commit/galaxy-central: 5 new changesets
5 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d7ebdeca53d2/ Changeset: d7ebdeca53d2 User: jmchilton Date: 2014-08-08 15:16:55 Summary: More RESTful shared workflow import. Previous route was "POST /api/workflows/shared", this still works but should be condisdered deprecated in favor of POSTing to /api/workflows with shared_workflow_id in the payload. Affected #: 2 files diff -r 5f663734a26e8e2d1c462320741c86c9b5d9aef6 -r d7ebdeca53d28ac3d21e7e242629811a81f68082 lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -161,8 +161,13 @@ :param workflow_name: If from_history_id is set - name of the workflow to create when extracting a workflow from history :type workflow_name: str """ - - if len( set( ['workflow_id', 'installed_repository_file', 'from_history_id'] ).intersection( payload ) ) > 1: + ways_to_create = set( [ + 'workflow_id', + 'installed_repository_file', + 'from_history_id', + 'shared_workflow_id', + ] ) + if len( ways_to_create.intersection( payload ) ) > 1: trans.response.status = 403 return "Only one among 'workflow_id', 'installed_repository_file', 'from_history_id' must be specified" @@ -193,6 +198,10 @@ item[ 'url' ] = url_for( 'workflow', id=item[ 'id' ] ) return item + if 'shared_workflow_id' in payload: + workflow_id = payload[ 'shared_workflow_id' ] + return self.__api_import_shared_workflow( trans, workflow_id, payload ) + workflow_id = payload.get( 'workflow_id', None ) if not workflow_id: trans.response.status = 403 @@ -409,7 +418,7 @@ return item @expose_api - def import_shared_workflow(self, trans, payload, **kwd): + def import_shared_workflow_deprecated(self, trans, payload, **kwd): """ POST /api/workflows/import Import a workflow shared by other users. @@ -423,6 +432,9 @@ workflow_id = payload.get('workflow_id', None) if workflow_id is None: raise exceptions.ObjectAttributeMissingException( "Missing required parameter 'workflow_id'." ) + self.__api_import_shared_workflow( trans, workflow_id, payload ) + + def __api_import_shared_workflow( self, trans, workflow_id, payload, **kwd ): try: stored_workflow = self.get_stored_workflow( trans, workflow_id, check_ownership=False ) except: diff -r 5f663734a26e8e2d1c462320741c86c9b5d9aef6 -r d7ebdeca53d28ac3d21e7e242629811a81f68082 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -219,7 +219,8 @@ webapp.mapper.connect( 'workflow_dict', '/api/workflows/{workflow_id}/download', controller='workflows', action='workflow_dict', conditions=dict( method=['GET'] ) ) # Preserve the following download route for now for dependent applications -- deprecate at some point webapp.mapper.connect( 'workflow_dict', '/api/workflows/download/{workflow_id}', controller='workflows', action='workflow_dict', conditions=dict( method=['GET'] ) ) - webapp.mapper.connect( 'import_shared_workflow', '/api/workflows/import', controller='workflows', action='import_shared_workflow', conditions=dict( method=['POST'] ) ) + # Deprecated in favor of POST /api/workflows with shared_workflow_id in payload. + webapp.mapper.connect( 'import_shared_workflow_deprecated', '/api/workflows/import', controller='workflows', action='import_shared_workflow_deprecated', conditions=dict( method=['POST'] ) ) webapp.mapper.connect( 'workflow_usage', '/api/workflows/{workflow_id}/usage', controller='workflows', action='workflow_usage', conditions=dict(method=['GET'])) webapp.mapper.connect( 'workflow_usage_contents', '/api/workflows/{workflow_id}/usage/{usage_id}', controller='workflows', action='workflow_usage_contents', conditions=dict(method=['GET'])) https://bitbucket.org/galaxy/galaxy-central/commits/479397aedd2b/ Changeset: 479397aedd2b User: jmchilton Date: 2014-08-08 15:16:55 Summary: More RESTful direct workflow creation from JSON. Previous route was "POST /api/workflows/upload", this still works but should be condisdered deprecated in favor of POSTing to /api/workflows with 'workflow' in the payload. Affected #: 3 files diff -r d7ebdeca53d28ac3d21e7e242629811a81f68082 -r 479397aedd2b4cb074ac978377f4d27fa92476a6 lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -166,6 +166,7 @@ 'installed_repository_file', 'from_history_id', 'shared_workflow_id', + 'workflow', ] ) if len( ways_to_create.intersection( payload ) ) > 1: trans.response.status = 403 @@ -202,6 +203,9 @@ workflow_id = payload[ 'shared_workflow_id' ] return self.__api_import_shared_workflow( trans, workflow_id, payload ) + if 'workflow' in payload: + return self.__api_import_new_workflow( trans, payload, **kwd ) + workflow_id = payload.get( 'workflow_id', None ) if not workflow_id: trans.response.status = 403 @@ -389,15 +393,20 @@ return ( "Workflow '%s' successfully deleted" % stored_workflow.name ) @web.expose_api - def import_new_workflow(self, trans, payload, **kwd): + def import_new_workflow_deprecated(self, trans, payload, **kwd): """ POST /api/workflows/upload Importing dynamic workflows from the api. Return newly generated workflow id. Author: rpark # currently assumes payload['workflow'] is a json representation of a workflow to be inserted into the database + + Deprecated in favor to POST /api/workflows with encoded 'workflow' in + payload the same way. """ + return self.__api_import_new_workflow( trans, payload, **kwd ) + def __api_import_new_workflow( self, trans, payload, **kwd ): data = payload['workflow'] workflow, missing_tool_tups = self._workflow_from_dict( trans, data, source="API" ) diff -r d7ebdeca53d28ac3d21e7e242629811a81f68082 -r 479397aedd2b4cb074ac978377f4d27fa92476a6 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -213,9 +213,8 @@ webapp.add_route( '/visualization/show/:visualization_name', controller='visualization', action='render', visualization_name=None ) - # "POST /api/workflows/import" => ``workflows.import_workflow()``. - # Defines a named route "import_workflow". - webapp.mapper.connect( 'import_workflow', '/api/workflows/upload', controller='workflows', action='import_new_workflow', conditions=dict( method=['POST'] ) ) + # Deprecated in favor of POST /api/workflows with 'workflow' in payload. + webapp.mapper.connect( 'import_workflow_deprecated', '/api/workflows/upload', controller='workflows', action='import_new_workflow_deprecated', conditions=dict( method=['POST'] ) ) webapp.mapper.connect( 'workflow_dict', '/api/workflows/{workflow_id}/download', controller='workflows', action='workflow_dict', conditions=dict( method=['GET'] ) ) # Preserve the following download route for now for dependent applications -- deprecate at some point webapp.mapper.connect( 'workflow_dict', '/api/workflows/download/{workflow_id}', controller='workflows', action='workflow_dict', conditions=dict( method=['GET'] ) ) diff -r d7ebdeca53d28ac3d21e7e242629811a81f68082 -r 479397aedd2b4cb074ac978377f4d27fa92476a6 test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -46,11 +46,21 @@ self._assert_status_code_is( index_response, 200 ) assert isinstance( index_response.json(), list ) - def test_import( self ): + def test_upload( self ): + self.