def get_jobs():
"""
Return a list of jobs with optional job_status filter.
request['job_status'] str: see customjob.JobStatus properties for values
:return: json response with 'result' array of jobs.
"""
job_status = request.args.get("job_status")
result = []
for job in CustomJob.find_jobs(get_db(), job_status):
result.append(job.get_dict())
return make_json_response({'result': result})
def get_jobs():
"""
Return a list of jobs with optional job_status filter.
request['job_status'] str: see customjob.JobStatus properties for values
:return: json response with 'result' array of jobs.
"""
job_status = request.args.get("job_status")
result = []
for job in CustomJob.find_jobs(get_db(), job_status):
result.append(job.get_dict())
return make_json_response({'result': 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)
