ci.yml

name: CI

on:
  push:
    branches:
      - main
    tags:
      - '*.*.*'
  pull_request:

env:
  docker_repository: docker.synapse.org/syn22277123/i2b2-phi-dataset
  # github.event.repository.clone_url not available for on: schedule
  clone_url: https://github.com/nlpsandbox/i2b2-phi-dataset.git
  # github.event.repository.default_branch not available for on: schedule
  default_branch: main

jobs:
  configure:
    runs-on: ubuntu-latest
    steps:
    - name: Create configuration
      run: |
        DOCKER_IMAGE=${{ env.docker_repository }}
        VERSION=noop
        PUSH_IMAGE=false
        PUSH_NOTEBOOKS=false
        if [ "${{ github.event_name }}" = "schedule" ]; then
          VERSION=weekly
          PUSH_IMAGE=true
          PUSH_NOTEBOOKS=true
        elif [[ $GITHUB_REF == refs/tags/* ]]; then
          VERSION=${GITHUB_REF#refs/tags/}
        elif [[ $GITHUB_REF == refs/heads/* ]]; then
          VERSION=$(echo ${GITHUB_REF#refs/heads/} | sed -r 's#/+#-#g')
          if [ "${{ github.event.repository.default_branch }}" = "$VERSION" ]; then
            VERSION=edge
            PUSH_IMAGE=true
            PUSH_NOTEBOOKS=true
          fi
        elif [[ $GITHUB_REF == refs/pull/* ]]; then
          VERSION=pr-${{ github.event.number }}
          PUSH_IMAGE=false
          PUSH_NOTEBOOKS=true
        fi
        TAGS="${DOCKER_IMAGE}:${VERSION}"
        if [[ $VERSION == "edge" ]]; then
          TAGS="$TAGS,${DOCKER_IMAGE}:edge-${GITHUB_SHA::8}"
        elif [[ $VERSION =~ ^[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}$ ]]; then
          MINOR=${VERSION%.*}
          MAJOR=${MINOR%.*}
          TAGS="$TAGS,${DOCKER_IMAGE}:latest"
          PUSH_IMAGE=true
          PUSH_NOTEBOOKS=true
        fi
        printf "%s\n" \
          "version=${VERSION}" \
          "version_major=${MAJOR}" \
          "version_minor=${MINOR}" \
          "tags=${TAGS}" \
          "created=$(date -u +'%Y-%m-%dT%H:%M:%SZ')" \
          "push_image=${PUSH_IMAGE}" \
          "push_notebooks=${PUSH_NOTEBOOKS}" | tee -a .github_env

    - name: Upload .github_env
      uses: actions/upload-artifact@v2
      with:
        name: GITHUB_ENV
        path: .github_env

  lint:
    needs: [configure]
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v2
    - name: Lint Dockerfiles
      uses: docker://hadolint/hadolint:latest
      with:
        entrypoint: hadolint
        args: Dockerfile
    - name: Check that packages in requirements.txt files are in asc order
      run: |
        sort -f --check conda/i2b2-phi-dataset/requirements.txt

  test:
    needs: [lint]
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v2
    - name: Set environment variables
      run: |
        cp .env.example .env
        export $(grep -v '^#' .env | xargs -d '\n')
    - name: Validate docker-compose.yml
      run: docker-compose -f docker-compose.yml config >/dev/null

  build-and-publish:
    needs: [test]
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v2

    - name: Download .github_env
      uses: actions/download-artifact@v2
      with:
        name: GITHUB_ENV
        path: .

