def handle_dragen_wgs_qc_event(event):
logger.info(f"Handling {util.EventType.DRAGEN_WGS_QC} event")
event_type = event.get(util.BusEventKey.DETAIL_TYPE.value)
if event_type != util.EventType.WRSC.value:
raise ValueError(f"Unsupported event type: {event_type}")
payload = event.get(util.BusEventKey.DETAIL.value)
wrsc_event: wrsc.Event = wrsc.Marshaller.unmarshall(payload,
typeName=wrsc.Event)
if wrsc_event.status == "Succeeded":
logger.info(
f"{util.EventType.DRAGEN_WGS_QC.value} workflow succeeded! Proceeding to T/N."
)
# only progress some libraries to mock T/N case
lib_id = get_lib_id_from_wrsc_event(wrsc_event)
if lib_id in ["L210001", "L210003"]:
wfr_event = wfr.Event(library_id=lib_id)
logger.info(
f"Emitting DRAGEN_WGS_QC event with payload {wfr_event}")
util.send_event_to_bus_schema(
event_source=util.EventSource.ORCHESTRATOR,
event_type=util.EventType.DRAGEN_WGS_SOMATIC,
event_payload=wfr_event)
else:
# ignore other status for now
logger.info(
f"Received unsupported workflow status: {wrsc_event.status}")
def handle_bssh_runs_event(event):
logger.info("Handling bssh.runs event")
event_action = event['messageAttributes']['action']['stringValue']
if event_action != 'statuschanged':
raise ValueError(f"Unexpected event action: {event_action}")
message_body = json.loads(event['body'])
# TODO: check difference between run name and instrument run ID
srn = message_body['name']
iri = message_body['instrumentRunId']
if srn != iri:
raise ValueError(f"Sequence run name and instrumentRunId are not the same! {srn} != {iri}")
ev = srsc.Event(
sequence_run_name=srn,
sequence_run_id=message_body['id'],
gds_folder_path=message_body['gdsFolderPath'],
gds_volume_name=message_body['gdsVolumeName'],
status=message_body['status'],
timestamp=datetime.utcnow())
logger.info(f"Emitting {util.EventType.SRSC} event {ev}")
util.send_event_to_bus_schema(
event_type=util.EventType.SRSC,
event_source=util.EventSource.ENS_HANDLER,
event_payload=ev)
def handle_wes_runs_event(event):
logger.info("Handling wes.runs event")
event_action = event['messageAttributes']['action']['stringValue'] # TODO: check! should probably be 'updated'
message_body = json.loads(event['body'])
# TODO: convert SQS/ENS event into corresponding Portal event
event_status = message_body['EventType'] # RunSucceeded
event_time = message_body['Timestamp']
workflow_name = message_body['Name']
workflow_id = message_body['WorkflowRun']['Id'] # wfr.23487yq4508
workflow_status = message_body['WorkflowRun']['Status'] # Succeeded
# Convert Pending status of WES launcher to Succeeded (simulating a successful WES run)
if workflow_status == "Pending":
workflow_status = "Succeeded"
else:
# We are receiving mock events from the WES launcher directly, those have all Pending status
raise ValueError("Received non Pending WES run status! Only expect Pending at this point.")
