From 204a308be0f741726b9a620d88fbc22b22124c81 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Fri, 29 Dec 2023 18:55:37 +0000 Subject: Namespace all modules under gn2. We move all modules under a gn2 directory. This is important for "correct" packaging and deployment as a Guix service. --- wqflask/tests/unit/base/test_trait.py | 262 ---------------------------------- 1 file changed, 262 deletions(-) delete mode 100644 wqflask/tests/unit/base/test_trait.py (limited to 'wqflask/tests/unit/base/test_trait.py') diff --git a/wqflask/tests/unit/base/test_trait.py b/wqflask/tests/unit/base/test_trait.py deleted file mode 100644 index 5a27e243..00000000 --- a/wqflask/tests/unit/base/test_trait.py +++ /dev/null @@ -1,262 +0,0 @@ -# -*- coding: utf-8 -*- -"""Tests wqflask/base/trait.py""" -import unittest -from unittest import mock - -from base.trait import GeneralTrait -from base.trait import retrieve_trait_info - - -class TestResponse: - """Mock Test Response after a request""" - @property - def content(self): - """Mock the content from Requests.get(params).content""" - return "[1, 2, 3, 4]" - - -class TestNilResponse: - """Mock Test Response after a request""" - @property - def content(self): - """Mock the content from Requests.get(params).content""" - return "{}" - - -class MockTrait(GeneralTrait): - @property - def wikidata_alias_fmt(self): - return "Mock alias" - - -class TestRetrieveTraitInfo(unittest.TestCase): - """Tests for 'retrieve_trait_info'""" - @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""" - 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() - cursor = mock.MagicMock() - cursor.fetchone.return_value = {} - conn.cursor.return_value.__enter__.return_value = cursor - mock_db.return_value.__enter__.return_value = conn - requests_mock.return_value = TestNilResponse() - with self.assertRaises(KeyError): - retrieve_trait_info(trait=mock.MagicMock(), - dataset=mock.MagicMock()) - - @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() - cursor = mock.MagicMock() - cursor.fetchone.return_value = [1, 2, 3, 4] - conn.cursor.return_value.__enter__.return_value = cursor - 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"]) - test_trait = retrieve_trait_info(trait=MockTrait(dataset=mock_dataset), - dataset=mock_dataset) - self.assertEqual(test_trait.a, 1) - self.assertEqual(test_trait.b, 2) - self.assertEqual(test_trait.c, 3) - self.assertEqual(test_trait.d, 4) - - @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( - return_value=["a", "b", "c", "d"]) - type(mock_dataset).type = 'Publish' - - mock_trait = MockTrait( - dataset=mock_dataset, - pre_publication_description=utf_8_string - ) - trait_attrs = { - "group_code": "test_code", - "pre_publication_description": "test_pre_pub", - "pre_publication_abbreviation": "ファイルを画面毎に見て行くには、次のコマンドを使います。", - "post_publication_description": None, - "pubmed_id": None, - 'year': "2020", - "authors": "Jane Doe かいと", - } - for key, val in list(trait_attrs.items()): - setattr(mock_trait, key, val) - test_trait = retrieve_trait_info(trait=mock_trait, - dataset=mock_dataset) - self.assertEqual(test_trait.abbreviation, - "ファイルを画面毎に見て行くには、次のコマンドを使います。") - self.assertEqual(test_trait.authors, - "Jane Doe かいと") - - - @unittest.skip("Too complicated") - @mock.patch('base.trait.requests.get') - @mock.patch('base.trait.database_connection') - @mock.patch('base.trait.get_resource_id') - def test_retrieve_trait_info_with_non_empty_lrs(self, - resource_id_mock, - mock_db, - requests_mock): - """Test retrieve trait info when lrs has a value""" - resource_id_mock.return_value = 1 - conn = mock.MagicMock() - mock_db.return_value.