Fix long filename issue in SlicesDir (#1551)

Author: tsalo

xcp_d/interfaces/plotting.py

@@ -530,8 +530,9 @@ class _SlicesDirInputSpec(FSLCommandInputSpec):
         desc='output every second axial slice rather than just 9 ortho slices',
     )
 
+    # Copy in_files from the original location to the runtime.cwd
     in_files = InputMultiPath(
-        File(exists=True),
+        File(exists=True, copyfile=False),
         argstr='%s',
         mandatory=True,
         position=-1,
@@ -568,6 +569,58 @@ class SlicesDir(FSLCommand):
     _cmd = 'slicesdir'
     input_spec = _SlicesDirInputSpec
     output_spec = _SlicesDirOutputSpec
+    _short_basenames = None
+    _short_outline = None
+
+    def _run_interface(self, runtime):
+        """Create symlinks with short names before running slicesdir.
+
+        ``slicesdir`` names its output files by replacing path separators in the input
+        file paths with underscores. When input paths are long (e.g., in deep working
+        directories), the derived output filenames can exceed the OS's 255-character
+        filename limit (see https://github.com/PennLINC/xcp_d/issues/1545).
+
+        We work around this by creating symlinks with short names in the working
+        directory, and passing those short names to ``slicesdir`` instead of the
+        original long paths.
+        """
+        self._short_basenames = []
+        for i, f in enumerate(self.inputs.in_files):
+            ext = '.nii.gz' if f.endswith('.nii.gz') else os.path.splitext(f)[1]
+            basename = f'img{i}{ext}'
+            symlink_path = os.path.join(runtime.cwd, basename)
+            if os.path.lexists(symlink_path):
+                os.unlink(symlink_path)
+
+            os.symlink(os.path.abspath(f), symlink_path)
+            self._short_basenames.append(basename)
+
+        if isdefined(self.inputs.outline_image):
+            f = self.inputs.outline_image
+            ext = '.nii.gz' if f.endswith('.nii.gz') else os.path.splitext(f)[1]
+            self._short_outline = f'outline{ext}'
+            symlink_path = os.path.join(runtime.cwd, self._short_outline)
+            if os.path.lexists(symlink_path):
+                os.unlink(symlink_path)
+
+            os.symlink(os.path.abspath(f), symlink_path)
+
+        runtime = super()._run_interface(runtime)
+        return runtime
+
+    def _format_arg(self, name, spec, value):
+        """Use short symlink basenames for in_files and outline_image.
+
+        This ensures the ``slicesdir`` command line uses short paths, producing
+        short output filenames that won't exceed the OS filename length limit.
+        """
+        if name == 'in_files' and self._short_basenames is not None:
+            return ' '.join(self._short_basenames)
+
+        if name == 'outline_image' and self._short_outline is not None:
+            return spec.argstr % self._short_outline
+
+        return super()._format_arg(name, spec, value)
 
     def _list_outputs(self):
         """Create a Bunch which contains all possible files generated by running the interface.
@@ -586,13 +639,21 @@ def _list_outputs(self):
 
         out_dir = os.path.abspath(os.path.join(os.getcwd(), 'slicesdir'))
         outputs['out_dir'] = out_dir
+
+        # Use short basenames if available (set by _run_interface),
+        # otherwise fall back to the original path-based naming.
+        if self._short_basenames is not None:
+            in_basenames = self._short_basenames
+        else:
+            in_basenames = [f.replace(os.sep, '_') for f in self.inputs.in_files]
+
         outputs['out_files'] = [
             self._gen_fname(
-                basename=f.replace(os.sep, '_'),
+                basename=name,
                 cwd=out_dir,
                 ext=self.inputs.out_extension,
             )
-            for f in self.inputs.in_files
+            for name in in_basenames
         ]
         temp_files = [
             'grota.png',