log file annotation in RO manifest

Also avoid noisy warning that happens for any input files

Author: stain

cwltool/provenance.py

@@ -1026,6 +1026,7 @@ def open_log_file_for_activity(self, uuid_uri): # type: (Text) -> IO
             name = "activity"
         p = os.path.join(LOGS, "%s.%s.txt" % (name, activity_uuid))
         _logger.debug("[provenance] Opening log file for %s: %s" % (name, p))
+        self.add_annotation(activity_uuid.urn, [p], CWLPROV["log"].uri)
         return self.write_bag_file(p)
 
     def _finalize(self):  # type: () -> None
@@ -1567,8 +1568,7 @@ def _relativise_files(self, structure):
                 if not relative_path and "location" in structure:
                     # Register in RO; but why was this not picked
                     # up by used_artefacts?
-                    _logger.warning("File not previously registered in RO: %s",
-                                    yaml.dump(structure))
+                    _logger.info("Adding to RO %s", structure["location"])
                     fsaccess = self.make_fs_access("")
                     with fsaccess.open(structure["location"], "rb") as fp:
                         relative_path = self.add_data_file(fp)