Fix unit test after import and export feature changes

* #35

Author: Ezetowers

MLC/db/sqlite/sqlite_repository.py

@@ -12,6 +12,7 @@ class SQLiteRepository(MLCRepository):
     IN_MEMORY_DB = ":memory:"
 
     def __init__(self, database, init_db=False):
+        print database
         self._conn = sqlite3.connect(database)
         self._database = database
 
@@ -46,7 +47,9 @@ def __initialize_db(self):
     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
-        self._conn = sqlite3.connect(self._database)
+        if self._database != SQLiteRepository.IN_MEMORY_DB:
+            self._conn = sqlite3.connect(self._database)
+
         return self._conn
 
     def __insert_individuals_pending(self, individual):

tests/integration_tests/integration_tests.py

@@ -90,7 +90,7 @@ def setUpClass(cls):
             # clear static values
             if Config.get_instance().getboolean("BEHAVIOUR", "save"):
                 MLCRepository._instance = None
-            simulation = Simulation()
+            simulation = Simulation("integration_test")
             cls._app = Application(simulation)
 
             if isinstance(generation_params, int):
@@ -106,7 +106,7 @@ def setUpClass(cls):
         if Config.get_instance().getboolean("BEHAVIOUR", "save"):
             MLCRepository._instance._conn.close()
             MLCRepository._instance = None
-            cls._app = Application(Simulation())
+            cls._app = Application(Simulation("integration_test"))
 
         a = cls._app.get_simulation().number_of_generations()
         print "Number of populations: " + str(a)

tests/mlc/api/test_mlc.py

@@ -18,64 +18,59 @@
 
 import ConfigParser
 
+
 class MLCWorkspaceTest(unittest.TestCase):
     WORKSPACE_DIR = os.path.abspath("/tmp/mlc_workspace/")
-    DEFAULT_CONFIGURATION = {"BEHAVIOUR": {"save_dir"}}
-
+    FILE_WITH_RANDOMS = None
     ORIGINAL_EXPERIMENT = "test_first_experiment"
     ORIGINAL_CONFIGURATION = None
+    NEW_EXPERIMENT = "test_new_experiment"
+    NEW_CONFIGURATION = None
 
-    NEW_EXPERIMENT = "new_experiment"
-    NEW_CONFIGURATION = {"PARAMS": {"test_param": "test_value"}}
-
-    FILE_WITH_RANDOMS = None
 
     @classmethod
     def setUpClass(cls):
+        os.makedirs(MLCWorkspaceTest.WORKSPACE_DIR)
+        mlc = MLCLocal(working_dir=MLCWorkspaceTest.WORKSPACE_DIR)
         # general settings for MLC
         set_logger('console')
         set_working_directory(MLCWorkspaceTest.WORKSPACE_DIR)
 
         if not os.path.exists(MLCWorkspaceTest.WORKSPACE_DIR):
             os.makedirs(MLCWorkspaceTest.WORKSPACE_DIR)
 
-        # copy initial configuration file
-        experiment_cf, experiment_db = Experiment.get_experiment_files( MLCWorkspaceTest.WORKSPACE_DIR,
-                                                                        MLCWorkspaceTest.ORIGINAL_EXPERIMENT)
-
         this_dir = os.path.dirname(os.path.abspath(__file__))
-        shutil.copy(os.path.join(this_dir, MLCWorkspaceTest.ORIGINAL_EXPERIMENT+".conf"), experiment_cf)
-
-        # read configuration
-        original_config = ConfigParser.ConfigParser()
-        original_config.read(os.path.join(this_dir, MLCWorkspaceTest.ORIGINAL_EXPERIMENT+".conf"))
-        MLCWorkspaceTest.ORIGINAL_CONFIGURATION = Config.to_dictionary(original_config)
-
-        # create experiment database
-        Config.get_instance().read(experiment_cf)
-        s = Simulation()
+        MLCWorkspaceTest.ORIGINAL_CONFIGURATION = \
+            os.path.join(this_dir, MLCWorkspaceTest.ORIGINAL_EXPERIMENT + ".conf")
+        MLCWorkspaceTest.NEW_CONFIGURATION = \
+            os.path.join(this_dir, MLCWorkspaceTest.NEW_EXPERIMENT + ".conf")
+        mlc.new_experiment(MLCWorkspaceTest.ORIGINAL_EXPERIMENT,
+                           MLCWorkspaceTest.ORIGINAL_CONFIGURATION)
 
         # random file for simulations
-        this_dir = os.path.dirname(os.path.abspath(__file__))
         MLCWorkspaceTest.FILE_WITH_RANDOMS = os.path.join(this_dir, "matlab_randoms.txt")
 
