"""Tests for gn3.db.sample_data""" import pytest import gn3 from gn3.db.sample_data import __extract_actions from gn3.db.sample_data import delete_sample_data from gn3.db.sample_data import insert_sample_data 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, 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,Red,M", csv_header="Strain Name,Value,SE,Count,Color,Sex (13)", phenotype_id=10007, ) calls = [ mocker.call( "SELECT Id FROM PublishData where Id = %s AND StrainId = %s", (17373, 1), ), mocker.call( "INSERT INTO PublishData (StrainId, Id, value) " "VALUES (%s, %s, %s)", (1, 17373, "18"), ), mocker.call( "INSERT INTO PublishSE (StrainId, DataId, error) VALUES " "(%s, %s, %s)", (1, 17373, "3"), ), mocker.call( "INSERT INTO NStrain (StrainId, DataId, count) VALUES " "(%s, %s, %s)", (1, 17373, "0"), ), mocker.call( "SELECT Id FROM CaseAttribute WHERE Name = %s", ("Color",) ), mocker.call( "SELECT StrainId FROM CaseAttributeXRefNew WHERE " "StrainId = %s AND CaseAttributeId = %s AND InbredSetId = %s", (1, 19, 20), ), mocker.call( "INSERT INTO CaseAttributeXRefNew (StrainId, " "CaseAttributeId, Value, InbredSetId) VALUES " "(%s, %s, %s, %s)", (1, 19, "Red", 20), ), mocker.call( "SELECT StrainId FROM CaseAttributeXRefNew WHERE " "StrainId = %s AND CaseAttributeId = %s AND " "InbredSetId = %s", (1, "13", 20), ), mocker.call( "INSERT INTO CaseAttributeXRefNew (StrainId, " "CaseAttributeId, Value, InbredSetId) VALUES " "(%s, %s, %s, %s)", (1, "13", "M", 20), ), ] 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: 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,Red,M", csv_header="Strain Name,Value,SE,Count,Color,Sex (17)", 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, "Color", inbredset_id), ), mocker.call( "DELETE FROM CaseAttributeXRefNew WHERE " "StrainId = %s AND CaseAttributeId = %s " "AND InbredSetId = %s", (strain_id, "17", inbredset_id), ), ] cursor.execute.assert_has_calls(calls, any_order=False) @pytest.mark.unit_test def test_extract_actions(): """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: 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,M,x,Red", updated_data="BXD1,x,2,1,2,F,2,Green", csv_header="Strain Name,Value,SE,Count,pH,Sex (13),Age,Color", phenotype_id=10007, ) # pylint: disable=[E1101] gn3.db.sample_data.insert_sample_data.assert_called_once_with( conn=mock_conn, trait_name=35, data="BXD1,2,2,2", csv_header="Strain Name,SE,pH,Age", 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, ) cursor.execute.assert_has_calls( [ mocker.call( "UPDATE NStrain SET count = %s " "WHERE StrainId = %s AND DataId = %s", ("1", strain_id, data_id), ), mocker.call( "UPDATE CaseAttributeXRefNew SET Value = %s " "WHERE StrainId = %s AND CaseAttributeId = %s AND " "InbredSetId = %s", ("F", strain_id, "13", inbredset_id), ), mocker.call( "UPDATE CaseAttributeXRefNew SET Value = %s " "WHERE StrainId = %s AND CaseAttributeId = " "(SELECT CaseAttributeId FROM " "CaseAttribute WHERE Name = %s) " "AND InbredSetId = %s", ("Green", strain_id, "Color", inbredset_id), ), ], any_order=False, )