Source code for galaxy.dataset_collections.builder

from galaxy import model
from galaxy.util.odict import odict


[docs]def build_collection(type, dataset_instances): """ 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 = model.DatasetCollection() set_collection_elements(dataset_collection, type, dataset_instances) return dataset_collection
[docs]def set_collection_elements(dataset_collection, type, dataset_instances): element_index = 0 elements = [] for element in type.generate_elements(dataset_instances): element.element_index = element_index element.collection = dataset_collection elements.append(element) element_index += 1 dataset_collection.elements = elements dataset_collection.element_count = element_index return dataset_collection
[docs]class CollectionBuilder(object): """ 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 = odict()
[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 = odict() for identifier, element in elements.items(): new_elements[identifier] = element.build() elements = new_elements return elements
[docs] def build(self): type_plugin = self._collection_type_description.rank_type_plugin() collection = build_collection(type_plugin, self.build_elements()) collection.collection_type = self._collection_type_description.collection_type return 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, collection_type_description): self.dataset_collection = dataset_collection if dataset_collection.populated: raise Exception("Cannot reset elements of an already populated dataset collection.") super(BoundCollectionBuilder, self).__init__(collection_type_description)
[docs] def populate(self): elements = self.build_elements() type_plugin = self._collection_type_description.rank_type_plugin() set_collection_elements(self.dataset_collection, type_plugin, elements) self.dataset_collection.mark_as_populated()