Namespace mock paths under gn2.

19 files changed, 131 insertions, 131 deletions

diff --git a/gn2/tests/unit/base/test_data_set.py b/gn2/tests/unit/base/test_data_set.py
index 7341314c..9f9fb132 100644
--- a/gn2/tests/unit/base/test_data_set.py
+++ b/gn2/tests/unit/base/test_data_set.py
@@ -173,7 +173,7 @@ class TestDataSetTypes(unittest.TestCase):
                              ("All Phenotypes", redis_mock, cursor_mock), "Publish")
             redis_mock.get.assert_called_once_with("dataset_structure")
 
-    @mock.patch('base.data_set.datasettype.requests.get')
+    @mock.patch('gn2.base.data_set.datasettype.requests.get')
     def test_data_set_type_with_empty_redis(self, request_mock):
         """Test that DatasetType returns correctly if the Redis Instance is empty and
         the name variable exists in the dictionary
@@ -204,8 +204,8 @@ class TestDataSetTypes(unittest.TestCase):
 class TestDatasetAccessionId(unittest.TestCase):
     """Tests for the DataSetType class"""
 
-    @mock.patch("base.data_set.dataset.query_sql")
-    @mock.patch("base.data_set.dataset.DatasetGroup")
+    @mock.patch("gn2.base.data_set.dataset.query_sql")
+    @mock.patch("gn2.base.data_set.dataset.DatasetGroup")
     def test_get_accession_id(self, mock_dataset_group, mock_query_sql):
         def mock_fn():
             yield MonadicDict({"accession_id": 7})
@@ -221,8 +221,8 @@ class TestDatasetAccessionId(unittest.TestCase):
             .accession_id\
             .bind(lambda x: self.assertEqual(7, x))
 
-    @mock.patch("base.data_set.dataset.query_sql")
-    @mock.patch("base.data_set.dataset.DatasetGroup")
+    @mock.patch("gn2.base.data_set.dataset.query_sql")
+    @mock.patch("gn2.base.data_set.dataset.DatasetGroup")
     def test_get_accession_id_empty_return(self, mock_dataset_group,
                                            mock_query_sql):
         mock_dataset_group.return_value = MockGroup()
diff --git a/gn2/tests/unit/base/test_species.py b/gn2/tests/unit/base/test_species.py
index 239e8b3f..d2845b25 100644
--- a/gn2/tests/unit/base/test_species.py
+++ b/gn2/tests/unit/base/test_species.py
@@ -30,7 +30,7 @@ class MockDataset:
      (None, "Random Dataset", None, 1)))
 def test_species(mocker, species_name, dataset,
                  expected_name, chromosome_param):
-    _c = mocker.patch("base.species.Chromosomes",
+    _c = mocker.patch("gn2.base.species.Chromosomes",
                       return_value=chromosome_param)
     test_species = TheSpecies(dataset=dataset,
                               species_name=species_name)
diff --git a/gn2/tests/unit/base/test_trait.py b/gn2/tests/unit/base/test_trait.py
index 417956ae..2adb1fdf 100644
--- a/gn2/tests/unit/base/test_trait.py
+++ b/gn2/tests/unit/base/test_trait.py
@@ -31,7 +31,7 @@ class MockTrait(GeneralTrait):
 
 class TestRetrieveTraitInfo(unittest.TestCase):
     """Tests for 'retrieve_trait_info'"""
-    @mock.patch('base.trait.database_connection')
+    @mock.patch('gn2.base.trait.database_connection')
     def test_retrieve_trait_info_with_empty_dataset(self, mock_db):
         """Test that an exception is raised when dataset is empty"""
         conn = mock.MagicMock()
@@ -40,9 +40,9 @@ class TestRetrieveTraitInfo(unittest.TestCase):
             retrieve_trait_info(trait=mock.MagicMock(),
                                 dataset={})
 
-    @mock.patch('base.trait.requests.get')
-    @mock.patch('base.trait.g', mock.Mock())
-    @mock.patch('base.trait.database_connection')
+    @mock.patch('gn2.base.trait.requests.get')
+    @mock.patch('gn2.base.trait.g', mock.Mock())
+    @mock.patch('gn2.base.trait.database_connection')
     def test_retrieve_trait_info_with_empty_trait_info(self,
                                                        mock_db,
                                                        requests_mock):
@@ -57,9 +57,9 @@ class TestRetrieveTraitInfo(unittest.TestCase):
             retrieve_trait_info(trait=mock.MagicMock(),
                                 dataset=mock.MagicMock())
 
-    @mock.patch('base.trait.requests.get')
-    @mock.patch('base.trait.g', mock.Mock())
-    @mock.patch('base.trait.database_connection')
+    @mock.patch('gn2.base.trait.requests.get')
+    @mock.patch('gn2.base.trait.g', mock.Mock())
+    @mock.patch('gn2.base.trait.database_connection')
     def test_retrieve_trait_info_with_non_empty_trait_info(self,
                                                            mock_db,
                                                            requests_mock):
@@ -80,9 +80,9 @@ class TestRetrieveTraitInfo(unittest.TestCase):
         self.assertEqual(test_trait.c, 3)
         self.assertEqual(test_trait.d, 4)
 
-    @mock.patch('base.trait.requests.get')
-    @mock.patch('base.trait.g', mock.Mock())
-    @mock.patch('base.trait.database_connection')
+    @mock.patch('gn2.base.trait.requests.get')
+    @mock.patch('gn2.base.trait.g', mock.Mock())
+    @mock.patch('gn2.base.trait.database_connection')
     def test_retrieve_trait_info_utf8_parsing(self,
                                               mock_db,
                                               requests_mock):
@@ -120,9 +120,9 @@ class TestRetrieveTraitInfo(unittest.TestCase):
 
