This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.jobs.runners.cli

Job control via a command line interface (e.g. qsub/qstat), possibly over a remote connection (e.g. ssh).

import logging
import time

from galaxy import model
from galaxy.jobs import JobDestination
from galaxy.jobs.runners import (
from galaxy.util import asbool
from .util.cli import CliInterface, split_params

log = logging.getLogger(__name__)

__all__ = ('ShellJobRunner', )


[docs]class ShellJobRunner(AsynchronousJobRunner): """ Job runner backed by a finite pool of worker threads. FIFO scheduling """ runner_name = "ShellRunner"
[docs] def __init__(self, app, nworkers): """Start the job runner """ super().__init__(app, nworkers) self.cli_interface = CliInterface() self._init_monitor_thread() self._init_worker_threads()
[docs] def get_cli_plugins(self, shell_params, job_params): return self.cli_interface.get_plugins(shell_params, job_params)
[docs] def url_to_destination(self, url): params = {} shell_params, job_params = url.split('/')[2:4] # split 'foo=bar&baz=quux' into { 'foo' : 'bar', 'baz' : 'quux' } shell_params = {'shell_' + k: v for k, v in [kv.split('=', 1) for kv in shell_params.split('&')]} job_params = {'job_' + k: v for k, v in [kv.split('=', 1) for kv in job_params.split('&')]} params.update(shell_params) params.update(job_params) log.debug("Converted URL '{}' to destination runner=cli, params={}".format(url, params)) # Create a dynamic JobDestination return JobDestination(runner='cli', params=params)
[docs] def parse_destination_params(self, params): return split_params(params)
[docs] def queue_job(self, job_wrapper): """Create job script and submit it to the DRM""" # prepare the job include_metadata = asbool(job_wrapper.job_destination.params.get("embed_metadata_in_job", DEFAULT_EMBED_METADATA_IN_JOB)) if not self.prepare_job(job_wrapper, include_metadata=include_metadata): return # Get shell and job execution interface job_destination = job_wrapper.job_destination shell_params, job_params = self.parse_destination_params(job_destination.params) shell, job_interface = self.get_cli_plugins(shell_params, job_params) # wrapper.get_id_tag() instead of job_id for compatibility with TaskWrappers. galaxy_id_tag = job_wrapper.get_id_tag() # define job attributes ajs = AsynchronousJobState(files_dir=job_wrapper.working_directory, job_wrapper=job_wrapper) job_file_kwargs = job_interface.job_script_kwargs(ajs.output_file, ajs.error_file, ajs.job_name) script = self.get_job_file( job_wrapper, exit_code_path=ajs.exit_code_file, shell=job_wrapper.shell, **job_file_kwargs ) try: self.write_executable_script(ajs.job_file, script) except Exception: log.exception("(%s) failure writing job script" % galaxy_id_tag) job_wrapper.fail("failure preparing job script", exception=True) return # job was deleted while we were preparing it if job_wrapper.get_state() == model.Job.states.DELETED: log.info("(%s) Job deleted by user before it entered the queue" % galaxy_id_tag) if job_wrapper.cleanup_job in ("always", "onsuccess"): job_wrapper.cleanup() return log.debug("({}) submitting file: {}".format(galaxy_id_tag, ajs.job_file)) returncode, stdout = self.submit(shell, job_interface, ajs.job_file, galaxy_id_tag, retry=MAX_SUBMIT_RETRY) if returncode != 0: job_wrapper.fail("failure submitting job") return # Some job runners return something like 'Submitted batch job XXXX' # Strip and split to get job ID. external_job_id = stdout.strip().split()[-1] if not external_job_id: log.error('(%s) submission did not return a job identifier, failing job' % galaxy_id_tag) job_wrapper.fail("failure submitting job") return log.info("({}) queued with identifier: {}".format(galaxy_id_tag, external_job_id)) # store runner information for tracking if Galaxy restarts job_wrapper.set_external_id(external_job_id) # Store state information for job ajs.job_id = external_job_id ajs.old_state = 'new' ajs.job_destination = job_destination # Add to our 'queue' of jobs to monitor self.monitor_queue.put(ajs)
[docs] def submit(self, shell, job_interface, job_file, galaxy_id_tag, retry=MAX_SUBMIT_RETRY, timeout=10): """ Handles actual job script submission. If submission fails will retry `retry` time with a timeout of `timeout` seconds. Retuns the returncode of the submission and the stdout, which contains the external job_id. """ cmd_out = shell.execute(job_interface.submit(job_file)) if cmd_out.returncode == 0: return cmd_out.returncode, cmd_out.stdout stdout = '({}) submission failed (stdout): {}'.format(galaxy_id_tag, cmd_out.stdout) stderr = '({}) submission failed (stderr): {}'.format(galaxy_id_tag, cmd_out.stderr) if retry > 0: log.debug("%s, retrying in %s seconds", stdout, timeout) log.debug("%s, retrying in %s seconds", stderr, timeout) time.sleep(timeout) return self.submit(shell, job_interface, job_file, galaxy_id_tag, retry=retry - 1, timeout=timeout) else: log.error(stdout) log.error(stderr) return cmd_out.returncode, cmd_out.stdout
