Refactor fillInDefaults

Author: Peter Amstutz

cwltool/process.py

@@ -190,6 +190,17 @@ def checkFormat(actualFile, inputFormats, requirements, ontology):
                 return
         raise validate.ValidationException(u"Incompatible file format %s required format(s) %s" % (af["format"], inputFormats))
 
+def fillInDefaults(inputs, job):
+    for inp in inputs:
+        if shortname(inp["id"]) in job:
+            pass
+        elif shortname(inp["id"]) not in job and "default" in inp:
+            job[shortname(inp["id"])] = copy.copy(inp["default"])
+        elif shortname(inp["id"]) not in job and inp["type"][0] == "null":
+            pass
+        else:
+            raise validate.ValidationException("Missing input parameter `%s`" % shortname(inp["id"]))
+
 class Process(object):
     __metaclass__ = abc.ABCMeta
 
@@ -259,10 +270,7 @@ def _init_job(self, joborder, input_basedir, **kwargs):
         builder = Builder()
         builder.job = copy.deepcopy(joborder)
 
-        for i in self.tool["inputs"]:
-            d = shortname(i["id"])
-            if d not in builder.job and "default" in i:
-                builder.job[d] = i["default"]
+        fillInDefaults(self.tool["inputs"], builder.job)
 
         # Validate job order
         try: