TermSet Config

src/pynwb/core.py

@@ -2,11 +2,13 @@
 
 import numpy as np
 
-from hdmf import Container, Data
+import yaml
+
+from hdmf import Container, Data, TermSet, TermSetWrapper
 from hdmf.container import AbstractContainer, MultiContainerInterface as hdmf_MultiContainerInterface, Table
 from hdmf.common import DynamicTable, DynamicTableRegion  # noqa: F401
 from hdmf.common import VectorData, VectorIndex, ElementIdentifiers  # noqa: F401
-from hdmf.utils import docval, popargs
+from hdmf.utils import docval, popargs, get_docval
 from hdmf.utils import LabelledDict  # noqa: F401
 
 from . import CORE_NAMESPACE, register_class
@@ -54,6 +56,19 @@ class NWBContainer(NWBMixin, Container):
 
     __nwbfields__ = tuple()
 
+    def init_validation(self, kwargs):
+        # Before calling super().__init__() and before setting fields, check for termset_config.yaml.
+        # This file will be stored within nwb-schema
+        with open('src/pynwb/nwb-schema/termset_config/termset_config.yaml', 'r') as config:
+            termset_config = yaml.safe_load(config)
+            object_name = self.__class__.__name__ # the name field is not set yet
+            if object_name in termset_config:
+                for field in termset_config[object_name]:
+                    if field in kwargs: # make sure any custom fields are not handled (i.e., make an extension)
+                        termset_path = termset_config[object_name][field]
+                        termset = TermSet(term_schema_path=termset_path)
+                        kwargs[field] = TermSetWrapper(value=kwargs[field], termset=termset)
+
 
 @register_class('NWBDataInterface', CORE_NAMESPACE)
 class NWBDataInterface(NWBContainer):

src/pynwb/file.py

@@ -109,6 +109,7 @@ class Subject(NWBContainer):
         {'name': 'strain', 'type': str, 'doc': 'The strain of the subject, e.g., "C57BL/6J"', 'default': None},
     )
     def __init__(self, **kwargs):
+        self.init_validation(kwargs)
         keys_to_set = (
             "age",
             "age__reference",
@@ -122,8 +123,8 @@ def __init__(self, **kwargs):
             "strain",
         )
         args_to_set = popargs_to_dict(keys_to_set, kwargs)
-        super().__init__(name="subject", **kwargs)
-
+        kwargs['name'] = 'subject'
+        super().__init__(**kwargs)
         # NOTE when the Subject I/O mapper (see pynwb.io.file.py) reads an age__reference value of None from an
         # NWB 2.0-2.5 file, it sets the value to "unspecified" so that when Subject.__init__ is called, the incoming
         # age__reference value is NOT replaced by the default value ("birth") specified in the docval.