testing

src/hdmf/__init__.py

@@ -7,7 +7,7 @@
 
 
 # a global TermSetConfigurator
-TS_CONFIG = TermSetConfigurator()
+TS_CONFIG = TermSetConfigurator(path='src/hdmf/hdmf_config.yaml')
 
 def get_termset_config():
     return TS_CONFIG.config

src/hdmf/container.py

@@ -234,21 +234,22 @@ 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):
+    @docval({'name': 'constructor_args', 'type': dict, 'doc': 'The fields/parameters/attibutes for the object.'})
+    def init_validation(self, constructor_args):
         # load termset configuartion file from global Config
         from . import TS_CONFIG #update path
 
         termset_config = TS_CONFIG.config
-        breakpoint()
         if termset_config is None:
             msg = 'TermSet Configuration is not loaded.'
             raise ValueError(msg)
         object_name = self.__class__.__name__
 
         # Check that the object data_type is in the loaded namespace
         from .common import get_type_map
-        container_types_dict = get_type_map().container_types
+        tm = get_type_map()
+
+        container_types_dict = tm.container_types
         object_exists = False
         for namespace in container_types_dict:
             if object_name in container_types_dict[namespace]:
@@ -258,22 +259,37 @@ def init_validation(self, fields):
 
         if not object_exists:
             msg = "%s is not in the loaded Namespace(s)." % object_name
-            raise ValueError(msg)
+            raise warn(msg)
 
         # Wrap supported fields with TermSetWrapper
         obj_wrapped = False
         if object_name in termset_config:
             obj_wrapped = True
             for attr in termset_config[object_name]['fields']:
-                if attr in fields: # make sure any custom fields are not handled (i.e., make an extension)
+                obj_mapper = tm.get_map(self)
+                # get the spec according to attr name in schema
+                # Note: this is the name for the field in the config
+                spec = obj_mapper.get_attr_spec(attr)
+
+                # In the case of dealing with datasets directly or not defined in the spec.
+                # (Data/VectorData/DynamicTable/etc)
+                if spec is None:
+                #     constr_name= attr
+                    msg = "Spec not found for %s" % attr
+                    raise warn(msg)
+                # From the spec, get the corresponding constructor name
+                else:
+                    constr_name = obj_mapper.get_const_arg(spec)
+
+                if constr_name in constructor_args: # make sure any custom fields are not handled (i.e., make an extension)
                     termset_path = termset_config[object_name]['fields'][attr]
                     termset = TermSet(term_schema_path=termset_path)
-                    fields[attr] = TermSetWrapper(value=fields[attr], termset=termset)
+                    constructor_args[attr] = TermSetWrapper(value=constructor_args[attr], termset=termset)
 
         # Even if the data_type is in the namespace, it might not be in the configuration.
-        if not obj_wrapped:
+        if object_exists and not obj_wrapped:
             msg = "%s is not in the loaded TermSet Configuration." % object_name
-            raise ValueError(msg)
+            raise warn(msg)
 
     @property
     def read_io(self):
@@ -827,8 +843,8 @@ 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()
+        self.init_validation(constructor_args=kwargs)
+        # breakpoint()
         data = popargs('data', kwargs)
         super().__init__(**kwargs)
 

src/hdmf/hdmf_config.yaml

@@ -0,0 +1,12 @@
+VectorData:
+    namespace:
+    namespace_version:
+    fields:
+      data: /Users/mavaylon/Research/NWB/hdmf2/hdmf/tests/unit/example_test_term_set.yaml
+      field2: ...
+DataType2:
+    namespace:
+    namespace_version:
+    fields:
+      data: /Users/mavaylon/Research/NWB/hdmf2/hdmf/tests/unit/example_test_term_set.yaml
+      field2: ...

src/hdmf/term_set.py

@@ -310,8 +310,10 @@ class TermSetConfigurator:
     """
 
     """
-    def __init__(self):
-        self.path = ['/Users/mavaylon/Research/NWB/hdmf2/hdmf/docs/gallery/example_config.yaml']
+    @docval({'name': 'path', 'type': str, 'doc': 'Path to the configuartion file.',
+             'default': None})
+    def __init__(self, **kwargs):
+        self.path = [kwargs['path']]
         self.config = None
         self.load_termset_config()
 
@@ -339,10 +341,9 @@ def load_termset_config(self,config_path):
             # append path to new config to self.path
             self.path.append(config_path)
 
