need to clean

src/hdmf/common/__init__.py

@@ -20,13 +20,12 @@
 # a global type map
 global __TYPE_MAP
 
-def load_termset_config(config_path: str):
+def load_termset_config(config_path: str = None):
     """
-    This method will:
-    - Search the current configuration for data_types that are already present. These data_types will be
-    replaced with the new configuration.
-    - If the data_type is not present, then they will be loaded alongside the default curated configuration.
+    This method will either load the default config or the config provided by the path.
     """
+    if config_path is None:
+        config_path = path_to_config
     __TYPE_MAP.ts_config.load_termset_config(config_path)
 
 # a function to register a container classes with the global map

src/hdmf/container.py

@@ -37,7 +37,7 @@ class HERDManager:
     This class manages whether to set/attach an instance of HERD to the subclass.
     """
 
-    @docval({'name': 'herd', 'type': 'hdmf.common.resources.HERD',
+    @docval({'name': 'herd', 'type': 'HERD',
              'doc': 'The external resources to be used for the container.'},)
     def link_resources(self, **kwargs):
         """
@@ -78,7 +78,8 @@ def _setter(cls, field): # dada
         Make a setter function for creating a :py:func:`property`
         """
         name = field['name']
-        # breakpoint()
+        # if name == 'electrodes':
+        #     breakpoint()
         if not field.get('settable', True):
             return None
 
@@ -89,7 +90,6 @@ def setter(self, val):
                 msg = "can't set attribute '%s' -- already set" % name
                 raise AttributeError(msg)
             self.fields[name] = self._field_config(arg_name=name, val=val)
-            # self.fields[name] = val
 
         return setter
 
@@ -99,8 +99,6 @@ def _field_config(self, arg_name, val):
 
         """
         # load termset configuartion file from global Config
-        # if arg_name == 'location':
-            # breakpoint()
         configurator = self.type_map.ts_config
         if len(configurator.path)>0:
             CUR_DIR = os.path.dirname(os.path.realpath(configurator.path[0]))
@@ -120,6 +118,8 @@ def _field_config(self, arg_name, val):
                     msg = '%s not found within the configuration for %s' % (object_name, self.namespace)
                 else:
                     for attr in config_namespace['data_types'][object_name]:
+                        # if object_name == 'NWBFile':
+                        #     breakpoint()
                         # if the attr has been manually wrapped then skip checking the config for the attr
                         if type(attr) == TermSetWrapper:
                             continue
@@ -141,6 +141,7 @@ def _field_config(self, arg_name, val):
                             if constr_name == arg_name: # make sure any custom fields are not handled (i.e., make an extension)
                                 termset_path = os.path.join(CUR_DIR, config_namespace['data_types'][object_name][attr])
                                 termset = TermSet(term_schema_path=termset_path)
+
                                 val = TermSetWrapper(value=val, termset=termset)
                                 return val
                 return val
@@ -496,7 +497,7 @@ def set_modified(self, **kwargs):
     def children(self):
         return tuple(self.__children)
 
-    @docval({'name': 'child', 'type': 'hdmf.container.Container',
+    @docval({'name': 'child', 'type': 'Container',
              'doc': 'the child Container for this Container', 'default': None})
     def add_child(self, **kwargs):
         warn(DeprecationWarning('add_child is deprecated. Set the parent attribute instead.'))

src/hdmf/term_set.py

@@ -350,10 +350,11 @@ def load_termset_config(self,config_path):
                     msg = 'This configuration file path already exists within the configurator.'
                     raise ValueError(msg)
                 else:
-                    for namespace in termset_config:
+                    for namespace in termset_config['namespaces']:
                         if namespace not in self.config: # append namespace config if not present within self.config
                             self.config['namespaces'][namespace] = termset_config['namespaces'][namespace]
                         else: # check for any needed overrides within existing namespace configs
+                            breakpoint()
                             for data_type in termset_config['namespaces'][namespace]['data_types']:
                                 if data_type in self.config['namespaces'][namespace]['data_types']:
                                     replace_config = termset_config['namespaces'][namespace]['data_types'][data_type]

tests/unit/test_config.yaml

@@ -9,3 +9,7 @@ namespaces:
         field1: '...'
   hdmf-experimental:
     version: TBD
+    data_types:
+      type1:
+        field1: '/Users/mavaylon/Research/NWB/hdmf2/hdmf/tests/unit/example_test_term_set.yaml'
+        field2: '...'

tests/unit/test_extension_config.yaml

@@ -9,3 +9,8 @@ namespaces:
         field1: '...'
   hdmf-experimental:
     version: TBD
+  core:
+    data_types:
+      NWBFile:
+            experimenter: experimenter_termset2.yaml
+            blah: experimenter.yaml