Remove test cases related to sample data

Most of this functions were moved to their own module.

1 files changed, 0 insertions, 195 deletions

diff --git a/tests/unit/db/test_traits.py b/tests/unit/db/test_traits.py
index a1c1136..434f758 100644
--- a/tests/unit/db/test_traits.py
+++ b/tests/unit/db/test_traits.py
@@ -5,9 +5,7 @@ from gn3.db.traits import (
     build_trait_name,
     export_trait_data,
     export_informative,
-    get_trait_csv_sample_data,
     set_haveinfo_field,
-    update_sample_data,
     retrieve_trait_info,
     set_confidential_field,
     set_homologene_id_field,
@@ -203,56 +201,6 @@ class TestTraitsDBFunctions(TestCase):
                         expected)
 
     @pytest.mark.unit_test
-    def test_update_sample_data(self):
-        """Test that the SQL queries when calling update_sample_data are called with
-        the right calls.
-
-        """
-        # pylint: disable=C0103
-        db_mock = mock.MagicMock()
-        PUBLISH_DATA_SQL: str = (
-            "UPDATE PublishData SET value = %s "
-            "WHERE StrainId = %s AND Id = %s")
-        PUBLISH_SE_SQL: str = (
-            "UPDATE PublishSE SET error = %s "
-            "WHERE StrainId = %s AND DataId = %s")
-        N_STRAIN_SQL: str = (
-            "UPDATE NStrain SET count = %s "
-            "WHERE StrainId = %s AND DataId = %s")
-
-        with db_mock.cursor() as cursor:
-            type(cursor).rowcount = 1
-            mock_fetchone = mock.MagicMock()
-            mock_fetchone.return_value = (1, 1)
-            type(cursor).fetchone = mock_fetchone
-            self.assertEqual(update_sample_data(
-                conn=db_mock, strain_name="BXD11",
-                trait_name="1",
-                phenotype_id=10, value=18.7,
-                error=2.3, count=2),
-                             (1, 1, 1))
-            cursor.execute.assert_has_calls(
-                [mock.call(('SELECT Strain.Id, PublishData.Id FROM'
-                            ' (PublishData, Strain, PublishXRef, '
-                            'PublishFreeze) LEFT JOIN PublishSE ON '
-                            '(PublishSE.DataId = PublishData.Id '
-                            'AND PublishSE.StrainId = '
-                            'PublishData.StrainId) LEFT JOIN NStrain ON '
-                            '(NStrain.DataId = PublishData.Id AND '
-                            'NStrain.StrainId = PublishData.StrainId) WHERE '
-                            'PublishXRef.InbredSetId = '
-                            'PublishFreeze.InbredSetId AND PublishData.Id = '
-                            'PublishXRef.DataId AND PublishXRef.Id = %s AND '
-                            'PublishXRef.PhenotypeId = %s AND '
-                            'PublishData.StrainId = Strain.Id AND '
-                            'Strain.Name = %s'),
-                           ("1", 10, "BXD11")),
-                 mock.call(PUBLISH_DATA_SQL, (18.7, 1, 1)),
-                 mock.call(PUBLISH_SE_SQL, (2.3, 1, 1)),
-                 mock.call(N_STRAIN_SQL, (2, 1, 1))]
-            )
-
-    @pytest.mark.unit_test
     def test_set_haveinfo_field(self):
         """Test that the `haveinfo` field is set up correctly"""
         for trait_info, expected in [
@@ -432,146 +380,3 @@ class TestTraitsDBFunctions(TestCase):
             with self.subTest(trait_data=trait_data):
                 self.assertEqual(
                     export_informative(trait_data, inc_var), expected)
-
-
-class TestRetrieveCsvData(TestCase):