 
     @unittest.skip("Too complicated")
-    @mock.patch('base.trait.requests.get')
-    @mock.patch('base.trait.database_connection')
-    @mock.patch('base.trait.get_resource_id')
+    @mock.patch('gn2.base.trait.requests.get')
+    @mock.patch('gn2.base.trait.database_connection')
+    @mock.patch('gn2.base.trait.get_resource_id')
     def test_retrieve_trait_info_with_non_empty_lrs(self,
                                                     resource_id_mock,
                                                     mock_db,
@@ -169,9 +169,9 @@ class TestRetrieveTraitInfo(unittest.TestCase):
                              "2.4")
 
     @unittest.skip("Too complicated")
-    @mock.patch('base.trait.requests.get')
-    @mock.patch('base.trait.g')
-    @mock.patch('base.trait.get_resource_id')
+    @mock.patch('gn2.base.trait.requests.get')
+    @mock.patch('gn2.base.trait.g')
+    @mock.patch('gn2.base.trait.get_resource_id')
     def test_retrieve_trait_info_with_empty_lrs_field(self,
                                                       resource_id_mock,
                                                       g_mock,
@@ -215,9 +215,9 @@ class TestRetrieveTraitInfo(unittest.TestCase):
                          "Chr2: 3.000000")
         
     @unittest.skip("Too complicated")
-    @mock.patch('base.trait.requests.get')
-    @mock.patch('base.trait.g')
-    @mock.patch('base.trait.get_resource_id')
+    @mock.patch('gn2.base.trait.requests.get')
+    @mock.patch('gn2.base.trait.g')
+    @mock.patch('gn2.base.trait.get_resource_id')
     def test_retrieve_trait_info_with_empty_chr_field(self,
                                                       resource_id_mock,
                                                       g_mock,
diff --git a/gn2/tests/unit/utility/test_authentication_tools.py b/gn2/tests/unit/utility/test_authentication_tools.py
index 3b16ca94..90945b0f 100644
--- a/gn2/tests/unit/utility/test_authentication_tools.py
+++ b/gn2/tests/unit/utility/test_authentication_tools.py
@@ -38,10 +38,10 @@ def mock_add_resource(resource_ob, update=False):
 
 class TestCheckResourceAvailability(unittest.TestCase):
     """Test methods related to checking the resource availability"""
-    @mock.patch('utility.authentication_tools.add_new_resource')
-    @mock.patch('utility.authentication_tools.Redis')
-    @mock.patch('utility.authentication_tools.g', TestUserSession())
-    @mock.patch('utility.authentication_tools.get_resource_id')
+    @mock.patch('gn2.utility.authentication_tools.add_new_resource')
+    @mock.patch('gn2.utility.authentication_tools.Redis')
+    @mock.patch('gn2.utility.authentication_tools.g', TestUserSession())
+    @mock.patch('gn2.utility.authentication_tools.get_resource_id')
     def test_check_resource_availability_default_mask(
             self,
             resource_id_mock,
@@ -56,11 +56,11 @@ class TestCheckResourceAvailability(unittest.TestCase):
         add_new_resource_mock.return_value = {"default_mask": 2}
         self.assertEqual(check_resource_availability(test_dataset, user_id), 2)
 
-    @mock.patch('utility.authentication_tools.requests.get')
-    @mock.patch('utility.authentication_tools.add_new_resource')
-    @mock.patch('utility.authentication_tools.Redis')
-    @mock.patch('utility.authentication_tools.g', TestUserSession())
-    @mock.patch('utility.authentication_tools.get_resource_id')
+    @mock.patch('gn2.utility.authentication_tools.requests.get')
+    @mock.patch('gn2.utility.authentication_tools.add_new_resource')
+    @mock.patch('gn2.utility.authentication_tools.Redis')
+    @mock.patch('gn2.utility.authentication_tools.g', TestUserSession())
+    @mock.patch('gn2.utility.authentication_tools.get_resource_id')
     def test_check_resource_availability_non_default_mask(
             self,
             resource_id_mock,
@@ -77,13 +77,13 @@ class TestCheckResourceAvailability(unittest.TestCase):
         self.assertEqual(check_resource_availability(test_dataset, user_id),
                          ['foo'])
 
-    @mock.patch('utility.authentication_tools.webqtlConfig.SUPER_PRIVILEGES',
+    @mock.patch('gn2.utility.authentication_tools.webqtlConfig.SUPER_PRIVILEGES',
                 "SUPERUSER")
-    @mock.patch('utility.authentication_tools.requests.get')
-    @mock.patch('utility.authentication_tools.add_new_resource')
-    @mock.patch('utility.authentication_tools.Redis')
-    @mock.patch('utility.authentication_tools.g', TestUserSession())
-    @mock.patch('utility.authentication_tools.get_resource_id')
+    @mock.patch('gn2.utility.authentication_tools.requests.get')
+    @mock.patch('gn2.utility.authentication_tools.add_new_resource')
+    @mock.patch('gn2.utility.authentication_tools.Redis')
+    @mock.patch('gn2.utility.authentication_tools.g', TestUserSession())
+    @mock.patch('gn2.utility.authentication_tools.get_resource_id')
     def test_check_resource_availability_of_super_user(
             self,
             resource_id_mock,
@@ -100,14 +100,14 @@ class TestCheckResourceAvailability(unittest.TestCase):
         self.assertEqual(check_resource_availability(test_dataset, user_id),
                          "SUPERUSER")
 
