Add optional parameters to payload to import collections as single item in libraries.

Or else, use the default behavior of unpacking datasets.

Author: davelopez

lib/galaxy/webapps/galaxy/api/folder_contents.py

@@ -250,6 +250,13 @@ class CreateLibraryItemPayload(BaseModel):
         title="HDCA Encoded ID",
         description="The encoded identifier of the History Dataset Collection Association instance to add to the library.",
     )
+    collection_as_single_item: Optional[bool] = Field(
+        None,
+        title="Collection as single item",
+        description=(
+            "This will create the collection as a single item in the library instead of unpacking all the datasets."
+        ),
+    )
 
 
 # TODO: refactor and remove UsesLibraryMixinItems then move this class to lib/galaxy/managers/folder_contents.py
@@ -450,7 +457,9 @@ def create(self, trans, encoded_folder_id: EncodedDatabaseIdField, payload: Crea
                 return self._copy_hda_to_library_folder(trans, self.hda_manager, decoded_hda_id, encoded_folder_id_16, ldda_message)
             if from_hdca_id:
                 decoded_hdca_id = self._decode_id(from_hdca_id)
-                return self._copy_hdca_to_library_folder_single(trans, self.hdca_manager, decoded_hdca_id, encoded_folder_id_16)
+                if payload.collection_as_single_item:
+                    return self._copy_hdca_to_library_folder_single(trans, self.hdca_manager, decoded_hdca_id, encoded_folder_id_16)
+                return self._copy_hdca_to_library_folder(trans, self.hda_manager, decoded_hdca_id, encoded_folder_id_16, ldda_message)
         except Exception as exc:
             # TODO handle exceptions better within the mixins
             exc_message = util.unicodify(exc)

lib/galaxy_test/api/test_folder_contents.py

@@ -37,8 +37,20 @@ def test_create_hda_with_ldda_message(self):
     def test_create_hdca(self):
         contents = ["dataset01", "dataset02"]
         hdca_id = self._create_hdca_with_contents(name="Test Dataset Collection", contents=contents)
+        ldda_message = "Test message"
+        data = {
+            "from_hdca_id": hdca_id,
+            "ldda_message": ldda_message,
+        }
+        lddas = self._create_content_in_folder_with_payload(self.root_folder_id, data)
+        assert len(contents) == len(lddas)
+
+    def test_create_hdca_single_item(self):
+        contents = ["dataset01", "dataset02"]
+        hdca_id = self._create_hdca_with_contents(name="Test Dataset Collection Single", contents=contents)
         data = {
             "from_hdca_id": hdca_id,
+            "collection_as_single_item": True
         }
         ldca = self._create_content_in_folder_with_payload(self.root_folder_id, data)
         self._assert_has_keys(ldca, "name", "id", "element_count")
@@ -49,7 +61,7 @@ def test_index(self):
 
         self._create_subfolder_in(folder_id)
         self._create_dataset_in_folder(folder_id)
-        self._create_dataset_collection_in_folder(folder_id)
+        self._create_dataset_collection_in_folder(folder_id, single_item=True)
 
         response = self._get(f"folders/{folder_id}/contents")
         self._assert_status_code_is(response, 200)
@@ -85,7 +97,7 @@ def test_index_limit_offset(self):
 
         num_collections = 2
         for _ in range(num_collections):
-            self._create_dataset_collection_in_folder(folder_id)
+            self._create_dataset_collection_in_folder(folder_id, single_item=True)
 
         num_datasets = 5
         for _ in range(num_datasets):
@@ -234,11 +246,12 @@ def _create_dataset_in_folder(self, folder_id: str, name: Optional[str] = None)
         ldda = self._create_content_in_folder_with_payload(folder_id, data)
         return ldda["id"]
 
-    def _create_dataset_collection_in_folder(self, folder_id: str, name: Optional[str] = None, num_items: int = 3) -> str:
+    def _create_dataset_collection_in_folder(self, folder_id: str, name: Optional[str] = None, num_items: int = 3, single_item: bool = False) -> str:
         contents = [f"dataset{index}" for index in range(num_items)]
         hdca_id = self._create_hdca_with_contents(name or "Test Dataset Collection", contents)
         data = {
             "from_hdca_id": hdca_id,
+            "collection_as_single_item": single_item
         }
         ldca = self._create_content_in_folder_with_payload(folder_id, data)
         return ldca["id"]