From d3eb0a4e605b6af323babac811c6abcabbebbde8 Mon Sep 17 00:00:00 2001
From: Nayib Gloria <55710092+nayib-jose-gloria@users.noreply.github.com>
Date: Thu, 3 Oct 2024 11:26:37 -0400
Subject: [PATCH] fix: Revert "chore: resolve deprecation warning and update
 requirements (#7275)" (#7350)

---
 Dockerfile.backend                              |  2 +-
 backend/api_server/index.html                   |  4 ++--
 backend/common/auth0_manager.py                 |  2 +-
 backend/common/census_cube/utils.py             |  8 ++++----
 backend/common/server/config.py                 |  6 ++----
 backend/portal/api/app/v1/authentication.py     |  3 ++-
 .../backend/common/server/requirements.txt      |  6 +++---
 python_dependencies/backend/requirements.txt    | 17 +++++++++++++----
 8 files changed, 28 insertions(+), 20 deletions(-)

diff --git a/Dockerfile.backend b/Dockerfile.backend
index 22596d9642eef..1563bf75e66c8 100644
--- a/Dockerfile.backend
+++ b/Dockerfile.backend
@@ -22,7 +22,7 @@ RUN python3 -m pip install --upgrade pip setuptools
 # TODO: Determine if cmake is really needed for ddtrace
 # see ticket: https://github.com/chanzuckerberg/single-cell-data-portal/issues/5821
 RUN python3 -m pip install cmake
-RUN python3 -m pip install -r requirements.txt -r ./common/server/requirements.txt
+RUN python3 -m pip install -r requirements.txt
 RUN if [ "$INSTALL_DEV" = "true" ]; then python3 -m pip install -r requirements-dev.txt; fi
 # Install awscli to download wmg snapshot to the local disk
 RUN python3 -m pip install awscli
diff --git a/backend/api_server/index.html b/backend/api_server/index.html
index b9a9a13eb505b..148b2d3d43c72 100644
--- a/backend/api_server/index.html
+++ b/backend/api_server/index.html
@@ -9,8 +9,8 @@
     />
     <link
       rel="stylesheet"
-      href="https://cdnjs.cloudflare.com/ajax/libs/swagger-ui/5.17.14/swagger-ui.css"
-      integrity="sha512-MvYROlKG3cDBPskMQgPmkNgZh85LIf68y7SZ34TIppaIHQz1M/3S/yYqzIfufdKDJjzB9Qu1BV63SZjimJkPvw=="
+      href="https://cdnjs.cloudflare.com/ajax/libs/swagger-ui/3.0.13/swagger-ui.css"
+      integrity="sha256-Z7Z2kffooC4H3U4Myviypq5dO2IIGkmu7VRtd1YqNn8="
       crossorigin="anonymous"
     />
     <style>
diff --git a/backend/common/auth0_manager.py b/backend/common/auth0_manager.py
index 1814b71dcc997..cf85e59954879 100644
--- a/backend/common/auth0_manager.py
+++ b/backend/common/auth0_manager.py
@@ -30,7 +30,7 @@ def session(self):
                 total=3,
                 backoff_factor=1,
                 status_forcelist=self.config.retry_status_forcelist,
-                allowed_methods=["POST", "HEAD", "GET", "PUT", "DELETE", "OPTIONS"],
+                method_whitelist=["POST", "HEAD", "GET", "PUT", "DELETE", "OPTIONS"],
             )
             session.mount("https://", HTTPAdapter(max_retries=retry_config))
 
diff --git a/backend/common/census_cube/utils.py b/backend/common/census_cube/utils.py
index 759b1bbea1d9a..2c85da6a72b4e 100644
--- a/backend/common/census_cube/utils.py
+++ b/backend/common/census_cube/utils.py
@@ -96,17 +96,17 @@ def depluralize(x):
     return x[:-1] if x[-1] == "s" else x
 
 
-def setup_retry_session(retries=3, backoff_factor=2, status_forcelist=(500, 502, 503, 504), allowed_methods=None):
+def setup_retry_session(retries=3, backoff_factor=2, status_forcelist=(500, 502, 503, 504), method_whitelist=None):
     session = requests.Session()
 
