Source code for

Base classes for job runner plugins.

import datetime
import os
import string
import subprocess
import sys
import threading
import time
import traceback
import typing
import uuid
from queue import (

from sqlalchemy import select
from sqlalchemy.orm import object_session

from galaxy import model
from galaxy.exceptions import ConfigurationError
from galaxy.job_execution.output_collect import (
from import build_command
from import runner_states
from import env_to_statement
from import (
from galaxy.model.base import (
from galaxy.tool_util.deps.dependencies import (
from galaxy.tool_util.output_checker import DETECTED_JOB_STATE
from galaxy.util import (
from galaxy.util.custom_logging import get_logger
from galaxy.util.monitors import Monitors
from .state_handler_factory import build_state_handlers

if typing.TYPE_CHECKING:
    from import GalaxyManagerApplication
    from import (

log = get_logger(__name__)

STOP_SIGNAL = object()

JOB_RUNNER_PARAMETER_UNKNOWN_MESSAGE = "Invalid job runner parameter for this plugin: %s"
    "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_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: runner_name = "BaseJobRunner" start_methods = ["_init_monitor_thread", "_init_worker_threads"] DEFAULT_SPECS = dict(recheck_missing_job_retries=dict(map=int, valid=lambda x: int(x) >= 0, default=0))
[docs] def __init__(self, app: "GalaxyManagerApplication", nworkers: int, **kwargs): """Start the job runner""" = app self.redact_email_in_job_name = 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() self._should_stop = False
[docs] def start(self): for start_method in self.start_methods: getattr(self, start_method, lambda: None)()
def _init_worker_threads(self): """Start ``nworkers`` worker threads.""" self.work_queue = Queue() self.work_threads = [] log.debug(f"Starting {self.nworkers} {self.runner_name} workers") for i in range(self.nworkers): worker = threading.Thread(name="%s.work_thread-%d" % (self.runner_name, i), target=self.run_next) worker.daemon = True worker.start() self.work_threads.append(worker) def _alive_worker_threads(self, cycle=False): # yield endlessly as long as there are alive threads if cycle is True alive = True while alive: alive = False for thread in self.work_threads: if thread.is_alive(): if cycle: alive = True yield thread
[docs] def run_next(self): """Run the next item in the work queue (a job waiting to run)""" while self._should_stop is False: with # Create a Session instance and ensure it's closed. try: (method, arg) = self.work_queue.get(timeout=1) except Empty: continue 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 # Ensure a Job object belongs to a session self._ensure_db_session(arg) try: action_str = f"{self.__class__.__name__.lower()}.{name}" action_timer = f"internals.{action_str}", "job runner action %s for job ${job_id} executed" % (action_str) ) method(arg) log.trace(action_timer.to_str(job_id=job_id)) except Exception: log.exception(f"({job_id}) Unhandled exception calling {name}") if not isinstance(arg, JobState): job_state = JobState(job_wrapper=arg, job_destination={}) else: job_state = arg if method != self.fail_job: # Prevent fail_job cycle in the work_queue self.work_queue.put((self.fail_job, job_state))
def _ensure_db_session(self, arg: typing.Union["JobWrapper", "JobState"]) -> None: """Ensure Job object belongs to current session.""" try: job_wrapper = arg.job_wrapper # type: ignore[union-attr] except AttributeError: job_wrapper = arg if job_wrapper._job_io: job = job_wrapper._job_io.job if object_session(job) is None: # Causes a runner's `queue_job` method to be called from a worker thread
[docs] def put(self, job_wrapper: "MinimalJobWrapper"): """Add a job to the queue (by job identifier), indicate that the job is ready to run.""" put_timer = ExecutionTimer() try: queue_job = job_wrapper.enqueue() except Exception as e: queue_job = False # Required for exceptions thrown by object store incompatibility. # tested by test/integration/objectstore/ message = e.client_message if hasattr(e, "client_message") else str(e), exception=e) log.debug(f"Job [{job_wrapper.job_id}] failed to queue {put_timer}") return if queue_job: self.mark_as_queued(job_wrapper) log.debug(f"Job [{job_wrapper.job_id}] queued {put_timer}")
[docs] def mark_as_queued(self, job_wrapper: "MinimalJobWrapper"): self.work_queue.put((self.queue_job, job_wrapper))
