🔄 Synced file(s) with jhudsl/AnVIL_Template #10

cansavvy · 2025-01-15T21:14:12Z

Synced local file(s) with jhudsl/AnVIL_Template.

Changed files

Synced local directory .github/workflows/ with remote directory .github/workflows/
Created local .github/AnVIL_Feedback_Script.sh from remote .github/AnVIL_Feedback_Script.sh
Synced local directory style-sets with remote directory style-sets
Synced local directory assets/box_images/ with remote directory assets/box_images/
Synced local directory assets/AnVIL_style/ with remote directory assets/AnVIL_style/
Synced local directory assets/GDSCN_style/ with remote directory assets/GDSCN_style/
Synced local assets/style.css with remote assets/style.css
Synced local config_automation.yml with remote config_automation.yml
Synced local _output.yml with remote _output.yml

This PR was created automatically by the repo-file-sync-action workflow run #14837576330

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…ub/AnVIL_Feedback_Script.sh' release-null

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github-actions · 2025-05-05T13:29:08Z

⚠️ broken url errors ⚠️
There are broken url errors that need to be addressed.
Click here ➡️ for broken url errors! ❗
Add errors that aren't errors to the resources/ignore-urls.txt file of this repo.
If you are having troubles see this guide
Comment updated at 2025-05-05-13:30:18 with changes from e909b38

github-actions · 2025-05-05T13:29:12Z

⚠️ spelling errors ⚠️
There are spelling errors that need to be addressed.
Click here ➡️ for spelling errors! ❗
Add errors that aren't errors to the resources/dictionary.txt file of this repo.
If you are having troubles see this guide
Comment updated at 2025-05-05-13:31:06 with changes from e909b38

.github/workflows/check-url.yml

+    name: Load user automation choices
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+        # Use the yaml-env-action action.
+      - name: Load environment from YAML
+        uses: doughepi/yaml-env-action@v1.0.0
+        with:
+            files: config_automation.yml # Pass a space-separated list of configuration files. Rightmost files take precedence.
+    outputs:
+      toggle_url_check_periodically: "${{ env.URL_CHECK_PERIODICALLY }}"
+
+  url-check:


To fix the issue, we will add a permissions block to the workflow. This block will specify the minimal permissions required for the workflow to function correctly. Based on the workflow's operations, the following permissions are needed:

contents: write for checking out code, creating branches, and pushing changes.

actions: read for interacting with GitHub Actions.

The permissions block will be added at the root level of the workflow to apply to all jobs. If any job requires additional or fewer permissions, a job-specific permissions block can be added.