__test_upload( use_deprecated_route=False ) + + def test_upload_deprecated( self ): + self.__test_upload( use_deprecated_route=True ) + + def __test_upload( self, use_deprecated_route ): data = dict( workflow=dumps( self.workflow_populator.load_workflow( name="test_import" ) ), ) - upload_response = self._post( "workflows/upload", data=data ) + if use_deprecated_route: + route = "workflows/upload" + else: + route = "workflows" + upload_response = self._post( route, data=data ) self._assert_status_code_is( upload_response, 200 ) self._assert_user_has_workflow_with_name( "test_import (imported from API)" ) https://bitbucket.org/galaxy/galaxy-central/commits/ecc4c38e0529/ Changeset: ecc4c38e0529 User: jmchilton Date: 2014-08-08 15:16:55 Summary: Work toward making workflows API use newer standards. Convert workflow API to use new-style API decorator throughout. Improved workflow exception handling - now more explicit status code setting and returning of raw error strings in the API. Most obvious exceptional paths out of the API are now coming through MessageExceptions of things even more specific. Add API tests for many of these exceptional conditions. Use more helper methods to reduce method length, duplication. Affected #: 2 files diff -r 479397aedd2b4cb074ac978377f4d27fa92476a6 -r ecc4c38e0529fb3352ad0534e71929f6f6b29e7f lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -6,8 +6,9 @@ import logging from sqlalchemy import desc, or_ -from galaxy import exceptions, util, web +from galaxy import exceptions, util from galaxy.model.item_attrs import UsesAnnotations +from galaxy.managers import histories from galaxy.web import _future_expose_api as expose_api from galaxy.web.base.controller import BaseAPIController, url_for, UsesStoredWorkflowMixin from galaxy.web.base.controller import UsesHistoryMixin @@ -20,7 +21,11 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesHistoryMixin, UsesAnnotations): - @web.expose_api + def __init__( self, app ): + super( BaseAPIController, self ).__init__( app ) + self.history_manager = histories.HistoryManager() + + @expose_api def index(self, trans, **kwd): """ GET /api/workflows @@ -54,30 +59,21 @@ rval.append(item) return rval - @web.expose_api + @expose_api def show(self, trans, id, **kwd): """ GET /api/workflows/{encoded_workflow_id} Displays information needed to run a workflow from the command line. """ - workflow_id = id - try: - decoded_workflow_id = trans.security.decode_id(workflow_id) - except TypeError: - trans.response.status = 400 - return "Malformed workflow id ( %s ) specified, unable to decode." % str(workflow_id) - try: - stored_workflow = trans.sa_session.query(trans.app.model.StoredWorkflow).get(decoded_workflow_id) - if stored_workflow.importable is False and stored_workflow.user != trans.user and not trans.user_is_admin(): - if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: - trans.response.status = 400 - return("Workflow is neither importable, nor owned by or shared with current user") - except: - trans.response.status = 400 - return "That workflow does not exist." + stored_workflow = self.__get_stored_workflow( trans, id ) + if stored_workflow.importable is False and stored_workflow.user != trans.user and not trans.user_is_admin(): + if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: + message = "Workflow is neither importable, nor owned by or shared with current user" + raise exceptions.ItemAccessibilityException( message ) + item = stored_workflow.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id } ) - item['url'] = url_for('workflow', id=workflow_id) + item['url'] = url_for('workflow', id=id) item['owner'] = stored_workflow.user.username latest_workflow = stored_workflow.latest_workflow inputs = {} @@ -114,7 +110,7 @@ item['steps'] = steps return item - @web.expose_api + @expose_api def create(self, trans, payload, **kwd): """ POST /api/workflows @@ -167,10 +163,14 @@ 'from_history_id', 'shared_workflow_id', 'workflow', - ] ) - if len( ways_to_create.intersection( payload ) ) > 1: - trans.response.status = 403 - return "Only one among 'workflow_id', 'installed_repository_file', 'from_history_id' must be specified" + ] ).intersection( payload ) + if len( ways_to_create ) == 0: + message = "One parameter among - %s - must be specified" % ", ".join( ways_to_create ) + raise exceptions.RequestParameterMissingException( message ) + + if len( ways_to_create ) > 1: + message = "Only one parameter among - %s - must be specified" % ", ".join( ways_to_create ) + raise exceptions.RequestParameterInvalidException( message ) if 'installed_repository_file' in payload: workflow_controller = trans.webapp.controllers[ 'workflow' ] @@ -208,8 +208,8 @@ workflow_id = payload.get( 'workflow_id', None ) if not workflow_id: - trans.response.status = 403 - return "Either workflow_id, installed_repository_file or from_history_id must be specified" + message = "Invalid workflow_id specified." + raise exceptions.RequestParameterInvalidException( message ) # Pull other parameters out of payload. param_map = payload.get( 'parameters', {} ) @@ -238,34 +238,24 @@ history_param = payload.get('history', '') # Get workflow + accessibility check. - stored_workflow = trans.sa_session.query(self.app.model.StoredWorkflow).get(trans.security.decode_id(workflow_id)) - if stored_workflow.user != trans.user and not trans.user_is_admin(): - if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: - trans.response.status = 400 - return("Workflow is not owned by or shared with current user") + stored_workflow = self.