Add copy_elements parameter to ``HistoryClient.create_dataset_col…

…lection()`` and BioBlend.objects ``History.create_dataset_collection()`` methods Fix tests broken by galaxyproject/galaxy#16717 .
nsoranzo · Sep 26, 2023 · c07ed28 · c07ed28
1 parent fe48906
commit c07ed28
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Showing 4 changed files with 25 additions and 6 deletions.
diff --git a/bioblend/_tests/TestGalaxyDatasetCollections.py b/bioblend/_tests/TestGalaxyDatasetCollections.py
@@ -29,6 +29,7 @@ def test_create_list_in_history(self):
                     dataset_collections.HistoryDatasetElement(name="sample3", id=dataset3_id),
                 ],
             ),
+            copy_elements=False,
         )
         assert collection_response["name"] == "MyDatasetList"
         assert collection_response["collection_type"] == "list"
@@ -70,6 +71,7 @@ def test_create_list_of_paired_datasets_in_history(self):
                     ),
                 ],
             ),
+            copy_elements=False,
         )
         assert collection_response["name"] == "MyListOfPairedDatasets"
         assert collection_response["collection_type"] == "list:paired"
@@ -197,5 +199,6 @@ def _create_pair_in_history(self, history_id: str) -> Dict[str, Any]:
                     dataset_collections.HistoryDatasetElement(name="reverse", id=dataset2_id),
                 ],
             ),
+            copy_elements=False,
         )
         return collection_response
diff --git a/bioblend/_tests/TestGalaxyObjects.py b/bioblend/_tests/TestGalaxyObjects.py
@@ -898,7 +898,7 @@ def test_update(self):
 
     def test_create_dataset_collection(self):
         self._create_collection_description()
-        hdca = self.hist.create_dataset_collection(self.collection_description)
+        hdca = self.hist.create_dataset_collection(self.collection_description, copy_elements=False)
         assert isinstance(hdca, wrappers.HistoryDatasetCollectionAssociation)
         assert hdca.collection_type == "list"
         assert hdca.container is self.hist
@@ -908,7 +908,7 @@ def test_create_dataset_collection(self):
 
     def test_delete_dataset_collection(self):
         self._create_collection_description()
-        hdca = self.hist.create_dataset_collection(self.collection_description)
+        hdca = self.hist.create_dataset_collection(self.collection_description, copy_elements=False)
         hdca.delete()
         assert hdca.deleted
 
@@ -1045,7 +1045,7 @@ def test_run_workflow_with_dataset_collection(self):
                 dataset_collections.HistoryDatasetElement(name="sample2", id=dataset2.id),
             ],
         )
-        dataset_collection = self.hist.create_dataset_collection(collection_description)
+        dataset_collection = self.hist.create_dataset_collection(collection_description, copy_elements=False)
         assert len(self.hist.content_infos) == 3
         input_map = {"0": dataset_collection, "1": dataset1}
         inv = self.wf.invoke(input_map, history=self.hist)

diff --git a/bioblend/galaxy/histories/__init__.py b/bioblend/galaxy/histories/__init__.py
@@ -582,7 +582,10 @@ def upload_dataset_from_library(self, history_id: str, lib_dataset_id: str) -> D
         return self._post(payload, id=history_id, contents=True)
 
     def create_dataset_collection(
-        self, history_id: str, collection_description: Union["CollectionDescription", Dict[str, Any]]
+        self,
+        history_id: str,
+        collection_description: Union["CollectionDescription", Dict[str, Any]],
+        copy_elements: bool = True,
     ) -> Dict[str, Any]:
         """
         Create a new dataset collection
@@ -603,6 +606,10 @@ def create_dataset_collection(
                                       'src': 'hda'}],
              'name': 'My collection list'}
 
+        :type copy_elements: bool
+        :param copy_elements: Whether to make a copy of the elements of the
+          collection being created
+
         :rtype: dict
         :return: Information about the new HDCA
         """
@@ -616,6 +623,7 @@ def create_dataset_collection(
             type="dataset_collection",
             collection_type=collection_description_dict["collection_type"],
             element_identifiers=collection_description_dict["element_identifiers"],
+            copy_elements=copy_elements,
         )
         return self._post(payload, id=history_id, contents=True)
 

diff --git a/bioblend/galaxy/objects/wrappers.py b/bioblend/galaxy/objects/wrappers.py
@@ -1475,18 +1475,26 @@ def download(self, jeha_id: str, outf: IO[bytes], chunk_size: int = bioblend.CHU
         return self.gi.gi.histories.download_history(self.id, jeha_id, outf, chunk_size=chunk_size)
 
     def create_dataset_collection(
-        self, collection_description: bioblend.galaxy.dataset_collections.CollectionDescription
+        self,
+        collection_description: bioblend.galaxy.dataset_collections.CollectionDescription,
+        copy_elements: bool = True,
     ) -> "HistoryDatasetCollectionAssociation":
         """
         Create a new dataset collection in the history by providing a collection description.
 
         :type collection_description: bioblend.galaxy.dataset_collections.CollectionDescription
         :param collection_description: a description of the dataset collection
 
+        :type copy_elements: bool
+        :param copy_elements: Whether to make a copy of the elements of the
+          collection being created
+
         :rtype: :class:`~.HistoryDatasetCollectionAssociation`
         :return: the new dataset collection
         """
-        dataset_collection = self.gi.gi.histories.create_dataset_collection(self.id, collection_description)
+        dataset_collection = self.gi.gi.histories.create_dataset_collection(
+            self.id, collection_description, copy_elements=copy_elements
+        )
         self.refresh()
         return self.get_dataset_collection(dataset_collection["id"])