🔄 Synced file(s) with ottrproject/OTTR_Template by jhudsl-robot · Pull Request #27 · fhdsl/Clinical_Data_Management

jhudsl-robot · 2025-06-06T19:37:10Z

Synced local file(s) with ottrproject/OTTR_Template.

Changed files

Synced local directory .github/workflows/ with remote directory .github/workflows/
Synced local assets/style.css with remote assets/style.css
Created local assets/style_config_default.css from remote assets/style_config_default.css
Synced local config_automation.yml with remote config_automation.yml

This PR was created automatically by the repo-file-sync-action workflow run #15498355326

release-renderAction

…/style_config_default.css' release-renderAction

….yml' release-renderAction

github-actions · 2025-06-06T19:37:41Z

OTTR Check Results

Summary

Spelling check: ❌ FAILED (2 errors found, threshold: 0)
URL check: ❌ FAILED (3 errors found, threshold: 0)

⚠️ Some Checks Failed Click here to download detailed error reports

Last Updated: 2025-07-15-18:19:39

+    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 actions, the following permissions are needed:

contents: write for checking out code 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 specific jobs require different permissions, they can override the root-level permissions.

+    name: Check URLs
+    needs: set-up
+    if: ${{needs.set-up.outputs.toggle_url_check_periodically == 'true'}}
+    runs-on: ubuntu-latest
+
+    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 $GITHUB_WORKSPACE
+        git config --global user.name 'github-actions[bot]'
+        git config --global user.email 'github-actions[bot]@users.noreply.github.com'
+
+        echo branch doesnt exist
+        git checkout -b preview-spell-error || echo branch exists
+        git push --set-upstream origin preview-spell-error || echo echo branch exists remotely
+      shell: bash
+
+    - name: Run the check
+      uses: ottrproject/ottr-reports@main
+      id: check_results
+      continue-on-error: true
+      with:
+        check_spelling: false
+        spelling_error_min: 1
+        check_urls: true
+        url_error_min: 1
+        check_quiz_form: false
+        quiz_error_min: 1
+        sort_dictionary: false
+
+    - name: Declare file path and time
+      id: check-report
+      run: |
+        error_num=$(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/ottrproject/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 in the workflow. The permissions should be set at the job level for each job (set-up and url-check) to ensure that only the necessary permissions are granted.

For the set-up job, no write permissions are required, so contents: read is sufficient. For the url-check job, write permissions are needed for contents (to commit and push changes) and issues (to create issues).

The changes will be made by adding a permissions block to each job.

github-actions · 2025-06-06T19:38:58Z

Re-rendered previews from the latest commit:

👀 Quick preview of course website here *
🔬 Comprehensive download of the course website here

* note not all html features will be properly displayed in the "quick preview" but it will give you a rough idea.

Updated at 2025-07-15 with changes from the latest commit f761cba

kweav · 2025-07-15T17:29:48Z

Thought this had a docx file originally in the comment before I edited coursera: false. Going to switch it back and see what happens

jhudsl-robot added 4 commits June 6, 2025 19:37

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

af3e3ee

release-renderAction

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

7bc30fc

release-renderAction

🔄 Created local 'assets/style_config_default.css' from remote 'assets…

60d42e3

…/style_config_default.css' release-renderAction

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

4385d29

….yml' release-renderAction

jhudsl-robot added the sync label Jun 6, 2025

github-advanced-security AI found potential problems Jun 6, 2025

View reviewed changes

kweav reviewed Jul 15, 2025

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Comment thread config_automation.yml

Update config_automation.yml coursera toggle to match previous

e7d8216

kweav reviewed Jul 15, 2025

View reviewed changes

Comment thread config_automation.yml Outdated

Update config_automation.yml to switch coursera back to true

3edede2

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🔄 Synced file(s) with ottrproject/OTTR_Template#27

🔄 Synced file(s) with ottrproject/OTTR_Template#27
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@@ -2,2 +2,5 @@
+            permissions:
+              contents: write
+              actions: read

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OTTR Check Results

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⚠️ Some Checks Failed Click here to download detailed error reports

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