Fix pylint errors in unit_tests

2 files changed, 189 insertions, 135 deletions

diff --git a/tests/unit/db/test_sample_data.py b/tests/unit/db/test_sample_data.py
index 0fa2604..2524e07 100644
--- a/tests/unit/db/test_sample_data.py
+++ b/tests/unit/db/test_sample_data.py
@@ -1,3 +1,4 @@
+"""Tests for gn3.db.sample_data"""
 import pytest
 import gn3
 
@@ -9,132 +10,179 @@ from gn3.db.sample_data import update_sample_data
 
 @pytest.mark.unit_test
 def test_insert_sample_data(mocker):
+    """Test that inserts work properly"""
     mock_conn = mocker.MagicMock()
     strain_id, data_id, inbredset_id = 1, 17373, 20
     with mock_conn.cursor() as cursor:
-        cursor.fetchone.side_effect = (0, [19, ], 0)
-        mocker.patch('gn3.db.sample_data.get_sample_data_ids',
-                     return_value=(strain_id, data_id, inbredset_id))
-        insert_sample_data(conn=mock_conn,
-                           trait_name=35,
-                           data="BXD1,18,3,0,M",
-                           csv_header="Strain Name,Value,SE,Count,Sex",
-                           phenotype_id=10007)
-        calls = [mocker.call("SELECT Id FROM PublishData where Id = %s "
-                             "AND StrainId = %s",
-                             (data_id, strain_id)),
-                 mocker.call("INSERT INTO PublishData "
-                             "(StrainId, Id, value) VALUES (%s, %s, %s)",
-                             (strain_id, data_id, '18')),
-                 mocker.call("INSERT INTO PublishSE "
-                             "(StrainId, DataId, error) VALUES (%s, %s, %s)",
-                             (strain_id, data_id, '3')),
-                 mocker.call("INSERT INTO NStrain "
-                             "(StrainId, DataId, count) VALUES (%s, %s, %s)",
-                             (strain_id, data_id, '0')),
-                 mocker.call("SELECT Id FROM CaseAttribute WHERE Name = %s",
-                             ("Sex",)),
-                 mocker.call("SELECT StrainId FROM CaseAttributeXRefNew "
-                             "WHERE StrainId = %s AND "
-                             "CaseAttributeId = %s AND InbredSetId = %s",
-                             (strain_id, 19, inbredset_id)),
-                 mocker.call("INSERT INTO CaseAttributeXRefNew "
-                             "(StrainId, CaseAttributeId, Value, "
-                             "InbredSetId) VALUES (%s, %s, %s, %s)",
-                             (strain_id, 19, 'M', inbredset_id))
-                 ]
+        cursor.fetchone.side_effect = (
+            0,
+            [
+                19,
+            ],
+            0,
+        )
+        mocker.patch(
+            "gn3.db.sample_data.get_sample_data_ids",
+            return_value=(strain_id, data_id, inbredset_id),
+        )
+        insert_sample_data(
+            conn=mock_conn,
+            trait_name=35,
+            data="BXD1,18,3,0,M",
+            csv_header="Strain Name,Value,SE,Count,Sex",
+            phenotype_id=10007,
+        )
+        calls = [
+            mocker.call(
+                "SELECT Id FROM PublishData where Id = %s " "AND StrainId = %s",
+                (data_id, strain_id),
+            ),
+            mocker.call(
+                "INSERT INTO PublishData " "(StrainId, Id, value) VALUES (%s, %s, %s)",
+                (strain_id, data_id, "18"),
+            ),
+            mocker.call(
+                "INSERT INTO PublishSE "
+                "(StrainId, DataId, error) VALUES (%s, %s, %s)",
+                (strain_id, data_id, "3"),
+            ),
+            mocker.call(
+                "INSERT INTO NStrain " "(StrainId, DataId, count) VALUES (%s, %s, %s)",
+                (strain_id, data_id, "0"),
+            ),
+            mocker.call("SELECT Id FROM CaseAttribute WHERE Name = %s", ("Sex",)),
+            mocker.call(
+                "SELECT StrainId FROM CaseAttributeXRefNew "
+                "WHERE StrainId = %s AND "
+                "CaseAttributeId = %s AND InbredSetId = %s",
+                (strain_id, 19, inbredset_id),
+            ),
+            mocker.call(
+                "INSERT INTO CaseAttributeXRefNew "
+                "(StrainId, CaseAttributeId, Value, "
+                "InbredSetId) VALUES (%s, %s, %s, %s)",
+                (strain_id, 19, "M", inbredset_id),
+            ),
+        ]
         cursor.execute.assert_has_calls(calls, any_order=False)
 
