add escaping, full pipeline

ccb-hms · Feb 20, 2022 · da9ddc6 · da9ddc6
1 parent ea3e124
commit da9ddc6
Showing 1 changed file with 54 additions and 67 deletions.
diff --git a/.github/workflows/mapper-test.yml b/.github/workflows/mapper-test.yml
@@ -10,10 +10,38 @@ on:
         branches: [task5-workflow]
 
 jobs:
-    test_bash_script:
+    run_mapper:
         runs-on: ubuntu-latest
-        name: Test script
+        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 "," <<< "${{ github.event.head_commit.message }}"
@@ -22,68 +50,27 @@ jobs:
                   else
                     MSG='${{ github.event.head_commit.message }}'
                   fi
-                  echo -n "${GITHUB_REF},${GITHUB_SHA},${MSG},ukb-efo/${GITHUB_SHA}.csv,"
-    # 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 "," <<< "${{ github.event.head_commit.message }}"
-    #               then
-    #                 TEST=\"${MSG}\"
-    #               else
-    #                 TEST=${MSG}
-    #               fi
-    #               echo -n "${GITHUB_REF},${GITHUB_SHA},${{ github.event.head_commit.message }},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: ${{ secrets.MAPPER_TESTING }}
-    #               directory: "tests"
+                  echo -n "${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"