Merge pull request #172 from mila-iqia/fix-werkzeug-version-bug

Update python libraries

clockwork_dev.Dockerfile

@@ -12,7 +12,7 @@ ENV CLOCKWORK_ENABLE_TESTING_LOGIN=True
 ENV MONGODB_DATABASE_NAME="clockwork"
 
 # to have gcc to build `dulwich` used by poetry
-RUN apt update && apt install -y build-essential
+RUN apt update && apt install -y build-essential git
 
 RUN pip install --upgrade pip poetry
 

clockwork_tools_test/requirements.txt

@@ -1,3 +1,3 @@
-pytest==7.1
-pymongo==4.0
-coverage==6.3
+coverage==7.3.2
+pymongo==4.5.0
+pytest==7.4.2

clockwork_tools_test/requirements_orig.txt

@@ -0,0 +1,9 @@
+coverage==7.3.2
+dnspython==2.4.2
+exceptiongroup==1.1.3
+iniconfig==2.0.0
+packaging==23.2
+pluggy==1.3.0
+pymongo==4.5.0
+pytest==7.4.2
+tomli==2.0.1

clockwork_web/Dockerfile

@@ -10,6 +10,7 @@ WORKDIR ${CLOCKWORK_ROOT}
 ENV FLASK_APP=clockwork_web.main:app
 ENV MONGODB_DATABASE_NAME="clockwork"
 
+RUN apt-get update && apt-get install -y --no-install-recommends git
 RUN pip install --upgrade pip
 
 COPY requirements.txt /requirements_web.txt

clockwork_web/browser_routes/admin.py

@@ -11,7 +11,8 @@
 # Use of "Markup" described there to avoid Flask escaping it when passing to a template.
 # https://stackoverflow.com/questions/3206344/passing-html-to-template-using-flask-jinja2
 
-from flask import Flask, Response, url_for, request, redirect, make_response, Markup
+from markupsafe import Markup
+from flask import Flask, Response, url_for, request, redirect, make_response
 from flask import request, send_file
 from flask import jsonify
 from werkzeug.utils import secure_filename

clockwork_web/browser_routes/gpu.py

@@ -1,5 +1,5 @@
 import logging
-from flask import Blueprint, Markup, request
+from flask import Blueprint, request
 from flask.json import jsonify
 from flask_login import current_user, login_required
 from flask_babel import gettext

clockwork_web/browser_routes/jobs.py

@@ -9,8 +9,8 @@
 
 # Use of "Markup" described there to avoid Flask escaping it when passing to a template.
 # https://stackoverflow.com/questions/3206344/passing-html-to-template-using-flask-jinja2
-
-from flask import Flask, Response, url_for, request, redirect, make_response, Markup
+from markupsafe import Markup
+from flask import Flask, Response, url_for, request, redirect, make_response
 from flask import request, send_file
 from flask import jsonify
 from werkzeug.utils import secure_filename

clockwork_web/browser_routes/nodes.py

@@ -10,11 +10,9 @@
 
 # Use of "Markup" described there to avoid Flask escaping it when passing to a template.
 # https://stackoverflow.com/questions/3206344/passing-html-to-template-using-flask-jinja2
-
-from flask import Flask, Response, url_for, request, redirect, make_response, Markup
-from flask import request, send_file
-from flask import jsonify
-from werkzeug.utils import secure_filename
+from markupsafe import Markup
+from flask import Flask, Response, request
+from flask import request
 from werkzeug.wsgi import FileWrapper
 
