From 5e3dc3bad03e3ed4e134a733bed417fc7e360543 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Tue, 17 Mar 2015 12:25:59 -0400 Subject: [PATCH] pep8 datasets manager --- lib/galaxy/managers/datasets.py | 61 +++++++++++++++++---------------- 1 file changed, 31 insertions(+), 30 deletions(-) diff --git a/lib/galaxy/managers/datasets.py b/lib/galaxy/managers/datasets.py index f1e2bc7e41a..802845d8063 100644 --- a/lib/galaxy/managers/datasets.py +++ b/lib/galaxy/managers/datasets.py @@ -20,7 +20,7 @@ class DatasetManager( base.ModelManager, secured.AccessibleManagerMixin, deletab model_class = model.Dataset foreign_key_name = 'dataset' - #TODO:?? get + error_if_uploading is common pattern, should upload check be worked into access/owed? + # TODO:?? get + error_if_uploading is common pattern, should upload check be worked into access/owed? def __init__( self, app ): super( DatasetManager, self ).__init__( app ) @@ -40,26 +40,26 @@ class DatasetManager( base.ModelManager, secured.AccessibleManagerMixin, deletab self.app.model.context.flush() return dataset - #def copy( self, dataset, **kwargs ): + # def copy( self, dataset, **kwargs ): # """ # Clone, update, and return the given dataset. # """ # pass - #def to_hda( self, trans, dataset, history, **kwargs ): + # def to_hda( self, trans, dataset, history, **kwargs ): # """ # Create an hda from this dataset. # """ # pass - #def to_ldda( self, trans, dataset, library_folder, **kwargs ): + # def to_ldda( self, trans, dataset, library_folder, **kwargs ): # """ # Create an ldda from this dataset. # """ # pass - #TODO: this may be more conv. somewhere else -#TODO: how to allow admin bypass? + # TODO: this may be more conv. somewhere else + # TODO: how to allow admin bypass? def error_unless_dataset_purge_allowed( self, trans, item, msg=None ): if not self.app.config.allow_user_dataset_purge: msg = msg or 'This instance does not allow user dataset purging' @@ -102,7 +102,7 @@ class DatasetManager( base.ModelManager, secured.AccessibleManagerMixin, deletab roles = user.all_roles() if user else [] return self.app.security_agent.can_access_dataset( roles, dataset ) - #TODO: these need work + # TODO: these need work def _access_permission( self, trans, dataset, user=None, role=None ): """ Return most recent DatasetPermissions for the dataset and user. @@ -114,10 +114,10 @@ class DatasetManager( base.ModelManager, secured.AccessibleManagerMixin, deletab user_roles = [ role ] if role else user.all_roles() user_role_ids = [ r.id for r in user_roles ] query = ( self.app.model.context.query( model.DatasetPermissions ) - .filter( model.DatasetPermissions.action == access_action ) - .filter( model.DatasetPermissions.dataset == dataset ) - .filter( model.DatasetPermissions.role_id.in_( user_role_ids ) ) ) - #TODO:?? most recent? + .filter( model.DatasetPermissions.action == access_action ) + .filter( model.DatasetPermissions.dataset == dataset ) + .filter( model.DatasetPermissions.role_id.in_( user_role_ids ) ) ) + # TODO:?? most recent? return query.first() def _create_access_permission( self, trans, dataset, role, flush=True ): @@ -131,7 +131,7 @@ class DatasetManager( base.ModelManager, secured.AccessibleManagerMixin, deletab self.app.model.context.flush() return permission - #def give_access_permission( self, trans, dataset, user, flush=True ): + # def give_access_permission( self, trans, dataset, user, flush=True ): # """ # """ # # for now, use the user's private role @@ -160,29 +160,29 @@ class DatasetManager( base.ModelManager, secured.AccessibleManagerMixin, deletab # # return dataset - #def remove_access_permission( self, trans, dataset, user ): + # def remove_access_permission( self, trans, dataset, user ): # """ # """ # pass # .... manage/modify - #def has_manage_permission( self, trans, dataset, user ): + # def has_manage_permission( self, trans, dataset, user ): # """ # """ # pass # - #def give_manage_permission( self, trans, dataset, user ): + # def give_manage_permission( self, trans, dataset, user ): # """ # """ # pass # - #def remove_manage_permission( self, trans, dataset, user ): + # def remove_manage_permission( self, trans, dataset, user ): # """ # """ # pass - #TODO: implement above for groups - #TODO: datatypes? + # TODO: implement above for groups + # TODO: datatypes? # .... data, object_store @@ -198,9 +198,9 @@ class DatasetSerializer( base.ModelSerializer, deletable.PurgableSerializerMixin 'create_time', 'update_time', 'state', 'deleted', 'purged', 'purgable', - #'object_store_id', - #'external_filename', - #'extra_files_path', + # 'object_store_id', + # 'external_filename', + # 'extra_files_path', 'file_size', 'total_size', 'uuid', ]) @@ -211,10 +211,10 @@ class DatasetSerializer( base.ModelSerializer, deletable.PurgableSerializerMixin deletable.PurgableSerializerMixin.add_serializers( self ) self.serializers.update({ - 'id' : self.serialize_id, - 'create_time' : self.serialize_date, - 'update_time' : self.serialize_date, - 'uuid' : lambda t, i, k: str( i.uuid ) if i.uuid else None, + 'id': self.serialize_id, + 'create_time': self.serialize_date, + 'update_time': self.serialize_date, + 'uuid': lambda t, i, k: str( i.uuid ) if i.uuid else None, }) @@ -248,14 +248,14 @@ class DatasetAssociationManager( base.ModelManager, secured.AccessibleManagerMix # defer to the dataset return self.dataset_manager.is_accessible( trans, dataset_assoc.dataset, user ) - #def metadata( self, trans, dataset_assoc ): + # def metadata( self, trans, dataset_assoc ): # """ # Return the metadata collection. # """ # # get metadata # pass - #def is_being_used( self, trans, dataset_assoc ): + # def is_being_used( self, trans, dataset_assoc ): # """ # """ # #TODO: check history_associations, library_associations @@ -275,6 +275,7 @@ class DatasetAssociationDeserializer( base.ModelDeserializer, deletable.Purgable super( DatasetAssociationDeserializer, self ).add_deserializers() deletable.PurgableDeserializerMixin.add_deserializers( self ) + class DatasetAssociationFilters( base.ModelFilterParser, deletable.PurgableFiltersMixin ): def _add_parsers( self ): @@ -282,7 +283,7 @@ class DatasetAssociationFilters( base.ModelFilterParser, deletable.PurgableFilte deletable.PurgableFiltersMixin._add_parsers( self ) self.orm_filter_parsers.update({ - 'name' : { 'op': ( 'eq', 'contains', 'like' ) }, - 'state' : { 'op': ( 'eq', 'in' ) }, + 'name': { 'op': ( 'eq', 'contains', 'like' ) }, + 'state': { 'op': ( 'eq', 'in' ) }, }) - #self.fn_filter_parsers.update({}) + # self.fn_filter_parsers.update({})