Changes test data #11
Workflow file for this run
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| 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 |