-    @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+    @mock.patch('gn2.utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
                 "John Doe")
     def test_check_resource_availability_string_dataset(self):
         """Test the resource availability if the dataset is a string"""
         self.assertEqual(check_resource_availability("Test", user_id),
                          "John Doe")
 
-    @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+    @mock.patch('gn2.utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
                 "John Doe")
     def test_check_resource_availability_temp(self):
         """Test the resource availability if the dataset is a string"""
@@ -119,10 +119,10 @@ class TestCheckResourceAvailability(unittest.TestCase):
 
 class TestAddNewResource(unittest.TestCase):
     """Test cases for add_new_resource method"""
-    @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+    @mock.patch('gn2.utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
                 "John Doe")
-    @mock.patch('utility.authentication_tools.add_resource', mock_add_resource)
-    @mock.patch('utility.authentication_tools.get_group_code')
+    @mock.patch('gn2.utility.authentication_tools.add_resource', mock_add_resource)
+    @mock.patch('gn2.utility.authentication_tools.get_group_code')
     def test_add_new_resource_if_publish_datatype(self, group_code_mock):
         """Test add_new_resource if dataset type is 'publish'"""
         group_code_mock.return_value = "Test"
@@ -143,10 +143,10 @@ class TestAddNewResource(unittest.TestCase):
         self.assertEqual(add_new_resource(test_dataset),
                          expected_value)
 
-    @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+    @mock.patch('gn2.utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
                 "John Doe")
-    @mock.patch('utility.authentication_tools.add_resource', mock_add_resource)
-    @mock.patch('utility.authentication_tools.get_group_code')
+    @mock.patch('gn2.utility.authentication_tools.add_resource', mock_add_resource)
+    @mock.patch('gn2.utility.authentication_tools.get_group_code')
     def test_add_new_resource_if_geno_datatype(self, group_code_mock):
         """Test add_new_resource if dataset type is 'geno'"""
         group_code_mock.return_value = "Test"
@@ -167,10 +167,10 @@ class TestAddNewResource(unittest.TestCase):
         self.assertEqual(add_new_resource(test_dataset),
                          expected_value)
 
-    @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+    @mock.patch('gn2.utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
                 "John Doe")
-    @mock.patch('utility.authentication_tools.add_resource', mock_add_resource)
-    @mock.patch('utility.authentication_tools.get_group_code')
+    @mock.patch('gn2.utility.authentication_tools.add_resource', mock_add_resource)
+    @mock.patch('gn2.utility.authentication_tools.get_group_code')
     def test_add_new_resource_if_other_datatype(self, group_code_mock):
         """Test add_new_resource if dataset type is not 'geno' or 'publish'"""
         group_code_mock.return_value = "Test"
diff --git a/gn2/tests/unit/utility/test_hmac.py b/gn2/tests/unit/utility/test_hmac.py
index 2b428588..f148ea5b 100644
--- a/gn2/tests/unit/utility/test_hmac.py
+++ b/gn2/tests/unit/utility/test_hmac.py
@@ -11,12 +11,12 @@ from gn2.utility.hmac import hmac_creation
 class TestHmacUtil(unittest.TestCase):
     """Test Utility method for hmac creation"""
 
-    @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
+    @mock.patch("gn2.utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
     def test_hmac_creation(self):
         """Test hmac creation with a utf-8 string"""
         self.assertEqual(hmac_creation("ファイ"), "7410466338cfe109e946")
 
-    @mock.patch("utility.hmac.app.config",
+    @mock.patch("gn2.utility.hmac.app.config",
                 {'SECRET_HMAC_CODE': ('\x08\xdf\xfa\x93N\x80'
                                       '\xd9\\H@\\\x9f`\x98d^'
                                       '\xb4a;\xc6OM\x946a\xbc'
@@ -29,21 +29,21 @@ class TestHmacUtil(unittest.TestCase):
             hmac_creation(uuid_),
             "af4fcf5eace9e7c864ce")
 
-    @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
+    @mock.patch("gn2.utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
     def test_data_hmac(self):
         """Test data_hmac fn with a utf-8 string"""
         self.assertEqual(data_hmac("ファイ"), "ファイ:7410466338cfe109e946")
 
-    @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
-    @mock.patch("utility.hmac.url_for")
+    @mock.patch("gn2.utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
+    @mock.patch("gn2.utility.hmac.url_for")
     def test_url_for_hmac_with_plain_url(self, mock_url):
         """Test url_for_hmac without params"""
         mock_url.return_value = "https://mock_url.com/ファイ/"
         self.assertEqual(url_for_hmac("ファイ"),
                          "https://mock_url.com/ファイ/?hm=05bc39e659b1948f41e7")
 
-    @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
-    @mock.patch("utility.hmac.url_for")
+    @mock.patch("gn2.utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
+    @mock.patch("gn2.utility.hmac.url_for")
     def test_url_for_hmac_with_param_in_url(self, mock_url):
         """Test url_for_hmac with params"""
         mock_url.return_value = "https://mock_url.com/?ファイ=1"
diff --git a/gn2/tests/unit/wqflask/api/test_correlation.py b/gn2/tests/unit/wqflask/api/test_correlation.py
index 8835375d..2a1907af 100644
--- a/gn2/tests/unit/wqflask/api/test_correlation.py
+++ b/gn2/tests/unit/wqflask/api/test_correlation.py
@@ -39,7 +39,7 @@ class TestCorrelations(unittest.TestCase):
 
         self.assertEqual(corr_params_results, expected_results)
 
