Bugfixs: pathmap on "Any" type, don't crash subgraph when inport has no source (#966)

* Bugfix: should apply to pathmapper to files in "Any" inputs

* Fix subgraph, don't crash when inport doesn't have a source.

Author: tetron

cwltool/builder.py

@@ -264,6 +264,10 @@ def bind_input(self,
                         self.bind_input(itemschema, item, lead_pos=n, tail_pos=tail_pos, discover_secondaryFiles=discover_secondaryFiles))
                 binding = None
 
+            def _capture_files(f):
+                self.files.append(f)
+                return f
+
             if schema["type"] == "File":
                 self.files.append(datum)
                 if (binding and binding.get("loadContents")) or schema.get("loadContents"):
@@ -308,10 +312,6 @@ def bind_input(self,
                             "Expected value of '%s' to have format %s but\n "
                             " %s" % (schema["name"], schema["format"], ve))
 
-                def _capture_files(f):
-                    self.files.append(f)
-                    return f
-
                 visit_class(datum.get("secondaryFiles", []), ("File", "Directory"), _capture_files)
 
             if schema["type"] == "Directory":
@@ -320,6 +320,9 @@ def _capture_files(f):
                     get_listing(self.fs_access, datum, (ll == "deep_listing"))
                 self.files.append(datum)
 
+            if schema["type"] == "Any":
+                visit_class(datum, ("File", "Directory"), _capture_files)
+
         # Position to front of the sort key
         if binding is not None:
             for bi in bindings:

cwltool/subgraph.py

@@ -128,6 +128,8 @@ def find_step(stepid):  # type: (Text) -> Optional[MutableMapping]
                 if i["id"] in visited:
                     if f == "steps":
                         for inport in i["in"]:
+                            if "source" not in inport:
+                                continue
                             if isinstance(inport["source"], MutableSequence):
                                 inport["source"] = [rewire[s][0] for s in inport["source"] if s in rewire]
                             elif inport["source"] in rewire: