diff --git a/.github/workflows/database-update.yml b/.github/workflows/database-update.yml index 56c95f1..6edc3e1 100644 --- a/.github/workflows/database-update.yml +++ b/.github/workflows/database-update.yml @@ -3,144 +3,211 @@ name: Build-database on: push: branches: - - '**' + - "**" paths: - - ./data/ - - # Allows you to run this workflow manually from the Actions tab + - data/ + + # Allows running workflow manually from 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 + # Placeholder + build-bmd: + #if: github.actor != 'github-actions[bot]' + runs-on: ubuntu-latest + # 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-zfbmd + - name: Run bmd python command + run: | + docker run -v $PWD:/tmp sgosline/srp-zfbmd --morpho /app/zfBmd/test_files/test_morphology.csv --lpr /app/zfBmd/test_files/test_behavioral.csv --output /tmp + - name: List files cwd + run: ls -la + - name: Move files + run: | + mkdir bmd-files + mv *.csv bmd-files + - name: Upload artifacts + uses: actions/upload-artifact@v4 + with: + name: bmd-files + path: bmd-files + + build-samples: + #if: github.actor != 'github-actions[bot]' + runs-on: ubuntu-latest + 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-latest + 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-latest + 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 + + create-figshare-article: + runs-on: ubuntu-latest + outputs: + article_id: ${{ steps.create_article.outputs.article_id }} + steps: + - name: Create new private Figshare article + id: create_article + run: | + # Generate timestamp for unique article title + TIMESTAMP=$(date +"%Y-%m-%d_%H-%M-%S") + COMMIT_SHA="${{ github.sha }}" + BRANCH_NAME="${{ github.ref_name }}" + PROJECT_ID="${{ secrets.FIGSHARE_PROJECT_ID }}" + + # Define article metadata + METADATA=$(cat <> $GITHUB_OUTPUT - 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/github-upload-action@v1.1 - with: - FIGSHARE_TOKEN: ${{ secrets.FIGSHARE_TOKEN }} - FIGSHARE_ENDPOINT: 'https://api.figshare.com/v2' - FIGSHARE_ARTICLE_ID: 26240471 -# FIGSHARE_PROJECT_ID: 177459 - DATA_DIR: 'srpAnalytics' + # metadata field: "tags": ["srp-analytics", "database"], + artifact-test: + needs: + [ + build-bmd, + build-samples, + build-expo, + build-expr, + create-figshare-article, + ] + runs-on: ubuntu-latest + steps: + - name: Checkout Repo + uses: actions/checkout@v2 + - name: Download artifacts from bmd + uses: actions/download-artifact@v4 + with: + name: bmd-files + - name: Download artifacts from expression + uses: actions/download-artifact@v4 + with: + name: expr-files + - name: Download artifacts from exposome + uses: actions/download-artifact@v4 + with: + name: expo-files + - name: Download 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/github-upload-action@v1.1 + continue-on-error: true + with: + FIGSHARE_TOKEN: ${{ secrets.FIGSHARE_TOKEN }} + FIGSHARE_ENDPOINT: "https://api.figshare.com/v2" + FIGSHARE_ARTICLE_ID: ${{ needs.create-figshare-article.outputs.article_id }} + DATA_DIR: "srpAnalytics" #zipfiles push to figshare