-    if allowed_methods is None:
-        allowed_methods = {"GET"}
+    if method_whitelist is None:
+        method_whitelist = {"GET"}
 
     retry = Retry(
         total=retries,
         backoff_factor=backoff_factor,
         status_forcelist=status_forcelist,
-        allowed_methods=allowed_methods,
+        allowed_methods=method_whitelist,
     )
 
     adapter = HTTPAdapter(max_retries=retry)
diff --git a/backend/common/server/config.py b/backend/common/server/config.py
index a494c34f66d23..0306c658eb9e9 100644
--- a/backend/common/server/config.py
+++ b/backend/common/server/config.py
@@ -51,10 +51,9 @@ def configure_flask_app(flask_app):
         SESSION_COOKIE_SECURE=require_secure_cookies,
         SESSION_COOKIE_HTTPONLY=True,
         SESSION_COOKIE_SAMESITE="Lax",
+        JSON_SORT_KEYS=True,
     )
     flask_app.json_encoder = CustomJSONEncoder
-    flask_app.json.sort_keys = True
-
     return flask_app
 
 
@@ -142,8 +141,7 @@ def create_api_app(api_paths_and_spec_files, **server_args):
     based on the deployment stage.
 
     Args:
-        api_paths_and_spec_files (list of tuples): A list where each tuple contains a base path and a specification
-        file.
+        api_paths_and_spec_files (list of tuples): A list where each tuple contains a base path and a specification file.
         **server_args: Additional arguments to be passed to the FlaskApp.
 
     Returns:
diff --git a/backend/portal/api/app/v1/authentication.py b/backend/portal/api/app/v1/authentication.py
index 3beb65c48d844..8bae005871878 100644
--- a/backend/portal/api/app/v1/authentication.py
+++ b/backend/portal/api/app/v1/authentication.py
@@ -8,6 +8,7 @@
 
 import requests
 from authlib.integrations.flask_client import OAuth
+from authlib.integrations.flask_client.remote_app import FlaskRemoteApp
 from flask import Response, after_this_request, current_app, g, jsonify, make_response, redirect, request, session
 
 from backend.common.authorizer import assert_authorized_token, get_userinfo_from_auth0
@@ -19,7 +20,7 @@
 oauth_client = None
 
 
-def get_oauth_client(config: CorporaAuthConfig) -> OAuth:
+def get_oauth_client(config: CorporaAuthConfig) -> FlaskRemoteApp:
     """Create an oauth client on the first invocation, then return oauth client for subsequent calls.
 
     :param config:  An object containing the auth configuration.
diff --git a/python_dependencies/backend/common/server/requirements.txt b/python_dependencies/backend/common/server/requirements.txt
index f3e2362d1f09e..b5465d1f437b7 100644
--- a/python_dependencies/backend/common/server/requirements.txt
+++ b/python_dependencies/backend/common/server/requirements.txt
@@ -1,8 +1,8 @@
 connexion[swagger-ui]~=2.14.2
 gunicorn[gevent]~=22.0.0
 furl~=2.1.2
-Flask-Cors~=4.0.1
+Flask-Cors~=3.0.6
 flask-server-timing~=0.1.2
-ddtrace~=2.9.2
+ddtrace~=2.8.5
 python-json-logger
-boto3~=1.34.114
+boto3~=1.34.114
\ No newline at end of file
diff --git a/python_dependencies/backend/requirements.txt b/python_dependencies/backend/requirements.txt
index 26bd21aaacfae..ca313b3780a24 100644
--- a/python_dependencies/backend/requirements.txt
+++ b/python_dependencies/backend/requirements.txt
@@ -1,16 +1,24 @@
 alembic==1.*
-Authlib==1.3.1
+Authlib==0.14.3
+boto3>=1.11.17
 botocore>=1.14.17
-dataclasses-json==0.6.7
+connexion[swagger-ui]==2.14.2
+dataclasses-json==0.6.6
 cellxgene-ontology-guide<2
 # TODO: Check if this is really essential for APM tracing
 # see ticket: https://github.com/chanzuckerberg/single-cell-data-portal/issues/5821
 datadog==0.49.1
-Flask # verison determined by connexion
-psutil>=6, <7
+ddtrace>=2.1.4, <3
+Flask>=2.2.3, <3
+Flask-Cors>=3.0.6
+flask-server-timing>=0.1.2
+gunicorn[gevent]==22.0.0
+matplotlib>=3.6.3, <3.7 # 3.7.0 isn't compatible with scanpy: https://github.com/scverse/scanpy/issues/2411
+psutil>=5.9.5, <6
 psycopg2-binary==2.*
 pydantic>=1.10.7, <2
 python-jose[cryptography]>=3.1.0
+python-json-logger
 requests>=2.22.0
 rsa>=4.7 # not directly required, pinned by Snyk to avoid a vulnerability
 setproctitle>1.3,<2 # for gunicorn integration with datadog
@@ -18,3 +26,4 @@ SQLAlchemy-Utils
 SQLAlchemy==2.*
 tenacity
 tiledb
+Werkzeug==2.2.3