Test Illumina Genotyping Array #599
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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", "staging", "master" ] | |
| # Only run if files in these paths changed: | |
| #################################### | |
| # SET PIPELINE SPECIFIC PATHS HERE # | |
| #################################### | |
| paths: | |
| - 'pipelines/broad/genotyping/illumina/**' | |
| - 'tasks/broad/IlluminaGenotypingArrayTasks.wdl' | |
| - 'tasks/broad/Qc.wdl' | |
| - 'verification/VerifyIlluminaGenotypingArray.wdl' | |
| - 'verification/test-wdls/TestIlluminaGenotypingArray.wdl' | |
| - 'tasks/broad/Utilities.wdl' | |
| - 'tasks/broad/TerraCopyFilesFromCloudToCloud.wdl' | |
| - '.github/workflows/test_illumina_genotyping_array.yml' | |
| # Allows you to run this workflow manually from the Actions tab | |
| workflow_dispatch: | |
| inputs: | |
| useCallCache: | |
| description: 'Use call cache (default: true)' | |
| required: false | |
| default: "true" | |
| updateTruth: | |
| description: 'Update truth files (default: false)' | |
| required: false | |
| default: "false" | |
| testType: | |
| description: 'Specify the type of test (Plumbing or Scientific)' | |
| required: true | |
| truthBranch: | |
| description: 'Specify the branch for truth files (default: master)' | |
| required: false | |
| default: "master" | |
| env: | |
| PROJECT_NAME: WARP | |
| # Github repo name | |
| REPOSITORY_NAME: ${{ github.event.repository.name }} | |
| SA_JSON_B64: ${{ secrets.PDT_TESTER_SA_B64 }} | |
| jobs: | |
| run_pipeline: | |
| runs-on: ubuntu-latest | |
| # Add "id-token" with the intended permissions. | |
| permissions: | |
| contents: 'read' | |
| id-token: 'write' | |
| steps: | |
| # Add a step to wait to account for github -> dockstore -> terra delays | |
| - name: Wait Before Starting | |
| run: | | |
| echo "Waiting for 5 minutes before starting..." | |
| sleep 1 # time in seconds, update this when we really want a delay | |
| # actions/checkout MUST come before auth | |
| - uses: actions/checkout@v3 | |
| with: | |
| ref: ${{ github.ref }} | |
| # id: 'auth' | |
| # name: 'Authenticate to Google Cloud' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # token_format: 'access_token' | |
| # # Centralized in dsp-tools-k8s; ask in #dsp-devops-champions for help troubleshooting | |
| # # This is provided by the DevOps team - do not change! | |
| # workload_identity_provider: 'projects/1038484894585/locations/global/workloadIdentityPools/github-wi-pool/providers/github-wi-provider' | |
| # # This is our tester service account | |
| # service_account: '[email protected]' | |
| # access_token_lifetime: '3600' # seconds, default is 3600 | |
| # access_token_scopes: 'profile, email, openid' | |
| - name: Set up python | |
| id: setup-python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.11' | |
| - name: Install dependencies | |
| run: | | |
| pwd | |
| cd scripts/firecloud_api/ | |
| pip install -r requirements.txt | |
| - name: Set Commit Hash | |
| id: set_commit_hash | |
| run: echo "COMMIT_HASH=${{ github.sha }}" >> $GITHUB_ENV | |
| # Set the branch name. | |