-    @mock.patch("wqflask.api.correlation.database_connection")
+    @mock.patch("gn2.wqflask.api.correlation.database_connection")
     def test_convert_to_mouse_gene_id(self, mock_db):
         conn = mock.MagicMock()
         mock_db.return_value.__enter__.return_value = conn
@@ -59,8 +59,8 @@ class TestCorrelations(unittest.TestCase):
                 convert_to_mouse_gene_id(species="human", gene_id="H1"), "MG-2"
             )
 
-    @mock.patch("wqflask.api.correlation.database_connection")
-    @mock.patch("wqflask.api.correlation.convert_to_mouse_gene_id")
+    @mock.patch("gn2.wqflask.api.correlation.database_connection")
+    @mock.patch("gn2.wqflask.api.correlation.convert_to_mouse_gene_id")
     def test_do_literature_correlation_for_all_traits(
         self, mock_convert_to_mouse_geneid, mock_db
     ):
@@ -88,7 +88,7 @@ class TestCorrelations(unittest.TestCase):
             }
             self.assertEqual(results, expected_results)
 
-    @mock.patch("wqflask.api.correlation.corr_result_helpers.normalize_values")
+    @mock.patch("gn2.wqflask.api.correlation.corr_result_helpers.normalize_values")
     def test_get_sample_r_and_p_values(self, mock_normalize):
 
         group = AttributeSetter(
@@ -146,7 +146,7 @@ class TestCorrelations(unittest.TestCase):
             self.assertAlmostEqual(val, results_spearmanr[i], 4)
         self.assertEqual(results_num_overlap, None)
 
-    @mock.patch("wqflask.api.correlation.do_literature_correlation_for_all_traits")
+    @mock.patch("gn2.wqflask.api.correlation.do_literature_correlation_for_all_traits")
     def test_calculate_results(self, literature_correlation):
 
         literature_correlation.return_value = {
diff --git a/gn2/tests/unit/wqflask/api/test_gen_menu.py b/gn2/tests/unit/wqflask/api/test_gen_menu.py
index a6081e99..2416b3f6 100644
--- a/gn2/tests/unit/wqflask/api/test_gen_menu.py
+++ b/gn2/tests/unit/wqflask/api/test_gen_menu.py
@@ -258,7 +258,7 @@ class TestGenMenu(unittest.TestCase):
                 "ORDER BY -ProbeSetFreeze.OrderList DESC, "
                 "ProbeSetFreeze.CreateTime DESC")
 
-    @mock.patch('wqflask.api.gen_menu.build_datasets')
+    @mock.patch('gn2.wqflask.api.gen_menu.build_datasets')
     def test_build_types(self, datasets_mock):
         """Test that correct tissue metadata is returned"""
         db_mock = mock.MagicMock()
@@ -286,9 +286,9 @@ class TestGenMenu(unittest.TestCase):
                 "ORDER BY Tissue.Name"
             )
 
-    @mock.patch('wqflask.api.gen_menu.build_types')
-    @mock.patch('wqflask.api.gen_menu.genotypes_exist')
-    @mock.patch('wqflask.api.gen_menu.phenotypes_exist')
+    @mock.patch('gn2.wqflask.api.gen_menu.build_types')
+    @mock.patch('gn2.wqflask.api.gen_menu.genotypes_exist')
+    @mock.patch('gn2.wqflask.api.gen_menu.phenotypes_exist')
     def test_get_types_with_existing_genotype_and_phenotypes(
             self,
             phenotypes_exist_mock,
@@ -310,9 +310,9 @@ class TestGenMenu(unittest.TestCase):
                                    mock.MagicMock()),
                          expected_result)
 
-    @mock.patch('wqflask.api.gen_menu.build_types')
-    @mock.patch('wqflask.api.gen_menu.genotypes_exist')
-    @mock.patch('wqflask.api.gen_menu.phenotypes_exist')
+    @mock.patch('gn2.wqflask.api.gen_menu.build_types')
+    @mock.patch('gn2.wqflask.api.gen_menu.genotypes_exist')
+    @mock.patch('gn2.wqflask.api.gen_menu.phenotypes_exist')
     def test_get_types_with_buildtype_and_non_existent_genotype_and_phenotypes(
             self,
             phenotypes_exist_mock,
@@ -329,9 +329,9 @@ class TestGenMenu(unittest.TestCase):
         self.assertEqual(get_types(self.test_group, mock.MagicMock()),
                          {'mouse': {}, 'human': {}})
 
-    @mock.patch('wqflask.api.gen_menu.build_types')
-    @mock.patch('wqflask.api.gen_menu.genotypes_exist')
-    @mock.patch('wqflask.api.gen_menu.phenotypes_exist')
+    @mock.patch('gn2.wqflask.api.gen_menu.build_types')
+    @mock.patch('gn2.wqflask.api.gen_menu.genotypes_exist')
+    @mock.patch('gn2.wqflask.api.gen_menu.phenotypes_exist')
     def test_get_types_with_non_existent_genotype_phenotypes_and_buildtype(
             self,
             phenotypes_exist_mock,
@@ -357,7 +357,7 @@ class TestGenMenu(unittest.TestCase):
         self.assertEqual(get_types(self.test_group, mock.MagicMock()),
                          expected_result)
 
-    @mock.patch('wqflask.api.gen_menu.build_datasets')
+    @mock.patch('gn2.wqflask.api.gen_menu.build_datasets')
     def test_get_datasets_with_existent_datasets(self,
                                                  build_datasets_mock):
         """Test correct dataset is returned with existent build_datasets"""
@@ -379,7 +379,7 @@ class TestGenMenu(unittest.TestCase):
         self.assertEqual(get_datasets(self.test_type, mock.MagicMock()),
                          expected_result)
 
