Merge pull request #11732 from assuntad23/copy_collections_dbkey

Copy collections dbkey

lib/galaxy/managers/collections.py

@@ -287,7 +287,7 @@ class DatasetCollectionManager:
         changed = self._set_from_dict(trans, dataset_collection_instance, payload)
         return changed
 
-    def copy(self, trans, parent, source, encoded_source_id, copy_elements=False):
+    def copy(self, trans, parent, source, encoded_source_id, copy_elements=False, dataset_instance_attributes=None):
         """
         PRECONDITION: security checks on ability to add to parent occurred
         during load.
@@ -296,7 +296,9 @@ class DatasetCollectionManager:
         source_hdca = self.__get_history_collection_instance(trans, encoded_source_id)
         copy_kwds = {}
         if copy_elements:
-            copy_kwds["element_destination"] = parent
+            copy_kwds["element_destination"] = parent  # e.g. a history
+        if dataset_instance_attributes is not None:
+            copy_kwds["dataset_instance_attributes"] = dataset_instance_attributes
         new_hdca = source_hdca.copy(**copy_kwds)
         new_hdca.copy_tags_from(target_user=trans.get_user(), source=source_hdca)
         if not copy_elements:

lib/galaxy/model/__init__.py

@@ -4289,7 +4289,7 @@ class DatasetCollection(Dictifiable, UsesAnnotations, RepresentById):
         error_message = f"Dataset collection has no {get_by_attribute} with key {key}."
         raise KeyError(error_message)
 
-    def copy(self, destination=None, element_destination=None, flush=True):
+    def copy(self, destination=None, element_destination=None, dataset_instance_attributes=None, flush=True):
         new_collection = DatasetCollection(
             collection_type=self.collection_type,
             element_count=self.element_count
@@ -4299,6 +4299,7 @@ class DatasetCollection(Dictifiable, UsesAnnotations, RepresentById):
                 new_collection,
                 destination=destination,
                 element_destination=element_destination,
+                dataset_instance_attributes=dataset_instance_attributes,
                 flush=flush
             )
         object_session(self).add(new_collection)
@@ -4540,7 +4541,7 @@ class HistoryDatasetCollectionAssociation(DatasetCollectionInstance,
                 break
         return matching_collection
 
-    def copy(self, element_destination=None):
+    def copy(self, element_destination=None, dataset_instance_attributes=None):
         """
         Create a copy of this history dataset collection association. Copy
         underlying collection.
@@ -4561,6 +4562,7 @@ class HistoryDatasetCollectionAssociation(DatasetCollectionInstance,
         collection_copy = self.collection.copy(
             destination=hdca,
             element_destination=element_destination,
+            dataset_instance_attributes=dataset_instance_attributes,
             flush=False,
         )
         hdca.collection = collection_copy
@@ -4722,17 +4724,22 @@ class DatasetCollectionElement(Dictifiable, RepresentById):
         else:
             return [element_object]
 
-    def copy_to_collection(self, collection, destination=None, element_destination=None, flush=True):
+    def copy_to_collection(self, collection, destination=None, element_destination=None, dataset_instance_attributes=None, flush=True):
+        dataset_instance_attributes = dataset_instance_attributes or {}
         element_object = self.element_object
         if element_destination:
             if self.is_collection:
                 element_object = element_object.copy(
                     destination=destination,
                     element_destination=element_destination,
+                    dataset_instance_attributes=dataset_instance_attributes,
                     flush=flush
                 )
             else:
                 new_element_object = element_object.copy(flush=flush, copy_tags=element_object.tags)
+                for attribute, value in dataset_instance_attributes.items():
+                    setattr(new_element_object, attribute, value)
+
                 new_element_object.visible = False
                 if destination is not None and element_object.hidden_beneath_collection_instance:
                     new_element_object.hidden_beneath_collection_instance = destination

lib/galaxy/webapps/galaxy/api/history_contents.py

@@ -530,13 +530,21 @@ class HistoryContentsController(BaseGalaxyAPIController, UsesLibraryMixin, UsesL
             content = payload.get('content', None)
             if content is None:
                 raise exceptions.RequestParameterMissingException("'content' id of target to copy is missing")
-            copy_elements = payload.get('copy_elements', False)
+            dbkey = payload.get("dbkey")
+            copy_required = dbkey is not None
+            copy_elements = payload.get('copy_elements', copy_required)
+            if copy_required and not copy_elements:
+                raise exceptions.RequestParameterMissingException("copy_elements passed as 'false' but it is required to change specified attributes")
+            dataset_instance_attributes = {}
+            if dbkey is not None:
+                dataset_instance_attributes["dbkey"] = dbkey
             dataset_collection_instance = service.copy(
                 trans=trans,
                 parent=history,
                 source="hdca",
                 encoded_source_id=content,
                 copy_elements=copy_elements,
+                dataset_instance_attributes=dataset_instance_attributes,
             )
         else:
             message = "Invalid 'source' parameter in request %s" % source

lib/galaxy_test/api/test_history_contents.py

@@ -440,6 +440,18 @@ class HistoryContentsApiTestCase(ApiTestCase):
         self._assert_has_keys(new_forward, "history_id")
         assert new_forward["history_id"] == self.history_id
 
+    def test_hdca_copy_with_new_dbkey(self):
+        hdca = self.dataset_collection_populator.create_pair_in_history(self.history_id).json()
+        hdca_id = hdca["id"]
+        assert hdca["elements"][0]["object"]["metadata_dbkey"] == "?"
+        assert hdca["elements"][0]["object"]["genome_build"] == "?"
+        create_data = {'source': 'hdca', 'content': hdca_id, 'dbkey': 'hg19'}
+        create_response = self._post(f"histories/{self.history_id}/contents/dataset_collections", create_data)
+        collection = self.__check_create_collection_response(create_response)
+        new_forward = collection['elements'][0]['object']
+        assert new_forward["metadata_dbkey"] == "hg19"
+        assert new_forward["genome_build"] == "hg19"
+
     def test_hdca_copy_and_elements(self):
         hdca = self.dataset_collection_populator.create_pair_in_history(self.history_id).json()
         hdca_id = hdca["id"]