fix for the biophysical node validation (#67)

* fix for the biophysical node validation

bluepysnap/circuit_validation.py

@@ -5,6 +5,7 @@
 import click
 from pathlib2 import Path
 import h5py
+import six
 
 from bluepysnap.config import Config
 
@@ -248,6 +249,18 @@ def _check_rotations():
     return errors
 
 
+def _is_biophysical(group):
+    """Check if a group contains biophysical nodes."""
+    if group['model_type'][0] == 'biophysical':
+        return True
+    if "@library/model_type" in group:
+        model_type_int = group['model_type'][0]
+        model_type = group["@library/model_type"][model_type_int]
+        if six.ensure_str(model_type) == 'biophysical':
+            return True
+    return False
+
+
 def _check_nodes_group(group, config):
     """Validates nodes group in nodes population.
 
@@ -264,7 +277,7 @@ def _check_nodes_group(group, config):
         return [fatal('Group {} of {} misses required fields: {}'
                       .format(_get_group_name(group, parents=1), group.file.filename,
                               missing_fields))]
-    elif 'biophysical' in group['model_type'][:]:
+    elif _is_biophysical(group):
         return _check_bio_nodes_group(group, config)
     return []
 
@@ -430,7 +443,7 @@ def _check_edge_population_data(population, groups, nodes):
                                               'Cannot be read via bluepysnap or libsonata'.
                                format(population_name, population.file.filename)))
 
-    children_object_names = set(population.keys())
+    children_object_names = set(population)
     group_datasets = ["edge_group_id", "edge_group_index"]
     required_datasets = ['edge_type_id', 'source_node_id', 'target_node_id']
     if len(groups) > 1:

tests/test_circuit_validation.py

@@ -11,9 +11,11 @@
 except ImportError:
     from pathlib2 import Path
 import h5py
-from six import u as unicode
+
+import six
 import bluepysnap.circuit_validation as test_module
 from bluepysnap.circuit_validation import Error, BbpError
+import numpy as np
 
 from utils import setup_tempdir, TEST_DATA_DIR
 
@@ -50,7 +52,7 @@ def _edit_config(config_path):
         yield config
     finally:
         with config_path.open('w') as f:
-            f.write(unicode(json.dumps(config)))
+            f.write(six.u(json.dumps(config)))
 
 
 def test_error_comparison():
@@ -207,6 +209,20 @@ def test_no_required_bio_node_group_datasets():
                                 .format(nodes_file, required_datasets))]
 
 
+def test_ok_bio_model_type_in_library():
+    with _copy_circuit() as (circuit_copy_path, config_copy_path):
+        nodes_file = circuit_copy_path / 'nodes.h5'
+        with h5py.File(nodes_file, 'r+') as h5f:
+            data = h5f['nodes/default/0/model_type'][:]
+            del h5f['nodes/default/0/model_type']
+            h5f.create_dataset('nodes/default/0/model_type', data=np.zeros_like(data, dtype=int))
+            dt = h5py.special_dtype(vlen=six.text_type)
+            h5f.create_dataset('nodes/default/0/@library/model_type',
+                               data=np.array(["biophysical", ], dtype=object), dtype=dt)
+        errors = test_module.validate(str(config_copy_path))
+        assert errors == []
+
+
 def test_no_rotation_bio_node_group_datasets():
     angle_datasets = ['rotation_angle_xaxis', 'rotation_angle_yaxis', 'rotation_angle_zaxis']
     with _copy_circuit() as (circuit_copy_path, config_copy_path):