Merge pull request #215 from oncokb/update-clinical-header #109
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| # This workflow will install Python dependencies, run annotation against the master annotation for a particular study | |
| name: Compare Genomic Change Annotation | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - next-minor-release | |
| pull_request: | |
| branches: | |
| - master | |
| - next-minor-release | |
| jobs: | |
| build: | |
| if: github.repository == 'oncokb/oncokb-annotator' | |
| runs-on: macos-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - 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 flake8 | |
| pip install -r requirements/common.txt -r requirements/pip3.txt | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Annotate | |
| id: annotate | |
| env: | |
| ONCOKB_API_TOKEN: ${{ secrets.ONCOKB_BOT_API_TOKEN }} | |
| ONCOKB_OAUTH_TOKEN: ${{ secrets.ONCOKB_OAUTH_TOKEN }} | |
| run: | | |
| git checkout -b compare | |
| MUTATION_DATA_NAME=data_mutations_mskcc.txt | |
| CLINICAL_DATA_NAME=data_clinical_sample.txt | |
| cd data | |
| curl -s -H "Authorization: token ${ONCOKB_OAUTH_TOKEN}" https://api.github.com/repos/knowledgesystems/oncokb-data/contents/annotation/annotator-test/data | jq -r '.[] | .download_url + " " + .name' | while IFS=' ' read -r downloadurl name; do | |
| if [[ "$name" == "$MUTATION_DATA_NAME" || "$name" == "$CLINICAL_DATA_NAME" ]]; then | |
| curl -s "$downloadurl" -o $name | |
| fi | |
| done | |
| cd .. | |
| # create compare folder to add all annotated files | |
| mkdir compare | |
| OGCMAF=oncokb_genomic_change_$MUTATION_DATA_NAME | |
| python MafAnnotator.py -i data/$MUTATION_DATA_NAME -o compare/$OGCMAF -c data/$CLINICAL_DATA_NAME -b $ONCOKB_API_TOKEN -q Genomic_Change | |
| git config user.name oncokb-bot | |
| git config user.email [email protected] | |
| git add . | |
| git commit -m 'add analysis' | |
| echo "::set-output name=FILE_NAME::$OGCMAF" | |
| - name: Compare annotation result with the ones from master | |
| id: compare | |
| env: | |
| FILE_NAME: ${{steps.annotate.outputs.FILE_NAME}} | |
| ONCOKB_OAUTH_TOKEN: ${{ secrets.ONCOKB_OAUTH_TOKEN }} | |
| run: | | |
| # remove everything under compare folder and replace wiht the ones from oncokb-data | |
| rm -f compare/*.txt | |
| cd compare | |
| curl -s -H "Authorization: token ${ONCOKB_OAUTH_TOKEN}" https://api.github.com/repos/knowledgesystems/oncokb-data/contents/annotation/annotator-test/annotation | jq -r '.[] | .download_url + " " + .name' | while IFS=' ' read -r downloadurl name; do | |
| if [[ "$name" == "$FILE_NAME" ]]; then | |
| curl -s "$downloadurl" -o $name | |
| fi | |
| done | |
| cd .. | |
| # compare | |
| CHANGED=$(git diff --name-only HEAD --) | |
| if [ -n "$CHANGED" ] | |
| then | |
| git diff | |
| exit 1 | |
| fi | |