+    @classmethod
+    def teardownClass(cls):
+        shutil.rmtree(MLCWorkspaceTest.WORKSPACE_DIR)
+
     def test_obtain_experiments(self):
         mlc = MLCLocal(working_dir=MLCWorkspaceTest.WORKSPACE_DIR)
         experiments = mlc.get_workspace_experiments()
         self.assertEqual(len(experiments), 1)
         self.assertEqual(experiments[0], MLCWorkspaceTest.ORIGINAL_EXPERIMENT)
 
     def test_obtain_configuration_from_a_closed_experiment(self):
-        mlc = MLCLocal(working_dir=MLCWorkspaceTest.WORKSPACE_DIR)
         try:
+            mlc = MLCLocal(working_dir=MLCWorkspaceTest.WORKSPACE_DIR)
             mlc.get_experiment_configuration(MLCWorkspaceTest.ORIGINAL_EXPERIMENT)
             self.assertTrue(False, "Configuration from a closed experiment should not be obtained")
         except MLC.api.mlc.ClosedExperimentException:
             self.assertTrue(True)
 
     def test_open_invalid_experiment(self):
-        mlc = MLCLocal(working_dir=MLCWorkspaceTest.WORKSPACE_DIR)
         try:
+            mlc = MLCLocal(working_dir=MLCWorkspaceTest.WORKSPACE_DIR)
             mlc.open_experiment("invalid_name")
             self.assertTrue(False)
         except MLC.api.mlc.ExperimentNotExistException:
@@ -106,17 +101,21 @@ def test_open_and_close_experiment(self):
     def test_create_duplicated_experiment(self):
         try:
             mlc = MLCLocal(working_dir=MLCWorkspaceTest.WORKSPACE_DIR)
-            mlc.new_experiment(MLCWorkspaceTest.ORIGINAL_EXPERIMENT, MLCWorkspaceTest.DEFAULT_CONFIGURATION)
+            mlc.new_experiment(MLCWorkspaceTest.ORIGINAL_EXPERIMENT,
+                               MLCWorkspaceTest.ORIGINAL_CONFIGURATION)
             self.assertTrue(False)
         except MLC.api.mlc.DuplicatedExperimentError:
             self.assertTrue(True)
 
     def test_create_experiment_and_obtain_configuration(self):
         try:
             mlc = MLCLocal(working_dir=MLCWorkspaceTest.WORKSPACE_DIR)
-            mlc.new_experiment(MLCWorkspaceTest.NEW_EXPERIMENT, MLCWorkspaceTest.NEW_CONFIGURATION)
+            mlc.new_experiment(MLCWorkspaceTest.NEW_EXPERIMENT,
+                               MLCWorkspaceTest.NEW_CONFIGURATION)
             mlc.open_experiment(MLCWorkspaceTest.NEW_EXPERIMENT)
             configuration = mlc.get_experiment_configuration(MLCWorkspaceTest.NEW_EXPERIMENT)
+            print configuration
+            mlc.close_experiment(MLCWorkspaceTest.NEW_EXPERIMENT)
 
             # check configuration structure
             self.assertIsInstance(configuration, dict)
@@ -127,34 +126,24 @@ def test_create_experiment_and_obtain_configuration(self):
 
         finally:
             # FIXME: use Setup/TearDown testcase
-            os.unlink(os.path.join(MLCWorkspaceTest.WORKSPACE_DIR, MLCWorkspaceTest.NEW_EXPERIMENT)+".conf")
-            os.unlink(os.path.join(MLCWorkspaceTest.WORKSPACE_DIR, MLCWorkspaceTest.NEW_EXPERIMENT)+".mlc")
-
+            mlc.delete_experiment(MLCWorkspaceTest.NEW_EXPERIMENT)
 
     def test_delete_experiment(self):
-        mlc = MLCLocal(working_dir=MLCWorkspaceTest.WORKSPACE_DIR)
-
+        # delete an experiment that not exists
         try:
-            # delete an experiment that not exists
-            try:
-                mlc.delete_experiment_from_workspace(MLCWorkspaceTest.NEW_EXPERIMENT)
-                self.assertTrue(False)
-            except MLC.api.mlc.ExperimentNotExistException:
-                self.assertTrue(True)
-
-            mlc.new_experiment(MLCWorkspaceTest.NEW_EXPERIMENT, MLCWorkspaceTest.NEW_CONFIGURATION)
-            mlc.delete_experiment_from_workspace(MLCWorkspaceTest.NEW_EXPERIMENT)
-            self.assertFalse(os.path.exists(os.path.join(MLCWorkspaceTest.WORKSPACE_DIR, MLCWorkspaceTest.NEW_EXPERIMENT)+".conf"))
-            self.assertFalse(os.path.exists(os.path.join(MLCWorkspaceTest.WORKSPACE_DIR, MLCWorkspaceTest.NEW_EXPERIMENT)+".mlc"))
+            mlc = MLCLocal(working_dir=MLCWorkspaceTest.WORKSPACE_DIR)
+            mlc.delete_experiment(MLCWorkspaceTest.NEW_EXPERIMENT)
+            self.assertTrue(False)
+        except MLC.api.mlc.ExperimentNotExistException:
+            self.assertTrue(True)
 
