Fix circuit validation (#72)

* Fix circuit validation * Move 'components' errors to BbpError * Consider '@library' enum when checking files
BlueBrain · Jul 8, 2020 · 92e836d · 92e836d
1 parent 8903edf
commit 92e836d
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Showing 3 changed files with 11 additions and 9 deletions.
diff --git a/bluepysnap/circuit_validation.py b/bluepysnap/circuit_validation.py
@@ -67,7 +67,7 @@ def _check_components_dir(name, components):
     """
     dirpath = components.get(name)
     if not dirpath or not Path(dirpath).is_dir():
-        return [fatal('Invalid components "{}": {}'.format(name, dirpath))]
+        return [BbpError(Error.FATAL, 'Invalid components "{}": {}'.format(name, dirpath))]
     return []
 
 
@@ -233,18 +233,21 @@ def _check_rotations():
     _check_rotations()
     components = config['components']
     errors += _check_components_dir('morphologies_dir', components)
-    errors += _check_components_dir('mechanisms_dir', components)
     errors += _check_components_dir('biophysical_neuron_models_dir', components)
     if errors:
         return errors
+    morph_files = group['morphology'] if _get_h5_data(group, '@library/morphology') is None \
+        else group['@library/morphology']
     errors += _check_files(
         'morphology: {}[{}]'.format(group_name, group.file.filename),
-        (Path(components['morphologies_dir'], m + '.swc') for m in group['morphology']),
+        (Path(components['morphologies_dir'], m + '.swc') for m in morph_files),
         Error.WARNING)
+    bio_files = group['model_template'] if _get_h5_data(group, '@library/model_template') is None \
+        else group['@library/model_template']
     bio_path = Path(components['biophysical_neuron_models_dir'])
     errors += _check_files(
         'model_template: {}[{}]'.format(group_name, group.file.filename),
-        (bio_path / _get_model_template_file(m) for m in group['model_template']),
+        (bio_path / _get_model_template_file(m) for m in bio_files),
         Error.WARNING)
     return errors
 

diff --git a/tests/data/circuit_config.json b/tests/data/circuit_config.json
@@ -6,7 +6,6 @@
   },
   "components": {
     "morphologies_dir": "$COMPONENT_DIR/morphologies",
-    "mechanisms_dir": "$COMPONENT_DIR/mechanisms_dir",
     "biophysical_neuron_models_dir": "$COMPONENT_DIR/biophysical_neuron_models"
   },
   "node_sets_file": "$BASE_DIR/node_sets.json",

diff --git a/tests/test_circuit_validation.py b/tests/test_circuit_validation.py
@@ -213,15 +213,15 @@ def test_no_rotation_bbp_node_group_datasets():
 
 
 def test_no_bio_component_dirs():
-    dirs = ['morphologies_dir', 'mechanisms_dir', 'biophysical_neuron_models_dir']
+    dirs = ['morphologies_dir', 'biophysical_neuron_models_dir']
     for dir_ in dirs:
         with copy_circuit() as (_, config_copy_path):
             with edit_config(config_copy_path) as config:
                 del config['components'][dir_]
-            errors = test_module.validate(str(config_copy_path))
+            errors = test_module.validate(str(config_copy_path), True)
             # multiplication by 2 because we have 2 populations, each produces the same error.
-            assert errors == 2 * [Error(Error.FATAL,
-                                        'Invalid components "{}": {}'.format(dir_, None))]
+            assert errors == 2 * [BbpError(Error.FATAL,
+                                           'Invalid components "{}": {}'.format(dir_, None))]
 
 
 @patch('bluepysnap.circuit_validation.MAX_MISSING_FILES_DISPLAY', 1)