__get_stored_accessible_workflow( trans, workflow_id ) workflow = stored_workflow.latest_workflow # Sanity checks. - if not workflow: - trans.response.status = 400 - return "Workflow not found." if len( workflow.steps ) == 0: - trans.response.status = 400 - return "Workflow cannot be run because it does not have any steps" + raise exceptions.MessageException( "Workflow cannot be run because it does not have any steps" ) if workflow.has_cycles: - trans.response.status = 400 - return "Workflow cannot be run because it contains cycles" + raise exceptions.MessageException( "Workflow cannot be run because it contains cycles" ) if workflow.has_errors: - trans.response.status = 400 - return "Workflow cannot be run because of validation errors in some steps" + message = "Workflow cannot be run because of validation errors in some steps" + raise exceptions.MessageException( message ) # Get target history. if history_param.startswith('hist_id='): # Passing an existing history to use. - history = trans.sa_session.query(self.app.model.History).get(trans.security.decode_id(history_param[8:])) - if history.user != trans.user and not trans.user_is_admin(): - trans.response.status = 400 - return "Invalid History specified." + encoded_history_id = history_param[ 8: ] + history_id = self.__decode_id( trans, encoded_history_id, model_type="history" ) + history = self.history_manager.get( trans, history_id, check_ownership=True ) else: # Send workflow outputs to new history. history = self.app.model.History(name=history_param, user=trans.user) @@ -297,8 +287,8 @@ inputs[k]['id'] ) else: - trans.response.status = 400 - return "Unknown dataset source '%s' specified." % inputs[k]['src'] + message = "Unknown workflow input source '%s' specified." % inputs[k]['src'] + raise exceptions.RequestParameterInvalidException( message ) if add_to_history and content.history != history: content = content.copy() if isinstance( content, self.app.model.HistoryDatasetAssociation ): @@ -307,8 +297,8 @@ history.add_dataset_collection( content ) inputs[k]['hda'] = content # TODO: rename key to 'content', prescreen input ensure not populated explicitly except AssertionError: - trans.response.status = 400 - return "Invalid Dataset '%s' Specified" % inputs[k]['id'] + message = "Invalid workflow input '%s' specified" % inputs[k]['id'] + raise exceptions.ItemAccessibilityException( message ) # Run each step, connecting outputs to inputs replacement_dict = payload.get('replacement_params', {}) @@ -321,6 +311,8 @@ param_map=param_map, ) + # invoke may throw MessageExceptions on tool erors, failure + # to match up inputs, etc... outputs = invoke( trans=trans, workflow=workflow, @@ -340,30 +332,22 @@ return rval - @web.expose_api + @expose_api def workflow_dict( self, trans, workflow_id, **kwd ): """ GET /api/workflows/{encoded_workflow_id}/download Returns a selected workflow as a json dictionary. """ - try: - stored_workflow = trans.sa_session.query(self.app.model.StoredWorkflow).get(trans.security.decode_id(workflow_id)) - except Exception, e: - return ("Workflow with ID='%s' can not be found\n Exception: %s") % (workflow_id, str( e )) - # check to see if user has permissions to selected workflow - if stored_workflow.user != trans.user and not trans.user_is_admin(): - if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: - trans.response.status = 400 - return("Workflow is not owned by or shared with current user") + stored_workflow = self.__get_stored_accessible_workflow( trans, workflow_id ) ret_dict = self._workflow_to_dict( trans, stored_workflow ) if not ret_dict: # This workflow has a tool that's missing from the distribution - trans.response.status = 400 - return "Workflow cannot be exported due to missing tools." + message = "Workflow cannot be exported due to missing tools." + raise exceptions.MessageException( message ) return ret_dict - @web.expose_api + @expose_api def delete( self, trans, id, **kwd ): """ DELETE /api/workflows/{encoded_workflow_id} @@ -392,7 +376,7 @@ # TODO: Unsure of response message to let api know that a workflow was successfully deleted return ( "Workflow '%s' successfully deleted" % stored_workflow.name ) - @web.expose_api + @expose_api def import_new_workflow_deprecated(self, trans, payload, **kwd): """ POST /api/workflows/upload @@ -512,3 +496,32 @@ if out is not None: return self.encode_all_ids( trans, out.to_dict('element'), True) return None + + def __get_stored_accessible_workflow( self, trans, workflow_id ): + stored_workflow = self.__get_stored_workflow( trans, workflow_id ) + + # check to see if user has permissions to selected workflow + if stored_workflow.user != trans.user and not trans.user_is_admin(): + if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: + message = "Workflow is not owned by or shared with current user" + raise exceptions.ItemAccessibilityException( message ) + + return stored_workflow + + def __get_stored_workflow( self, trans, workflow_id ): + try: + workflow_id = self.__decode_id( trans, workflow_id ) + query = trans.sa_session.query( trans.app.model.StoredWorkflow ) + stored_workflow = query.get( workflow_id ) + except Exception: + raise exceptions.ObjectNotFound( "No such workflow found - invalid workflow identifier." ) + if stored_workflow is None: + raise exceptions.ObjectNotFound( "No such workflow found." ) + return stored_workflow + + def __decode_id( self, trans, workflow_id, model_type="workflow" ): + try: + return trans.security.decode_id( workflow_id ) + except Exception: + message = "Malformed %s id ( %s ) specified, unable to decode" % ( model_type, workflow_id ) + raise exceptions.MalformedId( message ) diff -r 479397aedd2b4cb074ac978377f4d27fa92476a6 -r ecc4c38e0529fb3352ad0534e71929f6f6b29e7f test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -9,6 +9,7 @@ from .helpers import skip_without_tool from base.interactor import delete_request # requests like delete +from galaxy.exceptions import error_codes # Workflow API TODO: @@ -24,6 +25,16 @@ self.dataset_populator = DatasetPopulator( self.galaxy_interactor ) self.dataset_collection_populator = DatasetCollectionPopulator( self.galaxy_interactor ) + def test_show_invalid_is_404( self ): + show_response = self._get( "workflow/%s" % self._random_key() ) + self._assert_status_code_is( show_response, 404 ) + + def test_cannot_show_private_workflow( self ): + workflow_id = self.workflow_populator.simple_workflow( "test_not_importportable" ) + with self._different_user(): + show_response = self._get( "workflows/%s" % workflow_id ) + self._assert_status_code_is( show_response, 403 ) + def test_delete( self ): workflow_id = self.workflow_populator.simple_workflow( "test_delete" ) workflow_name = "test_delete (imported from API)" @@ -95,6 +106,29 @@ self._assert_status_code_is( run_workflow_response, 200 ) self.dataset_populator.wait_for_history( history_id, assert_ok=True ) + def test_cannot_run_inaccessible_workflow( self ): + workflow = self.workflow_populator.load_workflow( name="test_for_run_cannot_access" ) + workflow_request, history_id = self._setup_workflow_run( workflow ) + with self._different_user(): + run_workflow_response = self._post( "workflows", data=workflow_request ) + self._assert_status_code_is( run_workflow_response, 403 ) + + def test_404_on_invalid_workflow( self ): + workflow = self.workflow_populator.load_workflow( name="test_for_run_does_not_exist" ) + workflow_request, history_id = self._setup_workflow_run( workflow ) + workflow_request[ "workflow_id" ] = self._random_key() + run_workflow_response = self._post( "workflows", data=workflow_request ) + self._assert_status_code_is( run_workflow_response, 404 ) + + def test_cannot_run_against_other_users_history( self ): + workflow = self.workflow_populator.load_workflow( name="test_for_run_does_not_exist" ) + workflow_request, history_id = self._setup_workflow_run( workflow ) + with self._different_user(): + other_history_id = self.dataset_populator.new_history() + workflow_request[ "history" ] = "hist_id=%s" % other_history_id + run_workflow_response = self._post( "workflows", data=workflow_request ) + self._assert_status_code_is( run_workflow_response, 403 ) + @skip_without_tool( "cat1" ) @skip_without_tool( "collection_two_paired" ) def test_run_workflow_collection_params( self ): @@ -243,6 +277,20 @@ collection_step_state = loads( collection_step[ "tool_state" ] ) self.assertEquals( collection_step_state[ "collection_type" ], u"paired" ) + def test_empty_create( self ): + response = self._post( "workflows" ) + self._assert_status_code_is( response, 400 ) + self._assert_error_code_is( response, error_codes.USER_REQUEST_MISSING_PARAMETER ) + + def test_invalid_create_multiple_types( self ): + data = { + 'shared_workflow_id': '1234567890abcdef', + 'from_history_id': '1234567890abcdef' + } + response = self._post( "workflows", data ) + self._assert_status_code_is( response, 400 ) + self._assert_error_code_is( response, error_codes.USER_REQUEST_INVALID_PARAMETER ) + @skip_without_tool( "random_lines1" ) def test_extract_mapping_workflow_from_history( self ): history_id = self.dataset_populator.new_history() https://bitbucket.org/galaxy/galaxy-central/commits/a3ac64b85faa/ Changeset: a3ac64b85faa User: jmchilton Date: 2014-08-08 15:16:55 Summary: Allow workflow uploads to specify publishable/importable. Use new capabilities to improve workflow testing. Affected #: 3 files diff -r ecc4c38e0529fb3352ad0534e71929f6f6b29e7f -r a3ac64b85faa4e59d331277a801a2b5570a8ca7e lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -1664,7 +1664,7 @@ session.flush() return imported_stored - def _workflow_from_dict( self, trans, data, source=None, add_to_menu=False ): + def _workflow_from_dict( self, trans, data, source=None, add_to_menu=False, publish=False ): """ Creates a workflow from a dict. Created workflow is stored in the database and returned. """ @@ -1752,6 +1752,7 @@ workflow.stored_workflow = stored stored.latest_workflow = workflow stored.user = trans.user + stored.published = publish if data[ 'annotation' ]: self.add_item_annotation( trans.sa_session, stored.user, stored, data[ 'annotation' ] ) diff -r ecc4c38e0529fb3352ad0534e71929f6f6b29e7f -r a3ac64b85faa4e59d331277a801a2b5570a8ca7e lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -12,6 +12,7 @@ from galaxy.web import _future_expose_api as expose_api from galaxy.web.base.controller import BaseAPIController, url_for, UsesStoredWorkflowMixin from galaxy.web.base.controller import UsesHistoryMixin +from galaxy.web.base.controller import SharableMixin from galaxy.workflow.extract import extract_workflow from galaxy.workflow.run import invoke from galaxy.workflow.run import WorkflowRunConfig @@ -19,7 +20,7 @@ log = logging.getLogger(__name__) -class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesHistoryMixin, UsesAnnotations): +class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesHistoryMixin, UsesAnnotations, SharableMixin): def __init__( self, app ): super( BaseAPIController, self ).__init__( app ) @@ -393,7 +394,22 @@ def __api_import_new_workflow( self, trans, payload, **kwd ): data = payload['workflow'] - workflow, missing_tool_tups = self._workflow_from_dict( trans, data, source="API" ) + publish = util.string_as_bool( payload.get( "publish", False ) ) + # If 'publish' set, default to importable. + importable = util.string_as_bool( payload.get( "importable", publish ) ) + + if publish and not importable: + raise exceptions.RequestParameterInvalidException( "Published workflow must be importable." ) + + from_dict_kwds = dict( + source="API", + publish=publish, + ) + workflow, missing_tool_tups = self._workflow_from_dict( trans, data, **from_dict_kwds ) + + if importable: + self._make_item_accessible( trans.sa_session, workflow ) + trans.sa_session.flush() # galaxy workflow newly created id workflow_id = workflow.id @@ -433,9 +449,9 @@ except: raise exceptions.ObjectNotFound( "Malformed workflow id ( %s ) specified." % workflow_id ) if stored_workflow.importable is False: - raise exceptions.MessageException( 'The owner of this workflow has disabled imports via this link.' ) + raise exceptions.ItemAccessibilityException( 'The owner of this workflow has disabled imports via this link.' ) elif stored_workflow.deleted: - raise exceptions.MessageException( "You can't import this workflow because it has been deleted." ) + raise exceptions.ItemDeletionException( "You can't import this workflow because it has been deleted." ) imported_workflow = self._import_shared_workflow( trans, stored_workflow ) item = imported_workflow.to_dict( value_mapper={ 'id': trans.security.encode_id } ) encoded_id = trans.security.encode_id(imported_workflow.id) diff -r ecc4c38e0529fb3352ad0534e71929f6f6b29e7f -r a3ac64b85faa4e59d331277a801a2b5570a8ca7e test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -75,6 +75,26 @@ self._assert_status_code_is( upload_response, 200 ) self._assert_user_has_workflow_with_name( "test_import (imported from API)" ) + def test_import_deprecated( self ): + workflow_id = self.workflow_populator.simple_workflow( "test_import_published_deprecated", publish=True ) + with self._different_user(): + other_import_response = self.__import_workflow( workflow_id ) + self._assert_status_code_is( other_import_response, 200 ) + self._assert_user_has_workflow_with_name( "imported: test_import_published_deprecated (imported from API)") + + def test_not_importable_prevents_import( self ): + workflow_id = self.workflow_populator.simple_workflow( "test_not_importportable" ) + with self._different_user(): + other_import_response = self.__import_workflow( workflow_id ) + self._assert_status_code_is( other_import_response, 403 ) + + def test_import_published( self ): + workflow_id = self.workflow_populator.simple_workflow( "test_import_published", publish=True ) + with self._different_user(): + other_import_response = self.__import_workflow( workflow_id, deprecated_route=True ) + self._assert_status_code_is( other_import_response, 200 ) + self._assert_user_has_workflow_with_name( "imported: test_import_published (imported from API)") + def test_export( self ): uploaded_workflow_id = self.workflow_populator.simple_workflow( "test_for_export" ) download_response = self._get( "workflows/%s/download" % uploaded_workflow_id ) @@ -609,3 +629,16 @@ self._assert_status_code_is( index_response, 200 ) names = map( lambda w: w[ "name" ], index_response.json() ) return names + + def __import_workflow( self, workflow_id, deprecated_route=False ): + if deprecated_route: + route = "workflows/import" + import_data = dict( + workflow_id=workflow_id, + ) + else: + route = "workflows" + import_data = dict( + shared_workflow_id=workflow_id, + ) + return self._post( route, import_data ) https://bitbucket.org/galaxy/galaxy-central/commits/de2e33813275/ Changeset: de2e33813275 User: jmchilton Date: 2014-08-09 15:15:11 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #452) More RESTful workflow API (attempt 3) Affected #: 4 files diff -r fcbd2849ebd17a80e66e0fbdac9df7bb37f88fa2 -r de2e33813275b89a04e7de4e95b21f6d2e100d4e lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -1664,7 +1664,7 @@ session.flush() return imported_stored - def _workflow_from_dict( self, trans, data, source=None, add_to_menu=False ): + def _workflow_from_dict( self, trans, data, source=None, add_to_menu=False, publish=False ): """ Creates a workflow from a dict. Created workflow is stored in the database and returned. """ @@ -1752,6 +1752,7 @@ workflow.stored_workflow = stored stored.latest_workflow = workflow stored.user = trans.user + stored.published = publish if data[ 'annotation' ]: self.add_item_annotation( trans.sa_session, stored.user, stored, data[ 'annotation' ] ) diff -r fcbd2849ebd17a80e66e0fbdac9df7bb37f88fa2 -r de2e33813275b89a04e7de4e95b21f6d2e100d4e lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -6,11 +6,13 @@ import logging from sqlalchemy import desc, or_ -from galaxy import exceptions, util, web +from galaxy import exceptions, util from galaxy.model.item_attrs import UsesAnnotations +from galaxy.managers import histories from galaxy.web import _future_expose_api as expose_api from galaxy.web.base.controller import BaseAPIController, url_for, UsesStoredWorkflowMixin from galaxy.web.base.controller import UsesHistoryMixin +from galaxy.web.base.controller import SharableMixin from galaxy.workflow.extract import extract_workflow from galaxy.workflow.run import invoke from galaxy.workflow.run import WorkflowRunConfig @@ -18,9 +20,13 @@ log = logging.getLogger(__name__) -class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesHistoryMixin, UsesAnnotations): +class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesHistoryMixin, UsesAnnotations, SharableMixin): - @web.expose_api + def __init__( self, app ): + super( BaseAPIController, self ).__init__( app ) + self.history_manager = histories.HistoryManager() + + @expose_api def index(self, trans, **kwd): """ GET /api/workflows @@ -54,30 +60,21 @@ rval.append(item) return rval - @web.expose_api + @expose_api def show(self, trans, id, **kwd): """ GET /api/workflows/{encoded_workflow_id} Displays information needed to run a workflow from the command line. """ - workflow_id = id - try: - decoded_workflow_id = trans.security.decode_id(workflow_id) - except TypeError: - trans.response.status = 400 - return "Malformed workflow id ( %s ) specified, unable to decode." % str(workflow_id) - try: - stored_workflow = trans.sa_session.query(trans.app.model.StoredWorkflow).get(decoded_workflow_id) - if stored_workflow.importable is False and stored_workflow.user != trans.user and not trans.user_is_admin(): - if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: - trans.response.status = 400 - return("Workflow is neither importable, nor owned by or shared with current user") - except: - trans.response.status = 400 - return "That workflow does not exist." + stored_workflow = self.__get_stored_workflow( trans, id ) + if stored_workflow.importable is False and stored_workflow.user != trans.user and not trans.user_is_admin(): + if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: + message = "Workflow is neither importable, nor owned by or shared with current user" + raise exceptions.ItemAccessibilityException( message ) + item = stored_workflow.