Removed unnecessary print statement. Added optionally argument loading. ...

Removed unnecessary print statement.  Added optionally argument loading.  Fixed valid workflow generation test.

chipathlon/test/workflow_job_tests.py

@@ -145,11 +145,6 @@ class WorkflowJobTests(unittest.TestCase):
                     "name": "url",
                     "type": "string",
                     "value": "some.encode.url.org/asdf"
-                },
-                "md5": {
-                    "name": "md5",
-                    "type": "string",
-                    "value": "asdfasdf"
                 }
             },
             {
@@ -161,7 +156,7 @@ class WorkflowJobTests(unittest.TestCase):
                 }
             }
         )
-        self.assertEqual(pegasus_job, None, msg=job.get_error_string())
+        self.assertNotEqual(pegasus_job, None, msg=job.get_error_string())
         return
 
 if __name__ == "__main__":

chipathlon/workflow_job.py

@@ -461,7 +461,6 @@ class WorkflowJob(object):
                 elif output_info["type"] == "stderr":
                     job.setStderr(output_file["name"])
             arg_list = self._create_arg_list(inputs, outputs)
-            print "Created arg_list: %s" % (arg_list,)
             job.addArguments(*self._create_arg_list(inputs, outputs))
             self._add_job_resources(job)
             return job
@@ -515,12 +514,19 @@ class WorkflowJob(object):
                 add_value = []
                 for file_dict in inputs[arg_value]["values"]:
                     add_value.append(file_dict["file"])
-            elif arg_info["type"] in chipathlon.conf.argument_types["file"]:
-                # Need to load from inputs / outputs conditionally
-                add_value = (inputs if arg_value in inputs else outputs)[arg_value]["file"]
             else:
-                # No such thing as argument outputs
-                add_value = inputs[arg_value]["value"]
+                # Conditionally load from inputs / outputs
+                # This will only load the dict of information though, not
+                # the actual value we want
+                add_value = (inputs if arg_value in inputs else outputs).get(arg_value)
+                # If the value is None we wan't to avoid adding anything
+                if add_value is not None:
+                    if arg_info["type"] in chipathlon.conf.argument_types["file"]:
+                        # Want the actual Pegasus file obj
+                        add_value = add_value.get("file")
+                    else:
+                        # Get the actual argumnet value
+                        add_value = add_value.get("value")
         return add_value
 
     def _create_arg_list(self, inputs, outputs):
@@ -550,20 +556,22 @@ class WorkflowJob(object):
             # 1. Should we add the argument name?
             # 2. What's the correct value to add?
             add_value = self._interpolate_value(inputs, outputs, arg_name, arg_info)
-            # Now we actually add the argument
-            if arg_info["has_value"]:
-                # If it's a file we want to add the actual Pegasus.File instance
-                if isinstance(add_value, File):
-                    arg_list.append(arg_name)
-                    arg_list.append(add_value)
-                # If it's a list we want to add each of the Pegasus.File instances
-                elif isinstance(add_value, list):
-                    arg_list.append(arg_name)
-                    for f in add_value:
-                        arg_list.append(f)
-                # Otherwise, add stuff as a string
+            # Only add arguments that have a value
+            if add_value is not None:
+                # Need to add in the arg_name and the arg_value
+                if arg_info["has_value"]:
+                    # If it's a file we want to add the actual Pegasus.File instance
+                    if isinstance(add_value, File):
+                        arg_list.append(arg_name)
+                        arg_list.append(add_value)
+                    # If it's a list we want to add each of the Pegasus.File instances
+                    elif isinstance(add_value, list):
+                        arg_list.append(arg_name)
+                        for f in add_value:
+                            arg_list.append(f)
+                    # Otherwise, add stuff as a string
+                    else:
+                        arg_list.append("%s %s" % (arg_name, add_value))
                 else:
-                    arg_list.append("%s %s" % (arg_name, add_value))
-            else:
-                arg_list.append(add_value)
+                    arg_list.append(add_value)
         return arg_list