Merge pull request #688 from wtsi-hgi/fix-687

Fix #687

Author: mr-c

cwltool/builder.py

@@ -93,27 +93,34 @@ def bind_input(self, schema, datum, lead_pos=None, tail_pos=None):
 
         # Handle union types
         if isinstance(schema["type"], list):
-            if not value_from_expression:
-                for t in schema["type"]:
-                    if isinstance(t, (str, Text)) and self.names.has_name(t, ""):
-                        avsc = self.names.get_name(t, "")
-                    elif isinstance(t, dict) and "name" in t and self.names.has_name(t["name"], ""):
-                        avsc = self.names.get_name(t["name"], "")
-                    else:
-                        avsc = AvroSchemaFromJSONData(t, self.names)
-                    if validate.validate(avsc, datum):
-                        schema = copy.deepcopy(schema)
-                        schema["type"] = t
+            bound_input = False
+            for t in schema["type"]:
+                if isinstance(t, (str, Text)) and self.names.has_name(t, ""):
+                    avsc = self.names.get_name(t, "")
+                elif isinstance(t, dict) and "name" in t and self.names.has_name(t["name"], ""):
+                    avsc = self.names.get_name(t["name"], "")
+                else:
+                    avsc = AvroSchemaFromJSONData(t, self.names)
+                if validate.validate(avsc, datum):
+                    schema = copy.deepcopy(schema)
+                    schema["type"] = t
+                    if not value_from_expression:
                         return self.bind_input(schema, datum, lead_pos=lead_pos, tail_pos=tail_pos)
+                    else:
+                        self.bind_input(schema, datum, lead_pos=lead_pos, tail_pos=tail_pos)
+                        bound_input = True
+            if not bound_input:
                 raise validate.ValidationException(u"'%s' is not a valid union %s" % (datum, schema["type"]))
         elif isinstance(schema["type"], dict):
-            if not value_from_expression:
-                st = copy.deepcopy(schema["type"])
-                if binding and "inputBinding" not in st and st["type"] == "array" and "itemSeparator" not in binding:
-                    st["inputBinding"] = {}
-                for k in ("secondaryFiles", "format", "streamable"):
-                    if k in schema:
-                        st[k] = schema[k]
+            st = copy.deepcopy(schema["type"])
+            if binding and "inputBinding" not in st and st["type"] == "array" and "itemSeparator" not in binding:
+                st["inputBinding"] = {}
+            for k in ("secondaryFiles", "format", "streamable"):
+                if k in schema:
+                    st[k] = schema[k]
+            if value_from_expression:
+                self.bind_input(st, datum, lead_pos=lead_pos, tail_pos=tail_pos)
+            else:
                 bindings.extend(self.bind_input(st, datum, lead_pos=lead_pos, tail_pos=tail_pos))
         else:
             if schema["type"] in self.schemaDefs: