ENH: Add better error detection for nipype node errors

migas/error/__init__.py

@@ -53,4 +53,4 @@ def strip_filenames(text: str) -> str:
     paths = set(re.findall(r'(?:/[^/]+)[/\w\.-]*', text))
     for path in paths:
         text = text.replace(path, '<redacted>')
-    return text
+    return text

migas/error/nipype.py

@@ -0,0 +1,34 @@
+import re
+import typing as ty
+from types import TracebackType
+
+from migas.error import strip_filenames
+
+
+def node_execution_error(etype: type, evalue: str, etb: TracebackType) -> dict:
+    strpval = evalue.replace('\n', ' ').replace('\t', ' ').strip()
+    node, cmd, stdout, stderr, tb = None, None, None, None, None
+
+    if m := re.search(r'(?P<node>(?<=Exception raised while executing Node )\w+)', strpval):
+        node = m.group('node').strip()
+
+    if m := re.search(r'(?P<cmdline>(?<=Cmdline:).*(?=Stdout:))', strpval):
+        cmd = strip_filenames(m.group('cmdline')).strip()
+
+    if m := re.search(r'(?P<stdout>(?<=Stdout:).*(?=Stderr:))', strpval):
+        stdout = strip_filenames(m.group('stdout')).strip()
+
+    if m := re.search(r'(?P<stderr>(?<=Stderr:).*(?=Traceback:))', strpval):
+        stderr = strip_filenames(m.group('stderr')).strip()
+
+    if m := re.search(r'(?P<tb>(?<=Traceback:).*)', strpval):
+        tb = strip_filenames(m.group('tb')).strip()
+
+    print(node, cmd, stdout, stderr, tb)
+
+    return {
+        'status': 'F',
+        'status_desc': f'Exception raised from node {node or "<?>"}',
+        'error_type': 'NodeExecutionError',
+        'error_desc': tb or "No traceback available",
+    }

migas/error/tests/test_nipype.py

@@ -0,0 +1,65 @@
+import sys
+
+from migas.error.nipype import node_execution_error
+
+ERROR_TEXT = """
+nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node failingnode.
+
+Cmdline:
+	mri_convert --out_type mgz --input_volume /tmp/sample/file.txt --output_volume /tmp/wf/conv1/README_out.mgz
+Stdout:
+	mri_convert --out_type mgz --input_volume /tmp/sample/file.txt --output_volume /tmp/wf/conv1/README_out.mgz
+	ERROR: cannot determine file type for /tmp/sample/file.txt
+Stderr:
+
+Traceback:
+	Traceback (most recent call last):
+	  File "/code/nipype/nipype/interfaces/base/core.py", line 454, in aggregate_outputs
+	    setattr(outputs, key, val)
+	  File "/code/nipype/nipype/interfaces/base/traits_extension.py", line 425, in validate
+	    value = super(MultiObject, self).validate(objekt, name, newvalue)
+	  File "/code/.pyenv/versions/nipreps/lib/python3.10/site-packages/traits/trait_types.py", line 2699, in validate
+	    return TraitListObject(self, object, name, value)
+	  File "/code/.pyenv/versions/nipreps/lib/python3.10/site-packages/traits/trait_list_object.py", line 582, in __init__
+	    super().__init__(
+	  File "/code/.pyenv/versions/nipreps/lib/python3.10/site-packages/traits/trait_list_object.py", line 213, in __init__
+	    super().__init__(self.item_validator(item) for item in iterable)
+	  File "/code/.pyenv/versions/nipreps/lib/python3.10/site-packages/traits/trait_list_object.py", line 213, in <genexpr>
+	    super().__init__(self.item_validator(item) for item in iterable)
+	  File "/code/.pyenv/versions/nipreps/lib/python3.10/site-packages/traits/trait_list_object.py", line 865, in _item_validator
+	    return trait_validator(object, self.name, value)
+	  File "/code/nipype/nipype/interfaces/base/traits_extension.py", line 330, in validate
+	    value = super(File, self).validate(objekt, name, value, return_pathlike=True)
+	  File "/code/nipype/nipype/interfaces/base/traits_extension.py", line 135, in validate
+	    self.error(objekt, name, str(value))
+	  File "/code/.pyenv/versions/nipreps/lib/python3.10/site-packages/traits/base_trait_handler.py", line 74, in error
+	    raise TraitError(
+	traits.trait_errors.TraitError: Each element of the 'out_file' trait of a MRIConvertOutputSpec instance must be a pathlike object or string representing an existing file, but a value of '/tmp/wf/conv1/README_out.mgz' <class 'str'> was specified.
+
+	During handling of the above exception, another exception occurred:
+
+	Traceback (most recent call last):
+	  File "/code/nipype/nipype/interfaces/base/core.py", line 401, in run
+	    outputs = self.aggregate_outputs(runtime)
+	  File "/code/nipype/nipype/interfaces/base/core.py", line 461, in aggregate_outputs
+	    raise FileNotFoundError(msg)
+	FileNotFoundError: No such file or directory '/tmp/wf/conv1/README_out.mgz' for output 'out_file' of a MRIConvert interface
+"""
+
+
+class NodeExecutionError(Exception):
+    ...
+
+
+TB = None
+try:
+    1 + 'a'
+except Exception:
+    _, _, TB = sys.exc_info()
+
+
+def test_node_execution_error():
+    kwargs = node_execution_error(NodeExecutionError, ERROR_TEXT, TB)
+    assert kwargs['status'] == 'F'
+    assert kwargs['error_type'] == 'NodeExecutionError'
+    assert 'FileNotFoundError' in kwargs['error_desc']