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Source code for galaxy.jobs.runners.pulsar
"""Job runner used to execute Galaxy jobs through Pulsar.
More information on Pulsar can be found at https://pulsar.readthedocs.io/ .
"""
from __future__ import absolute_import # Need to import pulsar_client absolutely.
import errno
import logging
import os
import subprocess
from time import sleep
import packaging.version
import pulsar.core
import yaml
from pulsar.client import (
build_client_manager,
ClientJobDescription,
ClientOutputs,
finish_job as pulsar_finish_job,
PathMapper,
PulsarClientTransportError,
PulsarOutputs,
submit_job as pulsar_submit_job,
url_to_destination_params
)
from galaxy import model
from galaxy.jobs import (
ComputeEnvironment,
JobDestination
)
from galaxy.jobs.command_factory import build_command
from galaxy.jobs.runners import (
AsynchronousJobRunner,
AsynchronousJobState
)
from galaxy.tools.deps import dependencies
from galaxy.util import (
galaxy_directory,
specs,
string_as_bool_or_none
)
from galaxy.util.bunch import Bunch
log = logging.getLogger(__name__)
__all__ = (
'PulsarLegacyJobRunner',
'PulsarRESTJobRunner',
'PulsarMQJobRunner',
'PulsarEmbeddedJobRunner',
)
MINIMUM_PULSAR_VERSIONS = {
'_default_': packaging.version.parse("0.7.0.dev3"),
'remote_metadata': packaging.version.parse("0.8.0"),
}
NO_REMOTE_GALAXY_FOR_METADATA_MESSAGE = "Pulsar misconfiguration - Pulsar client configured to set metadata remotely, but remote Pulsar isn't properly configured with a galaxy_home directory."
NO_REMOTE_DATATYPES_CONFIG = "Pulsar client is configured to use remote datatypes configuration when setting metadata externally, but Pulsar is not configured with this information. Defaulting to datatypes_conf.xml."
GENERIC_REMOTE_ERROR = "Failed to communicate with remote job server."
FAILED_REMOTE_ERROR = "Remote job server indicated a problem running or monitoring this job."
LOST_REMOTE_ERROR = "Remote job server could not determine this job's state."
UPGRADE_PULSAR_ERROR = "Galaxy is misconfigured, please contact administrator. The target Pulsar server is unsupported, this version of Galaxy requires Pulsar version %s or newer."
# Is there a good way to infer some default for this? Can only use
# url_for from web threads. https://gist.github.com/jmchilton/9098762
DEFAULT_GALAXY_URL = "http://localhost:8080"
PULSAR_PARAM_SPECS = dict(
transport=dict(
map=specs.to_str_or_none,
valid=specs.is_in("urllib", "curl", None),
default=None
),
transport_timeout=dict(
map=lambda val: None if val == "None" else int(val),
default=None,
),
cache=dict(
map=specs.to_bool_or_none,
default=None,
),
amqp_url=dict(
map=specs.to_str_or_none,
default=None,
),
galaxy_url=dict(
map=specs.to_str_or_none,
default=None,
),
pulsar_config=dict(
map=specs.to_str_or_none,
default=None,
),
manager=dict(
map=specs.to_str_or_none,
default=None,
),
persistence_directory=dict(
map=specs.to_str_or_none,
default=None,
),
amqp_acknowledge=dict(
map=specs.to_bool_or_none,
default=None
),
amqp_ack_republish_time=dict(
map=lambda val: None if val == "None" else int(val),
default=None,
),
amqp_consumer_timeout=dict(
map=lambda val: None if val == "None" else float(val),
default=None,
),
amqp_connect_ssl_ca_certs=dict(
map=specs.to_str_or_none,
default=None,
),
amqp_connect_ssl_keyfile=dict(
map=specs.to_str_or_none,
default=None,
),
amqp_connect_ssl_certfile=dict(
map=specs.to_str_or_none,
default=None,
),
amqp_connect_ssl_cert_reqs=dict(
map=specs.to_str_or_none,
default=None,
),
# https://kombu.readthedocs.io/en/latest/reference/kombu.html#kombu.Producer.publish
amqp_publish_retry=dict(
map=specs.to_bool,
default=False,
),
amqp_publish_priority=dict(
map=int,
valid=lambda x: 0 <= x and x <= 9,
default=0,
),
# https://kombu.readthedocs.io/en/latest/reference/kombu.html#kombu.Exchange.delivery_mode
amqp_publish_delivery_mode=dict(
map=str,
valid=specs.is_in("transient", "persistent"),
default="persistent",
),
amqp_publish_retry_max_retries=dict(
map=int,
default=None,
),
amqp_publish_retry_interval_start=dict(
map=int,
default=None,
),
amqp_publish_retry_interval_step=dict(
map=int,
default=None,
),
amqp_publish_retry_interval_max=dict(
map=int,
default=None,
),
)
PARAMETER_SPECIFICATION_REQUIRED = object()
PARAMETER_SPECIFICATION_IGNORED = object()
class PulsarJobRunner(AsynchronousJobRunner):
"""Base class for pulsar job runners."""