| # github.head_ref contains the name of the branch in the context of a pull request | |
| # if github.head_ref is empty, it implies the workflow was triggered manually | |
| # ${GITHUB_REF##*/} extracts the branch name from GITHUB_REF. | |
| # The ##*/ is a parameter expansion that removes the refs/heads/ prefix, leaving just the branch name. | |
| - name: Set Branch Name | |
| id: set_branch | |
| run: | | |
| if [ -z "${{ github.head_ref }}" ]; then | |
| echo "Branch name is missing, using ${GITHUB_REF##*/}" | |
| echo "branch_name=${GITHUB_REF##*/}" >> $GITHUB_ENV | |
| else | |
| echo "Branch name from PR: ${{ github.head_ref }}" | |
| echo "branch_name=${{ github.head_ref }}" >> $GITHUB_ENV | |
| fi | |
| - name: Set Test Type for PRs | |
| if: ${{ github.event_name == 'pull_request' }} | |
| id: set_test_type | |
| run: | | |
| # Default to "Scientific" if targeting master | |
| if [ "${{ github.base_ref }}" == "master" ]; then | |
| echo "testType=Scientific" >> $GITHUB_ENV | |
| else | |
| echo "testType=Plumbing" >> $GITHUB_ENV | |
| fi | |
| - name: Use Provided Test Type | |
| if: ${{ github.event_name == 'workflow_dispatch' }} | |
| id: use_provided_test_type | |
| run: | | |
| # Use the testType provided by the user | |
| echo "testType=${{ github.event.inputs.testType }}" >> $GITHUB_ENV | |
| - name: Update test inputs and Upload to Terra | |
| run: | | |
| UPDATE_TRUTH="${{ github.event.inputs.updateTruth || 'false' }}" | |
| USE_CALL_CACHE="${{ github.event.inputs.useCallCache || 'true' }}" | |
| TRUTH_BRANCH="${{ github.event.inputs.truthBranch || 'master' }}" | |
| CURRENT_TIME=$(date +"%Y-%m-%d-%H-%M-%S") | |
| MAX_RETRIES=2 | |
| RETRY_DELAY=300 # 300 seconds = 5 minutes | |
| # Initialize variables to aggregate statuses and outputs | |
| ALL_WORKFLOW_STATUSES="Workflow ID | Status"$'\n'"--- | ---" | |
| ALL_OUTPUTS="" | |
| # Initialize arrays to track submission and workflow statuses | |
| declare -a SUBMISSION_IDS | |
| declare -A WORKFLOW_STATUSES | |
| # Convert UPDATE_TRUTH and USE_CALL_CACHE to a boolean-friendly format ("true" -> true, "false" -> false) | |
| if [ "$UPDATE_TRUTH" = "true" ]; then | |
| UPDATE_TRUTH_BOOL=true | |
| else | |
| UPDATE_TRUTH_BOOL=false | |
| fi | |
| if [ "$USE_CALL_CACHE" == "true" ]; then | |
| USE_CALL_CACHE_BOOL=true | |
| else | |
| USE_CALL_CACHE_BOOL=false | |
| fi | |
| PIPELINE_NAME="TestIlluminaGenotypingArray" | |
| PIPELINE_DIR="pipelines/broad/genotyping/illumina" | |
| TEST_TYPE="${{ env.testType }}" | |
| INPUTS_DIR="$PIPELINE_DIR/test_inputs/$TEST_TYPE" | |
| echo "Running tests with test type: $TEST_TYPE" | |
| TRUTH_PATH="gs://broad-gotc-test-storage/IlluminaGenotypingArray/truth/$(echo "$TEST_TYPE" | tr '[:upper:]' '[:lower:]')/$TRUTH_BRANCH" | |
| echo "Truth path: $TRUTH_PATH" | |
| RESULTS_PATH="gs://broad-gotc-test-storage/IlluminaGenotypingArray/results/$CURRENT_TIME" | |
| # Create the submission_data.json file which will be the same for all inputs | |
| SUBMISSION_DATA_FILE="submission_data.json" | |
| # Use a heredoc to generate the JSON file content dynamically | |
| cat <<EOF > "$SUBMISSION_DATA_FILE" | |
| { | |
