diff options
Diffstat (limited to 'tests')
| -rw-r--r-- | tests/unit/computations/test_correlation.py | 1 | ||||
| -rw-r--r-- | tests/unit/db/test_datasets.py | 14 | ||||
| -rw-r--r-- | tests/unit/db/test_traits.py | 33 |
3 files changed, 32 insertions, 16 deletions
diff --git a/tests/unit/computations/test_correlation.py b/tests/unit/computations/test_correlation.py index 0de347d..7523d99 100644 --- a/tests/unit/computations/test_correlation.py +++ b/tests/unit/computations/test_correlation.py @@ -1,7 +1,6 @@ """Module contains the tests for correlation""" from unittest import TestCase from unittest import mock -import unittest from collections import namedtuple import math diff --git a/tests/unit/db/test_datasets.py b/tests/unit/db/test_datasets.py index 39f4af9..0b8c2fe 100644 --- a/tests/unit/db/test_datasets.py +++ b/tests/unit/db/test_datasets.py @@ -13,15 +13,17 @@ class TestDatasetsDBFunctions(TestCase): def test_retrieve_dataset_name(self): """Test that the function is called correctly.""" - for trait_type, thresh, trait_name, dataset_name, columns, table in [ + for trait_type, thresh, trait_name, dataset_name, columns, table, expected in [ ["ProbeSet", 9, "probesetTraitName", "probesetDatasetName", - "Id, Name, FullName, ShortName, DataScale", "ProbeSetFreeze"], + "Id, Name, FullName, ShortName, DataScale", "ProbeSetFreeze", + {"dataset_id": None, "dataset_name": "probesetDatasetName", + "dataset_fullname": "probesetDatasetName"}], ["Geno", 3, "genoTraitName", "genoDatasetName", - "Id, Name, FullName, ShortName", "GenoFreeze"], + "Id, Name, FullName, ShortName", "GenoFreeze", {}], ["Publish", 6, "publishTraitName", "publishDatasetName", - "Id, Name, FullName, ShortName", "PublishFreeze"], + "Id, Name, FullName, ShortName", "PublishFreeze", {}], ["Temp", 4, "tempTraitName", "tempTraitName", - "Id, Name, FullName, ShortName", "TempFreeze"]]: + "Id, Name, FullName, ShortName", "TempFreeze", {}]]: db_mock = mock.MagicMock() with self.subTest(trait_type=trait_type): with db_mock.cursor() as cursor: @@ -29,7 +31,7 @@ class TestDatasetsDBFunctions(TestCase): self.assertEqual( retrieve_dataset_name( trait_type, thresh, trait_name, dataset_name, db_mock), - {}) + expected) cursor.execute.assert_called_once_with( "SELECT {cols} " "FROM {table} " diff --git a/tests/unit/db/test_traits.py b/tests/unit/db/test_traits.py index 4aa9389..75f3d4c 100644 --- a/tests/unit/db/test_traits.py +++ b/tests/unit/db/test_traits.py @@ -202,8 +202,6 @@ class TestTraitsDBFunctions(TestCase): """ # pylint: disable=C0103 db_mock = mock.MagicMock() - - STRAIN_ID_SQL: str = "UPDATE Strain SET Name = %s WHERE Id = %s" PUBLISH_DATA_SQL: str = ( "UPDATE PublishData SET value = %s " "WHERE StrainId = %s AND Id = %s") @@ -216,16 +214,33 @@ class TestTraitsDBFunctions(TestCase): 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", - strain_id=10, publish_data_id=8967049, - value=18.7, error=2.3, count=2), - (1, 1, 1, 1)) + trait_name="1", + phenotype_id=10, value=18.7, + error=2.3, count=2), + (1, 1, 1)) cursor.execute.assert_has_calls( - [mock.call(STRAIN_ID_SQL, ('BXD11', 10)), - mock.call(PUBLISH_DATA_SQL, (18.7, 10, 8967049)), - mock.call(PUBLISH_SE_SQL, (2.3, 10, 8967049)), - mock.call(N_STRAIN_SQL, (2, 10, 8967049))] + [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 = 1 AND ' + 'PublishXRef.PhenotypeId = 10 AND ' + 'PublishData.StrainId = Strain.Id AND ' + 'Strain.Name = "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))] ) def test_set_haveinfo_field(self): |