Merge pull request #3395 from oesteban/fix/commandline-nodes-issue

FIX: Improve error handling of ``CommandLine`` interfaces

Author: effigies

nipype/interfaces/base/core.py

@@ -607,6 +607,7 @@ class must be instantiated with a command argument
     _cmd = None
     _version = None
     _terminal_output = "stream"
+    _write_cmdline = False
 
     @classmethod
     def set_default_terminal_output(cls, output_type):
@@ -623,7 +624,9 @@ def set_default_terminal_output(cls, output_type):
         else:
             raise AttributeError("Invalid terminal output_type: %s" % output_type)
 
-    def __init__(self, command=None, terminal_output=None, **inputs):
+    def __init__(
+        self, command=None, terminal_output=None, write_cmdline=False, **inputs
+    ):
         super(CommandLine, self).__init__(**inputs)
         self._environ = None
         # Set command. Input argument takes precedence
@@ -638,6 +641,8 @@ def __init__(self, command=None, terminal_output=None, **inputs):
         if terminal_output is not None:
             self.terminal_output = terminal_output
 
+        self._write_cmdline = write_cmdline
+
     @property
     def cmd(self):
         """sets base command, immutable"""
@@ -669,6 +674,14 @@ def terminal_output(self, value):
             )
         self._terminal_output = value
 
+    @property
+    def write_cmdline(self):
+        return self._write_cmdline
+
+    @write_cmdline.setter
+    def write_cmdline(self, value):
+        self._write_cmdline = value is True
+
     def raise_exception(self, runtime):
         raise RuntimeError(
             (
@@ -716,9 +729,16 @@ def _run_interface(self, runtime, correct_return_codes=(0,)):
             adds stdout, stderr, merged, cmdline, dependencies, command_path
 
         """
-
         out_environ = self._get_environ()
         # Initialize runtime Bunch
+
+        try:
+            runtime.cmdline = self.cmdline
+        except Exception as exc:
+            raise RuntimeError(
+                "Error raised when interpolating the command line"
+            ) from exc
+
         runtime.stdout = None
         runtime.stderr = None
         runtime.cmdline = self.cmdline
@@ -742,7 +762,11 @@ def _run_interface(self, runtime, correct_return_codes=(0,)):
             if self._ldd
             else "<skipped>"
         )
-        runtime = run_command(runtime, output=self.terminal_output)
+        runtime = run_command(
+            runtime,
+            output=self.terminal_output,
+            write_cmdline=self.write_cmdline,
+        )
         return runtime
 
     def _format_arg(self, name, trait_spec, value):
@@ -907,7 +931,14 @@ def _parse_inputs(self, skip=None):
 
             if not isdefined(value):
                 continue
-            arg = self._format_arg(name, spec, value)
+
+            try:
+                arg = self._format_arg(name, spec, value)
+            except Exception as exc:
+                raise ValueError(
+                    f"Error formatting command line argument '{name}' with value '{value}'"
+                ) from exc
+
             if arg is None:
                 continue
             pos = spec.position

nipype/pipeline/engine/nodes.py

@@ -209,6 +209,9 @@ def __init__(
         self.needed_outputs = needed_outputs
         self.config = None
 
+        if hasattr(self._interface, "write_cmdline"):
+            self._interface.write_cmdline = True
+
     @property
     def interface(self):
         """Return the underlying interface object"""
@@ -711,16 +714,13 @@ def _run_command(self, execute, copyfiles=True):
             f'[Node] Executing "{self.name}" <{self._interface.__module__}'
             f".{self._interface.__class__.__name__}>"
         )
+
         # Invoke core run method of the interface ignoring exceptions
         result = self._interface.run(cwd=outdir, ignore_exception=True)
         logger.info(
             f'[Node] Finished "{self.name}", elapsed time {result.runtime.duration}s.'
         )
 
-        if issubclass(self._interface.__class__, CommandLine):
-            # Write out command line as it happened
-            Path.write_text(outdir / "command.txt", f"{result.runtime.cmdline}\n")
-
         exc_tb = getattr(result.runtime, "traceback", None)
 
         if not exc_tb:

nipype/utils/subprocess.py

@@ -10,6 +10,7 @@
 import select
 import locale
 import datetime
+from pathlib import Path
 from subprocess import Popen, STDOUT, PIPE
 from .filemanip import canonicalize_env, read_stream
 
@@ -69,7 +70,7 @@ def _read(self, drain):
         self._lastidx = len(self._rows)
 
 
-def run_command(runtime, output=None, timeout=0.01):
+def run_command(runtime, output=None, timeout=0.01, write_cmdline=False):
     """Run a command, read stdout and stderr, prefix with timestamp.
 
     The returned runtime contains a merged stdout+stderr log with timestamps
@@ -100,6 +101,9 @@ def run_command(runtime, output=None, timeout=0.01):
         errfile = os.path.join(runtime.cwd, "stderr.nipype")
         stderr = open(errfile, "wb")
 
+    if write_cmdline:
+        (Path(runtime.cwd) / "command.txt").write_text(cmdline)
+
     proc = Popen(
         cmdline,
         stdout=stdout,