Don't raise errors when node_id is defined implicitly. (#78)

bluepysnap/circuit_validation.py

@@ -295,17 +295,19 @@ def _check_nodes_population(nodes_dict, config):
     Returns:
         list: List of errors, empty if no errors
     """
-    POPULATION_DATASET_NAMES = ['node_type_id', 'node_group_id', 'node_group_index']
+    required_datasets = ['node_type_id']
     errors = []
     nodes_file = nodes_dict.get('nodes_file')
     with h5py.File(nodes_file, 'r') as h5f:
         nodes = _get_h5_data(h5f, 'nodes')
         if not nodes or len(nodes) == 0:
             errors.append(fatal('No "nodes" in {}.'.format(nodes_file)))
             return errors
+        if len(nodes.keys()) > 1:
+            required_datasets += ['node_group_id', 'node_group_index']
         for population_name in nodes:
             population = nodes[population_name]
-            missing_datasets = sorted(set(POPULATION_DATASET_NAMES) - set(population))
+            missing_datasets = sorted(set(required_datasets) - set(population))
             if missing_datasets:
                 errors.append(fatal('Population {} of {} misses datasets {}'.
                                     format(population_name, nodes_file, missing_datasets)))
@@ -355,10 +357,12 @@ def _get_node_ids(node_population):
     if 'node_id' in node_population:
         node_ids = node_population['node_id'][:]
     else:
-        node_size_ds = _get_h5_data(node_population, 'node_type_id') \
-            or _get_h5_data(node_population, 'node_group_id')
-        if node_size_ds:
-            node_ids = np.arange(len(node_size_ds))
+        grp = _get_h5_data(node_population, '0')
+        if grp:
+            for attr in grp:
+                if isinstance(grp[attr], h5py.Dataset):
+                    node_ids = np.arange(len(grp[attr]))
+                    break
     return node_ids
 
 

tests/test_circuit_validation.py

@@ -123,7 +123,23 @@ def test_ok_node_ids_dataset():
         assert errors == []
 
 
-def test_no_required_node_population_datasets():
+def test_no_required_node_single_population_datasets():
+    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:
+            del h5f['nodes/default2/']
+            del h5f['nodes/default/node_group_id']
+            del h5f['nodes/default/node_group_index']
+        errors = test_module.validate(str(config_copy_path))
+        assert errors == []
+        with h5py.File(nodes_file, 'r+') as h5f:
+            del h5f['nodes/default/node_type_id']
+        errors = test_module.validate(str(config_copy_path))
+        assert errors == [Error(Error.FATAL, 'Population default of {} misses datasets {}'.
+                                format(nodes_file, ['node_type_id']))]
+
+
+def test_no_required_node_multi_population_datasets():
     required_datasets = ['node_type_id', 'node_group_id', 'node_group_index']
     for ds in required_datasets:
         with copy_circuit() as (circuit_copy_path, config_copy_path):
@@ -504,16 +520,12 @@ def test_no_edge_source_to_target():
 
 
 def test_no_edge_all_node_ids():
-    node_ids_ds = ['node_group_id', 'node_type_id']
     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:
-            for ds in node_ids_ds:
-                del h5f['nodes/default/' + ds]
+            del h5f['nodes/default/0']
         errors = test_module.validate(str(config_copy_path))
         assert errors == [
-            Error(Error.FATAL,
-                  'Population default of {} misses datasets {}'.format(nodes_file, node_ids_ds)),
             Error(Error.FATAL,
                   '/edges/default/source_node_id does not have node ids in its node population'),
             Error(Error.FATAL,