-    "Test cases for retrieving csv data"
-    def test_get_trait_csv_sample_data_with_case_attributes(self):
-        """Test that correct csv is returned when all samples have case attribute
-values"""
-        mock_conn = mock.MagicMock()
-        with mock_conn.cursor() as cursor:
-            cursor.fetchall.return_value = [
-                ['H1044,25.900000,x,1', 'Strain', 'BXD29'],
-                ['H1044,25.900000,x,1', 'Condition', 'CD'],
-                ['H1044,25.900000,x,1', 'EarTag', 1044],
-                ['H1044,25.900000,x,1', 'Age', 724],
-                ['H1096,23.700001,x,1', 'EarTag', 1096],
-                ['H1096,23.700001,x,1', 'Age', 732],
-                ['H1096,23.700001,x,1', 'Strain', 'BXD90'],
-                ['H1096,23.700001,x,1', 'Condition', 'CD'],
-                ['H1163,95.000000,x,1', 'Strain', 'D2B6F1'],
-                ['H1163,95.000000,x,1', 'Condition', 'HF'],
-                ['H1163,95.000000,x,1', 'EarTag', 1163],
-                ['H1163,95.000000,x,1', 'Age', 1114],
-                ['H1230,88.099998,x,1', 'EarTag', 1230],
-                ['H1230,88.099998,x,1', 'Age', 726],
-                ['H1230,88.099998,x,1', 'Strain', 'B6D2F1'],
-                ['H1230,88.099998,x,1', 'Condition', 'HF'],
-                ['H1251,24.100000,x,1', 'EarTag', 1251],
-                ['H1251,24.100000,x,1', 'Age', 711],
-                ['H1251,24.100000,x,1', 'Strain', 'C57BL/6J'],
-                ['H1251,24.100000,x,1', 'Condition', 'CD'],
-                ['H1292,24.900000,x,1', 'Strain', 'C57BL/6J'],
-                ['H1292,24.900000,x,1', 'Condition', 'CD'],
-                ['H1292,24.900000,x,1', 'EarTag', 1292],
-                ['H1292,24.900000,x,1', 'Age', 705],
-            ]
-        csv = get_trait_csv_sample_data(conn=mock_conn,
-                                        trait_name=10006,
-                                        phenotype_id=28409)
-        self.assertEqual(csv, """Strain Name,Value,SE,Count,Age,Condition,EarTag,Strain
-H1044,25.900000,x,1,724,CD,1044,BXD29
-H1096,23.700001,x,1,732,CD,1096,BXD90
-H1163,95.000000,x,1,1114,HF,1163,D2B6F1
-H1230,88.099998,x,1,726,HF,1230,B6D2F1
-H1251,24.100000,x,1,711,CD,1251,C57BL/6J
-H1292,24.900000,x,1,705,CD,1292,C57BL/6J
-""")
-
-    def test_get_trait_csv_sample_data_with_missing_case_attributes(self):
-        """Test that the correct csv is returned when some case attributes are not
-present from some samples"""
-        mock_conn = mock.MagicMock()
-        with mock_conn.cursor() as cursor:
-            cursor.fetchall.return_value = [
-                ['H1044,25.900000,x,1', 'Strain', 'BXD29'],
-                ['H1044,25.900000,x,1', 'Condition', 'CD'],
-                ['H1044,25.900000,x,1', 'Age', 724],
-                ['H1096,23.700001,x,1', 'Age', 732],
-                ['H1096,23.700001,x,1', 'Strain', 'BXD90'],
-                ['H1096,23.700001,x,1', 'Condition', 'CD'],
-                ['H1163,95.000000,x,1', 'Condition', 'HF'],
-                ['H1163,95.000000,x,1', 'EarTag', 1163],
-                ['H1163,95.000000,x,1', 'Age', 1114],
-                ['H1230,88.099998,x,1', 'EarTag', 1230],
-                ['H1230,88.099998,x,1', 'Age', 726],
-                ['H1230,88.099998,x,1', 'Strain', 'B6D2F1'],
-                ['H1230,88.099998,x,1', 'Condition', 'HF'],
-                ['H1251,24.100000,x,1', 'EarTag', 1251],
-                ['H1251,24.100000,x,1', 'Age', 711],
-                ['H1251,24.100000,x,1', 'Strain', 'C57BL/6J'],