runner_name = "PulsarJobRunner"
default_build_pulsar_app = False
def __init__(self, app, nworkers, **kwds):
"""Start the job runner."""
super(PulsarJobRunner, self).__init__(app, nworkers, runner_param_specs=PULSAR_PARAM_SPECS, **kwds)
self._init_worker_threads()
galaxy_url = self.runner_params.galaxy_url
if not galaxy_url:
galaxy_url = app.config.galaxy_infrastructure_url
if galaxy_url:
galaxy_url = galaxy_url.rstrip("/")
self.galaxy_url = galaxy_url
self.__init_client_manager()
self._monitor()
def _monitor(self):
# Extension point allow MQ variant to setup callback instead
self._init_monitor_thread()
def __init_client_manager(self):
pulsar_conf = self.runner_params.get('pulsar_config', None)
self.__init_pulsar_app(pulsar_conf)
client_manager_kwargs = {}
for kwd in 'manager', 'cache', 'transport', 'persistence_directory':
client_manager_kwargs[kwd] = self.runner_params[kwd]
if self.pulsar_app is not None:
client_manager_kwargs["pulsar_app"] = self.pulsar_app
# TODO: Hack remove this following line pulsar lib update
# that includes https://github.com/galaxyproject/pulsar/commit/ce0636a5b64fae52d165bcad77b2caa3f0e9c232
client_manager_kwargs["file_cache"] = None
for kwd in self.runner_params.keys():
if kwd.startswith('amqp_') or kwd.startswith('transport_'):
client_manager_kwargs[kwd] = self.runner_params[kwd]
self.client_manager = build_client_manager(**client_manager_kwargs)
def __init_pulsar_app(self, pulsar_conf_path):
if pulsar_conf_path is None and not self.default_build_pulsar_app:
self.pulsar_app = None
return
conf = {}
if pulsar_conf_path is None:
log.info("Creating a Pulsar app with default configuration (no pulsar_conf specified).")
else:
log.info("Loading Pulsar app configuration from %s" % pulsar_conf_path)
with open(pulsar_conf_path, "r") as f:
conf.update(yaml.safe_load(f) or {})
if "job_metrics_config_file" not in conf:
conf["job_metrics"] = self.app.job_metrics
if "staging_directory" not in conf:
conf["staging_directory"] = "database/pulsar_staging"
if "persistence_directory" not in conf:
conf["persistence_directory"] = "database/pulsar_persisted_data"
if "galaxy_home" not in conf:
conf["galaxy_home"] = galaxy_directory()
self.pulsar_app = pulsar.core.PulsarApp(**conf)
def url_to_destination(self, url):
"""Convert a legacy URL to a job destination."""
return JobDestination(runner="pulsar", params=url_to_destination_params(url))
def check_watched_item(self, job_state):
try:
client = self.get_client_from_state(job_state)
status = client.get_status()
except PulsarClientTransportError as exc:
log.error("Communication error with Pulsar server on state check, will retry: %s", exc)
return job_state
except Exception:
# An orphaned job was put into the queue at app startup, so remote server went down
# either way we are done I guess.
self.mark_as_finished(job_state)
return None
job_state = self._update_job_state_for_status(job_state, status)
return job_state
def _update_job_state_for_status(self, job_state, pulsar_status, full_status=None):
if pulsar_status == "complete":
self.mark_as_finished(job_state)
return None
if pulsar_status in ["failed", "lost"]:
if pulsar_status == "failed":
message = FAILED_REMOTE_ERROR
else:
message = LOST_REMOTE_ERROR
if not job_state.job_wrapper.get_job().finished:
self.fail_job(job_state, message, full_status=full_status)
return None
if pulsar_status == "running" and not job_state.running:
job_state.running = True
job_state.job_wrapper.change_state(model.Job.states.RUNNING)
return job_state
def queue_job(self, job_wrapper):
job_destination = job_wrapper.job_destination
self._populate_parameter_defaults(job_destination)
command_line, client, remote_job_config, compute_environment = self.__prepare_job(job_wrapper, job_destination)
if not command_line:
return
try:
dependencies_description = PulsarJobRunner.__dependencies_description(client, job_wrapper)
rewrite_paths = not PulsarJobRunner.__rewrite_parameters(client)
unstructured_path_rewrites = {}
output_names = []
if compute_environment:
unstructured_path_rewrites = compute_environment.unstructured_path_rewrites
output_names = compute_environment.output_names()
client_job_description = ClientJobDescription(
command_line=command_line,
input_files=self.get_input_files(job_wrapper),
client_outputs=self.__client_outputs(client, job_wrapper),
working_directory=job_wrapper.tool_working_directory,
metadata_directory=job_wrapper.working_directory,
tool=job_wrapper.tool,
config_files=job_wrapper.extra_filenames,
dependencies_description=dependencies_description,
env=client.env,
rewrite_paths=rewrite_paths,
arbitrary_files=unstructured_path_rewrites,
touch_outputs=output_names,
)
job_id = pulsar_submit_job(client, client_job_description, remote_job_config)
log.info("Pulsar job submitted with job_id %s" % job_id)
job_wrapper.set_job_destination(job_destination, job_id)
job_wrapper.change_state(model.Job.states.QUEUED)
except Exception:
job_wrapper.fail("failure running job", exception=True)
log.exception("failure running job %d", job_wrapper.job_id)
return
pulsar_job_state = AsynchronousJobState()
pulsar_job_state.job_wrapper = job_wrapper
pulsar_job_state.job_id = job_id
pulsar_job_state.old_state = True
pulsar_job_state.running = False
pulsar_job_state.job_destination = job_destination
self.monitor_job(pulsar_job_state)
def __needed_features(self, client):
return {
'remote_metadata': PulsarJobRunner.__remote_metadata(client),
}
def __prepare_job(self, job_wrapper, job_destination):
"""Build command-line and Pulsar client for this job."""
command_line = None
client = None
remote_job_config = None
compute_environment = None
try:
client = self.get_client_from_wrapper(job_wrapper)
tool = job_wrapper.tool
remote_job_config = client.setup(tool.id, tool.version, tool.requires_galaxy_python_environment)
needed_features = self.__needed_features(client)
PulsarJobRunner.check_job_config(remote_job_config, check_features=needed_features)
rewrite_parameters = PulsarJobRunner.__rewrite_parameters(client)
prepare_kwds = {}
if rewrite_parameters:
compute_environment = PulsarComputeEnvironment(client, job_wrapper, remote_job_config)
prepare_kwds['compute_environment'] = compute_environment
job_wrapper.prepare(**prepare_kwds)
self.__prepare_input_files_locally(job_wrapper)
remote_metadata = PulsarJobRunner.__remote_metadata(client)
dependency_resolution = PulsarJobRunner.__dependency_resolution(client)
metadata_kwds = self.__build_metadata_configuration(client, job_wrapper, remote_metadata, remote_job_config)
remote_command_params = dict(
working_directory=remote_job_config['metadata_directory'],
metadata_kwds=metadata_kwds,
dependency_resolution=dependency_resolution,
)
remote_working_directory = remote_job_config['working_directory']
