Detect and display error for duplicate reaction names (keys) - Issue #235

src/acom_music_box/main.py

@@ -152,6 +152,7 @@ def main():
     myBox = MusicBox()
     logger.debug(f"Configuration file = {musicBoxConfigFile}")
     myBox.readConditionsFromJson(musicBoxConfigFile)
+    myBox.check_config(os.path.join(os.getcwd(), musicBoxConfigFile))
 
     # Create solver and solve
     config_path = os.path.join(

src/acom_music_box/music_box.py

@@ -89,6 +89,47 @@ def create_solver(
             solver_type,
             number_of_grid_cells)
 
+    def check_config(self, boxConfigPath):
+        """
+        Verifies correct configuration of the MusicBox object.
+        There is intentionally no check for the presence of a solver;
+        this test function is for the loaded configuration only.
+
+        Args:
+            boxConfigPath = filename and path of MusicBox configuration file
+                This filename is supplied only for the error message;
+                the configuration should already be loaded.
+
+        Returns:
+            True if all checks passed
+            Throws error for the first check failed.
+        """
+
+        # look for duplicate reaction names
+        if (self.initial_conditions):
+            if (self.initial_conditions.reaction_rates):
+                reactionNames = []
+                for rate in self.initial_conditions.reaction_rates:
+                    # watch out for Nones in here
+                    if not rate.reaction:
+                        continue
+                    if not rate.reaction.name:
+                        continue
+                    reactionNames.append(rate.reaction.name)
+
+                # look for name already seen
+                seen = set()
+                dupNames = [name for name in reactionNames if name in seen or seen.add(name)]
+
+                if (len(dupNames) > 0):
+                    # inform user of the error and its remedy
+                    errString = ("Error: Duplicate reaction names specified within {}: {}."
+                            .format(boxConfigPath, dupNames))
+                    errString += " Please remove or rename the duplicates."
+                    raise Exception(errString)
+
+        return(True)
+
     def solve(self, output_path=None, callback=None):
         """
         Solves the box model simulation and optionally writes the output to a file.

tests/integration/test_duplicate_reactions.py

@@ -0,0 +1,42 @@
+from acom_music_box import MusicBox, Reaction, ReactionRate, Conditions
+from acom_music_box.reaction_list import ReactionList
+
+import os
+import csv
+import math
+
+
+class TestDuplicateReactions:
+    def test_run(self):
+        # set up dummy reactions
+        abc123 = ReactionRate(Reaction("abc"), 12.3)
+        def456 = ReactionRate(Reaction("def"), 45.6)
+        abc789 = ReactionRate(Reaction("abc"), 78.9)
+
+        # Pass: unique reaction names
+        pass_reactions = [abc123, def456]
+        pass_conditions = Conditions(reaction_rates=pass_reactions)
+        box_model = MusicBox(initial_conditions=pass_conditions)
+        box_model.check_config("Loaded from string.")
+
+        # Pass test should throw an error above if it fails
+        assert True, f"All is good."        # example of assertion
+
+        # Fail: duplicate reaction names
+        fail_reactions = reactions=[abc123, abc789]
+        fail_conditions = Conditions(reaction_rates=fail_reactions)
+        box_model = MusicBox(initial_conditions=fail_conditions)    # new instance
+
+        # catching the exception is a Pass for the duplicate case
+        caughtExcept = False
+        try:
+            box_model.check_config("Loaded from string.")
+        except Exception as myExcept:
+            caughtExcept = True
+        assert caughtExcept, f"Failed to detect duplicate reaction names."
+
+
+if __name__ == "__main__":
+    test = TestDuplicateReactions()
+    test.test_run()
+