Update GitHub actions and Python Dependencies

.github/workflows/backend.yml

@@ -30,7 +30,7 @@ jobs:
             github.com:443
             storage.googleapis.com:443
             uploader.codecov.io:443
-      - uses: actions/checkout@755da8c3cf115ac066823e79a1e1788f8940201b # v3.2.0
+      - uses: actions/checkout@ac593985615ec2ede58e132d2e21d2b1cbd6127c # v3.3.0
       - name: Setup dotnet
         uses: actions/setup-dotnet@607fce577a46308457984d59e4954e075820f10a # v3.0.3
         with:
@@ -79,7 +79,7 @@ jobs:
             github.com:443
 
       - name: Checkout repository
-        uses: actions/checkout@755da8c3cf115ac066823e79a1e1788f8940201b # v3.2.0
+        uses: actions/checkout@ac593985615ec2ede58e132d2e21d2b1cbd6127c # v3.3.0
       # Manually install .NET to work around:
       # https://github.com/github/codeql-action/issues/757
       - name: Setup .NET
@@ -93,7 +93,7 @@ jobs:
       - name: Autobuild
         uses: github/codeql-action/autobuild@959cbb7472c4d4ad70cdfe6f4976053fe48ab394 # v2.1.37
       - name: Upload artifacts if build failed
-        uses: actions/upload-artifact@82c141cc518b40d92cc801eee768e7aafc9c2fa2 # v2.3.1
+        uses: actions/upload-artifact@0b7f8abb1508181956e8e162db84b466c27e18ce # v3.1.2
         if: ${{ failure() }}
         with:
           name: tracer-logs
@@ -103,7 +103,7 @@ jobs:
 
   docker_build:
     runs-on: ubuntu-22.04
-    if: ${{ github.event.type }} == "PullRequest"
+    #    if: ${{ github.event.type }} == "PullRequest"
     steps:
       # For subfolders, currently a full checkout is required.
       # See: https://github.com/marketplace/actions/build-and-push-docker-images#path-context
@@ -117,12 +117,12 @@ jobs:
             dc.services.visualstudio.com:443
             deb.debian.org:80
             github.com:443
-            mcr.microsoft.com:443
-            eastus.data.mcr.microsoft.com:443
-            centralus.data.mcr.microsoft.com:443
-            westcentralus.data.mcr.microsoft.com:443
-            westus.data.mcr.microsoft.com:443
-      - uses: actions/checkout@755da8c3cf115ac066823e79a1e1788f8940201b # v3.2.0
+            docker.io:443
+            auth.docker.io:443
+            registry-1.docker.io:443
+            production.cloudflare.docker.com
+            security.debian.org
+      - uses: actions/checkout@ac593985615ec2ede58e132d2e21d2b1cbd6127c # v3.3.0
         with:
           fetch-depth: 0
       - name: Build backend

.github/workflows/codeql.yml

@@ -65,7 +65,7 @@ jobs:
           egress-policy: block
           allowed-endpoints: ${{ matrix.language.endpoints }}
       - name: Checkout repository
-        uses: actions/checkout@755da8c3cf115ac066823e79a1e1788f8940201b # v3.2.0
+        uses: actions/checkout@ac593985615ec2ede58e132d2e21d2b1cbd6127c # v3.3.0
 
       # Initializes the CodeQL tools for scanning.
       - name: Initialize CodeQL

.github/workflows/combine_deploy_image.yml

@@ -35,7 +35,7 @@ jobs:
           username: ${{ secrets.AWS_ACCESS_KEY_ID }}
           password: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
       - name: Build combine_deploy
-        uses: docker/build-push-action@c56af957549030174b10d6867f20e78cfd7debc5 # v3.2.0
+        uses: docker/build-push-action@37abcedcc1da61a57767b7588cb9d03eb57e28b3 # v3.3.0
         with:
           context: "{{defaultContext}}:deploy"
           push: true

.github/workflows/database.yml

@@ -19,7 +19,7 @@ jobs:
         with:
           egress-policy: audit # TODO: change to 'egress-policy: block' after couple of runs
 
-      - uses: actions/checkout@755da8c3cf115ac066823e79a1e1788f8940201b # v3.2.0
+      - uses: actions/checkout@ac593985615ec2ede58e132d2e21d2b1cbd6127c # v3.3.0
         with:
           fetch-depth: 0
       - name: Build database image

