release.yml

name: Upload assets to release

on:
  release:
    types: [published]

jobs:
  release:
    name: Upload assets to release
    runs-on: ubuntu-latest

    steps:
      - name: Checkout code
        uses: actions/checkout@v4

      - name: Set appVersion
        uses: bhowell2/github-substring-action@v1
        id: appVersion
        with:
          value: ${{github.ref}}
          index_of_str: "refs/tags/v"

      - run: echo "Version = ${{steps.appVersion.outputs.substring}}"

      - name: Set up JDK
        uses: actions/setup-java@v4
        with:
          distribution: temurin
          java-version: 17
          cache: gradle

      - name: Package PharmCAT
        run: make pipelinePkg scriptPkg

      - name: Upload jar to release
        uses: svenstaro/upload-release-action@v2
        with:
          repo_token: ${{ secrets.GITHUB_TOKEN }}
          tag: ${{ github.ref }}
          file: build/libs/pharmcat-${{steps.appVersion.outputs.substring}}-all.jar
          overwrite: true

      - name: Upload pipeline to release
        uses: svenstaro/upload-release-action@v2
        with:
          repo_token: ${{ secrets.GITHUB_TOKEN }}
          tag: ${{ github.ref }}
          file: build/pipeline.tar.gz
          asset_name: pharmcat-pipeline-${{steps.appVersion.outputs.substring}}.tar.gz
          overwrite: true

      - name: Upload preprocessor to release
        uses: svenstaro/upload-release-action@v2
        with:
          repo_token: ${{ secrets.GITHUB_TOKEN }}
          tag: ${{ github.ref }}
          file: build/preprocessor.tar.gz
          asset_name: pharmcat-preprocessor-${{steps.appVersion.outputs.substring}}.tar.gz
          overwrite: true

      - name: Upload positions.vcf to release
        uses: svenstaro/upload-release-action@v2
        with:
          repo_token: ${{ secrets.GITHUB_TOKEN }}
          tag: ${{ github.ref }}
          file: pharmcat_positions.vcf
          asset_name: pharmcat_positions_${{steps.appVersion.outputs.substring}}.vcf
          overwrite: true

      - name: Upload positions.vcf.bgz to release
        uses: svenstaro/upload-release-action@v2
        with:
          repo_token: ${{ secrets.GITHUB_TOKEN }}
          tag: ${{ github.ref }}
          file: pharmcat_positions.vcf.bgz
          asset_name: pharmcat_positions_${{steps.appVersion.outputs.substring}}.vcf.bgz
          overwrite: true

      - name: Upload positions.vcf.bgz.csi to release
        uses: svenstaro/upload-release-action@v2
        with:
          repo_token: ${{ secrets.GITHUB_TOKEN }}
          tag: ${{ github.ref }}
          file: pharmcat_positions.vcf.bgz.csi
          asset_name: pharmcat_positions_${{steps.appVersion.outputs.substring}}.vcf.bgz.csi
          overwrite: true

      - name: Upload positions.uniallelic.vcf.bgz to release
        uses: svenstaro/upload-release-action@v2
        with:
          repo_token: ${{ secrets.GITHUB_TOKEN }}
          tag: ${{ github.ref }}
          file: pharmcat_positions.uniallelic.vcf.bgz
          asset_name: pharmcat_positions_${{steps.appVersion.outputs.substring}}.uniallelic.vcf.bgz
          overwrite: true

      - name: Upload positions.uniallelic.vcf.bgz.csi to release
        uses: svenstaro/upload-release-action@v2
        with:
          repo_token: ${{ secrets.GITHUB_TOKEN }}
          tag: ${{ github.ref }}
          file: pharmcat_positions.uniallelic.vcf.bgz.csi
          asset_name: pharmcat_positions_${{steps.appVersion.outputs.substring}}.uniallelic.vcf.bgz.csi
          overwrite: true


      - name: Send Slack notification on failure
        if: failure()
        uses: slackapi/slack-github-action@v1
        with:
          channel-id: 'dev'
          payload: |
            {
              "attachments": [{
                "color": "#ff0000",
                "blocks": [
                  {
                    "type": "section",
                    "text": {
                      "type": "mrkdwn",
                      "text": ":stop: <https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}|FAILED ${{ github.workflow }}!>"
                    }
                  },
                  {
                    "type": "section",
                    "text": {
                      "type": "mrkdwn",
                      "text": "Triggered by ${{ github.event_name }} on <${{ github.event.pull_request.html_url || github.event.head_commit.url }}|${{ github.ref_name }}> by ${{ github.actor }}."
                    }
                  },
                  {
                    "type": "context",
                    "elements": [
                      {
                        "type": "mrkdwn",
                        "text": "Last commit:\n${{ github.event.head_commit.message }}"
                      }
                    ]
                  }
                ]
            }]
            }
        env:
          SLACK_BOT_TOKEN: ${{ secrets.SLACK_NOTIFICATIONS_BOT_TOKEN }}