Allow unknown attributes in parameters and allow to skip the validation

Change-Id: Iccb3b20c1847cd0555a7ef0f1a4c65b0a983da6d
BlueBrain · Oct 14, 2020 · 8af8acf · 8af8acf
1 parent c9927b1
commit 8af8acf
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Showing 4 changed files with 15 additions and 56 deletions.
diff --git a/tests/test_validator.py b/tests/test_validator.py
@@ -33,6 +33,11 @@ def test_validate_params():
     data['apical']['orientation'] = [0, 0, 0]
     assert_raises(ValidationError, tested.validate_neuron_params, data)
 
+    # Unknown parameters can be added at the root
+    params = dummy_params()
+    params["unknown_param"] = 0
+    tested.validate_neuron_params(params)
+
 def test_empty_params_raises():
     data = {'apical': {},
             'axon': {},

diff --git a/tns/generate/grower.py b/tns/generate/grower.py
@@ -26,22 +26,26 @@ class NeuronGrower:
     """
 
     def __init__(self, input_parameters, input_distributions,
-                 context=None, external_diametrizer=None):
+                 context=None, external_diametrizer=None, skip_validation=False):
         """TNS NeuronGrower
         input_parameters: the user-defined parameters
         input_distributions: distributions extracted from biological data
         context: an object containing contextual information
-        extremal_diametrizer: diametrizer function for external diametrizer module
+        external_diametrizer: diametrizer function for external diametrizer module
+        skip_validation: if set to False, the parameters and distributions are validated
         """
         self.neuron = Morphology()
         self.context = context
 
         self.input_parameters = copy.deepcopy(input_parameters)
         L.debug('Input Parameters: %s', input_parameters)
-        self.validate_params()
 
         self.input_distributions = copy.deepcopy(input_distributions)
-        self.validate_distribs()
+
+        # Validate parameters and distributions
+        if not skip_validation:
+            self.validate_params()
+            self.validate_distribs()
 
         # Consistency check between parameters and distributions
         for tree_type in self.input_parameters['grow_types']:

diff --git a/tns/schemas/parameters.json b/tns/schemas/parameters.json
@@ -53,30 +53,6 @@
                 "tree_type"
             ],
             "additionalProperties": false
-        },
-
-        "limit": {
-            "type": "object",
-            "properties": {
-                "layer": {
-                    "type": "integer"
-                },
-                "fraction": {
-                    "type": "number"
-                }
-            },
-            "required": ["layer", "fraction"],
-            "additionalProperties": false
-        },
-
-        "limits": {
-            "type": "object",
-            "properties": {
-                "min": {"$ref": "#/definitions/limit"},
-                "target": {"$ref": "#/definitions/limit"},
-                "max": {"$ref": "#/definitions/limit"}
-            },
-            "additionalProperties": false
         }
     },
 
@@ -95,34 +71,8 @@
             "type": "object",
             "properties": {"method": {"type": "string"}},
             "required": ["method"]
-        },
-        "context_constraints": {
-            "type": "object",
-            "properties": {
-                "apical": {"anyOf": [
-                    {"$ref": "#/definitions/limits"},
-                    {
-                        "extent_to_path": {
-                            "type": "object",
-                            "properties": {
-                                "slope": {
-                                    "type": "number"
-                                },
-                                "intercept": {
-                                    "type": "number"
-                                }
-                            },
-                            "required": ["slope", "intercept"],
-                            "additionalProperties": false
-                        }
-                    }
-                ]},
-                "basal": {"$ref": "#/definitions/limits"}
-            },
-            "additionalProperties": false
         }
     },
 
-    "required": ["origin", "diameter_params", "grow_types"],
-    "additionalProperties": false
+    "required": ["origin", "diameter_params", "grow_types"]
 }
diff --git a/tns/version.py b/tns/version.py
@@ -1,2 +1,2 @@
 """ tns version """
-VERSION = "2.2.4"
+VERSION = "2.2.5.dev0"