Support Tumor_Sample_Barcode as column name in clinical file #108
Workflow file for this run
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| # This workflow will install Python dependencies, run annotation against the master annotation | |
| name: Compare 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 | |
| FUSION_DATA_NAME=data_fusions.txt | |
| INDIVIDUAL_CNA_DATA_NAME=data_individual_CNA.txt | |
| cd data || exit | |
| 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" == "$FIEL_NAME_PREFIX"* ]]; then | |
| curl -s "$downloadurl" -o $name | |
| fi | |
| done | |
| cd .. | |
| # create compare folder to add all annotated files | |
| mkdir compare | |
| PREFIX=oncokb | |
| IMAF=data/"$MUTATION_DATA_NAME" | |
| OMAF=compare/"$PREFIX"_"$MUTATION_DATA_NAME" | |
| IC=data/"$CLINICAL_DATA_NAME" | |
| OC=compare/"$PREFIX"_"$CLINICAL_DATA_NAME" | |
| IF=data/"$FUSION_DATA_NAME" | |
| OF=compare/"$PREFIX"_"$FUSION_DATA_NAME" | |
| IICNA=data/"$INDIVIDUAL_CNA_DATA_NAME" | |
| OICNA=compare/"$PREFIX"_"$INDIVIDUAL_CNA_DATA_NAME" | |
| python MafAnnotator.py -i "$IMAF" -o "$OMAF" -c "$IC" -b "$ONCOKB_API_TOKEN" | |
| python FusionAnnotator.py -i "$IF" -o "$OF" -c "$IC" -b "$ONCOKB_API_TOKEN" | |
| python CnaAnnotator.py -i "$IICNA" -o "$OICNA" -c "$IC" -b "$ONCOKB_API_TOKEN" -f "individual" | |
| python ClinicalDataAnnotator.py -i "$IC" -o "$OC" -a "$OMAF,$OICNA,$OF" | |
| git config user.name oncokb-bot | |
| git config user.email [email protected] | |
| git add . | |
| git commit -m 'add analysis' | |
| - name: Compare annotation result with the ones from master | |
| id: compare | |
| env: | |
| ONCOKB_OAUTH_TOKEN: ${{ secrets.ONCOKB_OAUTH_TOKEN }} | |
| FIEL_NAME_PREFIX: 'oncokb_data' | |
| run: | | |
| # remove everything under compare folder and replace wiht the ones from oncokb-data | |
| rm -f compare/*.txt | |
| cd compare || exit | |
| 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" == "$FIEL_NAME_PREFIX"* ]]; then | |
| curl -s "$downloadurl" -o $name | |
| fi | |
| done | |
| cd .. | |
| # compare | |
| CHANGED=$(git diff --name-only HEAD --) | |
| if [ -n "$CHANGED" ] | |
| then | |
| git diff | |
| exit 1 | |
| fi | |