[galaxy-commits] commit/galaxy-central: 3 new changesets

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7cd7546f107e/ Changeset: 7cd7546f107e User: dannon Date: 2015-01-22 21:48:26+00:00 Summary: cleanup, pep8 base manager Affected #: 1 file diff -r 89daa32d57d16834ce02d78b3dec4072351007d3 -r 7cd7546f107eff39603d4ee4b70a639f6ebf316e lib/galaxy/managers/base.py --- a/lib/galaxy/managers/base.py +++ b/lib/galaxy/managers/base.py @@ -20,21 +20,18 @@ ModelDeserializers control how a model validates and process an incoming attribute change to a model object. """ -#TODO: it may be there's a better way to combine the above three classes +# TODO: it may be there's a better way to combine the above three classes # such as: a single flat class, serializers being singletons in the manager, etc. # instead of the three separate classes. With no 'apparent' perfect scheme # I'm opting to just keep them separate. -import re - import pkg_resources pkg_resources.require( "SQLAlchemy >= 0.4" ) import sqlalchemy +from galaxy import exceptions from galaxy import model -from galaxy import exceptions from galaxy.model import tool_shed_install -from galaxy.util import sanitize_html import logging @@ -169,7 +166,7 @@ """ return ( self.model_class.create_time, ) - #NOTE: at this layer, all ids are expected to be decoded and in int form + # NOTE: at this layer, all ids are expected to be decoded and in int form # ------------------------------------------------------------------------- get/read/query def query( self, trans, eagerloads=True, filters=None, order_by=None, limit=None, offset=None, **kwargs ): """ @@ -177,14 +174,13 @@ Set eagerloads to False to disable them for this query. """ - #print 'query:', eagerloads, filters, order_by, limit, offset, kwargs query = trans.sa_session.query( self.model_class ) # joined table loading if eagerloads is False: query = query.enable_eagerloads( False ) - #TODO: if non-orm filters are the only option, here is where they'd go + # TODO: if non-orm filters are the only option, here is where they'd go query = self._apply_filters( query, filters ) query = self._apply_order_by_limit_offset( query, order_by, limit, offset ) return query @@ -198,7 +194,7 @@ if not isinstance( filters, list ): filters = [ filters ] - #note: implicit AND + # note: implicit AND for filter in filters: query = query.filter( filter ) return query @@ -209,7 +205,7 @@ (While allowing them to be None, non-lists, or lists.) """ - #TODO: there's nothing specifically filter or model-related here - move to util + # TODO: there's nothing specifically filter or model-related here - move to util if filtersA is None: return filtersB if filtersB is None: @@ -268,9 +264,9 @@ # overridden to raise serializable errors try: return query.one() - except sqlalchemy.orm.exc.NoResultFound, not_found: + except sqlalchemy.orm.exc.NoResultFound: raise exceptions.ObjectNotFound( self.model_class.__name__ + ' not found' ) - except sqlalchemy.orm.exc.MultipleResultsFound, multi_found: + except sqlalchemy.orm.exc.MultipleResultsFound: raise exceptions.InconsistentDatabase( 'found more than one ' + self.model_class.__name__ ) def _one_or_none( self, query ): @@ -281,10 +277,10 @@ """ try: return self._one_with_recast_errors( query ) - except exceptions.ObjectNotFound, not_found: + except exceptions.ObjectNotFound: return None - #TODO: get? + # TODO: get? def by_id( self, trans, id, **kwargs ): """ @@ -312,14 +308,13 @@ Returns an in-order list of models with the matching ids in `ids`. """ found = self._query_by_ids( trans, ids, **kwargs ).all() - #TODO: this does not order by the original 'ids' array + # TODO: this does not order by the original 'ids' array # ...could use get (supposedly since found are in the session, the db won't be hit twice) - #return map( trans.sa_session.query( self.model_class ).get, ids ) + # return map( trans.sa_session.query( self.model_class ).get, ids ) # ...could implement own version here - slow? return self._order_items_by_id( ids, found ) - #return found def _order_items_by_id( self, ids, items ): """ @@ -330,9 +325,9 @@ id, they will not be in the returned list. """ ID_ATTR_NAME = 'id' - #TODO:?? aside from sqlalx.get mentioned above, I haven't seen an in-SQL way + # TODO:?? aside from sqlalx.get mentioned above, I haven't seen an in-SQL way # to make this happen. This may not be the most efficient way either. - #NOTE: that this isn't sorting by id - this is matching the order in items to the order in ids + # NOTE: that this isn't sorting by id - this is matching the order in items to the order in ids # move items list into dict by id item_dict = {} for item in items: @@ -379,7 +374,7 @@ trans.sa_session.flush() return item - #TODO: yagni? + # TODO: yagni? def associate( self, trans, associate_with, item, foreign_key_name=None ): """ Generically associate `item` with `associate_with` based on `foreign_key_name`. @@ -398,7 +393,7 @@ # ------------------------------------------------------------------------- delete # a rename of sql DELETE to differentiate from the Galaxy notion of mark_as_deleted - #def destroy( self, trans, item, **kwargs ): + # def destroy( self, trans, item, **kwargs ): # return item @@ -442,7 +437,7 @@ self.serializers = {} # a list of valid serializable keys that can use the default (string) serializer # this allows us to: 'mention' the key without adding the default serializer - #NOTE: if a key is requested that is in neither serializable_keys or serializers, it is not returned + # NOTE: if a key is requested that is in neither serializable_keys or serializers, it is not returned self.serializable_keys = [] # add subclass serializers defined there self.add_serializers() @@ -484,7 +479,7 @@ """ Serialize the `item`'s attribute named `key`. """ - #TODO:?? point of change but not really necessary? + # TODO:?? point of change but not really necessary? return getattr( item, key ) # ......................................................................... serializers for common galaxy objects @@ -568,7 +563,7 @@ # create a generically accessible manager for the model this deserializer works with/for self.manager = None if self.model_manager_class: - self.manager = self.model_manager_class( self.app ) + self.manager = self.model_manager_class( self.app ) def add_deserializers( self ): """ @@ -588,9 +583,9 @@ for key, val in data.items(): if key in self.deserializers: new_dict[ key ] = self.deserializers[ key ]( trans, item, key, val ) - #!important: don't error on unreg. keys -- many clients will add weird ass keys onto the model + # !important: don't error on unreg. keys -- many clients will add weird ass keys onto the model - #TODO:?? add and flush here or in manager? + # TODO:?? add and flush here or in manager? if flush and len( new_dict ): sa_session.add( item ) sa_session.flush() @@ -603,7 +598,7 @@ If the incoming `val` is different than the `item` value change it and, in either case, return the value. """ - #TODO: sets the item attribute to value (this may not work in all instances) + # TODO: sets the item attribute to value (this may not work in all instances) # only do the following if val == getattr( item, key ) if hasattr( item, key ) and getattr( item, key ) != val: @@ -632,7 +627,7 @@ # ----------------------------------------------------------------------------- -#TODO:?? a larger question is: which should be first? Deserialize then validate - or - validate then deserialize? +# TODO:?? a larger question is: which should be first? Deserialize then validate - or - validate then deserialize? class ModelValidator( object ): """ An object that inspects a dictionary (generally meant to be a set of @@ -685,7 +680,7 @@ """ Must be a list of basestrings. """ - #TODO: Here's where compound types start becoming a nightmare. Any more or more complex + # TODO: Here's where compound types start becoming a nightmare. Any more or more complex # and should find a different way. val = self.type( key, val, list ) return [ self.basestring( key, elem ) for elem in val ] @@ -695,7 +690,7 @@ """ Must be a valid genome_build/dbkey/reference/whatever-the-hell-were-calling-them-now. """ - #TODO: is this correct? + # TODO: is this correct? if val is None: return '?' for genome_build_shortname, longname in self.app.genome_builds.get_genome_build_names( trans=trans ): @@ -703,7 +698,7 @@ return val raise exceptions.RequestParameterInvalidException( "invalid reference", key=key, val=val ) - #def slug( self, trans, item, key, val ): + # def slug( self, trans, item, key, val ): # """validate slug""" # pass @@ -746,7 +741,7 @@ return item raise exceptions.ItemAccessibilityException( "%s is not accessible by user" % ( self.model_class.__name__ ) ) - #TODO:?? are these even useful? + # TODO:?? are these even useful? def list_accessible( self, trans, user, **kwargs ): """ Return a list of items accessible to the user, raising an error if ANY @@ -755,18 +750,18 @@ :raises exceptions.ItemAccessibilityException: """ raise exceptions.NotImplemented( "Abstract Interface Method" ) - #NOTE: this will be a large, inefficient list if filters are not passed in kwargs - #items = ModelManager.list( self, trans, **kwargs ) - #return [ self.error_unless_accessible( trans, item, user ) for item in items ] + # NOTE: this will be a large, inefficient list if filters are not passed in kwargs + # items = ModelManager.list( self, trans, **kwargs ) + # return [ self.error_unless_accessible( trans, item, user ) for item in items ] def filter_accessible( self, trans, user, **kwargs ): """ Return a list of items accessible to the user. """ raise exceptions.NotImplemented( "Abstract Interface