# TODO: Following defs work for Pulsar, always worked for Pulsar but should be
# calculated at some other level.
remote_job_directory = os.path.abspath(os.path.join(remote_working_directory, os.path.pardir))
remote_tool_directory = os.path.abspath(os.path.join(remote_job_directory, "tool_files"))
container = self._find_container(
job_wrapper,
compute_working_directory=remote_working_directory,
compute_tool_directory=remote_tool_directory,
compute_job_directory=remote_job_directory,
)
job_wrapper.disable_commands_in_new_shell()
metadata_directory = None
if remote_metadata:
metadata_directory = remote_job_config['metadata_directory']
# Pulsar handles ``create_tool_working_directory`` and
# ``include_work_dir_outputs`` details.
command_line = build_command(
self,
job_wrapper=job_wrapper,
container=container,
include_metadata=remote_metadata,
metadata_directory=metadata_directory,
create_tool_working_directory=False,
include_work_dir_outputs=False,
remote_command_params=remote_command_params,
)
except UnsupportedPulsarException as e:
job_wrapper.fail(str(e), exception=False)
log.exception("failure running job %d", job_wrapper.job_id)
except Exception:
job_wrapper.fail("failure preparing job", exception=True)
log.exception("failure running job %d", job_wrapper.job_id)
# If we were able to get a command line, run the job
if not command_line:
job_wrapper.finish('', '')
return command_line, client, remote_job_config, compute_environment
def __prepare_input_files_locally(self, job_wrapper):
"""Run task splitting commands locally."""
prepare_input_files_cmds = getattr(job_wrapper, 'prepare_input_files_cmds', None)
if prepare_input_files_cmds is not None:
for cmd in prepare_input_files_cmds: # run the commands to stage the input files
subprocess.check_call(cmd, shell=True)
job_wrapper.prepare_input_files_cmds = None # prevent them from being used in-line
def _populate_parameter_defaults(self, job_destination):
updated = False
params = job_destination.params
for key, value in self.destination_defaults.items():
if key in params:
if value is PARAMETER_SPECIFICATION_IGNORED:
log.warning("Pulsar runner in selected configuration ignores parameter %s" % key)
continue
# if self.runner_params.get( key, None ):
# # Let plugin define defaults for some parameters -
# # for instance that way jobs_directory can be
# # configured next to AMQP url (where it belongs).
# params[ key ] = self.runner_params[ key ]
# continue
if not value:
continue
if value is PARAMETER_SPECIFICATION_REQUIRED:
raise Exception("Pulsar destination does not define required parameter %s" % key)
elif value is not PARAMETER_SPECIFICATION_IGNORED:
params[key] = value
updated = True
return updated
def get_output_files(self, job_wrapper):
output_paths = job_wrapper.get_output_fnames()
return [str(o) for o in output_paths] # Force job_path from DatasetPath objects.
def get_input_files(self, job_wrapper):
input_paths = job_wrapper.get_input_paths()
return [str(i) for i in input_paths] # Force job_path from DatasetPath objects.
def get_client_from_wrapper(self, job_wrapper):
job_id = job_wrapper.job_id
if hasattr(job_wrapper, 'task_id'):
job_id = "%s_%s" % (job_id, job_wrapper.task_id)
params = job_wrapper.job_destination.params.copy()
for key, value in params.items():
if value:
params[key] = model.User.expand_user_properties(job_wrapper.get_job().user, value)
env = getattr(job_wrapper.job_destination, "env", [])
return self.get_client(params, job_id, env)
def get_client_from_state(self, job_state):
job_destination_params = job_state.job_destination.params
job_id = job_state.job_id
return self.get_client(job_destination_params, job_id)
def get_client(self, job_destination_params, job_id, env=[]):
# Cannot use url_for outside of web thread.
# files_endpoint = url_for( controller="job_files", job_id=encoded_job_id )
encoded_job_id = self.app.security.encode_id(job_id)
job_key = self.app.security.encode_id(job_id, kind="jobs_files")
endpoint_base = "%s/api/jobs/%s/files?job_key=%s"
if self.app.config.nginx_upload_job_files_path:
endpoint_base = "%s" + \
self.app.config.nginx_upload_job_files_path + \
"?job_id=%s&job_key=%s"
files_endpoint = endpoint_base % (
self.galaxy_url,
encoded_job_id,
job_key
)
get_client_kwds = dict(
job_id=str(job_id),
files_endpoint=files_endpoint,
env=env
)
return self.client_manager.get_client(job_destination_params, **get_client_kwds)
def finish_job(self, job_state):
stderr = stdout = ''
job_wrapper = job_state.job_wrapper
try:
client = self.get_client_from_state(job_state)
run_results = client.full_status()
remote_working_directory = run_results.get("working_directory", None)
remote_metadata_directory = run_results.get("metadata_directory", None)
stdout = run_results.get('stdout', '')
stderr = run_results.get('stderr', '')
exit_code = run_results.get('returncode', None)
pulsar_outputs = PulsarOutputs.from_status_response(run_results)
