Merge remote-tracking branch 'origin/cwlprov_conf_fixes' into toil-prov

Author: mb1069

cwltool/main.py

@@ -836,6 +836,18 @@ def my_represent_none(self, data):  # pylint: disable=unused-argument
                 if runtimeContext.research_obj is not None:
                     runtimeContext.research_obj.create_job(
                         out, None, True)
+                    def remove_at_id(doc):  # type: MutableMapping -> None
+                        for key in list(doc.keys()):
+                            if key == '@id':
+                                del doc[key]
+                            else:
+                                value = doc[key]
+                                if isinstance(value, MutableMapping):
+                                    remove_at_id(value)
+                                elif isinstance(value, MutableSequence):
+                                    for entry in value:
+                                        remove_at_id(entry)
+                    remove_at_id(out)
 
                 def loc_to_path(obj):  # type: (Dict[Text, Any]) -> None
                     for field in ("path", "nameext", "nameroot", "dirname"):

cwltool/provenance.py

@@ -549,7 +549,12 @@ def declare_file(self, value):
         # Check for secondaries
         for sec in value.get("secondaryFiles", ()):
             # TODO: Record these in a specializationOf entity with UUID?
-            (sec_entity, _, _) = self.declare_file(sec)
+            if sec['class'] == "File":
+                (sec_entity, _, _) = self.declare_file(sec)
+            elif sec['class'] == "Directory":
+                sec_entity = self.declare_directory(sec)
+            else:
+                raise ValueError("Got unexpected secondaryFiles value: {}".format(sec))
             # We don't know how/when/where the secondary file was generated,
             # but CWL convention is a kind of summary/index derived
             # from the original file. As its generally in a different format