removed adding requirements #2
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| name: Task1 QC | |
| on: | |
| push: | |
| branches: | |
| - main | |
| jobs: | |
| process_raw: | |
| runs-on: self-hosted | |
| outputs: | |
| sub: ${{ steps.set_vars.outputs.sub }} | |
| task: ${{ steps.set_vars.outputs.task }} | |
| version: ${{ steps.set_vars.outputs.version }} | |
| steps: | |
| - name: checkout code and return recently uploaded file in /data | |
| uses: actions/checkout@v3 | |
| - name: Get changed files | |
| run: | | |
| #!/bin/bash | |
| # Get the list of CSV files changed in the last 24 hours | |
| data=$(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 $data; do | |
| filename=$(basename "$file") | |
| IFS='_' read -r sub task version <<< "$filename" | |
| version="${version%.csv}" # Remove the .csv extension from version | |
| echo "::set-output name=sub::$sub" | |
| echo "::set-output name=task::$task" | |
| echo "::set-output name=version::$version" | |
| 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 }}" | |
| - name: run quality control | |
| run: | | |
| sub=${{ needs.process_raw.outputs.sub }} | |
| task=${{ needs.process_raw.outputs.task }} | |
| vers=${{ needs.process_raw.outputs.version }} | |
| 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/${sub}_${task}_${vers}.csv" | |
| log_file="./data/${sub}/qc_${task}_${vers}.log" | |
| echo "CSV file: $csv_file" | |
| echo "Log file: $log_file" | |
| if [ -f "$csv_file" ]; then | |
| python ./code/ATSqC.py -s "$csv_file" -o "./data/${sub}/" -sub "$sub" | tee "$log_file" | |
| echo "QC for ${sub}_${task}_${vers} running" | |
| else | |
| echo "CSV file $csv_file does not exist" | |
| fi | |
| done | |
| done | |
| done | |
| push: | |
| runs-on: self-hosted | |
| needs: run_qc | |
| steps: | |
| - name: Commit and Push Changes | |
| run: | | |
| git config --global user.name "miloswrath" | |
| git config --global user.email "[email protected]" | |
| git remote set-url origin https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/$GITHUB_REPOSITORY | |
| git add . | |
| git commit -m "Automated commit by GitHub Actions" | |
| git push | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GIT_PAT }} |