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Source code for galaxy.managers.containers

Manager mixins to unify the interface into things that can contain: Datasets
and other (nested) containers.

(e.g. DatasetCollections, Histories, LibraryFolders)
# Histories should be DatasetCollections.
# Libraries should be DatasetCollections.
import logging
import operator
from typing import Optional

import galaxy.exceptions
import galaxy.util
from galaxy import model

log = logging.getLogger(__name__)

# ====
[docs]class ContainerManagerMixin: """ A class that tracks/contains two types of items: 1) some non-container object (such as datasets) 2) other sub-containers nested within this one Levels of nesting are not considered here; In other words, each of the methods below only work on the first level of nesting. """ # TODO: terminology is getting a bit convoluted and silly at this point: rename three public below? # TODO: this should be an open mapping (not just 2) #: the classes that can be contained contained_class: type subcontainer_class: type #: how any contents lists produced are ordered - (string) attribute name to sort on or tuple of attribute names default_order_by: Optional[str] = None # ---- interface
[docs] def contents(self, container): """ Returns both types of contents: filtered and in some order. """ iters = [] iters.append(self.contained(container)) iters.append(self.subcontainers(container)) return galaxy.util.merge_sorted_iterables(self.order_contents_on, *iters)
[docs] def contained(self, container, **kwargs): """ Returns non-container objects. """ return self._filter_contents(container, self.contained_class, **kwargs)
[docs] def subcontainers(self, container, **kwargs): """ Returns only the containers within this one. """ return self._filter_contents(container, self.subcontainer_class, **kwargs)
# ---- private def _filter_contents(self, container, content_class, **kwargs): # TODO: use list (or by_history etc.) container_filter = self._filter_to_contained(container, content_class) query = self.session().query(content_class).filter(container_filter) return query def _get_filter_for_contained(self, container, content_class): raise galaxy.exceptions.NotImplemented('Abstract class') def _content_manager(self, content): raise galaxy.exceptions.NotImplemented('Abstract class')
[docs]class LibraryFolderAsContainerManagerMixin(ContainerManagerMixin): # can contain two types of subcontainer: LibraryFolder, LibraryDatasetCollectionAssociation # has as the top level container: Library contained_class = model.LibraryDataset subcontainer_class = model.LibraryFolder # subcontainer_class = model.LibraryDatasetCollectionAssociation order_contents_on = operator.attrgetter('create_time') def _get_filter_for_contained(self, container, content_class): if content_class == self.subcontainer_class: return self.subcontainer_class.parent == container return self.contained_class.folder == container def _content_manager(self, content): # type snifffing is inevitable if isinstance(content, model.LibraryDataset): return self.lda_manager elif isinstance(content, model.LibraryFolder): return self.folder_manager raise TypeError('Unknown contents class: ' + str(content))
[docs]class DatasetCollectionAsContainerManagerMixin(ContainerManagerMixin): # (note: unlike the other collections, dc's wrap both contained and subcontainers in this class) contained_class = model.DatasetCollectionElement subcontainer_class = model.DatasetCollection order_contents_on = operator.attrgetter('element_index') def _get_filter_for_contained(self, container, content_class): return content_class.collection == container def _content_manager(self, content): # type snifffing is inevitable if isinstance(content, model.DatasetCollectionElement): return self.collection_manager elif isinstance(content, model.DatasetCollection): return self.collection_manager raise TypeError('Unknown contents class: ' + str(content))