[docs] def shutdown(self): """Attempts to gracefully shut down the worker threads""""%s: Sending stop signal to %s job worker threads", self.runner_name, len(self.work_threads)) self._should_stop = True for _ in range(len(self.work_threads)): self.work_queue.put((STOP_SIGNAL, None)) if (join_timeout := > 0:"Waiting up to %d seconds for job worker threads to shutdown...", join_timeout) start = time.time() # NOTE: threads that have already joined by now are not going to be logged for thread in self._alive_worker_threads(cycle=True): if time.time() > (start + join_timeout): break try: thread.join(2) except Exception: log.exception("Caught exception attempting to shutdown job worker thread %s:", if not thread.is_alive(): log.debug("Job worker thread terminated: %s", else:"All job worker threads shutdown cleanly") return for thread in self._alive_worker_threads(): try: frame = sys._current_frames()[thread.ident] except KeyError: # thread is now stopped continue log.warning( "Timed out waiting for job worker thread %s to terminate, shutdown will be unclean! Thread " "stack is:\n%s",, "".join(traceback.format_stack(frame)), )
# Most runners should override the legacy URL handler methods and destination param method
[docs] def url_to_destination(self, url: str): """ 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":")[0])
[docs] def parse_destination_params(self, params: typing.Dict[str, typing.Any]): """Parse the JobDestination ``params`` dict and return the runner's native representation of those params.""" raise NotImplementedError()
[docs] def prepare_job( self, job_wrapper: "MinimalJobWrapper", include_metadata: bool = False, include_work_dir_outputs: bool = True, modify_command_for_container: bool = True, stream_stdout_stderr: bool = False, ): """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.runner_command_line = None # Make sure the job hasn't been deleted if job_state == model.Job.states.DELETED: log.debug(f"({job_id}) Job deleted by user before it entered the {self.runner_name} queue") if in ("always", "onsuccess"): job_wrapper.cleanup() return False elif job_state != model.Job.states.QUEUED:"({job_id}) Job is in state {job_state}, skipping execution") # 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, stream_stdout_stderr=stream_stdout_stderr, ) except Exception as e: log.exception("(%s) Failure preparing job", job_id), 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 queue_job(self, job_wrapper: "MinimalJobWrapper") -> None: raise NotImplementedError()
[docs] def stop_job(self, job_wrapper): raise NotImplementedError()
[docs] def recover(self, job, job_wrapper): raise NotImplementedError()
[docs] def build_command_line( self, job_wrapper: "MinimalJobWrapper", include_metadata: bool = False, include_work_dir_outputs: bool = True, modify_command_for_container: bool = True, stream_stdout_stderr=False, ): 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, stream_stdout_stderr=stream_stdout_stderr, )
[docs] def get_work_dir_outputs( self, job_wrapper: "MinimalJobWrapper", job_working_directory: typing.Optional[str] = None, tool_working_directory: typing.Optional[str] = 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) assert job_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.job_io.get_output_fnames(): path = dataset_path.real_path if asbool(job_wrapper.get_destination_configuration("outputs_to_working_directory", False)): 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: if dataset.dataset.purged: "Output dataset %s for job %s purged before job completed, skipping output collection.",,, ) continue hda_tool_output = job_tool.find_output_def( 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: model.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, stmt = ( select( .filter_by(job=job, dataset=dataset) .limit(1) ) joda = self.sa_session.scalars(stmt).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 _verify_celery_config(self): if not raise ConfigurationError("Can't request celery metadata without enabling celery tasks") celery_conf = if not celery_conf and not celery_conf["result_backend"]: raise ConfigurationError( "Celery backend not set. Please set `result_backend` on the `celery_conf` config option." ) def _handle_metadata_externally(self, job_wrapper: "MinimalJobWrapper", resolve_requirements: bool = 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]: external_metadata_script = job_wrapper.setup_external_metadata( output_fnames=job_wrapper.job_io.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}, ) metadata_strategy = job_wrapper.metadata_strategy if "celery" in metadata_strategy: self._verify_celery_config() from galaxy.celery.tasks import set_job_metadata # We're synchronously waiting for a task here. This means we have to have a result backend. # That is bad practice and also means this can never become part of another task. try: set_job_metadata.delay( tool_job_working_directory=job_wrapper.working_directory, job_id=job_wrapper.job_id, extended_metadata_collection="extended" in metadata_strategy, ).get() except Exception: log.exception("Metadata task failed") return else: lib_adjust = GALAXY_LIB_ADJUST_TEMPLATE % job_wrapper.galaxy_lib_dir venv = GALAXY_VENV_TEMPLATE % job_wrapper.galaxy_virtual_env external_metadata_script = f"{lib_adjust} {venv} {external_metadata_script}" if resolve_requirements: 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 = f"{dependency_shell_commands}&&{external_metadata_script}" log.debug( "executing external set_meta script for job %d: %s", job_wrapper.job_id, external_metadata_script ) args=external_metadata_script, shell=True, cwd=job_wrapper.working_directory, env=os.environ, preexec_fn=os.setpgrp, ) log.debug("execution of external set_meta for job %d finished" % job_wrapper.job_id)
[docs] def get_job_file(self, job_wrapper: "MinimalJobWrapper", **kwds) -> str: job_metrics = job_instrumenter = job_metrics.job_instrumenters[] env_setup_commands = kwds.get("env_setup_commands", []) env_setup_commands.append(job_wrapper.get_env_setup_clause() or "") destination = job_wrapper.job_destination 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,, 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(f"({job_id}) command is: {command_line}") options.update(**kwds) return job_script(**options)
[docs] def write_executable_script(self, path: str, contents: str, job_io: DescribesScriptIntegrityChecks) -> None: write_script(path, contents, job_io)
def _find_container( self, job_wrapper: "MinimalJobWrapper", compute_working_directory: typing.Optional[str] = None, compute_tool_directory: typing.Optional[str] = None, compute_job_directory: typing.Optional[str] = None, compute_tmp_directory: typing.Optional[str] = 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 guest_ports = job_wrapper.guest_ports tool_info = ToolInfo( tool.containers, tool.requirements, tool.requires_galaxy_python_environment, tool.docker_env_pass_through, guest_ports=guest_ports,, tool_version=tool.version, profile=tool.profile, ) job_info = JobInfo( working_directory=compute_working_directory, tool_directory=compute_tool_directory, job_directory=compute_job_directory, tmp_directory=compute_tmp_directory, home_directory=job_wrapper.home_directory(), job_directory_type=job_directory_type, ) destination_info = job_wrapper.job_destination.params container =, destination_info, job_info) if container: job_wrapper.set_container(container) return container def _handle_runner_state(self, runner_state, job_state: "JobState"): try: for handler in self.runner_state_handlers.get(runner_state, []): handler(, 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: "JobState", exception=False, message="Job failed", full_status=None): if getattr(job_state, "stop_job", True): self.stop_job(job_state.job_wrapper) job_state.job_wrapper.reclaim_ownership() 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: # full_status currently only passed in pulsar runner, # but might be useful for other runners in the future. full_status = full_status or {} tool_stdout = full_status.get("stdout") tool_stderr = full_status.get("stderr") fail_message = getattr(job_state, "fail_message", message) fail_message, tool_stdout=tool_stdout, tool_stderr=tool_stderr, exception=exception )
[docs] def mark_as_resubmitted(self, job_state: "JobState", info: typing.Optional[str] = None): job_state.job_wrapper.mark_as_resubmitted(info=info) if not job_state.job_wrapper.change_state(model.Job.states.QUEUED)
def _job_io_for_db(self, stream): return shrink_stream_by_size( stream, DATABASE_MAX_STRING_SIZE, join_by="\n..\n", left_larger=True, beginning_on_size_error=True ) def _finish_or_resubmit_job(self, job_state: "JobState", job_stdout, job_stderr, job_id=None, external_job_id=None): job_wrapper = job_state.job_wrapper try: job = job_state.job_wrapper.get_job() if job_id is None: job_id = job.get_id_tag() if external_job_id is None: external_job_id = job.get_job_runner_external_id() exit_code = job_state.read_exit_code() outputs_directory = os.path.join(job_wrapper.working_directory, "outputs") if not os.path.exists(outputs_directory): outputs_directory = job_wrapper.working_directory tool_stdout_path = os.path.join(outputs_directory, "tool_stdout") tool_stderr_path = os.path.join(outputs_directory, "tool_stderr") try: with open(tool_stdout_path, "rb") as stdout_file: tool_stdout = self._job_io_for_db(stdout_file) with open(tool_stderr_path, "rb") as stderr_file: tool_stderr = self._job_io_for_db(stderr_file) except FileNotFoundError: if job.state in (model.Job.states.DELETING, model.Job.states.DELETED): # We killed the job, so we may not even have the tool stdout / tool stderr tool_stdout = "" tool_stderr = "Job cancelled" else: # Should we instead just move on ? # In the end the only consequence here is that we won't be able to determine # if the job failed for known tool reasons (check_tool_output). # OTOH I don't know if this can even be reached # Deal with it if we ever get reports about this. raise check_output_detected_state = job_wrapper.check_tool_output( tool_stdout, tool_stderr, tool_exit_code=exit_code, job=job, job_stdout=job_stdout, job_stderr=job_stderr, ) job_ok = check_output_detected_state == DETECTED_JOB_STATE.OK # clean up the job files cleanup_job = job_state.job_wrapper.cleanup_job if cleanup_job == "always" or (job_ok and cleanup_job == "onsuccess"): job_state.cleanup() # Flush with streams... self.sa_session.add(job) with transaction(self.sa_session): self.sa_session.commit() if not job_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_wrapper.finish( tool_stdout, tool_stderr, exit_code, check_output_detected_state=check_output_detected_state, job_stdout=job_stdout, job_stderr=job_stderr, ) except Exception: log.exception(f"({job_id or ''}/{external_job_id or ''}) Job wrapper finish method failed")"Unable to finish job", exception=True)
[docs]class JobState: """ Encapsulate state of jobs. """ runner_states = runner_states
[docs] def __init__(self, job_wrapper: "JobWrapper", job_destination: "JobDestination"): self.runner_state_handled = False self.job_wrapper = job_wrapper self.job_destination = job_destination self.runner_state = None self.redact_email_in_job_name = True self._exit_code_file = None if self.job_wrapper: self.redact_email_in_job_name = self.cleanup_file_attributes = ["job_file", "output_file", "error_file", "exit_code_file"]
@property def exit_code_file(self) -> str: return self._exit_code_file or default_exit_code_file( self.job_wrapper.working_directory, self.job_wrapper.get_id_tag() )
[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, f"galaxy_{id_tag}.o") self.error_file = os.path.join(files_dir, f"galaxy_{id_tag}.e") job_name = f"g{id_tag}" if self.job_wrapper.tool.old_id: job_name += f"_{self.job_wrapper.tool.old_id}" if not self.redact_email_in_job_name and self.job_wrapper.user: job_name += f"_{self.job_wrapper.user}" self.job_name = "".join(x if x in (f"{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, f"galaxy_{id_tag}.sh")
[docs] def read_exit_code(self): return read_exit_code_from(self.exit_code_file, self.job_wrapper.get_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 = f"({self.job_wrapper.get_id_tag()})" else: prefix = f"({self.job_wrapper.get_id_tag()}/{self.job_id})" log.debug(f"{prefix} Unable to cleanup {file}: {unicodify(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().__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 if exit_code_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 =
[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 = - (self.start_time or 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(BaseJobRunner, Monitors): """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().__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 = f"{self.runner_name}.monitor_thread" super()._init_monitor_thread(name=name, target=self.monitor, start=True,
[docs] def handle_stop(self): # DRMAA and SGE runners should override this and disconnect. pass
[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 # Ideally we'd construct a sqlalchemy session now and pass it into `check_watched_items` # and have that be the only session being used. The next best thing is to scope # the session and discard it after each check_watched_item loop scoped_id = str(uuid.uuid4()) # Iterate over the list of watched jobs and check state try: check_database_connection(self.sa_session) self.check_watched_items() except Exception: log.exception("Unhandled exception checking active jobs") finally: # Sleep a bit before the next state check time.sleep(
[docs] def monitor_job(self, job_state): self.monitor_queue.put(job_state)
[docs] def shutdown(self): """Attempts to gracefully shut down the monitor thread""""{self.runner_name}: Sending stop signal to monitor thread") self.monitor_queue.put(STOP_SIGNAL) # Call the parent's shutdown method to stop workers self.shutdown_monitor() super().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 check_watched_item(self, job_state): raise NotImplementedError()
[docs] def finish_job(self, job_state: AsynchronousJobState): """ 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 < + 1: try: with open(job_state.output_file, "rb") as stdout_file, open(job_state.error_file, "rb") as stderr_file: stdout = self._job_io_for_db(stdout_file) stderr = self._job_io_for_db(stderr_file) break except Exception as e: if which_try == 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, unicodify(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 self._finish_or_resubmit_job(job_state, stdout, stderr, job_id=galaxy_id_tag, external_job_id=external_job_id)
[docs] def mark_as_finished(self, job_state): self.work_queue.put((self.finish_job, job_state))
[docs] def mark_as_failed(self, job_state): self.work_queue.put((self.fail_job, job_state))