Template standardization #7
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 |