Merge pull request #7 from Parsl/bug-fixes

bug fixes
1. Fix handling CWL input arguments in list form
2. Maintain order listed in CWL for input args if position is not mentioned
3. Update handling optional boolean flags (remove unnecessary space in the command)

cwl/cwl_app.py

@@ -153,7 +153,7 @@ def __process_array_value(self, value: Any, str_quote="") -> str:
 
     def __lt__(self, other) -> bool:
         if self.position is None:
-            return other.position is None
+            return other.position is not None
         return True if other.position is None else self.position < other.position
 
 
@@ -331,7 +331,7 @@ def validate_cwl(cls, cwl_content: Dict[str, any]) -> Dict[str, any]:
                             "id": Regex(
                                 r"^[a-zA-Z_][a-zA-Z0-9_]*$",
                             ),
-                            "type": input_simple_types,
+                            "type": input_types_schema,
                             Opt("items"): Or(*input_simple_types),
                             Opt("default"): Or(
                                 int, float, str, bool, list, error="Invalid default value"
@@ -499,7 +499,7 @@ def get_command(self, **kwargs) -> str:
             else:
                 raise ArgumentMissing(f"missing required value for argument: {input_arg.arg_id}")
 
-        return f"{self.__base_command} {' '.join(input_args)}"
+        return f"{self.__base_command} {' '.join(filter(None, input_args))}"
 
     def __get_parsl_bash_app_args(self, **kwargs) -> Dict[str, Any]:
         """Args needed to run the command using Parsl