deferred Package¶

`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>¶

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

db_dataset_for(dbkey)[source]¶

get_current_user_roles()[source]¶

get_galaxy_session()[source]¶

log_event(message, tool_id=None)[source]¶

class galaxy.jobs.deferred.Sleeper[source]¶

Bases: object

Provides a ‘sleep’ method that sleeps for a number of seconds unless the notify method is called (from a different thread).

sleep(seconds)[source]¶

wake()[source]¶

`data_transfer` Module¶

Module for managing data transfer jobs.

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

Bases: object

check_interval = 15¶

check_job(job)[source]¶

create_job(trans, **kwd)[source]¶

dataset_datatype_re = <_sre.SRE_Pattern object>¶

dataset_name_re = <_sre.SRE_Pattern object>¶

run_job(job)[source]¶

`genome_index` Module¶

`genome_transfer` Module¶

`liftover_transfer` Module¶

`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

check_job(job)[source]¶

create_job(trans, **kwd)[source]¶

`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'¶

check_job(job)[source]¶

create_job(trans, **kwd)[source]¶

deferred Package¶