Fixed a validation error with jobs with non-required arguments. Trying to...

Fixed a validation error with jobs with non-required arguments.  Trying to evaluate numeric types without a value.

chipathlon/workflow_job.py

@@ -235,34 +235,35 @@ class WorkflowJob(object):
         the size of the list.
         """
         arg_value = self._get_arg_value(arg_name, arg_info)
-        if arg_info["type"] == "numeric":
-            # We need this as two seperate if statements otherwise we try
-            # to interpolate numeric arguments
-            if not is_number(arg_value):
-                return (False, "[Error parsing job %s]: Argument '%s' with value '%s' must be numeric." % (self, arg_name, arg_value))
-        elif arg_info["type"] in chipathlon.conf.argument_types["file"]:
-            # If the argument is a rawfile, validate it's extension & existance
-            if arg_info["type"] == "rawfile":
-                if os.path.isfile(arg_value):
-                    if not arg_value.endswith(tuple(chipathlon.conf.file_extensions[arg_info["file_type"]])):
-                        return (False, "[Error parsing job %s] Argument '%s' with file path '%s' is not of file type '%s'. \
-                                    Should match one of these extensions: %s." % (
-                                        self,
-                                        arg_name,
-                                        arg_value,
-                                        arg_info["file_type"],
-                                        chipathlon.conf.file_extensions[arg_info["file_type"]]
+        if arg_value is not None:
+            if arg_info["type"] == "numeric":
+                # We need this as two seperate if statements otherwise we try
+                # to interpolate numeric arguments
+                if not is_number(arg_value):
+                    return (False, "[Error parsing job %s]: Argument '%s' with value '%s' must be numeric." % (self, arg_name, arg_value))
+            elif arg_info["type"] in chipathlon.conf.argument_types["file"]:
+                # If the argument is a rawfile, validate it's extension & existance
+                if arg_info["type"] == "rawfile":
+                    if os.path.isfile(arg_value):
+                        if not arg_value.endswith(tuple(chipathlon.conf.file_extensions[arg_info["file_type"]])):
+                            return (False, "[Error parsing job %s] Argument '%s' with file path '%s' is not of file type '%s'. \
+                                        Should match one of these extensions: %s." % (
+                                            self,
+                                            arg_name,
+                                            arg_value,
+                                            arg_info["file_type"],
+                                            chipathlon.conf.file_extensions[arg_info["file_type"]]
+                                        )
                                     )
-                                )
-                else:
-                    return (False, "[Error parsing job %s]: Argument '%s' is a rawfile, however the specified path '%s' does not exist. " % (self, arg_name, arg_value))
-            # If the argument is a 'regular' file, we need to make sure that it
-            # references one of the keys of the inputs / outputs
-            elif not arg_value.startswith("$"):
-                return (False, "[Error parsing job %s]: Argument '%s' has value '%s'.  File references must start with a '$'." % (self, arg_name, arg_value))
-        elif isinstance(arg_value, str) and arg_value.startswith("$"):
-            if not any([str(arg_value)[1:] == ref for ref in (self.valid_inputs + self.valid_outputs)]):
-                return (False, "[Error parsing job %s]: Argument '%s' has reference '%s'.  No such input / output exists." % (self, arg_name, arg_value))
+                    else:
+                        return (False, "[Error parsing job %s]: Argument '%s' is a rawfile, however the specified path '%s' does not exist. " % (self, arg_name, arg_value))
+                # If the argument is a 'regular' file, we need to make sure that it
+                # references one of the keys of the inputs / outputs
+                elif not arg_value.startswith("$"):
+                    return (False, "[Error parsing job %s]: Argument '%s' has value '%s'.  File references must start with a '$'." % (self, arg_name, arg_value))
+            elif isinstance(arg_value, str) and arg_value.startswith("$"):
+                if not any([str(arg_value)[1:] == ref for ref in (self.valid_inputs + self.valid_outputs)]):
+                    return (False, "[Error parsing job %s]: Argument '%s' has reference '%s'.  No such input / output exists." % (self, arg_name, arg_value))
         return (True, None)
 
     def _get_arg_value(self, arg_name, arg_info):
@@ -285,10 +286,10 @@ class WorkflowJob(object):
             elif "path" in arg_info:
                 return self._get_path(arg_info["path"]) + arg_info["default"]
             else:
-                return arg_info["default"]
+                return arg_info.get("default")
         else:
             if arg_info["has_value"]:
-                return arg_info["default"]
+                return arg_info.get("default")
             elif "path" in arg_info:
                 return self._get_path(arg_info["path"]) + arg_name
             else: