Automated Commit -> New Data #117
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| # .github/workflows/deploy.yml | |
| name: Task1 QC and Deploy | |
| on: | |
| push: | |
| branches: | |
| - main | |
| permissions: | |
| contents: write | |
| packages: write | |
| issues: write | |
| id-token: write | |
| pages: write | |
| jobs: | |
| process_raw: | |
| name: Process Raw CSV Files | |
| runs-on: self-hosted | |
| outputs: | |
| data: ${{ steps.set_vars.outputs.json }} | |
| has_data: ${{ steps.set_vars.outputs.has_data }} | |
| steps: | |
| - name: Checkout Code | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Get Changed CSV Files | |
| run: | | |
| #!/bin/bash | |
| # Get the list of CSV files changed in the last 24 hours | |
| data=$(git log --since="24 hours ago" --name-only --pretty=format: -- '*.csv' | sort | uniq) | |
| # Convert the list into a multi-line format | |
| formatted_data=$(echo "$data" | tr ' ' '\n') | |
| # Export the formatted data variable to the environment | |
| echo "data<<EOF" >> $GITHUB_ENV | |
| echo "$formatted_data" >> $GITHUB_ENV | |
| echo "EOF" >> $GITHUB_ENV | |
| # Print the changed CSV files | |
| echo "Changed CSV files in the last 24 hours:" | |
| echo "$formatted_data" | |
| - name: Parse Raw CSV Files | |
| id: set_vars | |
| run: | | |
| # Initialize an empty JSON array | |
| json_array="[" | |
| first_item=true | |
| # 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="${version%.csv}" # Remove the .csv extension from version | |
| # Escape variables for JSON | |
| sub_escaped=$(printf '%s' "$sub" | sed 's/"/\\"/g') | |
| task_escaped=$(printf '%s' "$task" | sed 's/"/\\"/g') | |
| version_escaped=$(printf '%s' "$version" | sed 's/"/\\"/g') | |
| run_part_escaped=$(printf '%s' "$run_part" | sed 's/"/\\"/g') | |
| # Build JSON object | |
| json_object="{\"sub\":\"$sub_escaped\",\"task\":\"$task_escaped\",\"version\":\"$version_escaped\",\"run_part\":\"$run_part_escaped\"}" | |
| # Append to JSON array | |
| if [ "$first_item" = true ]; then | |
| json_array="$json_array$json_object" | |
| first_item=false | |
| else | |
| json_array="$json_array,$json_object" | |
| fi | |
| # Print the extracted values | |
| echo "Run Part: $run_part" | |
| echo "Subject: $sub" | |
| echo "Task: $task" | |
| echo "Version: $version" | |
| done | |
| json_array="$json_array]" | |
| # Output the JSON array | |
| echo "json=$json_array" >> $GITHUB_OUTPUT | |
| # Determine if json_array is empty | |
| if [ "$json_array" = "[]" ]; then | |
| echo "has_data=false" >> $GITHUB_OUTPUT | |
| else | |
| echo "has_data=true" >> $GITHUB_OUTPUT | |
| fi | |
| # Output the JSON array | |
| echo "json=$json_array" >> $GITHUB_OUTPUT | |
| run_qc: | |
| name: Run Quality Control | |
| runs-on: self-hosted | |
| needs: process_raw | |
| if: needs.process_raw.outputs.has_data == 'true' | |
| strategy: | |
| matrix: | |
| config: ${{ fromJson(needs.process_raw.outputs.data) }} | |
| steps: | |
| - name: Checkout Code | |
| uses: actions/checkout@v3 | |
| - name: Debug Environment Variables | |
| run: | | |
| echo "Subject: ${{ matrix.config.sub }}" | |
| echo "Task: ${{ matrix.config.task }}" | |
| echo "Version: ${{ matrix.config.version }}" | |
| echo "Run Part: ${{ matrix.config.run_part }}" | |
| - name: Install Python Dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| - name: Run Quality Control Script | |
| env: | |
| TEASE: ${{ secrets.TEASE }} | |
| run: | | |
| sub=${{ matrix.config.sub }} | |
| task=${{ matrix.config.task }} | |
| vers=${{ matrix.config.version }} | |
| run_part=${{ matrix.config.run_part }} | |
| echo "Processing subject: $sub" | |
| echo "Processing task: $task" | |
| 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" | |
| echo "Log file: $log_file" | |
| if [ -f "$csv_file" ]; then | |
| python ./code/NTSqC.py -s "$csv_file" -o "./data/${sub}/${run_part}" -sub "$sub" | tee "$log_file" | |
| echo "QC for ${sub}_${task}_${vers} completed" | |
| else | |
| echo "CSV file $csv_file does not exist" | |
| fi | |
| - name: Upload QC Results | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: qc-results-${{ matrix.config.sub }}-${{ matrix.config.task }}-${{ matrix.config.version }}-${{ matrix.config.run_part }} | |
| path: | | |
| ./data/${{ matrix.config.sub }}/${{ matrix.config.run_part }}/*.png | |
| ./data/${{ matrix.config.sub }}/${{ matrix.config.run_part }}/*.log | |
| commit_results: | |
| name: Commit and Push QC Results | |
| runs-on: self-hosted | |
| needs: [process_raw, run_qc] | |
| if: needs.process_raw.outputs.has_data == 'true' | |
| steps: | |
| - name: Checkout Code | |
| uses: actions/checkout@v3 | |
| - name: Download all artifacts | |
| uses: actions/download-artifact@v3 | |
| with: | |
| path: ./ | |
| - name: Move QC Results | |
| run: | | |
| echo "Moving QC results to data directory..." | |
| for dir in qc-results-*; do | |
| echo "Processing artifact directory: $dir" | |
| # Extract sub, task, version, and run_part from the directory name | |
| IFS='-' read -r _ _ sub task version run_part <<< "$dir" | |
| echo "Subject: $sub, Task: $task, Version: $version, Run Part: $run_part" | |
| # Define the target directories | |
