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Source code for galaxy.managers.taggable
"""
Mixins for Taggable model managers and serializers.
"""
# from galaxy import exceptions as galaxy_exceptions
import logging
from typing import Type
from sqlalchemy import sql
from galaxy import model
from galaxy.util import unicodify
log = logging.getLogger(__name__)
# TODO: work out the relation between serializers and managers and then fold these into the parent of the two
def _tag_str_gen(item):
# TODO: which user is this? all?
for tag in item.tags:
tag_str = tag.user_tname
if tag.value is not None:
tag_str += ":" + tag.user_value
yield tag_str
def _tags_to_strings(item):
if not hasattr(item, 'tags'):
return None
return sorted(list(_tag_str_gen(item)))
def _tags_from_strings(item, tag_handler, new_tags_list, user=None):
# TODO: have to assume trans.user here...
if not user:
# raise galaxy_exceptions.RequestParameterMissingException( 'User required for tags on ' + str( item ) )
# TODO: this becomes a 'silent failure' - no tags are set. This is a questionable approach but
# I haven't found a better one for anon users copying items with tags
return
# TODO: duped from tags manager - de-dupe when moved to taggable mixin
tag_handler.delete_item_tags(user, item)
new_tags_str = ','.join(new_tags_list)
tag_handler.apply_item_tags(user, item, unicodify(new_tags_str, 'utf-8'))
# TODO:!! does the creation of new_tags_list mean there are now more and more unused tag rows in the db?
[docs]class TaggableManagerMixin:
tag_assoc: Type[model.ItemTagAssociation]
# TODO: most of this can be done by delegating to the GalaxyTagHandler?
[docs] def get_tags(self, item):
"""
Return a list of tag strings.
"""
return _tags_to_strings(item)
[docs] def set_tags(self, item, new_tags, user=None):
"""
Set an `item`'s tags from a list of strings.
"""
return _tags_from_strings(item, self.app.tag_handler, new_tags, user=user)
# def tags_by_user( self, user, **kwargs ):
# TODO: here or GalaxyTagHandler
# pass
[docs]class TaggableSerializerMixin:
[docs] def serialize_tags(self, item, key, **context):
"""
Return tags as a list of strings.
"""
return _tags_to_strings(item)
[docs]class TaggableDeserializerMixin:
[docs] def deserialize_tags(self, item, key, val, user=None, **context):
"""
Make sure `val` is a valid list of tag strings and assign them.
Note: this will erase any previous tags.
"""
new_tags_list = self.validate.basestring_list(key, val)
_tags_from_strings(item, self.app.tag_handler, new_tags_list, user=user)
return item.tags
[docs]class TaggableFilterMixin:
valid_ops = ('eq', 'contains', 'has')
[docs] def create_tag_filter(self, attr, op, val):
def _create_tag_filter(model_class=None):
if op not in TaggableFilterMixin.valid_ops:
self.raise_filter_err(attr, op, val, 'bad op in filter')
if model_class is None:
return True
class_name = model_class.__name__
if class_name == 'HistoryDatasetCollectionAssociation':
# Unfortunately we were a little inconsistent with out naming scheme
class_name = 'HistoryDatasetCollection'
target_model = getattr(model, "%sTagAssociation" % class_name)
id_column = "%s_id" % target_model.table.name.rsplit('_tag_association')[0]
column = target_model.table.c.user_tname + ":" + target_model.table.c.user_value
if op == 'eq':
if ':' not in val:
# We require an exact match and the tag to look for has no user_value,
# so we can't just concatenate user_tname, ':' and user_vale
cond = target_model.table.c.user_tname == val
else:
cond = column == val
else:
cond = column.contains(val, autoescape=True)
return sql.expression.and_(
model_class.table.c.id == getattr(target_model.table.c, id_column),
cond
)
return _create_tag_filter
def _add_parsers(self):
self.orm_filter_parsers.update({
'tag': self.create_tag_filter
})