galaxy.jobs.actions package

This package contains job action classes.

Submodules

galaxy.jobs.actions.post module

Actions to be run at job completion (or output hda creation, as in the case of immediate_actions listed below. Currently only used in workflows.

class galaxy.jobs.actions.post.DefaultJobAction[source]

Bases: object

Base job action.

name = 'DefaultJobAction'
verbose_name = 'Default Job'
classmethod execute(app, sa_session, action, job, replacement_dict=None)[source]
classmethod get_short_str(pja)[source]
class galaxy.jobs.actions.post.EmailAction[source]

Bases: galaxy.jobs.actions.post.DefaultJobAction

This action sends an email to the galaxy user responsible for a job.

name = 'EmailAction'
verbose_name = 'Email Notification'
classmethod execute(app, sa_session, action, job, replacement_dict)[source]
classmethod get_short_str(pja)[source]
class galaxy.jobs.actions.post.ChangeDatatypeAction[source]

Bases: galaxy.jobs.actions.post.DefaultJobAction

name = 'ChangeDatatypeAction'
verbose_name = 'Change Datatype'
classmethod execute(app, sa_session, action, job, replacement_dict)[source]
classmethod get_short_str(pja)[source]
class galaxy.jobs.actions.post.RenameDatasetAction[source]

Bases: galaxy.jobs.actions.post.DefaultJobAction

name = 'RenameDatasetAction'
verbose_name = 'Rename Dataset'
classmethod execute_on_mapped_over(trans, sa_session, action, step_inputs, step_outputs, replacement_dict)[source]
classmethod execute(app, sa_session, action, job, replacement_dict)[source]
classmethod get_short_str(pja)[source]
class galaxy.jobs.actions.post.HideDatasetAction[source]

Bases: galaxy.jobs.actions.post.DefaultJobAction

name = 'HideDatasetAction'
verbose_name = 'Hide Dataset'
classmethod execute(app, sa_session, action, job, replacement_dict)[source]
classmethod execute_on_mapped_over(trans, sa_session, action, step_inputs, step_outputs, replacement_dict)[source]
classmethod get_short_str(pja)[source]
class galaxy.jobs.actions.post.DeleteDatasetAction[source]

Bases: galaxy.jobs.actions.post.DefaultJobAction

name = 'DeleteDatasetAction'
verbose_name = 'Delete Dataset'
classmethod execute(app, sa_session, action, job, replacement_dict)[source]
classmethod execute_on_mapped_over(trans, sa_session, action, step_inputs, step_outputs, replacement_dict)[source]
classmethod get_short_str(pja)[source]
class galaxy.jobs.actions.post.ColumnSetAction[source]

Bases: galaxy.jobs.actions.post.DefaultJobAction

name = 'ColumnSetAction'
verbose_name = 'Assign Columns'
classmethod execute(app, sa_session, action, job, replacement_dict)[source]
classmethod get_short_str(pja)[source]
class galaxy.jobs.actions.post.SetMetadataAction[source]

Bases: galaxy.jobs.actions.post.DefaultJobAction

name = 'SetMetadataAction'
classmethod execute(app, sa_session, action, job, replacement_dict)[source]
class galaxy.jobs.actions.post.DeleteIntermediatesAction[source]

Bases: galaxy.jobs.actions.post.DefaultJobAction

name = 'DeleteIntermediatesAction'
verbose_name = 'Delete Non-Output Completed Intermediate Steps'
classmethod execute(app, sa_session, action, job, replacement_dict)[source]
classmethod get_short_str(pja)[source]
class galaxy.jobs.actions.post.TagDatasetAction[source]

Bases: galaxy.jobs.actions.post.DefaultJobAction

name = 'TagDatasetAction'
verbose_name = 'Add tag to dataset'
action = 'Add'
direction = 'to'
classmethod execute_on_mapped_over(trans, sa_session, action, step_inputs, step_outputs, replacement_dict)[source]
classmethod execute(app, sa_session, action, job, replacement_dict)[source]
classmethod get_short_str(pja)[source]
class galaxy.jobs.actions.post.RemoveTagDatasetAction[source]

Bases: galaxy.jobs.actions.post.TagDatasetAction

name = 'RemoveTagDatasetAction'
verbose_name = 'Remove tag from dataset'
action = 'Remove'
direction = 'from'
class galaxy.jobs.actions.post.ActionBox[source]

Bases: object

actions = {'ChangeDatatypeAction': <class 'galaxy.jobs.actions.post.ChangeDatatypeAction'>, 'ColumnSetAction': <class 'galaxy.jobs.actions.post.ColumnSetAction'>, 'DeleteIntermediatesAction': <class 'galaxy.jobs.actions.post.DeleteIntermediatesAction'>, 'EmailAction': <class 'galaxy.jobs.actions.post.EmailAction'>, 'HideDatasetAction': <class 'galaxy.jobs.actions.post.HideDatasetAction'>, 'RemoveTagDatasetAction': <class 'galaxy.jobs.actions.post.RemoveTagDatasetAction'>, 'RenameDatasetAction': <class 'galaxy.jobs.actions.post.RenameDatasetAction'>, 'TagDatasetAction': <class 'galaxy.jobs.actions.post.TagDatasetAction'>}
public_actions = ['RenameDatasetAction', 'ChangeDatatypeAction', 'ColumnSetAction', 'EmailAction', 'DeleteIntermediatesAction', 'TagDatasetAction', 'RemoveTagDatasetAction']
immediate_actions = ['ChangeDatatypeAction', 'RenameDatasetAction', 'TagDatasetAction', 'RemoveTagDatasetAction']
mapped_over_output_actions = ['RenameDatasetAction', 'HideDatasetAction', 'TagDatasetAction', 'RemoveTagDatasetAction']
classmethod get_short_str(action)[source]
classmethod handle_incoming(incoming)[source]
classmethod execute_on_mapped_over(trans, sa_session, pja, step_inputs, step_outputs, replacement_dict=None)[source]
classmethod execute(app, sa_session, pja, job, replacement_dict=None)[source]