Python AsynchronousJobState.exit_code_file方法代码示例

# 需要导入模块: from galaxy.jobs.runners import AsynchronousJobState [as 别名]
# 或者: from galaxy.jobs.runners.AsynchronousJobState import exit_code_file [as 别名]
 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)

# 需要导入模块: from galaxy.jobs.runners import AsynchronousJobState [as 别名]
# 或者: from galaxy.jobs.runners.AsynchronousJobState import exit_code_file [as 别名]

#.........这里部分代码省略.........
        if self.app.config.pbs_application_server:
            pbs_ofile = self.app.config.pbs_application_server + ':' + ofile
            pbs_efile = self.app.config.pbs_application_server + ':' + efile
            output_files = [ str( o ) for o in output_fnames ]
            output_files.append(ecfile)
            stagein = self.get_stage_in_out( job_wrapper.get_input_fnames() + output_files, symlink=True )
            stageout = self.get_stage_in_out( output_files )
            attrs = [
                dict( name=pbs.ATTR_o, value=pbs_ofile ),
                dict( name=pbs.ATTR_e, value=pbs_efile ),
                dict( name=pbs.ATTR_stagein, value=stagein ),
                dict( name=pbs.ATTR_stageout, value=stageout ),
            ]
        # If not, we're using NFS
        else:
            attrs = [
                dict( name=pbs.ATTR_o, value=ofile ),
                dict( name=pbs.ATTR_e, value=efile ),
            ]

        # define PBS job options
        attrs.append( dict( name=pbs.ATTR_N, value=str( "%s_%s_%s" % ( job_wrapper.job_id, job_wrapper.tool.id, job_wrapper.user ) ) ) )
        job_attrs = pbs.new_attropl( len( attrs ) + len( pbs_options ) )
        for i, attr in enumerate( attrs + pbs_options ):
            job_attrs[i].name = attr['name']
            job_attrs[i].value = attr['value']
            if 'resource' in attr:
                job_attrs[i].resource = attr['resource']
        exec_dir = os.path.abspath( job_wrapper.working_directory )

        # write the job script
        if self.app.config.pbs_stage_path != '':
            # touch the ecfile so that it gets staged
            with open(ecfile, 'a'):
                os.utime(ecfile, None)

            stage_commands = pbs_symlink_template % (
                " ".join( job_wrapper.get_input_fnames() + output_files ),
                self.app.config.pbs_stage_path,
                exec_dir,
            )
        else:
            stage_commands = ''

        env_setup_commands = [ stage_commands ]
        script = self.get_job_file(job_wrapper, exit_code_path=ecfile, env_setup_commands=env_setup_commands)
        job_file = "%s/%s.sh" % (self.app.config.cluster_files_directory, job_wrapper.job_id)
        self.write_executable_script( job_file, script )
        # job was deleted while we were preparing it
        if job_wrapper.get_state() == model.Job.states.DELETED:
            log.debug( "Job %s deleted by user before it entered the PBS queue" % job_wrapper.job_id )
            pbs.pbs_disconnect(c)
            if job_wrapper.cleanup_job in ( "always", "onsuccess" ):
                self.cleanup( ( ofile, efile, ecfile, job_file ) )
                job_wrapper.cleanup()
            return

        # submit
        # The job tag includes the job and the task identifier
        # (if a TaskWrapper was passed in):
        galaxy_job_id = job_wrapper.get_id_tag()
        log.debug("(%s) submitting file %s" % ( galaxy_job_id, job_file ) )

        tries = 0
        while tries < 5:
            job_id = pbs.pbs_submit(c, job_attrs, job_file, pbs_queue_name, None)
            tries += 1
            if job_id:
                pbs.pbs_disconnect(c)
                break
            errno, text = pbs.error()
            log.warning( "(%s) pbs_submit failed (try %d/5), PBS error %d: %s" % (galaxy_job_id, tries, errno, text) )
            time.sleep(2)
        else:
            log.error( "(%s) All attempts to submit job failed" % galaxy_job_id )
            job_wrapper.fail( "Unable to run this job due to a cluster error, please retry it later" )
            return

        if pbs_queue_name is None:
            log.debug("(%s) queued in default queue as %s" % (galaxy_job_id, job_id) )
        else:
            log.debug("(%s) queued in %s queue as %s" % (galaxy_job_id, pbs_queue_name, job_id) )

        # persist destination
        job_wrapper.set_job_destination( job_destination, job_id )

        # Store PBS related state information for job
        job_state = AsynchronousJobState()
        job_state.job_wrapper = job_wrapper
        job_state.job_id = job_id
        job_state.job_file = job_file
        job_state.output_file = ofile
        job_state.error_file = efile
        job_state.exit_code_file = ecfile
        job_state.old_state = 'N'
        job_state.running = False
        job_state.job_destination = job_destination

        # Add to our 'queue' of jobs to monitor
        self.monitor_queue.put( job_state )