# Use Pulsar client code to transfer/copy files back
# and cleanup job if needed.
completed_normally = \
job_wrapper.get_state() not in [model.Job.states.ERROR, model.Job.states.DELETED]
cleanup_job = job_wrapper.cleanup_job
client_outputs = self.__client_outputs(client, job_wrapper)
finish_args = dict(client=client,
job_completed_normally=completed_normally,
cleanup_job=cleanup_job,
client_outputs=client_outputs,
pulsar_outputs=pulsar_outputs)
failed = pulsar_finish_job(**finish_args)
if failed:
job_wrapper.fail("Failed to find or download one or more job outputs from remote server.", exception=True)
except Exception:
message = GENERIC_REMOTE_ERROR
job_wrapper.fail(message, exception=True)
log.exception("failure finishing job %d", job_wrapper.job_id)
return
if not PulsarJobRunner.__remote_metadata(client):
self._handle_metadata_externally(job_wrapper, resolve_requirements=True)
# Finish the job
try:
job_wrapper.finish(
stdout,
stderr,
exit_code,
remote_working_directory=remote_working_directory,
remote_metadata_directory=remote_metadata_directory,
)
except Exception:
log.exception("Job wrapper finish method failed")
job_wrapper.fail("Unable to finish job", exception=True)
def fail_job(self, job_state, message=GENERIC_REMOTE_ERROR, full_status=None):
"""Seperated out so we can use the worker threads for it."""
self.stop_job(self.sa_session.query(self.app.model.Job).get(job_state.job_wrapper.job_id))
stdout = ""
stderr = ""
if full_status:
stdout = full_status.get("stdout", "")
stderr = full_status.get("stderr", "")
job_state.job_wrapper.fail(getattr(job_state, "fail_message", message), stdout=stdout, stderr=stderr)
def check_pid(self, pid):
try:
os.kill(pid, 0)
return True
except OSError as e:
if e.errno == errno.ESRCH:
log.debug("check_pid(): PID %d is dead" % pid)
else:
log.warning("check_pid(): Got errno %s when attempting to check PID %d: %s" % (errno.errorcode[e.errno], pid, e.strerror))
return False
def stop_job(self, job):
# if our local job has JobExternalOutputMetadata associated, then our primary job has to have already finished
client = self.get_client(job.destination_params, job.job_runner_external_id)
job_ext_output_metadata = job.get_external_output_metadata()
if not PulsarJobRunner.__remote_metadata(client) and job_ext_output_metadata:
pid = job_ext_output_metadata[0].job_runner_external_pid # every JobExternalOutputMetadata has a pid set, we just need to take from one of them
if pid in [None, '']:
log.warning("stop_job(): %s: no PID in database for job, unable to stop" % job.id)
return
pid = int(pid)
if not self.check_pid(pid):
log.warning("stop_job(): %s: PID %d was already dead or can't be signaled" % (job.id, pid))
return
for sig in [15, 9]:
try:
os.killpg(pid, sig)
except OSError as e:
log.warning("stop_job(): %s: Got errno %s when attempting to signal %d to PID %d: %s" % (job.id, errno.errorcode[e.errno], sig, pid, e.strerror))
return # give up
sleep(2)
if not self.check_pid(pid):
log.debug("stop_job(): %s: PID %d successfully killed with signal %d" % (job.id, pid, sig))
return
else:
log.warning("stop_job(): %s: PID %d refuses to die after signaling TERM/KILL" % (job.id, pid))
else:
# Remote kill
pulsar_url = job.job_runner_name
job_id = job.job_runner_external_id
log.debug("Attempt remote Pulsar kill of job with url %s and id %s" % (pulsar_url, job_id))
client = self.get_client(job.destination_params, job_id)
client.kill()
def recover(self, job, job_wrapper):
"""Recover jobs stuck in the queued/running state when Galaxy started."""
