diff --git a/lib/galaxy/webapps/galaxy/api/datasets.py b/lib/galaxy/webapps/galaxy/api/datasets.py index 0f24ba1e2ce..8d203a7bd64 100644 --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -67,7 +67,7 @@ class DatasetsController( BaseAPIController, UsesVisualizationMixin ): # Default: return dataset as dict. if hda_ldda == 'hda': return self.hda_serializer.serialize_to_view( dataset, - view=kwd.get( 'view', 'detailed' ), user=trans.user, trans=trans ) + view=kwd.get( 'view', 'detailed' ), user=trans.user, trans=trans ) else: rval = dataset.to_dict() @@ -111,7 +111,7 @@ class DatasetsController( BaseAPIController, UsesVisualizationMixin ): # If there is a chrom, check for data on the chrom. if chrom: data_provider = trans.app.data_provider_registry.get_data_provider( trans, - original_dataset=dataset, source='index' ) + original_dataset=dataset, source='index' ) if not data_provider.has_data( chrom ): return dataset.conversion_messages.NO_DATA @@ -286,7 +286,7 @@ class DatasetsController( BaseAPIController, UsesVisualizationMixin ): if raw: if filename and filename != 'index': file_path = trans.app.object_store.get_filename( hda.dataset, - extra_dir=( 'dataset_%s_files' % hda.dataset.id ), alt_name=filename) + extra_dir=( 'dataset_%s_files' % hda.dataset.id ), alt_name=filename) else: file_path = hda.file_name rval = open( file_path ) diff --git a/lib/galaxy/webapps/galaxy/api/group_roles.py b/lib/galaxy/webapps/galaxy/api/group_roles.py index bf85a1669c2..b4d40b4d0f3 100644 --- a/lib/galaxy/webapps/galaxy/api/group_roles.py +++ b/lib/galaxy/webapps/galaxy/api/group_roles.py @@ -56,8 +56,8 @@ class GroupRolesAPIController( BaseAPIController ): for gra in group.roles: if gra.role == role: item = dict( id=role_id, - name=role.name, - url=url_for( 'group_role', group_id=group_id, id=role_id) ) # TODO Fix This + name=role.name, + url=url_for( 'group_role', group_id=group_id, id=role_id) ) # TODO Fix This if not item: item = "role %s not in group %s" % (role.name, group.name) except Exception, e: @@ -82,8 +82,8 @@ class GroupRolesAPIController( BaseAPIController ): for gra in group.roles: if gra.role == role: item = dict( id=role_id, - name=role.name, - url=url_for( 'group_role', group_id=group_id, id=role_id) ) + name=role.name, + url=url_for( 'group_role', group_id=group_id, id=role_id) ) if not item: gra = trans.app.model.GroupRoleAssociation( group, role ) # Add GroupRoleAssociation diff --git a/lib/galaxy/webapps/galaxy/api/group_users.py b/lib/galaxy/webapps/galaxy/api/group_users.py index e06ca581c63..51dae1f3265 100644 --- a/lib/galaxy/webapps/galaxy/api/group_users.py +++ b/lib/galaxy/webapps/galaxy/api/group_users.py @@ -56,8 +56,8 @@ class GroupUsersAPIController( BaseAPIController ): for uga in group.users: if uga.user == user: item = dict( id=user_id, - email=user.email, - url=url_for( 'group_user', group_id=group_id, id=user_id) ) # TODO Fix This + email=user.email, + url=url_for( 'group_user', group_id=group_id, id=user_id) ) # TODO Fix This if not item: item = "user %s not in group %s" % (user.email, group.name) except Exception, e: @@ -82,8 +82,8 @@ class GroupUsersAPIController( BaseAPIController ): for uga in group.users: if uga.user == user: item = dict( id=user_id, - email=user.email, - url=url_for( 'group_user', group_id=group_id, id=user_id) ) + email=user.email, + url=url_for( 'group_user', group_id=group_id, id=user_id) ) if not item: uga = trans.app.model.UserGroupAssociation( user, group ) # Add UserGroupAssociations diff --git a/lib/galaxy/webapps/galaxy/api/histories.py b/lib/galaxy/webapps/galaxy/api/histories.py index af8e75b42a1..183fbe1b2a2 100644 --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -123,7 +123,7 @@ class HistoriesController( BaseAPIController, ExportsHistoryMixin, ImportsHistor rval = [] for history in histories: history_dict = self.history_serializer.serialize_to_view( history, - user=trans.user, trans=trans, **serialization_params ) + user=trans.user, trans=trans, **serialization_params ) rval.append( history_dict ) return rval @@ -183,7 +183,7 @@ class HistoriesController( BaseAPIController, ExportsHistoryMixin, ImportsHistor history = self.history_manager.get_accessible( self.decode_id( history_id ), trans.user, current_history=trans.history ) return self.history_serializer.serialize_to_view( history, - user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) ) + user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) ) @expose_api_anonymous def citations( self, trans, history_id, **kwd ): @@ -249,7 +249,7 @@ class HistoriesController( BaseAPIController, ExportsHistoryMixin, ImportsHistor trans.sa_session.flush() return self.history_serializer.serialize_to_view( new_history, - user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) ) + user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) ) @expose_api def delete( self, trans, id, **kwd ): @@ -288,7 +288,7 @@ class HistoriesController( BaseAPIController, ExportsHistoryMixin, ImportsHistor self.history_manager.purge( history ) return self.history_serializer.serialize_to_view( history, - user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) ) + user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) ) @expose_api