def post(self, request):
request_ids = request.data.get('request_ids', [])
run_ids = request.data.get('run_ids', [])
job_group_id = request.data.get('job_group_id', [])
pipeline_name = request.data['pipeline_name']
pipeline = get_object_or_404(Pipeline, name=pipeline_name)
if request_ids:
for request_id in request_ids:
logging.info("Submitting requestId %s to pipeline %s" %
(request_id, pipeline_name))
if not job_group_id:
job_group = JobGroup.objects.create()
job_group_id = str(job_group.id)
create_jobs_from_request.delay(request_id,
pipeline.operator_id,
job_group_id)
body = {"details": "Operator Job submitted %s" % str(request_ids)}
else:
if run_ids:
operator_model = Operator.objects.get(id=pipeline.operator_id)
if job_group_id:
operator = OperatorFactory.get_by_model(
operator_model,
run_ids=run_ids,
job_group_id=job_group_id)
create_jobs_from_operator(operator, job_group_id)
body = {
"details":
"Operator Job submitted to pipeline %s, job group id %s, with runs %s"
% (pipeline_name, job_group_id, str(run_ids))
}
else:
operator = OperatorFactory.get_by_model(operator_model,
run_ids=run_ids)
create_jobs_from_operator(operator)
body = {
"details":
"Operator Job submitted to pipeline %s with runs %s" %
(pipeline_name, str(run_ids))
}
else:
operator_model = Operator.objects.get(id=pipeline.operator_id)
if job_group_id:
operator = OperatorFactory.get_by_model(
operator_model, job_group_id=job_group_id)
run_routine_operator_job(operator, job_group_id)
body = {
"details":
"Operator Job submitted to operator %s (JobGroupId: %s)"
% (operator, job_group_id)
}
else:
operator = OperatorFactory.get_by_model(operator_model)
run_routine_operator_job(operator)
body = {
"details":
"Operator Job submitted to operator %s" % operator
}
return Response(body, status=status.HTTP_200_OK)
def post(self, request):
request_ids = request.data.get('request_ids')
pipeline_name = request.data.get('pipeline')
job_group_id = request.data.get('job_group_id', None)
for_each = request.data.get('for_each', True)
pipeline = get_object_or_404(Pipeline, name=pipeline_name)
errors = []
if not request_ids:
errors.append('request_ids needs to be specified')
if not pipeline:
errors.append('pipeline needs to be specified')
if errors:
return Response({'details': errors},
status=status.HTTP_400_BAD_REQUEST)
if not job_group_id:
if for_each:
for req in request_ids:
job_group = JobGroup()
job_group.save()
job_group_id = str(job_group.id)
logging.info("Submitting requestId %s to pipeline %s" %
(req, pipeline))
create_jobs_from_request.delay(req,
pipeline.operator_id,
job_group_id,
pipeline=str(pipeline.id))
else:
return Response({'details': 'Not Implemented'},
status=status.HTTP_400_BAD_REQUEST)
else:
if for_each:
for req in request_ids:
logging.info("Submitting requestId %s to pipeline %s" %
(req, pipeline))
try:
job_group_notifier = JobGroupNotifier.objects.get(
job_group_id=job_group_id,
notifier_type_id=pipeline.operator.notifier_id)
job_group_notifier_id = str(job_group_notifier.id)
except JobGroupNotifier.DoesNotExist:
job_group_notifier_id = notifier_start(
job_group_id, req, pipeline.operator)
create_jobs_from_request.delay(
req,
pipeline.operator_id,
job_group_id,
job_group_notifier_id=job_group_notifier_id,
pipeline=str(pipeline.id))
else:
return Response({'details': 'Not Implemented'},
status=status.HTTP_400_BAD_REQUEST)
body = {"details": "Operator Job submitted %s" % str(request_ids)}
return Response(body, status=status.HTTP_202_ACCEPTED)
def request_callback(request_id, job_group=None, job_group_notifier=None):
jg = None
jgn = None
try:
jgn = JobGroupNotifier.objects.get(id=job_group_notifier)
logger.debug("[RequestCallback] JobGroup id: %s", job_group)
except JobGroupNotifier.DoesNotExist:
logger.debug("[RequestCallback] JobGroup not set")
job_group_notifier_id = str(jgn.id) if jgn else None
assays = ETLConfiguration.objects.first()
recipe = LIMSClient.get_request_samples(request_id).get("recipe", None)
if (not all([
JobStatus(job["status"]) == JobStatus.COMPLETED for job in
Job.objects.filter(job_group=job_group,
run=TYPES["SAMPLE"],
args__igocomplete=True).values("status")