 
 @pytest.mark.unit_test
 def test_delete_sample_data(mocker):
+    """Test that deletes work properly"""
     mock_conn = mocker.MagicMock()
     strain_id, data_id, inbredset_id = 1, 17373, 20
     with mock_conn.cursor() as cursor:
-        cursor.fetchone.side_effect = (0, [19, ], 0)
-        mocker.patch('gn3.db.sample_data.get_sample_data_ids',
-                     return_value=(strain_id, data_id, inbredset_id))
-        delete_sample_data(conn=mock_conn,
-                           trait_name=35,
-                           data="BXD1,18,3,0,M",
-                           csv_header="Strain Name,Value,SE,Count,Sex",
-                           phenotype_id=10007)
-        calls = [mocker.call("DELETE FROM PublishData WHERE "
-                             "StrainId = %s AND Id = %s",
-                             (strain_id, data_id)),
-                 mocker.call("DELETE FROM PublishSE WHERE "
-                             "StrainId = %s AND DataId = %s",
-                             (strain_id, data_id)),
-                 mocker.call("DELETE FROM NStrain WHERE "
-                             "StrainId = %s AND DataId = %s",
-                             (strain_id, data_id)),
-                 mocker.call("DELETE FROM CaseAttributeXRefNew WHERE "
-                             "StrainId = %s AND CaseAttributeId = "
-                             "(SELECT CaseAttributeId FROM "
-                             "CaseAttribute WHERE Name = %s) "
-                             "AND InbredSetId = %s",
-                             (strain_id, "Sex", inbredset_id)),
-                 ]
+        cursor.fetchone.side_effect = (
+            0,
+            [
+                19,
+            ],
+            0,
+        )
+        mocker.patch(
+            "gn3.db.sample_data.get_sample_data_ids",
+            return_value=(strain_id, data_id, inbredset_id),
+        )
+        delete_sample_data(
+            conn=mock_conn,
+            trait_name=35,
+            data="BXD1,18,3,0,M",
+            csv_header="Strain Name,Value,SE,Count,Sex",
+            phenotype_id=10007,
+        )
+        calls = [
+            mocker.call(
+                "DELETE FROM PublishData WHERE " "StrainId = %s AND Id = %s",
+                (strain_id, data_id),
+            ),
+            mocker.call(
+                "DELETE FROM PublishSE WHERE " "StrainId = %s AND DataId = %s",
+                (strain_id, data_id),
+            ),
+            mocker.call(
+                "DELETE FROM NStrain WHERE " "StrainId = %s AND DataId = %s",
+                (strain_id, data_id),
+            ),
+            mocker.call(
+                "DELETE FROM CaseAttributeXRefNew WHERE "
+                "StrainId = %s AND CaseAttributeId = "
+                "(SELECT CaseAttributeId FROM "
+                "CaseAttribute WHERE Name = %s) "
+                "AND InbredSetId = %s",
+                (strain_id, "Sex", inbredset_id),
+            ),
+        ]
         cursor.execute.assert_has_calls(calls, any_order=False)
 
 
 @pytest.mark.unit_test
 def test_extract_actions():
-    assert (__extract_actions(original_data="BXD1,18,x,0,x",
-                              updated_data="BXD1,x,2,1,F",
-                              csv_header="Strain Name,Value,SE,Count,Sex") ==
-            {
-                "delete": {"data": "BXD1,18",
-                           "csv_header": "Strain Name,Value"},
-                "insert": {"data": "BXD1,2,F",
-                           "csv_header": "Strain Name,SE,Sex"},
-                "update": {"data": "BXD1,1",
-                           "csv_header": "Strain Name,Count"},
-    })
-    assert(__extract_actions(original_data="BXD1,18,x,0,x",
-                             updated_data="BXD1,19,2,1,F",
-                             csv_header="Strain Name,Value,SE,Count,Sex") ==
-           {
-               "delete": None,
-               "insert": {"data": "BXD1,2,F",
-                          "csv_header": "Strain Name,SE,Sex"},
-               "update": {"data": "BXD1,19,1",
-                          "csv_header": "Strain Name,Value,Count"},
-    })
+    """Test that extracting the correct dict of 'actions' work properly"""
+    assert __extract_actions(
+        original_data="BXD1,18,x,0,x",
+        updated_data="BXD1,x,2,1,F",
+        csv_header="Strain Name,Value,SE,Count,Sex",
+    ) == {
+        "delete": {"data": "BXD1,18", "csv_header": "Strain Name,Value"},
+        "insert": {"data": "BXD1,2,F", "csv_header": "Strain Name,SE,Sex"},
+        "update": {"data": "BXD1,1", "csv_header": "Strain Name,Count"},
+    }
+    assert __extract_actions(
+        original_data="BXD1,18,x,0,x",
+        updated_data="BXD1,19,2,1,F",
+        csv_header="Strain Name,Value,SE,Count,Sex",
+    ) == {
+        "delete": None,
+        "insert": {"data": "BXD1,2,F", "csv_header": "Strain Name,SE,Sex"},
+        "update": {"data": "BXD1,19,1", "csv_header": "Strain Name,Value,Count"},
+    }
 
