log(ex)
return list()
def run(self):
run_pipeline(self.pipeline, self.pipelinetype, self.job, self.owner)
def complete(self):
status = jobs.get_job_status(str(self.job), util.conn_string)
return status['status'] == jobs.COMPLETED or status[
'status'] == jobs.WARNING or status['status'] == jobs.FAILURE
if __name__ == "__main__":
owner = "tester"
p_id = "11469"
the_job_id = data_access.create_new_job(
data_access.NlpJob(job_id=-1,
name="Test Phenotype",
description="Test Phenotype",
owner=owner,
status=data_access.STARTED,
date_ended=None,
phenotype_id=int(p_id),
pipeline_id=-1,
date_started=datetime.datetime.now(),
job_type='PHENOTYPE'), util.conn_string)
luigi.run([
'PhenotypeTask', '--phenotype', p_id, '--job',
str(the_job_id), '--owner', 'tester'
])
task = registered_pipelines[str(self.pipelinetype)]
matches = [task(pipeline=self.pipeline, job=self.job, start=n, solr_query=self.solr_query, batch=n)
for n in ranges]
return matches
except Exception as ex:
traceback.print_exc(file=sys.stderr)
jobs.update_job_status(str(self.job), util.conn_string, jobs.WARNING, ''.join(traceback.format_stack()))
print(ex)
return list()
def run(self):
run_pipeline(self.pipeline, self.pipelinetype, self.job, self.owner)
def complete(self):
status = jobs.get_job_status(str(self.job), util.conn_string)
return status['status'] == jobs.COMPLETED or status['status'] == jobs.WARNING or status[
'status'] == jobs.FAILURE
if __name__ == "__main__":
owner = "tester"
p_id = "1000"
the_job_id = data_access.create_new_job(
data_access.NlpJob(job_id=-1, name="Test Phenotype", description="Test Phenotype",
owner=owner, status=data_access.STARTED, date_ended=None,
phenotype_id=int(p_id), pipeline_id=-1, date_started=datetime.datetime.now(),
job_type='PHENOTYPE'), util.conn_string)
luigi.run(['PhenotypeTask', '--phenotype', p_id, '--job', str(the_job_id), '--owner', 'tester'])