def recover(self, job, job_wrapper): """Recovers jobs stuck in the queued/running state when Galaxy started""" job_id = job.get_job_runner_external_id() pbs_job_state = AsynchronousJobState() pbs_job_state.output_file = "%s/%s.o" % ( self.app.config.cluster_files_directory, job.id) pbs_job_state.error_file = "%s/%s.e" % ( self.app.config.cluster_files_directory, job.id) pbs_job_state.exit_code_file = "%s/%s.ec" % ( self.app.config.cluster_files_directory, job.id) pbs_job_state.job_file = "%s/%s.sh" % ( self.app.config.cluster_files_directory, job.id) pbs_job_state.job_id = str(job_id) pbs_job_state.runner_url = job_wrapper.get_job_runner_url() pbs_job_state.job_destination = job_wrapper.job_destination job_wrapper.command_line = job.command_line pbs_job_state.job_wrapper = job_wrapper if job.state == model.Job.states.RUNNING: log.debug( "(%s/%s) is still in running state, adding to the PBS queue" % (job.id, job.get_job_runner_external_id())) pbs_job_state.old_state = 'R' pbs_job_state.running = True self.monitor_queue.put(pbs_job_state) elif job.state == model.Job.states.QUEUED: log.debug( "(%s/%s) is still in PBS queued state, adding to the PBS queue" % (job.id, job.get_job_runner_external_id())) pbs_job_state.old_state = 'Q' pbs_job_state.running = False self.monitor_queue.put(pbs_job_state)
def recover(self, job, job_wrapper): """Recovers jobs stuck in the queued/running state when Galaxy started""" job_id = job.get_job_runner_external_id() pbs_job_state = AsynchronousJobState() pbs_job_state.output_file = "%s/%s.o" % (self.app.config.cluster_files_directory, job.id) pbs_job_state.error_file = "%s/%s.e" % (self.app.config.cluster_files_directory, job.id) pbs_job_state.exit_code_file = "%s/%s.ec" % (self.app.config.cluster_files_directory, job.id) pbs_job_state.job_file = "%s/%s.sh" % (self.app.config.cluster_files_directory, job.id) pbs_job_state.job_id = str(job_id) pbs_job_state.runner_url = job_wrapper.get_job_runner_url() pbs_job_state.job_destination = job_wrapper.job_destination job_wrapper.command_line = job.command_line pbs_job_state.job_wrapper = job_wrapper if job.state == model.Job.states.RUNNING: log.debug( "(%s/%s) is still in running state, adding to the PBS queue" % (job.id, job.get_job_runner_external_id()) ) pbs_job_state.old_state = "R" pbs_job_state.running = True self.monitor_queue.put(pbs_job_state) elif job.state == model.Job.states.QUEUED: log.debug( "(%s/%s) is still in PBS queued state, adding to the PBS queue" % (job.id, job.get_job_runner_external_id()) ) pbs_job_state.old_state = "Q" pbs_job_state.running = False self.monitor_queue.put(pbs_job_state)
def _job_state(self, job, job_wrapper): job_state = AsynchronousJobState() # TODO: Determine why this is set when using normal message queue updates # but not CLI submitted MQ updates... raw_job_id = job.get_job_runner_external_id() or job_wrapper.job_id job_state.job_id = str(raw_job_id) job_state.runner_url = job_wrapper.get_job_runner_url() job_state.job_destination = job_wrapper.job_destination job_state.job_wrapper = job_wrapper return job_state
def _job_state( self, job, job_wrapper ): job_state = AsynchronousJobState() # TODO: Determine why this is set when using normal message queue updates # but not CLI submitted MQ updates... raw_job_id = job.get_job_runner_external_id() or job_wrapper.job_id job_state.job_id = str( raw_job_id ) job_state.runner_url = job_wrapper.get_job_runner_url() job_state.job_destination = job_wrapper.job_destination job_state.job_wrapper = job_wrapper return job_state
def recover( self, job, job_wrapper ): """Recovers jobs stuck in the queued/running state when Galaxy started""" job_state = AsynchronousJobState() job_state.job_id = str( job.get_job_runner_external_id() ) job_state.runner_url = job_wrapper.get_job_runner_url() job_state.job_destination = job_wrapper.job_destination job_wrapper.command_line = job.get_command_line() job_state.job_wrapper = job_wrapper state = job.get_state() if state in [model.Job.states.RUNNING, model.Job.states.QUEUED]: log.debug( "(LWR/%s) is still in running state, adding to the LWR queue" % ( job.get_id()) ) job_state.old_state = True job_state.running = state == model.Job.states.RUNNING self.monitor_queue.put( job_state )
def recover(self, job, job_wrapper): """Recovers jobs stuck in the queued/running state when Galaxy started""" job_state = AsynchronousJobState() job_state.job_id = str(job.get_job_runner_external_id()) job_state.runner_url = job_wrapper.get_job_runner_url() job_state.job_destination = job_wrapper.job_destination job_wrapper.command_line = job.get_command_line() job_state.job_wrapper = job_wrapper state = job.get_state() if state in [model.Job.states.RUNNING, model.Job.states.QUEUED]: log.debug( "(LWR/%s) is still in running state, adding to the LWR queue" % (job.get_id())) job_state.old_state = True job_state.running = state == model.Job.states.RUNNING self.monitor_queue.put(job_state)