-
     def unload_termset_config():
         """
         Remove validation according to termset configuration file.
         """
-        self.path = ['/Users/mavaylon/Research/NWB/hdmf2/hdmf/docs/gallery/example_config.yaml']
+        self.path = ['src/hdmf/hdmf_config.yaml']
         self.config = None

tests/unit/common/test_table.py

@@ -39,6 +39,31 @@
 class TestVDConfig(TestCase):
     def test_init_config(self):
         vd = VectorData(name='data', description='',data=['Homo sapiens'])
+        tb = DynamicTable(name="with_table_columns", description='a test table', columns=[vd])
+        from hdmf.common import get_type_map
+        htm = get_type_map()
+        om = htm.get_map(tb)
+        from datetime import datetime
+        from uuid import uuid4
+
+        # import numpy as np
+        # from dateutil.tz import tzlocal
+        #
+        # from pynwb import NWBHDF5IO, NWBFile
+        # from pynwb.behavior import SpatialSeries
+        # from pynwb import get_type_map
+        # tm = get_type_map()
+        # timestamps = np.linspace(0, 50) / 200
+        # position_data = np.array([np.linspace(0, 10, 50), np.linspace(0, 8, 50)]).T
+        #
+        # position_spatial_series = SpatialSeries(
+        #     name="SpatialSeries",
+        #     description="Position (x, y) in an open field.",
+        #     data=position_data,
+        #     timestamps=timestamps,
+        #     reference_frame="(0,0) is bottom left corner",
+        # )
+        breakpoint()
 
 
 class TestDynamicTable(TestCase):

tests/unit/test_config.yaml

@@ -0,0 +1,12 @@
+VectorData:
+    namespace:
+    namespace_version:
+    fields:
+      data: /Users/mavaylon/Research/NWB/hdmf2/hdmf/tests/unit/example_test_term_set.yaml
+      field2: ...
+DataType2:
+    namespace:
+    namespace_version:
+    fields:
+      data: /Users/mavaylon/Research/NWB/hdmf2/hdmf/tests/unit/example_test_term_set.yaml
+      field2: ...

tests/unit/test_extension_config.yaml

@@ -0,0 +1,12 @@
+VectorData:
+    namespace:
+    namespace_version:
+    fields:
+      data: /Users/mavaylon/Research/NWB/hdmf2/hdmf/tests/unit/example_test_term_set.yaml
+      field2: ...
+DataType2:
+    namespace:
+    namespace_version:
+    fields:
+      data: /Users/mavaylon/Research/NWB/hdmf2/hdmf/tests/unit/example_test_term_set.yaml
+      field2: ...

tests/unit/test_termset_config.py

@@ -0,0 +1,68 @@
+from hdmf.testing import TestCase
+from hdmf import get_termset_config, load_termset_config, unload_termset_config
+from hdmf.term_set import TermSetConfigurator
+
+class TestConfig(TestCase):
+    self.test_config = {}
+    self.test_merged_extension_config = {}
+    self.hdmf_config = {}
+
+    def test_construct_config(self):
+        # add asserts for self.path and self.config
+        test_config = TermSetConfigurator(path='tests/unit/test_config.yaml')
+        self.assertEqual(test_config.path, ['tests/unit/test_config.yaml'])
+        # self.assertEqual(test_config.config, None)
+
+    def test_load_termset_config(self):
+        test_config = TermSetConfigurator(path='tests/unit/test_config.yaml')
+        test_config.load_termset_config(path='tests/unit/test_extension_config.yaml')
+        self.assertEqual(config.path, ['tests/unit/test_config.yaml', 'tests/unit/test_extension_config.yaml'])
+        # self.assertEqual(config.config, None)
+
+    def test_unload_termset_config(self):
+        test_config = TermSetConfigurator(path='tests/unit/test_config.yaml')
+        test_config.unload_termset_config()
+        self.assertEqual(config.path, ['src/hdmf/hdmf_config.yaml'])
+        self.assertEqual(config.config, None)
+
+    def test_get_termset_config(self):
+        config = get_termset_config()
+        self.assertEqual(config.path, ['src/hdmf/hdmf_config.yaml'])
+        # self.assertEqual(config.config, None)
+
+    def test_unload_global_config(self):
+        config = get_termset_config()
+        unload_termset_config()
+        self.assertEqual(config.path, ['src/hdmf/hdmf_config.yaml'])
+        self.assertEqual(config.config, None)
+
+    def test_load_global_config_reset(self):
+        load_termset_config()
+        self.assertEqual(config.path, ['src/hdmf/hdmf_config.yaml'])
+        # self.assertEqual(config.config, None)
+
+    def test_load_global_config_extension_config(self):
+        load_termset_config()
+        self.assertEqual(config.path, ['tests/unit/test_config.yaml', 'tests/unit/test_extension_config.yaml'])
+        # self.assertEqual(config.config, None)
+
+    def test_data(self):
+        pass
+
+    def test_dataset_not_in_spec(self):
+        pass
+
+    def test_attribute_not_in_spec(self):
+        pass
+
+    def test_attriute_in_spec(self):
+        pass
+
+    def test_dataset_in_spec(self):
+        pass
+
+    def test_data_type_not_in_namespace(self):
+        pass
+
+    def test_warn_not_wrapped(self):
+        pass