add overwrite argument to json load

Author: oesteban

nipype/interfaces/base.py

@@ -56,6 +56,8 @@
 
 iflogger = logging.getLogger('interface')
 
+PY35 = sys.version_info >= (3, 5)
+
 if runtime_profile:
     try:
         import psutil
@@ -762,12 +764,13 @@ def __init__(self, from_file=None, **inputs):
         if not self.input_spec:
             raise Exception('No input_spec in class: %s' %
                             self.__class__.__name__)
+
         self.inputs = self.input_spec(**inputs)
         self.estimated_memory_gb = 1
         self.num_threads = 1
 
         if from_file is not None:
-            self.load_inputs_from_json(from_file)
+            self.load_inputs_from_json(from_file, overwrite=False)
 
 
     @classmethod
@@ -1152,24 +1155,33 @@ def version(self):
                                  self.__class__.__name__)
         return self._version
 
-    def load_inputs_from_json(self, json_file):
+    def load_inputs_from_json(self, json_file, overwrite=True):
         """
         A convenient way to load pre-set inputs from a JSON file.
         """
 
         with open(json_file) as fhandle:
             inputs_dict = json.load(fhandle)
 
-        for key, val in list(inputs_dict.items()):
+        for key, newval in list(inputs_dict.items()):
             if not hasattr(self.inputs, key):
-                setattr(self.inputs, key, val)
+                continue
+            val = getattr(self.inputs, key)
+            if overwrite or not isdefined(val):
+                setattr(self.inputs, key, newval)
 
     def save_inputs_to_json(self, json_file):
         """
         A convenient way to save current inputs to a JSON file.
         """
+        inputs = self.inputs.get()
+        for key, val in list(inputs.items()):
+            if not isdefined(val):
+                inputs.pop(key, None)
+
+        iflogger.debug('saving inputs {}', inputs)
         with open(json_file, 'w') as fhandle:
-            json.dump(self.inputs.get(), fhandle, indent=4)
+            json.dump(inputs, fhandle, indent=4)
 
 
 class Stream(object):

nipype/interfaces/tests/test_base.py

@@ -459,6 +459,11 @@ def test_BaseInterface_load_save_inputs():
     tmp_dir = tempfile.mkdtemp()
     tmp_json = os.path.join(tmp_dir, 'settings.json')
 
+    def _rem_undefined(indict):
+        for key, val in list(indict.items()):
+            if not nib.isdefined(val):
+                indict.pop(key, None)
+        return indict
 
     class InputSpec(nib.TraitedSpec):
         input1 = nib.traits.Int()
@@ -472,16 +477,20 @@ class DerivedInterface(nib.BaseInterface):
         def __init__(self, **inputs):
             super(DerivedInterface, self).__init__(**inputs)
 
-    inputs_dict = {'input1': 12, 'input2': 3.4, 'input3': True,
+    inputs_dict = {'input1': 12, 'input3': True,
                    'input4': 'some string'}
     bif = DerivedInterface(**inputs_dict)
     bif.save_inputs_to_json(tmp_json)
     bif2 = DerivedInterface()
     bif2.load_inputs_from_json(tmp_json)
-    yield assert_equal, inputs_dict, bif2.inputs.get()
+    yield assert_equal, _rem_undefined(bif2.inputs.get()), inputs_dict
 
     bif3 = DerivedInterface(from_file=tmp_json)
-    yield assert_equal, inputs_dict, bif3.inputs.get()
+    yield assert_equal, _rem_undefined(bif3.inputs.get()), inputs_dict
+
+    inputs_dict.update({'input4': 'some other string'})
+    bif4 = DerivedInterface(from_file=tmp_json, input4='some other string')
+    yield assert_equal, _rem_undefined(bif4.inputs.get()), inputs_dict
 
 def assert_not_raises(fn, *args, **kwargs):
     fn(*args, **kwargs)