Merge pull request #3505 from mgxd/fix/node-execution-info

mgxd · web-flow · commit fd39c1f53cbc · 2022-09-14T16:52:31.000-04:00
FIX: Provide more runtime information when node execution fails
diff --git a/nipype/pipeline/engine/nodes.py b/nipype/pipeline/engine/nodes.py
@@ -750,9 +750,25 @@ def _run_command(self, execute, copyfiles=True):
         )
 
         if exc_tb:
-            raise NodeExecutionError(
-                f"Exception raised while executing Node {self.name}.\n\n{result.runtime.traceback}"
-            )
+            runtime = result.runtime
+
+            def _tab(text):
+                from textwrap import indent
+
+                if not text:
+                    return ""
+                return indent(text, '\t')
+
+            msg = f"Exception raised while executing Node {self.name}.\n\n"
+            if hasattr(runtime, 'cmdline'):
+                msg += (
+                    f"Cmdline:\n{_tab(runtime.cmdline)}\n"
+                    f"Stdout:\n{_tab(runtime.stdout)}\n"
+                    f"Stderr:\n{_tab(runtime.stderr)}\n"
+                )
+            # Always pass along the traceback
+            msg += f"Traceback:\n{_tab(runtime.traceback)}"
+            raise NodeExecutionError(msg)
 
         return result
 
diff --git a/nipype/pipeline/engine/tests/test_nodes.py b/nipype/pipeline/engine/tests/test_nodes.py
@@ -7,6 +7,7 @@
 
 from .... import config
 from ....interfaces import utility as niu
+from ....interfaces import base as nib
 from ... import engine as pe
 from ..utils import merge_dict
 from .test_base import EngineTestInterface
@@ -334,3 +335,45 @@ def _producer(num=1, deadly_num=7):
     wf.base_dir = os.path.abspath("./test_output")
     with pytest.raises(RuntimeError):
         wf.run(plugin="MultiProc")
+
+
+class FailCommandLine(nib.CommandLine):
+    input_spec = nib.CommandLineInputSpec
+    output_spec = nib.TraitedSpec
+    _cmd = 'nipype-node-execution-fail'
+
+
+def test_NodeExecutionError(tmp_path, monkeypatch):
+    import stat
+
+    monkeypatch.chdir(tmp_path)
+
+    # create basic executable and add to PATH
+    exebin = tmp_path / 'bin'
+    exebin.mkdir()
+    exe = exebin / 'nipype-node-execution-fail'
+    exe.write_text('#!/bin/bash\necho "Running"\necho "This should fail" >&2\nexit 1')
+    exe.chmod(exe.stat().st_mode | stat.S_IEXEC)
+    monkeypatch.setenv("PATH", str(exe.parent.absolute()), prepend=os.pathsep)
+
+    # Test with cmdline interface
+    cmd = pe.Node(FailCommandLine(), name="cmd-fail", base_dir='cmd')
+    with pytest.raises(pe.nodes.NodeExecutionError) as exc:
+        cmd.run()
+    error_msg = str(exc.value)
+
+    for attr in ("Cmdline:", "Stdout:", "Stderr:", "Traceback:"):
+        assert attr in error_msg
+    assert "This should fail" in error_msg
+
+    # Test with function interface
+    def fail():
+        raise Exception("Functions can fail too")
+
+    func = pe.Node(niu.Function(function=fail), name='func-fail', base_dir='func')
+    with pytest.raises(pe.nodes.NodeExecutionError) as exc:
+        func.run()
+    error_msg = str(exc.value)
+    assert "Traceback:" in error_msg
+    assert "Cmdline:" not in error_msg
+    assert "Functions can fail too" in error_msg
