def queue_job(self, job_wrapper):
command_line = ''
job_destination = job_wrapper.job_destination
try:
job_wrapper.prepare()
if hasattr(job_wrapper, 'prepare_input_files_cmds'
) and job_wrapper.prepare_input_files_cmds is not None:
for cmd in job_wrapper.prepare_input_files_cmds: # run the commands to stage the input files
#log.debug( 'executing: %s' % cmd )
if 0 != os.system(cmd):
raise Exception(
'Error running file staging command: %s' % cmd)
job_wrapper.prepare_input_files_cmds = None # prevent them from being used in-line
command_line = self.build_command_line(
job_wrapper,
include_metadata=False,
include_work_dir_outputs=False)
except:
job_wrapper.fail("failure preparing job", exception=True)
log.exception("failure running job %d" % job_wrapper.job_id)
return
# If we were able to get a command line, run the job
if not command_line:
job_wrapper.finish('', '')
return
try:
client = self.get_client_from_wrapper(job_wrapper)
output_files = self.get_output_files(job_wrapper)
input_files = job_wrapper.get_input_fnames()
working_directory = job_wrapper.working_directory
tool = job_wrapper.tool
file_stager = FileStager(client, tool, command_line,
job_wrapper.extra_filenames, input_files,
output_files, working_directory)
rebuilt_command_line = file_stager.get_rewritten_command_line()
job_id = file_stager.job_id
client.launch(rebuilt_command_line)
job_wrapper.set_job_destination(job_destination, job_id)
job_wrapper.change_state(model.Job.states.QUEUED)
except:
job_wrapper.fail("failure running job", exception=True)
log.exception("failure running job %d" % job_wrapper.job_id)
return
lwr_job_state = AsynchronousJobState()
lwr_job_state.job_wrapper = job_wrapper
lwr_job_state.job_id = job_id
lwr_job_state.old_state = True
lwr_job_state.running = False
lwr_job_state.job_destination = job_destination
self.monitor_job(lwr_job_state)
def queue_job(self, job_wrapper):
stderr = stdout = command_line = ""
runner_url = job_wrapper.get_job_runner_url()
try:
job_wrapper.prepare()
if hasattr(job_wrapper, "prepare_input_files_cmds") and job_wrapper.prepare_input_files_cmds is not None:
for cmd in job_wrapper.prepare_input_files_cmds: # run the commands to stage the input files
# log.debug( 'executing: %s' % cmd )
if 0 != os.system(cmd):
raise Exception("Error running file staging command: %s" % cmd)
job_wrapper.prepare_input_files_cmds = None # prevent them from being used in-line
command_line = self.build_command_line(job_wrapper, include_metadata=False, include_work_dir_outputs=False)
except:
job_wrapper.fail("failure preparing job", exception=True)
log.exception("failure running job %d" % job_wrapper.job_id)
return
# If we were able to get a command line, run the job
if not command_line:
job_wrapper.finish("", "")
return
try:
# log.debug( 'executing: %s' % command_line )
client = self.get_client_from_wrapper(job_wrapper)
output_files = self.get_output_files(job_wrapper)
input_files = job_wrapper.get_input_fnames()
working_directory = job_wrapper.working_directory
file_stager = FileStager(
client,
command_line,
job_wrapper.extra_filenames,
input_files,
output_files,
job_wrapper.tool.tool_dir,
working_directory,
)
rebuilt_command_line = file_stager.get_rewritten_command_line()
job_id = file_stager.job_id
client.launch(rebuilt_command_line)
job_wrapper.set_runner(runner_url, job_id)
job_wrapper.change_state(model.Job.states.RUNNING)
except Exception, exc:
job_wrapper.fail("failure running job", exception=True)
log.exception("failure running job %d" % job_wrapper.job_id)
return
def queue_job(self, job_wrapper):
command_line = ''
job_destination = job_wrapper.job_destination
try:
job_wrapper.prepare()
if hasattr(job_wrapper, 'prepare_input_files_cmds') and job_wrapper.prepare_input_files_cmds is not None:
for cmd in job_wrapper.prepare_input_files_cmds: # run the commands to stage the input files
#log.debug( 'executing: %s' % cmd )
if 0 != os.system(cmd):
raise Exception('Error running file staging command: %s' % cmd)
job_wrapper.prepare_input_files_cmds = None # prevent them from being used in-line
command_line = self.build_command_line( job_wrapper, include_metadata=False, include_work_dir_outputs=False )
except:
job_wrapper.fail( "failure preparing job", exception=True )
log.exception("failure running job %d" % job_wrapper.job_id)
return
# If we were able to get a command line, run the job
if not command_line:
job_wrapper.finish( '', '' )
return
try:
client = self.get_client_from_wrapper(job_wrapper)
output_files = self.get_output_files(job_wrapper)
input_files = job_wrapper.get_input_fnames()
working_directory = job_wrapper.working_directory
tool = job_wrapper.tool
file_stager = FileStager(client, tool, command_line, job_wrapper.extra_filenames, input_files, output_files, working_directory)
rebuilt_command_line = file_stager.get_rewritten_command_line()
job_id = file_stager.job_id
client.launch( rebuilt_command_line )
job_wrapper.set_job_destination( job_destination, job_id )
job_wrapper.change_state( model.Job.states.QUEUED )
except:
job_wrapper.fail( "failure running job", exception=True )
log.exception("failure running job %d" % job_wrapper.job_id)
return
lwr_job_state = AsynchronousJobState()
lwr_job_state.job_wrapper = job_wrapper
lwr_job_state.job_id = job_id
lwr_job_state.old_state = True
lwr_job_state.running = False
lwr_job_state.job_destination = job_destination
self.monitor_job(lwr_job_state)
def queue_job(self, job_wrapper):
stderr = stdout = command_line = ''
runner_url = job_wrapper.get_job_runner_url()
try:
job_wrapper.prepare()
if hasattr(job_wrapper, 'prepare_input_files_cmds') and job_wrapper.prepare_input_files_cmds is not None:
for cmd in job_wrapper.prepare_input_files_cmds: # run the commands to stage the input files
#log.debug( 'executing: %s' % cmd )
if 0 != os.system(cmd):
raise Exception('Error running file staging command: %s' % cmd)
job_wrapper.prepare_input_files_cmds = None # prevent them from being used in-line
command_line = self.build_command_line( job_wrapper, include_metadata=False, include_work_dir_outputs=False )
except:
job_wrapper.fail( "failure preparing job", exception=True )
log.exception("failure running job %d" % job_wrapper.job_id)
return
# If we were able to get a command line, run the job
if not command_line:
job_wrapper.finish( '', '' )
return
try:
#log.debug( 'executing: %s' % command_line )
client = self.get_client_from_wrapper(job_wrapper)
output_files = self.get_output_files(job_wrapper)
input_files = job_wrapper.get_input_fnames()
working_directory = job_wrapper.working_directory
file_stager = FileStager(client, command_line, job_wrapper.extra_filenames, input_files, output_files, job_wrapper.tool.tool_dir, working_directory)
rebuilt_command_line = file_stager.get_rewritten_command_line()
job_id = file_stager.job_id
client.launch( rebuilt_command_line )
job_wrapper.set_runner( runner_url, job_id )
job_wrapper.change_state( model.Job.states.RUNNING )
except Exception, exc:
job_wrapper.fail( "failure running job", exception=True )
log.exception("failure running job %d" % job_wrapper.job_id)
return