.github/workflows/deploy_qa.yml

@@ -2,7 +2,11 @@ name: "Deploy Update to QA Server"
 
 on:
   push:
-    branches: [master]
+    branches:
+      - master
+
+permissions:
+  contents: read
 
 jobs:
   build:
@@ -22,26 +26,25 @@ jobs:
           allowed-endpoints: >
             ${{ secrets.AWS_ACCOUNT }}.dkr.ecr.${{ secrets.AWS_DEFAULT_REGION }}.amazonaws.com
             api.ecr.${{ secrets.AWS_DEFAULT_REGION }}.amazonaws.com:443
-            auth.docker.io:443
-            files.pythonhosted.org:443
-            github.com:443
+            sts.${{ secrets.AWS_DEFAULT_REGION }}.amazonaws.com:443
+            dotnetcli.azureedge.net:443
+            codecov.io:443
+            uploader.codecov.io:443
             production.cloudflare.docker.com:443
-            pypi.org:443
+            docker.io:443
+            auth.docker.io:443
             registry-1.docker.io:443
+            github.com:443
+            api.github.com:443
+            storage.googleapis.com:443
             registry.npmjs.org:443
-            sts.${{ secrets.AWS_DEFAULT_REGION }}.amazonaws.com:443
             api.nuget.org:443
+            pypi.org:443
+            files.pythonhosted.org:443
+            security.ubuntu.com:443
+            archive.ubuntu.com:443
             dc.services.visualstudio.com:443
-            deb.debian.org:80
-            mcr.microsoft.com:443
-            eastus.data.mcr.microsoft.com:443
-            centralus.data.mcr.microsoft.com:443
-            westcentralus.data.mcr.microsoft.com:443
-            westus.data.mcr.microsoft.com:443
-            archive.ubuntu.com:80
-            security.ubuntu.com:80
-            api.github.com:443
-      - uses: actions/checkout@755da8c3cf115ac066823e79a1e1788f8940201b # v3.2.0
+      - uses: actions/checkout@ac593985615ec2ede58e132d2e21d2b1cbd6127c # v3.3.0
         with:
           fetch-depth: 0
       - name: Build The Combine
@@ -69,7 +72,7 @@ jobs:
             api.ecr.${{ secrets.AWS_DEFAULT_REGION }}.amazonaws.com:443
             github.com:443
             sts.${{ secrets.AWS_DEFAULT_REGION }}.amazonaws.com:443
-      - uses: actions/checkout@755da8c3cf115ac066823e79a1e1788f8940201b # v3.2.0
+      - uses: actions/checkout@ac593985615ec2ede58e132d2e21d2b1cbd6127c # v3.3.0
       - name: Configure AWS credentials
         uses: aws-actions/configure-aws-credentials@97271860067ec931c45b8d104fbf0d15954ab85c # v1-node16
         with:
@@ -82,7 +85,7 @@ jobs:
     needs: build
     runs-on: [self-hosted, thecombine]
     steps:
-      - uses: actions/checkout@755da8c3cf115ac066823e79a1e1788f8940201b # v3.2.0
+      - uses: actions/checkout@ac593985615ec2ede58e132d2e21d2b1cbd6127c # v3.3.0
       - name: Deploy The Combine Update
         uses: ./.github/actions/combine-deploy-update
         with:

.github/workflows/deploy_release.yml

@@ -5,6 +5,9 @@ on:
     branches: [master]
     types: [published]
 
+permissions:
+  contents: read
+
 jobs:
   build:
     strategy:
@@ -19,7 +22,7 @@ jobs:
         with:
           egress-policy: audit # TODO: change to 'egress-policy: block' after couple of runs
 
-      - uses: actions/checkout@755da8c3cf115ac066823e79a1e1788f8940201b # v3.2.0
+      - uses: actions/checkout@ac593985615ec2ede58e132d2e21d2b1cbd6127c # v3.3.0
       - name: Build The Combine
         id: build_combine
         uses: ./.github/actions/combine-build
@@ -38,7 +41,7 @@ jobs:
     needs: build
     runs-on: [self-hosted, thecombine]
     steps:
-      - uses: actions/checkout@755da8c3cf115ac066823e79a1e1788f8940201b # v3.2.0
+      - uses: actions/checkout@ac593985615ec2ede58e132d2e21d2b1cbd6127c # v3.3.0
         with:
           fetch-depth: 0
       - name: Deploy The Combine Update

