✅ Fix get_nested to handle empty config

Author: shnizzedy

CPAC/utils/configuration/configuration.py

@@ -322,13 +322,15 @@ def update(self, key, val=ConfigurationDictUpdateConflation):
         setattr(self, key, val)
 
     def get_nested(self, d, keys):
+        if d is None:
+            d = {}
         if isinstance(keys, str):
             return d[keys]
-        elif isinstance(keys, tuple) or isinstance(keys, list):
+        if isinstance(keys, (list, tuple)):
             if len(keys) > 1:
                 return self.get_nested(d[keys[0]], keys[1:])
-            else:
-                return d[keys[0]]
+            return d[keys[0]]
+        return d
 
     def set_nested(self, d, keys, value):  # pylint: disable=invalid-name
         if isinstance(keys, str):

CPAC/utils/configuration/yaml_template.py

@@ -108,12 +108,7 @@ def dump(self, new_dict, parents=None):
             fsldir = self.get_nested(self._dict,
                                      ['pipeline_setup', 'system_config',
                                       'FSLDIR'])
-        try:
-            self.get_nested(new_dict, ['surface_analysis', 'freesurfer', 'ingress_reconall'])
-        except KeyError:
-            new_dict = set_nested_value(new_dict, ['surface_analysis', 'freesurfer', 
-                            'ingress_reconall'], False)
-        
+
         # Add YAML version directive to top of document and ensure
         # C-PAC version comment and 'FROM' are at the top of the YAML
         # output
@@ -125,8 +120,16 @@ def dump(self, new_dict, parents=None):
             # Insert automatically-changed value in original dict
             if freesurfer_extraction:
                 new_dict = set_nested_value(
-                    new_dict, ['surface_analysis', 'freesurfer', 
+                    new_dict, ['surface_analysis', 'freesurfer',
                     'run_reconall'], False)
+            try:
+                self.get_nested(new_dict,
+                                ['surface_analysis', 'freesurfer',
+                                 'ingress_reconall'])
+            except KeyError:
+                new_dict = set_nested_value(new_dict,
+                                            ['surface_analysis', 'freesurfer',
+                                             'ingress_reconall'], False)
         else:
             _dump = []
         # Prepare for indentation