 # https://flask.palletsprojects.com/en/1.1.x/appcontext/
@@ -36,10 +34,7 @@
 
 from clockwork_web.core.clusters_helper import get_all_clusters
 from clockwork_web.core.nodes_helper import get_nodes
-from clockwork_web.core.jobs_helper import (
-    get_filter_cluster_name,
-    combine_all_mongodb_filters,
-)
+from clockwork_web.core.jobs_helper import combine_all_mongodb_filters
 from clockwork_web.core.nodes_helper import (
     get_filter_node_name,
     strip_artificial_fields_from_node,

clockwork_web/browser_routes/settings.py

@@ -6,7 +6,8 @@
 import secrets
 import logging
 
-from flask import Flask, Response, url_for, request, redirect, make_response, Markup
+from markupsafe import Markup
+from flask import Flask, Response, url_for, request, redirect, make_response
 from flask import request, send_file
 from flask import jsonify
 

clockwork_web/requirements.txt

@@ -1,10 +1,23 @@
-requests==2.27
-Flask==2.1
-oauthlib==3.2
-Werkzeug==2.2.2
-Flask-Login==0.6.0
-Flask-Babel==2.0.0
-pymongo==4.0
+Babel==2.13.0
+blinker==1.6.3
+certifi==2023.7.22
+charset-normalizer==3.3.0
+click==8.1.7
+dnspython==2.4.2
+Flask==3.0.0
+flask-babel==4.0.0
+Flask-Login @ git+https://github.com/maxcountryman/flask-login.git@2204b4eee7b215977ba5a1bf85e2061f7fa65e20
+idna==3.4
+importlib-metadata==6.8.0
+itsdangerous==2.1.2
+Jinja2==3.1.2
+MarkupSafe==2.1.3
+oauthlib==3.2.2
+pymongo==4.5.0
+pytz==2023.3.post1
+requests==2.31.0
+sentry-sdk==1.32.0
 toml==0.10.2
-sentry-sdk[flask]
-
+urllib3==2.0.7
+Werkzeug==3.0.0
+zipp==3.17.0

clockwork_web/requirements_orig.txt

@@ -0,0 +1,9 @@
+Flask==3.0.0
+flask-babel==4.0.0
+Flask-Login @ git+https://github.com/maxcountryman/flask-login.git@2204b4eee7b215977ba5a1bf85e2061f7fa65e20
+oauthlib==3.2.2
+pymongo==4.5.0
+requests==2.31.0
+sentry-sdk==1.32.0
+toml==0.10.2
+Werkzeug==3.0.0

clockwork_web/server_app.py

@@ -41,7 +41,7 @@
 from .core.jobs_helper import job_state_to_aggregated
 
 
-from werkzeug.urls import url_encode
+from urllib.parse import urlencode
 
 register_config("flask.secret_key", validator=string)
 register_config("translation.translations_folder", default="", validator=string)
@@ -128,7 +128,7 @@ def modify_query(**new_values):
         for key, value in new_values.items():
             args[key] = value
 
-        return "{}?{}".format(request.path, url_encode(args))
+        return "{}?{}".format(request.path, urlencode(args))
 
     # Adding a function to help comparing two usernames
     @app.template_global()
@@ -146,9 +146,6 @@ def have_same_users(user1: str, user2: str):
         )
 
     # Initialize Babel
-    babel = Babel(app)
-
-    @babel.localeselector
     def get_locale():
         # If the user is authenticated
         if current_user and current_user.is_authenticated():
@@ -167,6 +164,8 @@ def get_locale():
 
             return session["language"]
 
+    babel = Babel(app, locale_selector=get_locale, timezone_selector=None)
+
     # Initialize templates filters
     @app.template_filter()
     def format_date(float_timestamp, expected_date_format, expected_time_format):

clockwork_web_test/requirements.txt

@@ -1,3 +1,14 @@
-pytest==7.1
-coverage==6.3
-requests-mock==1.9
+certifi==2023.7.22
+charset-normalizer==3.3.0
+coverage==7.3.2
+exceptiongroup==1.1.3
+idna==3.4
+iniconfig==2.0.0
+packaging==23.2
+pluggy==1.3.0
+pytest==7.4.2
+requests==2.31.0
+requests-mock==1.11.0
+six==1.16.0
+tomli==2.0.1
+urllib3==2.0.7

clockwork_web_test/requirements_orig.txt

@@ -0,0 +1,4 @@
+coverage==7.3.2
+pytest==7.4.2
+requests-mock==1.11.0
+toml==0.10.2