-    @mock.patch('wqflask.api.gen_menu.build_datasets')
+    @mock.patch('gn2.wqflask.api.gen_menu.build_datasets')
     def test_get_datasets_with_non_existent_datasets(self,
                                                      build_datasets_mock):
         """Test correct dataset is returned with non-existent build_datasets"""
@@ -393,10 +393,10 @@ class TestGenMenu(unittest.TestCase):
         self.assertEqual(get_datasets(self.test_type, mock.MagicMock()),
                          expected_result)
 
-    @mock.patch('wqflask.api.gen_menu.get_datasets')
-    @mock.patch('wqflask.api.gen_menu.get_types')
-    @mock.patch('wqflask.api.gen_menu.get_groups')
-    @mock.patch('wqflask.api.gen_menu.get_all_species')
+    @mock.patch('gn2.wqflask.api.gen_menu.get_datasets')
+    @mock.patch('gn2.wqflask.api.gen_menu.get_types')
+    @mock.patch('gn2.wqflask.api.gen_menu.get_groups')
+    @mock.patch('gn2.wqflask.api.gen_menu.get_all_species')
     def test_gen_dropdown_json(self,
                                species_mock,
                                groups_mock,
diff --git a/gn2/tests/unit/wqflask/api/test_mapping.py b/gn2/tests/unit/wqflask/api/test_mapping.py
index 1553cbf6..226e2a9b 100644
--- a/gn2/tests/unit/wqflask/api/test_mapping.py
+++ b/gn2/tests/unit/wqflask/api/test_mapping.py
@@ -63,12 +63,12 @@ class TestMapping(unittest.TestCase):
 
         self.assertEqual(results_2, expected_results)
 
-    @mock.patch("wqflask.api.mapping.rqtl_mapping.run_rqtl")
-    @mock.patch("wqflask.api.mapping.gemma_mapping.run_gemma")
-    @mock.patch("wqflask.api.mapping.initialize_parameters")
-    @mock.patch("wqflask.api.mapping.retrieve_sample_data")
-    @mock.patch("wqflask.api.mapping.create_trait")
-    @mock.patch("wqflask.api.mapping.data_set.create_dataset")
+    @mock.patch("gn2.wqflask.api.mapping.rqtl_mapping.run_rqtl")
+    @mock.patch("gn2.wqflask.api.mapping.gemma_mapping.run_gemma")
+    @mock.patch("gn2.wqflask.api.mapping.initialize_parameters")
+    @mock.patch("gn2.wqflask.api.mapping.retrieve_sample_data")
+    @mock.patch("gn2.wqflask.api.mapping.create_trait")
+    @mock.patch("gn2.wqflask.api.mapping.data_set.create_dataset")
     def test_do_mapping_for_api(self, mock_create_dataset, mock_trait, mock_retrieve_sample, mock_param, run_gemma, run_rqtl_geno):
         start_vars = {
             "db": "Temp",
diff --git a/gn2/tests/unit/wqflask/api/test_markdown_routes.py b/gn2/tests/unit/wqflask/api/test_markdown_routes.py
index f0f93bc1..ecf64a81 100644
--- a/gn2/tests/unit/wqflask/api/test_markdown_routes.py
+++ b/gn2/tests/unit/wqflask/api/test_markdown_routes.py
@@ -26,7 +26,7 @@ This is another sub-heading"""
 class TestMarkdownRoutesFunctions(unittest.TestCase):
     """Test cases for functions in markdown"""
 
-    @mock.patch('wqflask.api.markdown.requests.get')
+    @mock.patch('gn2.wqflask.api.markdown.requests.get')
     def test_render_markdown_when_fetching_locally(self, requests_mock):
         requests_mock.return_value = MockRequests404()
         markdown_content = render_markdown("general/glossary/glossary.md")
@@ -38,7 +38,7 @@ class TestMarkdownRoutesFunctions(unittest.TestCase):
         self.assertRegex(markdown_content,
                          "Content for general/glossary/glossary.md not available.")
 
-    @mock.patch('wqflask.api.markdown.requests.get')
+    @mock.patch('gn2.wqflask.api.markdown.requests.get')
     def test_render_markdown_when_fetching_remotely(self, requests_mock):
         requests_mock.return_value = MockRequests200()
         markdown_content = render_markdown("general/glossary/glossary.md")
diff --git a/gn2/tests/unit/wqflask/correlation/test_correlation_functions.py b/gn2/tests/unit/wqflask/correlation/test_correlation_functions.py
index c0f57141..f76ef57e 100644
--- a/gn2/tests/unit/wqflask/correlation/test_correlation_functions.py
+++ b/gn2/tests/unit/wqflask/correlation/test_correlation_functions.py
@@ -11,7 +11,7 @@ def test_tissue_corr_computation(mocker):
     """Test for cal_zero_order_corr_for_tiss"""
     primary_values = [9.288, 9.313, 8.988, 9.660, 8.21]
     target_values = [9.586, 8.498, 9.362, 8.820, 8.786]
-    _m = mocker.patch(("wqflask.correlation.correlation_functions."
+    _m = mocker.patch(("gn2.wqflask.correlation.correlation_functions."
                        "compute_corr_coeff_p_value"),
                       return_value=(0.51, 0.7))
     results = cal_zero_order_corr_for_tiss(primary_values, target_values)
diff --git a/gn2/tests/unit/wqflask/marker_regression/test_gemma_mapping.py b/gn2/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
index 26f0c50a..b4d80ad7 100644
--- a/gn2/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
+++ b/gn2/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
@@ -22,7 +22,7 @@ class MockGroup(AttributeSetter):
 
 class TestGemmaMapping(unittest.TestCase):
 
