fixed format issue pt3 #114
Workflow file for this run
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - builder_branch_JJ | |
| jobs: | |
| build-hcmi: | |
| runs-on: ubuntu-20.04 | |
| environment: build | |
| steps: | |
| - name: Checkout HCMI | |
| uses: actions/checkout@v2 | |
| - name: Build HCMI Image | |
| run: docker build -t hcmi-builder -f build/docker/Dockerfile.hcmi . | |
| - name: Run HCMI Container | |
| run: docker run --name hcmi-container hcmi-builder | |
| - name: Copy files from HCMI Container | |
| run: | | |
| mkdir hcmi-files | |
| for file in hcmi_samples.csv hcmi_transcriptomics.csv hcmi_copy_number.csv hcmi_mutations.csv; do | |
| docker cp hcmi-container:/usr/src/app/$file hcmi-files/$file | |
| done | |
| - name: Get HCMI container logs | |
| run: docker logs hcmi-container | |
| # - name: dummy hcmi | |
| # run: | | |
| # mkdir hcmi-files | |
| # echo "This is some sample text." > hcmi-files/d.txt | |
| # echo "Another line of text." > hcmi-files/c.gz | |
| - name: Upload artifacts for HCMI | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: hcmi-files | |
| path: hcmi-files | |
| build-beataml: | |
| runs-on: ubuntu-20.04 | |
| environment: build | |
| steps: | |
| - name: Checkout code BeatAML | |
| uses: actions/checkout@v2 | |
| - name: Build BeatAML Image | |
| run: docker build -t beataml-builder -f build/docker/Dockerfile.beataml . | |
| - name: Run BeatAML Container | |
| run: docker run --name beataml-container -e SYNAPSE_TOKEN=${{ secrets.SYNAPSE_TOKEN_SECRET }} beataml-builder | |
| - name: Copy files from BeatAML Container | |
| run: | | |
| mkdir beataml-files | |
| for file in beataml_samples.csv beataml_transcriptomics.csv beataml_proteomics.csv beataml_mutations.csv beataml_drugs.tsv beataml_experiments.csv; do | |
| docker cp beataml-container:/usr/src/app/$file beataml-files/$file | |
| done | |
| - name: Get BeatAML container logs | |
| run: docker logs beataml-container | |
| - name: Upload artifact for BeatAML | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: beataml-files | |
| path: beataml-files | |
| data-visualization: | |
| environment: build | |
| runs-on: ubuntu-20.04 | |
| if: always() | |
| steps: | |
| - name: checkout repo content | |
| uses: actions/checkout@v2 | |
| - name: Download artifacts from HCMI | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: hcmi-files | |
| - name: Download artifacts from BeatAML | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: beataml-files | |
| - name: Create all-files directory | |
| run: mkdir all-files | |
| - name: List files cwd | |
| run: ls -lah | |
| - name: Set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| - name: Run Visualization02 | |
| if: success() || failure() | |
| run: Rscript visualization02.r | |
| - name: Run Visualization01 | |
| if: success() || failure() | |
| run: Rscript visualization01.r | |
| - name: setup data-vis dir | |
| if: success() || failure() | |
| run: | | |
| mkdir data-vis | |
| mv *.png data-vis | |
| mv *.pdf data-vis | |
| mv *table.csv data-vis | |
| - name: Upload artifacts | |
| if: success() || failure() | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: data-vis | |
| path: data-vis | |
| data-visualization-save-to-docs: | |
| environment: build | |
| runs-on: ubuntu-20.04 | |
| if: always() | |
| steps: | |
| - name: Checkout repo content | |
| uses: actions/checkout@v2 | |
| - name: Download artifacts from data-vis | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: data-vis | |
| - name: Move files to docs directory | |
| run: | | |
| mv data-vis/* docs/ | |
| - name: Setup Git config | |
| run: | | |
| git config user.name "jjacobson95" | |
| git config user.email "[email protected]" | |
| - name: Commit and push changes | |
| run: | | |
| git add . | |
| git commit -m "Add data visualization artifacts to docs" | |
| if git diff --staged --quiet; then | |
| echo "No changes to commit." | |
| else | |
| git push | |
| fi | |
| upload-to-figshare: | |
| needs: [build-hcmi, build-beataml] | |
| environment: build | |
| runs-on: ubuntu-20.04 | |
| if: always() | |
| steps: | |
| - name: checkout repo content | |
| uses: actions/checkout@v2 | |
| - name: Download artifacts from HCMI | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: hcmi-files | |
| - name: Download artifacts from BeatAML | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: beataml-files | |
| - name: Create all-files directory | |
| run: mkdir all-files | |
| - name: List files cwd | |
| run: ls -lah | |
| - name: Move files to all-files | |
| run: | | |
| rsync -av --remove-source-files --include='*.csv' --include='*.tsv' --include='*.gz' --exclude='*' . all-files/ | |
| - name: List files in all-files | |
| run: ls -lah all-files/ | |
| - name: Upload to Figshare | |
| # This can be updated to trigger with tag releases. | |
| # run: python scripts/push_to_figshare.py --directory all-files --title "CODERData${{ github.event.release.tag_name }}" --token ${{ secrets.FIGSHARE_TOKEN_SECRET }} -p False | |
| #This is a short term alternative. Links to branch. Not as pretty but okay for now. | |
| #To do: Extract version number from setup.py and run there. This can occur after merge with package dev branch. | |
| run: python scripts/push_to_figshare.py --directory all-files --title "CODERData${{ github.ref }}" --token ${{ secrets.FIGSHARE_TOKEN_SECRET }} -p False |