[docs] def check_watched_items(self): """ Called by the monitor thread to look at each watched job and deal with state changes. """ new_watched = [] job_states = self.__get_job_states() for ajs in self.watched: external_job_id = ajs.job_id id_tag = ajs.job_wrapper.get_id_tag() old_state = ajs.old_state state = job_states.get(external_job_id, None) if state is None: if ajs.job_wrapper.get_state() == model.Job.states.DELETED: continue log.debug("({}/{}) job not found in batch state check".format(id_tag, external_job_id)) shell_params, job_params = self.parse_destination_params(ajs.job_destination.params) shell, job_interface = self.get_cli_plugins(shell_params, job_params) cmd_out = shell.execute(job_interface.get_single_status(external_job_id)) state = job_interface.parse_single_status(cmd_out.stdout, external_job_id) if not state == model.Job.states.OK: log.warning('({}/{}) job not found in batch state check, but found in individual state check'.format(id_tag, external_job_id)) if state != old_state: log.debug("({}/{}) state change: from {} to {}".format(id_tag, external_job_id, old_state, state)) if not state == model.Job.states.OK: # No need to change_state when the state is OK, this will be handled by `self.finish_job` ajs.job_wrapper.change_state(state) if state == model.Job.states.ERROR: # Try to find out the reason for exiting self.__handle_out_of_memory(ajs, external_job_id) self.work_queue.put((self.mark_as_failed, ajs)) # Don't add the job to the watched items once it fails, deals with https://github.com/galaxyproject/galaxy/issues/7820 continue if state == model.Job.states.RUNNING and not ajs.running: ajs.running = True ajs.old_state = state if state == model.Job.states.OK: external_metadata = not asbool(ajs.job_wrapper.job_destination.params.get("embed_metadata_in_job", DEFAULT_EMBED_METADATA_IN_JOB)) if external_metadata: self.work_queue.put((self.handle_metadata_externally, ajs)) log.debug('({}/{}) job execution finished, running job wrapper finish method'.format(id_tag, external_job_id)) self.work_queue.put((self.finish_job, ajs)) else: new_watched.append(ajs) # Replace the watch list with the updated version self.watched = new_watched
[docs] def handle_metadata_externally(self, ajs): self._handle_metadata_externally(ajs.job_wrapper, resolve_requirements=True)
def __handle_out_of_memory(self, ajs, external_job_id): shell_params, job_params = self.parse_destination_params(ajs.job_destination.params) shell, job_interface = self.get_cli_plugins(shell_params, job_params) cmd_out = shell.execute(job_interface.get_failure_reason(external_job_id)) if cmd_out is not None: if job_interface.parse_failure_reason(cmd_out.stdout, external_job_id) \ == JobState.runner_states.MEMORY_LIMIT_REACHED: ajs.runner_state = JobState.runner_states.MEMORY_LIMIT_REACHED ajs.fail_message = "Tool failed due to insufficient memory. Try with more memory." def __get_job_states(self): job_destinations = {} job_states = {} # unique the list of destinations for ajs in self.watched: if ajs.job_destination.id not in job_destinations: job_destinations[ajs.job_destination.id] = dict(job_destination=ajs.job_destination, job_ids=[ajs.job_id]) else: job_destinations[ajs.job_destination.id]['job_ids'].append(ajs.job_id) # check each destination for the listed job ids for v in job_destinations.values(): job_destination = v['job_destination'] job_ids = v['job_ids'] shell_params, job_params = self.parse_destination_params(job_destination.params) shell, job_interface = self.get_cli_plugins(shell_params, job_params) cmd_out = shell.execute(job_interface.get_status(job_ids)) assert cmd_out.returncode == 0, cmd_out.stderr job_states.update(job_interface.parse_status(cmd_out.stdout, job_ids)) return job_states
[docs] def stop_job(self, job_wrapper): """Attempts to delete a dispatched job""" job = job_wrapper.get_job() try: shell_params, job_params = self.parse_destination_params(job.destination_params) shell, job_interface = self.get_cli_plugins(shell_params, job_params) cmd_out = shell.execute(job_interface.delete(job.job_runner_external_id)) assert cmd_out.returncode == 0, cmd_out.stderr log.debug("({}/{}) Terminated at user's request".format(job.id, job.job_runner_external_id)) except Exception as e: log.debug("({}/{}) User killed running job, but error encountered during termination: {}".format(job.id, job.job_runner_external_id, e))
[docs] 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.command_line ajs.job_wrapper = job_wrapper ajs.job_destination = job_wrapper.job_destination if job.state == model.Job.states.RUNNING: log.debug("({}/{}) is still in running state, adding to the runner monitor queue".format(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("({}/{}) is still in queued state, adding to the runner monitor queue".format(job.id, job.job_runner_external_id)) ajs.old_state = model.Job.states.QUEUED ajs.running = False self.monitor_queue.put(ajs)