def insert(self, db):
if not self.type or not self.sequence_list or not self.status or not self.model_name:
raise ValueError(
"Type, sequence_list, model_name, and status properties "
"must be filled in before calling insert.")
insert_sql = "insert into job(id, type, model_name, seq_id, status) values(%s, %s, %s, %s, %s)"
update_database(db, insert_sql, [
self.uuid, self.type, self.model_name, self.sequence_list,
self.status
])
def set_job_running(db, job_uuid):
"""
Set job to RUNNING state.
Requires job to be at NEW status.
:param db: DatabaseConnection: database to update
:param job_uuid: str: uuid of this job
"""
update_sql = "update job set status = %s where id = %s and status = %s"
rowcount = update_database(db, update_sql, [JobStatus.RUNNING, job_uuid, JobStatus.NEW])
if rowcount == 0:
raise ValueError("No job found for {} at status {}".format(job_uuid, JobStatus.NEW))
def set_job_complete(db, job_uuid):
"""
Set job to COMPLETE state.
Requires job to be at RUNNING status.
Updates the finished date/time.
:param db: DatabaseConnection: database to update
:param job_uuid: str: uuid of this job
"""
update_sql = "update job set status = %s, finished = CURRENT_TIMESTAMP where id = %s and status = %s"
rowcount = update_database(db, update_sql, [JobStatus.COMPLETE, job_uuid, JobStatus.RUNNING])
if rowcount == 0:
raise ValueError("No job found for {} at status {}".format(job_uuid, JobStatus.RUNNING))
def set_job_running(db, job_uuid):
"""
Set job to RUNNING state.
Requires job to be at NEW status.
:param db: DatabaseConnection: database to update
:param job_uuid: str: uuid of this job
"""
update_sql = "update job set status = %s where id = %s and status = %s"
rowcount = update_database(
db, update_sql, [JobStatus.RUNNING, job_uuid, JobStatus.NEW])
if rowcount == 0:
raise ValueError("No job found for {} at status {}".format(
job_uuid, JobStatus.NEW))
def set_job_as_error(db, job_uuid, error_message):
"""
Set job to ERROR state.
Updates the finished date/time.
:param db: DatabaseConnection: database to update
:param job_uuid: str: uuid of this job
:param error_message: str: error associated with the failure
"""
if not error_message:
raise ValueError("Missing required error_message.")
update_sql = "update job set status = %s, error_msg = %s, finished = CURRENT_TIMESTAMP where id = %s"
rowcount = update_database(db, update_sql, [JobStatus.ERROR, error_message, job_uuid])
if rowcount == 0:
raise ValueError("No job found for {}.".format(job_uuid))
def set_job_complete(db, job_uuid):
"""
Set job to COMPLETE state.
Requires job to be at RUNNING status.
Updates the finished date/time.
:param db: DatabaseConnection: database to update
:param job_uuid: str: uuid of this job
"""
update_sql = "update job set status = %s, finished = CURRENT_TIMESTAMP where id = %s and status = %s"
rowcount = update_database(
db, update_sql, [JobStatus.COMPLETE, job_uuid, JobStatus.RUNNING])
if rowcount == 0:
raise ValueError("No job found for {} at status {}".format(
job_uuid, JobStatus.RUNNING))
def set_job_as_error(db, job_uuid, error_message):
"""
Set job to ERROR state.
Updates the finished date/time.
:param db: DatabaseConnection: database to update
:param job_uuid: str: uuid of this job
:param error_message: str: error associated with the failure
"""
if not error_message:
raise ValueError("Missing required error_message.")
update_sql = "update job set status = %s, error_msg = %s, finished = CURRENT_TIMESTAMP where id = %s"
rowcount = update_database(db, update_sql,
[JobStatus.ERROR, error_message, job_uuid])
if rowcount == 0:
raise ValueError("No job found for {}.".format(job_uuid))
def insert(self, db):
if not self.type or not self.sequence_list or not self.status or not self.model_name:
raise ValueError("Type, sequence_list, model_name, and status properties "
"must be filled in before calling insert.")
insert_sql = "insert into job(id, type, model_name, seq_id, status) values(%s, %s, %s, %s, %s)"
update_database(db, insert_sql, [self.uuid, self.type, self.model_name, self.sequence_list, self.status])
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)