| "methodConfigurationNamespace": "warp-pipelines", | |
| "methodConfigurationName": "$PIPELINE_NAME", | |
| "useCallCache": $USE_CALL_CACHE_BOOL, | |
| "deleteIntermediateOutputFiles": false, | |
| "useReferenceDisks": true, | |
| "memoryRetryMultiplier": 1.2, | |
| "workflowFailureMode": "NoNewCalls", | |
| "userComment": "Automated submission", | |
| "ignoreEmptyOutputs": false | |
| } | |
| EOF | |
| echo "Created submission data file: $SUBMISSION_DATA_FILE" | |
| # 1. Submit all jobs first and store their submission IDs | |
| for input_file in "$INPUTS_DIR"/*.json; do | |
| test_input_file=$(python3 scripts/firecloud_api/UpdateTestInputs.py --truth_path "$TRUTH_PATH" \ | |
| --results_path "$RESULTS_PATH" \ | |
| --inputs_json "$input_file" \ | |
| --update_truth "$UPDATE_TRUTH_BOOL" \ | |
| --commit_hash "$COMMIT_HASH" ) | |
| echo "Uploading the test input file: $test_input_file" | |
| python3 scripts/firecloud_api/firecloud_api2.py \ | |
| upload_test_inputs \ | |
| --workspace-namespace warp-pipelines \ | |
| --workspace-name "WARP Tests" \ | |
| --pipeline_name "$PIPELINE_NAME" \ | |
| --test_input_file "$test_input_file" \ | |
| --branch_name "$branch_name" \ | |
| --sa-json-b64 "$SA_JSON_B64" \ | |
| --user "[email protected]" | |
| attempt=1 | |
| while [ $attempt -le $MAX_RETRIES ]; do | |
| SUBMISSION_ID=$(python3 scripts/firecloud_api/firecloud_api2.py submit_job \ | |
| --workspace-namespace "warp-pipelines" \ | |
| --workspace-name "WARP Tests" \ | |
| --sa-json-b64 "$SA_JSON_B64" \ | |
| --user "[email protected]" \ | |
| --submission_data_file "$SUBMISSION_DATA_FILE") | |
| echo "Submission ID: $SUBMISSION_ID" | |
| if [[ "$SUBMISSION_ID" == *"404"* || -z "$SUBMISSION_ID" ]]; then | |
| echo "Error in submission, retrying in $RETRY_DELAY seconds..." | |
| ((attempt++)) | |
| if [ $attempt -gt $MAX_RETRIES ]; then | |
| echo "Max retries reached. Exiting..." | |
| exit 1 | |
| fi | |
| sleep $RETRY_DELAY | |
| continue | |
| fi | |
| echo "Submission successful. Submission ID: $SUBMISSION_ID" | |
| SUBMISSION_IDS+=("$SUBMISSION_ID") | |
| break | |
| done | |
| done | |
| echo "All jobs have been submitted. Starting to poll for statuses..." | |
| # 2. After all submissions are done, start polling for statuses of all jobs | |
| for SUBMISSION_ID in "${SUBMISSION_IDS[@]}"; do | |
| attempt=1 | |
| while [ $attempt -le $MAX_RETRIES ]; do | |
| echo "Polling for Submission ID: $SUBMISSION_ID" | |
| RESPONSE=$(python3 scripts/firecloud_api/firecloud_api2.py poll_job_status \ | |
| --submission_id "$SUBMISSION_ID" \ | |
| --sa-json-b64 "$SA_JSON_B64" \ | |
| --user "[email protected]" \ | |
| --workspace-namespace "warp-pipelines" \ | |
| --workspace-name "WARP Tests") | |
| if [ -z "$RESPONSE" ]; then | |
| echo "Failed to retrieve Workflow IDs for submission: $SUBMISSION_ID" | |
| ((attempt++)) | |
| if [ $attempt -gt $MAX_RETRIES ]; then | |
| echo "Max retries reached. Exiting..." | |
| exit 1 | |
| fi | |
| sleep $RETRY_DELAY | |
| continue | |
| fi | |
| WORKFLOW_STATUSES_FOR_SUBMISSION=$(echo "$RESPONSE" | jq -r 'to_entries | map(.key + " | " + .value) | .[]') | |