job_state = self._job_state(job, job_wrapper)
job_wrapper.command_line = job.get_command_line()
state = job.get_state()
if state in [model.Job.states.RUNNING, model.Job.states.QUEUED]:
log.debug("(Pulsar/%s) is still in running state, adding to the Pulsar queue" % (job.get_id()))
job_state.old_state = True
job_state.running = state == model.Job.states.RUNNING
self.monitor_queue.put(job_state)
def shutdown(self):
super(PulsarJobRunner, self).shutdown()
self.client_manager.shutdown()
def _job_state(self, job, job_wrapper):
job_state = AsynchronousJobState()
# TODO: Determine why this is set when using normal message queue updates
# but not CLI submitted MQ updates...
raw_job_id = job.get_job_runner_external_id() or job_wrapper.job_id
job_state.job_id = str(raw_job_id)
job_state.runner_url = job_wrapper.get_job_runner_url()
job_state.job_destination = job_wrapper.job_destination
job_state.job_wrapper = job_wrapper
return job_state
def __client_outputs(self, client, job_wrapper):
work_dir_outputs = self.get_work_dir_outputs(job_wrapper)
output_files = self.get_output_files(job_wrapper)
client_outputs = ClientOutputs(
working_directory=job_wrapper.tool_working_directory,
metadata_directory=job_wrapper.working_directory,
work_dir_outputs=work_dir_outputs,
output_files=output_files,
version_file=job_wrapper.get_version_string_path(),
)
return client_outputs
@staticmethod
def check_job_config(remote_job_config, check_features=None):
check_features = check_features or {}
# 0.6.0 was newest Pulsar version that did not report it's version.
pulsar_version = packaging.version.parse(remote_job_config.get('pulsar_version', "0.6.0"))
needed_version = packaging.version.parse("0.0.0")
log.info("pulsar_version is %s" % pulsar_version)
for feature in list(check_features.keys()) + ['_default_']:
if pulsar_version < MINIMUM_PULSAR_VERSIONS[feature]:
needed_version = max(needed_version, MINIMUM_PULSAR_VERSIONS[feature])
if pulsar_version < needed_version:
raise UnsupportedPulsarException(needed_version)
@staticmethod
def __dependencies_description(pulsar_client, job_wrapper):
dependency_resolution = PulsarJobRunner.__dependency_resolution(pulsar_client)
remote_dependency_resolution = dependency_resolution == "remote"
if not remote_dependency_resolution:
return None
requirements = job_wrapper.tool.requirements or []
installed_tool_dependencies = job_wrapper.tool.installed_tool_dependencies or []
return dependencies.DependenciesDescription(
requirements=requirements,
installed_tool_dependencies=installed_tool_dependencies,
)
@staticmethod
def __dependency_resolution(pulsar_client):
dependency_resolution = pulsar_client.destination_params.get("dependency_resolution", "remote")
if dependency_resolution not in ["none", "local", "remote"]:
raise Exception("Unknown dependency_resolution value encountered %s" % dependency_resolution)
return dependency_resolution
@staticmethod
def __remote_metadata(pulsar_client):
remote_metadata = string_as_bool_or_none(pulsar_client.destination_params.get("remote_metadata", False))
return remote_metadata
@staticmethod
def __use_remote_datatypes_conf(pulsar_client):
"""Use remote metadata datatypes instead of Galaxy's.
When setting remote metadata, use integrated datatypes from this
Galaxy instance or use the datatypes config configured via the remote
Pulsar.
Both options are broken in different ways for same reason - datatypes
may not match. One can push the local datatypes config to the remote
server - but there is no guarentee these datatypes will be defined
there. Alternatively, one can use the remote datatype config - but
there is no guarentee that it will contain all the datatypes available
to this Galaxy.
