rough draft

docs/gallery/example_config.yaml

@@ -0,0 +1,16 @@
+- data_type: VectorData
+  namespace:
+  namespace_version:
+  fields:
+    data: /Users/mavaylon/Research/NWB/hdmf2/hdmf/tests/unit/example_test_term_set.yaml
+    field2: ...
+# - data_type: #Container2
+#   namespace:
+#   namespace_version:
+#   fields:
+#     - name:
+#       doc:
+#       termset_path:
+#     - name:
+#       doc:
+#       termset_path:

src/hdmf/__init__.py

@@ -3,9 +3,13 @@
 from .container import Container, Data, DataRegion, HERDManager
 from .region import ListSlicer
 from .utils import docval, getargs
-from .term_set import TermSet, TermSetWrapper
+from .term_set import TermSet, TermSetWrapper, TermSetConfigurator
 
 
+# a global TermSetConfigurator
+global TS_CONFIG
+TS_CONFIG = TermSetConfigurator()
+
 @docval(
     {"name": "dataset", "type": None, "doc": "the HDF5 dataset to slice"},
     {"name": "region", "type": None, "doc": "the region reference to use to slice"},

src/hdmf/build/manager.py

@@ -410,6 +410,7 @@ def __init__(self, **kwargs):
         self.__data_types = dict()
         self.__default_mapper_cls = mapper_cls
         self.__class_generator = ClassGenerator()
+        self.__load_termset_config = True
         self.register_generator(CustomClassGenerator)
         self.register_generator(MCIClassGenerator)
 
@@ -480,9 +481,6 @@ def load_namespaces(self, **kwargs):
                     self.register_container_type(new_ns, dt, container_cls)
         return deps
 
-    def load_config(self, **kwargs):
-        pass
-
     @docval({"name": "namespace", "type": str, "doc": "the namespace containing the data_type"},
             {"name": "data_type", "type": str, "doc": "the data type to create a AbstractContainer class for"},
             {"name": "autogen", "type": bool, "doc": "autogenerate class if one does not exist", "default": True},

src/hdmf/common/__init__.py

@@ -107,6 +107,23 @@ def available_namespaces():
     return __TYPE_MAP.namespace_catalog.namespaces
 
 
+@docval({'name': 'config_path', 'type': str, 'doc': 'Path to the configuartion file.',
+         'default': '/Users/mavaylon/Research/NWB/hdmf2/hdmf/docs/gallery/example_config.yaml'}) #update path
+def load_termset_config(config_path: str):
+    """
+    Load the configuration file for validation on the fields defined for the objects within the file.
+    By default, the curated configuration file is used, but can take in a custom file.
+    """
+    return __TS_CONFIG.load_termset_config(config_path)
+
+
+def unload_termset_config():
+    """
+    Remove validation according to termset configuration file.
+    """
+    return __TS_CONFIG.unload_termset_config()
+
+
 # a function to get the container class for a give type
 @docval({'name': 'data_type', 'type': str,
          'doc': 'the data_type to get the Container class for'},

src/hdmf/container.py

@@ -5,6 +5,7 @@
 from typing import Type
 from uuid import uuid4
 from warnings import warn
+import yaml
 
 import h5py
 import numpy as np
@@ -13,6 +14,8 @@
 from .data_utils import DataIO, append_data, extend_data
 from .utils import docval, get_docval, getargs, ExtenderMeta, get_data_shape, popargs, LabelledDict
 
+from .term_set import TermSet, TermSetWrapper
+
 
 def _set_exp(cls):
     """Set a class as being experimental"""
@@ -232,6 +235,24 @@ def __init__(self, **kwargs):
         self.__read_io = None
         self.__obj = None
 
+    @docval({'name': 'fields', 'type': dict, 'doc': 'The fields/parameters/attibutes for the object.'})
+    def init_validation(self, fields):
+        # load termset configuartion file from global Config
+        from . import TS_CONFIG #update path
+        # Before calling super().__init__() and before setting fields, check for config file for
+        # validation via TermSetWrapper.
+        with open(TS_CONFIG.path, 'r') as config:
+            termset_config = yaml.safe_load(config)
+            object_name = self.__class__.__name__
+
+            for obj_config in termset_config:
+                if obj_config['data_type'] == object_name:
+                    for attr in obj_config['fields']:
+                        if attr in fields: # make sure any custom fields are not handled (i.e., make an extension)
+                            termset_path = obj_config['fields'][attr]
+                            termset = TermSet(term_schema_path=termset_path)
+                            fields[attr] = TermSetWrapper(value=fields[attr], termset=termset)
+
     @property
     def read_io(self):
         """
@@ -785,6 +806,8 @@ class Data(AbstractContainer):
     @docval({'name': 'name', 'type': str, 'doc': 'the name of this container'},
             {'name': 'data', 'type': ('scalar_data', 'array_data', 'data'), 'doc': 'the source of the data'})
     def __init__(self, **kwargs):
+        self.init_validation(fields=kwargs)
+        breakpoint()
         data = popargs('data', kwargs)
         super().__init__(**kwargs)
 

src/hdmf/term_set.py

@@ -304,3 +304,28 @@ def extend(self, arg):
         else:
             msg = ('"%s" is not in the term set.' % ', '.join([str(item) for item in bad_data]))
             raise ValueError(msg)
+
+class TermSetConfigurator:
+    """
+
+    """
+    def __init__(self):
+        self.path = '/Users/mavaylon/Research/NWB/hdmf2/hdmf/docs/gallery/example_config.yaml'
+
+    # @property
+    # def config_path(self):
+    #     return self.__config_path
+
+    @docval({'name': 'config_path', 'type': str, 'doc': 'Path to the configuartion file.'})
+    def load_termset_config(config_path: str):
+        """
+        Load the configuration file for validation on the fields defined for the objects within the file.
+        By default, the curated configuration file is used, but can take in a custom file.
+        """
+        self.path = config_path
+
+    def unload_termset_config():
+        """
+        Remove validation according to termset configuration file.
+        """
+        self.path = None

tests/unit/common/test_table.py

@@ -36,6 +36,10 @@
 except ImportError:
     LINKML_INSTALLED = False
 
+class TestVDConfig(TestCase):
+    def test_init_config(self):
+        vd = VectorData(name='data', description='',data=['Homo sapiens'])
+
 
 class TestDynamicTable(TestCase):
 

tests/unit/test_container.py

@@ -32,6 +32,10 @@ def test_link_and_get_resources(self):
         er_get = em.get_linked_resources()
         self.assertEqual(er, er_get)
 
+class TestContainerConfig(TestCase):
+    def test_init_config(self):
+        obj = Container('obj1')
+
 
 class TestContainer(TestCase):