debugging support for new KiSAO terms for CVODE parameters

biosimulators · Jun 1, 2021 · 5fabc66 · 5fabc66
1 parent f521f0b
commit 5fabc66
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Showing 3 changed files with 33 additions and 39 deletions.
diff --git a/biosimulators.json b/biosimulators.json
@@ -193,11 +193,11 @@
         {
           "name": "Iteration type",
           "id": "IterationTypeId",
-          "type": "string",
-          "value": "Newton",
+          "type": "kisaoId",
+          "value": "KISAO_0000408",
           "recommendedRange": [
-            "Newton",
-            "Functional"
+            "KISAO_0000408",
+            "KISAO_0000632"
           ],
           "kisaoId": {
             "namespace": "KISAO",
@@ -211,15 +211,15 @@
         {
           "name": "Linear solver",
           "id": "LinearSolverId",
-          "type": "string",
-          "value": "Dense",
+          "type": "kisaoId",
+          "value": "KISAO_0000625",
           "recommendedRange": [
-            "Dense",
-            "Banded",
-            "Diagonal",
-            "GMRES",
-            "BiCGStab",
-            "TFQMR"
+            "KISAO_0000625",
+            "KISAO_0000626",
+            "KISAO_0000627",
+            "KISAO_0000353",
+            "KISAO_0000392",
+            "KISAO_0000396"
           ],
           "kisaoId": {
             "namespace": "KISAO",
@@ -233,11 +233,11 @@
         {
           "name": "Preconditioner",
           "id": "PreconditionerId",
-          "type": "string",
-          "value": "Banded",
+          "type": "kisaoId",
+          "value": "KISAO_0000626",
           "recommendedRange": [
-            "Banded",
-            "None"
+            "KISAO_0000626",
+            "KISAO_0000629"
           ],
           "kisaoId": {
             "namespace": "KISAO",
@@ -730,14 +730,14 @@
         {
           "name": "LinearSolverId",
           "id": "LinearSolverId",
-          "type": "string",
-          "value": "Dense",
+          "type": "kisaoId",
+          "value": "KISAO_0000625",
           "recommendedRange": [
-            "Dense",
-            "Banded",
-            "GMRES",
-            "BiCGStab",
-            "TFQMR"
+            "KISAO_0000625",
+            "KISAO_0000626",
+            "KISAO_0000353",
+            "KISAO_0000392",
+            "KISAO_0000396"
           ],
           "kisaoId": {
             "namespace": "KISAO",

diff --git a/biosimulators_opencor/data_model.py b/biosimulators_opencor/data_model.py
@@ -78,28 +78,28 @@ class KinsolLinearSolver(str, enum.Enum):
                 'id': 'IntegrationMethodId',
                 'name': 'integration method',
                 'type': ValueType.string,
-                'default': CvodeIntegrationMethod.KISAO_0000288.value,
+                'default': CvodeIntegrationMethod.KISAO_0000288.name,
                 'enum': CvodeIntegrationMethod,
             },
             'KISAO_0000476': {
                 'id': 'IterationTypeId',
                 'name': 'iteration type',
                 'type': ValueType.string,
-                'default': CvodeIterationType.KISAO_0000408.value,
+                'default': CvodeIterationType.KISAO_0000408.name,
                 'enum': CvodeIterationType,
             },
             'KISAO_0000477': {
                 'id': 'LinearSolverId',
                 'name': 'linear solver',
                 'type': ValueType.string,
-                'default': CvodeLinearSolver.KISAO_0000625.value,
+                'default': CvodeLinearSolver.KISAO_0000625.name,
                 'enum': CvodeLinearSolver,
             },
             'KISAO_0000478': {
                 'id': 'PreconditionerId',
                 'name': 'preconditioner',
                 'type': ValueType.string,
-                'default': CvodePreconditioner.KISAO_0000626.value,
+                'default': CvodePreconditioner.KISAO_0000626.name,
                 'enum': CvodePreconditioner,
             },
             'KISAO_0000479': {
@@ -201,7 +201,7 @@ class KinsolLinearSolver(str, enum.Enum):
                 'id': 'LinearSolverId',
                 'name': 'linear solver',
                 'type': ValueType.string,
-                'default': KinsolLinearSolver.KISAO_0000625.value,
+                'default': KinsolLinearSolver.KISAO_0000625.name,
                 "enum": KinsolLinearSolver,
             },
             'KISAO_0000479': {

diff --git a/tests/test_data_model.py b/tests/test_data_model.py
@@ -17,10 +17,10 @@
 class DataModelTestCase(unittest.TestCase):
     def test(self):
         self.assertEqual(data_model.CvodeIntegrationMethod.KISAO_0000288.value, 'BDF')
-        self.assertEqual(data_model.CvodeIterationType.Newton.value, 'Newton')
-        self.assertEqual(data_model.CvodeLinearSolver.Dense.value, 'Dense')
-        self.assertEqual(data_model.CvodePreconditioner['None'].value, 'None')
-        self.assertEqual(data_model.KinsolLinearSolver.Dense.value, 'Dense')
+        self.assertEqual(data_model.CvodeIterationType.KISAO_0000408.value, 'Newton')
+        self.assertEqual(data_model.CvodeLinearSolver.KISAO_0000625.value, 'Dense')
+        self.assertEqual(data_model.CvodePreconditioner.KISAO_0000629.value, 'None')
+        self.assertEqual(data_model.KinsolLinearSolver.KISAO_0000625.value, 'Dense')
         self.assertEqual(data_model.KISAO_ALGORITHM_MAP['KISAO_0000019']['kisao_id'], 'KISAO_0000019')
 
     def test_consistent_with_specs(self):
@@ -44,13 +44,7 @@ def test_consistent_with_specs(self):
 
                 if param_props['type'] == ValueType.float and param_specs['value'] is None and param_props['default'] == 0:
                     pass
-                elif param_specs['type'] == 'kisaoId' and param_specs['value'] == 'KISAO_0000288' and param_props['default'] == 'BDF':
-                    pass
-                elif (
-                    param_specs['type'] == 'kisaoId'
-                    and param_specs['value'] == 'KISAO_0000280'
-                    and param_props['default'] == 'Adams-Moulton'
-                ):
+                elif param_specs['type'] == 'kisaoId' and param_specs['value'] == param_props['default']:
                     pass
                 else:
                     self.assertEqual(param_props['default'], parse_value(param_specs['value'], param_props['type']))