FIX/TEST: Fixes minor bugs in BoutiqueInterface

nipype/interfaces/base/__init__.py

@@ -8,6 +8,8 @@
 This module defines the API of all nipype interfaces.
 
 """
+from .boutiques import (BoutiqueInterface)
+
 from .core import (Interface, BaseInterface, SimpleInterface, CommandLine,
                    StdOutCommandLine, MpiCommandLine, SEMLikeCommandLine,
                    LibraryBaseInterface, PackageInfo)

nipype/interfaces/base/boutiques.py

@@ -7,6 +7,7 @@
 from itertools import chain
 import json
 import os
+import re
 
 from .core import CommandLine
 from .specs import DynamicTraitedSpec
@@ -187,7 +188,6 @@ def _populate_input_spec(self, input_list):
                                (self.input_spec,),
                                input_spec)
 
-        # TODO: value-keys aren't necessarily mutually exclusive; use id as key
         self.value_keys = value_keys
 
     def _populate_output_spec(self, output_list):
@@ -243,8 +243,10 @@ def _list_outputs(self):
 
             # replace all value-keys in output name
             for name, valkey in self.value_keys.items():
+                if valkey not in output_filename:
+                    continue
                 repl = self.inputs.trait_get().get(name)
-                # if input is specified, strip extensions + replace in output
+                # if input is specified, strip ext + replace value in output
                 if repl is not None and isdefined(repl):
                     for ext in strip:
                         repl = repl[:-len(ext)] if repl.endswith(ext) else repl
@@ -271,14 +273,13 @@ def aggregate_outputs(self, runtime=None, needed_outputs=None):
                 if len(val) == 0:
                     val = Undefined
                 setattr(outputs, key, val)
-            else:
+            if isdefined(val):
                 if not os.path.exists(val):
-                    val = Undefined
-            if not os.path.exists(val):
-                setattr(outputs, key, Undefined)
+                    setattr(outputs, key, Undefined)
 
         return outputs
 
+    @property
     def cmdline(self):
         """ Prints command line with all specified arguments
         """
@@ -295,12 +296,12 @@ def cmdline(self):
             elif spec.argstr:
                 value = self._format_arg(name, spec, value)
             args = args.replace(valkey, value)
-        return self._cmd + ' ' + args
+        # normalize excessive whitespace before returning
+        return re.sub(r'\s\s+', ' ', self._cmd + ' ' + args).strip()
 
     def help(self, returnhelp=False):
         """ Prints interface help
         """
-
         docs = self.boutique_spec.get('description')
         if docs is not None:
             docstring = trim(docs).split('\n') + ['']

nipype/interfaces/base/tests/test_boutiques.py

@@ -0,0 +1,44 @@
+# -*- coding: utf-8 -*-
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+
+from ...base import BoutiqueInterface
+from ....testing import example_data
+
+
+EXAMPLE_SPECS = [
+    dict(
+        spec=example_data('boutiques_fslbet.json'),
+        inputs=[
+            'additional_surfaces_flag', 'additional_surfaces_t2',
+            'approx_skull_flag', 'binary_mask_flag', 'center_of_gravity',
+            'debug_flag', 'fractional_intensity', 'head_radius', 'in_file',
+            'no_seg_output_flag', 'out_file', 'overlay_flag',
+            'reduce_bias_flag', 'residual_optic_cleanup_flag',
+            'robust_iters_flag', 'slice_padding_flag', 'thresholding_flag',
+            'verbose_flag', 'vg_fractional_intensity', 'vtk_mesh',
+            'whole_set_mask_flag'
+        ],
+        outputs=[
+            'approx_skull_img_file', 'binary_skull_file', 'inskull_mask_file',
+            'inskull_mesh_file', 'inskull_off_file', 'output_file',
+            'outskin_mask_file', 'outskin_mesh_file', 'outskin_off_file',
+            'outskull_mask_file', 'outskull_mesh_file', 'outskull_off_file',
+            'overlay_file', 'skull_mask_file', 'vtk_mesh_file'
+        ]
+    )
+]
+
+
+def test_BoutiqueInterface():
+    for example in EXAMPLE_SPECS:
+        interface = BoutiqueInterface(example['spec'])
+
+        # check interface input/output spec generation
+        inputs = list(interface.input_spec().get())
+        outputs = list(interface.output_spec().get())
+        assert all([f in inputs for f in example['inputs']])
+        assert all([f in outputs for f in example['outputs']])
+
+        # confirm help works
+        assert isinstance(interface.help(True), str)