Method" ) - #NOTE: this will be a large, inefficient list if filters are not passed in kwargs - #items = ModelManager.list( self, trans, **kwargs ) - #return filter( lambda item: self.is_accessible( trans, item, user ), items ) + # NOTE: this will be a large, inefficient list if filters are not passed in kwargs + # items = ModelManager.list( self, trans, **kwargs ) + # return filter( lambda item: self.is_accessible( trans, item, user ), items ) # ============================================================================= @@ -862,7 +857,7 @@ pass -#TODO: these are of questionable value if we don't want to enable users to delete/purge via update +# TODO: these are of questionable value if we don't want to enable users to delete/purge via update class DeletableModelDeserializer( object ): def add_deserializers( self ): @@ -875,7 +870,7 @@ new_deleted = self.validate.bool( key, val ) if new_deleted == item.deleted: return item.deleted - #TODO:?? flush=False? + # TODO:?? flush=False? if new_deleted: self.manager.delete( trans, item, flush=False ) else: https://bitbucket.org/galaxy/galaxy-central/commits/11227c92c3cc/ Changeset: 11227c92c3cc User: dannon Date: 2015-01-22 21:51:14+00:00 Summary: Prevent redefinition of model, cleanup/pep8 in annotatable manager. Affected #: 1 file diff -r 7cd7546f107eff39603d4ee4b70a639f6ebf316e -r 11227c92c3cc71ded407e447dfeb80f1f922c633 lib/galaxy/managers/annotatable.py --- a/lib/galaxy/managers/annotatable.py +++ b/lib/galaxy/managers/annotatable.py @@ -2,9 +2,6 @@ Mixins for Annotatable model managers and serializers. """ -from galaxy import exceptions -from galaxy import model - import logging log = logging.getLogger( __name__ ) @@ -13,7 +10,7 @@ class AnnotatableManagerInterface( object ): annotation_assoc = None - #TODO: most of this seems to be covered by item_attrs.UsesAnnotations + # TODO: most of this seems to be covered by item_attrs.UsesAnnotations # ============================================================================= @@ -26,8 +23,8 @@ """ Get and serialize an `item`'s annotation. """ - #TODO: have to assume trans.user here... - #user = item.user + # TODO: have to assume trans.user here... + # user = item.user user = trans.user sa_session = self.app.model.context returned = item.get_item_annotation_str( sa_session, user, item ) @@ -49,11 +46,11 @@ val = self.validate.nullable_basestring( key, val ) sa_session = self.app.model.context - #TODO: have to assume trans.user here... + # TODO: have to assume trans.user here... user = trans.user if val is None: item.delete_item_annotation( sa_session, user, item ) return None - model = item.add_item_annotation( sa_session, user, item, val ) - return model.annotation + annotated_item = item.add_item_annotation( sa_session, user, item, val ) + return annotated_item.annotation https://bitbucket.org/galaxy/galaxy-central/commits/b32080c9b454/ Changeset: b32080c9b454 User: dannon Date: 2015-01-22 21:52:27+00:00 Summary: Import cleanup, organization in collections manager. Affected #: 1 file diff -r 11227c92c3cc71ded407e447dfeb80f1f922c633 -r b32080c9b45492b9fe341271edbc884d7460734e lib/galaxy/managers/collections.py --- a/lib/galaxy/managers/collections.py +++ b/lib/galaxy/managers/collections.py @@ -1,21 +1,18 @@ +from galaxy import model +from galaxy.dataset_collections import builder +from galaxy.dataset_collections.matching import MatchingCollections from galaxy.dataset_collections.registry import DatasetCollectionTypesRegistry -from galaxy.dataset_collections.matching import MatchingCollections from galaxy.dataset_collections.type_description import CollectionTypeDescriptionFactory -from galaxy.dataset_collections import builder - -from galaxy import model +from galaxy.exceptions import ItemAccessibilityException from galaxy.exceptions import MessageException -from galaxy.exceptions import ItemAccessibilityException from galaxy.exceptions import RequestParameterInvalidException -from galaxy.managers import base from galaxy.managers import hdas # TODO: Refactor all mixin use into managers. from galaxy.managers import histories from galaxy.managers import lddas from galaxy.managers import tags from galaxy.managers.collections_util import validate_input_element_identifiers +from galaxy.util import odict from galaxy.util import validation -from galaxy.util import odict - import logging log = logging.getLogger( __name__ ) @@ -259,7 +256,7 @@ return elements def __load_element( self, trans, element_identifier ): - #if not isinstance( element_identifier, dict ): + # if not isinstance( element_identifier, dict ): # # Is allowing this to just be the id of an hda too clever? Somewhat # # consistent with other API methods though. # element_identifier = dict( src='hda', id=str( element_identifier ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.