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)
