- fix an issue where expressions retrieved were wrong

get_xxx functions now pass along the model parameter, so that the correct model elements can be found.
copasi · Mar 14, 2024 · 606924a · 606924a
1 parent 1282b47
commit 606924a
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Showing 2 changed files with 19 additions and 6 deletions.
diff --git a/basico/model_info.py b/basico/model_info.py
@@ -370,8 +370,8 @@ def get_species(name=None, exact=False, **kwargs):
             'unit': unit,
             'initial_concentration': metab.getInitialConcentration(),
             'initial_particle_number': metab.getInitialValue(),
-            'initial_expression': _replace_cns_with_names(metab.getInitialExpression()),
-            'expression': _replace_cns_with_names(metab.getExpression()),
+            'initial_expression': _replace_cns_with_names(metab.getInitialExpression(), model=dm),
+            'expression': _replace_cns_with_names(metab.getExpression(), model=dm),
             'concentration': metab.getConcentration(),
             'particle_number': metab.getValue(),
             'rate': metab.getConcentrationRate(),
@@ -2206,9 +2206,9 @@ def get_compartments(name=None, exact=False, **kwargs):
             'type': __status_to_string(compartment.getStatus()),
             'unit': unit,
             'initial_size': compartment.getInitialValue(),
-            'initial_expression': _replace_cns_with_names(compartment.getInitialExpression()),
+            'initial_expression': _replace_cns_with_names(compartment.getInitialExpression(), model=dm),
             'dimensionality': compartment.getDimensionality(),
-            'expression': _replace_cns_with_names(compartment.getExpression()),
+            'expression': _replace_cns_with_names(compartment.getExpression(), model=dm),
             'size': compartment.getValue(),
             'rate': compartment.getRate(),
             'key': compartment.getKey(),
@@ -2281,8 +2281,8 @@ def get_parameters(name=None, exact=False, **kwargs):
             'type': __status_to_string(param.getStatus()),
             'unit': unit,
             'initial_value': param.getInitialValue(),
-            'initial_expression': _replace_cns_with_names(param.getInitialExpression()),
-            'expression': _replace_cns_with_names(param.getExpression()),
+            'initial_expression': _replace_cns_with_names(param.getInitialExpression(), model=dm),
+            'expression': _replace_cns_with_names(param.getExpression(), model=dm),
             'value': param.getValue(),
             'rate': param.getRate(),
             'key': param.getKey(),

diff --git a/tests/test_basico_info.py b/tests/test_basico_info.py
@@ -1,4 +1,5 @@
 import logging
+from math import exp
 import sys
 import unittest
 import basico
@@ -518,6 +519,18 @@ def test_parameter_sets(self):
 
         basico.remove_datamodel(dm)
 
+    def test_retrieval_from_multiple_models(self):
+        dm1 = basico.load_example('bruss')
+        basico.add_parameter('xy_sum', expression='[X] + [Y]', type='assignment')
+        basico.add_parameter('xy_initial_half', expression='Values[xy_sum].InitialValue / 2', type='assignment')
+        param1 =  basico.as_dict(basico.get_parameters())
+        dm2 = basico.new_model(name='empty')
+        param2 = basico.as_dict(basico.get_parameters(model=dm1))
+        self.assertEqual(len(param1), len(param2))
+        self.assertEqual(param1[0]['expression'], param2[0]['expression'])
+        self.assertEqual(param1[1]['expression'], param2[1]['expression'])
+        basico.remove_datamodel(dm1)
+        basico.remove_datamodel(dm2)
 
 if __name__ == "__main__":
     unittest.main()