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Merge pull request #383.
This commit is contained in:
John Chilton
@@ -1,9 +1,9 @@
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from __future__ import absolute_import
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"""
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API operations for Workflows
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"""
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from __future__ import absolute_import
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import logging
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from sqlalchemy import desc, or_
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from galaxy import exceptions
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@@ -12,7 +12,6 @@ from galaxy import web
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from galaxy.web import _future_expose_api as expose_api
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from galaxy.web.base.controller import BaseAPIController, url_for, UsesStoredWorkflowMixin
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from galaxy.web.base.controller import UsesHistoryMixin
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from galaxy.workflow.modules import module_factory
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from galaxy.workflow.run import invoke
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from galaxy.workflow.run import WorkflowRunConfig
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from galaxy.workflow.extract import extract_workflow
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@@ -120,79 +119,85 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesHis
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workflow will be created for this user. Otherwise, workflow_id must be
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specified and this API method will cause a workflow to execute.
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:param installed_repository_file The path of a workflow to import. Either workflow_id or installed_repository_file must be specified
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:param installed_repository_file The path of a workflow to import. Either workflow_id, installed_repository_file or from_history_id must be specified
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:type installed_repository_file str
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:param workflow_id: an existing workflow id. Either workflow_id or installed_repository_file must be specified
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:param workflow_id: An existing workflow id. Either workflow_id, installed_repository_file or from_history_id must be specified
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:type workflow_id: str
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:param parameters: See _update_step_parameters()
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:param parameters: If workflow_id is set - see _update_step_parameters()
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:type parameters: dict
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:param ds_map: A dictionary mapping each input step id to a dictionary with 2 keys: 'src' (which can be 'ldda', 'ld' or 'hda') and 'id' (which should be the id of a LibraryDatasetDatasetAssociation, LibraryDataset or HistoryDatasetAssociation respectively)
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:param ds_map: If workflow_id is set - a dictionary mapping each input step id to a dictionary with 2 keys: 'src' (which can be 'ldda', 'ld' or 'hda') and 'id' (which should be the id of a LibraryDatasetDatasetAssociation, LibraryDataset or HistoryDatasetAssociation respectively)
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:type ds_map: dict
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:param no_add_to_history: if present in the payload with any value, the input datasets will not be added to the selected history
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:param no_add_to_history: If workflow_id is set - if present in the payload with any value, the input datasets will not be added to the selected history
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:type no_add_to_history: str
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:param history: Either the name of a new history or "hist_id=HIST_ID" where HIST_ID is the id of an existing history
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:param history: If workflow_id is set - optional history where to run the workflow, either the name of a new history or "hist_id=HIST_ID" where HIST_ID is the id of an existing history. If not specified, the workflow will be run a new unnamed history
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:type history: str
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:param replacement_params: A dictionary used when renaming datasets
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:param replacement_params: If workflow_id is set - an optional dictionary used when renaming datasets
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:type replacement_params: dict
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:param from_history_id: Id of history to extract a workflow from. Should not be used with worfklow_id or installed_repository_file.
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:param from_history_id: Id of history to extract a workflow from. Either workflow_id, installed_repository_file or from_history_id must be specified
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:type from_history_id: str
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:param job_ids: If from_history_id is set - this should be a list of jobs to include when extracting workflow from history.
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:param job_ids: If from_history_id is set - optional list of jobs to include when extracting a workflow from history
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:type job_ids: str
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:param dataset_ids: If from_history_id is set - this should be a list of HDA ids corresponding to workflow inputs when extracting workflow from history.
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:param dataset_ids: If from_history_id is set - optional list of HDA ids corresponding to workflow inputs when extracting a workflow from history
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:type dataset_ids: str
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:param dataset_collection_ids: If from_history_id is set - optional list of HDCA ids corresponding to workflow inputs when extracting a workflow from history
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:type dataset_collection_ids: str
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:param workflow_name: If from_history_id is set - name of the workflow to create when extracting a workflow from history
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:type workflow_name: str
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"""
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# Pull parameters out of payload.
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workflow_id = payload.get('workflow_id', None)
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param_map = payload.get('parameters', {})
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ds_map = payload.get('ds_map', {})
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if len( set( ['workflow_id', 'installed_repository_file', 'from_history_id'] ).intersection( payload ) ) > 1:
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trans.response.status = 403
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return "Only one among 'workflow_id', 'installed_repository_file', 'from_history_id' must be specified"
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if 'installed_repository_file' in payload:
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workflow_controller = trans.webapp.controllers[ 'workflow' ]
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result = workflow_controller.import_workflow( trans=trans,
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cntrller='api',
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**payload)
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return result
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if 'from_history_id' in payload:
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from_history_id = payload.get( 'from_history_id' )
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history = self.get_history( trans, from_history_id, check_ownership=False, check_accessible=True )
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job_ids = map( trans.security.decode_id, payload.get( 'job_ids', [] ) )
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dataset_ids = payload.get( 'dataset_ids', [] )
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dataset_collection_ids = payload.get( 'dataset_collection_ids', [] )
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workflow_name = payload[ 'workflow_name' ]
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stored_workflow = extract_workflow(
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trans=trans,
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user=trans.get_user(),
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history=history,
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job_ids=job_ids,
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dataset_ids=dataset_ids,
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dataset_collection_ids=dataset_collection_ids,
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workflow_name=workflow_name,
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)
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item = stored_workflow.to_dict( value_mapper={ 'id': trans.security.encode_id } )
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item[ 'url' ] = url_for( 'workflow', id=item[ 'id' ] )
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return item
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workflow_id = payload.get( 'workflow_id', None )
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if not workflow_id:
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trans.response.status = 403
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return "Either workflow_id, installed_repository_file or from_history_id must be specified"
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# Pull other parameters out of payload.
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param_map = payload.get( 'parameters', {} )
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ds_map = payload.get( 'ds_map', {} )
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add_to_history = 'no_add_to_history' not in payload
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history_param = payload.get('history', '')
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# Get/create workflow.
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if not workflow_id:
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# create new
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if 'installed_repository_file' in payload:
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workflow_controller = trans.webapp.controllers[ 'workflow' ]
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result = workflow_controller.import_workflow( trans=trans,
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cntrller='api',
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**payload)
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return result
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if 'from_history_id' in payload:
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from_history_id = payload.get( 'from_history_id' )
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history = self.get_history( trans, from_history_id, check_ownership=False, check_accessible=True )
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job_ids = map( trans.security.decode_id, payload.get( "job_ids", [] ) )
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dataset_ids = payload.get( "dataset_ids", [] )
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dataset_collection_ids = payload.get( "dataset_collection_ids", [] )
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workflow_name = payload[ "workflow_name" ]
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stored_workflow = extract_workflow(
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trans=trans,
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user=trans.get_user(),
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history=history,
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job_ids=job_ids,
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dataset_ids=dataset_ids,
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dataset_collection_ids=dataset_collection_ids,
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workflow_name=workflow_name,
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)
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item = stored_workflow.to_dict( value_mapper={ "id": trans.security.encode_id } )
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item[ 'url' ] = url_for( 'workflow', id=item[ "id" ] )
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return item
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trans.response.status = 403
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return "Either workflow_id or installed_repository_file must be specified"
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if 'installed_repository_file' in payload:
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trans.response.status = 403
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return "installed_repository_file may not be specified with workflow_id"
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# Get workflow + accessibility check.
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stored_workflow = trans.sa_session.query(self.app.model.StoredWorkflow).get(
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trans.security.decode_id(workflow_id))
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