-        finally:
-            pass
-            # FIXME: use Setup/TearDown testcase
-            # os.unlink(os.path.join(MLCWorkspaceTest.WORKSPACE_DIR, MLCWorkspaceTest.NEW_EXPERIMENT) + ".conf")
-            # os.unlink(os.path.join(MLCWorkspaceTest.WORKSPACE_DIR, MLCWorkspaceTest.NEW_EXPERIMENT) + ".mlc")
+        mlc.new_experiment(MLCWorkspaceTest.NEW_EXPERIMENT,
+                           MLCWorkspaceTest.NEW_CONFIGURATION)
+        mlc.delete_experiment(MLCWorkspaceTest.NEW_EXPERIMENT)
+        self.assertFalse(os.path.exists(os.path.join(MLCWorkspaceTest.WORKSPACE_DIR,
+                                                     MLCWorkspaceTest.NEW_EXPERIMENT)))
 
     def test_set_configuration(self):
-
         try:
             mlc = MLCLocal(working_dir=MLCWorkspaceTest.WORKSPACE_DIR)
 
@@ -163,25 +152,30 @@ def test_set_configuration(self):
             mlc.open_experiment(MLCWorkspaceTest.NEW_EXPERIMENT)
             original_config = mlc.get_experiment_configuration(MLCWorkspaceTest.NEW_EXPERIMENT)
             self.assertEqual(original_config["PARAMS"]["test_param"], "test_value")
-
             # chage paramenter value
             mlc.set_experiment_configuration(MLCWorkspaceTest.NEW_EXPERIMENT, {"PARAMS": {"test_param": "new_value"}})
+            mlc.close_experiment(MLCWorkspaceTest.NEW_EXPERIMENT)
 
             # reload mlc_workspace
             mlc_reloaded = MLCLocal(working_dir=MLCWorkspaceTest.WORKSPACE_DIR)
-            mlc.open_experiment(MLCWorkspaceTest.NEW_EXPERIMENT)
-            original_config = mlc.get_experiment_configuration(MLCWorkspaceTest.NEW_EXPERIMENT)
+            mlc_reloaded.open_experiment(MLCWorkspaceTest.NEW_EXPERIMENT)
+            original_config = mlc_reloaded.get_experiment_configuration(MLCWorkspaceTest.NEW_EXPERIMENT)
             self.assertEqual(original_config["PARAMS"]["test_param"], "new_value")
+            mlc_reloaded.close_experiment(MLCWorkspaceTest.NEW_EXPERIMENT)
 
             # set specific parameter
             mlc = MLCLocal(working_dir=MLCWorkspaceTest.WORKSPACE_DIR)
             mlc.open_experiment(MLCWorkspaceTest.NEW_EXPERIMENT)
-            mlc.set_experiment_configuration_parameter(MLCWorkspaceTest.NEW_EXPERIMENT, "another_section", "another_param", "another_value")
+            mlc.set_experiment_configuration_parameter(MLCWorkspaceTest.NEW_EXPERIMENT,
+                                                       "another_section", "another_param",
+                                                       "another_value")
+            mlc.close_experiment(MLCWorkspaceTest.NEW_EXPERIMENT)
 
             # reload mlc_workspace
             mlc_reloaded = MLCLocal(working_dir=MLCWorkspaceTest.WORKSPACE_DIR)
             mlc_reloaded.open_experiment(MLCWorkspaceTest.NEW_EXPERIMENT)
             config = mlc_reloaded.get_experiment_configuration(MLCWorkspaceTest.NEW_EXPERIMENT)
+            mlc_reloaded.close_experiment(MLCWorkspaceTest.NEW_EXPERIMENT)
             self.assertEqual(config["PARAMS"]["test_param"], "new_value")
 
             self.assertIn("another_section", config)
@@ -190,8 +184,7 @@ def test_set_configuration(self):
 
         finally:
             # FIXME: use Setup/TearDown testcase
-            os.unlink(os.path.join(MLCWorkspaceTest.WORKSPACE_DIR, MLCWorkspaceTest.NEW_EXPERIMENT) + ".conf")
-            os.unlink(os.path.join(MLCWorkspaceTest.WORKSPACE_DIR, MLCWorkspaceTest.NEW_EXPERIMENT) + ".mlc")
+            mlc.delete_experiment(MLCWorkspaceTest.NEW_EXPERIMENT)
             pass
 
