text: """Job runner used to execute Galaxy jobs through Pulsar.
  
  More information on Pulsar can be found at https://pulsar.readthedocs.io/ .
  """
  
  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,
      CLIENT_INPUT_PATH_TYPES,
      ClientInput,
      ClientInputs,
      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.tool_util.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',
      'PulsarEmbeddedMQJobRunner',
  )
  
  MINIMUM_PULSAR_VERSIONS = {
      '_default_': packaging.version.parse("0.7.0.dev3"),
      'remote_metadata': packaging.version.parse("0.8.0"),
      'remote_container_handling': packaging.version.parse("0.9.1.dev0")  # probably 0.10 ultimately?
  }
  
  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,
      ),
      remote_container_handling=dict(
          map=specs.to_bool,
          default=False,
      ),
      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,
      ),
      pulsar_app_config=dict(
          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
      use_mq = False
      poll = True
  
      def __init__(self, app, nworkers, **kwds):
          """Start the job runner."""
          super().__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):
          if self.use_mq:
              # 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()
  
          if self.poll:
              self._init_monitor_thread()
          else:
              self._init_noop_monitor()
  
      def __init_client_manager(self):
          pulsar_conf = self.runner_params.get('pulsar_app_config', None)
          pulsar_conf_file = None
          if pulsar_conf is None:
              pulsar_conf_file = self.runner_params.get('pulsar_config', None)
          self.__init_pulsar_app(pulsar_conf, pulsar_conf_file)
  
          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, conf, pulsar_conf_path):
          if conf is None and pulsar_conf_path is None and not self.default_build_pulsar_app:
              self.pulsar_app = None
              return
          if conf is None:
              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) 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"] = os.path.join(self.app.config.data_dir, "pulsar_staging")
          if "persistence_directory" not in conf:
              conf["persistence_directory"] = os.path.join(self.app.config.data_dir, "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):
          if self.use_mq:
              # Might still need to check pod IPs.
              job_wrapper = job_state.job_wrapper
              guest_ports = job_wrapper.guest_ports
              if len(guest_ports) > 0:
                  persisted_state = job_wrapper.get_state()
                  if persisted_state in model.Job.terminal_states + [model.Job.states.DELETED_NEW]:
                      log.debug("(%s) Watched job in terminal state, will stop monitoring: %s", job_state.job_id, persisted_state)
                      job_state = None
                  elif persisted_state == model.Job.states.RUNNING:
                      client = self.get_client_from_state(job_state)
                      job_ip = client.job_ip()
                      if job_ip:
                          ports_dict = {}
                          for guest_port in guest_ports:
                              ports_dict[str(guest_port)] = dict(host=job_ip, port=guest_port, protocol="http")
                          self.app.interactivetool_manager.configure_entry_points(job_wrapper.get_job(), ports_dict)
                          log.debug("(%s) Got ports for entry point: %s", job_state.job_id, str(ports_dict))
                          job_state = None
              else:
                  # No need to monitor MQ jobs that have no entry points
                  job_state = None
              return job_state
          else:
              return self.check_watched_item_state(job_state)
  
      def check_watched_item_state(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):
          log.debug('(%s) Received status update: %s %s', job_state.job_id, type(pulsar_status), pulsar_status)
          if pulsar_status in ["complete", "cancelled"] or job_state.job_wrapper.get_state() == model.Job.states.STOPPED:
              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, remote_container = 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)
              path_rewrites_unstructured = {}
              output_names = []
              if compute_environment:
                  path_rewrites_unstructured = compute_environment.path_rewrites_unstructured
                  output_names = compute_environment.output_names()
  