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id } ) - item['url'] = url_for('workflow', id=workflow_id) + item['url'] = url_for('workflow', id=id) item['owner'] = stored_workflow.user.username latest_workflow = stored_workflow.latest_workflow inputs = {} @@ -114,7 +111,7 @@ item['steps'] = steps return item - @web.expose_api + @expose_api def create(self, trans, payload, **kwd): """ POST /api/workflows @@ -161,10 +158,20 @@ :param workflow_name: If from_history_id is set - name of the workflow to create when extracting a workflow from history :type workflow_name: str """ + ways_to_create = set( [ + 'workflow_id', + 'installed_repository_file', + 'from_history_id', + 'shared_workflow_id', + 'workflow', + ] ).intersection( payload ) + if len( ways_to_create ) == 0: + message = "One parameter among - %s - must be specified" % ", ".join( ways_to_create ) + raise exceptions.RequestParameterMissingException( message ) - if len( set( ['workflow_id', 'installed_repository_file', 'from_history_id'] ).intersection( payload ) ) > 1: - trans.response.status = 403 - return "Only one among 'workflow_id', 'installed_repository_file', 'from_history_id' must be specified" + if len( ways_to_create ) > 1: + message = "Only one parameter among - %s - must be specified" % ", ".join( ways_to_create ) + raise exceptions.RequestParameterInvalidException( message ) if 'installed_repository_file' in payload: workflow_controller = trans.webapp.controllers[ 'workflow' ] @@ -193,10 +200,17 @@ item[ 'url' ] = url_for( 'workflow', id=item[ 'id' ] ) return item + if 'shared_workflow_id' in payload: + workflow_id = payload[ 'shared_workflow_id' ] + return self.__api_import_shared_workflow( trans, workflow_id, payload ) + + if 'workflow' in payload: + return self.__api_import_new_workflow( trans, payload, **kwd ) + workflow_id = payload.get( 'workflow_id', None ) if not workflow_id: - trans.response.status = 403 - return "Either workflow_id, installed_repository_file or from_history_id must be specified" + message = "Invalid workflow_id specified." + raise exceptions.RequestParameterInvalidException( message ) # Pull other parameters out of payload. param_map = payload.get( 'parameters', {} ) @@ -225,34 +239,24 @@ history_param = payload.get('history', '') # Get workflow + accessibility check. - stored_workflow = trans.sa_session.query(self.app.model.StoredWorkflow).get(trans.security.decode_id(workflow_id)) - if stored_workflow.user != trans.user and not trans.user_is_admin(): - if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: - trans.response.status = 400 - return("Workflow is not owned by or shared with current user") + stored_workflow = self.__get_stored_accessible_workflow( trans, workflow_id ) workflow = stored_workflow.latest_workflow # Sanity checks. - if not workflow: - trans.response.status = 400 - return "Workflow not found." if len( workflow.steps ) == 0: - trans.response.status = 400 - return "Workflow cannot be run because it does not have any steps" + raise exceptions.MessageException( "Workflow cannot be run because it does not have any steps" ) if workflow.has_cycles: - trans.response.status = 400 - return "Workflow cannot be run because it contains cycles" + raise exceptions.MessageException( "Workflow cannot be run because it contains cycles" ) if workflow.has_errors: - trans.response.status = 400 - return "Workflow cannot be run because of validation errors in some steps" + message = "Workflow cannot be run because of validation errors in some steps" + raise exceptions.MessageException( message ) # Get target history. if history_param.startswith('hist_id='): # Passing an existing history to use. - history = trans.sa_session.query(self.app.model.History).get(trans.security.decode_id(history_param[8:])) - if history.user != trans.user and not trans.user_is_admin(): - trans.response.status = 400 - return "Invalid History specified." + encoded_history_id = history_param[ 8: ] + history_id = self.__decode_id( trans, encoded_history_id, model_type="history" ) + history = self.history_manager.get( trans, history_id, check_ownership=True ) else: # Send workflow outputs to new history. history = self.app.model.History(name=history_param, user=trans.user) @@ -284,8 +288,8 @@ inputs[k]['id'] ) else: - trans.response.status = 400 - return "Unknown dataset source '%s' specified." % inputs[k]['src'] + message = "Unknown workflow input source '%s' specified." % inputs[k]['src'] + raise exceptions.RequestParameterInvalidException( message ) if add_to_history and content.history != history: content = content.copy() if isinstance( content, self.app.model.HistoryDatasetAssociation ): @@ -294,8 +298,8 @@ history.add_dataset_collection( content ) inputs[k]['hda'] = content # TODO: rename key to 'content', prescreen input ensure not populated explicitly except AssertionError: - trans.response.status = 400 - return "Invalid Dataset '%s' Specified" % inputs[k]['id'] + message = "Invalid workflow input '%s' specified" % inputs[k]['id'] + raise exceptions.ItemAccessibilityException( message ) # Run each step, connecting outputs to inputs replacement_dict = payload.get('replacement_params', {}) @@ -308,6 +312,8 @@ param_map=param_map, ) + # invoke may throw MessageExceptions on tool erors, failure + # to match up inputs, etc... outputs = invoke( trans=trans, workflow=workflow, @@ -327,30 +333,22 @@ return rval - @web.expose_api + @expose_api def workflow_dict( self, trans, workflow_id, **kwd ): """ GET /api/workflows/{encoded_workflow_id}/download Returns a selected workflow as a json dictionary. """ - try: - stored_workflow = trans.sa_session.query(self.app.model.StoredWorkflow).get(trans.security.decode_id(workflow_id)) - except Exception, e: - return ("Workflow with ID='%s' can not be found\n Exception: %s") % (workflow_id, str( e )) - # check to see if user has permissions to selected workflow - if stored_workflow.user != trans.user and not trans.user_is_admin(): - if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: - trans.response.status = 400 - return("Workflow is not owned by or shared with current user") + stored_workflow = self.