Merge pull request #410 from SciDAP/master

Fix #409: checkFormat fails for Null input

Author: mr-c

cwltool/process.py

@@ -344,6 +344,8 @@ def formatSubclassOf(fmt, cls, ontology, visited):
 def checkFormat(actualFile, inputFormats, ontology):
     # type: (Union[Dict[Text, Any], List, Text], Union[List[Text], Text], Graph) -> None
     for af in aslist(actualFile):
+        if not af:
+            continue
         if "format" not in af:
             raise validate.ValidationException(u"Missing required 'format' for File %s" % af)
         for inpf in aslist(inputFormats):

cwltool/workflow.py

@@ -66,13 +66,13 @@ def match_types(sinktype, src, iid, inputobj, linkMerge, valueFrom):
                 return True
     elif isinstance(src.parameter["type"], list):
         # Source is union type
-        # Check that every source type is compatible with the sink.
+        # Check that at least one source type is compatible with the sink.
         for st in src.parameter["type"]:
             srccopy = copy.deepcopy(src)
             srccopy.parameter["type"] = st
-            if not match_types(st, srccopy, iid, inputobj, linkMerge, valueFrom):
-                return False
-        return True
+            if match_types(sinktype, srccopy, iid, inputobj, linkMerge, valueFrom):
+                return True
+        return False
     elif linkMerge:
         if iid not in inputobj:
             inputobj[iid] = []