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Source code for galaxy.jobs.runners
"""
Base classes for job runner plugins.
"""
import datetime
import logging
import os
import string
import subprocess
import threading
import time
from six.moves.queue import (
Empty,
Queue
)
import galaxy.jobs
from galaxy import model
from galaxy.jobs.command_factory import build_command
from galaxy.jobs.output_checker import DETECTED_JOB_STATE
from galaxy.jobs.runners.util.env import env_to_statement
from galaxy.jobs.runners.util.job_script import (
job_script,
write_script
)
from galaxy.util import (
DATABASE_MAX_STRING_SIZE,
ExecutionTimer,
in_directory,
ParamsWithSpecs,
shrink_stream_by_size
)
from galaxy.util.bunch import Bunch
from galaxy.util.monitors import Monitors
from .state_handler_factory import build_state_handlers
log = logging.getLogger(__name__)
STOP_SIGNAL = object()
JOB_RUNNER_PARAMETER_UNKNOWN_MESSAGE = "Invalid job runner parameter for this plugin: %s"
JOB_RUNNER_PARAMETER_MAP_PROBLEM_MESSAGE = "Job runner parameter '%s' value '%s' could not be converted to the correct type"
JOB_RUNNER_PARAMETER_VALIDATION_FAILED_MESSAGE = "Job runner parameter %s failed validation"
GALAXY_LIB_ADJUST_TEMPLATE = """GALAXY_LIB="%s"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi;"""
GALAXY_VENV_TEMPLATE = """GALAXY_VIRTUAL_ENV="%s"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi;"""
[docs]class RunnerParams(ParamsWithSpecs):
def _param_unknown_error(self, name):
raise Exception(JOB_RUNNER_PARAMETER_UNKNOWN_MESSAGE % name)
def _param_map_error(self, name, value):
raise Exception(JOB_RUNNER_PARAMETER_MAP_PROBLEM_MESSAGE % (name, value))
def _param_vaildation_error(self, name, value):
raise Exception(JOB_RUNNER_PARAMETER_VALIDATION_FAILED_MESSAGE % name)
[docs]class BaseJobRunner(object):
DEFAULT_SPECS = dict(recheck_missing_job_retries=dict(map=int, valid=lambda x: x >= 0, default=0))
[docs] def __init__(self, app, nworkers, **kwargs):
"""Start the job runner
"""
self.app = app
self.sa_session = app.model.context
self.nworkers = nworkers
runner_param_specs = self.DEFAULT_SPECS.copy()
if 'runner_param_specs' in kwargs:
runner_param_specs.update(kwargs.pop('runner_param_specs'))
if kwargs:
log.debug('Loading %s with params: %s', self.runner_name, kwargs)
self.runner_params = RunnerParams(specs=runner_param_specs, params=kwargs)
self.runner_state_handlers = build_state_handlers()
def _init_worker_threads(self):
"""Start ``nworkers`` worker threads.
"""
self.work_queue = Queue()
self.work_threads = []
log.debug('Starting %s %s workers' % (self.nworkers, self.runner_name))
for i in range(self.nworkers):
worker = threading.Thread(name="%s.work_thread-%d" % (self.runner_name, i), target=self.run_next)
worker.setDaemon(True)
self.app.application_stack.register_postfork_function(worker.start)
self.work_threads.append(worker)
[docs] def run_next(self):
"""Run the next item in the work queue (a job waiting to run)
"""
while True:
(method, arg) = self.work_queue.get()
if method is STOP_SIGNAL:
return
# id and name are collected first so that the call of method() is the last exception.
try:
if isinstance(arg, AsynchronousJobState):
job_id = arg.job_wrapper.get_id_tag()
else:
# arg should be a JobWrapper/TaskWrapper
job_id = arg.get_id_tag()
except Exception:
job_id = 'unknown'
try:
name = method.__name__
except Exception:
name = 'unknown'
try:
method(arg)
except Exception:
log.exception("(%s) Unhandled exception calling %s" % (job_id, name))
# Causes a runner's `queue_job` method to be called from a worker thread
[docs] def put(self, job_wrapper):
"""Add a job to the queue (by job identifier), indicate that the job is ready to run.
"""
put_timer = ExecutionTimer()
job = job_wrapper.get_job()
# Change to queued state before handing to worker thread so the runner won't pick it up again
job_wrapper.change_state(model.Job.states.QUEUED, flush=False, job=job)
# Persist the destination so that the job will be included in counts if using concurrency limits
job_wrapper.set_job_destination(job_wrapper.job_destination, None, flush=False, job=job)
self.sa_session.flush()
self.mark_as_queued(job_wrapper)
log.debug("Job [%s] queued %s" % (job_wrapper.job_id, put_timer))
[docs] def shutdown(self):
"""Attempts to gracefully shut down the worker threads
"""
log.info("%s: Sending stop signal to %s worker threads" % (self.runner_name, len(self.work_threads)))
for i in range(len(self.work_threads)):
self.work_queue.put((STOP_SIGNAL, None))
join_timeout = self.app.config.monitor_thread_join_timeout
if join_timeout > 0:
exception = None
for thread in self.work_threads:
try:
thread.join(join_timeout)
except Exception as e:
exception = e
log.exception("Faild to shutdown worker thread")
if exception:
raise exception
# Most runners should override the legacy URL handler methods and destination param method
[docs] def url_to_destination(self, url):
"""
Convert a legacy URL to a JobDestination.
Job runner URLs are deprecated, JobDestinations should be used instead.
This base class method converts from a URL to a very basic
JobDestination without destination params.
"""
return galaxy.jobs.JobDestination(runner=url.split(':')[0])
[docs] def parse_destination_params(self, params):
"""Parse the JobDestination ``params`` dict and return the runner's native representation of those params.
"""
raise NotImplementedError()
[docs] def prepare_job(self, job_wrapper, include_metadata=False, include_work_dir_outputs=True,
modify_command_for_container=True):
"""Some sanity checks that all runners' queue_job() methods are likely to want to do
"""
job_id = job_wrapper.get_id_tag()
job_state = job_wrapper.get_state()
job_wrapper.is_ready = False
job_wrapper.runner_command_line = None
# Make sure the job hasn't been deleted
if job_state == model.Job.states.DELETED:
log.debug("(%s) Job deleted by user before it entered the %s queue" % (job_id, self.runner_name))
if self.app.config.cleanup_job in ("always", "onsuccess"):
job_wrapper.cleanup()
return False
elif job_state != model.Job.states.QUEUED:
log.info("(%s) Job is in state %s, skipping execution" % (job_id, job_state))
# cleanup may not be safe in all states
return False
# Prepare the job
try:
job_wrapper.prepare()
job_wrapper.runner_command_line = self.build_command_line(
job_wrapper,
include_metadata=include_metadata,
include_work_dir_outputs=include_work_dir_outputs,
modify_command_for_container=modify_command_for_container
)
except Exception as e:
log.exception("(%s) Failure preparing job" % job_id)
job_wrapper.fail(e.message if hasattr(e, 'message') else "Job preparation failed", exception=True)
return False
if not job_wrapper.runner_command_line:
job_wrapper.finish('', '')
return False
return True
# Runners must override the job handling methods
[docs] def build_command_line(self, job_wrapper, include_metadata=False, include_work_dir_outputs=True,
modify_command_for_container=True):
container = self._find_container(job_wrapper)
if not container and job_wrapper.requires_containerization:
raise Exception("Failed to find a container when required, contact Galaxy admin.")
return build_command(
self,
job_wrapper,
include_metadata=include_metadata,
include_work_dir_outputs=include_work_dir_outputs,
modify_command_for_container=modify_command_for_container,
container=container
)
[docs] def get_work_dir_outputs(self, job_wrapper, job_working_directory=None, tool_working_directory=None):
"""
Returns list of pairs (source_file, destination) describing path
to work_dir output file and ultimate destination.
"""
if tool_working_directory is not None and job_working_directory is not None:
raise Exception("get_work_dir_outputs called with both a job and tool working directory, only one may be specified")
if tool_working_directory is None:
if not job_working_directory:
job_working_directory = os.path.abspath(job_wrapper.working_directory)
tool_working_directory = os.path.join(job_working_directory, "working")
# Set up dict of dataset id --> output path; output path can be real or
# false depending on outputs_to_working_directory
output_paths = {}
for dataset_path in job_wrapper.get_output_fnames():
path = dataset_path.real_path
if self.app.config.outputs_to_working_directory:
path = dataset_path.false_path
output_paths[dataset_path.dataset_id] = path
output_pairs = []
# Walk job's output associations to find and use from_work_dir attributes.
job = job_wrapper.get_job()
job_tool = job_wrapper.tool
for (joda, dataset) in self._walk_dataset_outputs(job):
if joda and job_tool:
hda_tool_output = job_tool.find_output_def(joda.name)
if hda_tool_output and hda_tool_output.from_work_dir:
# Copy from working dir to HDA.
# TODO: move instead of copy to save time?
source_file = os.path.join(tool_working_directory, hda_tool_output.from_work_dir)
destination = job_wrapper.get_output_destination(output_paths[dataset.dataset_id])
if in_directory(source_file, tool_working_directory):
output_pairs.append((source_file, destination))
else:
# Security violation.
log.exception("from_work_dir specified a location not in the working directory: %s, %s", source_file, job_wrapper.working_directory)
return output_pairs
def _walk_dataset_outputs(self, job):
for dataset_assoc in job.output_datasets + job.output_library_datasets:
for dataset in dataset_assoc.dataset.dataset.history_associations + dataset_assoc.dataset.dataset.library_associations:
if isinstance(dataset, self.app.model.HistoryDatasetAssociation):
joda = self.sa_session.query(self.app.model.JobToOutputDatasetAssociation).filter_by(job=job, dataset=dataset).first()
yield (joda, dataset)
# TODO: why is this not just something easy like:
# for dataset_assoc in job.output_datasets + job.output_library_datasets:
# yield (dataset_assoc, dataset_assoc.dataset)
# I don't understand the reworking it backwards. -John
def _handle_metadata_externally(self, job_wrapper, resolve_requirements=False):
"""
Set metadata externally. Used by the Pulsar job runner where this
shouldn't be attached to command line to execute.
"""
# run the metadata setting script here
# this is terminate-able when output dataset/job is deleted
# so that long running set_meta()s can be canceled without having to reboot the server
if job_wrapper.get_state() not in [model.Job.states.ERROR, model.Job.states.DELETED] and job_wrapper.output_paths:
lib_adjust = GALAXY_LIB_ADJUST_TEMPLATE % job_wrapper.galaxy_lib_dir
venv = GALAXY_VENV_TEMPLATE % job_wrapper.galaxy_virtual_env
external_metadata_script = job_wrapper.setup_external_metadata(output_fnames=job_wrapper.get_output_fnames(),
set_extension=True,
tmp_dir=job_wrapper.working_directory,
# We don't want to overwrite metadata that was copied over in init_meta(), as per established behavior
kwds={'overwrite' : False})
external_metadata_script = "%s %s %s" % (lib_adjust, venv, external_metadata_script)
if resolve_requirements:
dependency_shell_commands = self.app.datatypes_registry.set_external_metadata_tool.build_dependency_shell_commands(job_directory=job_wrapper.working_directory)
if dependency_shell_commands:
if isinstance(dependency_shell_commands, list):
dependency_shell_commands = "&&".join(dependency_shell_commands)
external_metadata_script = "%s&&%s" % (dependency_shell_commands, external_metadata_script)
log.debug('executing external set_meta script for job %d: %s' % (job_wrapper.job_id, external_metadata_script))
external_metadata_proc = subprocess.Popen(args=external_metadata_script,
shell=True,
cwd=job_wrapper.working_directory,
env=os.environ,
preexec_fn=os.setpgrp)
job_wrapper.external_output_metadata.set_job_runner_external_pid(external_metadata_proc.pid, self.sa_session)
external_metadata_proc.wait()
log.debug('execution of external set_meta for job %d finished' % job_wrapper.job_id)
[docs] def get_job_file(self, job_wrapper, **kwds):
job_metrics = job_wrapper.app.job_metrics
job_instrumenter = job_metrics.job_instrumenters[job_wrapper.job_destination.id]
env_setup_commands = kwds.get('env_setup_commands', [])
env_setup_commands.append(job_wrapper.get_env_setup_clause() or '')
destination = job_wrapper.job_destination or {}
envs = destination.get("env", [])
envs.extend(job_wrapper.environment_variables)
for env in envs:
env_setup_commands.append(env_to_statement(env))
command_line = job_wrapper.runner_command_line
tmp_dir_creation_statement = job_wrapper.tmp_dir_creation_statement
options = dict(
tmp_dir_creation_statement=tmp_dir_creation_statement,
job_instrumenter=job_instrumenter,
galaxy_lib=job_wrapper.galaxy_lib_dir,
galaxy_virtual_env=job_wrapper.galaxy_virtual_env,
env_setup_commands=env_setup_commands,
working_directory=os.path.abspath(job_wrapper.working_directory),
command=command_line,
shell=job_wrapper.shell,
preserve_python_environment=job_wrapper.tool.requires_galaxy_python_environment,
)