.github/workflows/frontend.yml

@@ -27,9 +27,9 @@ jobs:
             registry.npmjs.org:443
             storage.googleapis.com:443
             uploader.codecov.io:443
-      - uses: actions/checkout@755da8c3cf115ac066823e79a1e1788f8940201b # v3.2.0
+      - uses: actions/checkout@ac593985615ec2ede58e132d2e21d2b1cbd6127c # v3.3.0
       - name: Use Node.js ${{ matrix.node-version }}
-        uses: actions/setup-node@8c91899e586c5b171469028077307d293428b516 # v3.5.1
+        uses: actions/setup-node@64ed1c7eab4cce3362f8c340dee64e5eaeef8f7c # v3.6.0
         with:
           node-version: ${{ matrix.node-version }}
       - run: npm ci
@@ -68,7 +68,7 @@ jobs:
             pypi.org:443
             registry-1.docker.io:443
             registry.npmjs.org:443
-      - uses: actions/checkout@755da8c3cf115ac066823e79a1e1788f8940201b # v3.2.0
+      - uses: actions/checkout@ac593985615ec2ede58e132d2e21d2b1cbd6127c # v3.3.0
         with:
           fetch-depth: 0
       - name: Build frontend

.github/workflows/maintenance.yml

@@ -28,7 +28,7 @@ jobs:
             pypi.org:443
             registry-1.docker.io:443
             security.ubuntu.com:80
-      - uses: actions/checkout@755da8c3cf115ac066823e79a1e1788f8940201b # v3.2.0
+      - uses: actions/checkout@ac593985615ec2ede58e132d2e21d2b1cbd6127c # v3.3.0
         with:
           fetch-depth: 0
       - name: Build maintenance image

.github/workflows/pages.yml

@@ -23,7 +23,7 @@ jobs:
             files.pythonhosted.org:443
             github.com:443
             pypi.org:443
-      - uses: actions/checkout@755da8c3cf115ac066823e79a1e1788f8940201b # v3.2.0
+      - uses: actions/checkout@ac593985615ec2ede58e132d2e21d2b1cbd6127c # v3.3.0
       - uses: actions/setup-python@5ccb29d8773c3f3f653e1705f474dfaa8a06a912 # v4.4.0
         with:
           python-version: 3.9

.github/workflows/python.yml

@@ -25,7 +25,7 @@ jobs:
             files.pythonhosted.org:443
             github.com:443
             pypi.org:443
-      - uses: actions/checkout@755da8c3cf115ac066823e79a1e1788f8940201b # v3.2.0
+      - uses: actions/checkout@ac593985615ec2ede58e132d2e21d2b1cbd6127c # v3.3.0
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@5ccb29d8773c3f3f653e1705f474dfaa8a06a912 # v4.4.0
         with:

.github/workflows/scorecards.yml

@@ -13,8 +13,6 @@ on:
     - cron: "18 6 * * 0"
   push:
     branches: [master]
-  pull_request:
-    branches: [master]
 
 # Declare default permissions as read only.
 permissions: read-all
@@ -49,13 +47,14 @@ jobs:
             sigstore-tuf-root.storage.googleapis.com:443
             auth.docker.io:443
             rekor.sigstore.dev:443
+            api.securityscorecards.dev
       - name: "Checkout code"
-        uses: actions/checkout@93ea575cb5d8a053eaa0ac8fa3b40d7e05a33cc8 # v3.1.0
+        uses: actions/checkout@ac593985615ec2ede58e132d2e21d2b1cbd6127c # v3.3.0
         with:
           persist-credentials: false
 
       - name: "Run analysis"
-        uses: ossf/scorecard-action@99c53751e09b9529366343771cc321ec74e9bd3d # v2.0.6
+        uses: ossf/scorecard-action@e38b1902ae4f44df626f11ba0734b14fb91f8f86 # v2.1.2
         with:
           results_file: results.sarif
           results_format: sarif
@@ -77,7 +76,7 @@ jobs:
       # Upload the results as artifacts (optional). Commenting out will disable uploads of run results in SARIF
       # format to the repository Actions tab.
       - name: "Upload artifact"
-        uses: actions/upload-artifact@3cea5372237819ed00197afe530f5a7ea3e805c8 # v3.1.0
+        uses: actions/upload-artifact@0b7f8abb1508181956e8e162db84b466c27e18ce # v3.1.2
         with:
           name: SARIF file
           path: results.sarif

