproject.toml +++ b/pyproject.toml @@ -29,7 +29,7 @@ flask-restful = ">=0.3.8" email_validator = "^1.1.1" gen3authz = "^1.5.1" gen3cirrus = "^2.0.0" -gen3config = {git = "https://github.com/uc-cdis/gen3config", rev = "feat/poetry"} +gen3config = ">=1.1.0" gen3users = "^0.6.0" idna = "^2.10" # https://github.com/python-poetry/poetry/issues/3555 markdown = "^3.1.1" @@ -48,7 +48,7 @@ requests = ">=2.18.0" retry = "^0.9.2" sqlalchemy = "^1.3.3" storageclient = {git = "https://github.com/uc-cdis/storage-client", rev = "1.0.2"} -userdatamodel = {git = "https://github.com/uc-cdis/userdatamodel", rev = "fix/deps"} +userdatamodel = ">=2.4.3" werkzeug = ">=2.2.3" cachelib = "^0.2.0" azure-storage-blob = "^12.6.0" From 36287965fc7af1ad18748abeb55fff39739ac02b Mon Sep 17 00:00:00 2001 From: Alex VanTol Date: Tue, 25 Apr 2023 13:26:52 -0500 Subject: [PATCH 05/11] fix(warnings): fix deprecation warnings --- fence/sync/sync_users.py | 7 +++---- migrations/versions/e4c7b0ab68d3_create_tables.py | 5 ++++- 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/fence/sync/sync_users.py b/fence/sync/sync_users.py index 0a9a24514..e6dc77d17 100644 --- a/fence/sync/sync_users.py +++ b/fence/sync/sync_users.py @@ -378,7 +378,7 @@ def _match_pattern(filepath, id_patterns, encrypted=True): # when converting the YAML from fence-config, # python reads it as Python string literal. So "\" turns into "\\" # which messes with the regex match - pattern = pattern.encode().decode("unicode_escape") + pattern.replace("\\\\", "\\") if re.match(pattern, os.path.basename(filepath)): return True return False @@ -500,7 +500,7 @@ def _parse_csv(self, file_dict, sess, dbgap_config={}, encrypted=True): self.id_patterns += ( [ - r"{}".format(item) + item.replace("\\\\", "\\") for item in dbgap_config.get("allowed_whitelist_patterns", []) ] if dbgap_config.get("allow_non_dbGaP_whitelist", False) @@ -523,8 +523,7 @@ def _parse_csv(self, file_dict, sess, dbgap_config={}, encrypted=True): if "additional_allowed_project_id_patterns" in dbgap_config: patterns = dbgap_config.get("additional_allowed_project_id_patterns") patterns = [ - r"{}".format(pattern.encode().decode("unicode_escape")) - for pattern in patterns + pattern.replace("\\\\", "\\") for pattern in patterns ] # when converting the YAML from fence-config, python reads it as Python string literal. So "\" turns into "\\" which messes with the regex match project_id_patterns += patterns diff --git a/migrations/versions/e4c7b0ab68d3_create_tables.py b/migrations/versions/e4c7b0ab68d3_create_tables.py index 2e2f05d03..40e9f4940 100644 --- a/migrations/versions/e4c7b0ab68d3_create_tables.py +++ b/migrations/versions/e4c7b0ab68d3_create_tables.py @@ -36,7 +36,10 @@ def upgrade(): # The state of the DB after the old migration script runs is the same as # after this initial Alembic migration. conn = op.get_bind() - inspector = sa.engine.reflection.Inspector.from_engine(conn) + + # the below was previously: `sa.engine.reflection.Inspector.from_engine(conn)` + # but that is deprecated and will be removed soon. + inspector = sa.inspect(conn) tables = inspector.get_table_names() if len(tables) > 0 and tables != ["alembic_version"]: logger.info( From fa3f08528d2cc895f65990904fc708d172fe978d Mon Sep 17 00:00:00 2001 From: Alexander VanTol Date: Thu, 27 Apr 2023 12:40:13 -0500 Subject: [PATCH 06/11] Update pyproject.toml --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index fd57ced3d..02d665c50 100755 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "fence" -version = "6.1.0" +version = "9.0.0" description = "Gen3 AuthN/AuthZ OIDC Service" authors = ["CTDS UChicago "] license = "Apache-2.0" From 215b90fb8feac7808ec524a7d6fded1e099db52b Mon Sep 17 00:00:00 2001 From: Alex VanTol Date: Fri, 28 Apr 2023 12:06:13 -0500 Subject: [PATCH 07/11] fix(test): re-add removed test --- fence/resources/google/utils.py | 2 +- tests/data/test_data.py | 40 +++++++++++++++++++++++++++++++++ 2 files changed, 41 insertions(+), 1 deletion(-) diff --git a/fence/resources/google/utils.py b/fence/resources/google/utils.py index ab1005b4b..6c7a3ccd9 100644 --- a/fence/resources/google/utils.py +++ b/fence/resources/google/utils.py @@ -565,7 +565,7 @@ def _update_service_account_db_entry( current_app.scoped_session().commit() logger.info( - "Created service account {} for proxy group {}.".format( + "Created or updated service account {} for proxy group {}.".format( new_service_account["email"], proxy_group_id ) ) diff --git a/tests/data/test_data.py b/tests/data/test_data.py index bea09c9bd..3da5febc8 100755 --- a/tests/data/test_data.py +++ b/tests/data/test_data.py @@ -107,6 +107,46 @@ def test_indexd_download_file( ) +@pytest.mark.parametrize( + "indexd_client", + ["gs", "s3", "gs_acl", "s3_acl", "s3_external", "no_urls", "az", "https"], + indirect=True, +) +def test_indexd_upload_file( + client, + oauth_client, + user_client, + indexd_client, + kid, + rsa_private_key, + google_proxy_group, + primary_google_service_account, + cloud_manager, + google_signed_url, +): + """ + Test ``GET /data/download/1``. + """ + file_id = "1" + indexed_file_location = indexd_client["indexed_file_location"] + path = f"/data/upload/{file_id}?protocol=" + indexed_file_location + headers = { + "Authorization": "Bearer " + + jwt.encode( + utils.authorized_upload_context_claims( + user_client.username, user_client.user_id + ), + key=rsa_private_key, + headers={"kid": kid}, + algorithm="RS256", + ) + } + response = client.get(path, headers=headers) + assert response.status_code == 200 + assert "url" in list(response.json.keys()) + assert file_id in response.json.get("url") + + @pytest.mark.parametrize( "indexd_client", ["gs", "s3", "gs_acl", "s3_acl", "s3_external", "az", "https"], From af1da74f6c93113931709456f24647e5f4a0da49 Mon Sep 17 00:00:00 2001 From: Alex VanTol Date: Wed, 3 May 2023 11:21:39 -0500 Subject: [PATCH 08/11] feat(deps): update flask to latest b/c of another high severity flag --- poetry.lock | 179 ++++++++++++++++++++++++++++------------------------ 1 file changed, 96 insertions(+), 83 deletions(-) diff --git a/poetry.lock b/poetry.lock index 928410313..a1c4498b8 100644 --- a/poetry.lock +++ b/poetry.lock @@ -14,14 +14,14 @@ files = [ [[package]] name = "alembic" -version = "1.10.3" +version = "1.10.4" description = "A database migration tool for SQLAlchemy." category = "main" optional = false python-versions = ">=3.7" files = [ - {file = "alembic-1.10.3-py3-none-any.whl", hash = "sha256:b2e0a6cfd3a8ce936a1168320bcbe94aefa3f4463cd773a968a55071beb3cd37"}, - {file = "alembic-1.10.3.tar.gz", hash = "sha256:32a69b13a613aeb7e8093f242da60eff9daed13c0df02fff279c1b06c32965d2"}, + {file = "alembic-1.10.4-py3-none-any.whl", hash = "sha256:43942c3d4bf2620c466b91c0f4fca136fe51ae972394a0cc8b90810d664e4f5c"}, + {file = "alembic-1.10.4.tar.gz", hash = "sha256:295b54bbb92c4008ab6a7dcd1e227e668416d6f84b98b3c4446a2bc6214a556b"}, ] [package.dependencies] @@ -236,6 +236,18 @@ cffi = ">=1.1" tests = ["pytest (>=3.2.1,!