Merge pull request #47 from nipreps/fix/error-desc

ENH: Improve error description, add handler for NodeExecutionError

migas/error/__init__.py

@@ -0,0 +1,6 @@
+from migas.error.base import inspect_error, strip_filenames
+
+__all__ = [
+    "inspect_error",
+    "strip_filenames",
+]

migas/error/base.py

@@ -0,0 +1,56 @@
+from __future__ import annotations
+
+import re
+import sys
+
+
+def inspect_error(error_funcs: dict | None = None) -> dict:
+    # Catch handled errors as well
+    etype, err, etb = sys.exc_info()
+
+    if (etype, err, etb) == (None, None, None):
+        # Python 3.12, new method
+        # MG: Cannot reproduce behavior while testing with 3.12.0
+        # if hasattr(sys, 'last_exc'):
+        #     etype, evalue, etb = sys.last_exc
+
+        # < 3.11
+        if hasattr(sys, 'last_type'):
+            etype = sys.last_type
+            err = sys.last_value
+            etb = sys.last_traceback
+
+    if err and etype:
+        evalue = err.args[0]
+        ename = etype.__name__
+
+        if isinstance(error_funcs, dict) and ename in error_funcs:
+            func = error_funcs[ename]
+            kwargs = func(etype, evalue, etb)
+
+        elif ename in ('KeyboardInterrupt', 'BdbQuit'):
+            kwargs = {
+                'status': 'S',
+                'status_desc': 'Suspended',
+            }
+
+        else:
+            kwargs = {
+                'status': 'F',
+                'status_desc': 'Errored',
+                'error_type': ename,
+                'error_desc': evalue,
+            }
+    else:
+        kwargs = {
+            'status': 'C',
+            'status_desc': 'Completed',
+        }
+    return kwargs
+
+
+def strip_filenames(text: str) -> str:
+    paths = set(re.findall(r'(?:/[^/]+)[/\w\.-]*', text))
+    for path in paths:
+        text = text.replace(path, '<redacted>')
+    return text

migas/error/nipype.py

@@ -0,0 +1,31 @@
+import re
+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()
+
+    return {
+        'status': 'F',
+        'status_desc': f'Exception raised from node {node or "<?>"}',
+        'error_type': 'NodeExecutionError',
+        'error_desc': tb or "No traceback available",
+    }

migas/tests/test_helpers.py → migas/error/tests/test_error.py

@@ -2,14 +2,12 @@
 
 import pytest
 
-import migas
-
 
 class CustomException(Exception):
     ...
 
 
-def sample_error_func(etype: Exception, evalue: str, etb: str):
+def sample_error_func(etype: type, evalue: str, etb: str):
     ename = etype.__name__
     if ename == "CustomException":
         return {
@@ -20,23 +18,24 @@ def sample_error_func(etype: Exception, evalue: str, etb: str):
         }
 
 
-@pytest.mark.parametrize('error_funcs,error,status,error_desc', [
+@pytest.mark.parametrize('error_funcs,error_type,status,error_desc', [
     (None, None, 'C', None),
     (None, KeyboardInterrupt, 'S', None),
-    (None, KeyError, 'F', 'KeyError: \'foo\''),
+    (None, FileNotFoundError, 'F', "i'm a teapot"),
     ({'CustomException': sample_error_func}, CustomException, 'F', 'Custom Error!'),
 ])
-def test_inspect_error(monkeypatch, error_funcs, error, status, error_desc):
+def test_inspect_error(monkeypatch, error_funcs, error_type, status, error_desc):
 
     # do not actually call the server
-    if error is not None:
-        monkeypatch.setattr(sys, 'last_type', error, raising=False)
-        monkeypatch.setattr(sys, 'last_value', error_desc, raising=False)
+    if error_type:
+        error = error_type(error_desc)
+        monkeypatch.setattr(sys, 'last_type', error_type, raising=False)
+        monkeypatch.setattr(sys, 'last_value', error, raising=False)
         monkeypatch.setattr(sys, 'last_traceback', 'Traceback...', raising=False)
 
-    from migas.helpers import _inspect_error
-    res = _inspect_error(error_funcs)
+    from migas.error import inspect_error
+    res = inspect_error(error_funcs)
 
     assert res.get('status') == status
-    if error_desc is not None:
+    if error_desc:
         assert res.get('error_desc') == error_desc

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:
+    raise RuntimeError("Testing")
+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']

migas/helpers.py

@@ -1,12 +1,23 @@
 from __future__ import annotations
 
 import atexit
-import sys
 
 from migas.operations import add_project
+from migas.error import inspect_error
 
 
 def track_exit(project: str, version: str, error_funcs: dict | None = None, **kwargs) -> None:
+    """
+    Registers a final breadcrumb to be sent upon process termination.
+
+    This supplements `migas.operations.add_breadcrumb` by inferring the final process status
+    on whether exception information is available. If so, rough exception information is relayed
+    to the server.
+
+    Additional customization is supported by using the `error_funcs` parameters, which accepts
+    a dictionary consisting of <error-name, function-to-handle-error> key/value pairs. Note that
+    expected outputs of the function are keyword arguments for `migas.operations.add_breadcrumb`.
+    """
     atexit.register(_final_breadcrumb, project, version, error_funcs, **kwargs)
 
 def _final_breadcrumb(
@@ -15,49 +26,6 @@ def _final_breadcrumb(
     error_funcs: dict | None = None,
     **ping_kwargs,
 ) -> dict:
-    status = _inspect_error(error_funcs)
-    kwargs = {**ping_kwargs, **status}
+    status_kwargs = inspect_error(error_funcs)
+    kwargs = {**ping_kwargs, **status_kwargs}
     return add_project(project, version, **kwargs)
-
-
-def _inspect_error(error_funcs: dict | None) -> dict:
-    etype, evalue, etb = None, None, None
-
-    # Python 3.12, new method
-    # MG: Cannot reproduce behavior while testing with 3.12.0
-    # if hasattr(sys, 'last_exc'):
-    #     etype, evalue, etb = sys.last_exc
-
-    # < 3.11
-    if hasattr(sys, 'last_type'):
-        etype = sys.last_type
-        evalue = sys.last_value
-        etb = sys.last_traceback
-
-    if etype:
-        ename = etype.__name__
-
-        if isinstance(error_funcs, dict) and ename in error_funcs:
-            func = error_funcs[ename]
-            kwargs = func(etype, evalue, etb)
-
-        elif ename in ('KeyboardInterrupt', 'BdbQuit'):
-            kwargs = {
-                'status': 'S',
-                'status_desc': 'Suspended',
-            }
-
-        else:
-            kwargs = {
-                'status': 'F',
-                'status_desc': 'Errored',
-                'error_type': ename,
-                'error_desc': evalue,
-            }
-    else:
-        kwargs = {
-            'status': 'C',
-            'status_desc': 'Completed',
-        }
-
-    return kwargs