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()
log.debug("k8s trying to recover job: " + job_id)
if job_id is None:
self.put(job_wrapper)
return
ajs = AsynchronousJobState(files_dir=job_wrapper.working_directory,
job_wrapper=job_wrapper)
ajs.job_id = str(job_id)
ajs.command_line = job.command_line
ajs.job_wrapper = job_wrapper
ajs.job_destination = job_wrapper.job_destination
if job.state == model.Job.states.RUNNING:
log.debug(
"(%s/%s) is still in running state, adding to the runner monitor queue"
% (job.id, job.job_runner_external_id))
ajs.old_state = model.Job.states.RUNNING
ajs.running = True
self.monitor_queue.put(ajs)
elif job.state == model.Job.states.QUEUED:
log.debug(
"(%s/%s) is still in queued state, adding to the runner monitor queue"
% (job.id, job.job_runner_external_id))
ajs.old_state = model.Job.states.QUEUED
ajs.running = False
self.monitor_queue.put(ajs)
def recover(self, job, job_wrapper):
msg = ('(name!r/runner!r) is still in {state!s} state, adding to'
' the runner monitor queue')
job_id = job.get_job_runner_external_id()
ajs = AsynchronousJobState(files_dir=job_wrapper.working_directory,
job_wrapper=job_wrapper)
ajs.job_id = self.JOB_NAME_PREFIX + str(job_id)
ajs.command_line = job.command_line
ajs.job_wrapper = job_wrapper
ajs.job_destination = job_wrapper.job_destination
if job.state in (model.Job.states.RUNNING, model.Job.states.STOPPED):
LOGGER.debug(
msg.format(name=job.id,
runner=job.job_runner_external_id,
state=job.state))
ajs.old_state = model.Job.states.RUNNING
ajs.running = True
self.monitor_queue.put(ajs)
elif job.state == model.Job.states.QUEUED:
LOGGER.debug(
msg.format(name=job.id,
runner=job.job_runner_external_id,
state='queued'))
ajs.old_state = model.Job.states.QUEUED
ajs.running = False
self.monitor_queue.put(ajs)
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()
if job_id is None:
self.put(job_wrapper)
return
ajs = AsynchronousJobState(files_dir=job_wrapper.working_directory,
job_wrapper=job_wrapper)
ajs.job_id = str(job_id)
ajs.command_line = job.get_command_line()
ajs.job_wrapper = job_wrapper
ajs.job_destination = job_wrapper.job_destination
self.__old_state_paths(ajs)
if job.state == model.Job.states.RUNNING:
log.debug(
"(%s/%s) is still in running state, adding to the DRM queue" %
(job.get_id(), job.get_job_runner_external_id()))
ajs.old_state = drmaa.JobState.RUNNING
ajs.running = True
self.monitor_queue.put(ajs)
elif job.get_state() == model.Job.states.QUEUED:
log.debug(
"(%s/%s) is still in DRM queued state, adding to the DRM queue"
% (job.get_id(), job.get_job_runner_external_id()))
ajs.old_state = drmaa.JobState.QUEUED_ACTIVE
ajs.running = False
self.monitor_queue.put(ajs)
def recover(self, job, job_wrapper):
"""Recovers jobs stuck in the queued/running state when Galaxy started"""
# TODO this needs to be implemented to override unimplemented base method
job_id = job.get_job_runner_external_id()
log.debug("k8s trying to recover job: " + job_id)
if job_id is None:
self.put(job_wrapper)
return
ajs = AsynchronousJobState(files_dir=job_wrapper.working_directory, job_wrapper=job_wrapper)
ajs.job_id = str(job_id)
ajs.command_line = job.command_line
ajs.job_wrapper = job_wrapper
ajs.job_destination = job_wrapper.job_destination
if job.state == model.Job.states.RUNNING:
log.debug("(%s/%s) is still in running state, adding to the runner monitor queue" % (
job.id, job.job_runner_external_id))
ajs.old_state = model.Job.states.RUNNING
ajs.running = True
self.monitor_queue.put(ajs)
elif job.state == model.Job.states.QUEUED:
log.debug("(%s/%s) is still in queued state, adding to the runner monitor queue" % (
job.id, job.job_runner_external_id))
ajs.old_state = model.Job.states.QUEUED
ajs.running = False
self.monitor_queue.put(ajs)
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()
if job_id is None:
self.put( job_wrapper )
return
ajs = AsynchronousJobState( files_dir=job_wrapper.working_directory, job_wrapper=job_wrapper )
ajs.job_id = str( job_id )
ajs.command_line = job.get_command_line()
ajs.job_wrapper = job_wrapper
ajs.job_destination = job_wrapper.job_destination
if job.state == model.Job.states.RUNNING:
log.debug( "(%s/%s) is still in running state, adding to the DRM queue" % ( job.get_id(), job.get_job_runner_external_id() ) )
ajs.old_state = drmaa.JobState.RUNNING
ajs.running = True
self.monitor_queue.put( ajs )
elif job.get_state() == model.Job.states.QUEUED:
log.debug( "(%s/%s) is still in DRM queued state, adding to the DRM queue" % ( job.get_id(), job.get_job_runner_external_id() ) )
ajs.old_state = drmaa.JobState.QUEUED_ACTIVE
ajs.running = False
self.monitor_queue.put( ajs )
def recover(self, job, job_wrapper):
msg = ('(name!r/runner!r) is still in {state!s} state, adding to'
' the runner monitor queue')
job_id = job.get_job_runner_external_id()
ajs = AsynchronousJobState(files_dir=job_wrapper.working_directory,
job_wrapper=job_wrapper)
ajs.job_id = self.JOB_NAME_PREFIX + str(job_id)
ajs.command_line = job.command_line
ajs.job_wrapper = job_wrapper
ajs.job_destination = job_wrapper.job_destination
if job.state == model.Job.states.RUNNING:
LOGGER.debug(msg.format(
name=job.id, runner=job.job_runner_external_id,
state='running'))
ajs.old_state = model.Job.states.RUNNING
ajs.running = True
self.monitor_queue.put(ajs)
elif job.state == model.Job.states.QUEUED:
LOGGER.debug(msg.format(
name=job.id, runner=job.job_runner_external_id,
state='queued'))
ajs.old_state = model.Job.states.QUEUED
ajs.running = False
self.monitor_queue.put(ajs)
