diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/tests/unit/base/test_trait.py | 28 | ||||
| -rw-r--r-- | wqflask/tests/wqflask/show_trait/test_show_trait.py | 68 |
2 files changed, 56 insertions, 40 deletions
diff --git a/wqflask/tests/unit/base/test_trait.py b/wqflask/tests/unit/base/test_trait.py index 71fe0a44..e8c01ca9 100644 --- a/wqflask/tests/unit/base/test_trait.py +++ b/wqflask/tests/unit/base/test_trait.py @@ -3,7 +3,6 @@ import unittest from unittest import mock -from wqflask import app from base.trait import GeneralTrait from base.trait import retrieve_trait_info @@ -32,25 +31,24 @@ class MockTrait(GeneralTrait): class TestRetrieveTraitInfo(unittest.TestCase): """Tests for 'retrieve_trait_info'""" - - def setUp(self): - self.app_context = app.app_context() - self.app_context.push() - - def tearDown(self): - self.app_context.pop() - - def test_retrieve_trait_info_with_empty_dataset(self): + @mock.patch('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""" - with self.assertRaises(AssertionError): + conn = mock.MagicMock() + mock_db.return_value.__enter__.return_value = conn + with self.assertRaises(ValueError): 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') def test_retrieve_trait_info_with_empty_trait_info(self, + mock_db, requests_mock): """Empty trait info""" + conn = mock.MagicMock() + mock_db.return_value.__enter__.return_value = conn requests_mock.return_value = TestNilResponse() with self.assertRaises(KeyError): retrieve_trait_info(trait=mock.MagicMock(), @@ -58,10 +56,14 @@ class TestRetrieveTraitInfo(unittest.TestCase): @mock.patch('base.trait.requests.get') @mock.patch('base.trait.g', mock.Mock()) + @mock.patch('base.trait.database_connection') def test_retrieve_trait_info_with_non_empty_trait_info(self, + mock_db, requests_mock): """Test that attributes are set""" mock_dataset = mock.MagicMock() + conn = mock.MagicMock() + mock_db.return_value.__enter__.return_value = conn requests_mock.return_value = TestResponse() type(mock_dataset).display_fields = mock.PropertyMock( return_value=["a", "b", "c", "d"]) @@ -74,10 +76,14 @@ class TestRetrieveTraitInfo(unittest.TestCase): @mock.patch('base.trait.requests.get') @mock.patch('base.trait.g', mock.Mock()) + @mock.patch('base.trait.database_connection') def test_retrieve_trait_info_utf8_parsing(self, + mock_db, requests_mock): """Test that utf-8 strings are parsed correctly""" utf_8_string = "test_string" + conn = mock.MagicMock() + mock_db.return_value.__enter__.return_value = conn mock_dataset = mock.MagicMock() requests_mock.return_value = TestResponse() type(mock_dataset).display_fields = mock.PropertyMock( diff --git a/wqflask/tests/wqflask/show_trait/test_show_trait.py b/wqflask/tests/wqflask/show_trait/test_show_trait.py index 5f4598f5..6a6b1587 100644 --- a/wqflask/tests/wqflask/show_trait/test_show_trait.py +++ b/wqflask/tests/wqflask/show_trait/test_show_trait.py @@ -143,39 +143,49 @@ class TestTraits(unittest.TestCase): self.assertEqual(results, "this is a descriptionN/A") self.assertEqual(results_no_unit, "Value") - @mock.patch("wqflask.show_trait.show_trait.g") + @mock.patch("wqflask.show_trait.show_trait.database_connection") def test_get_nearest_marker(self, mock_db): """test for getting nearest marker with non-empty db""" - - mock_db.db.execute.return_value.fetchall.return_value = [ - ["Geno1", "Geno2"], ["Geno3"]] - - trait = TraitObject({"locus_chr": "test_chr", "locus_mb": "test_mb"}) - group_name = TraitObject({"name": "group_name"}) - this_db = TraitObject({"group": group_name}) - results_with_item_db = get_nearest_marker(trait, this_db) - called_with_value = """SELECT Geno.Name - FROM Geno, GenoXRef, GenoFreeze - WHERE Geno.Chr = 'test_chr' AND - GenoXRef.GenoId = Geno.Id AND - GenoFreeze.Id = GenoXRef.GenoFreezeId AND - GenoFreeze.Name = 'group_nameGeno' - ORDER BY ABS( Geno.Mb - test_mb) LIMIT 1""" - - mock_db.db.execute.assert_called_with(called_with_value) - - self.assertEqual(results_with_item_db, "Geno1") - - @mock.patch("wqflask.show_trait.show_trait.g") + conn = mock.MagicMock() + mock_db.return_value.__enter__.return_value = conn + with conn.cursor() as cursor: + cursor.fetchall.return_value = [ + ["Geno1", "Geno2"], ["Geno3"]] + + trait = TraitObject({ + "locus_chr": "test_chr", + "locus_mb": "test_mb" + }) + group_name = TraitObject({"name": "group_name"}) + this_db = TraitObject({"group": group_name}) + results_with_item_db = get_nearest_marker(trait, this_db) + cursor.execute.assert_called_with( + "SELECT Geno.Name FROM Geno, GenoXRef, " + "GenoFreeze WHERE Geno.Chr = %s " + "AND GenoXRef.GenoId = Geno.Id AND " + "GenoFreeze.Id = GenoXRef.GenoFreezeId " + "AND GenoFreeze.Name = %s " + "ORDER BY ABS( Geno.Mb - %s) LIMIT 1", + ('test_chr', 'group_nameGeno', 'test_mb')) + + self.assertEqual(results_with_item_db, "Geno1") + + @mock.patch("wqflask.show_trait.show_trait.database_connection") def test_get_nearest_marker_empty_db(self, mock_db): """test for getting nearest marker with empty db""" - mock_db.db.execute.return_value.fetchall.return_value = [] - trait = TraitObject({"locus_chr": "test_chr", "locus_mb": "test_mb"}) - group_name = TraitObject({"name": "group_name"}) - this_db = TraitObject({"group": group_name}) - results_empty_db = get_nearest_marker(trait, this_db) - mock_db.db.execute.assert_called_once() - self.assertEqual(results_empty_db, "") + conn = mock.MagicMock() + mock_db.return_value.__enter__.return_value = conn + with conn.cursor() as cursor: + cursor.fetchall.return_value = [] + trait = TraitObject({ + "locus_chr": "test_chr", + "locus_mb": "test_mb" + }) + group_name = TraitObject({"name": "group_name"}) + this_db = TraitObject({"group": group_name}) + results_empty_db = get_nearest_marker(trait, this_db) + cursor.execute.assert_called_once() + self.assertEqual(results_empty_db, "") @mock.patch("wqflask.show_trait.show_trait.get_scales_from_genofile") def test_get_genotype_scales_with_genofile_is_list(self, mock_get_scales): |