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Automated commit by GitHub Actions #82
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| name: Task1 QC | |
| on: | |
| push: | |
| branches: | |
| - main | |
| permissions: | |
| contents: write | |
| packages: write | |
| issues: write | |
| id-token: write | |
| pages: write | |
| jobs: | |
| process_raw: | |
| runs-on: self-hosted | |
| outputs: | |
| sub: ${{ steps.set_vars.outputs.sub }} | |
| task: ${{ steps.set_vars.outputs.task }} | |
| version: ${{ steps.set_vars.outputs.version }} | |
| run_part: ${{ steps.set_vars.outputs.run_part }} | |
| steps: | |
| - name: checkout code and return recently uploaded file in /data | |
| uses: actions/checkout@v3 | |
| - name: Get changed files | |
| run: | | |
| #!/bin/bash | |
| # Get the list of CSV files changed in the last 24 hours | |
| data=$(git log --since="24 hours ago" --name-only --pretty=format: -- '*.csv' | sort | uniq) | |
| # Export the data variable to the environment | |
| echo "data=$data" >> $GITHUB_ENV | |
| # Print the changed CSV files | |
| echo "Changed CSV files in the last 24 hours: $data" | |
| - name: set up python | |
| run: | | |
| python -m pip install --upgrade pip | |
| - name: parse raw | |
| id: set_vars | |
| run: | | |
| # Loop through each CSV file in $data | |
| for file in $data; do | |
| # Extract the directory and filename | |
| dir=$(dirname "$file") | |
| filename=$(basename "$file") | |
| # Extract the run-* part from the directory | |
| run_part=$(basename "$dir") | |
| # Split the filename into sub, task, and version | |
| IFS='_' read -r sub task version <<< "$filename" | |
| version="${version%.csv}" # Remove the .csv extension from version | |
| # Set outputs | |
| echo "::set-output name=run_part::$run_part" | |
| echo "::set-output name=sub::$sub" | |
| echo "::set-output name=task::$task" | |
| echo "::set-output name=version::$version" | |
| # Print the extracted values | |
| echo "Run Part: $run_part" | |
| echo "Subject: $sub" | |
| echo "Task: $task" | |
| echo "Version: $version" | |
| done | |
| run_qc: | |
| runs-on: self-hosted | |
| needs: process_raw | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| - name: Debug env vars | |
| run: | | |
| echo "sub=${{ needs.process_raw.outputs.sub }}" | |
| echo "task=${{ needs.process_raw.outputs.task }}" | |
| echo "version=${{ needs.process_raw.outputs.version }}" | |
| echo "run_part=${{ needs.process_raw.outputs.run_part }}" | |
| - name: run quality control | |
| run: | | |
| sub=${{ needs.process_raw.outputs.sub }} | |
| task=${{ needs.process_raw.outputs.task }} | |
| vers=${{ needs.process_raw.outputs.version }} | |
| run_part=${{ needs.process_raw.outputs.run_part }} | |
| for sub in ${sub}; do | |
| echo "Processing subject: $sub" | |
| for task in ${task}; do | |
| echo "Processing task: $task" | |
| for vers in ${vers}; do | |
| echo "Processing version: $vers" | |
| csv_file="./data/${sub}/processed/${run_part}/${sub}_${task}_${vers}.csv" | |
| mkdir -p "./data/${sub}/${run_part}" | |
| log_file="./data/${sub}/${run_part}/qc_${task}_${vers}.log" | |
| echo "CSV file: $csv_file"s | |
| echo "Log file: $log_file" | |
| if [ -f "$csv_file" ]; then | |
| python ./code/AFqC.py -s "$csv_file" -o "./data/${sub}/${run_part}" -sub "$sub" | tee "$log_file" | |
| echo "QC for ${sub}_${task}_${vers} running" | |
| else | |
| echo "CSV file $csv_file does not exist" | |
| fi | |
| done | |
| done | |
| done | |
| add: | |
| concurrency: | |
| group: "pages" | |
| cancel-in-progress: false | |