def undelete( self, trans, id, **kwd ): @@ -311,7 +311,7 @@ class HistoriesController( BaseAPIController, ExportsHistoryMixin, ImportsHistor self.history_manager.undelete( history ) return self.history_serializer.serialize_to_view( history, - user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) ) + user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) ) @expose_api def update( self, trans, id, payload, **kwd ): @@ -340,7 +340,7 @@ class HistoriesController( BaseAPIController, ExportsHistoryMixin, ImportsHistor self.history_deserializer.deserialize( history, payload, user=trans.user, trans=trans ) return self.history_serializer.serialize_to_view( history, - user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) ) + user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) ) @expose_api def archive_export( self, trans, id, **kwds ): diff --git a/lib/galaxy/webapps/galaxy/api/history_contents.py b/lib/galaxy/webapps/galaxy/api/history_contents.py index 65ad3bfc51c..6841fd86f99 100644 --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -111,7 +111,7 @@ class HistoryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar def __collection_dict( self, trans, dataset_collection_instance, view="collection" ): return dictify_dataset_collection_instance( dataset_collection_instance, - security=trans.security, parent=dataset_collection_instance.history, view=view ) + security=trans.security, parent=dataset_collection_instance.history, view=view ) @expose_api_anonymous def show( self, trans, id, history_id, **kwd ): @@ -140,7 +140,7 @@ class HistoryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar def __show_dataset( self, trans, id, **kwd ): hda = self.hda_manager.get_accessible( self.decode_id( id ), trans.user ) return self.hda_serializer.serialize_to_view( hda, - user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) ) + user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) ) def __show_dataset_collection( self, trans, id, history_id, **kwd ): try: @@ -210,7 +210,7 @@ class HistoryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar # examples. See also bioblend and API tests for specific examples. history = self.history_manager.get_owned( self.decode_id( history_id ), trans.user, - current_history=trans.history ) + current_history=trans.history ) type = payload.get( 'type', 'dataset' ) if type == 'dataset': @@ -253,7 +253,7 @@ class HistoryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar if not hda: return None return self.hda_serializer.serialize_to_view( hda, - user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) ) + user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) ) def __create_dataset_collection( self, trans, history, payload, **kwd ): source = kwd.get("source", "new_collection") @@ -344,7 +344,7 @@ class HistoryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar if payload.get( 'deleted', False ): self.hda_manager.stop_creating_job( hda ) return self.hda_serializer.serialize_to_view( hda, - user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) ) + user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) ) return {} @@ -403,7 +403,7 @@ class HistoryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar else: self.hda_manager.delete( hda ) return self.hda_serializer.serialize_to_view( hda, - user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) ) + user=trans.user, trans=trans, **self._parse_serialization_params( kwd, 'detailed' ) ) def __handle_unknown_contents_type( self, trans, contents_type ): raise exceptions.UnknownContentsType('Unknown contents type: %s' % type) diff --git a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py index ab31b4b3548..e9ac154736e 100644 --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -120,7 +120,7 @@ class ToolShedRepositoriesController( BaseAPIController ): def __get_value_mapper( self, trans, tool_shed_repository ): value_mapper = { 'id' : trans.security.encode_id( tool_shed_repository.id ), - 'error_message' : tool_shed_repository.error_message or '' } + 'error_message' : tool_shed_repository.error_message or '' } return value_mapper @expose_api diff --git a/lib/galaxy/webapps/galaxy/api/visualizations.py b/lib/galaxy/webapps/galaxy/api/visualizations.py index f360f725dd0..17a3afd3f5c 100644 --- a/lib/galaxy/webapps/galaxy/api/visualizations.py +++ b/lib/galaxy/webapps/galaxy/api/visualizations.py @@ -63,7 +63,7 @@ class VisualizationsController( BaseAPIController, UsesVisualizationMixin, Shara visualization = self.get_visualization( trans, id, check_ownership=False, check_accessible=True ) dictionary = trans.security.encode_dict_ids( self.get_visualization_dict( visualization ) ) dictionary[ 'url' ] = web.url_for( controller='visualization', - action="display_by_username_and_slug", username=visualization.user.username, slug=visualization.slug ) + action="display_by_username_and_slug", username=visualization.user.username, slug=visualization.slug ) dictionary[ 'annotation' ] = self.get_item_annotation_str( trans.sa_session, trans.user, visualization ) # need to encode ids in revisions as well