.github/workflows/check-url.yml

+    name: Check URLs
+    needs: set-up
+    if: ${{needs.set-up.outputs.toggle_url_check_periodically == 'yes'}}
+    runs-on: ubuntu-latest
+    container:
+      image: jhudsl/base_ottr:main
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
+
+    # Delete the branch if this has been run before
+    - name: Delete branch locally and remotely
+      run: git push origin --delete preview-spell-error || echo "No branch to delete"
+
+    # Make the branch fresh
+    - name: Make the branch fresh
+      run: |
+        git config --global --add safe.directory $GITHUB_WORKSPACE
+        git config --global user.name 'github-actions[bot]'
+        git config --global user.email 'github-actions[bot]@users.noreply.github.com'
+
+        echo branch doesnt exist
+        git checkout -b preview-spell-error || echo branch exists
+        git push --set-upstream origin preview-spell-error || echo echo branch exists remotely
+      shell: bash
+
+    - name: Run the check
+      uses: jhudsl/ottr-reports@main
+      id: check_results
+      continue-on-error: true
+      with:
+        check_type: urls
+        error_min: 1
+
+    - name: Declare file path and time
+      id: check-report
+      run: |
+        error_num=$(cat check_reports/url_checks.tsv | wc -l)
+        error_num="$((error_num-1))"
+        echo "error_num=$error_num" >> $GITHUB_OUTPUT
+        echo "error_url=https://github.com/${GITHUB_REPOSITORY}/blob/preview-spell-error/check_reports/url_checks.tsv" >> $GITHUB_OUTPUT
+      shell: bash
+
+    - name: Stop if failure
+      if: steps.check_results.outcome == 'failure'
+      run: exit 1
+
+    - name: Print out error variables
+      run: |
+        echo ${{ steps.check-report.outputs.error_url }}
+        echo ${{ steps.check-report.outputs.error_num }}
+
+      # Commit file
+    - name: Commit tocless bookdown files
+      if: ${{ steps.check-report.outputs.error_num >= 1 }}
+      env:
+        GH_PAT: ${{ secrets.GH_PAT }}
+      run: |
+        git add --force check_reports/url_checks.tsv
+        git commit -m 'Add spell check file' || echo "No changes to commit"
+        git push --set-upstream origin preview-spell-error || echo echo branch exists remotely
+
+    - name: Find issues
+      id: find-issue
+      env:
+        GH_PAT: ${{ secrets.GH_PAT }}
+      run: |
+        echo "$GITHUB_REPOSITORY"
+        curl -o find_issue.R https://raw.githubusercontent.com/jhudsl/ottr-reports/main/scripts/find_issue.R
+        issue_exists=$(Rscript --vanilla find_issue.R --repo $GITHUB_REPOSITORY --git_pat $GH_PAT)
+        echo URL issue exists: $issue_exists
+        echo "issue_existence=$issue_exists" >> $GITHUB_OUTPUT
+
+    - name: If too many URL errors, then make an issue
+      if: ${{ steps.check-report.outputs.error_num >= 1 && steps.find-issue.outputs.issue_existence == 0}}
+      uses: JasonEtco/create-an-issue@v2
+      with:
+        filename: .github/ISSUE_TEMPLATE/url-error.md
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        FILE_URL: ${{ steps.check-report.outputs.error_url }}
+        ERROR_NUM: ${{ steps.check-report.outputs.error_num }}
+
+    - name: If no URL errors than delete the branch we made
+      if: ${{ steps.check-report.outputs.error_num < 1 }}
+      run: |
+        git config --system --add safe.directory "$GITHUB_WORKSPACE"
+        git push origin --delete preview-spell-error || echo "No branch to delete"


To fix the issue, we need to explicitly define the permissions for the GITHUB_TOKEN at the workflow level or for individual jobs. Since the workflow performs actions like committing files, pushing branches, and creating issues, we will grant the minimal required permissions. Specifically:

contents: write is needed for committing and pushing changes.

issues: write is needed for creating issues.

We will add a permissions block at the workflow level to apply these permissions to all jobs. This ensures that the workflow has only the necessary permissions and adheres to the principle of least privilege.

cansavvy added the sync label Jan 15, 2025

cansavvy force-pushed the repo-sync/AnVIL_Template/default branch from aca1395 to f335615 Compare January 28, 2025 14:33

kweav added 9 commits May 5, 2025 13:28

🔄 Synced local '.github/workflows/' with remote '.github/workflows/'

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🔄 Created local '.github/AnVIL_Feedback_Script.sh' from remote '.gith…

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…ub/AnVIL_Feedback_Script.sh' release-null

🔄 Synced local 'style-sets' with remote 'style-sets'

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🔄 Synced local 'assets/box_images/' with remote 'assets/box_images/'

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🔄 Synced local 'assets/AnVIL_style/' with remote 'assets/AnVIL_style/'

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🔄 Synced local 'assets/GDSCN_style/' with remote 'assets/GDSCN_style/'

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🔄 Synced local 'assets/style.css' with remote 'assets/style.css'

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🔄 Synced local 'config_automation.yml' with remote 'config_automation…

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….yml' release-null

🔄 Synced local '_output.yml' with remote '_output.yml'

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kweav force-pushed the repo-sync/AnVIL_Template/default branch from f335615 to 559175f Compare May 5, 2025 13:28

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🔄 Synced file(s) with jhudsl/AnVIL_Template #10

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cansavvy commented Jan 15, 2025 •

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@@ -7,2 +7,6 @@
+            permissions:
+              contents: write
+              actions: read
             jobs:

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