| runs-on: ubuntu-latest | |
| needs: run_qc # Ensure 'run_qc' job exists if referenced | |
| steps: | |
| # 1. Checkout the Repository | |
| - name: Checkout Repository | |
| uses: actions/checkout@v4 | |
| with: | |
| persist-credentials: false # Recommended for security | |
| fetch-depth: 0 # Ensure full history is fetched for git commands | |
| # 2. Find New PNG Files | |
| - name: Find New PNG Files | |
| id: find_png | |
| run: | | |
| # Find newly added PNG files in this commit | |
| png_files=$(git diff --name-only --relative --diff-filter=A HEAD^ HEAD -- '*.png') | |
| echo "PNG_FILES=$png_files" >> $GITHUB_ENV | |
| # 3. Generate Jekyll Posts | |
| - name: Add _posts | |
| run: | | |
| POSTS_DIR="_posts" | |
| mkdir -p $POSTS_DIR # Ensure the _posts directory exists | |
| # Initialize an associative array to group images by subject | |
| declare -A subjects | |
| # Iterate over each PNG file and group them by subject number | |
| for file in $PNG_FILES; do | |
| # Extract the subject number (assuming it's the first part of the filename before '_') | |
| subject=$(echo "$file" | awk -F_ '{print $1}') | |
| # Append the filename to the subject's array | |
| subjects["$subject"]+="$file " | |
| done | |
| # Generate Jekyll posts for each subject | |
| for subject in "${!subjects[@]}"; do | |
| # Define the post filename with current date and subject number | |
| post_filename="$POSTS_DIR/$(date +%Y-%m-%d)-subject-$subject.md" | |
| # Create the Jekyll post | |
| { | |
| echo "---" | |
| echo "layout: post" | |
| echo "title: Subject $subject" | |
| echo "date: $(date +%Y-%m-%d)" | |
| echo "categories: subjects" | |
| echo "---" | |
| echo "" | |
| echo "# $subject" | |
| # Add images to the post | |
| for image in ${subjects["$subject"]}; do | |
| echo "" | |
| done | |
| } > "$post_filename" | |
| echo "Created post: $post_filename" | |
| done | |
| # 4. (Optional) Commit and Push Generated Posts | |
| # This step commits the newly created posts back to the repository. | |
| # 5. Set Up Ruby Environment | |
| - name: Setup Ruby | |
| uses: ruby/setup-ruby@v1 | |
| with: | |
| ruby-version: '3.1' # Specify your Ruby version | |
| bundler-cache: true # Caches installed gems automatically | |
| cache-version: 1 # Increment if you need to reset the cache | |
| # 6. Install Dependencies | |
| - name: Install Dependencies | |
| run: bundle install | |
| # 7. Build the Jekyll Site | |
| - name: Build with Jekyll | |
| run: bundle exec jekyll build --baseurl "${{ github.event.inputs.base_path || '' }}" | |
| env: | |
| JEKYLL_ENV: production | |
| # Alternatively, if you prefer using GitHub's built-in Pages action: | |
| # Uncomment the following steps and remove the above Deploy step | |
| # | |
| - name: Configure GitHub Pages | |
| uses: actions/configure-pages@v5 | |
| # | |
| - name: Upload Pages Artifact | |
| uses: actions/upload-pages-artifact@v1 | |
| with: | |
| path: ./_site | |
| - name: Deploy to GitHub Pages | |
| uses: actions/deploy-pages@v1 | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| push: | |
| runs-on: self-hosted | |
| needs: add | |
| steps: | |
| - name: Commit and Push Changes | |
| run: | | |
| git config --global user.name "miloswrath" | |
| git config --global user.email "[email protected]" | |
| git remote set-url origin https://x-access-token:${{ secrets.GIT_TOKEN }}@github.com/$GITHUB_REPOSITORY | |
| git add . | |
| git commit -m "Automated commit by GitHub Actions" | |
| git push | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GIT_TOKEN }} |