wrsc_event = wrsc.Event(
workflow_run_name=workflow_name,
workflow_run_id=workflow_id,
status=workflow_status,
timestamp=event_time
)
logger.info(f"Emitting {util.EventType.SRSC} event {wrsc_event}")
util.send_event_to_bus_schema(
event_type=util.EventType.WRSC,
event_source=util.EventSource.ENS_HANDLER,
event_payload=wrsc_event)
def handler(event, context):
logger.info("Starting dragen_wgs_qc handler")
logger.info(json.dumps(event))
event_type = event.get(util.BusEventKey.DETAIL_TYPE.value)
if event_type != util.EventType.DRAGEN_WGS_QC.value:
raise ValueError(f"Unsupported event type: {event_type}")
payload = event.get(util.BusEventKey.DETAIL.value)
wfr_event: wfr.Event = wfr.Marshaller.unmarshall(payload,
typeName=wfr.Event)
workflow_input = {
"library_id": wfr_event.library_id,
"fastq_list_rows": {}
}
logger.info(f"Created workflow input: {workflow_input}")
wf_name = f"{util.WorkflowType.DRAGEN_WGS_QC}_workflow_{wfr_event.library_id}"
logger.info(f"Sending WES launch request for workflow {wf_name}")
wes_launch_request = wlr.Event(workflow_run_name=wf_name,
workflow_id="wfl.w94tygian4p8g4",
workflow_version="3.7.5-34afe2c",
workflow_input=workflow_input,
timestamp=datetime.utcnow(),
workflow_engine_parameters={})
logger.info(
f"Emitting {util.EventType.WES_LAUNCH} request event: {wes_launch_request}"
)
util.send_event_to_bus_schema(event_type=util.EventType.WES_LAUNCH,
event_source=util.EventSource.DRAGEN_WGS_QC,
event_payload=wes_launch_request)
logger.info("All done.")
def submit_dragen_tso_ctdna_requests(libraries: list):
# TODO: make sure that's not blocking other runs (i.e. a single WF failure should not prevent others)
for lib in libraries:
if lib.type == "TSO": # TODO:
wfr_event = wfr.Event(library_id=lib.library_id)
logger.info(
f"Emitting DRAGEN_TSO_CTDNA event with payload {wfr_event}")
util.send_event_to_bus_schema(
event_source=util.EventSource.ORCHESTRATOR,
event_type=util.EventType.DRAGEN_TSO_CTDNA,
event_payload=wfr_event)
def handler(event, context):
"""
Lambda to prepare and trigger BCL CONVERT workflow runs.
An event payload (detail) of the following format is expected:
SequenceRunStateChange:
{
"sequence_run_name": "210525_A00100_0999_AHYYKD8MYX",
"sequence_run_id": "r.c1IvasRL4U2MubrbB13cI4",
'gds_volume_name': "bssh.xxxx",
'gds_folder_path': "/Runs/210525_A00100_0999_AHYYKD8MYX_r.c1IvasRL4U2MubrbB13cI4",
'status': "",
'timestamp': ""
}
:param event: An AWSEvent with a SequenceRunStateChange event payload (detail) and SequenceRunStateChange detail-type
:param context: Not used.
:return:
"""
logger.info("Starting bcl_convert handler")
logger.info(json.dumps(event))
event_type = event.get(util.BusEventKey.DETAIL_TYPE.value)
if event_type != util.EventType.SRSC.value:
raise ValueError(f"Unsupported event type: {event_type}")
payload = event.get(util.BusEventKey.DETAIL.value)
srsc_event: srsc.Event = srsc.Marshaller.unmarshall(payload,
typeName=srsc.Event)
workflow_input = {
"seq_run_name":
srsc_event.sequence_run_name,
"seq_run_id":
srsc_event.sequence_run_id,
"gds_volume":
srsc_event.gds_volume_name,
"gds_path":
srsc_event.gds_folder_path,
"sample_sheet":
f"gds://{srsc_event.gds_volume_name}{srsc_event.gds_folder_path}/SampleSheet.csv"
}
logger.info(f"Created workflow input: {workflow_input}")
wf_name = f"{util.WorkflowType.BCL_CONVERT}_workflow_{srsc_event.sequence_run_name}_{srsc_event.sequence_run_id}"
logger.info(f"Sending WES launch request for workflow {wf_name}")
wes_launch_request = wlr.Event(workflow_run_name=wf_name,
workflow_id="wfl.w94tygian4p8g4",
workflow_version="3.7.5-34afe2c",
workflow_input=workflow_input,
timestamp=datetime.utcnow(),
workflow_engine_parameters={})
logger.info(
f"Emitting {util.EventType.WES_LAUNCH} request event: {wes_launch_request}"
)
# mock: just forward on the payload
util.send_event_to_bus_schema(event_type=util.EventType.WES_LAUNCH,
event_source=util.EventSource.BCL_CONVERT,
event_payload=wes_launch_request)
logger.info("All done.")