__get_stored_accessible_workflow( trans, workflow_id ) ret_dict = self._workflow_to_dict( trans, stored_workflow ) if not ret_dict: # This workflow has a tool that's missing from the distribution - trans.response.status = 400 - return "Workflow cannot be exported due to missing tools." + message = "Workflow cannot be exported due to missing tools." + raise exceptions.MessageException( message ) return ret_dict - @web.expose_api + @expose_api def delete( self, trans, id, **kwd ): """ DELETE /api/workflows/{encoded_workflow_id} @@ -379,19 +377,39 @@ # TODO: Unsure of response message to let api know that a workflow was successfully deleted return ( "Workflow '%s' successfully deleted" % stored_workflow.name ) - @web.expose_api - def import_new_workflow(self, trans, payload, **kwd): + @expose_api + def import_new_workflow_deprecated(self, trans, payload, **kwd): """ POST /api/workflows/upload Importing dynamic workflows from the api. Return newly generated workflow id. Author: rpark # currently assumes payload['workflow'] is a json representation of a workflow to be inserted into the database + + Deprecated in favor to POST /api/workflows with encoded 'workflow' in + payload the same way. """ + return self.__api_import_new_workflow( trans, payload, **kwd ) + def __api_import_new_workflow( self, trans, payload, **kwd ): data = payload['workflow'] - workflow, missing_tool_tups = self._workflow_from_dict( trans, data, source="API" ) + publish = util.string_as_bool( payload.get( "publish", False ) ) + # If 'publish' set, default to importable. + importable = util.string_as_bool( payload.get( "importable", publish ) ) + + if publish and not importable: + raise exceptions.RequestParameterInvalidException( "Published workflow must be importable." ) + + from_dict_kwds = dict( + source="API", + publish=publish, + ) + workflow, missing_tool_tups = self._workflow_from_dict( trans, data, **from_dict_kwds ) + + if importable: + self._make_item_accessible( trans.sa_session, workflow ) + trans.sa_session.flush() # galaxy workflow newly created id workflow_id = workflow.id @@ -409,7 +427,7 @@ return item @expose_api - def import_shared_workflow(self, trans, payload, **kwd): + def import_shared_workflow_deprecated(self, trans, payload, **kwd): """ POST /api/workflows/import Import a workflow shared by other users. @@ -423,14 +441,17 @@ workflow_id = payload.get('workflow_id', None) if workflow_id is None: raise exceptions.ObjectAttributeMissingException( "Missing required parameter 'workflow_id'." ) + self.__api_import_shared_workflow( trans, workflow_id, payload ) + + def __api_import_shared_workflow( self, trans, workflow_id, payload, **kwd ): try: stored_workflow = self.get_stored_workflow( trans, workflow_id, check_ownership=False ) except: raise exceptions.ObjectNotFound( "Malformed workflow id ( %s ) specified." % workflow_id ) if stored_workflow.importable is False: - raise exceptions.MessageException( 'The owner of this workflow has disabled imports via this link.' ) + raise exceptions.ItemAccessibilityException( 'The owner of this workflow has disabled imports via this link.' ) elif stored_workflow.deleted: - raise exceptions.MessageException( "You can't import this workflow because it has been deleted." ) + raise exceptions.ItemDeletionException( "You can't import this workflow because it has been deleted." ) imported_workflow = self._import_shared_workflow( trans, stored_workflow ) item = imported_workflow.to_dict( value_mapper={ 'id': trans.security.encode_id } ) encoded_id = trans.security.encode_id(imported_workflow.id) @@ -491,3 +512,32 @@ if out is not None: return self.encode_all_ids( trans, out.to_dict('element'), True) return None + + def __get_stored_accessible_workflow( self, trans, workflow_id ): + stored_workflow = self.__get_stored_workflow( trans, workflow_id ) + + # check to see if user has permissions to selected workflow + if stored_workflow.user != trans.user and not trans.user_is_admin(): + if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: + message = "Workflow is not owned by or shared with current user" + raise exceptions.ItemAccessibilityException( message ) + + return stored_workflow + + def __get_stored_workflow( self, trans, workflow_id ): + try: + workflow_id = self.__decode_id( trans, workflow_id ) + query = trans.sa_session.query( trans.app.model.StoredWorkflow ) + stored_workflow = query.get( workflow_id ) + except Exception: + raise exceptions.ObjectNotFound( "No such workflow found - invalid workflow identifier." ) + if stored_workflow is None: + raise exceptions.ObjectNotFound( "No such workflow found." ) + return stored_workflow + + def __decode_id( self, trans, workflow_id, model_type="workflow" ): + try: + return trans.security.decode_id( workflow_id ) + except Exception: + message = "Malformed %s id ( %s ) specified, unable to decode" % ( model_type, workflow_id ) + raise exceptions.MalformedId( message ) diff -r fcbd2849ebd17a80e66e0fbdac9df7bb37f88fa2 -r de2e33813275b89a04e7de4e95b21f6d2e100d4e lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -213,13 +213,13 @@ webapp.add_route( '/visualization/show/:visualization_name', controller='visualization', action='render', visualization_name=None ) - # "POST /api/workflows/import" => ``workflows.import_workflow()``. - # Defines a named route "import_workflow". - webapp.mapper.connect( 'import_workflow', '/api/workflows/upload', controller='workflows', action='import_new_workflow', conditions=dict( method=['POST'] ) ) + # Deprecated in favor of POST /api/workflows with 'workflow' in payload. + webapp.mapper.connect( 'import_workflow_deprecated', '/api/workflows/upload', controller='workflows', action='import_new_workflow_deprecated', conditions=dict( method=['POST'] ) ) webapp.mapper.connect( 'workflow_dict', '/api/workflows/{workflow_id}/download', controller='workflows', action='workflow_dict', conditions=dict( method=['GET'] ) ) # Preserve the following download route for now for dependent applications -- deprecate at some point webapp.mapper.connect( 'workflow_dict', '/api/workflows/download/{workflow_id}', controller='workflows', action='workflow_dict', conditions=dict( method=['GET'] ) ) - webapp.mapper.connect( 'import_shared_workflow', '/api/workflows/import', controller='workflows', action='import_shared_workflow', conditions=dict( method=['POST'] ) ) + # Deprecated in favor of POST /api/workflows with shared_workflow_id in payload. + webapp.mapper.connect( 'import_shared_workflow_deprecated', '/api/workflows/import', controller='workflows', action='import_shared_workflow_deprecated', conditions=dict( method=['POST'] ) ) webapp.mapper.connect( 'workflow_usage', '/api/workflows/{workflow_id}/usage', controller='workflows', action='workflow_usage', conditions=dict(method=['GET'])) webapp.mapper.connect( 