main.yml

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 "jeremy.jacobson3402@gmail.com"
      - 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