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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.
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class
galaxy.job_execution.actions.post.
ActionBox
[source]¶ Bases:
object
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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'>}¶
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classmethod
execute
(app, sa_session, pja, job, replacement_dict=None, final_job_state=None)[source]¶
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classmethod
execute_on_mapped_over
(trans, sa_session, pja, step_inputs, step_outputs, replacement_dict=None, final_job_state=None)[source]¶
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immediate_actions
= ['ChangeDatatypeAction', 'RenameDatasetAction', 'TagDatasetAction', 'RemoveTagDatasetAction']¶
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mapped_over_output_actions
= ['RenameDatasetAction', 'HideDatasetAction', 'TagDatasetAction', 'RemoveTagDatasetAction']¶
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public_actions
= ['RenameDatasetAction', 'ChangeDatatypeAction', 'ColumnSetAction', 'EmailAction', 'DeleteIntermediatesAction', 'TagDatasetAction', 'RemoveTagDatasetAction']¶
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class
galaxy.job_execution.actions.post.
ChangeDatatypeAction
[source]¶ Bases:
galaxy.job_execution.actions.post.DefaultJobAction
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name
= 'ChangeDatatypeAction'¶
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verbose_name
= 'Change Datatype'¶
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class
galaxy.job_execution.actions.post.
ColumnSetAction
[source]¶ Bases:
galaxy.job_execution.actions.post.DefaultJobAction
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name
= 'ColumnSetAction'¶
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verbose_name
= 'Assign Columns'¶
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class
galaxy.job_execution.actions.post.
DefaultJobAction
[source]¶ Bases:
object
Base job action.
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classmethod
execute
(app, sa_session, action, job, replacement_dict=None, final_job_state=None)[source]¶
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classmethod
execute_on_mapped_over
(trans, sa_session, action, step_inputs, step_outputs, replacement_dict, final_job_state=None)[source]¶
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name
= 'DefaultJobAction'¶
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verbose_name
= 'Default Job'¶
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classmethod
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class
galaxy.job_execution.actions.post.
DeleteDatasetAction
[source]¶ Bases:
galaxy.job_execution.actions.post.DefaultJobAction
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classmethod
execute_on_mapped_over
(trans, sa_session, action, step_inputs, step_outputs, replacement_dict, final_job_state=None)[source]¶
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name
= 'DeleteDatasetAction'¶
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verbose_name
= 'Delete Dataset'¶
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classmethod
-
class
galaxy.job_execution.actions.post.
DeleteIntermediatesAction
[source]¶ Bases:
galaxy.job_execution.actions.post.DefaultJobAction
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name
= 'DeleteIntermediatesAction'¶
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verbose_name
= 'Delete Non-Output Completed Intermediate Steps'¶
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class
galaxy.job_execution.actions.post.
EmailAction
[source]¶ Bases:
galaxy.job_execution.actions.post.DefaultJobAction
This action sends an email to the galaxy user responsible for a job.
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name
= 'EmailAction'¶
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verbose_name
= 'Email Notification'¶
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class
galaxy.job_execution.actions.post.
HideDatasetAction
[source]¶ Bases:
galaxy.job_execution.actions.post.DefaultJobAction
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classmethod
execute_on_mapped_over
(trans, sa_session, action, step_inputs, step_outputs, replacement_dict, final_job_state=None)[source]¶
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name
= 'HideDatasetAction'¶
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verbose_name
= 'Hide Dataset'¶
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classmethod
-
class
galaxy.job_execution.actions.post.
RemoveTagDatasetAction
[source]¶ Bases:
galaxy.job_execution.actions.post.TagDatasetAction
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action
= 'Remove'¶
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direction
= 'from'¶
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name
= 'RemoveTagDatasetAction'¶
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verbose_name
= 'Remove tag from dataset'¶
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class
galaxy.job_execution.actions.post.
RenameDatasetAction
[source]¶ Bases:
galaxy.job_execution.actions.post.DefaultJobAction
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classmethod
execute_on_mapped_over
(trans, sa_session, action, step_inputs, step_outputs, replacement_dict, final_job_state=None)[source]¶
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name
= 'RenameDatasetAction'¶
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verbose_name
= 'Rename Dataset'¶
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classmethod
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class
galaxy.job_execution.actions.post.
SetMetadataAction
[source]¶ Bases:
galaxy.job_execution.actions.post.DefaultJobAction
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name
= 'SetMetadataAction'¶
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class
galaxy.job_execution.actions.post.
TagDatasetAction
[source]¶ Bases:
galaxy.job_execution.actions.post.DefaultJobAction
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action
= 'Add'¶
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direction
= 'to'¶
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classmethod
execute_on_mapped_over
(trans, sa_session, action, step_inputs, step_outputs, replacement_dict, final_job_state=None)[source]¶
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name
= 'TagDatasetAction'¶
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verbose_name
= 'Add tag to dataset'¶
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class
galaxy.job_execution.actions.post.
ValidateOutputsAction
[source]¶ Bases:
galaxy.job_execution.actions.post.DefaultJobAction
This action validates the produced outputs against the expected datatype.
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name
= 'ValidateOutputsAction'¶
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verbose_name
= 'Validate Tool Outputs'¶
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