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Source code for galaxy.managers.annotatable

"""
Mixins for Annotatable model managers and serializers.
"""

import logging
log = logging.getLogger( __name__ )


# needed to extract this for use in manager *and* serializer, ideally, would use self.manager.annotation
# from serializer, but history_contents has no self.manager
# TODO: fix
def _match_by_user( item, user ):
    if not user:
        return None
    for annotation in item.annotations:
        if annotation.user_id == user.id:
            return annotation.annotation
    return None


[docs]class AnnotatableManagerMixin( object ): #: class of AnnotationAssociation (e.g. HistoryAnnotationAssociation) annotation_assoc = None
[docs] def annotation( self, item ): """ Return the annotation string made by the `item`'s owner or `None` if there is no annotation. """ # NOTE: only works with sharable (.user) return self._user_annotation( item, item.user )
# TODO: should/do we support multiple, non-owner annotation of items?
[docs] def annotate( self, item, annotation, user=None, flush=True ): """ Create a new annotation on `item` or delete the existing if annotation is `None`. """ if not user: return None if annotation is None: self._delete_annotation( item, user, flush=flush ) return None annotation_obj = item.add_item_annotation( self.session(), user, item, annotation ) if flush: self.session().flush() return annotation_obj
def _user_annotation( self, item, user ): return _match_by_user( item, user ) def _delete_annotation( self, item, user, flush=True ): returned = item.delete_item_annotation( self.session(), user, item ) if flush: self.session().flush() return returned
[docs]class AnnotatableSerializerMixin( object ):
[docs] def add_serializers( self ): self.serializers[ 'annotation' ] = self.serialize_annotation
[docs] def serialize_annotation( self, item, key, user=None, **context ): """ Get and serialize an `item`'s annotation. """ annotation = _match_by_user( item, user ) return annotation.strip() if annotation else None
[docs]class AnnotatableDeserializerMixin( object ):
[docs] def add_deserializers( self ): self.deserializers[ 'annotation' ] = self.deserialize_annotation
[docs] def deserialize_annotation( self, item, key, val, user=None, **context ): """ Make sure `val` is a valid annotation and assign it, deleting any existing if `val` is None. """ val = self.validate.nullable_basestring( key, val ) return self.manager.annotate( item, val, user=user, flush=False )
# TODO: I'm not entirely convinced this (or tags) are a good idea for filters since they involve a/the user
[docs]class AnnotatableFilterMixin( object ): def _owner_annotation( self, item ): """ Get the annotation by the item's owner. """ return _match_by_user( item, item.user )
[docs] def filter_annotation_contains( self, item, val ): """ Test whether `val` is in the owner's annotation. """ owner_annotation = self._owner_annotation( item ) if owner_annotation is None: return False return val in owner_annotation
def _add_parsers( self ): self.fn_filter_parsers.update({ 'annotation' : { 'op': { 'has': self.filter_annotation_contains, } }, })