chore(deps): update backend

Dockerfile.backend

@@ -1,4 +1,4 @@
-FROM ubuntu:22.04
+FROM ubuntu:24.04
 
 ENV APP_NAME=corpora-api
 ENV EXPORT_ENV_VARS_TO_LAMBDA="APP_NAME DEPLOYMENT_STAGE"

Dockerfile.backend_de

@@ -1,4 +1,4 @@
-FROM ubuntu:22.04
+FROM ubuntu:24.04
 
 ENV APP_NAME=corpora-api-de
 ENV EXPORT_ENV_VARS_TO_LAMBDA="APP_NAME DEPLOYMENT_STAGE"

Dockerfile.backend_wmg

@@ -1,4 +1,4 @@
-FROM ubuntu:22.04
+FROM ubuntu:24.04
 
 ENV APP_NAME=corpora-api-wmg
 ENV EXPORT_ENV_VARS_TO_LAMBDA="APP_NAME DEPLOYMENT_STAGE"

backend/api_server/index.html

@@ -9,8 +9,8 @@
     />
     <link
       rel="stylesheet"
-      href="https://cdnjs.cloudflare.com/ajax/libs/swagger-ui/3.0.13/swagger-ui.css"
-      integrity="sha256-Z7Z2kffooC4H3U4Myviypq5dO2IIGkmu7VRtd1YqNn8="
+      href="https://cdnjs.cloudflare.com/ajax/libs/swagger-ui/5.18.2/swagger-ui.css"
+      integrity="sha512-Fx2bx472ykst5EwyqNnGgXC2pPBxuxRnxHSa5Elf7sVbYA1vj2M/J50eJ0aXDal5hDjdSl3EEaQCaO5y69HmcQ=="
       crossorigin="anonymous"
     />
     <style>
@@ -84,13 +84,13 @@
     <div id="swagger-ui"></div>
 
     <script
-      src="https://cdnjs.cloudflare.com/ajax/libs/swagger-ui/3.23.11/swagger-ui-bundle.js"
-      integrity="sha256-wmWvmMbIQjnhA5qXYJAw60JjO3/zvM2T/BMnbdBD26w="
+      src="https://cdnjs.cloudflare.com/ajax/libs/swagger-ui/5.18.2/swagger-ui-bundle.js"
+      integrity="sha512-J8sV3czWF0DcwmhzNrUbzjxvu3KefHg9Sn6YweslZnSsRFrLqx/y/ePkiiLvppzgwM73KjBt5G7xQ6kxEvvdvA=="
       crossorigin="anonymous"
     ></script>
     <script
-      src="https://cdnjs.cloudflare.com/ajax/libs/swagger-ui/3.23.11/swagger-ui-standalone-preset.js"
-      integrity="sha256-AGfcF/HKnhqGTZNL+pNGJ+yemAzr2tuvbP69pYbn+GU="
+      src="https://cdnjs.cloudflare.com/ajax/libs/swagger-ui/5.18.2/swagger-ui-standalone-preset.js"
+      integrity="sha512-qvzEUMlxl6BHnALvxzMNZhtG6Ygu6K9j4kDefViA/+Ht++/N8nTBA+HnI4qaUj8SfyjBf11PhW5nxMdZTDm5Og=="
       crossorigin="anonymous"
     ></script>
     <script>

python_dependencies/backend/common/server/requirements.txt

@@ -1,8 +1,8 @@
-connexion[swagger-ui]~=2.14.2
-gunicorn[gevent]~=22.0.0
+connexion[swagger-ui]~=3.1.0
+gunicorn[gevent]~=23.0.0
 furl~=2.1.2
 Flask-Cors~=3.0.6
 flask-server-timing~=0.1.2
-ddtrace~=2.8.5
+ddtrace~=2.16.2
 python-json-logger
-boto3~=1.34.114
+boto3~=1.35.61

python_dependencies/backend/de/requirements.txt

@@ -1,8 +1,8 @@
 pandas~=2.2.2
-scipy~=1.13.1
-pydantic~=1.10.7
-numba~=0.59.1
-cellxgene-ontology-guide~=1.0.0
+scipy~=1.14.1
+pydantic~=2.9.2
+numba~=0.60.0
+cellxgene-ontology-guide~=1.2.0
 tiledb
-psutil~=5.9.8
-pyarrow==16.0.0
+psutil~=6.1.0
+pyarrow==18.0.0

python_dependencies/backend/requirements.txt

@@ -2,21 +2,21 @@ alembic==1.*
 Authlib==0.14.3
 boto3>=1.11.17
 botocore>=1.14.17
-connexion[swagger-ui]==2.14.2
-dataclasses-json==0.6.6
+connexion[swagger-ui]==3.1.0
+dataclasses-json==0.6.7
 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
+datadog==0.50.1
 ddtrace>=2.1.4, <3
-Flask>=2.2.3, <3
+Flask>=3.1, <4
 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
+gunicorn[gevent]==23.0.0
+matplotlib>=3.9.2, <3.10 # 3.7.0 isn't compatible with scanpy: https://github.com/scverse/scanpy/issues/2411
+psutil>=6.1, <7
 psycopg2-binary==2.*
-pydantic>=1.10.7, <2
+pydantic>=2.9.2, <3
 python-jose[cryptography]>=3.1.0
 python-json-logger
 requests>=2.22.0

python_dependencies/backend/wmg/requirements.txt

@@ -1,7 +1,7 @@
 pandas~=2.2.2
-pydantic~=1.10.7
-numba~=0.59.1
-cellxgene-ontology-guide~=1.0.0
+pydantic~=2.9.2
+numba~=0.60.0
+cellxgene-ontology-guide~=1.2.0
 tiledb
-psutil~=5.9.8
-pyarrow==16.0.0
+psutil~=6.1.0
+pyarrow==18.0.0