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Source code for galaxy.jobs.runners
"""
Base classes for job runner plugins.
"""
import datetime
import os
import string
import subprocess
import sys
import threading
import time
import traceback
import typing
from queue import (
Empty,
Queue,
)
from sqlalchemy.orm import object_session
import galaxy.jobs
from galaxy import model
from galaxy.exceptions import ConfigurationError
from galaxy.job_execution.output_collect import (
default_exit_code_file,
read_exit_code_from,
)
from galaxy.jobs.command_factory import build_command
from galaxy.jobs.runners.util import runner_states
from galaxy.jobs.runners.util.env import env_to_statement
from galaxy.jobs.runners.util.job_script import (
DescribesScriptIntegrityChecks,
job_script,
write_script,
)
from galaxy.model.base import transaction
from galaxy.tool_util.deps.dependencies import (
JobInfo,
ToolInfo,
)
from galaxy.tool_util.output_checker import DETECTED_JOB_STATE
from galaxy.util import (
asbool,
DATABASE_MAX_STRING_SIZE,
ExecutionTimer,
in_directory,
ParamsWithSpecs,
shrink_stream_by_size,
unicodify,
UNKNOWN,
)
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 galaxy.app import GalaxyManagerApplication
from galaxy.jobs import (
JobDestination,
JobWrapper,
MinimalJobWrapper,
)
log = get_logger(__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:
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"""
self.app = app
self.redact_email_in_job_name = self.app.config.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 self.app.model.session(): # 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"galaxy.jobs.runners.{self.__class__.__name__.lower()}.{name}"
action_timer = self.app.execution_timer_factory.get_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:
self.app.model.session().add(job)
# 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 incompatiblity.
# tested by test/integration/objectstore/test_private_handling.py
job_wrapper.fail(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"""
log.info("%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))
join_timeout = self.app.config.monitor_thread_join_timeout
if join_timeout > 0:
log.info("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:", thread.name)
if not thread.is_alive():
log.debug("Job worker thread terminated: %s", thread.name)
else:
log.info("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",
thread.name,
"".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 galaxy.jobs.JobDestination(runner=url.split(":")[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 self.app.config.cleanup_job in ("always", "onsuccess"):
job_wrapper.cleanup()
return False
elif job_state != model.Job.states.QUEUED:
log.info(f"({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)
job_wrapper.fail(unicodify(e), 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: "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:
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: 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, 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 _verify_celery_config(self):
if not self.app.config.enable_celery_tasks:
raise ConfigurationError("Can't request celery metadata without enabling celery tasks")
celery_conf = self.app.config.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 = (
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 = 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
)
subprocess.call(
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_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
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(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_id=tool.id,
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 = self.app.container_finder.find_container(tool_info, 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.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: "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)
job_state.job_wrapper.fail(
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 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 _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")
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)
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")
job_wrapper.fail("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.exit_code_file = default_exit_code_file(job_wrapper.working_directory, job_wrapper.get_id_tag())
self.redact_email_in_job_name = True
if self.job_wrapper:
self.redact_email_in_job_name = self.job_wrapper.app.config.redact_email_in_job_name
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, 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 = 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(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, 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(self.app.config.job_runner_monitor_sleep)
[docs] def shutdown(self):
"""Attempts to gracefully shut down the monitor thread"""
log.info(f"{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 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 < self.app.config.retry_job_output_collection + 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 == 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, 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)