Merge pull request #718 from bigbio/dev #2468
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # This workflow will install Python dependencies and run the included validation script. | |
| name: Validate annotations | |
| on: | |
| push: | |
| branches: [ master, dev ] | |
| paths: | |
| - 'annotated-projects/**' | |
| pull_request: | |
| branches: [ master, dev ] | |
| paths: | |
| - 'annotated-projects/**' | |
| jobs: | |
| sdrf_proteomics_validations: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.8 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install wheel | |
| pip install git+https://github.com/bigbio/sdrf-pipelines | |
| - name: Get a list of changed files | |
| if: github.event_name != 'schedule' | |
| id: getfiles | |
| run: | | |
| export OUTFILE=$HOME/filelist.txt | |
| if [ "${{ github.event_name }}" == pull_request ]; then | |
| echo 'Changed files:' | |
| git diff-tree --no-commit-id --name-only -r origin/${{ github.event.pull_request.base.ref }} ${{ github.sha }} | tee "$OUTFILE" | |
| else | |
| # push | |
| if [ "${{ github.event.before }}" == "0000000000000000000000000000000000000000" ]; then | |
| parent="origin/master" # compare with master as a last resort | |
| else | |
| parent="${{ github.event.before }}" | |
| fi | |
| git diff-tree --no-commit-id --name-only -r "$parent" ${{ github.sha }} | tee "$OUTFILE" | |
| fi | |
| - name: Run validation | |
| run: | | |
| if [ ${{ github.event_name }} == "schedule" ]; then | |
| echo "Validating all projects (schedule)" | |
| python validate.py -v | |
| else | |
| export FILELIST=$HOME/filelist.txt | |
| cat "$FILELIST" | grep "*sdrf.tsv" | while read line; do echo "Changed file: $line"; parse_sdrf validate-sdrf --sdrf_file $line --skip_factor_validation --skip_experimental_design_validation --use_ols_cache_only; done | |
| fi | |