cloudos_ci_test.yml

name: CI test on CloudOS
# This workflow is triggered on PRs of type review_requested or ready_for_review, against dev or main
on:
  pull_request:
    types: [review_requested, ready_for_review]
    branches:
      - main
      - dev
  workflow_dispatch:

jobs:
  test_on_cloudos_prod:
    runs-on: ubuntu-20.04
    if: github.event.pull_request.draft == false
    steps:
      - name: Checkout
        uses: actions/checkout@v2
        with:
          ref: ${{ github.event.pull_request.head.sha }}

      - name: Install pip
        run: sudo apt-get --assume-yes install python3-pip

      - name: Clone CloudOS repo
        uses: actions/checkout@v2
        with:
          repository: lifebit-ai/cloudos-py
          token: ${{ secrets.GH_PAT }}
          path: cloudos-py 
          ref: ce114ef7ba89f9c0bd8c013d08ac6254d6d9f654

      - name: Submit job using cloudos-py
        env:
          CLOUDOS_TOKEN: ${{ secrets.CLOUDOS_TOKEN }}
          GIT_COMMIT: ${{ github.event.pull_request.head.sha }}
          PR_NUM: ${{ github.event.number }}
        run: |
          set -o pipefail
          cd cloudos-py
          pip3 install -r requirements.txt
          pip3 install .
          # Production command
          cloudos job run \
              -k $CLOUDOS_TOKEN \
              --cloudos-url https://cloudos.lifebit.ai \
              --workspace-id 5c6d3e9bd954e800b23f8c62 \
              --project-name ci-test \
              --workflow-name exomiser-nf \
              --job-config ${GITHUB_WORKSPACE}/conf/test.config \
              --git-commit $GIT_COMMIT \
              --job-name exomiser-nf-CI-test-GithubCommit[${GIT_COMMIT:0:6}]-PR_Number[${PR_NUM}] \
              --spot | tee ../out_cloudos.txt
          # Processing outputs to get the PR message
          printf "**CloudOS CI test** - :rocket: " > pr_message.txt
          awk '{if (NR==6) print $0}' ../out_cloudos.txt >> pr_message.txt
          printf "\nThere will be a following **Status update** comment in the PR, once the CloudOS job completes. Please wait for that.\n" >> pr_message.txt
          echo 'CLOUDOS_STATUS<<EOF' >> $GITHUB_ENV
          cat pr_message.txt >> $GITHUB_ENV
          echo 'EOF' >> $GITHUB_ENV

      - name: Send cloudos start message to PR comment
        uses: mshick/add-pr-comment@v1
        with:
          message: ${{ env.CLOUDOS_STATUS }}
          repo-token: ${{ secrets.GH_PAT }}
          repo-token-user-login: 'github-actions[bot]'
          allow-repeats: true

      - name: Check job using cloudos-py
        env:
          CLOUDOS_TOKEN: ${{ secrets.CLOUDOS_TOKEN }}
          GIT_COMMIT: ${{ github.event.pull_request.head.sha }}
          JOB_IDMSG: ${{ env.CLOUDOS_STATUS }}
        run: |
          set -o pipefail
          cd cloudos-py
          echo "$JOB_IDMSG" > job_idmsg.txt
          JOB_ID=`head -1 job_idmsg.txt | rev | cut -f 1 -d '/' | rev`
          # Check job status every minute
          JOB_OUT=""
          TRY_NUM=1
          while [[ $JOB_OUT = "" ]] && [[ $TRY_NUM -le 120 ]]
          do
              cloudos job status \
                  -k $CLOUDOS_TOKEN \
                  --cloudos-url https://cloudos.lifebit.ai \
                  --job-id $JOB_ID | tee ../out_cloudos.txt
              if grep -q -e "completed" ../out_cloudos.txt
              then
                  JOB_OUT="**Status update** - :white_check_mark: CloudOS CI test job has finished with status - **COMPLETED**. You can check it in https://cloudos.lifebit.ai/app/job/$JOB_ID"
              elif grep -q -e "failed" ../out_cloudos.txt
              then
                  JOB_OUT="**Status update** - :x: CloudOS CI test job has finished with status - **FAILED**. You can check it in https://cloudos.lifebit.ai/app/job/$JOB_ID"
              elif grep -q -e "aborted" ../out_cloudos.txt
              then
                  JOB_OUT="**Status update** - :x: CloudOS CI test job has finished with status - **ABORTED**. You can check it in https://cloudos.lifebit.ai/app/job/$JOB_ID"
              elif [[ $TRY_NUM -eq 120 ]]
              then
                  JOB_OUT="**Status update** - :warning: CloudOS CI test job has not finished but you exceeded the maximum monitoring time. Please check its status in https://cloudos.lifebit.ai/app/job/$JOB_ID"
              else
                  sleep 1m
                  TRY_NUM=$((TRY_NUM+1))
              fi
          done
          # Processing outputs to get the PR message
          echo 'CLOUDOS_STATUS<<EOF' >> $GITHUB_ENV
          echo $JOB_OUT  >> $GITHUB_ENV
          echo 'EOF' >> $GITHUB_ENV

      - name: Send cloudos final message to PR comment
        uses: mshick/add-pr-comment@v1
        with:
          message: ${{ env.CLOUDOS_STATUS }}
          repo-token: ${{ secrets.GH_PAT }}
          repo-token-user-login: 'github-actions[bot]'
          allow-repeats: true

      - name: Make the CI fail when CloudOS fails
        env:
          JOB_OUT: ${{ env.CLOUDOS_STATUS }}
        run: |
          set -o pipefail
          echo $JOB_OUT > job_out.txt
          if grep -q -v -e "COMPLETED" job_out.txt
          then
              echo "Exiting with code 1 as CloudOS CI test was not successful"
              exit 1
          fi