| WORKFLOW_STATUSES["$SUBMISSION_ID"]="$WORKFLOW_STATUSES_FOR_SUBMISSION" | |
| # retrieve workflow outputs | |
| echo "Retrieving workflow outputs for Submission ID: $SUBMISSION_ID..." | |
| for WORKFLOW_ID in $(echo "$RESPONSE" | jq -r 'keys[]'); do | |
| WORKFLOW_OUTPUT=$(python3 scripts/firecloud_api/firecloud_api2.py get_workflow_outputs \ | |
| --user "[email protected]" \ | |
| --sa-json-b64 "$SA_JSON_B64" \ | |
| --submission_id "$SUBMISSION_ID" \ | |
| --workspace-namespace warp-pipelines \ | |
| --workspace-name "WARP Tests" \ | |
| --workflow_id "$WORKFLOW_ID" \ | |
| --pipeline_name "$PIPELINE_NAME") | |
| ALL_OUTPUTS+="$WORKFLOW_OUTPUT"$'\n' | |
| done | |
| break | |
| done | |
| # Generate final summary tables with hyperlinks for Submission IDs | |
| echo "## Combined Workflow Statuses" >> $GITHUB_STEP_SUMMARY | |
| for SUBMISSION_ID in "${!WORKFLOW_STATUSES[@]}"; do | |
| # Generate the Terra URL for the submission | |
| SUBMISSION_URL="https://app.terra.bio/#workspaces/$NAMESPACE/${WORKSPACE// /%20}/job_history/$SUBMISSION_ID" | |
| # Add the Submission ID as a hyperlink | |
| echo "[Submission ID: $SUBMISSION_ID]($SUBMISSION_URL)" >> $GITHUB_STEP_SUMMARY | |
| # Add the workflows and statuses for this submission | |
| echo "${WORKFLOW_STATUSES[$SUBMISSION_ID]}" >> $GITHUB_STEP_SUMMARY | |
| # Add a blank line for separation | |
| echo "" >> $GITHUB_STEP_SUMMARY | |
| done | |
| done | |
| # - name: Monitor Workflow Status | |
| # run: | | |
| # echo "Monitoring the status of submitted workflows..." | |
| # # Convert the space-separated string into an array | |
| # IFS=' ' read -r -a submission_ids_array <<< "$submission_ids" | |
| # | |
| # # Ensure the array is populated | |
| # if [ ${#submission_ids_array[@]} -eq 0 ]; then | |
| # echo "No submission IDs found. Exiting..." | |
| # exit 1 | |
| # fi | |
| # | |
| # declare -A WORKFLOW_STATUSES | |
| # | |
| # echo "submission_ids_array: ${submission_ids_array[@]}" | |
| # | |
| # for SUBMISSION_ID in "${submission_ids_array[@]}"; do | |
| # echo "Polling submission status for Submission ID: $SUBMISSION_ID" | |
| # RESPONSE=$(python3 scripts/firecloud_api/firecloud_api2.py poll_job_status \ | |
| # --submission_id "$SUBMISSION_ID" \ | |
| # --sa-json-b64 "$SA_JSON_B64" \ | |
| # --user "[email protected]" \ | |
| # --workspace-namespace "warp-pipelines" \ | |
| # --workspace-name "WARP Tests") | |
| # | |
| # if [ -z "$RESPONSE" ]; then | |
| # echo "Failed to retrieve Workflow IDs for submission: $SUBMISSION_ID" | |
| # continue | |
| # fi | |
| # | |
| # # Debug raw response | |
| # echo "Raw Workflow Statuses:" | |
| # echo "$RESPONSE" | |
| # | |
| # # Parse and store workflow statuses | |
| # echo "Parsing workflow statuses for submissions" | |
| # WORKFLOW_STATUSES_FOR_SUBMISSION=$(echo "$RESPONSE" | jq -r 'to_entries | map(.key + " | " + .value) | .[]') | |
| # echo "Raw Workflow Statuses: $WORKFLOW_STATUSES_FOR_SUBMISSION" | |
| # #up until here there are no issues with the script | |
| # | |
| # # Remove duplicates and sanitize | |
| # CLEANED_WORKFLOW_STATUSES=$(echo "$WORKFLOW_STATUSES_FOR_SUBMISSION" | awk '!seen[$0]++') | |