 
 @pytest.mark.unit_test
 def test_update_sample_data(mocker):
+    """Test that updates work properly"""
     mock_conn = mocker.MagicMock()
     strain_id, data_id, inbredset_id = 1, 17373, 20
     with mock_conn.cursor() as cursor:
         # cursor.fetchone.side_effect = (0, [19, ], 0)
-        mocker.patch('gn3.db.sample_data.get_sample_data_ids',
-                     return_value=(strain_id, data_id, inbredset_id))
-        mocker.patch('gn3.db.sample_data.insert_sample_data',
-                     return_value=1)
-        mocker.patch('gn3.db.sample_data.delete_sample_data',
-                     return_value=1)
-        update_sample_data(conn=mock_conn,
-                           trait_name=35,
-                           original_data="BXD1,18,x,0,x",
-                           updated_data="BXD1,x,2,1,F",
-                           csv_header="Strain Name,Value,SE,Count,Sex",
-                           phenotype_id=10007)
+        mocker.patch(
+            "gn3.db.sample_data.get_sample_data_ids",
+            return_value=(strain_id, data_id, inbredset_id),
+        )
+        mocker.patch("gn3.db.sample_data.insert_sample_data", return_value=1)
+        mocker.patch("gn3.db.sample_data.delete_sample_data", return_value=1)
+        update_sample_data(
+            conn=mock_conn,
+            trait_name=35,
+            original_data="BXD1,18,x,0,x",
+            updated_data="BXD1,x,2,1,F",
+            csv_header="Strain Name,Value,SE,Count,Sex",
+            phenotype_id=10007,
+        )
+        # pylint: disable=[E1101]
         gn3.db.sample_data.insert_sample_data.assert_called_once_with(
             conn=mock_conn,
             trait_name=35,
             data="BXD1,2,F",
             csv_header="Strain Name,SE,Sex",
-            phenotype_id=10007)
+            phenotype_id=10007,
+        )
+        # pylint: disable=[E1101]
         gn3.db.sample_data.delete_sample_data.assert_called_once_with(
             conn=mock_conn,
             trait_name=35,
             data="BXD1,18",
             csv_header="Strain Name,Value",
-            phenotype_id=10007)
+            phenotype_id=10007,
+        )
         cursor.execute.assert_has_calls(
-            [mocker.call("UPDATE NStrain SET count = %s "
-                         "WHERE StrainId = %s AND DataId = %s",
-                         ('1', strain_id, data_id))],
-            any_order=False)
+            [
+                mocker.call(
+                    "UPDATE NStrain SET count = %s "
+                    "WHERE StrainId = %s AND DataId = %s",
+                    ("1", strain_id, data_id),
+                )
+            ],
+            any_order=False,
+        )
diff --git a/tests/unit/test_csvcmp.py b/tests/unit/test_csvcmp.py
index 3c9ba33..c7ffe2f 100644
--- a/tests/unit/test_csvcmp.py
+++ b/tests/unit/test_csvcmp.py
@@ -1,13 +1,15 @@
+"""Tests for gn3.csvcmp"""
+import pytest
+
 from gn3.csvcmp import csv_diff
 from gn3.csvcmp import fill_csv
 from gn3.csvcmp import remove_insignificant_edits
 from gn3.csvcmp import extract_strain_name
 
-import pytest
-
 
 @pytest.mark.unit_test
 def test_fill_csv():
+    """Test that filling a csv works properly"""
     test_input = """
 Strain Name,Value,SE,Count,Sex
 BXD1,18,x,0,
@@ -20,45 +22,47 @@ BXD1,18,x,0,x
 BXD12,16,x,x,x
 BXD14,15,x,x,x
 BXD15,14,x,x,x"""
-    assert(fill_csv(test_input, width=5, value="x") == expected_output)
+    assert fill_csv(test_input, width=5, value="x") == expected_output
+
 
