Fix Clavel2023 #2894
Workflow file for this run
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| name: check_dataset | |
| # This workflow is triggered on pushes and PRs to the repository. | |
| on: | |
| pull_request: | |
| branches: [master] | |
| jobs: | |
| AMDirT: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.9" | |
| architecture: "x64" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install amdirt==1.4.6 | |
| pip install jsonschema==4.17.0 | |
| - name: Make validation results directory | |
| run: mkdir validation/ | |
| - name: Add AMDirT validate version | |
| run: | | |
| echo "$(AMDirT --version)" > validation/validation_results_raw.txt | |
| - name: SAMPLES test ancient host-associated metagenome (e.g. microbiomes) | |
| if: always() | |
| run: | | |
| echo "# Samples" >> validation/validation_results_raw.txt | |
| echo "## Ancient Metagenome Host Associated" >> validation/validation_results_raw.txt | |
| AMDirT validate -s -d -c -i -m --multi_values archive_accession ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples_schema.json &>> validation/validation_results_raw.txt | |
| - name: SAMPLES test ancient single microbial genomes (e.g. pathogens) | |
| if: always() | |
| run: | | |
| echo "## Ancient Single Genome Host Associated" >> validation/validation_results_raw.txt | |
| AMDirT validate -s -d -c -i -m --multi_values archive_accession ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples_schema.json &>> validation/validation_results_raw.txt | |
| - name: SAMPLES test ancient environmental (e.g. sediment) | |
| if: always() | |
| run: | | |
| echo "## Ancient Metagenome Environmental" >> validation/validation_results_raw.txt | |
| AMDirT validate -s -d -c -i -m --multi_values archive_accession ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples.tsv ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples_schema.json &>> validation/validation_results_raw.txt | |
| - name: LIBRARIES test ancient host-associated metagenome (e.g. microbiomes) | |
| if: always() | |
| run: | | |
| echo "# Libraries" >> validation/validation_results_raw.txt | |
| echo "## Ancient Metagenome Host Associated" >> validation/validation_results_raw.txt | |
| AMDirT validate -s -d -c -m ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries_schema.json &>> validation/validation_results_raw.txt | |
| - name: LIBRARIES test ancient host-associated single-genomes (e.g. pathogens) | |
| if: always() | |
| run: | | |
| echo "## Ancient Single Genome Host Associated" >> validation/validation_results_raw.txt | |
| AMDirT validate -s -d -c -m ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries_schema.json &>> validation/validation_results_raw.txt | |
| - name: LIBRARIES test ancient environmental metagenomes (e.g. sedaDNA) | |
| if: always() | |
| run: | | |
| echo "## Ancient Metagenome Environmental" >> validation/validation_results_raw.txt | |
| AMDirT validate -s -d -c -m ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_libraries.tsv ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_libraries_schema.json &>> validation/validation_results_raw.txt | |
| - name: cleanup validation results from streamlit warnings | |
| if: always() | |
| run: | | |
| grep -v streamlit validation/validation_results_raw.txt > validation/validation_results.txt | |
| - uses: actions/upload-artifact@v3 | |
| if: always() | |
| with: | |
| name: results | |
| path: validation/validation_results.txt | |
| - uses: actions/download-artifact@v3 | |
| if: always() | |
| with: | |
| name: results | |
| - name: comment PR | |
| if: always() | |
| uses: machine-learning-apps/[email protected] | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| path: validation/validation_results.txt |