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galaxy.jobs.deferred package

Queue for running deferred code via plugins.

class galaxy.jobs.deferred.DeferredJobQueue(app)[source]

Bases: object

job_states = <galaxy.util.bunch.Bunch object>
__init__(app)[source]
shutdown()[source]
class galaxy.jobs.deferred.FakeTrans(app, history=None, user=None)[source]

Bases: object

A fake trans for calling the external set metadata tool

__init__(app, history=None, user=None)[source]
get_galaxy_session()[source]
log_event(message, tool_id=None)[source]
get_current_user_roles()[source]
db_dataset_for(dbkey)[source]

Submodules

galaxy.jobs.deferred.data_transfer module

Module for managing data transfer jobs.

class galaxy.jobs.deferred.data_transfer.DataTransfer(app)[source]

Bases: object

check_interval = 15
dataset_name_re = <_sre.SRE_Pattern object>
dataset_datatype_re = <_sre.SRE_Pattern object>
__init__(app)[source]
create_job(trans, **kwd)[source]
check_job(job)[source]
run_job(job)[source]

galaxy.jobs.deferred.manual_data_transfer module

Generic module for managing manual data transfer jobs using Galaxy’s built-in file browser. This module can be used by various external services that are configured to transfer data manually.

class galaxy.jobs.deferred.manual_data_transfer.ManualDataTransferPlugin(app)[source]

Bases: galaxy.jobs.deferred.data_transfer.DataTransfer

__init__(app)[source]
create_job(trans, **kwd)[source]
check_job(job)[source]

galaxy.jobs.deferred.pacific_biosciences_smrt_portal module

Module for managing jobs in Pacific Bioscience’s SMRT Portal and automatically transferring files produced by SMRT Portal.

class galaxy.jobs.deferred.pacific_biosciences_smrt_portal.SMRTPortalPlugin(app)[source]

Bases: galaxy.jobs.deferred.data_transfer.DataTransfer

api_path = '/smrtportal/api'
__init__(app)[source]
create_job(trans, **kwd)[source]
check_job(job)[source]