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

src/acom_music_box/music_box.py

@@ -69,6 +69,67 @@ def add_evolving_condition(self, time_point, conditions):
             time=[time_point], conditions=[conditions])
         self.evolvingConditions.append(evolving_condition)
 
+    def create_solver(
+        self,
+        path_to_config,
+        solver_type=musica.micmsolver.rosenbrock,
+        number_of_grid_cells=1):
+        """
+        Creates a micm solver object using the CAMP configuration files.
+
+        Args:
+            path_to_config (str): The path to CAMP configuration directory.
+
+        Returns:
+            None
+        """
+        # Create a solver object using the configuration file
+        self.solver = musica.create_solver(
+            path_to_config,
+            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.
@@ -260,6 +321,8 @@ def loadJson(self, path_to_json):
             self.evolving_conditions = EvolvingConditions.from_config_JSON(
                 path_to_json, data, self.species_list, self.reaction_list)
 
+        self.check_config(os.path.join(os.getcwd(), path_to_json))
+
         camp_path = os.path.join(
             os.path.dirname(path_to_json),
             self.config_file)

tests/unit/test_duplicate_reactions.py

@@ -0,0 +1,33 @@
+from acom_music_box import MusicBox, Reaction, ReactionRate, Conditions
+from acom_music_box.reaction_list import ReactionList
+
+import pytest
+
+
+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)
+        assert box_model.check_config("Loaded from string.")
+
+        # 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
+
+        # verify that the fail exception was properly raised
+        with pytest.raises(Exception):
+            box_model.check_config("Loaded from string.")
+
+
+if __name__ == "__main__":
+    test = TestDuplicateReactions()
+    test.test_run()
+