def run_analysis_job(sal, job_name, pipeline_id, service_entry_points, block=False, time_out=None, task_options=()):
"""Run analysis (pbsmrtpipe) job
:rtype ServiceJob:
"""
if time_out is None:
time_out = sal.JOB_DEFAULT_TIMEOUT
status = sal.get_status()
log.info("System:{i} v:{v} Status:{x}".format(x=status['message'], i=status['id'], v=status['version']))
resolved_service_entry_points = []
for service_entry_point in service_entry_points:
# Always lookup/resolve the dataset by looking up the id
ds = sal.get_dataset_by_uuid(service_entry_point.resource)
if ds is None:
raise ValueError("Failed to find DataSet with id {r} {s}".format(s=service_entry_point, r=service_entry_point.resource))
dataset_id = ds['id']
ep = ServiceEntryPoint(service_entry_point.entry_id, service_entry_point.dataset_type, dataset_id)
log.debug("Resolved dataset {e}".format(e=ep))
resolved_service_entry_points.append(ep)
if block:
job_result = sal.run_by_pipeline_template_id(job_name, pipeline_id, resolved_service_entry_points, time_out=time_out, task_options=task_options)
job_id = job_result.job.id
# service job
result = sal.get_analysis_job_by_id(job_id)
if not result.was_successful():
raise JobExeError("Job {i} failed:\n{e}".format(i=job_id, e=job_result.job.error_message))
else:
# service job or error
result = sal.create_by_pipeline_template_id(job_name, pipeline_id, resolved_service_entry_points)
log.info("Result {r}".format(r=result))
return result
def args_emit_analysis_template(args):
ep1 = ServiceEntryPoint("eid_ref_dataset", FileTypes.DS_REF.file_type_id, 1)
ep1_d = ep1.to_d()
ep1_d['_comment'] = "datasetId can be provided as the DataSet UUID or Int. The entryId(s) can be obtained by running 'pbsmrtpipe show-pipeline-templates {PIPELINE-ID}'"
d = dict(name="Job name",
pipelineId="pbsmrtpipe.pipelines.dev_diagnostic",
entryPoints=[ep1_d],
taskOptions=[],
workflowOptions=[])
sx = json.dumps(d, sort_keys=True, indent=4, separators=(',', ': '))
print sx
return 0