-                ['H1251,24.100000,x,1', 'Condition', 'CD'],
-                ['H1292,24.900000,x,1', 'Strain', 'C57BL/6J'],
-                ['H1292,24.900000,x,1', 'Condition', 'CD'],
-                ['H1292,24.900000,x,1', 'EarTag', 1292],
-            ]
-        csv = get_trait_csv_sample_data(conn=mock_conn,
-                                        trait_name=10006,
-                                        phenotype_id=28409)
-        self.assertEqual(csv, """Strain Name,Value,SE,Count,Age,Condition,EarTag,Strain
-H1044,25.900000,x,1,724,CD,x,BXD29
-H1096,23.700001,x,1,732,CD,x,BXD90
-H1163,95.000000,x,1,1114,HF,1163,x
-H1230,88.099998,x,1,726,HF,1230,B6D2F1
-H1251,24.100000,x,1,711,CD,1251,C57BL/6J
-H1292,24.900000,x,1,x,CD,1292,C57BL/6J
-""")
-
-    def test_get_trait_csv_sample_data_with_varying_case_attributes(self):
-        """Test that the correct csv is returned when case attributes are entirely
-missing from same samples, and only one sample has a case attribute that is
-not present in all other samples"""
-        mock_conn = mock.MagicMock()
-        with mock_conn.cursor() as cursor:
-            cursor.fetchall.return_value = [
-                ['H1044,25.900000,x,1', 'x', 'x'],
-                ['H1096,23.700001,x,1', 'x', 'x'],
-                ['H1163,95.000000,x,1', 'x', 'x'],
-                ['H1230,88.099998,x,1', 'x', 'x'],
-                ['H1251,24.100000,x,1', 'x', 'x'],
-                ['H1292,24.900000,x,1', 'x', 'x'],
-            ]
-        csv = get_trait_csv_sample_data(conn=mock_conn,
-                                        trait_name=10006,
-                                        phenotype_id=28409)
-        self.assertEqual(csv, """Strain Name,Value,SE,Count
-H1044,25.900000,x,1
-H1096,23.700001,x,1
-H1163,95.000000,x,1
-H1230,88.099998,x,1
-H1251,24.100000,x,1
-H1292,24.900000,x,1""")
-
-    def test_get_trait_csv_sample_data_with_empty_case_attributes(self):
-        mock_conn = mock.MagicMock()
-        with mock_conn.cursor() as cursor:
-            cursor.fetchall.return_value = [
-                ['H1044,25.900000,x,1', 'x', 'x'],
-                ['H1096,23.700001,x,1', 'Age', 732],
-                ['H1096,23.700001,x,1', 'Sex', "M"],
-                ['H1096,23.700001,x,1', 'Strain', 'BXD90'],
-                ['H1096,23.700001,x,1', 'Condition', 'CD'],
-                ['H1163,95.000000,x,1', 'Condition', 'HF'],
-                ['H1163,95.000000,x,1', 'EarTag', 1163],
-                ['H1163,95.000000,x,1', 'Age', 1114],
-                ['H1230,88.099998,x,1', 'EarTag', 1230],
-                ['H1230,88.099998,x,1', 'Age', 726],
-                ['H1230,88.099998,x,1', 'Strain', 'B6D2F1'],
-                ['H1230,88.099998,x,1', 'Condition', 'HF'],
-                ['H1251,24.100000,x,1', 'x', 'x'],
-                ['H1292,24.900000,x,1', 'Strain', 'C57BL/6J'],
-                ['H1292,24.900000,x,1', 'Condition', 'CD'],
-                ['H1292,24.900000,x,1', 'EarTag', 1292],
-            ]
-        csv = get_trait_csv_sample_data(conn=mock_conn,
-                                        trait_name=10006,
-                                        phenotype_id=28409)
-        self.assertEqual(csv, """Strain Name,Value,SE,Count,Age,Condition,EarTag,Sex,Strain
-H1044,25.900000,x,1,x,x,x,x,x
-H1096,23.700001,x,1,732,CD,x,M,BXD90
-H1163,95.000000,x,1,1114,HF,1163,x,x
-H1230,88.099998,x,1,726,HF,1230,x,B6D2F1
-H1251,24.100000,x,1,x,x,x,x,x
-H1292,24.900000,x,1,x,CD,1292,x,C57BL/6J
-""")