CORE Test Suite Validation #1
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| name: CORE Test Suite Validation | |
| on: | |
| workflow_dispatch: | |
| env: | |
| DATASET_SIZE_THRESHOLD: 1000000000 | |
| PANDAS_DIFF: False | |
| DASK_DIFF: False | |
| jobs: | |
| validate: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Get Engine Changes | |
| uses: actions/checkout@v3 | |
| - name: Get Test Suite Repository | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: cdisc-org/CORE_Test_Suite | |
| path: CORE_Test_Suite | |
| token: ${{ secrets.ACCESS_TOKEN }} | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - name: Install dependencies | |
| run: | | |
| pip install -r requirements.txt | |
| - name: Update rules cache | |
| env: | |
| CDISC_LIBRARY_API_KEY: ${{ secrets.CDISC_LIBRARY_API_KEY }} | |
| run: | | |
| python core.py update-cache | |
| - name: Parse rule list and run validation | |
| run: | | |
| rules=$(cat CORE_Test_Suite/rulelist/testrulelist.txt | sed 's/^/-r /' | tr '\n' ' ') | |
| python core.py validate -s sdtmig -v 3-3 $rules -d CORE_Test_Suite/data -ct sdtmct-2020-03-27 -o CORE_Test_Suite/pandas-results | |
| - name: Pandas comparison script | |
| run: | | |
| cd CORE_Test_Suite | |
| result=$(python comparison.py pandas-results.xlsx CORE-Report.xlsx pandas_comparison.xlsx) | |
| echo "PANDAS_DIFF=$result" >> $GITHUB_ENV | |
| echo "Pandas comparison result: $result" | |
| - name: Run validation with Dask | |
| env: | |
| DATASET_SIZE_THRESHOLD: 0 | |
| run: | | |
| rules=$(cat CORE_Test_Suite/rulelist/testrulelist.txt | sed 's/^/-r /' | tr '\n' ' ') | |
| python core.py validate -s sdtmig -v 3-3 $rules -d CORE_Test_Suite/data -ct sdtmct-2020-03-27 -o CORE_Test_Suite/dask-results | |
| - name: Dask comparison script | |
| run: | | |
| cd CORE_Test_Suite | |
| result=$(python comparison.py dask-results.xlsx DASK-Report.xlsx dask_comparison.xlsx) | |
| echo "DASK_DIFF=$result" >> $GITHUB_ENV | |
| echo "Dask comparison result: $result" | |
| cd .. | |
| - name: Upload test results | |
| if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: comparison-results | |
| path: | | |
| CORE_Test_Suite/pandas_comparison.xlsx | |
| CORE_Test_Suite/pandas-results.xlsx | |
| CORE_Test_Suite/dask_comparison.xlsx | |
| CORE_Test_Suite/dask-results.xlsx | |
| if-no-files-found: warn | |
| - name: Check for differences | |
| if: always() | |
| run: | | |
| if [[ "${{ env.PANDAS_DIFF }}" == "true" || "${{ env.DASK_DIFF }}" == "true" ]]; then | |
| echo "Differences found in either Pandas or Dask comparison" | |
| exit 1 | |
| elif [[ "${{ env.PANDAS_DIFF }}" == "false" && "${{ env.DASK_DIFF }}" == "false" ]]; then | |
| echo "No differences found in either comparison" | |
| exit 0 | |
| else | |
| echo "Issue with comparison script" | |
| exit 1 | |
| fi |