Source code for galaxy.managers.taggable

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

# from galaxy import exceptions as galaxy_exceptions

import logging
import re
from typing import Type

from sqlalchemy import (
    func,
    sql,
)

from galaxy import model
from galaxy.model.tags import GalaxyTagHandler
from galaxy.util import unicodify
from .base import (
    ModelValidator,
    raise_filter_err,
)

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 += f":{tag.user_value}"
        yield tag_str


def _tags_to_strings(item):
    if not hasattr(item, "tags"):
        return None
    tag_list = list(_tag_str_gen(item))
    # consider named tags while sorting
    return sorted(tag_list, key=lambda str: re.sub("^name:", "#", str))


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]
    tag_handler: GalaxyTagHandler

    # 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.tag_handler, new_tags, user=user)

    # def tags_by_user( self, user, **kwargs ):
    # TODO: here or GalaxyTagHandler
    #    pass


[docs]class TaggableSerializerMixin:
[docs]    def add_serializers(self):
        self.serializers["tags"] = self.serialize_tags

[docs]    def serialize_tags(self, item, key, **context):
        """
        Return tags as a list of strings.
        """
        return _tags_to_strings(item)


[docs]class TaggableDeserializerMixin:
    tag_handler: GalaxyTagHandler
    validate: ModelValidator

[docs]    def add_deserializers(self):
        self.deserializers["tags"] = self.deserialize_tags

[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.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:
                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 our naming scheme
                class_name = "HistoryDatasetCollection"
            target_model = getattr(model, f"{class_name}TagAssociation")
            id_column = f"{target_model.table.name.rsplit('_tag_association')[0]}_id"
            column = target_model.table.c.user_tname + ":" + target_model.table.c.user_value
            lower_val = val.lower()  # Ignore case
            if op == "eq":
                if ":" not in lower_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 = func.lower(target_model.table.c.user_tname) == lower_val
                else:
                    cond = func.lower(column) == lower_val
            else:
                cond = func.lower(column).contains(lower_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})