nipype/testing/data/boutiques_fslbet.json

@@ -14,7 +14,7 @@
         {
             "description": "Name of generated, skulltripped image (e.g. img_bet.nii.gz)",
             "value-key": "[OUT_FILE]",
-            "type": "File",
+            "type": "String",
             "optional": false,
             "id": "out_file",
             "name": "Output file"
@@ -249,15 +249,15 @@
             "path-template": "[OUT_FILE].nii.gz",
             "description": "Default skullstripped image generated by BET",
             "optional": true,
-            "id": "outfile",
-            "name": "Output mask file",
+            "id": "output_file",
+            "name": "Output skullstripped file",
             "path-template-stripped-extensions": [".nii.gz", ".nii"]
         },
         {
             "path-template": "[OUT_FILE]_mask.nii.gz",
             "description": "Binary mask file (from -m option)",
             "optional": true,
-            "id": "binary_mask",
+            "id": "binary_skull_file",
             "name": "Output binary mask file",
             "path-template-stripped-extensions": [".nii.gz", ".nii"]
         },
@@ -273,95 +273,95 @@
             "path-template": "[OUT_FILE]_skull.nii.gz",
             "description": "Approximate skull image file",
             "optional": true,
-            "id": "approx_skull_img",
+            "id": "approx_skull_img_file",
             "name": "Approximate skull file",
             "path-template-stripped-extensions": [".nii.gz", ".nii"]
         },
         {
             "path-template": "[OUT_FILE]_mesh.vtk",
             "description": "Mesh in VTK format",
             "optional": true,
-            "id": "output_vtk_mesh",
+            "id": "vtk_mesh_file",
             "name": "VTK mesh",
             "path-template-stripped-extensions": [".nii.gz", ".nii"]
         },
         {
             "path-template": "[OUT_FILE]_skull_mask.nii.gz",
             "description": "Output mask for skull image",
             "optional": true,
-            "id": "skull_mask",
+            "id": "skull_mask_file",
             "name": "Skull mask image",
             "path-template-stripped-extensions": [".nii.gz", ".nii"]
         },
         {
             "path-template": "[OUT_FILE]_inskull_mask.nii.gz",
             "description": "The in-skull mask file from betsurf (from -A or -A2)",
             "optional": true,
-            "id": "out_inskull_mask",
+            "id": "inskull_mask_file",
             "name": "Output in-skull mask file",
             "path-template-stripped-extensions": [".nii.gz", ".nii"]
         },
         {
             "path-template": "[OUT_FILE]_inskull_mesh.nii.gz",
             "description": "The in-skull mesh file from betsurf (from -A or -A2)",
             "optional": true,
-            "id": "out_inskull_mesh",
+            "id": "inskull_mesh_file",
             "name": "Output in-skull mesh file",
             "path-template-stripped-extensions": [".nii.gz", ".nii"]
         },
         {
             "path-template": "[OUT_FILE]_inskull_mesh.off",
             "description": "The in-skull mesh .off file from betsurf (from -A or -A2)",
             "optional": true,
-            "id": "out_inskull_off",
+            "id": "inskull_off_file",
             "name": "Output in-skull mesh off file",
             "path-template-stripped-extensions": [".nii.gz", ".nii"]
         },
         {
             "path-template": "[OUT_FILE]_outskin_mask.nii.gz",
             "description": "The out-skin mask file from betsurf (from -A or -A2)",
             "optional": true,
-            "id": "out_outskin_mask",
+            "id": "outskin_mask_file",
             "name": "Output out-skin mask file",
             "path-template-stripped-extensions": [".nii.gz", ".nii"]
         },
         {
             "path-template": "[OUT_FILE]_outskin_mesh.nii.gz",
             "description": "The out-skin mesh file from betsurf (from -A or -A2)",
             "optional": true,
-            "id": "out_outskin_mesh",
+            "id": "outskin_mesh_file",
             "name": "Output out-skin mesh file",
             "path-template-stripped-extensions": [".nii.gz", ".nii"]
         },
         {
             "path-template": "[OUT_FILE]_outskin_mesh.off",
             "description": "The out-skin mesh .off file from betsurf (from -A or -A2)",
             "optional": true,
-            "id": "out_outskin_off",
+            "id": "outskin_off_file",
             "name": "Output out-skin mesh off file",
             "path-template-stripped-extensions": [".nii.gz", ".nii"]
         },
         {
             "path-template": "[OUT_FILE]_outskull_mask.nii.gz",
             "description": "The out-skull mask file from betsurf (from -A or -A2)",
             "optional": true,
-            "id": "out_outskull_mask",
+            "id": "outskull_mask_file",
             "name": "Output out-skull mask file",
             "path-template-stripped-extensions": [".nii.gz", ".nii"]
         },
         {
             "path-template": "[OUT_FILE]_outskull_mesh.nii.gz",
             "description": "The out-skull mesh file from betsurf (from -A or -A2)",
             "optional": true,
-            "id": "out_outskull_mesh",
+            "id": "outskull_mesh_file",
             "name": "Output out-skull mesh file",
             "path-template-stripped-extensions": [".nii.gz", ".nii"]
         },
         {
             "path-template": "[OUT_FILE]_outskull_mesh.off",
             "description": "The out-skull mesh .off file from betsurf (from -A or -A2)",
             "optional": true,
-            "id": "out_outskull_off",
+            "id": "outskull_off_file",
             "name": "Output out-skull mesh off file",
             "path-template-stripped-extensions": [".nii.gz", ".nii"]
         }