    - name: Restore $GITHUB_ENV
      run: cat .github_env >> $GITHUB_ENV

    - name: Set up QEMU
      uses: docker/setup-qemu-action@v1

    - name: Set up Docker Buildx
      id: buildx
      uses: docker/setup-buildx-action@v1

    - name: Cache Docker layers
      uses: actions/cache@v2
      with:
        path: /tmp/.buildx-cache
        key: ${{ runner.os }}-single-buildx-${{ github.sha }}
        restore-keys: |
          ${{ runner.os }}-single-buildx

    - name: Login to Docker Hub
      uses: docker/login-action@v1
      with:
        registry: docker.synapse.org
        username: ${{ secrets.SYNAPSE_USERNAME }}
        password: ${{ secrets.SYNAPSE_TOKEN }}

    - name: Build image
      uses: docker/build-push-action@v2
      with:
        context: .
        file: Dockerfile
        builder: ${{ steps.buildx.outputs.name }}
        load: true
        push: false
        platforms: linux/amd64
        tags: rstudio-cached:latest

    - name: Create .env
      run: |
        cp .env.example .env
        printf "%s\n" \
          "PASSWORD=${{ secrets.RSTUDIO_PASSWORD }}" \
          "USERID=$(id -u)" \
          "GROUPID=$(id -g)" \
          "SYNAPSE_TOKEN=${{ secrets.SYNAPSE_TOKEN }}" | tee -a .env >/dev/null

    - name: Generate HTML notebooks
      run: |
        docker run --rm \
          --env-file .env \
          -v $(pwd):/project \
          rstudio-cached:latest \
          render /project/notebooks/*.Rmd

    - name: Push image
      if: env.push_image == 'true'
      id: docker_push
      uses: docker/build-push-action@v2
      with:
        registry: docker.synapse.org
        context: .
        file: Dockerfile
        builder: ${{ steps.buildx.outputs.name }}
        push: true
        platforms: linux/amd64
        tags: ${{ env.tags }}
        labels: |
          org.opencontainers.image.created=${{ env.created }}
          org.opencontainers.image.source=${{ github.repositoryUrl }}
          org.opencontainers.image.version=${{ env.version }}
          org.opencontainers.image.revision=${{ github.sha }}
          org.opencontainers.image.licenses=${{ github.event.repository.license.name }}

    - name: Prepare to publish HTML notebooks to GH Pages
      if: env.push_notebooks == 'true'
      run: |
        git clone ${{ env.clone_url }} \
          --branch gh-pages --single-branch gh-pages

        # Update gh-pages: version specified
        NOTEBOOKS_TARGET_DIR=gh-pages/${{ env.version }}/notebooks
        rm -fr ${NOTEBOOKS_TARGET_DIR}
        mkdir -p ${NOTEBOOKS_TARGET_DIR}
        cp -R notebooks/*.html ${NOTEBOOKS_TARGET_DIR}

        # Update gh-pages: latest, major, and minor versions
        if [ ! -z "${{ env.version_major }}" ]; then
          # Update latest (e.g. "1.2.3" => "latest")
          NOTEBOOKS_TARGET_DIR=gh-pages/latest/notebooks
          rm -fr ${NOTEBOOKS_TARGET_DIR}
          mkdir -p ${NOTEBOOKS_TARGET_DIR}
          cp -R notebooks/*.html ${NOTEBOOKS_TARGET_DIR}

          # Update major version (e.g. "1.2.3" => "1")
          NOTEBOOKS_TARGET_DIR=gh-pages/${{ env.version_major }}/notebooks
          rm -fr ${NOTEBOOKS_TARGET_DIR}
          mkdir -p ${NOTEBOOKS_TARGET_DIR}
          cp -R notebooks/*.html ${NOTEBOOKS_TARGET_DIR}

          # Update minor version (e.g. "1.2.3" => "1.2")
          NOTEBOOKS_TARGET_DIR=gh-pages/${{ env.version_minor }}/notebooks
          rm -fr ${NOTEBOOKS_TARGET_DIR}
          mkdir -p ${NOTEBOOKS_TARGET_DIR}
          cp -R notebooks/*.html ${NOTEBOOKS_TARGET_DIR}
        fi
        cd gh-pages
        git config --local user.email "action@github.com"
        git config --local user.name "GitHub Action"
        git add .
        git commit -m "Update notebooks" -a || true
        # The above command will fail if no changes were present, so we ignore
        # that.

    - name: Push to gh-pages
      if: env.push_notebooks == 'true'
      uses: ad-m/github-push-action@master
      with:
        branch: gh-pages
        directory: gh-pages
        github_token: ${{ secrets.GITHUB_TOKEN }}
        force: true