| run_part_dir="./data/${sub}/${run_part}" | |
| # Create the target directories if they don't exist | |
| mkdir -p "$run_part_dir" | |
| # Move .png files to the processed directory | |
| mv "$dir"/*.png "$run_part_dir/" 2>/dev/null || : | |
| # Move .log files to the run_part directory | |
| mv "$dir"/*.log "$run_part_dir/" 2>/dev/null || : | |
| done | |
| - name: Commit and Push QC Results | |
| run: | | |
| git config --global user.name "miloswrath" | |
| git config --global user.email "[email protected]" | |
| git remote set-url origin https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/$GITHUB_REPOSITORY | |
| git add ./data/*/*/*.png ./data/*/*/*.log | |
| git commit -m "Add QC results for subjects $(date +%Y-%m-%d)" | |
| git push origin main | |
| - name: List Directory After QC | |
| run: | | |
| echo "Listing directory after running QC:" | |
| find ./data -type d | |
| find ./data -type f | |
| add: | |
| name: Generate Jekyll Posts and Deploy | |
| runs-on: ubuntu-latest | |
| needs: [process_raw, run_qc, commit_results] | |
| if: ${{ always() }} | |
| steps: | |
| # 1. Checkout the Repository | |
| - name: Checkout Repository | |
| uses: actions/checkout@v4 | |
| with: | |
| persist-credentials: false # Recommended for security | |
| fetch-depth: 0 | |
| ref: main | |
| - name: Pull Latest Changes | |
| run: git pull origin main | |
| # 4. Set Up Ruby Environment | |
| - name: Setup Ruby | |
| uses: ruby/setup-ruby@v1 | |
| with: | |
| ruby-version: '3.1' # Specify your Ruby version | |
| bundler-cache: true # Caches installed gems automatically | |
| cache-version: 1 # Increment if you need to reset the cache | |
| # 5. Install Ruby Dependencies | |
| - name: Install Dependencies | |
| run: bundle install | |
| # 6. Generate Jekyll Posts from PNGs | |
| - name: Generate Jekyll Posts | |
| run: | | |
| set -e # Exit immediately if a command exits with a non-zero status | |
| set -x # Print commands and their arguments as they are executed | |
| run_part=${{ needs.process_raw.outputs.run_part }} | |
| POSTS_DIR="_posts" | |
| mkdir -p "$POSTS_DIR" # Ensure the _posts directory exists | |
| # Initialize an associative array to group images by subject | |
| declare -A subjects | |
| # Get the list of PNG files added in the latest commit | |
| images=$(git diff --name-only HEAD~1 HEAD | grep '\.png$' || true) | |
| echo "Images: $images" | |
| if [ -z "$images" ]; then | |
| echo "No new images found. Skipping post generation." | |
| exit 0 | |
| fi | |
| # Iterate over each PNG file and group them by subject number | |
| for file in $images; do | |
| # Check if the file exists to avoid errors | |
| if [ ! -f "$file" ]; then | |
| continue | |
| fi | |
| # Extract the subject number from the filename (assuming it's the first part before '_') | |
| filename=$(basename "$file") | |
| subject=$(echo "$filename" | 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 | |
| timestamp=$(date +%H%M%S) | |
| post_filename="$POSTS_DIR/$(date +%Y-%m-%d)-subject-$subject-$timestamp.md" | |
| # Create the Jekyll post | |
| { | |
| echo "---" | |
| echo "layout: post" | |
| echo "title: Subject $subject" | |
| echo "date: $(date +%Y-%m-%d)" | |
| echo "categories: subjects" | |
| echo "---" | |
| echo "" | |
| # Add images to the post | |
| for image in ${subjects["$subject"]}; do | |
| # Adjust the image path based on your site structure | |
| # Assuming images are served from the root | |
| echo "" | |
| done | |
| } > "$post_filename" | |
| echo "Created post: $post_filename" | |
| done | |
| # 7. List _posts Directory for Verification (Optional) | |
| - name: List _posts Directory | |
| run: | | |
| echo "Listing _posts directory:" | |
| ls -la _posts | |
| # 8. Commit and Push Generated Posts | |
| - name: Commit and Push Posts | |
| run: | | |
| git config --global user.name "miloswrath" | |
| git config --global user.email "[email protected]" | |
| git remote set-url origin https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/$GITHUB_REPOSITORY | |
| # Add new posts to git | |
| git add _posts/*.md | |
| # Commit changes if there are any | |
| if ! git diff --cached --exit-code > /dev/null; then | |
| git commit -m "Add new posts for subjects $(date +%Y-%m-%d)" | |
| git push origin main # Replace 'main' with your default branch if different | |
| else | |
| echo "No changes to commit." | |
| fi | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| # 9. Build the Jekyll Site | |
| - name: Build with Jekyll | |
| run: bundle exec jekyll build --verbose --baseurl "${{ github.event.inputs.base_path || '' }}" | |
| env: | |
| JEKYLL_ENV: production | |
| # 10. Deploy to GitHub Pages | |
| # Using GitHub's built-in Pages action | |
| - name: Configure GitHub Pages | |
| uses: actions/configure-pages@v5 | |
| - name: Upload Pages Artifact | |
| uses: actions/upload-pages-artifact@v1 | |
| with: | |
| path: ./_site # Ensure this matches your Jekyll build output | |
| - name: List _site Directory | |
| run: | | |
| echo "Listing _site directory:" | |
| ls -la _site | |
| - name: Deploy to GitHub Pages | |
| uses: actions/deploy-pages@v1 | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} |