| # # Debug cleaned statuses | |
| # echo "Cleaned Workflow Statuses: $CLEANED_WORKFLOW_STATUSES" | |
| # | |
| # # Reset and assign to associative array | |
| # WORKFLOW_STATUSES["$SUBMISSION_ID"]="$CLEANED_WORKFLOW_STATUSES" | |
| # | |
| # #Debug stored status | |
| # echo "Stored Workflow Statuses for $SUBMISSION_ID: ${WORKFLOW_STATUSES[$SUBMISSION_ID]}" | |
| # | |
| # # Append to aggregate statuses | |
| # echo "Appending to aggregate statuses" | |
| # CLEANED_WORKFLOW_STATUSES=$(echo "$WORKFLOW_STATUSES_FOR_SUBMISSION" | tr -d '\n' | tr -d '\r') | |
| # echo "CLEANED_WORKFLOW_STATUSES: $CLEANED_WORKFLOW_STATUSES" | |
| # WORKFLOW_STATUSES["$SUBMISSION_ID"]="$CLEANED_WORKFLOW_STATUSES" | |
| # done | |
| # # # Retrieve workflow outputs | |
| # # echo "Retrieving workflow outputs for Submission ID: $SUBMISSION_ID..." | |
| # # for WORKFLOW_ID in $(echo "$RESPONSE" | jq -r 'keys[]'); do | |
| # # WORKFLOW_OUTPUT=$(python3 scripts/firecloud_api/firecloud_api2.py get_outputs \ | |
| # # --submission_id "$SUBMISSION_ID" \ | |
| # # --workflow_id "$WORKFLOW_ID" \ | |
| # # --pipeline_name "$PIPELINE_NAME") | |
| # # ALL_OUTPUTS+="$WORKFLOW_OUTPUT"$'\n' | |
| # # done | |
| # # done | |
| # # Generate summary for Submission IDs | |
| # echo "## Combined Workflow Statuses" >> $GITHUB_STEP_SUMMARY | |
| # for SUBMISSION_ID in "${!WORKFLOW_STATUSES[@]}"; do | |
| # # Generate the Terra URL for the submission | |
| # SUBMISSION_URL="https://app.terra.bio/#workspaces/$NAMESPACE/${WORKSPACE// /%20}/job_history/$SUBMISSION_ID" | |
| # | |
| # # Add the Submission ID as a hyperlink | |
| # echo "[Submission ID: $SUBMISSION_ID]($SUBMISSION_URL)" >> $GITHUB_STEP_SUMMARY | |
| # | |
| # # Add the workflows and statuses for this submission | |
| # echo "${WORKFLOW_STATUSES[$SUBMISSION_ID]}" >> $GITHUB_STEP_SUMMARY | |
| # | |
| # # Add a blank line for separation | |
| # echo "" >> $GITHUB_STEP_SUMMARY | |
| # done | |
| env: | |
| #SUBMISSION_IDS: ${{ steps.submit_jobs.outputs.submission_ids }} # Pass IDs from a previous step | |
| PIPELINE_NAME: TestIlluminaGenotypingArray | |
| NAMESPACE: warp-pipelines | |
| WORKSPACE: WARP Tests | |
| #- name: Download Commit Hash from GCP | |
| # run: | | |
| # gsutil cp gs://fc-cddd72b5-323c-495c-9557-5057fff0275a/commit_hash.txt ./commit_hash.txt | |
| #- name: Check Commit Hash | |
| # id: check_commit_hash | |
| # run: | | |
| # # Read the commit hash from the downloaded file | |
| # COMMIT_HASH_FROM_WDL=$(cat commit_hash.txt) | |
| # | |
| # # Compare the two commit hashes | |
| # if [ "$COMMIT_HASH_FROM_WDL" != "${{ env.COMMIT_HASH }}" ]; then | |
| # echo "Error: The commit hash from the WDL output does not match the expected commit hash." | |
| # exit 1 | |
| # else | |
| # echo "Commit hash match successful: $COMMIT_HASH_FROM_WDL" | |
| # fi | |
| - name: Print Summary on Success | |
| if: success() | |
| run: | | |
| echo "# :white_check_mark: Pipeline Execution Summary :white_check_mark:" >> $GITHUB_STEP_SUMMARY | |
| - name: Print Summary on Failure | |
| if: failure() | |
| run: | | |
| echo "# :x: Pipeline Execution Summary (on Failure) :x: " >> $GITHUB_STEP_SUMMARY |