def run_main(path, host, port, job_name, pipeline_id, referenceset_uuid, block=False, custom_options=None):
"""
:param path: Path to SubreadSet XML will be imported (if it's not already been imported)
:param host: SL Host
:param port: SL Port
:param job_name: Job name
:param pipeline_id: Pipeline Id (e.g, pbsmrtpipe.pipelines.my_pipeline
:param referenceset_uuid: UUID of Rset. This *must* already be imported
:param block: To block and poll for the analysis job to complete
:param custom_options: Dictionary of task options for the provided
Pipeline in the form
{"pbalign.task_options.concordant":True}
:type custom_options: dict | None
:rtype: int
"""
# look up the reference set UUID from pbservice CLI util or
# http://smrtlink-beta:8081/secondary-analysis/datasets/references
# TODO. 1. Import SubreadSet if it's not already imported
# TODO. 2. Check and see if the Job with the SubreadSet UUID was already submitted
# TODO. 3. Add option to force a new submission to override (2)
# TODO. 4. Enable custom pipeline options json file at the CLI
# sanity test
sset = SubreadSet(path)
log.info("Loaded SubreadSet {}".format(sset))
sal = ServiceAccessLayer(host, port)
# Sanity Check
_ = sal.get_status()
# Step 1. Import SubreadSet (and block) if it's not imported already
service_sset = sal.get_subreadset_by_id(sset.uuid)
# TODO. Add check to see if Job was successful
if service_sset is None:
log.info("Running Import-DataSet job with {}".format(path))
sset_import_job = sal.run_import_dataset_subread(path)
log.info("Import-DataSet job {}".format(sset_import_job))
else:
log.info("Found already imported SubreadSet {}".format(service_sset))
# Step 2. Check and See if an previous analysis job has already been run
# Immediately exit if an analysis job is found
analysis_job = get_job_by_subreadset_uuid_or_none(sal, sset.uuid)
if analysis_job is not None:
log.info("Found exiting job {} for SubreadSet {}".format(analysis_job, sset))
return 0
# Step 3. Create a new Analysis job with custom task options (if provided)
task_options = {} if custom_options is None else custom_options
# Get the already Successfully imported DataSets
service_sset_d = sal.get_dataset_by_uuid(sset.uuid)
service_rset_d = sal.get_dataset_by_uuid(referenceset_uuid)
f = sal.run_by_pipeline_template_id if block else sal.create_by_pipeline_template_id
# The API takes the Int id of the DataSet
epoints = (ServiceEntryPoint("eid_subread", FileTypes.DS_SUBREADS.file_type_id, service_sset_d['id']),
ServiceEntryPoint("eid_ref_dataset", FileTypes.DS_REF.file_type_id, service_rset_d['id']))
job = f(job_name, pipeline_id, epoints, task_options=task_options)
log.info("Analysis Job {}".format(job))
if block:
exit_code = 0 if job.state == JobStates.SUCCESSFUL else 1
else:
# the job is in the created state
exit_code = 0
return exit_code