# Additional logging to enable if debugging from_work_dir handling, metadata
# commands, etc... (or just peak in the job script.)
job_id = job_wrapper.job_id
log.debug('(%s) command is: %s' % (job_id, command_line))
options.update(**kwds)
return job_script(**options)
[docs] def write_executable_script(self, path, contents, mode=0o755):
write_script(path, contents, self.app.config, mode=mode)
def _find_container(
self,
job_wrapper,
compute_working_directory=None,
compute_tool_directory=None,
compute_job_directory=None,
compute_tmp_directory=None,
):
job_directory_type = "galaxy" if compute_working_directory is None else "pulsar"
if not compute_working_directory:
compute_working_directory = job_wrapper.tool_working_directory
if not compute_job_directory:
compute_job_directory = job_wrapper.working_directory
if not compute_tool_directory:
compute_tool_directory = job_wrapper.tool.tool_dir
if not compute_tmp_directory:
compute_tmp_directory = job_wrapper.tmp_directory()
tool = job_wrapper.tool
from galaxy.tools.deps import containers
tool_info = containers.ToolInfo(tool.containers, tool.requirements, tool.requires_galaxy_python_environment, tool.docker_env_pass_through)
job_info = containers.JobInfo(
compute_working_directory,
compute_tool_directory,
compute_job_directory,
compute_tmp_directory,
job_directory_type,
)
destination_info = job_wrapper.job_destination.params
return self.app.container_finder.find_container(
tool_info,
destination_info,
job_info
)
def _handle_runner_state(self, runner_state, job_state):
try:
for handler in self.runner_state_handlers.get(runner_state, []):
handler(self.app, self, job_state)
if job_state.runner_state_handled:
break
except Exception:
log.exception('Caught exception in runner state handler')
[docs] def fail_job(self, job_state, exception=False):
if getattr(job_state, 'stop_job', True):
self.stop_job(self.sa_session.query(self.app.model.Job).get(job_state.job_wrapper.job_id))
self._handle_runner_state('failure', job_state)
# Not convinced this is the best way to indicate this state, but
# something necessary
if not job_state.runner_state_handled:
job_state.job_wrapper.fail(getattr(job_state, 'fail_message', 'Job failed'), exception=exception)
if job_state.job_wrapper.cleanup_job == "always":
job_state.cleanup()
[docs] def mark_as_resubmitted(self, job_state, info=None):
job_state.job_wrapper.mark_as_resubmitted(info=info)
if not self.app.config.track_jobs_in_database:
job_state.job_wrapper.change_state(model.Job.states.QUEUED)
self.app.job_manager.job_handler.dispatcher.put(job_state.job_wrapper)
def _finish_or_resubmit_job(self, job_state, stdout, stderr, exit_code):
job = job_state.job_wrapper.get_job()
check_output_detected_state = job_state.job_wrapper.check_tool_output(stdout, stderr, exit_code, job)
# Flush with streams...
self.sa_session.add(job)
self.sa_session.flush()
if check_output_detected_state != DETECTED_JOB_STATE.OK:
job_runner_state = JobState.runner_states.TOOL_DETECT_ERROR
if check_output_detected_state == DETECTED_JOB_STATE.OUT_OF_MEMORY_ERROR:
job_runner_state = JobState.runner_states.MEMORY_LIMIT_REACHED
job_state.runner_state = job_runner_state
self._handle_runner_state('failure', job_state)
# Was resubmitted or something - I think we are done with it.
if job_state.runner_state_handled:
return
job_state.job_wrapper.finish(stdout, stderr, exit_code, check_output_detected_state=check_output_detected_state)
[docs]class JobState(object):
"""
Encapsulate state of jobs.