-    @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.parse_loco_output")
     def test_run_gemma_firstrun_set_false(self, mock_parse_loco):
         """add tests for gemma function where  first run is set to false"""
         dataset = AttributeSetter(
@@ -38,17 +38,17 @@ class TestGemmaMapping(unittest.TestCase):
         expected_results = ([], "file1")
         self.assertEqual(expected_results, result)
 
-    @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img")
-    @mock.patch("wqflask.marker_regression.gemma_mapping.GEMMAOPTS", "-debug")
-    @mock.patch("wqflask.marker_regression.gemma_mapping.GEMMA_WRAPPER_COMMAND", "ghc")
-    @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR",
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.GEMMAOPTS", "-debug")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.GEMMA_WRAPPER_COMMAND", "ghc")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.TEMPDIR",
                 os.path.join(os.path.dirname(__file__), "user/data"))
-    @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output")
-    @mock.patch("wqflask.marker_regression.gemma_mapping.flat_files")
-    @mock.patch("wqflask.marker_regression.gemma_mapping.gen_covariates_file")
-    @mock.patch("wqflask.marker_regression.run_mapping.random.choice")
-    @mock.patch("wqflask.marker_regression.gemma_mapping.os")
-    @mock.patch("wqflask.marker_regression.gemma_mapping.gen_pheno_txt_file")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.parse_loco_output")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.flat_files")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.gen_covariates_file")
+    @mock.patch("gn2.wqflask.marker_regression.run_mapping.random.choice")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.os")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.gen_pheno_txt_file")
     def test_run_gemma_firstrun_set_true(self, mock_gen_pheno_txt, mock_os, mock_choice, mock_gen_covar, mock_flat_files, mock_parse_loco):
         """add tests for run_gemma where first run is set to true"""
         this_chromosomes = {}
@@ -78,7 +78,7 @@ class TestGemmaMapping(unittest.TestCase):
             ('/home/user/imgfile_output.assoc.txt'))
         self.assertEqual(results, ([], "GP1_GWA_RRRRRR"))
 
-    @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data")
     def test_gen_pheno_txt_file(self):
         """add tests for generating pheno txt file"""
         with mock.patch("builtins.open", mock.mock_open())as mock_open:
@@ -95,9 +95,9 @@ class TestGemmaMapping(unittest.TestCase):
 
             filehandler.write.assert_has_calls(write_calls)
 
-    @mock.patch("wqflask.marker_regression.gemma_mapping.flat_files")
-    @mock.patch("wqflask.marker_regression.gemma_mapping.create_trait")
-    @mock.patch("wqflask.marker_regression.gemma_mapping.create_dataset")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.flat_files")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.create_trait")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.create_dataset")
     def test_gen_covariates_file(self, create_dataset, create_trait, flat_files):
         """add tests for generating covariates files"""
         covariates = "X1:X2,Y1:Y2,M1:M3,V1:V2"
@@ -140,9 +140,9 @@ class TestGemmaMapping(unittest.TestCase):
             filehandler.write.assert_has_calls([mock.call(
                 '-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('\n')])
 
-    @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp")
-    @mock.patch("wqflask.marker_regression.gemma_mapping.os")
-    @mock.patch("wqflask.marker_regression.gemma_mapping.json")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.os")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.json")
     def test_parse_loco_outputfile_found(self, mock_json, mock_os):
         """add tests for parse loco output file found"""
         mock_json.load.return_value = {
@@ -174,8 +174,8 @@ X\tM5\t12\tQ\tE\tMMB\tR\t21.1\tW\t0.65\t0.6"""
                 {'name': 'M5', 'chr': 'X', 'Mb': 1.2e-05, 'p_value': 0.6, 'additive': -10.55, 'lod_score': 0.22184874961635637}]
             self.assertEqual(expected_results, results)
 
-    @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp")
-    @mock.patch("wqflask.marker_regression.gemma_mapping.os")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp")
+    @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.os")
     def test_parse_loco_outputfile_not_found(self, mock_os):
         """add tests for parse loco output where  output file not found"""
 
diff --git a/gn2/tests/unit/wqflask/marker_regression/test_plink_mapping.py b/gn2/tests/unit/wqflask/marker_regression/test_plink_mapping.py
index 4c13b907..7542e15a 100644
--- a/gn2/tests/unit/wqflask/marker_regression/test_plink_mapping.py
+++ b/gn2/tests/unit/wqflask/marker_regression/test_plink_mapping.py
@@ -27,7 +27,7 @@ class TestPlinkMapping(unittest.TestCase):
         self.assertEqual([], build_line_list())
         self.assertEqual(["this", "is", "an,", "irregular", "line"], results)
 
-    @mock.patch("wqflask.marker_regression.plink_mapping.flat_files")
+    @mock.patch("gn2.wqflask.marker_regression.plink_mapping.flat_files")
     def test_get_samples_from_ped_file(self, mock_flat_files):
         """test for getting samples from ped file"""
         dataset = AttributeSetter({"group": AttributeSetter({"name": "n_1"})})
@@ -42,8 +42,8 @@ Expected_2\there
             self.assertEqual(
                 ["Expected_1", "Expected_2", "Expected_3"], results)
 
