opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-24 02:04:04 +08:00
Code Issues Packages Projects Releases Wiki Activity

Restore hiding of dataset instances

Browse Source
This commit is contained in:
mvdbeek
2018-08-26 22:13:50 +02:00
parent 5dd63dd6d0
commit ce892a028c
1 changed files with 21 additions and 15 deletions
Download Patch File Download Diff File Expand all files Collapse all files
lib/galaxy/managers/collections.py
+21 -15
View File
@@ -173,26 +173,25 @@ class DatasetCollectionManager(object):
# If we have elements, this is an internal request, don't need to load
# objects from identifiers.
if elements is None:
elements = self._element_identifiers_to_elements(trans, collection_type_description, element_identifiers)
elements = self._element_identifiers_to_elements(trans,
collection_type_description=collection_type_description,
element_identifiers=element_identifiers,
hide_source_items=hide_source_items)
else:
if has_subcollections:
# Nested collection - recursively create collections as needed.
self.__recursively_create_collections_for_elements(trans, elements)
self.__recursively_create_collections_for_elements(trans, elements, hide_source_items)
# else if elements is set, it better be an ordered dict!
if elements is not self.ELEMENTS_UNINITIALIZED:
type_plugin = collection_type_description.rank_type_plugin()
dataset_collection = builder.build_collection(type_plugin, elements)
if hide_source_items:
log.debug("Hiding source items during dataset collection creation")
for dataset in dataset_collection.dataset_instances:
dataset.visible = False
else:
dataset_collection = model.DatasetCollection(populated=False)
dataset_collection.collection_type = collection_type
return dataset_collection
def _element_identifiers_to_elements(self, trans, collection_type_description, element_identifiers):
def _element_identifiers_to_elements(self, trans, collection_type_description, element_identifiers, hide_source_items=False):
if collection_type_description.has_subcollections():
# Nested collection - recursively create collections and update identifiers.
self.__recursively_create_collections_for_identifiers(trans, element_identifiers)
@@ -200,9 +199,13 @@ class DatasetCollectionManager(object):
for element_identifier in element_identifiers:
if element_identifier.get("src") == "new_collection" and element_identifier.get('collection_type') == '':
new_collection = True
elements = self.__load_elements(trans, element_identifier['element_identifiers'])
elements = self.__load_elements(trans=trans,
element_identifiers=element_identifier['element_identifiers'],
hide_source_items=hide_source_items)
if not new_collection:
elements = self.__load_elements(trans, element_identifiers)
elements = self.__load_elements(trans=trans,
element_identifiers=element_identifiers,
hide_source_items=hide_source_items)
return elements
def _append_tags(self, dataset_collection_instance, implicit_inputs=None, tags=None):
@@ -342,7 +345,7 @@ class DatasetCollectionManager(object):
return element_identifiers
def __recursively_create_collections_for_elements(self, trans, elements):
def __recursively_create_collections_for_elements(self, trans, elements, hide_source_items):
if elements is self.ELEMENTS_UNINITIALIZED:
return
@@ -362,17 +365,18 @@ class DatasetCollectionManager(object):
trans=trans,
collection_type=collection_type,
elements=sub_elements,
hide_source_items=hide_source_items
)
new_elements[key] = collection
elements.update(new_elements)
def __load_elements(self, trans, element_identifiers):
def __load_elements(self, trans, element_identifiers, hide_source_items=False):
elements = odict.odict()
for element_identifier in element_identifiers:
elements[element_identifier["name"]] = self.__load_element(trans, element_identifier)
elements[element_identifier["name"]] = self.__load_element(trans, element_identifier, hide_source_items)
return elements
def __load_element(self, trans, element_identifier):
def __load_element(self, trans, element_identifier, hide_source_items):
# if not isinstance( element_identifier, dict ):
# # Is allowing this to just be the id of an hda too clever? Somewhat
# # consistent with other API methods though.
@@ -401,8 +405,10 @@ class DatasetCollectionManager(object):
if src_type == 'hda':
decoded_id = int(trans.app.security.decode_id(encoded_id))
element = self.hda_manager.get_accessible(decoded_id, trans.user)
element = self.hda_manager.copy(element, history=element.history, hide_copy=True)
hda = self.hda_manager.get_accessible(decoded_id, trans.user)
element = self.hda_manager.copy(hda, history=hda.history, hide_copy=True)
if hide_source_items:
hda.visible = False
tags = element_identifier.pop('tags', [])
if tags:
self.tag_manager.apply_item_tags(user=trans.user, item=element, tags_str=",".join(str(_) for _ in tags))