]) and recipe in settings.WES_ASSAYS):
wes_job_failed = WESJobFailedEvent(job_group_notifier_id, recipe)
send_notification.delay(wes_job_failed.to_dict())
if not recipe:
raise FailedToSubmitToOperatorException(
"Not enough metadata to choose the operator for requestId:%s" %
request_id)
if not all(item in assays.all_recipes for item in [recipe]):
ci_review_e = SetCIReviewEvent(job_group_notifier_id).to_dict()
send_notification.delay(ci_review_e)
set_unknown_assay_label = SetLabelEvent(
job_group_notifier_id, "unrecognized_assay").to_dict()
send_notification.delay(set_unknown_assay_label)
unknown_assay_event = UnknownAssayEvent(job_group_notifier_id,
recipe).to_dict()
send_notification.delay(unknown_assay_event)
return []
if any(item in assays.hold_recipes for item in [
recipe,
]):
admin_hold_event = AdminHoldEvent(job_group_notifier_id).to_dict()
send_notification.delay(admin_hold_event)
custom_capture_event = CustomCaptureCCEvent(job_group_notifier_id,
recipe).to_dict()
send_notification.delay(custom_capture_event)
return []
if any(item in assays.disabled_recipes for item in [
recipe,
]):
not_for_ci = NotForCIReviewEvent(job_group_notifier_id).to_dict()
send_notification.delay(not_for_ci)
disabled_assay_event = DisabledAssayEvent(job_group_notifier_id,
recipe).to_dict()
send_notification.delay(disabled_assay_event)
return []
if len(
FileRepository.filter(metadata={
"requestId": request_id
},
values_metadata="recipe").all()) == 0:
no_samples_event = AdminHoldEvent(job_group_notifier_id).to_dict()
send_notification.delay(no_samples_event)
return []
if not all([
JobStatus(job["status"]) == JobStatus.COMPLETED
for job in Job.objects.filter(job_group=job_group).values("status")
]):
ci_review_e = SetCIReviewEvent(job_group_notifier_id).to_dict()
send_notification.delay(ci_review_e)
lab_head_email = FileRepository.filter(
metadata={
"requestId": request_id
}, values_metadata="labHeadEmail").first()
try:
if lab_head_email.split("@")[1] != "mskcc.org":
event = ExternalEmailEvent(job_group_notifier_id,
request_id).to_dict()
send_notification.delay(event)
except Exception:
logger.error("Failed to check labHeadEmail")
if len(
FileRepository.filter(metadata={
"requestId": request_id,
"tumorOrNormal": "Tumor"
})) == 0:
only_normal_samples_event = OnlyNormalSamplesEvent(
job_group_notifier_id, request_id).to_dict()
send_notification.delay(only_normal_samples_event)
if recipe in settings.ASSAYS_ADMIN_HOLD_ONLY_NORMALS:
admin_hold_event = AdminHoldEvent(job_group_notifier_id).to_dict()
send_notification.delay(admin_hold_event)
return []
operators = Operator.objects.filter(recipes__overlap=[recipe])
if not operators:
# TODO: Import ticket will have CIReviewNeeded
msg = "No operator defined for requestId %s with recipe %s" % (
request_id, recipe)
logger.error(msg)
e = OperatorRequestEvent(job_group_notifier_id,
"[CIReviewEvent] %s" % msg).to_dict()
send_notification.delay(e)
ci_review_e = SetCIReviewEvent(job_group_notifier_id).to_dict()
send_notification.delay(ci_review_e)
raise FailedToSubmitToOperatorException(msg)
for operator in operators:
if not operator.active:
msg = "Operator not active: %s" % operator.class_name
logger.info(msg)
e = OperatorRequestEvent(job_group_notifier_id,
"[CIReviewEvent] %s" % msg).to_dict()
send_notification.delay(e)
error_label = SetLabelEvent(job_group_notifier_id,
"operator_inactive").to_dict()
send_notification.delay(error_label)
ci_review_e = SetCIReviewEvent(job_group_notifier_id).to_dict()
send_notification.delay(ci_review_e)
else:
logger.info("Submitting request_id %s to %s operator" %
(request_id, operator.class_name))
if Job.objects.filter(job_group=job_group,
args__request_id=request_id,
run=TYPES["SAMPLE"],
status=JobStatus.FAILED).all():
partialy_complete_event = ETLImportPartiallyCompleteEvent(
job_notifier=job_group_notifier_id).to_dict()
send_notification.delay(partialy_complete_event)
else:
complete_event = ETLImportCompleteEvent(
job_notifier=job_group_notifier_id).to_dict()
send_notification.delay(complete_event)
create_jobs_from_request.delay(request_id, operator.id, job_group)
return []