'workflow_usage_contents', '/api/workflows/{workflow_id}/usage/{usage_id}', controller='workflows', action='workflow_usage_contents', conditions=dict(method=['GET'])) diff -r fcbd2849ebd17a80e66e0fbdac9df7bb37f88fa2 -r de2e33813275b89a04e7de4e95b21f6d2e100d4e test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -9,6 +9,7 @@ from .helpers import skip_without_tool from base.interactor import delete_request # requests like delete +from galaxy.exceptions import error_codes # Workflow API TODO: @@ -24,6 +25,16 @@ self.dataset_populator = DatasetPopulator( self.galaxy_interactor ) self.dataset_collection_populator = DatasetCollectionPopulator( self.galaxy_interactor ) + def test_show_invalid_is_404( self ): + show_response = self._get( "workflow/%s" % self._random_key() ) + self._assert_status_code_is( show_response, 404 ) + + def test_cannot_show_private_workflow( self ): + workflow_id = self.workflow_populator.simple_workflow( "test_not_importportable" ) + with self._different_user(): + show_response = self._get( "workflows/%s" % workflow_id ) + self._assert_status_code_is( show_response, 403 ) + def test_delete( self ): workflow_id = self.workflow_populator.simple_workflow( "test_delete" ) workflow_name = "test_delete (imported from API)" @@ -46,14 +57,44 @@ self._assert_status_code_is( index_response, 200 ) assert isinstance( index_response.json(), list ) - def test_import( self ): + def test_upload( self ): + self.__test_upload( use_deprecated_route=False ) + + def test_upload_deprecated( self ): + self.__test_upload( use_deprecated_route=True ) + + def __test_upload( self, use_deprecated_route ): data = dict( workflow=dumps( self.workflow_populator.load_workflow( name="test_import" ) ), ) - upload_response = self._post( "workflows/upload", data=data ) + if use_deprecated_route: + route = "workflows/upload" + else: + route = "workflows" + upload_response = self._post( route, data=data ) self._assert_status_code_is( upload_response, 200 ) self._assert_user_has_workflow_with_name( "test_import (imported from API)" ) + def test_import_deprecated( self ): + workflow_id = self.workflow_populator.simple_workflow( "test_import_published_deprecated", publish=True ) + with self._different_user(): + other_import_response = self.__import_workflow( workflow_id ) + self._assert_status_code_is( other_import_response, 200 ) + self._assert_user_has_workflow_with_name( "imported: test_import_published_deprecated (imported from API)") + + def test_not_importable_prevents_import( self ): + workflow_id = self.workflow_populator.simple_workflow( "test_not_importportable" ) + with self._different_user(): + other_import_response = self.__import_workflow( workflow_id ) + self._assert_status_code_is( other_import_response, 403 ) + + def test_import_published( self ): + workflow_id = self.workflow_populator.simple_workflow( "test_import_published", publish=True ) + with self._different_user(): + other_import_response = self.__import_workflow( workflow_id, deprecated_route=True ) + self._assert_status_code_is( other_import_response, 200 ) + self._assert_user_has_workflow_with_name( "imported: test_import_published (imported from API)") + def test_export( self ): uploaded_workflow_id = self.workflow_populator.simple_workflow( "test_for_export" ) download_response = self._get( "workflows/%s/download" % uploaded_workflow_id ) @@ -85,6 +126,29 @@ self._assert_status_code_is( run_workflow_response, 200 ) self.dataset_populator.wait_for_history( history_id, assert_ok=True ) + def test_cannot_run_inaccessible_workflow( self ): + workflow = self.workflow_populator.load_workflow( name="test_for_run_cannot_access" ) + workflow_request, history_id = self._setup_workflow_run( workflow ) + with self._different_user(): + run_workflow_response = self._post( "workflows", data=workflow_request ) + self._assert_status_code_is( run_workflow_response, 403 ) + + def test_404_on_invalid_workflow( self ): + workflow = self.workflow_populator.load_workflow( name="test_for_run_does_not_exist" ) + workflow_request, history_id = self._setup_workflow_run( workflow ) + workflow_request[ "workflow_id" ] = self._random_key() + run_workflow_response = self._post( "workflows", data=workflow_request ) + self._assert_status_code_is( run_workflow_response, 404 ) + + def test_cannot_run_against_other_users_history( self ): + workflow = self.workflow_populator.load_workflow( name="test_for_run_does_not_exist" ) + workflow_request, history_id = self._setup_workflow_run( workflow ) + with self._different_user(): + other_history_id = self.dataset_populator.new_history() + workflow_request[ "history" ] = "hist_id=%s" % other_history_id + run_workflow_response = self._post( "workflows", data=workflow_request ) + self._assert_status_code_is( run_workflow_response, 403 ) + @skip_without_tool( "cat1" ) @skip_without_tool( "collection_two_paired" ) def test_run_workflow_collection_params( self ): @@ -233,6 +297,20 @@ collection_step_state = loads( collection_step[ "tool_state" ] ) self.assertEquals( collection_step_state[ "collection_type" ], u"paired" ) + def test_empty_create( self ): + response = self._post( "workflows" ) + self._assert_status_code_is( response, 400 ) + self._assert_error_code_is( response, error_codes.USER_REQUEST_MISSING_PARAMETER ) + + def test_invalid_create_multiple_types( self ): + data = { + 'shared_workflow_id': '1234567890abcdef', + 'from_history_id': '1234567890abcdef' + } + response = self._post( "workflows", data ) + self._assert_status_code_is( response, 400 ) + self._assert_error_code_is( response, error_codes.USER_REQUEST_INVALID_PARAMETER ) + @skip_without_tool( "random_lines1" ) def test_extract_mapping_workflow_from_history( self ): history_id = self.dataset_populator.new_history() @@ -551,3 +629,16 @@ self._assert_status_code_is( index_response, 200 ) names = map( lambda w: w[ "name" ], index_response.json() ) return names + + def __import_workflow( self, workflow_id, deprecated_route=False ): + if deprecated_route: + route = "workflows/import" + import_data = dict( + workflow_id=workflow_id, + ) + else: + route = "workflows" + import_data = dict( + shared_workflow_id=workflow_id, + ) + return self._post( route, import_data ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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