-    @mock.patch("wqflask.marker_regression.plink_mapping.TMPDIR", "/home/user/data/")
-    @mock.patch("wqflask.marker_regression.plink_mapping.get_samples_from_ped_file")
+    @mock.patch("gn2.wqflask.marker_regression.plink_mapping.TMPDIR", "/home/user/data/")
+    @mock.patch("gn2.wqflask.marker_regression.plink_mapping.get_samples_from_ped_file")
     def test_gen_pheno_txt_file_plink(self, mock_samples):
         """test for getting gen_pheno txt file"""
         mock_samples.return_value = ["Expected_1", "Expected_2", "Expected_3"]
@@ -64,8 +64,8 @@ Expected_2\there
 
             filehandler.close.assert_called_once()
 
-    @mock.patch("wqflask.marker_regression.plink_mapping.TMPDIR", "/home/user/data/")
-    @mock.patch("wqflask.marker_regression.plink_mapping.build_line_list")
+    @mock.patch("gn2.wqflask.marker_regression.plink_mapping.TMPDIR", "/home/user/data/")
+    @mock.patch("gn2.wqflask.marker_regression.plink_mapping.build_line_list")
     def test_parse_plink_output(self, mock_line_list):
         """test for parsing plink output"""
         chromosomes = [0, 34, 110, 89, 123, 23, 2]
diff --git a/gn2/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py b/gn2/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
index 2268f4cb..c2753141 100644
--- a/gn2/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
+++ b/gn2/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
@@ -7,7 +7,7 @@ from gn2.wqflask.marker_regression.qtlreaper_mapping import gen_pheno_txt_file
 
 
 class TestQtlReaperMapping(unittest.TestCase):
-    @mock.patch("wqflask.marker_regression.qtlreaper_mapping.TEMPDIR", "/home/user/data")
+    @mock.patch("gn2.wqflask.marker_regression.qtlreaper_mapping.TEMPDIR", "/home/user/data")
     def test_gen_pheno_txt_file(self):
         vals = ["V1", "x", "V4", "V3", "x"]
         samples = ["S1", "S2", "S3", "S4", "S5"]
diff --git a/gn2/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py b/gn2/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
index 5cfce28c..9f646fb0 100644
--- a/gn2/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
+++ b/gn2/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
@@ -15,9 +15,9 @@ class MockDataset:
 
 class TestRqtlMapping(unittest.TestCase):
     """Tests for functions in rqtl_mapping.py"""
-    @mock.patch("wqflask.marker_regression.rqtl_mapping.requests.post")
-    @mock.patch("wqflask.marker_regression.rqtl_mapping.locate")
-    @mock.patch("wqflask.marker_regression.rqtl_mapping.write_phenotype_file")
+    @mock.patch("gn2.wqflask.marker_regression.rqtl_mapping.requests.post")
+    @mock.patch("gn2.wqflask.marker_regression.rqtl_mapping.locate")
+    @mock.patch("gn2.wqflask.marker_regression.rqtl_mapping.write_phenotype_file")
     def test_run_rqtl_with_perm(self, mock_write_pheno_file, mock_locate, mock_post):
         """Test for run_rqtl with permutations > 0"""
         dataset_group = MockGroup("GP1", "file_geno")
diff --git a/gn2/tests/unit/wqflask/marker_regression/test_run_mapping.py b/gn2/tests/unit/wqflask/marker_regression/test_run_mapping.py
index dd67ce49..817bf2b9 100644
--- a/gn2/tests/unit/wqflask/marker_regression/test_run_mapping.py
+++ b/gn2/tests/unit/wqflask/marker_regression/test_run_mapping.py
@@ -61,7 +61,7 @@ class TestRunMapping(unittest.TestCase):
         result_2 = get_genofile_samplelist(self.dataset)
         self.assertEqual(result_2, [])
 
-    @mock.patch("wqflask.marker_regression.run_mapping.data_set")
+    @mock.patch("gn2.wqflask.marker_regression.run_mapping.data_set")
     def test_if_geno_db_exists(self, mock_data_set):
         mock_data_set.create_dataset.side_effect = [
             AttributeSetter({}), Exception()]
@@ -178,7 +178,7 @@ class TestRunMapping(unittest.TestCase):
 
         with mock.patch("builtins.open", mock.mock_open()) as mock_open:
 
-            with mock.patch("wqflask.marker_regression.run_mapping.datetime.datetime", new=datetime_mock):
+            with mock.patch("gn2.wqflask.marker_regression.run_mapping.datetime.datetime", new=datetime_mock):
                 export_mapping_results(dataset=self.dataset, trait=self.trait, markers=markers,
                                        results_path="~/results", mapping_method="gemma", mapping_scale="physic",
                                        score_type="-logP", transform="qnorm",
@@ -215,7 +215,7 @@ class TestRunMapping(unittest.TestCase):
                 filehandler = mock_open()
                 filehandler.write.assert_has_calls(write_calls)
 
-    @mock.patch("wqflask.marker_regression.run_mapping.random.choice")
+    @mock.patch("gn2.wqflask.marker_regression.run_mapping.random.choice")
     def test_write_input_for_browser(self, mock_choice):
         """test for writing input for browser"""
         mock_choice.side_effect = ["F", "i", "l", "e", "s", "x"]
diff --git a/gn2/tests/unit/wqflask/show_trait/test_export_trait_data.py b/gn2/tests/unit/wqflask/show_trait/test_export_trait_data.py
index a933d0bf..1ecf394b 100644
--- a/gn2/tests/unit/wqflask/show_trait/test_export_trait_data.py
+++ b/gn2/tests/unit/wqflask/show_trait/test_export_trait_data.py
@@ -16,9 +16,9 @@ class AttributesSetter:
 class TestExportTraits(unittest.TestCase):
     """Test methods for exporting traits and metadata"""
 