     def test_get_info_empty_simulation(self):
@@ -200,7 +193,7 @@ def test_get_info_empty_simulation(self):
         info = mlc.get_experiment_info(MLCWorkspaceTest.ORIGINAL_EXPERIMENT)
 
         self._assert_key_value(info, "name", MLCWorkspaceTest.ORIGINAL_EXPERIMENT)
-        self._assert_key_value(info, "filename", MLCWorkspaceTest.ORIGINAL_EXPERIMENT+".mlc")
+        self._assert_key_value(info, "filename", MLCWorkspaceTest.ORIGINAL_EXPERIMENT + ".mlc")
         self._assert_key_value(info, "generations", 0)
         self._assert_key_value(info, "individuals", 0)
         self._assert_key_value(info, "individuals_per_generation", 10)
@@ -260,47 +253,46 @@ def test_go_and_get_individuals(self):
             indiv_data = mlc.get_individuals("test_go_and_check")[2]
             self.assertEqual(indiv_data.get_appearances(), 2)
             self.assertEqual(indiv_data.get_cost_history(), {1: [(1000.0, 1001)], 2: [(1000.0, 1001)]})
+            mlc.close_experiment("test_go_and_check")
         finally:
             # FIXME: use Setup/TearDown testcase
-            os.unlink(os.path.join(MLCWorkspaceTest.WORKSPACE_DIR, "test_go_and_check") + ".conf")
-            os.unlink(os.path.join(MLCWorkspaceTest.WORKSPACE_DIR, "test_go_and_check") + ".mlc")
-            pass
+            mlc.delete_experiment("test_go_and_check")
 
     @nottest
     def test_go_and_get_generations(self):
-            try:
+        try:
                 # load random values for the simulation
-                self._load_random_values()
-
-                # Execute a simulation
-                mlc = MLCLocal(working_dir=MLCWorkspaceTest.WORKSPACE_DIR)
-                mlc.new_experiment("test_go_and_check", MLCWorkspaceTest.ORIGINAL_CONFIGURATION)
-                mlc.open_experiment("test_go_and_check")
-                mlc.go("test_go_and_check", 2)
-
-                # get first population
-                first_generation = mlc.get_generation("test_go_and_check", 1)
-                self.assertIsInstance(first_generation, MLCPopulation)
-
-                # get second generation
-                second_generation = mlc.get_generation("test_go_and_check", 2)
-                self.assertIsInstance(second_generation, MLCPopulation)
-
-                # third generation does not exist and must raise an Exception
-                # TODO: Use a specific exception instead of IndexError
-
-                try:
-                    third_generation = mlc.get_generation("test_go_and_check", 3)
-                    self.assertIsInstance(third_generation, MLCPopulation)
-                    self.assertTrue(False)
-                except IndexError:
-                    self.assertTrue(True)
-
-            finally:
-                # FIXME: use Setup/TearDown testcase
-                os.unlink(os.path.join(MLCWorkspaceTest.WORKSPACE_DIR, "test_go_and_check") + ".conf")
-                os.unlink(os.path.join(MLCWorkspaceTest.WORKSPACE_DIR, "test_go_and_check") + ".mlc")
-                pass
+            self._load_random_values()
+
+            # Execute a simulation
+            mlc = MLCLocal(working_dir=MLCWorkspaceTest.WORKSPACE_DIR)
+            mlc.new_experiment("test_go_and_check", MLCWorkspaceTest.ORIGINAL_CONFIGURATION)
+            mlc.open_experiment("test_go_and_check")
+            mlc.go("test_go_and_check", 2)
+
+            # get first population
+            first_generation = mlc.get_generation("test_go_and_check", 1)
+            self.assertIsInstance(first_generation, MLCPopulation)
+
+            # get second generation
+            second_generation = mlc.get_generation("test_go_and_check", 2)
+            self.assertIsInstance(second_generation, MLCPopulation)
+
+            # third generation does not exist and must raise an Exception
+            # TODO: Use a specific exception instead of IndexError
+
+            try:
+                third_generation = mlc.get_generation("test_go_and_check", 3)
+                self.assertIsInstance(third_generation, MLCPopulation)
+                self.assertTrue(False)
+            except IndexError:
+                self.assertTrue(True)
+
+        finally:
+            # FIXME: use Setup/TearDown testcase
+            os.unlink(os.path.join(MLCWorkspaceTest.WORKSPACE_DIR, "test_go_and_check") + ".conf")
+            os.unlink(os.path.join(MLCWorkspaceTest.WORKSPACE_DIR, "test_go_and_check") + ".mlc")
+            pass
 
     def _assert_key_value(self, dictionary, key, value):
         self.assertIsInstance(dictionary, dict)

tests/mlc/api/test_new_experiment.conf

@@ -0,0 +1,2 @@
+[PARAMS]
+test_param = test_value