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 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)