__enter__.return_value = conn - with conn.cursor() as cursor: - cursor.fetchone.side_effect = [ - # trait_info = g.db.execute(query).fetchone() - [1, 2, 3, 4], - # trait_qtl = g.db.execute(query).fetchone() - [1, 2.37, 3, 4, 5], - # trait_info = g.db.execute(query).fetchone() - [2.7333, 2.1204] - ] - requests_mock.return_value = None - - mock_dataset = mock.MagicMock() - type(mock_dataset).display_fields = mock.PropertyMock( - return_value=["a", "b", "c", "d"]) - type(mock_dataset).type = "ProbeSet" - type(mock_dataset).name = "RandomName" - - mock_trait = MockTrait( - dataset=mock_dataset, - pre_publication_description="test_string" - ) - trait_attrs = { - "description": "some description", - "probe_target_description": "some description", - "cellid": False, - "chr": 2.733, - "mb": 2.1204 - } - - for key, val in list(trait_attrs.items()): - setattr(mock_trait, key, val) - test_trait = retrieve_trait_info(trait=mock_trait, - dataset=mock_dataset, - get_qtl_info=True) - self.assertEqual(test_trait.LRS_score_repr, - "2.4") - - @unittest.skip("Too complicated") - @mock.patch('base.trait.requests.get') - @mock.patch('base.trait.g') - @mock.patch('base.trait.get_resource_id') - def test_retrieve_trait_info_with_empty_lrs_field(self, - resource_id_mock, - g_mock, - requests_mock): - """Test retrieve trait info with empty lrs field""" - resource_id_mock.return_value = 1 - g_mock.db.execute.return_value.fetchone = mock.Mock() - g_mock.db.execute.return_value.fetchone.side_effect = [ - [1, 2, 3, 4], # trait_info = g.db.execute(query).fetchone() - [1, None, 3, 4, 5], # trait_qtl = g.db.execute(query).fetchone() - [2, 3] # trait_info = g.db.execute(query).fetchone() - ] - requests_mock.return_value = None - - mock_dataset = mock.MagicMock() - type(mock_dataset).display_fields = mock.PropertyMock( - return_value=["a", "b", "c", "d"]) - type(mock_dataset).type = "ProbeSet" - type(mock_dataset).name = "RandomName" - - mock_trait = MockTrait( - dataset=mock_dataset, - pre_publication_description="test_string" - ) - trait_attrs = { - "description": "some description", - "probe_target_description": "some description", - "cellid": False, - "chr": 2.733, - "mb": 2.1204 - } - - for key, val in list(trait_attrs.items()): - setattr(mock_trait, key, val) - test_trait = retrieve_trait_info(trait=mock_trait, - dataset=mock_dataset, - get_qtl_info=True) - self.assertEqual(test_trait.LRS_score_repr, - "N/A") - self.assertEqual(test_trait.LRS_location_repr, - "Chr2: 3.000000") - - @unittest.skip("Too complicated") - @mock.patch('base.trait.requests.get') - @mock.patch('base.trait.g') - @mock.patch('base.trait.get_resource_id') - def test_retrieve_trait_info_with_empty_chr_field(self, - resource_id_mock, - g_mock, - requests_mock): - """Test retrieve trait info with empty chr field""" - resource_id_mock.return_value = 1 - g_mock.db.execute.return_value.fetchone = mock.Mock() - g_mock.db.execute.return_value.fetchone.side_effect = [ - [1, 2, 3, 4], # trait_info = g.db.execute(query).fetchone() - [1, 2, 3, 4, 5], # trait_qtl = g.db.execute(query).fetchone() - [None, 3] # trait_info = g.db.execute(query).fetchone() - ] - - requests_mock.return_value = None - - mock_dataset = mock.MagicMock() - type(mock_dataset).display_fields = mock.PropertyMock( - return_value=["a", "b", "c", "d"]) - type(mock_dataset).type = "ProbeSet" - type(mock_dataset).name = "RandomName" - - mock_trait = MockTrait( - dataset=mock_dataset, - pre_publication_description="test_string" - ) - trait_attrs = { - "description": "some description", - "probe_target_description": "some description", - "cellid": False, - "chr": 2.733, - "mb": 2.1204 - } - - for key, val in list(trait_attrs.items()): - setattr(mock_trait, key, val) - test_trait = retrieve_trait_info(trait=mock_trait, - dataset=mock_dataset, - get_qtl_info=True) - self.assertEqual(test_trait.LRS_score_repr, - "N/A") - self.assertEqual(test_trait.LRS_location_repr, - "N/A") -- cgit v1.2.3