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A fake job runner for testing the walltime resubmission feature committed in https://bitbucket.org/galaxy/galaxy-central/commits/7b209e06ddb944e953d340754439f4e3e5dc339d
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<?xml version="1.0"?> | |
<job_conf> | |
<plugins> | |
<plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="8"/> | |
<plugin id="walltime" type="runner" load="galaxy.jobs.runners.walltime:WalltimeJobRunner" workers="4"/> | |
</plugins> | |
<handlers default="main"> | |
<handler id="main"/> | |
</handlers> | |
<destinations default="short"> | |
<destination id="short" runner="walltime"> | |
<resubmit condition="walltime_reached" destination="long" /> | |
<resubmit condition="memory_limit_reached" destination="long" /> | |
</destination> | |
<destination id="long" runner="local"/> | |
</destinations> | |
<tools> | |
<tool id="upload1" destination="long"/> | |
</tools> | |
</job_conf> |
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import time | |
import random | |
import logging | |
from galaxy import model | |
from galaxy.jobs.runners import AsynchronousJobState, AsynchronousJobRunner | |
log = logging.getLogger( __name__ ) | |
__all__ = [ 'WalltimeJobRunner' ] | |
class WalltimeJobRunner( AsynchronousJobRunner ): | |
runner_name = "WalltimeRunner" | |
def __init__( self, app, nworkers, **kwargs ): | |
"""Start the job runner""" | |
self.step_delay = int(kwargs.get( 'step_delay', 1 )) | |
super( WalltimeJobRunner, self ).__init__( app, nworkers, **kwargs ) | |
self._init_monitor_thread() | |
self._init_worker_threads() | |
self.current_job_id = 0 | |
def queue_job( self, job_wrapper ): | |
ajs = AsynchronousJobState( files_dir=job_wrapper.working_directory, job_wrapper=job_wrapper, job_name='walltime_job' ) | |
ajs.job_id = self.current_job_id | |
ajs.old_state = 'new' | |
ajs.job_destination = job_wrapper.job_destination | |
self.current_job_id += 1 | |
log.debug( '(%s) Job queued with external id %s', job_wrapper.get_id_tag(), ajs.job_id ) | |
self.monitor_queue.put( ajs ) | |
def check_watched_items( self ): | |
new_watched = [] | |
time.sleep( self.step_delay ) | |
for ajs in self.watched: | |
log.debug( '(%s/%s) State check, last state was: %s', ajs.job_wrapper.get_id_tag(), ajs.job_id, ajs.old_state ) | |
if ajs.old_state == model.Job.states.NEW: | |
log.debug( '(%s/%s) Job state changed to queued', ajs.job_wrapper.get_id_tag(), ajs.job_id ) | |
ajs.job_wrapper.change_state( model.Job.states.QUEUED ) | |
ajs.old_state = model.Job.states.QUEUED | |
new_watched.append( ajs ) | |
elif ajs.old_state == model.Job.states.QUEUED: | |
log.debug( '(%s/%s) Job state changed to running', ajs.job_wrapper.get_id_tag(), ajs.job_id ) | |
ajs.running = True | |
ajs.job_wrapper.change_state( model.Job.states.RUNNING ) | |
ajs.old_state = model.Job.states.RUNNING | |
new_watched.append( ajs ) | |
elif ajs.old_state == model.Job.states.RUNNING: | |
log.debug( '(%s/%s) Job state changed to failed', ajs.job_wrapper.get_id_tag(), ajs.job_id ) | |
ajs.stop_job = False | |
if random.randint(0,1): | |
ajs.fail_message = "Walltime reached" | |
ajs.runner_state = ajs.runner_states.WALLTIME_REACHED | |
else: | |
ajs.fail_message = "Memory exhausted" | |
ajs.runner_state = ajs.runner_states.MEMORY_LIMIT_REACHED | |
self.work_queue.put( ( self.fail_job, ajs ) ) | |
self.watched = new_watched |
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Update to also test the MEMORY_LIMIT_REACHED state.