Merge pull request #1086 from uc-cdis/fix/google_update

feat(google_update): updated Flask and deps, also don't fail early with Google errors PXP-10900

.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"

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()
 
 
@@ -509,28 +528,15 @@ 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):
@@ -569,3 +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}")

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)
@@ -120,16 +120,17 @@ 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()
     )
     if not idp:
         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()