from galaxy import model
from galaxy.model.orm.util import add_object_to_object_session
from galaxy.util.oset import OrderedSet
from .type_description import COLLECTION_TYPE_DESCRIPTION_FACTORY
[docs]def build_collection(type, dataset_instances, collection=None, associated_identifiers=None):
"""
Build DatasetCollection with populated DatasetcollectionElement objects
corresponding to the supplied dataset instances or throw exception if
this is not a valid collection of the specified type.
"""
dataset_collection = collection or model.DatasetCollection()
associated_identifiers = associated_identifiers or set()
set_collection_elements(dataset_collection, type, dataset_instances, associated_identifiers)
return dataset_collection
[docs]def set_collection_elements(dataset_collection, type, dataset_instances, associated_identifiers):
new_element_keys = OrderedSet(dataset_instances.keys()) - associated_identifiers
new_dataset_instances = {k: dataset_instances[k] for k in new_element_keys}
dataset_collection.element_count = dataset_collection.element_count or 0
element_index = dataset_collection.element_count
elements = []
for element in type.generate_elements(new_dataset_instances):
element.element_index = element_index
add_object_to_object_session(element, dataset_collection)
element.collection = dataset_collection
elements.append(element)
element_index += 1
associated_identifiers.add(element.element_identifier)
dataset_collection.element_count = element_index
return dataset_collection
[docs]class CollectionBuilder:
"""Purely functional builder pattern for building a dataset collection."""
[docs] def __init__(self, collection_type_description):
self._collection_type_description = collection_type_description
self._current_elements = {}
# Store collection here so we don't recreate the collection all the time
self.collection = None
self.associated_identifiers = set()
[docs] def replace_elements_in_collection(self, template_collection, replacement_dict):
self._current_elements = self._replace_elements_in_collection(
template_collection=template_collection,
replacement_dict=replacement_dict,
)
def _replace_elements_in_collection(self, template_collection, replacement_dict):
elements = {}
for element in template_collection.elements:
if element.is_collection:
collection_builder = CollectionBuilder(
collection_type_description=self._collection_type_description.child_collection_type_description()
)
collection_builder.replace_elements_in_collection(
template_collection=element.child_collection, replacement_dict=replacement_dict
)
elements[element.element_identifier] = collection_builder
else:
elements[element.element_identifier] = replacement_dict.get(
element.element_object, element.element_object
)
return elements
[docs] def get_level(self, identifier):
if not self._nested_collection:
message_template = "Cannot add nested collection to collection of type [%s]"
message = message_template % (self._collection_type_description)
raise AssertionError(message)
if identifier not in self._current_elements:
subcollection_builder = CollectionBuilder(self._subcollection_type_description)
self._current_elements[identifier] = subcollection_builder
return self._current_elements[identifier]
[docs] def add_dataset(self, identifier, dataset_instance):
self._current_elements[identifier] = dataset_instance
[docs] def build_elements(self):
elements = self._current_elements
if self._nested_collection:
new_elements = {}
for identifier, element in elements.items():
new_elements[identifier] = element.build()
elements = new_elements
else:
self._current_elements = {}
return elements
[docs] def build(self):
type_plugin = self._collection_type_description.rank_type_plugin()
self.collection = build_collection(
type_plugin, self.build_elements(), self.collection, self.associated_identifiers
)
self.collection.collection_type = self._collection_type_description.collection_type
return self.collection
@property
def _subcollection_type_description(self):
return self._collection_type_description.subcollection_type_description()
@property
def _nested_collection(self):
return self._collection_type_description.has_subcollections()
[docs]class BoundCollectionBuilder(CollectionBuilder):
"""More stateful builder that is bound to a particular model object."""
[docs] def __init__(self, dataset_collection):
self.dataset_collection = dataset_collection
if dataset_collection.populated:
raise Exception("Cannot reset elements of an already populated dataset collection.")
collection_type = dataset_collection.collection_type
collection_type_description = COLLECTION_TYPE_DESCRIPTION_FACTORY.for_collection_type(collection_type)
super().__init__(collection_type_description)
[docs] def populate_partial(self):
elements = self.build_elements()
type_plugin = self._collection_type_description.rank_type_plugin()
set_collection_elements(self.dataset_collection, type_plugin, elements, self.associated_identifiers)
[docs] def populate(self):
self.populate_partial()
self.dataset_collection.mark_as_populated()