                  client_inputs_list = []
                  for input_dataset_wrapper in job_wrapper.get_input_paths():
                      # str here to resolve false_path if set on a DatasetPath object.
                      path = str(input_dataset_wrapper)
                      object_store_ref = {
                          "dataset_id": input_dataset_wrapper.dataset_id,
                          "dataset_uuid": str(input_dataset_wrapper.dataset_uuid),
                          "object_store_id": input_dataset_wrapper.object_store_id,
                      }
                      client_inputs_list.append(ClientInput(path, CLIENT_INPUT_PATH_TYPES.INPUT_PATH, object_store_ref=object_store_ref))
  
                  for input_extra_path in compute_environment.path_rewrites_input_extra.keys():
                      # TODO: track dataset for object_Store_ref...
                      client_inputs_list.append(ClientInput(input_extra_path, CLIENT_INPUT_PATH_TYPES.INPUT_EXTRA_FILES_PATH))
  
                  for input_metadata_path in compute_environment.path_rewrites_input_metadata.keys():
                      # TODO: track dataset for object_Store_ref...
                      client_inputs_list.append(ClientInput(input_metadata_path, CLIENT_INPUT_PATH_TYPES.INPUT_METADATA_PATH))
  
                  input_files = None
                  client_inputs = ClientInputs(client_inputs_list)
              else:
                  input_files = self.get_input_files(job_wrapper)
                  client_inputs = None
  
              if self.app.config.metadata_strategy == "legacy":
                  # Drop this branch in 19.09.
                  metadata_directory = job_wrapper.working_directory
              else:
                  metadata_directory = os.path.join(job_wrapper.working_directory, "metadata")
  
              dest_params = job_destination.params
              remote_pulsar_app_config = dest_params.get("pulsar_app_config", {}).copy()
              if "pulsar_app_config_path" in dest_params:
                  pulsar_app_config_path = dest_params["pulsar_app_config_path"]
                  with open(pulsar_app_config_path, "r") as fh:
                      remote_pulsar_app_config.update(yaml.safe_load(fh))
              job_directory_files = []
              config_files = job_wrapper.extra_filenames
              tool_script = os.path.join(job_wrapper.working_directory, "tool_script.sh")
              if os.path.exists(tool_script):
                  log.debug("Registering tool_script for Pulsar transfer [%s]" % tool_script)
                  job_directory_files.append(tool_script)
                  config_files.append(tool_script)
              # Following is job destination environment variables
              env = client.env
              # extend it with tool defined environment variables
              tool_envs = job_wrapper.environment_variables
              env.extend(tool_envs)
              for tool_env in tool_envs:
                  job_directory_path = tool_env.get("job_directory_path")
                  if job_directory_path:
                      config_files.append(job_directory_path)
  
              client_job_description = ClientJobDescription(
                  command_line=command_line,
                  input_files=input_files,
                  client_inputs=client_inputs,  # Only one of these input defs should be non-None
                  client_outputs=self.__client_outputs(client, job_wrapper),
                  working_directory=job_wrapper.tool_working_directory,
                  metadata_directory=metadata_directory,
                  tool=job_wrapper.tool,
                  config_files=config_files,
                  dependencies_description=dependencies_description,
                  env=env,
                  rewrite_paths=rewrite_paths,
                  arbitrary_files=path_rewrites_unstructured,
                  touch_outputs=output_names,
                  remote_pulsar_app_config=remote_pulsar_app_config,
                  job_directory_files=job_directory_files,
                  container=None if not remote_container else remote_container.container_id,
                  guest_ports=job_wrapper.guest_ports,
              )
              job_id = pulsar_submit_job(client, client_job_description, remote_job_config)
              log.info("Pulsar job submitted with job_id %s" % job_id)
              job = job_wrapper.get_job()
              # Set the job destination here (unlike other runners) because there are likely additional job destination
              # params from the Pulsar client.
              # Flush with change_state.
              job_wrapper.set_job_destination(job_destination, external_id=job_id, flush=False, job=job)
              job_wrapper.change_state(model.Job.states.QUEUED, job=job)
          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),
              'remote_container_handling': PulsarJobRunner.__remote_container_handling(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
          remote_container = None
  
          fail_or_resubmit = False
          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)
              remote_container_handling = PulsarJobRunner.__remote_container_handling(client)
              if remote_container_handling:
                  # Handle this remotely and don't pass it to build_command
                  remote_container = self._find_container(
                      job_wrapper,
                  )
  