=3.3.0)"] typecheck = ["mypy"] +[[package]] +name = "blinker" +version = "1.6.2" +description = "Fast, simple object-to-object and broadcast signaling" +category = "main" +optional = false +python-versions = ">=3.7" +files = [ + {file = 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[package.dependencies] MarkupSafe = ">=2.1.1" [package.extras] -watchdog = ["watchdog"] +watchdog = ["watchdog (>=2.3)"] [[package]] name = "wrapt" From 35d961f235917aae75c301806fe73d9756697dcc Mon Sep 17 00:00:00 2001 From: Alex VanTol Date: Wed, 3 May 2023 12:46:22 -0500 Subject: [PATCH 09/11] fix(dep): update deprecated werkzeug cookie attribute to new attribute --- tests/session/test_session.py | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/tests/session/test_session.py b/tests/session/test_session.py index 1840b70c6..27ac626be 100644 --- a/tests/session/test_session.py +++ b/tests/session/test_session.py @@ -25,7 +25,7 @@ def test_session_cookie_creation(app): with client.session_transaction(): pass - client_cookies = [cookie.name for cookie in client.cookie_jar] + client_cookies = [cookie.key for cookie in client.cookie_jar] assert not client_cookies @@ -36,12 +36,15 @@ def test_session_cookie_creation_session_modified(app): with client.session_transaction() as session: session["username"] = "Captain Janeway" - client_cookies = [cookie.name for cookie in client.cookie_jar] + import pdb + + pdb.set_trace() + client_cookies = [cookie.key for cookie in client.cookie_jar] assert config["SESSION_COOKIE_NAME"] in client_cookies session_cookie = [ cookie for cookie in client.cookie_jar - if cookie.name == config["SESSION_COOKIE_NAME"] + if cookie.key == config["SESSION_COOKIE_NAME"] ] assert len(session_cookie) == 1 assert session_cookie[0].value # Make sure it's not empty @@ -89,7 +92,6 @@ def test_valid_session_modified(app): samesite="Lax", ) with client.session_transaction() as session: - assert session["username"] == username session["username"] = modified_username @@ -179,7 +181,7 @@ def test_session_cleared(app): session["username"] = username session.clear() assert session.get("username") != username - client_cookies = [cookie.name for cookie in client.cookie_jar] + client_cookies = [cookie.key for cookie in client.cookie_jar] assert config["SESSION_COOKIE_NAME"] not in client_cookies From 57b5b5d63fa760c14bc02d9044fed4368045bb43 Mon Sep 17 00:00:00 2001 From: Alex VanTol Date: Wed, 3 May 2023 12:50:14 -0500 Subject: [PATCH 10/11] fix(travis): upgrade pip before install --- .travis.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index fc33673c3..239ea50bb 100644 --- a/.travis.yml +++ b/.travis.yml @@ -11,8 +11,9 @@ addons: postgresql: "9.6" install: + - pip install --upgrade pip - pip install poetry - - poetry install -vv --no-interaction + - poetry install --all-extras -vv --no-interaction - poetry show -vv - psql -c 'SELECT version();' -U postgres - psql -U postgres -c "create database fence_test_tmp" From f5f5b255905d56fbe69d9455ca35c690b3a807d5 Mon Sep 17 00:00:00 2001 From: Alex VanTol Date: Wed, 3 May 2023 13:22:16 -0500 Subject: [PATCH 11/11] fix(tests): remove debugging --- tests/session/test_session.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/tests/session/test_session.py b/tests/session/test_session.py index 27ac626be..387dd7e98 100644 --- a/tests/session/test_session.py +++ b/tests/session/test_session.py @@ -36,9 +36,6 @@ def test_session_cookie_creation_session_modified(app): with client.session_transaction() as session: session["username"] = "Captain Janeway" - import pdb - - pdb.set_trace() client_cookies = [cookie.key for cookie in client.cookie_jar] assert config["SESSION_COOKIE_NAME"] in client_cookies session_cookie = [