-    @mock.patch("wqflask.show_trait.export_trait_data.datetime")
-    @mock.patch("wqflask.show_trait.export_trait_data.create_trait")
-    @mock.patch("wqflask.show_trait.export_trait_data.data_set")
+    @mock.patch("gn2.wqflask.show_trait.export_trait_data.datetime")
+    @mock.patch("gn2.wqflask.show_trait.export_trait_data.create_trait")
+    @mock.patch("gn2.wqflask.show_trait.export_trait_data.data_set")
     def test_get_export_metadata(self, data_mock, trait_mock, date_mock):
         """test for exporting metadata with dataset.type=Publish"""
         mock_dataset = AttributesSetter({"type": "Publish",
diff --git a/gn2/tests/unit/wqflask/snp_browser/test_snp_browser.py b/gn2/tests/unit/wqflask/snp_browser/test_snp_browser.py
index c33f46ef..bf0421c0 100644
--- a/gn2/tests/unit/wqflask/snp_browser/test_snp_browser.py
+++ b/gn2/tests/unit/wqflask/snp_browser/test_snp_browser.py
@@ -102,7 +102,7 @@ class TestSnpBrowser(unittest.TestCase):
         self.assertEqual(expected_results, results_with_snp)
         self.assertEqual(expected_results_with_indel, results_with_indel)
 
-    @mock.patch("wqflask.snp_browser.snp_browser.database_connection")
+    @mock.patch("gn2.wqflask.snp_browser.snp_browser.database_connection")
     def test_get_gene_id(self, mock_db):
         db_query_value = (
             "SELECT geneId FROM GeneList WHERE " "SpeciesId = %s AND geneSymbol = %s"
@@ -122,7 +122,7 @@ class TestSnpBrowser(unittest.TestCase):
             )
             self.assertEqual(results, "517d729f-aa13-4413-a885-40a3f7ff768a")
 
-    @mock.patch("wqflask.snp_browser.snp_browser.database_connection")
+    @mock.patch("gn2.wqflask.snp_browser.snp_browser.database_connection")
     def test_gene_id_name_dict(self, mock_db):
         no_gene_names = []
         conn = mock.MagicMock()
@@ -164,7 +164,7 @@ class TestSnpBrowser(unittest.TestCase):
             self.assertEqual(results_found, expected_found)
             self.assertEqual(no_results, {})
 
-    @mock.patch("wqflask.snp_browser.snp_browser.database_connection")
+    @mock.patch("gn2.wqflask.snp_browser.snp_browser.database_connection")
     def test_check_if_in_gene(self, mock_db):
         conn = mock.MagicMock()
         mock_db.return_value.__enter__.return_value = conn
@@ -196,7 +196,7 @@ class TestSnpBrowser(unittest.TestCase):
             )
             self.assertEqual(gene_not_found, "")
 
-    @mock.patch("wqflask.snp_browser.snp_browser.database_connection")
+    @mock.patch("gn2.wqflask.snp_browser.snp_browser.database_connection")
     def test_get_browser_sample_lists(self, mock_db):
         conn = mock.MagicMock()
         mock_db.return_value.__enter__.return_value = conn
diff --git a/gn2/tests/unit/wqflask/test_collect.py b/gn2/tests/unit/wqflask/test_collect.py
index 41d6bf74..6c1bafa5 100644
--- a/gn2/tests/unit/wqflask/test_collect.py
+++ b/gn2/tests/unit/wqflask/test_collect.py
@@ -42,7 +42,7 @@ class TestCollect(unittest.TestCase):
     def tearDown(self):
         self.app_context.pop()
 
-    @mock.patch("wqflask.collect.g", MockFlaskG())
+    @mock.patch("gn2.wqflask.collect.g", MockFlaskG())
     def test_process_traits_with_bytestring(self):
         """
         Test that the correct traits are returned when the user is logged
@@ -58,7 +58,7 @@ class TestCollect(unittest.TestCase):
                  '1452447_at:HC_M2_0606_P',
                  '1452452_at:HC_M2_0606_P']))
 
-    @mock.patch("wqflask.collect.g", MockFlaskG())
+    @mock.patch("gn2.wqflask.collect.g", MockFlaskG())
     def test_process_traits_with_normal_string(self):
         """
         Test that the correct traits are returned when the user is logged
diff --git a/gn2/tests/unit/wqflask/test_resource_manager.py b/gn2/tests/unit/wqflask/test_resource_manager.py
index f4335425..a4b3a0ee 100644
--- a/gn2/tests/unit/wqflask/test_resource_manager.py
+++ b/gn2/tests/unit/wqflask/test_resource_manager.py
@@ -58,7 +58,7 @@ class TestGetUserMembership(unittest.TestCase):
 class TestCheckUserAccessRole(unittest.TestCase):
     """Test cases for `get_highest_user_access_role`"""
 
-    @mock.patch("wqflask.resource_manager.requests.get")
+    @mock.patch("gn2.wqflask.resource_manager.requests.get")
     def test_edit_access(self, requests_mock):
         """Test that the right access roles are set"""
         response = mock.PropertyMock(return_value=json.dumps(
@@ -76,7 +76,7 @@ class TestCheckUserAccessRole(unittest.TestCase):
              "metadata": DataRole.EDIT,
              "admin": AdminRole.EDIT_ACCESS})
 
-    @mock.patch("wqflask.resource_manager.requests.get")
+    @mock.patch("gn2.wqflask.resource_manager.requests.get")
     def test_no_access(self, requests_mock):
         response = mock.PropertyMock(return_value=json.dumps(
             {