              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_working_directory = remote_job_config['working_directory']
              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"))
              remote_command_params = dict(
                  working_directory=remote_job_config['metadata_directory'],
                  script_directory=remote_job_directory,
                  metadata_kwds=metadata_kwds,
                  dependency_resolution=dependency_resolution,
              )
              # TODO: Following directories work for Pulsar, always worked for Pulsar - but should be
              # calculated at some other level.
              job_wrapper.disable_commands_in_new_shell()
              container = None
              if remote_container is None:
                  container = self._find_container(
                      job_wrapper,
                      compute_working_directory=remote_working_directory,
                      compute_tool_directory=remote_tool_directory,
                      compute_job_directory=remote_job_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,
                  create_tool_working_directory=False,
                  include_work_dir_outputs=False,
                  remote_command_params=remote_command_params,
                  remote_job_directory=remote_job_directory,
              )
          except UnsupportedPulsarException:
              log.exception("failure running job %d, unsupported Pulsar target", job_wrapper.job_id)
              fail_or_resubmit = True
          except PulsarClientTransportError:
              log.exception("failure running job %d, Pulsar connection failed", job_wrapper.job_id)
              fail_or_resubmit = True
          except Exception:
              log.exception("failure running job %d", job_wrapper.job_id)
              fail_or_resubmit = True
  
          # If we were unable to get a command line, there was problem
          fail_or_resubmit = fail_or_resubmit or not command_line
          if fail_or_resubmit:
              job_state = self._job_state(job_wrapper.get_job(), job_wrapper)
              self.work_queue.put((self.fail_job, job_state))
  
          return command_line, client, remote_job_config, compute_environment, remote_container
  
      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 = f"{job_id}_{job_wrapper.task_id}"
          params = job_wrapper.job_destination.params.copy()
          user = job_wrapper.get_job().user
          if user:
              for key, value in params.items():
                  if value and isinstance(value, str):
                      params[key] = model.User.expand_user_properties(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=None):
          # Cannot use url_for outside of web thread.
          # files_endpoint = url_for( controller="job_files", job_id=encoded_job_id )
          if env is None:
              env = []
          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
          )
          # Turn MutableDict into standard dict for pulsar consumption
          job_destination_params = dict(job_destination_params.items())
          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_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)
              job_state = job_wrapper.get_state()
              # Use Pulsar client code to transfer/copy files back
              # and cleanup job if needed.
              completed_normally = job_state not in [model.Job.states.ERROR, model.Job.states.DELETED]
              if completed_normally and job_state == model.Job.states.STOPPED:
                  # Discard pulsar exit code (probably -9), we know the user stopped the job
                  log.debug("Setting exit code for stopped job {job_wrapper.job_id} to 0 (was {exit_code})")
                  exit_code = 0
              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:
              self.fail_job(job_state, message=GENERIC_REMOTE_ERROR, 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_metrics_directory = os.path.join(job_wrapper.working_directory, "metadata")
              # Following check is a hack for jobs started during 19.01 or earlier release
              # and finishing with a 19.05 code base. Eliminate the hack in 19.09 or later
              # along with hacks for legacy metadata compute strategy.
              if not os.path.exists(job_metrics_directory) or not any(["__instrument" in f for f in os.listdir(job_metrics_directory)]):
                  job_metrics_directory = job_wrapper.working_directory
              job_wrapper.finish(
                  stdout,
                  stderr,
                  exit_code,
                  remote_metadata_directory=remote_metadata_directory,
                  job_metrics_directory=job_metrics_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, exception=False):
          """Seperated out so we can use the worker threads for it."""
          self.stop_job(job_state.job_wrapper)
          stdout = ""
          stderr = ""
          if full_status:
              stdout = full_status.get("stdout", "")
              stderr = full_status.get("stderr", "")
          self._handle_runner_state('failure', job_state)
          if not job_state.runner_state_handled:
              job_state.job_wrapper.fail(getattr(job_state, "fail_message", message),
                                         tool_stdout=stdout, tool_stderr=stderr, exception=exception)
  
      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_wrapper):
          job = job_wrapper.get_job()
          if not job.job_runner_external_id:
              return
          # 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(f"Attempt remote Pulsar kill of job with url {pulsar_url} and id {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, model.Job.states.STOPPED]:
              log.debug(f"(Pulsar/{job.id}) is still in {state} state, adding to the Pulsar queue")
              job_state.old_state = True
              job_state.running = state == model.Job.states.RUNNING
              self.monitor_queue.put(job_state)
  
      def shutdown(self):
          super().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)
          if self.app.config.metadata_strategy == "legacy":
              # Drop this branch in 19.09.
              metadata_directory = job_wrapper.working_directory
          else:
              metadata_directory = os.path.join(job_wrapper.working_directory, "metadata")
          client_outputs = ClientOutputs(
              working_directory=job_wrapper.tool_working_directory,
              metadata_directory=metadata_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, needed in list(check_features.items()) + [('_default_', True)]:
              if not needed:
                  continue
              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
          installed_tool_dependencies = job_wrapper.tool.installed_tool_dependencies
          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 __remote_container_handling(pulsar_client):
          remote_container_handling = string_as_bool_or_none(pulsar_client.destination_params.get("remote_container_handling", False))
          return remote_container_handling
  
      @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 and not job_wrapper.use_metadata_binary:
              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
  
      def __async_update(self, full_status):
          galaxy_job_id = None
          try:
              remote_job_id = full_status["job_id"]
              if len(remote_job_id) == 32:
                  # It is a UUID - assign_ids = uuid in destination params...
                  sa_session = self.app.model.context.current
                  galaxy_job_id = sa_session.query(model.Job).filter(model.Job.job_runner_external_id == remote_job_id).one().id
              else:
                  galaxy_job_id = remote_job_id
              job, job_wrapper = self.app.job_manager.job_handler.job_queue.job_pair_for_id(galaxy_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", galaxy_job_id)
              raise
              # Nothing else to do? - Attempt to fail the job?
  
  
  class PulsarLegacyJobRunner(PulsarJobRunner):
      """Flavor of Pulsar job runner mimicking behavior of old LWR runner."""
  
      destination_defaults = dict(
          rewrite_parameters="false",
          dependency_resolution="local",
      )
  
  
  class PulsarMQJobRunner(PulsarJobRunner):
      """Flavor of Pulsar job runner with sensible defaults for message queue communication."""
      use_mq = True
      poll = False
  
      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
      )
  
  
  KUBERNETES_DESTINATION_DEFAULTS = {
      "default_file_action": "remote_transfer",
      "rewrite_parameters": "true",
      "jobs_directory": "/pulsar_staging",
      "pulsar_container_image": "galaxy/pulsar-pod-staging:0.14.0",
      "remote_container_handling": True,
      "k8s_enabled": True,
      "url": PARAMETER_SPECIFICATION_IGNORED,
      "private_token": PARAMETER_SPECIFICATION_IGNORED,
  }
  
  
  class PulsarKubernetesJobRunner(PulsarMQJobRunner):
      destination_defaults = KUBERNETES_DESTINATION_DEFAULTS
      poll = True  # Poll so we can check API for pod IP for ITs.
  
      def _populate_parameter_defaults(self, job_destination):
          super()._populate_parameter_defaults(job_destination)
          params = job_destination.params
          # Set some sensible defaults for Pulsar application that runs in staging container.
          if "pulsar_app_config" not in params:
              params["pulsar_app_config"] = {}
          pulsar_app_config = params["pulsar_app_config"]
          if "staging_directory" not in pulsar_app_config:
              # coexecution always uses a fixed path for staging directory
              pulsar_app_config["staging_directory"] = params.get("jobs_directory")
  
  
  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,
      )
  
  
  class PulsarEmbeddedJobRunner(PulsarJobRunner):
      """Flavor of Puslar job runner 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 PulsarEmbeddedMQJobRunner(PulsarMQJobRunner):
      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.path_rewrites_unstructured = {}
          self.path_rewrites_input_extra = {}
          self.path_rewrites_input_metadata = {}
  
          # job_wrapper.prepare is going to expunge the job backing the following
          # computations, so precalculate these 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 input_path_rewrite(self, dataset):
          local_input_path_rewrite = self.local_path_config.input_path_rewrite(dataset)
          if local_input_path_rewrite is not None:
              local_input_path = local_input_path_rewrite
          else:
              local_input_path = dataset.file_name
          remote_path = self.path_mapper.remote_input_path_rewrite(local_input_path)
          return remote_path
  
      def output_path_rewrite(self, dataset):
          local_output_path_rewrite = self.local_path_config.output_path_rewrite(dataset)
          if local_output_path_rewrite is not None:
              local_output_path = local_output_path_rewrite
          else:
              local_output_path = dataset.file_name
          remote_path = self.path_mapper.remote_output_path_rewrite(local_output_path)
          return remote_path
  
      def input_extra_files_rewrite(self, dataset):
          input_path_rewrite = self.input_path_rewrite(dataset)
          base_input_path = input_path_rewrite[0:-len(".dat")]
          remote_extra_files_path_rewrite = "%s_files" % base_input_path
          self.path_rewrites_input_extra[dataset.extra_files_path] = remote_extra_files_path_rewrite
          return remote_extra_files_path_rewrite
  
      def output_extra_files_rewrite(self, dataset):
          output_path_rewrite = self.output_path_rewrite(dataset)
          base_output_path = output_path_rewrite[0:-len(".dat")]
          remote_extra_files_path_rewrite = "%s_files" % base_output_path
          return remote_extra_files_path_rewrite
  
      def input_metadata_rewrite(self, dataset, metadata_val):
          # May technically be incorrect to not pass through local_path_config.input_metadata_rewrite
          # first but that adds untested logic that wouln't ever be used.
          remote_input_path = self.path_mapper.remote_input_path_rewrite(metadata_val, client_input_path_type=CLIENT_INPUT_PATH_TYPES.INPUT_METADATA_PATH)
          if remote_input_path:
              log.info(f"input_metadata_rewrite is {remote_input_path} from {metadata_val}")
              self.path_rewrites_input_metadata[metadata_val] = remote_input_path
              return remote_input_path
  
          # No rewrite...
          return None
  
      def unstructured_path_rewrite(self, parameter_value):
          path_rewrites_unstructured = self.path_rewrites_unstructured
          if parameter_value in path_rewrites_unstructured:
              # Path previously mapped, use previous mapping.
              return path_rewrites_unstructured[parameter_value]
  
          rewrite, new_unstructured_path_rewrites = self.path_mapper.check_for_arbitrary_rewrite(parameter_value)
          if rewrite:
              path_rewrites_unstructured.update(new_unstructured_path_rewrites)
              return rewrite
          else:
              # Did not need to rewrite, use original path or value.
              return None
  
      def working_directory(self):
          return self._working_directory
  
      def env_config_directory(self):
          return self.config_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 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
  
      def galaxy_url(self):
          return self.job_wrapper.get_destination_configuration("galaxy_infrastructure_url")
  
  
  class UnsupportedPulsarException(Exception):
  
      def __init__(self, needed):
          super().__init__(UPGRADE_PULSAR_ERROR % needed)
  