removing run_task from boshtask, small edit to run_task from shellcommand task

Author: djarecka

pydra/engine/boutiques.py

@@ -217,18 +217,3 @@ def _bosh_invocation_file(self, state_ind, ind=None):
             json.dump(input_json, jsonfile)
 
         return str(filename)
-
-    def _run_task(self):
-        self.output_ = None
-        args = self.command_args
-        if args:
-            # removing empty strings
-            args = [str(el) for el in args if el not in ["", " "]]
-            keys = ["return_code", "stdout", "stderr"]
-            values = execute(args, strip=self.strip)
-            self.output_ = dict(zip(keys, values))
-            if self.output_["return_code"]:
-                if self.output_["stderr"]:
-                    raise RuntimeError(self.output_["stderr"])
-                else:
-                    raise RuntimeError(self.output_["stdout"])

pydra/engine/task.py

@@ -399,13 +399,16 @@ def _run_task(self):
         else:
             args = self.command_args
         if args:
-            # removing emty strings
+            # removing empty strings
             args = [str(el) for el in args if el not in ["", " "]]
             keys = ["return_code", "stdout", "stderr"]
             values = execute(args, strip=self.strip)
             self.output_ = dict(zip(keys, values))
             if self.output_["return_code"]:
-                raise RuntimeError(self.output_["stderr"])
+                if self.output_["stderr"]:
+                    raise RuntimeError(self.output_["stderr"])
+                else:
+                    raise RuntimeError(self.output_["stdout"])
 
 
 class ContainerTask(ShellCommandTask):