"""
use_remote_datatypes = string_as_bool_or_none(pulsar_client.destination_params.get("use_remote_datatypes", False))
return use_remote_datatypes
@staticmethod
def __rewrite_parameters(pulsar_client):
return string_as_bool_or_none(pulsar_client.destination_params.get("rewrite_parameters", False)) or False
def __build_metadata_configuration(self, client, job_wrapper, remote_metadata, remote_job_config):
metadata_kwds = {}
if remote_metadata:
remote_system_properties = remote_job_config.get("system_properties", {})
remote_galaxy_home = remote_system_properties.get("galaxy_home", None)
if not remote_galaxy_home:
raise Exception(NO_REMOTE_GALAXY_FOR_METADATA_MESSAGE)
metadata_kwds['exec_dir'] = remote_galaxy_home
outputs_directory = remote_job_config['outputs_directory']
working_directory = remote_job_config['working_directory']
metadata_directory = remote_job_config['metadata_directory']
# For metadata calculation, we need to build a list of of output
# file objects with real path indicating location on Galaxy server
# and false path indicating location on compute server. Since the
# Pulsar disables from_work_dir copying as part of the job command
# line we need to take the list of output locations on the Pulsar
# server (produced by self.get_output_files(job_wrapper)) and for
# each work_dir output substitute the effective path on the Pulsar
# server relative to the remote working directory as the
# false_path to send the metadata command generation module.
work_dir_outputs = self.get_work_dir_outputs(job_wrapper, tool_working_directory=working_directory)
outputs = [Bunch(false_path=os.path.join(outputs_directory, os.path.basename(path)), real_path=path) for path in self.get_output_files(job_wrapper)]
for output in outputs:
for pulsar_workdir_path, real_path in work_dir_outputs:
if real_path == output.real_path:
output.false_path = pulsar_workdir_path
metadata_kwds['output_fnames'] = outputs
metadata_kwds['compute_tmp_dir'] = metadata_directory
metadata_kwds['config_root'] = remote_galaxy_home
default_config_file = os.path.join(remote_galaxy_home, 'config/galaxy.ini')
metadata_kwds['config_file'] = remote_system_properties.get('galaxy_config_file', default_config_file)
metadata_kwds['dataset_files_path'] = remote_system_properties.get('galaxy_dataset_files_path', None)
if PulsarJobRunner.__use_remote_datatypes_conf(client):
remote_datatypes_config = remote_system_properties.get('galaxy_datatypes_config_file', None)
if not remote_datatypes_config:
log.warning(NO_REMOTE_DATATYPES_CONFIG)
remote_datatypes_config = os.path.join(remote_galaxy_home, 'datatypes_conf.xml')
metadata_kwds['datatypes_config'] = remote_datatypes_config
else:
datatypes_config = os.path.join(job_wrapper.working_directory, 'registry.xml')
self.app.datatypes_registry.to_xml_file(path=datatypes_config)
# Ensure this file gets pushed out to the remote config dir.
job_wrapper.extra_filenames.append(datatypes_config)
metadata_kwds['datatypes_config'] = datatypes_config
return metadata_kwds
[docs]class PulsarLegacyJobRunner(PulsarJobRunner):
"""Flavor of Pulsar job runner mimicking behavior of old LWR runner."""
destination_defaults = dict(
rewrite_parameters="false",
dependency_resolution="local",
)
[docs]class PulsarMQJobRunner(PulsarJobRunner):
"""Flavor of Pulsar job runner with sensible defaults for message queue communication."""
destination_defaults = dict(
default_file_action="remote_transfer",
rewrite_parameters="true",
dependency_resolution="remote",
jobs_directory=PARAMETER_SPECIFICATION_REQUIRED,
url=PARAMETER_SPECIFICATION_IGNORED,
private_token=PARAMETER_SPECIFICATION_IGNORED
)
def _monitor(self):
# This is a message queue driven runner, don't monitor
# just setup required callback.
self.client_manager.ensure_has_status_update_callback(self.__async_update)
self.client_manager.ensure_has_ack_consumers()
def __async_update(self, full_status):
job_id = None
try:
job_id = full_status["job_id"]
job, job_wrapper = self.app.job_manager.job_handler.job_queue.job_pair_for_id(job_id)
job_state = self._job_state(job, job_wrapper)
self._update_job_state_for_status(job_state, full_status["status"], full_status=full_status)
except Exception:
log.exception("Failed to update Pulsar job status for job_id %s", job_id)
raise
# Nothing else to do? - Attempt to fail the job?
[docs]class PulsarRESTJobRunner(PulsarJobRunner):
"""Flavor of Pulsar job runner with sensible defaults for RESTful usage."""
destination_defaults = dict(
default_file_action="transfer",
rewrite_parameters="true",
dependency_resolution="remote",
url=PARAMETER_SPECIFICATION_REQUIRED,
)
[docs]class PulsarEmbeddedJobRunner(PulsarJobRunner):
"""Flavor of Puslar job runnner that runs Pulsar's server code directly within Galaxy.
This is an appropriate job runner for when the desire is to use Pulsar staging
but their is not need to run a remote service.
"""
destination_defaults = dict(
default_file_action="copy",
rewrite_parameters="true",
dependency_resolution="remote",
)
default_build_pulsar_app = True
class PulsarComputeEnvironment(ComputeEnvironment):
def __init__(self, pulsar_client, job_wrapper, remote_job_config):
self.pulsar_client = pulsar_client
self.job_wrapper = job_wrapper
self.local_path_config = job_wrapper.default_compute_environment()
self.unstructured_path_rewrites = {}
# job_wrapper.prepare is going to expunge the job backing the following
# computations, so precalculate these paths.
self._wrapper_input_paths = self.local_path_config.input_paths()
self._wrapper_output_paths = self.local_path_config.output_paths()
self.path_mapper = PathMapper(pulsar_client, remote_job_config, self.local_path_config.working_directory())
self._config_directory = remote_job_config["configs_directory"]
self._working_directory = remote_job_config["working_directory"]
self._sep = remote_job_config["system_properties"]["separator"]
self._tool_dir = remote_job_config["tools_directory"]
version_path = self.local_path_config.version_path()
new_version_path = self.path_mapper.remote_version_path_rewrite(version_path)
if new_version_path:
version_path = new_version_path
self._version_path = version_path
def output_names(self):
# Maybe this should use the path mapper, but the path mapper just uses basenames
return self.job_wrapper.get_output_basenames()
def output_paths(self):
local_output_paths = self._wrapper_output_paths
results = []
for local_output_path in local_output_paths:
wrapper_path = str(local_output_path)
remote_path = self.path_mapper.remote_output_path_rewrite(wrapper_path)
results.append(self._dataset_path(local_output_path, remote_path))
return results
def input_paths(self):
local_input_paths = self._wrapper_input_paths
results = []
for local_input_path in local_input_paths:
wrapper_path = str(local_input_path)
# This will over-copy in some cases. For instance in the case of task
# splitting, this input will be copied even though only the work dir
# input will actually be used.
remote_path = self.path_mapper.remote_input_path_rewrite(wrapper_path)
results.append(self._dataset_path(local_input_path, remote_path))
return results
def _dataset_path(self, local_dataset_path, remote_path):
remote_extra_files_path = None
if remote_path:
remote_extra_files_path = "%s_files" % remote_path[0:-len(".dat")]
return local_dataset_path.with_path_for_job(remote_path, remote_extra_files_path)
def working_directory(self):
return self._working_directory
def config_directory(self):
return self._config_directory
def new_file_path(self):
return self.working_directory() # Problems with doing this?
def sep(self):
return self._sep
def version_path(self):
return self._version_path
def rewriter(self, parameter_value):
unstructured_path_rewrites = self.unstructured_path_rewrites
if parameter_value in unstructured_path_rewrites:
# Path previously mapped, use previous mapping.
return unstructured_path_rewrites[parameter_value]
if parameter_value in unstructured_path_rewrites.values():
# Path is a rewritten remote path (this might never occur,
# consider dropping check...)
return parameter_value
rewrite, new_unstructured_path_rewrites = self.path_mapper.check_for_arbitrary_rewrite(parameter_value)
if rewrite:
unstructured_path_rewrites.update(new_unstructured_path_rewrites)
return rewrite
else:
# Did need to rewrite, use original path or value.
return parameter_value
def unstructured_path_rewriter(self):
return self.rewriter
def tool_directory(self):
return self._tool_dir
def home_directory(self):
# TODO: revisit and implement this, won't break anything working in the
# meantime.
return None
def tmp_directory(self):
# TODO: revisit and implement this, won't break anything working in the
# meantime.
return None
class UnsupportedPulsarException(Exception):
def __init__(self, needed):
super(UnsupportedPulsarException, self).__init__(UPGRADE_PULSAR_ERROR % needed)