Backend/Dockerfile

@@ -1,5 +1,5 @@
 # Docker multi-stage build.
-FROM mcr.microsoft.com/dotnet/sdk:6.0 AS builder
+FROM bitnami/dotnet-sdk:6@sha256:b8426ee39b7ec43d905d3b198f7819552c791472485fae95275e3832ab251480 AS builder
 WORKDIR /app
 
 # Copy csproj and restore (fetch dependencies) as distinct layers.
@@ -11,7 +11,7 @@ COPY . ./
 RUN dotnet publish -c Release -o build
 
 # Build runtime image.
-FROM mcr.microsoft.com/dotnet/aspnet:6.0
+FROM bitnami/aspnet-core@sha256:1fa0ee4f642f484066b236a4cb8629cafbbc21c485939b0da52f6d0e9b36f3f7
 
 ENV ASPNETCORE_URLS=http://+:5000
 ENV COMBINE_IS_IN_CONTAINER=1

Dockerfile

@@ -1,5 +1,5 @@
 # User guide build environment.
-FROM python:3.10 AS user_guide_builder
+FROM python:3.11@sha256:a3c0c6766535f85f18e7304d3a0111de5208d73935bcf1b024217005ad5ce195 AS user_guide_builder
 
 ENV PYTHONDONTWRITEBYTECODE 1
 ENV PYTHONUNBUFFERED 1

deploy/requirements.txt

@@ -1,28 +1,28 @@
 #
-# This file is autogenerated by pip-compile with python 3.10
-# To update, run:
+# This file is autogenerated by pip-compile with Python 3.10
+# by the following command:
 #
 #    pip-compile requirements.in
 #
-ansible==6.5.0
+ansible==7.1.0
     # via -r requirements.in
-ansible-core==2.13.5
+ansible-core==2.14.1
     # via ansible
-cachetools==5.2.0
+cachetools==5.2.1
     # via google-auth
-certifi==2022.9.24
+certifi==2022.12.7
     # via
     #   kubernetes
     #   requests
 cffi==1.15.1
     # via cryptography
-charset-normalizer==2.1.1
+charset-normalizer==3.0.1
     # via requests
-cryptography==38.0.1
+cryptography==39.0.0
     # via
     #   ansible-core
     #   pyopenssl
-google-auth==2.12.0
+google-auth==2.16.0
     # via kubernetes
 idna==3.4
     # via requests
@@ -33,13 +33,13 @@ jinja2==3.1.2
     #   jinja2-base64-filters
 jinja2-base64-filters==0.1.4
     # via -r requirements.in
-kubernetes==24.2.0
+kubernetes==25.3.0
     # via -r requirements.in
-markupsafe==2.1.1
+markupsafe==2.1.2
     # via jinja2
-oauthlib==3.2.1
+oauthlib==3.2.2
     # via requests-oauthlib
-packaging==21.3
+packaging==23.0
     # via ansible-core
 pyasn1==0.4.8
     # via
@@ -49,18 +49,16 @@ pyasn1-modules==0.2.8
     # via google-auth
 pycparser==2.21
     # via cffi
-pyopenssl==22.1.0
+pyopenssl==23.0.0
     # via -r requirements.in
-pyparsing==3.0.9
-    # via packaging
 python-dateutil==2.8.2
     # via kubernetes
 pyyaml==6.0
     # via
     #   -r requirements.in
     #   ansible-core
     #   kubernetes
-requests==2.28.1
+requests==2.28.2
     # via
     #   kubernetes
     #   requests-oauthlib
@@ -75,11 +73,11 @@ six==1.16.0
     #   google-auth
     #   kubernetes
     #   python-dateutil
-urllib3==1.26.12
+urllib3==1.26.14
     # via
     #   kubernetes
     #   requests
-websocket-client==1.4.1
+websocket-client==1.4.2
     # via kubernetes
 
 # The following packages are considered to be unsafe in a requirements file:

deploy/scripts/build.py

@@ -65,7 +65,6 @@ def start_next(self) -> bool:
         running or if the queue is empty.
         """
         if self.curr_job is not None and self.curr_job.poll() is None:
-            logging.debug(f"{self.name}.start_next(): called while job is still running.")
             return False
         if len(self.job_list) > 0:
             next_job = self.job_list.pop(0)
@@ -95,7 +94,6 @@ def check_jobs(self) -> JobStatus:
         if self.curr_job is not None:
             # See if the job is still running
             if self.curr_job.poll() is None:
-                logging.debug(f"{self.name} job is running.")
                 return self.status
             # Current job has finished
             if self.curr_job.returncode == 0: