Added run error handling

chi_pet/chi_run.py

@@ -22,18 +22,20 @@ def run_args(workdir, state, args):
         if workdir.exists():
             os.chdir(workdir)
             action_file.touch()  # Keeps track of current pipeline state
-            status = run(args)
+            print("Running: ", args)
+            status = run(args) #TODO capture output when an error occurs
+            print("status: ", status)
             if status.returncode:
-                print(f"Run failed: State {state} did not succeed.")
+                raise OSError(f"Run failed: OSError occured at state {state}.")
             action_file.unlink()  # Remove once completed successfully
             return status.returncode
         else:
-            print(
-                f"Run failed: could not find work directory {workdir} to do action {state}.")
-            return 1
+            # error for not finding directory
+            raise FileNotFoundError(
+                f"Run failed: Work directory {workdir} not found to do action {state} .")
     except:
-        print(f"Run failed: State {state} did not succeed.")
-        return 1
+        (workdir / '.error').touch()
+        raise 
     finally:
         os.chdir(current_dir)
 
@@ -55,9 +57,8 @@ def run(self):
 
             # If sim action file exists then run the state
             if run_state in self._states:
-                if run_args(self._opts.workdir, run_state, args):
-                    (self._opts.workdir / '.error').touch()
-                elif sim_state.exists():
+                run_args(self._opts.workdir, run_state, args)
+                if sim_state.exists():
                     sim_state.unlink()
 
     def get_run_states(self):

tests/test_chi_node.py

@@ -218,3 +218,6 @@ def test_chi_node_matched_creation_runtime_error(mock_param_yaml_dict, mock_crea
     cnode.make_node_dir(root_path)
     with pytest.raises(RuntimeError):
         cnode.make_subnodes()
+
+
+FileNotFoundError

tests/test_chi_run.py

@@ -51,4 +51,20 @@ def test_chi_run_only_one_touch_with_opts(mock_leaf_dir, mock_run_opts):
     assert not (mock_leaf_path / 'mock_output2.txt').exists()
 
 
-# TODO NEXT TEST test run args to make sure it always returns you to the right directory
+def test_chi_run_error(mock_leaf_dir, mock_run_opts):
+    """Test chi_run."""
+    home_dir = Path.cwd()
+    mock_leaf_path = mock_leaf_dir
+    # Create and modify run optoins
+    mock_run_opts.args_dict = {'touch1': ['not_a_command', 'mock_output1.txt']}
+    mock_run_opts.states = mock_run_opts.args_dict.keys()
+    mock_run_opts.workdir = mock_leaf_path
+
+    # Make a ChiRun object
+    crun = ChiRun(mock_run_opts)
+    # Run the pipeline with failed state
+    with pytest.raises(OSError):
+        crun.run()
+    assert (mock_leaf_path / '.error').exists()
+    assert Path.cwd() == home_dir
+