def __command(self, **extra_kwds):
kwds = dict(runner=self.runner,
job_wrapper=self.job_wrapper,
include_metadata=self.include_metadata,
include_work_dir_outputs=self.include_work_dir_outputs,
**extra_kwds)
return build_command(**kwds)
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)
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['working_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()
command_line = build_command(
self,
job_wrapper=job_wrapper,
container=container,
include_metadata=remote_metadata,
include_work_dir_outputs=False,
remote_command_params=remote_command_params,
)
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 build_command_line(self, job_wrapper, include_metadata=False, include_work_dir_outputs=True):
container = self._find_container(job_wrapper)
return build_command(
self,
job_wrapper,
include_metadata=include_metadata,
include_work_dir_outputs=include_work_dir_outputs,
container=container,
)
def __command(self, **extra_kwds):
kwds = dict(
runner=self.runner,
job_wrapper=self.job_wrapper,
include_metadata=self.include_metadata,
include_work_dir_outputs=self.include_work_dir_outputs,
**extra_kwds
)
return build_command(**kwds)
def build_command_line(self,
job_wrapper,
include_metadata=False,
include_work_dir_outputs=True):
container = self._find_container(job_wrapper)
return build_command(self,
job_wrapper,
include_metadata=include_metadata,
include_work_dir_outputs=include_work_dir_outputs,
container=container)
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)
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['working_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()
command_line = build_command(
self,
job_wrapper=job_wrapper,
container=container,
include_metadata=remote_metadata,
include_work_dir_outputs=False,
remote_command_params=remote_command_params,
)
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 build_command_line( self, job_wrapper, include_metadata=False, include_work_dir_outputs=True ):
# TODO: Eliminate extra kwds no longer used (since LWR skips
# abstraction and calls build_command directly).
container = self._find_container( job_wrapper )
return build_command(
self,
job_wrapper,
include_metadata=include_metadata,
include_work_dir_outputs=include_work_dir_outputs,
container=container
)
def build_command_line( self, job_wrapper, include_metadata=False, include_work_dir_outputs=True ):
# TODO: Eliminate extra kwds no longer used (since LWR skips
# abstraction and calls build_command directly).
container = self._find_container( job_wrapper )
return build_command(
self,
job_wrapper,
include_metadata=include_metadata,
include_work_dir_outputs=include_work_dir_outputs,
container=container
)
def build_command_line( self, job_wrapper, include_metadata=False, include_work_dir_outputs=True,
modify_command_for_container=True ):
container = self._find_container( job_wrapper )
return build_command(
self,
job_wrapper,
this_app=self.app,
include_metadata=include_metadata,
include_work_dir_outputs=include_work_dir_outputs,
modify_command_for_container=modify_command_for_container,
container=container
)
def build_command_line( self, job_wrapper, include_metadata=False, include_work_dir_outputs=True,
modify_command_for_container=True ):
container = self._find_container( job_wrapper )
if not container and job_wrapper.requires_containerization:
raise Exception("Failed to find a container when required, contact Galaxy admin.")
return build_command(
self,
job_wrapper,
include_metadata=include_metadata,
include_work_dir_outputs=include_work_dir_outputs,
modify_command_for_container=modify_command_for_container,
container=container
)
def build_command_line(self, job_wrapper, include_metadata=False, include_work_dir_outputs=True,
modify_command_for_container=True):
container = self._find_container(job_wrapper)
if not container and job_wrapper.requires_containerization:
raise Exception("Failed to find a container when required, contact Galaxy admin.")
return build_command(
self,
job_wrapper,
include_metadata=include_metadata,
include_work_dir_outputs=include_work_dir_outputs,
modify_command_for_container=modify_command_for_container,
container=container
)
def build_command_line(self,
job_wrapper,
include_metadata=False,
include_work_dir_outputs=True,
modify_command_for_container=True):
container = self._find_container(job_wrapper)
return build_command(
self,
job_wrapper,
this_app=self.app,
include_metadata=include_metadata,
include_work_dir_outputs=include_work_dir_outputs,
modify_command_for_container=modify_command_for_container,
container=container)
def __prepare_job(self, job_wrapper, job_destination):
""" Build command-line and LWR client for this job. """
command_line = None
client = None
remote_job_config = None
try:
job_wrapper.prepare()
self.__prepare_input_files_locally(job_wrapper)
client = self.get_client_from_wrapper(job_wrapper)
tool = job_wrapper.tool
remote_job_config = client.setup(tool.id, tool.version)
remote_metadata = LwrJobRunner.__remote_metadata( client )
remote_work_dir_copy = LwrJobRunner.__remote_work_dir_copy( client )
dependency_resolution = LwrJobRunner.__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['working_directory'],
metadata_kwds=metadata_kwds,
dependency_resolution=dependency_resolution,
)
command_line = build_command(
self,
job_wrapper=job_wrapper,
include_metadata=remote_metadata,
include_work_dir_outputs=remote_work_dir_copy,
remote_command_params=remote_command_params,
)
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
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
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)
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"))
# This should be remote_job_directory ideally, this patch using configs is a workaround for
# older Pulsar versions that didn't support writing stuff to the job directory natively.
script_directory = os.path.join(remote_job_directory, "configs")
remote_command_params = dict(
working_directory=remote_job_config['metadata_directory'],
script_directory=script_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.
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()
# 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
def build_command_line( self, job_wrapper, include_metadata=False, include_work_dir_outputs=True ):
return build_command( self, job_wrapper, include_metadata=include_metadata, include_work_dir_outputs=include_work_dir_outputs )