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galaxy.job_execution.actions package

This package contains job action classes.

Submodules

galaxy.job_execution.actions.post module

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

class galaxy.job_execution.actions.post.DefaultJobAction

Bases: object

Base job action.

name = 'DefaultJobAction'

verbose_name = 'Default Job'

classmethod execute(app, sa_session, action, job, replacement_dict=None, final_job_state=None)

classmethod execute_on_mapped_over(trans, sa_session, action, step_inputs, step_outputs, replacement_dict, final_job_state=None)

classmethod get_short_str(pja)

class galaxy.job_execution.actions.post.EmailAction

Bases: galaxy.job_execution.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, final_job_state=None)

classmethod get_short_str(pja)

class galaxy.job_execution.actions.post.ValidateOutputsAction

Bases: galaxy.job_execution.actions.post.DefaultJobAction

This action validates the produced outputs against the expected datatype.

name = 'ValidateOutputsAction'

verbose_name = 'Validate Tool Outputs'

classmethod execute(app, sa_session, action, job, replacement_dict, final_job_state=None)

classmethod get_short_str(pja)

class galaxy.job_execution.actions.post.ChangeDatatypeAction

Bases: galaxy.job_execution.actions.post.DefaultJobAction

name = 'ChangeDatatypeAction'

verbose_name = 'Change Datatype'

classmethod execute(app, sa_session, action, job, replacement_dict, final_job_state=None)

classmethod get_short_str(pja)

class galaxy.job_execution.actions.post.RenameDatasetAction

Bases: galaxy.job_execution.actions.post.DefaultJobAction

name = 'RenameDatasetAction'

verbose_name = 'Rename Dataset'

classmethod execute_on_mapped_over(trans, sa_session, action, step_inputs, step_outputs, replacement_dict, final_job_state=None)

classmethod execute(app, sa_session, action, job, replacement_dict, final_job_state=None)

classmethod get_short_str(pja)

class galaxy.job_execution.actions.post.HideDatasetAction

Bases: galaxy.job_execution.actions.post.DefaultJobAction

name = 'HideDatasetAction'

verbose_name = 'Hide Dataset'

classmethod execute(app, sa_session, action, job, replacement_dict, final_job_state=None)

classmethod execute_on_mapped_over(trans, sa_session, action, step_inputs, step_outputs, replacement_dict, final_job_state=None)

classmethod get_short_str(pja)

class galaxy.job_execution.actions.post.DeleteDatasetAction

Bases: galaxy.job_execution.actions.post.DefaultJobAction

name = 'DeleteDatasetAction'

verbose_name = 'Delete Dataset'

classmethod execute(app, sa_session, action, job, replacement_dict, final_job_state=None)

classmethod execute_on_mapped_over(trans, sa_session, action, step_inputs, step_outputs, replacement_dict, final_job_state=None)

classmethod get_short_str(pja)

class galaxy.job_execution.actions.post.ColumnSetAction

Bases: galaxy.job_execution.actions.post.DefaultJobAction

name = 'ColumnSetAction'

verbose_name = 'Assign Columns'

classmethod execute(app, sa_session, action, job, replacement_dict, final_job_state=None)

classmethod get_short_str(pja)

class galaxy.job_execution.actions.post.SetMetadataAction

Bases: galaxy.job_execution.actions.post.DefaultJobAction

name = 'SetMetadataAction'

classmethod execute(app, sa_session, action, job, replacement_dict, final_job_state=None)

class galaxy.job_execution.actions.post.DeleteIntermediatesAction

Bases: galaxy.job_execution.actions.post.DefaultJobAction

name = 'DeleteIntermediatesAction'

verbose_name = 'Delete Non-Output Completed Intermediate Steps'

classmethod execute(app, sa_session, action, job, replacement_dict, final_job_state=None)

classmethod get_short_str(pja)

class galaxy.job_execution.actions.post.TagDatasetAction

Bases: galaxy.job_execution.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, final_job_state=None)

classmethod execute(app, sa_session, action, job, replacement_dict, final_job_state=None)

classmethod get_short_str(pja)

class galaxy.job_execution.actions.post.RemoveTagDatasetAction

Bases: galaxy.job_execution.actions.post.TagDatasetAction

name = 'RemoveTagDatasetAction'

verbose_name = 'Remove tag from dataset'

action = 'Remove'

direction = 'from'

class galaxy.job_execution.actions.post.ActionBox

Bases: object

actions = {'ChangeDatatypeAction': <class 'galaxy.job_execution.actions.post.ChangeDatatypeAction'>, 'ColumnSetAction': <class 'galaxy.job_execution.actions.post.ColumnSetAction'>, 'DeleteIntermediatesAction': <class 'galaxy.job_execution.actions.post.DeleteIntermediatesAction'>, 'EmailAction': <class 'galaxy.job_execution.actions.post.EmailAction'>, 'HideDatasetAction': <class 'galaxy.job_execution.actions.post.HideDatasetAction'>, 'RemoveTagDatasetAction': <class 'galaxy.job_execution.actions.post.RemoveTagDatasetAction'>, 'RenameDatasetAction': <class 'galaxy.job_execution.actions.post.RenameDatasetAction'>, 'TagDatasetAction': <class 'galaxy.job_execution.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)

classmethod handle_incoming(incoming)

classmethod execute_on_mapped_over(trans, sa_session, pja, step_inputs, step_outputs, replacement_dict=None, final_job_state=None)

classmethod execute(app, sa_session, pja, job, replacement_dict=None, final_job_state=None)