It looks like python printings messes up bash inputs. Cleaning it up. #47
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| name: Test Illumina Genotyping Array | |
| # Controls when the workflow will run | |
| on: | |
| #run on push to feature branch "kp_GHA_Terra_auth_PD-2682" - REMOVE WHEN DONE TESTING | |
| push: | |
| branches: | |
| - kp_GHA_Terra_auth_PD-2682 | |
| #pull_request: | |
| # branches: [ "develop" ] | |
| # Allows you to run this workflow manually from the Actions tab | |
| workflow_dispatch: | |
| # inputs: | |
| # image_tag: | |
| # description: 'Docker Image Tag (default: branch_name)' | |
| env: | |
| PROJECT_NAME: WARP | |
| # Github repo name | |
| REPOSITORY_NAME: ${{ github.event.repository.name }} | |
| jobs: | |
| run_pipeline: | |
| runs-on: ubuntu-latest | |
| # Add "id-token" with the intended permissions. | |
| permissions: | |
| contents: 'read' | |
| id-token: 'write' | |
| steps: | |
| # actions/checkout MUST come before auth | |
| - uses: 'actions/checkout@v3' | |
| - id: 'auth' | |
| name: 'Authenticate to Google Cloud' | |
| uses: 'google-github-actions/auth@v2' | |
| with: | |
| token_format: 'access_token' | |
| # Centralized in dsp-tools-k8s; ask in #dsp-devops-champions for help troubleshooting | |
| workload_identity_provider: 'projects/1038484894585/locations/global/workloadIdentityPools/github-wi-pool/providers/github-wi-provider' | |
| # This is our tester service account | |
| service_account: '[email protected]' | |
| access_token_lifetime: '1000s' # optional, default: '3600s' (1 hour) | |
| access_token_scopes: 'profile, email, openid' | |
| # ... further steps are automatically authenticated | |
| - name: Check working directory | |
| run: | | |
| echo "Current directory:" | |
| pwd | |
| ls -lht | |
| - name: Submit job, poll status, and get outputs | |
| run: | | |
| # Set these environment variables or replace with your actual values | |
| TOKEN="${{ steps.auth.outputs.access_token }}" | |
| NAMESPACE="warp-pipelines" | |
| WORKSPACE="WARP Tests" | |
| # Function to call the Firecloud API using the firecloud_api.py script | |
| firecloud_action() { | |
| python3 scripts/firecloud_api/firecloud_api.py --token "$TOKEN" --namespace "$NAMESPACE" --workspace "$WORKSPACE" --action "$1" "${@:2}" | |
| } | |
| # Create the submission_data.json file | |
| SUBMISSION_DATA_FILE="submission_data.json" | |
| # Use a heredoc to generate the JSON file content dynamically | |
| cat <<EOF > "$SUBMISSION_DATA_FILE" | |
| { | |
| "methodConfigurationNamespace": "warp-pipelines", | |
| "methodConfigurationName": "IlluminaGenotypingArray", | |
| "useCallCache": true, | |
| "deleteIntermediateOutputFiles": true, | |
| "useReferenceDisks": true, | |
| "memoryRetryMultiplier": 1.2, | |
| "workflowFailureMode": "NoNewCalls", | |
| "userComment": "Automated submission", | |
| "ignoreEmptyOutputs": false | |
| } | |
| EOF | |
| echo "Created submission data file: $SUBMISSION_DATA_FILE" | |
| # 1. Submit a new workflow using the generated submission_data.json | |
| SUBMISSION_ID=$(firecloud_action submit --submission_data_file "$SUBMISSION_DATA_FILE") | |
| # Check if submission was successful | |
| if [ -z "$SUBMISSION_ID" ]; then | |
| echo "Submission failed." | |
| exit 1 | |
| fi | |
| echo "Submission ID: $SUBMISSION_ID" | |
| # 2. Poll submission status and capture all Workflow IDs from the response | |
| RESPONSE=$(firecloud_action poll_status --submission_id "$SUBMISSION_ID") | |
| #print the response | |
| echo "Response: $RESPONSE" | |
| #Parse the response to get the workflow IDs | |
| WORKFLOW_IDS=$(echo "$RESPONSE" | grep -oP 'workflow_id:\s*\K\S+') | |
| #WORKFLOW_IDS=$(firecloud_action poll_status --submission_id "$SUBMISSION_ID" | grep -oP 'workflow_id:\s*\K\S+') | |
| # Check if Workflow IDs were retrieved | |
| if [ -z "$WORKFLOW_IDS" ]; then | |
| echo "Failed to retrieve Workflow IDs." | |
| exit 1 | |
| fi | |
| echo "Workflow IDs: $WORKFLOW_IDS" | |
| # 3. Iterate over all Workflow IDs to get outputs | |
| PIPELINE_NAME="IlluminaGenotypingArray" # Replace with your actual Pipeline name | |
| for WORKFLOW_ID in $WORKFLOW_IDS; do | |
| firecloud_action get_outputs --submission_id "$SUBMISSION_ID" --workflow_id "$WORKFLOW_ID" --pipeline_name "$PIPELINE_NAME" | |
| done | |
| echo "Workflow outputs retrieved successfully." | |
| # - name: Check the status of a Terra submission | |
| # run: | | |
| # submissionId="44d890f7-f6dd-4a2c-8841-a10faeab3a07" | |
| # namespace="warp-pipelines" | |
| # name="Illumina-Genotyping-Array_np_copy" | |
| # # Assign the access token to a variable | |
| # ACCESS_TOKEN="${{ steps.auth.outputs.access_token }}" | |
| # printf "\nFetching status for submission ID '%s':" "${submissionId}" | |
| # submissionDetails=$(curl \ | |
| # -X GET \ | |
| # --header 'Accept: application/json' \ | |
| # --header "Authorization: Bearer ${ACCESS_TOKEN}" \ | |
| # "https://api.firecloud.org/api/workspaces/$namespace/$name/submissions/$submissionId") | |
| # printf "\nFull JSON Response '%s':" "${submissionDetails}" | |
| # submissionStatus=$(jq -r '.status' <<< "${submissionDetails}") | |
| # workflowsStatus=$(jq -r '.workflows[] | .status' <<< "${submissionDetails}") | |
| # printf "\nSubmissionStatus '%s':" "${submissionStatus}" | |
| # printf "\nWorkflowsStatus '%s':" "${workflowsStatus}" | |
| # submissionList=$(curl -X 'GET' \ | |
| # "https://api.firecloud.org/api/workspaces/$namespace/$name/submissions" \ | |
| # -H 'accept: */*' \ | |
| # -H "Authorization: Bearer ${ACCESS_TOKEN}") | |
| # printf "\nSubmissionList '%s':" "${submissionList}" | |