def put_job(job_uuid):
"""
Update job status.
Secured via apache config: production/imads.conf.
request['job_status'] str: value from customjob.JobStatus properties
:param job_uuid: str: uuid of the job we want to update status
:return: json response
"""
db = get_db()
(job_status,) = get_required_json_props(request, ["job_status"])
error_message = request.get_json().get("error_message")
if job_status == JobStatus.RUNNING:
CustomJob.set_job_running(db, job_uuid)
elif job_status == JobStatus.COMPLETE:
CustomJob.set_job_complete(db, job_uuid)
elif job_status == JobStatus.ERROR:
CustomJob.set_job_as_error(db, job_uuid, error_message)
else:
raise ValueError("Invalid job status:{} for job:{}".format(job_status, job_uuid))
return json_ok_result()
def put_job(job_uuid):
"""
Update job status.
Secured via apache config: production/tfpredictions.conf.
request['job_status'] str: value from customjob.JobStatus properties
:param job_uuid: str: uuid of the job we want to update status
:return: json response
"""
db = get_db()
(job_status, ) = get_required_json_props(request, ["job_status"])
error_message = request.get_json().get("error_message")
if job_status == JobStatus.RUNNING:
CustomJob.set_job_running(db, job_uuid)
elif job_status == JobStatus.COMPLETE:
CustomJob.set_job_complete(db, job_uuid)
elif job_status == JobStatus.ERROR:
CustomJob.set_job_as_error(db, job_uuid, error_message)
else:
raise ValueError("Invalid job status:{} for job:{}".format(
job_status, job_uuid))
return json_ok_result()
def test_customjob(self):
FASTA_DATA1 = """>stuff\nAAACCCGGGGTT"""
db = create_db_connection(TestWithPostgres.config.dbconfig)
update_database(db, """
delete from custom_result_row;
delete from custom_result;
delete from job;
delete from sequence_list_item;
delete from sequence_list;
""", [])
# start out finding no jobs
jobs = CustomJob.find_jobs(db, None)
self.assertEqual(len(jobs), 0)
# create a new job that should be NEW status
sequence_list = SequenceList.create_with_content_and_title(db, FASTA_DATA1, "somelist")
job_uuid = CustomJob.create_job(db, DataType.PREDICTION, sequence_list, model_name="E2f1").uuid
job = CustomJob.read_job(db, job_uuid)
self.assertEqual(job_uuid, job.uuid)
self.assertEqual(JobStatus.NEW, job.status)
self.assertEqual(DataType.PREDICTION, job.type)
self.assertEqual(sequence_list, job.sequence_list)
self.assertIsNotNone(job.created)
self.assertIsNone(job.finished)
# find NEW job without filters
jobs = CustomJob.find_jobs(db, None)
self.assertEqual(len(jobs), 1)
self.assertEqual(jobs[0].uuid, job_uuid)
# find no for RUNNING jobs
jobs = CustomJob.find_jobs(db, JobStatus.RUNNING)
self.assertEqual(len(jobs), 0)
# find 1 for NEW jobs
jobs = CustomJob.find_jobs(db, JobStatus.NEW)
self.assertEqual(len(jobs), 1)
# Jobs can be set to running only once (when in NEW state)
CustomJob.set_job_running(db, job_uuid)
job = CustomJob.read_job(db, job_uuid)
self.assertEqual(JobStatus.RUNNING, job.status)
self.assertIsNone(job.finished)
# Disallow setting a job running twice (prevents two workers working on the same job)
with self.assertRaises(ValueError):
CustomJob.set_job_running(db, job_uuid)
# find 0 for NEW jobs
jobs = CustomJob.find_jobs(db, JobStatus.NEW)
self.assertEqual(len(jobs), 0)
# Jobs can be set to complete from RUNNING state
CustomJob.set_job_complete(db, job_uuid)
job = CustomJob.read_job(db, job_uuid)
self.assertEqual(JobStatus.COMPLETE, job.status)
self.assertIsNotNone(job.finished)
# find 0 for NEW jobs
jobs = CustomJob.find_jobs(db, JobStatus.NEW)
self.assertEqual(len(jobs), 0)
# Jobs can be set to complete from ERROR state
CustomJob.set_job_as_error(db, job_uuid, "Something failed.")
job = CustomJob.read_job(db, job_uuid)
self.assertEqual(JobStatus.ERROR, job.status)
self.assertEqual("Something failed.", job.error_msg)
self.assertIsNotNone(job.finished)
# find 0 for NEW jobs
jobs = CustomJob.find_jobs(db, JobStatus.NEW)
self.assertEqual(len(jobs), 0)
def test_customjob(self):
FASTA_DATA1 = """>stuff\nAAACCCGGGGTT"""
db = create_db_connection(TestWithPostgres.config.dbconfig)
update_database(db, """
delete from custom_result_row;
delete from custom_result;
delete from job;
delete from sequence_list_item;
delete from sequence_list;
""", [])
# start out finding no jobs
jobs = CustomJob.find_jobs(db, None)
self.assertEqual(len(jobs), 0)
# create a new job that should be NEW status
sequence_list = SequenceList.create_with_content_and_title(db, FASTA_DATA1, "somelist")
job_uuid = CustomJob.create_job(db, DataType.PREDICTION, sequence_list, model_name="E2f1").uuid
job = CustomJob.read_job(db, job_uuid)
self.assertEqual(job_uuid, job.uuid)
self.assertEqual(JobStatus.NEW, job.status)
self.assertEqual(DataType.PREDICTION, job.type)
self.assertEqual(sequence_list, job.sequence_list)
self.assertIsNotNone(job.created)
self.assertIsNone(job.finished)
# find NEW job without filters
jobs = CustomJob.find_jobs(db, None)
self.assertEqual(len(jobs), 1)
self.assertEqual(jobs[0].uuid, job_uuid)
# find no for RUNNING jobs
jobs = CustomJob.find_jobs(db, JobStatus.RUNNING)
self.assertEqual(len(jobs), 0)
# find 1 for NEW jobs
jobs = CustomJob.find_jobs(db, JobStatus.NEW)
self.assertEqual(len(jobs), 1)
# Jobs can be set to running only once (when in NEW state)
CustomJob.set_job_running(db, job_uuid)
job = CustomJob.read_job(db, job_uuid)
self.assertEqual(JobStatus.RUNNING, job.status)
self.assertIsNone(job.finished)
# Disallow setting a job running twice (prevents two workers working on the same job)
with self.assertRaises(ValueError):
CustomJob.set_job_running(db, job_uuid)
# find 0 for NEW jobs
jobs = CustomJob.find_jobs(db, JobStatus.NEW)
self.assertEqual(len(jobs), 0)
# Jobs can be set to complete from RUNNING state
CustomJob.set_job_complete(db, job_uuid)
job = CustomJob.read_job(db, job_uuid)
self.assertEqual(JobStatus.COMPLETE, job.status)
self.assertIsNotNone(job.finished)
# find 0 for NEW jobs
jobs = CustomJob.find_jobs(db, JobStatus.NEW)
self.assertEqual(len(jobs), 0)
# Jobs can be set to complete from ERROR state
CustomJob.set_job_as_error(db, job_uuid, "Something failed.")
job = CustomJob.read_job(db, job_uuid)
self.assertEqual(JobStatus.ERROR, job.status)
self.assertEqual("Something failed.", job.error_msg)
self.assertIsNotNone(job.finished)
# find 0 for NEW jobs
jobs = CustomJob.find_jobs(db, JobStatus.NEW)
self.assertEqual(len(jobs), 0)