"""
runner_states = Bunch(
WALLTIME_REACHED='walltime_reached',
MEMORY_LIMIT_REACHED='memory_limit_reached',
JOB_OUTPUT_NOT_RETURNED_FROM_CLUSTER='Job output not returned from cluster',
UNKNOWN_ERROR='unknown_error',
GLOBAL_WALLTIME_REACHED='global_walltime_reached',
OUTPUT_SIZE_LIMIT='output_size_limit',
TOOL_DETECT_ERROR='tool_detected', # job runner interaction worked fine but the tool indicated error
)
[docs] def __init__(self, job_wrapper, job_destination):
self.runner_state_handled = False
self.job_wrapper = job_wrapper
self.job_destination = job_destination
self.cleanup_file_attributes = ['job_file', 'output_file', 'error_file', 'exit_code_file']
[docs] def set_defaults(self, files_dir):
if self.job_wrapper is not None:
id_tag = self.job_wrapper.get_id_tag()
if files_dir is not None:
self.job_file = JobState.default_job_file(files_dir, id_tag)
self.output_file = os.path.join(files_dir, 'galaxy_%s.o' % id_tag)
self.error_file = os.path.join(files_dir, 'galaxy_%s.e' % id_tag)
self.exit_code_file = os.path.join(files_dir, 'galaxy_%s.ec' % id_tag)
job_name = 'g%s' % id_tag
if self.job_wrapper.tool.old_id:
job_name += '_%s' % self.job_wrapper.tool.old_id
if self.job_wrapper.user:
job_name += '_%s' % self.job_wrapper.user
self.job_name = ''.join(x if x in (string.ascii_letters + string.digits + '_') else '_' for x in job_name)
[docs] @staticmethod
def default_job_file(files_dir, id_tag):
return os.path.join(files_dir, 'galaxy_%s.sh' % id_tag)
[docs] @staticmethod
def default_exit_code_file(files_dir, id_tag):
return os.path.join(files_dir, 'galaxy_%s.ec' % id_tag)
[docs] def cleanup(self):
for file in [getattr(self, a) for a in self.cleanup_file_attributes if hasattr(self, a)]:
try:
os.unlink(file)
except Exception as e:
# TODO: Move this prefix stuff to a method so we don't have dispatch on attributes we may or may
# not have.
if not hasattr(self, "job_id"):
prefix = "(%s)" % self.job_wrapper.get_id_tag()
else:
prefix = "(%s/%s)" % (self.job_wrapper.get_id_tag(), self.job_id)
log.debug("%s Unable to cleanup %s: %s" % (prefix, file, str(e)))
[docs]class AsynchronousJobState(JobState):
"""
Encapsulate the state of an asynchronous job, this should be subclassed as
needed for various job runners to capture additional information needed
to communicate with distributed resource manager.
"""
[docs] def __init__(self, files_dir=None, job_wrapper=None, job_id=None, job_file=None, output_file=None, error_file=None, exit_code_file=None, job_name=None, job_destination=None):
super(AsynchronousJobState, self).__init__(job_wrapper, job_destination)
self.old_state = None
self._running = False
self.check_count = 0
self.start_time = None
# job_id is the DRM's job id, not the Galaxy job id
self.job_id = job_id
self.job_file = job_file
self.output_file = output_file
self.error_file = error_file
self.exit_code_file = exit_code_file
self.job_name = job_name
self.set_defaults(files_dir)
@property
def running(self):
return self._running
@running.setter
def running(self, is_running):
self._running = is_running
# This will be invalid for job recovery
if self.start_time is None:
self.start_time = datetime.datetime.now()
[docs] def check_limits(self, runtime=None):
limit_state = None
if self.job_wrapper.has_limits():
self.check_count += 1
if self.running and (self.check_count % 20 == 0):
if runtime is None:
runtime = datetime.datetime.now() - (self.start_time or datetime.datetime.now())
self.check_count = 0
limit_state = self.job_wrapper.check_limits(runtime=runtime)
if limit_state is not None:
# Set up the job for failure, but the runner will do the actual work
self.runner_state, self.fail_message = limit_state
self.stop_job = True
return True
return False
[docs] def register_cleanup_file_attribute(self, attribute):
if attribute not in self.cleanup_file_attributes:
self.cleanup_file_attributes.append(attribute)
[docs]class AsynchronousJobRunner(Monitors, BaseJobRunner):
"""Parent class for any job runner that runs jobs asynchronously (e.g. via
a distributed resource manager). Provides general methods for having a
thread to monitor the state of asynchronous jobs and submitting those jobs
to the correct methods (queue, finish, cleanup) at appropriate times..
