Don't add item to command line if input is null (#787)

Author: mr-c

cwltool/builder.py

@@ -179,7 +179,7 @@ def bind_input(self, schema, datum, lead_pos=None, tail_pos=None, discover_secon
 
             if schema["type"] == "record":
                 for f in schema["fields"]:
-                    if f["name"] in datum:
+                    if f["name"] in datum and datum[f["name"]] is not None:
                         bindings.extend(self.bind_input(f, datum[f["name"]], lead_pos=lead_pos, tail_pos=f["name"], discover_secondaryFiles=discover_secondaryFiles))
                     else:
                         datum[f["name"]] = f.get("default")

tests/test_js_sandbox.py

@@ -51,7 +51,10 @@ class TestValueFrom(unittest.TestCase):
     def test_value_from_two_concatenated_expressions(self):
         f = get_windows_safe_factory()
         echo = f.make(get_data("tests/wf/vf-concat.cwl"))
-        self.assertEqual(echo(), {u"out": u"a sting\n"})
+        self.assertEqual(echo(file1={
+            "class": "File",
+            "location": get_data("tests/wf/whale.txt")}),
+            {u"out": u"a string\n"})
 
 
 class ExecJsProcessTest(unittest.TestCase):

tests/wf/vf-concat.cwl

@@ -5,10 +5,10 @@ requirements:
 
 baseCommand: echo
 inputs:
-  - id: parameter
-    type: string?
+  file1:
+    type: File?
     inputBinding:
-      valueFrom: $("a ")$("sting")
+      valueFrom: $("a ")$("string")
 outputs:
   out:
     type: string