Fix in SQLite Connection. There were never closed

* There is still a fix when we want to close a SQLite connection
  created in a different thread

Author: Ezetowers

MLC/Simulation.py

@@ -46,6 +46,9 @@ def add_generation(self, population):
     def erase_generations(self, from_generation):
         self._mlc_repository.remove_population_from(from_generation)
 
+    def close(self):
+        self._mlc_repository.close()
+
     @staticmethod
     def create_empty_population_for(generation):
         from MLC.Population.Population import Population

MLC/api/Experiment.py

@@ -64,6 +64,9 @@ def get_simulation(self):
             Config.get_instance().read(self._config_file)
             set_logger(Config.get_instance().get('LOGGING', 'logmode'))
 
+            if Experiment.__last_simulation:
+                Experiment.__last_simulation.close()
+
             self._simulation = Simulation(self._name)
             Experiment.__last_simulation = self._simulation
 

MLC/api/MLCLocal.py

@@ -162,6 +162,7 @@ def close_experiment(self, experiment_name):
         # problems between Evaluation and Preevaluation scripts from other projects
         experiment_dir = os.path.join(self._working_dir, experiment_name)
         sys.path.remove(experiment_dir)
+        self._open_experiments[experiment_name].get_simulation().close()
         del self._open_experiments[experiment_name]
 
     def new_experiment(self, experiment_name,
@@ -246,10 +247,12 @@ def delete_experiment(self, experiment_name):
 
         experiment_dir = os.path.join(self._working_dir, experiment_name)
         try:
-            shutil.rmtree(experiment_dir)
             del self._experiments[experiment_name]
             if experiment_name in self._open_experiments:
+                simulation = self._open_experiments[experiment_name].get_simulation().close()
                 del self._open_experiments[experiment_name]
+
+            shutil.rmtree(experiment_dir)
         except OSError:
             logger.info("[MLC_LOCAL] Error while trying to delete experiment file: {0}".format(file))
             raise

MLC/db/mlc_repository.py

@@ -75,6 +75,9 @@ def _add_data(self, generation, cost, evaluation_time):
 class MLCRepository:
     _instance = None
 
+    # Close the Database opened
+    def close():
+        raise NotImplementedError("This method must be implemented")
     # operation over generations
     def add_population(self, population):
         raise NotImplementedError("This method must be implemented")

MLC/db/sqlite/sqlite_repository.py

@@ -32,6 +32,7 @@
 from MLC.arduino.protocol import ProtocolConfig
 from MLC.arduino.connection.serialconnection import SerialConnectionConfig
 from MLC.arduino.boards import types
+import traceback
 
 logger = get_gui_logger()
 
@@ -66,6 +67,9 @@ def __init__(self, database, init_db=False):
         self.__next_individual_id = 1 if not self.__individuals else max(self.__individuals.keys()) + 1
         self.__individuals_to_flush = {}
 
+    def close(self):
+        self._conn.close()
+
     def __initialize_db(self):
         cursor = self._conn.cursor()
 
@@ -84,11 +88,19 @@ def __initialize_db(self):
         self._conn.commit()
 
     def __get_db_connection(self, reopen_connection=False):
-        # TODO: Workaround. SQLite throw an exception when a connection is used in different threads. To solve it,
-        # we create a new connection every time a new connection is delivered
+        # TODO: Workaround. SQLite throw an exception when a connection is used 
+        # in different threads. To solve it, we create a new connection 
+        # every time a new connection is delivered
         if self._database != SQLiteRepository.IN_MEMORY_DB:
-            self._conn = sqlite3.connect(self._database)
+            # Close the previous connection
+            try:
+                self._conn.close()
+            except sqlite3.ProgrammingError:
+                # FIXME: There are open connections that cannot be closed for 
+                # the Thread bug. See what can be done
+                pass
 
+            self._conn = sqlite3.connect(self._database)
         return self._conn
 
     def __insert_individuals_pending(self, individual):

tests/mlc/api/test_new_experiment.conf

@@ -1,2 +1,5 @@
+[LOGGING]
+logmode = testing
+
 [PARAMS]
 test_param = test_value