Merge pull request #55 from ccb-hms/main

Update dev branch with task5-workflow

.github/workflows/mapper-test.yml

@@ -0,0 +1,76 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Mapper Test
+
+on:
+ push:
+ branches: [task5-workflow]
+ pull_request:
+ branches: [task5-workflow]
+
+jobs:
+ run_mapper:
+ runs-on: ubuntu-latest
+ name: Run Tests
+ steps:
+ - uses: actions/checkout@v2
+ name: Checkout out mapper repository
+ - uses: actions/checkout@v2
+ name: Checkout test repository
+ with:
+ path: tests
+ repository: "ccb-hms/ontology-mapper-tests"
+ token: ${{ secrets.MAPPER_TESTING }}
+ fetch-depth: 0 # otherwise, there would be errors pushing refs to the destination repository.
+ - name: Set up Python 3.9
+ uses: actions/setup-python@v2
+ with:
+ python-version: 3.9
+ - name: Install dependencies
+ run: |
+ python -m pip install --upgrade pip
+ pip install flake8 pytest
+ if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+ - name: Run mapper on UK Biobank source terms
+ run: |
+ python3 text2term.py -s $source_path -t $target_path -min 0 -o "./tests/mapper-outputs/ukb-efo/${GITHUB_SHA}.csv"
+ env:
+ source_path: ./tests/data/ukb-efo/terms.txt
+ # https://github.com/EBISPOT/efo/releases/tag/v2019-03-18
+ # 2019-03-18 EFO 2.106, as referenced by:
+ # https://github.com/EBISPOT/EFO-UKB-mappings/blob/master/ISMB_Mapping_UK_Biobank_to_EFO.pdf
+ # page 2, footnote 9
+ target_path: ./tests/data/ukb-efo/efo-v2019-03-18.owl
+ - name: Setup summary spreadsheet row
+ run: |
+ if grep -q "," <<< "${{ github.event.head_commit.message }}"
+ then
+ MSG='"${{ github.event.head_commit.message }}"'
+ else
+ MSG='${{ github.event.head_commit.message }}'
+ fi
+ echo -n "${GITHUB_REF},${GITHUB_SHA},${MSG},ukb-efo/${GITHUB_SHA}.csv," >> $summary_path
+ working-directory: tests
+ env:
+ summary_path: summary.csv
+ - name: Run coverage__one_error script
+ run: |
+ python3 $script_path
+ working-directory: tests/compare-scripts
+ env:
+ script_path: coverage_one_error.py
+ - name: Commit changes to tests repo
+ run: |
+ git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
+ git config --local user.name "github-actions[bot]"
+ git add mapper-outputs/*
+ git add summary.csv
+ git commit -m "Add files"
+ working-directory: tests
+ - name: Push changes
+ uses: ad-m/github-push-action@master
+ with:
+ repository: "ccb-hms/ontology-mapper-tests"
+ github_token: ${{ secrets.MAPPER_TESTING }}
+ directory: "tests"