black

lib/galaxy/job_execution/output_collect.py

@@ -106,7 +106,11 @@ def copy_dataset_permissions(self, init_from, primary_data):
 
 
 class MetadataSourceProvider(AbstractMetadataSourceProvider):
-    def __init__(self, inp_data: Dict[str, Optional["DatasetInstance"]], inp_collections: Dict[str, Union["DatasetCollectionInstance", "DatasetCollection"]]):
+    def __init__(
+        self,
+        inp_data: Dict[str, Optional["DatasetInstance"]],
+        inp_collections: Dict[str, Union["DatasetCollectionInstance", "DatasetCollection"]],
+    ):
         self._inp_data = inp_data or {}
         self._inp_collections = inp_collections or {}
 
@@ -116,10 +120,14 @@ def get_metadata_source(self, input_name: str) -> Optional["DatasetInstance"]:
         elif input_name in self._inp_collections:
             return self._inp_collections[input_name].dataset_instances[0]
         else:
-            raise KeyError(f"Could not find metadata source '{input_name}' in {list(self._inp_data)} or {list(self._inp_collections)}")
+            raise KeyError(
+                f"Could not find metadata source '{input_name}' in {list(self._inp_data)} or {list(self._inp_collections)}"
+            )
 
 
-def evaluate_source(source: str, output_collection_def: ToolOutputCollection, metadata_source_provider: AbstractMetadataSourceProvider) -> Optional[str]:
+def evaluate_source(
+    source: str, output_collection_def: ToolOutputCollection, metadata_source_provider: AbstractMetadataSourceProvider
+) -> Optional[str]:
     source_name = getattr(output_collection_def, source)
     if source_name is None:
         return None

lib/galaxy/jobs/__init__.py

@@ -1945,7 +1945,9 @@ def fail(message=job.info, exception=None):
         if not extended_metadata:
             # importing metadata will discover outputs if extended metadata
             try:
-                self.discover_outputs(job, inp_data, inp_collections, out_data, out_collections, final_job_state=final_job_state)
+                self.discover_outputs(
+                    job, inp_data, inp_collections, out_data, out_collections, final_job_state=final_job_state
+                )
             except MaxDiscoveredFilesExceededError as e:
                 final_job_state = job.states.ERROR
                 job.job_messages = [
@@ -2071,7 +2073,15 @@ def fail(message=job.info, exception=None):
         self.cleanup(delete_files=delete_files)
         log.debug(finish_timer.to_str(job_id=self.job_id, tool_id=job.tool_id))
 
-    def discover_outputs(self, job, inp_data: Dict[str, Optional["DatasetInstance"]], inp_collections: Dict[str, Union["DatasetCollectionInstance", "DatasetCollection"]], out_data, out_collections, final_job_state):
+    def discover_outputs(
+        self,
+        job,
+        inp_data: Dict[str, Optional["DatasetInstance"]],
+        inp_collections: Dict[str, Union["DatasetCollectionInstance", "DatasetCollection"]],
+        out_data,
+        out_collections,
+        final_job_state,
+    ):
         """
         Try to just recover input_ext and dbkey from job parameters (used and set in
         galaxy.tools.actions). Old jobs may have not set these in the job parameters

lib/galaxy/model/__init__.py

@@ -1560,7 +1560,9 @@ def finished(self):
 
     def io_dicts(self, exclude_implicit_outputs=False) -> IoDicts:
         inp_data: Dict[str, Optional[DatasetInstance]] = {da.name: da.dataset for da in self.input_datasets}
-        inp_collections: Dict[str, Optional[HistoryDatasetCollectionAssociation]] = {obj.name: obj.dataset_collection for obj in self.input_dataset_collections}
+        inp_collections: Dict[str, Optional[HistoryDatasetCollectionAssociation]] = {
+            obj.name: obj.dataset_collection for obj in self.input_dataset_collections
+        }
 
         out_data: Dict[str, DatasetInstance] = {da.name: da.dataset for da in self.output_datasets}
         inp_data.update([(da.name, da.dataset) for da in self.input_library_datasets])
@@ -4289,10 +4291,12 @@ def _calculate_size(self) -> int:
         return self.object_store.size(self)  # type:ignore[unreachable]
 
     @overload
-    def get_size(self, nice_size: Literal[False], calculate_size: bool = True) -> int: ...
+    def get_size(self, nice_size: Literal[False], calculate_size: bool = True) -> int:
+        ...
 
     @overload
-    def get_size(self, nice_size: Literal[True], calculate_size: bool = True) -> str: ...
+    def get_size(self, nice_size: Literal[True], calculate_size: bool = True) -> str:
+        ...
 
     def get_size(self, nice_size: bool = False, calculate_size: bool = True) -> Union[int, str]:
         """Returns the size of the data on disk"""
@@ -5977,7 +5981,6 @@ def to_dict(self, view="collection"):
 
 
 class LibraryDatasetDatasetAssociation(DatasetInstance, HasName, Serializable):
-
     def __init__(
         self,
         library_dataset=None,
@@ -7042,10 +7045,12 @@ def touch(self):
                 flag_modified(self.collection, "collection_type")
 
     @overload
-    def to_hda_representative(self, multiple: Literal[False] = False) -> Optional[HistoryDatasetAssociation]: ...
+    def to_hda_representative(self, multiple: Literal[False] = False) -> Optional[HistoryDatasetAssociation]:
+        ...
 
     @overload
-    def to_hda_representative(self, multiple: Literal[True]) -> List[HistoryDatasetAssociation]: ...
+    def to_hda_representative(self, multiple: Literal[True]) -> List[HistoryDatasetAssociation]:
+        ...
 
     def to_hda_representative(
         self, multiple: bool = False
@@ -7091,9 +7096,9 @@ def _serialize(self, id_encoder, serialization_options):
             copied_from_history_dataset_collection_association_chain.append(
                 serialization_options.get_identifier(id_encoder, src_hdca)
             )
-        rval["copied_from_history_dataset_collection_association_id_chain"] = (
-            copied_from_history_dataset_collection_association_chain
-        )
+        rval[
+            "copied_from_history_dataset_collection_association_id_chain"
+        ] = copied_from_history_dataset_collection_association_chain
         serialization_options.attach_identifier(id_encoder, self, rval)
         return rval
 

lib/galaxy/model/store/discover.py

@@ -324,7 +324,14 @@ def populate_collection_elements(
             )
 
     def _populate_elements(
-        self, chunk, name, root_collection_builder, metadata_source_name, default_format: Optional[str], final_job_state, change_datatype_actions
+        self,
+        chunk,
+        name,
+        root_collection_builder,
+        metadata_source_name,
+        default_format: Optional[str],
+        final_job_state,
+        change_datatype_actions,
     ):
         element_datasets: Dict[str, List[Any]] = {
             "element_identifiers": [],