"""
[docs] def __init__(self, app, nworkers, **kwargs):
super(AsynchronousJobRunner, self).__init__(app, nworkers, **kwargs)
# 'watched' and 'queue' are both used to keep track of jobs to watch.
# 'queue' is used to add new watched jobs, and can be called from
# any thread (usually by the 'queue_job' method). 'watched' must only
# be modified by the monitor thread, which will move items from 'queue'
# to 'watched' and then manage the watched jobs.
self.watched = []
self.monitor_queue = Queue()
def _init_monitor_thread(self):
name = "%s.monitor_thread" % self.runner_name
super(AsynchronousJobRunner, self)._init_monitor_thread(name=name, target=self.monitor, start=True, config=self.app.config)
[docs] def monitor(self):
"""
Watches jobs currently in the monitor queue and deals with state
changes (queued to running) and job completion.
"""
while True:
# Take any new watched jobs and put them on the monitor list
try:
while True:
async_job_state = self.monitor_queue.get_nowait()
if async_job_state is STOP_SIGNAL:
# TODO: This is where any cleanup would occur
self.handle_stop()
return
self.watched.append(async_job_state)
except Empty:
pass
# Iterate over the list of watched jobs and check state
try:
self.check_watched_items()
except Exception:
log.exception('Unhandled exception checking active jobs')
# Sleep a bit before the next state check
time.sleep(1)
[docs] def shutdown(self):
"""Attempts to gracefully shut down the monitor thread"""
log.info("%s: Sending stop signal to monitor thread" % self.runner_name)
self.monitor_queue.put(STOP_SIGNAL)
# Call the parent's shutdown method to stop workers
self.shutdown_monitor()
super(AsynchronousJobRunner, self).shutdown()
[docs] def check_watched_items(self):
"""
This method is responsible for iterating over self.watched and handling
state changes and updating self.watched with a new list of watched job
states. Subclasses can opt to override this directly (as older job runners will
initially) or just override check_watched_item and allow the list processing to
reuse the logic here.
"""
new_watched = []
for async_job_state in self.watched:
new_async_job_state = self.check_watched_item(async_job_state)
if new_async_job_state:
new_watched.append(new_async_job_state)
self.watched = new_watched
# Subclasses should implement this unless they override check_watched_items all together.
[docs] def finish_job(self, job_state):
"""
Get the output/error for a finished job, pass to `job_wrapper.finish`
and cleanup all the job's temporary files.
"""
galaxy_id_tag = job_state.job_wrapper.get_id_tag()
external_job_id = job_state.job_id
# To ensure that files below are readable, ownership must be reclaimed first
job_state.job_wrapper.reclaim_ownership()
# wait for the files to appear
which_try = 0
collect_output_success = True
while which_try < self.app.config.retry_job_output_collection + 1:
try:
stdout = shrink_stream_by_size(open(job_state.output_file, "r"), DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True)
stderr = shrink_stream_by_size(open(job_state.error_file, "r"), DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True)
break
except Exception as e:
if which_try == self.app.config.retry_job_output_collection:
stdout = ''
stderr = job_state.runner_states.JOB_OUTPUT_NOT_RETURNED_FROM_CLUSTER
log.error('(%s/%s) %s: %s' % (galaxy_id_tag, external_job_id, stderr, str(e)))
collect_output_success = False
else:
time.sleep(1)
which_try += 1
if not collect_output_success:
job_state.fail_message = stderr
job_state.runner_state = job_state.runner_states.JOB_OUTPUT_NOT_RETURNED_FROM_CLUSTER
self.mark_as_failed(job_state)
return
try:
# This should be an 8-bit exit code, but read ahead anyway:
exit_code_str = open(job_state.exit_code_file, "r").read(32)
except Exception:
# By default, the exit code is 0, which typically indicates success.
exit_code_str = "0"
try:
# Decode the exit code. If it's bogus, then just use 0.
exit_code = int(exit_code_str)
except ValueError:
log.warning("(%s/%s) Exit code '%s' invalid. Using 0." % (galaxy_id_tag, external_job_id, exit_code_str))
exit_code = 0
# clean up the job files
cleanup_job = job_state.job_wrapper.cleanup_job
if cleanup_job == "always" or (not stderr and cleanup_job == "onsuccess"):
job_state.cleanup()
try:
self._finish_or_resubmit_job(job_state, stdout, stderr, exit_code)
except Exception:
log.exception("(%s/%s) Job wrapper finish method failed" % (galaxy_id_tag, external_job_id))
job_state.job_wrapper.fail("Unable to finish job", exception=True)