Add nameroot and nameext to File objects in output, for use by

expressions/secondaryFiles.  Mypy fix.

Author: Peter Amstutz

cwltool/draft2tool.py

@@ -582,6 +582,8 @@ def collect_output(self, schema, builder, outdir, fs_access, compute_checksum=Tr
                             r.extend([{"location": g,
                                        "path": fs_access.join(builder.outdir, g[len(prefix[0])+1:]),
                                        "basename": os.path.basename(g),
+                                       "nameroot": os.path.splitext(os.path.basename(g))[0],
+                                       "nameext": os.path.splitext(os.path.basename(g))[1],
                                        "class": "File" if fs_access.isfile(g) else "Directory"}
                                       for g in fs_access.glob(fs_access.join(outdir, gb))])
                         except (OSError, IOError) as e:

cwltool/job.py

@@ -132,7 +132,7 @@ def __init__(self):  # type: () -> None
         self.name = None  # type: Text
         self.command_line = None  # type: List[Text]
         self.pathmapper = None  # type: PathMapper
-        self.make_pathmapper = None  # type: Callable[[List[Any], Text, **Any], PathMapper]
+        self.make_pathmapper = None  # type: Callable[[List[Any], Text, Any], PathMapper]
         self.generatemapper = None  # type: PathMapper
         self.collect_outputs = None  # type: Union[Callable[[Any], Any], functools.partial[Any]]
         self.output_callback = None  # type: Callable[[Any, Any], Any]