fix: fixed handling of duplicately defined XPP auxiliary variables

biosimulators_utils/model_lang/xpp/validation.py

@@ -8,6 +8,7 @@
 
 from ...config import Config  # noqa: F401
 from .data_model import SIMULATION_METHOD_KISAO_MAP
+from biosimulators_utils.sedml.data_model import Symbol
 import collections
 import glob
 import os
@@ -129,8 +130,10 @@ def validate_model(filename,
             'output': {},
             'ui': {},
             'other': {},
+            'outfile_column_names': [Symbol.time.value],
         }
         block = None
+        duplicate_ids = set()
         with open(var_param_filename, 'r') as file:
             for line in file:
                 line = line.strip()
@@ -141,7 +144,20 @@ def validate_model(filename,
                         block = 'initial_conditions'
                 elif block:
                     id, _, value = line.partition(' ')
-                    simulation[block][id] = float(value)
+                    if id in simulation[block]:
+                        duplicate_ids.add("{} '{}'".format(block[0:1].upper() + block[1:].replace('_', ' '), id))
+                    else:
+                        simulation[block][id] = float(value)
+
+                    if block == 'initial_conditions':
+                        simulation['outfile_column_names'].append(id)
+
+        if duplicate_ids:
+            msg = '{} parameters and variables were duplicately defined:\n  - {}'.format(
+                len(duplicate_ids),
+                '\n  - '.join(sorted(duplicate_ids)),
+            )
+            warnings.append([msg])
 
         parameter_ids = {key.lower(): key for key in simulation['parameters'].keys()}
         variable_ids = {key.upper(): key for key in simulation['initial_conditions'].keys()}
@@ -169,7 +185,8 @@ def validate_model(filename,
                         name, _, start_end = name[0:-1].partition('[')
                         start, _, end = start_end.partition('..')
                         for i_var in range(int(start), int(end) + 1):
-                            simulation['auxiliary_variables'][name + str(i_var)] = expr.replace('[j]', f'[{i_var}]')
+                            el_name = name + str(i_var)
+                            simulation['auxiliary_variables'][el_name] = expr.replace('[j]', f'[{i_var}]')
 
                     else:
                         simulation['auxiliary_variables'][name] = expr

tests/model_lang/xpp/test_xpp_validation.py

@@ -1,4 +1,5 @@
 from biosimulators_utils.model_lang.xpp import validation
+from biosimulators_utils.sedml.data_model import Symbol
 from biosimulators_utils.utils.core import flatten_nested_list_of_strings
 from unittest import mock
 import collections
@@ -40,6 +41,7 @@ def test(self):
             ('U', .1),
             ('V', .05),
         ])
+        outfile_column_names = [Symbol.time.value, 'U', 'V']
         simulation_method = {
             'total': '40',
         }
@@ -74,6 +76,7 @@ def test(self):
             'output': None,
             'ui': None,
             'other': None,
+            'outfile_column_names': outfile_column_names,
         })
         self.assertEqual(model['initial_conditions'], initial_conditions)
 
@@ -243,6 +246,7 @@ def test_from_directory(self):
             ('U', .2),
             ('V', .1),
         ])
+        outfile_column_names = [Symbol.time.value, 'U', 'V']
         simulation_method = {
             'total': '40',
         }
@@ -282,6 +286,7 @@ def test_from_directory(self):
             'output': None,
             'ui': None,
             'other': None,
+            'outfile_column_names': outfile_column_names,
         })
 
     def test_with_sets(self):
@@ -308,6 +313,7 @@ def test_with_sets(self):
             ('U', .3),
             ('V', .05),
         ])
+        outfile_column_names = [Symbol.time.value, 'U', 'V']
         sets = {
             'set1': {
                 'parameters': {'aee': 12.},
@@ -356,6 +362,7 @@ def test_with_sets(self):
             'output': None,
             'ui': None,
             'other': None,
+            'outfile_column_names': outfile_column_names,
         })
 
     def test_from_directory_2(self):
@@ -382,6 +389,7 @@ def test_from_directory_2(self):
             ('U', .1),
             ('V', .04),
         ])
+        outfile_column_names = [Symbol.time.value, 'U', 'V']
         sets = {}
         simulation_method = {
             'total': '40',
@@ -436,6 +444,7 @@ def test_from_directory_2(self):
             'output': None,
             'ui': None,
             'other': None,
+            'outfile_column_names': outfile_column_names,
         })
 
     def test_cannot_parse_other_formats(self):