Test Illumina Genotyping Array #646

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- run_pipeline
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- Workflow file

Workflow file for this run

.github/workflows/test_illumina_genotyping_array.yml at 53409b1

	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
	REPOSITORY_NAME: ${{ github.event.repository.name }}
	SA_JSON_B64: ${{ secrets.PDT_TESTER_SA_B64 }}
	PIPELINE_NAME: IlluminaGenotypingArray
	DOCKSTORE_PIPELINE_NAME: IlluminaGenotypingArray


	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
	with:
	ref: ${{ github.ref }}

	- 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 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: Fetch Dockstore Workflow CommitID
	run: \|
	# Wait for Dockstore to update
	sleep 1
	# Capture the output of the script (commit ID)
	DOCKSTORE_COMMIT_HASH_FROM_FETCH=$(python scripts/dockstore_api/fetch_dockstore_commit.py \
	$DOCKSTORE_TOKEN \
	$DOCKSTORE_PIPELINE_NAME \
	$branch_name)
	# Export the commit hash as an environment variable
	echo "DOCKSTORE_COMMIT_HASH=$DOCKSTORE_COMMIT_HASH_FROM_FETCH" >> $GITHUB_ENV
	echo "Dockstore Commit Hash: $DOCKSTORE_COMMIT_HASH_FROM_FETCH"

	env:
	## TODO NEED TO ADD DOCKSTORE_TOKEN FOR SERVICE ACCOUNT ##
	DOCKSTORE_TOKEN: ${{ secrets.DOCKSTORE_TOKEN }}
	DOCKSTORE_PIPELINE_NAME: ${{ env.DOCKSTORE_PIPELINE_NAME }}
	branch_name: ${{ env.branch_name }}

	- name: Fetch Github Commit Hash
	id: fetch_github_commit_hash
	run: \|
	echo "GITHUB_COMMIT_HASH=${{ github.sha }}" >> $GITHUB_ENV
	echo "GitHub Commit Hash: ${{ github.sha }}"

	# - name: Compare Dockstore and Commit Hashes
	# id: compare_hashes
	# run: \|
	# echo "Comparing hashes..."
	# echo "Dockstore Commit Hash: $DOCKSTORE_COMMIT_HASH"
	# echo "GitHub Commit Hash: $GITHUB_COMMIT_HASH"
	#
	# if [ "$DOCKSTORE_COMMIT_HASH" != "$GITHUB_COMMIT_HASH" ]; then
	# echo "Error: The Dockstore Commit Hash does not match the GitHub Commit Hash!"
	# echo "Mismatch found: $DOCKSTORE_COMMIT_HASH != $GITHUB_COMMIT_HASH"
	# exit 1
	# else
	# echo "Success: The Dockstore Commit Hash matches the GitHub Commit Hash."
	# fi
	# env:
	# DOCKSTORE_COMMIT_HASH: ${{ env.DOCKSTORE_COMMIT_HASH }}
	# GITHUB_COMMIT_HASH: ${{ env.GITHUB_COMMIT_HASH }}

	- 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, Upload to Terra, Submit, Monitor and Retrieve Outputs
	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 "$GITHUB_COMMIT_HASH" )
	echo "Uploading the test input file: $test_input_file"
	python3 scripts/firecloud_api/firecloud_api.py \
	upload_test_inputs \
	--workspace-namespace warp-pipelines \
	--workspace-name "WARP Tests" \
	--pipeline_name "$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_api.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_api.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=$(python3 scripts/firecloud_api/firecloud_api.py get_workflow_outputs \
	--user "[email protected]" \
	--sa-json-b64 "$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
	env:
	PIPELINE_NAME: TestIlluminaGenotypingArray
	NAMESPACE: warp-pipelines
	WORKSPACE: WARP Tests

	- name: Perform File Copy with gsutil
	run: \|
	python scripts/firecloud_api/firecloud_api.py gsutil_copy \
	--sa-json-b64 "$SA_JSON_B64" \
	--user "[email protected]" \
	--source "gs://fc-cddd72b5-323c-495c-9557-5057fff0275a/commit_hash.txt" \
	--destination . \
	--workspace-namespace warp-pipelines \
	--workspace-name "WARP Tests"
	env:
	SA_JSON_B64: ${{ secrets.PDT_TESTER_SA_B64 }}

	- 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

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Test Illumina Genotyping Array #646

Workflow file

Test Illumina Genotyping Array #646

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