clean execute

cwlkernel/CWLKernel.py

@@ -203,8 +203,8 @@ def _execute_workflow(self, code) -> Optional[Exception]:
         self._cwl_executor.set_data(self._yaml_input_data)
         self._cwl_executor.set_workflow(code)
         logger.debug('starting executing workflow ...')
-        run_id, results, stdout, stderr, exception = self._cwl_executor.execute()
-        logger.debug(f'\texecution results: {run_id}, {results}, {stdout}, {stderr}, {exception}')
+        run_id, results, exception = self._cwl_executor.execute()
+        logger.debug(f'\texecution results: {run_id}, {results}, {exception}')
         output_directory_for_that_run = str(run_id)
         for output in results:
             if isinstance(results[output], list):

cwlkernel/CoreExecutor.py

@@ -38,14 +38,11 @@ def set_workflow(self, workflow_str: str) -> str:
         self._workflow_path = self.file_manager.write(f'{str(uuid4())}.cwl', workflow_str.encode())
         return self._workflow_path
 
-    def execute(self) -> Tuple[UUID, Dict, StringIO, StringIO, Optional[Exception]]:
+    def execute(self) -> Tuple[UUID, Dict, Optional[Exception]]:
         """
-        :return: Run ID, List of new files, stdout, stderr, exception if there is any
+        :return: Run ID, dict with new files, exception if there is any
         """
         run_id = uuid4()
-        # args = [self._workflow_path, *self._data_paths]
-        stdout = StringIO()
-        stderr = StringIO()
 
         runtime_context = RuntimeContext()
         runtime_context.outdir = self.file_manager.ROOT_DIRECTORY
@@ -63,10 +60,10 @@ def execute(self) -> Tuple[UUID, Dict, StringIO, StringIO, Optional[Exception]]:
                 data = {**new_data, **data}
         try:
             result: Dict = executable(**data)
-            return run_id, result, stdout, stderr, None
+            return run_id, result, None
         except Exception as e:
             traceback.print_exc(file=sys.stderr)
-            return run_id, {}, stdout, stderr, e
+            return run_id, {}, e
 
     @classmethod
     def validate_input_files(cls, yaml_input: Dict, cwd: Path) -> NoReturn:

tests/test_CoreExecutor.py

@@ -31,11 +31,9 @@ def test_executor_execute(self):
             data_str = f.read()
         executor.set_data([data_str])
         try:
-            execution_id, new_files, stdout, stderr, exception = executor.execute()
+            execution_id, new_files, exception = executor.execute()
             self.assertIsNotNone(execution_id)
             self.assertDictEqual(new_files, {})
-            self.assertIsInstance(stdout, io.IOBase)
-            self.assertIsInstance(stderr, io.IOBase)
             self.assertIsNone(exception, 'An exception occurred while executing workflow')
         except Exception:
             self.fail("execution failed")