Validate annotations #587
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| # This workflow will install Python dependencies and run the included validation script. | |
| name: Validate annotations | |
| on: | |
| push: | |
| paths: | |
| - 'annotated-projects/**' | |
| - 'validate.py' | |
| pull_request: | |
| branches: [ master ] | |
| paths: | |
| - 'annotated-projects/**' | |
| - 'validate.py' | |
| schedule: | |
| - cron: '0 0 * * *' | |
| 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 "$FILELIST" | |
| if grep -q '^validate.py' "$FILELIST"; then | |
| echo "Validating all projects (script changed)" | |
| python validate.py -v | |
| else | |
| projects=$(cat "$FILELIST" | grep '^annotated-projects' | cut -d/ -f 2) | |
| echo "Validating projects:" $projects | |
| python validate.py -v $projects | |
| fi | |
| fi | |
| # mage_tab_validation: | |
| # runs-on: ubuntu-latest | |
| # steps: | |
| # - uses: actions/checkout@v2 | |
| # - name: Setup conda | |
| # uses: s-weigand/setup-conda@v1 | |
| # with: | |
| # update-conda: true | |
| # conda-channels: anaconda, bioconda, conda-forge | |
| # - name: Install perl-atlas-modules | |
| # run: conda create -n perl-atlas -c ebi-gene-expression-group -c bioconda perl-atlas-modules perl-graphviz | |
| # - name: Validate General MAGE-TAB | |
| # run: | | |
| # . /usr/share/miniconda/bin/activate /usr/share/miniconda/envs/perl-atlas | |
| # perl simple_validate_magetab.pl | |
| # - name: Archive production artifacts | |
| # uses: actions/upload-artifact@v2 | |
| # with: | |
| # name: sdrf-picture | |
| # path: graph_file_sdrf.png | |
| # retention-days: 5 | |
| # mage_tab_expression_atlas_validations: | |
| # runs-on: ubuntu-latest | |
| # steps: | |
| # - uses: actions/checkout@v2 | |
| # - name: Setup conda | |
| # uses: s-weigand/setup-conda@v1 | |
| # with: | |
| # update-conda: true | |
| # conda-channels: anaconda, bioconda, conda-forge | |
| # - name: Install perl-atlas-modules | |
| # run: conda create -n perl-atlas -c ebi-gene-expression-group perl-atlas-modules | |
| # - name: Validate Expression Atlas MAGE-TAB | |
| # id: atlas | |
| # run: | | |
| # . /usr/share/miniconda/bin/activate /usr/share/miniconda/envs/perl-atlas | |
| # perl validate_magetab.pl -i annotated-projects/PXD000288/PXD000288.idf.tsv -x -c -v | |
| # RSPEC_RESULT=$? | |
| # exit 0 | |