Build-database #31
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| name: Build-database | |
| on: | |
| push: | |
| branches: | |
| - '**' | |
| paths: | |
| - ./data/ | |
| # Allows you to run this workflow manually from the Actions tab | |
| workflow_dispatch: | |
| jobs: | |
| # Placeholder | |
| # build-bmd: | |
| # #if: github.actor != 'github-actions[bot]' | |
| # runs-on: ubuntu-20.04 | |
| # environment: build | |
| # steps: | |
| # - name: Checkout Repo | |
| # uses: actions/checkout@v3 | |
| # - name: Download artifacts from previous drug gen | |
| # uses: actions/download-artifact@v4 | |
| # - name: Pull sample image | |
| # run: docker pull sgosline/srp-bmd | |
| # - name: Run bmd python command | |
| # run: | | |
| # docker run -v $PWD:/tmp sgosline/srp-bmd | |
| # - name: List files cwd | |
| # run: ls -la | |
| build-samples: | |
| #if: github.actor != 'github-actions[bot]' | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Checkout Repo | |
| uses: actions/checkout@v3 | |
| - name: Download artifacts from previous drug gen | |
| uses: actions/download-artifact@v4 | |
| - name: Pull sample image | |
| run: docker pull sgosline/srp-samplechem | |
| - name: Run sample-chem python command | |
| run: | | |
| docker run -v $PWD:/tmp sgosline/srp-samplechem | |
| - name: List files cwd | |
| run: ls -la | |
| - name: move files | |
| run: | | |
| mkdir samp-files | |
| mv *csv samp-files | |
| - name: upload artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: samp-files | |
| path: samp-files | |
| build-expo: | |
| #if: github.actor != 'github-actions[bot]' | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Checkout Repo | |
| uses: actions/checkout@v3 | |
| - name: Download artifacts from previous drug gen | |
| uses: actions/download-artifact@v4 | |
| - name: Pull sample image | |
| run: docker pull sgosline/srp-exposome | |
| - name: Run sample-chem python command | |
| run: | | |
| docker run -v $PWD:/tmp sgosline/srp-exposome | |
| - name: List files cwd | |
| run: ls -la | |
| - name: Copy files to artifact | |
| run: | | |
| mkdir expo-files | |
| mv *.csv expo-files | |
| - name: upload artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: expo-files | |
| path: expo-files | |
| build-expr: | |
| #if: github.actor != 'github-actions[bot]' | |
| runs-on: ubuntu-20.04 | |
| needs: build-samples | |
| steps: | |
| - name: Checkout Repo | |
| uses: actions/checkout@v3 | |
| - name: Download artifacts from sample generation | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: samp-files | |
| path: samp-files | |
| - name: Pull sample image | |
| run: docker pull sgosline/srp-zfexp | |
| - name: move chemical list to tmp | |
| run: mv samp-files/chemicals.csv . | |
| - name: Run zfexp python command | |
| run: | | |
| docker run -v $PWD:/tmp sgosline/srp-zfexp | |
| - name: List files cwd | |
| run: ls -la | |
| - name: Copy files to artifact | |
| run: | | |
| mkdir expr-files | |
| mv *csv expr-files | |
| - name: upload artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: expr-files | |
| path: expr-files | |
| artifact-test: | |
| needs: [build-samples,build-expo,build-expr] | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Checkout Repo | |
| uses: actions/checkout@v2 | |
| - name: Download artifacts from expression | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: expr-files | |
| - name: Downlod artifacts from exposome | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: expo-files | |
| - name: Downlod artifacts from samples | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: samp-files | |
| - name: List files cwd | |
| run: ls -la * | |
| - name: Moves files to single directory | |
| run: | | |
| mkdir srpAnalytics | |
| mv *csv srpAnalytics | |
| #gzip -cvf srpAnalytics/* srpAnalytics.gz | |
| - name: Pushes to figshare | |
| uses: figshare/[email protected] | |
| with: | |
| FIGSHARE_TOKEN: ${{ secrets.FIGSHARE_TOKEN }} | |
| FIGSHARE_ENDPOINT: 'https://api.figshare.com/v2' | |
| FIGSHARE_ARTICLE_ID: 26240471 | |
| # FIGSHARE_PROJECT_ID: 177459 | |
| DATA_DIR: 'srpAnalytics' | |
| #zipfiles push to figshare | |