satisfy mypy

src/toil/cwl/cwltoil.py

@@ -54,7 +54,7 @@
     TypeVar,
     Union,
     cast,
-    Sequence,
+    Sequence, Literal,
 )
 from urllib.error import HTTPError
 from urllib.parse import quote, unquote, urlparse, urlsplit
@@ -1857,7 +1857,7 @@ def extract_files(
 
     if location in fileindex:
         file_metadata["location"] = fileindex[location]
-        return
+        return None
     if not location and file_metadata["path"]:
         file_metadata["location"] = location = schema_salad.ref_resolver.file_uri(
             cast(str, file_metadata["path"])
@@ -1944,7 +1944,7 @@ def visit_files(
 
     :param log_level: Log imported files at the given level.
     """
-    func_return = list()
+    func_return: List[Any] = list()
     tool_id = cwl_object.get("id", str(cwl_object)) if cwl_object else ""
 
     logger.debug("Importing files for %s", tool_id)
@@ -3653,7 +3653,7 @@ class CWLStartJob(CWLNamedJob):
 
     def __init__(
         self,
-        inputs: Promised[Tuple[CWLObjectType, CWLObjectType]],
+        inputs: Promised[Tuple[CWLObjectType, Process]],
         runtime_context: cwltool.context.RuntimeContext,
         **kwargs: Any,
     ) -> None:
@@ -3765,7 +3765,7 @@ def import_workflow_inputs(
     # always get a FileID out.
     def file_import_function(url: str) -> FileID:
         logger.log(log_level, "Loading %s...", url)
-        return cast(FileID, jobstore.import_file(url, symlink=True))
+        return jobstore.import_file(url, symlink=True)
 
     # Import all the input files, some of which may be missing optional
     # files.
@@ -3835,6 +3835,8 @@ def visitSteps(
             f"Unsupported type encountered in workflow "
             f"traversal: {type(cmdline_tool)}"
         )
+    # Satisfy mypy, but this branch should never be reached in practice
+    return []
 
 
 def rm_unprocessed_secondary_files(job_params: Any) -> None:

src/toil/job.py

@@ -3874,8 +3874,8 @@ class ImportsJob(Job):
     def __init__(
         self,
         file_to_data: Dict[str, FileMetadata],
-        import_workers_threshold,
-        **kwargs: Any,
+        import_workers_threshold: ParseableIndivisibleResource,
+        **kwargs: Any
     ):
         """
         Job to take the inputs from the WDL workflow and import them on a worker instead of a leader. Assumes all local and cloud files are accessible.

src/toil/wdl/wdltoil.py

@@ -1146,7 +1146,7 @@ def convert_file_to_uri(file: WDL.Value.File) -> WDL.Value.File:
         Calls import_filename to detect if a potential URI exists and imports it. Will modify the File object value to the new URI and tack on the virtualized file.
         """
         candidate_uri = file_to_data[file.value][0]
-        file_id = file_to_id.get(candidate_uri)
+        file_id = file_to_id[candidate_uri]
 
         # Work out what the basename for the file was
         file_basename = os.path.basename(urlsplit(candidate_uri).path)
@@ -4877,7 +4877,7 @@ def __init__(
         self,
         task_path: str,
         inputs: WDLBindings,
-        import_data: Promised[Tuple[Dict[str, FileID]], Dict[str, FileMetadata]],
+        import_data: Promised[Tuple[Dict[str, FileID], Dict[str, FileMetadata]]],
         **kwargs: Any,
     ) -> None:
         """
@@ -4915,9 +4915,9 @@ def __init__(
         target: Union[WDL.Tree.Workflow, WDL.Tree.Task],
         inputs: WDLBindings,
         wdl_options: WDLContext,
-        inputs_search_path,
-        import_remote_files,
-        import_workers_threshold,
+        inputs_search_path: List[str],
+        import_remote_files: bool,
+        import_workers_threshold: ParseableIndivisibleResource,
         **kwargs: Any,
     ):
         """
@@ -4960,13 +4960,13 @@ def run(self, file_store: AbstractFileStore) -> Promised[WDLBindings]:
 def make_root_job(
     target: WDL.Tree.Workflow | WDL.Tree.Task,
     inputs: WDLBindings,
-    inputs_search_path: list[str],
+    inputs_search_path: List[str],
     toil: Toil,
     wdl_options: WDLContext,
     options: Namespace,
 ) -> WDLSectionJob:
     if options.run_imports_on_workers:
-        root_job = WDLImportWrapper(
+        root_job: WDLSectionJob = WDLImportWrapper(
             target,
             inputs,
             wdl_options=wdl_options,