re-enable janky hdmf mapping test just to have it on the board for morale

Fix serializing datasets

nwb_linkml/src/nwb_linkml/types/ndarray.py

@@ -4,6 +4,7 @@ Extension of nptyping NDArray for pydantic that allows for JSON-Schema serializa
 * Order to store data in (row first)
 """
 import base64
+import pdb
 from pathlib import Path
 from typing import (
     Any,
@@ -119,6 +120,8 @@ class NDArray(_NDArray):
         def array_to_list(instance: np.ndarray | DaskArray) -> list|dict:
             if isinstance(instance, DaskArray):
                 arr = instance.__array__()
+            elif isinstance(instance, NDArrayProxy):
+                arr = instance[:]
             else:
                 arr = instance
 

nwb_linkml/tests/test_maps/test_hdmf.py

@@ -5,20 +5,27 @@ import h5py
 import time
 
 from nwb_linkml.maps.hdmf import model_from_dynamictable, dynamictable_to_model
+from ..fixtures import data_dir
 
 NWBFILE = '/Users/jonny/Dropbox/lab/p2p_ld/data/nwb/sub-738651046_ses-760693773.nwb'
 
-@pytest.mark.skip()
-def test_make_dynamictable():
-    h5f = h5py.File(NWBFILE, 'r')
+@pytest.mark.parametrize(
+    'dataset',
+    [
+        'aibs.nwb'
+    ]
+)
+def test_make_dynamictable(data_dir, dataset):
+    nwbfile = data_dir / dataset
+    h5f = h5py.File(nwbfile, 'r')
     group = h5f['units']
 
     start_time = time.time()
     model = model_from_dynamictable(group)
     data = dynamictable_to_model(group, model)
+
     ser = data.model_dump_json()
     end_time = time.time()
     total_time = end_time - start_time
-    pdb.set_trace()
 
 

nwb_linkml/tests/test_translate.py

@@ -1,16 +0,0 @@
-import pdb
-
-import pytest
-from pathlib import Path
-#from nwb_linkml.translate import generate_from_nwbfile
-
-# def test_generate_pydantic():
-#     # pass until we rig up smaller test data
-#     pass
-
-    #NWBFILE = Path('/Users/jonny/Dropbox/lab/p2p_ld/data/nwb/sub-738651046_ses-760693773.nwb')
-
-    #pydantic_module = generate_from_nwbfile(NWBFILE)
-
-    #pdb.set_trace()
-