 @pytest.mark.unit_test
 def test_remove_insignificant_data():
+    """Test that values outside ε are removed/ ignored"""
     diff_data = {
-        'Additions': [],
-        'Deletions': [],
-        'Modifications': [
-            {'Current': '1.000001,3', 'Original': '1,3'},
-            {'Current': '1,3', 'Original': '1.000001,3'},
-            {'Current': '2.000001,3', 'Original': '2,2'},
-            {'Current': '1.01,3', 'Original': '1,2'}
-        ]
+        "Additions": [],
+        "Deletions": [],
+        "Modifications": [
+            {"Current": "1.000001,3", "Original": "1,3"},
+            {"Current": "1,3", "Original": "1.000001,3"},
+            {"Current": "2.000001,3", "Original": "2,2"},
+            {"Current": "1.01,3", "Original": "1,2"},
+        ],
     }
     expected_json = {
-        'Additions': [],
-        'Deletions': [],
-        'Modifications': [
-            {'Current': '2,3', 'Original': '2,2'},
-            {'Current': '1.01,3', 'Original': '1,2'}
-        ]
+        "Additions": [],
+        "Deletions": [],
+        "Modifications": [
+            {"Current": "2,3", "Original": "2,2"},
+            {"Current": "1.01,3", "Original": "1,2"},
+        ],
     }
-    assert (remove_insignificant_edits(diff_data) ==
-            expected_json)
+    assert remove_insignificant_edits(diff_data) == expected_json
 
 
 @pytest.mark.unit_test
 def test_csv_diff_same_columns():
-    assert(csv_diff(base_csv="a,b\n1,2\n",
-                    delta_csv="a,b\n1,3") == {
-                        'Additions': [],
-                        'Deletions': [],
-                        'Columns': '',
-                        'Modifications': [{'Current': '1,3',
-                                           'Original': '1,2'}]})
+    """Test csv diffing on data with the same number of columns"""
+    assert csv_diff(base_csv="a,b\n1,2\n", delta_csv="a,b\n1,3") == {
+        "Additions": [],
+        "Deletions": [],
+        "Columns": "",
+        "Modifications": [{"Current": "1,3", "Original": "1,2"}],
+    }
 
 
 @pytest.mark.unit_test
 def test_csv_diff_different_columns():
+    """Test csv diffing on data with different columns"""
     base_csv = """
 Strain Name,Value,SE,Count
 BXD1,18,x,0
@@ -71,17 +75,17 @@ BXD1,18,x,0
 BXD12,16,x,x,1
 BXD14,15,x,x
 BXD15,14,x,x"""
-    assert(csv_diff(base_csv=base_csv,
-                    delta_csv=delta_csv) == {
-                        'Additions': [],
-                        'Columns': 'Strain Name,Value,SE,Count,Sex',
-                        'Deletions': [],
-                        'Modifications': [{'Current': 'BXD12,16,x,x,1',
-                                           'Original': 'BXD12,16,x,x,x'}]})
+    assert csv_diff(base_csv=base_csv, delta_csv=delta_csv) == {
+        "Additions": [],
+        "Columns": "Strain Name,Value,SE,Count,Sex",
+        "Deletions": [],
+        "Modifications": [{"Current": "BXD12,16,x,x,1", "Original": "BXD12,16,x,x,x"}],
+    }
 
 
 @pytest.mark.unit_test
 def test_csv_diff_only_column_change():
+    """Test csv diffing when only the column header change"""
     base_csv = """
 Strain Name,Value,SE,Count
 BXD1,18,x,0
@@ -95,15 +99,17 @@ BXD12,16,x,x
 BXD14,15,x,x
 BXD15,14,x,x
 """
-    assert(csv_diff(base_csv=base_csv,
-                    delta_csv=delta_csv) == {
-                        'Additions': [],
-                        'Deletions': [],
-                        'Modifications': []})
+    assert csv_diff(base_csv=base_csv, delta_csv=delta_csv) == {
+        "Additions": [],
+        "Deletions": [],
+        "Modifications": [],
+    }
 
 
 @pytest.mark.unit_test
 def test_extract_strain_name():
-    assert(extract_strain_name(csv_header="Strain Name,Value,SE,Count",
-                               data="BXD1,18,x,0") ==
-           "BXD1")
+    """Test that the strain's name is extracted given a csv header"""
+    assert (
+        extract_strain_name(csv_header="Strain Name,Value,SE,Count", data="BXD1,18,x,0")
+        == "BXD1"
+    )