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-rw-r--r--wqflask/tests/base/test_trait.py235
1 files changed, 235 insertions, 0 deletions
diff --git a/wqflask/tests/base/test_trait.py b/wqflask/tests/base/test_trait.py
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+++ b/wqflask/tests/base/test_trait.py
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+# -*- coding: utf-8 -*-
+"""Tests wqflask/base/trait.py"""
+import 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'"""
+ def test_retrieve_trait_info_with_empty_dataset(self):
+ """Test that an exception is raised when dataset is empty"""
+ with self.assertRaises(AssertionError):
+ retrieve_trait_info(trait=mock.MagicMock(),
+ dataset={})
+
+ @mock.patch('base.trait.requests.get')
+ @mock.patch('base.trait.g')
+ def test_retrieve_trait_info_with_empty_trait_info(self,
+ g_mock,
+ requests_mock):
+ """Empty trait info"""
+ 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')
+ def test_retrieve_trait_info_with_non_empty_trait_info(self,
+ g_mock,
+ requests_mock):
+ """Test that attributes are set"""
+ mock_dataset = mock.MagicMock()
+ 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')
+ def test_retrieve_trait_info_utf8_parsing(self,
+ g_mock,
+ requests_mock):
+ """Test that utf-8 strings are parsed correctly"""
+ utf_8_string = "test_string"
+ 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。".decode('utf-8'))
+ self.assertEqual(test_trait.authors,
+ "Jane Doe かいと".decode('utf-8'))
+
+ @mock.patch('base.trait.requests.get')
+ @mock.patch('base.trait.g')
+ @mock.patch('base.trait.get_resource_id')
+ def test_retrieve_trait_info_with_non_empty_lrs(self,
+ resource_id_mock,
+ g_mock,
+ requests_mock):
+ """Test """
+ 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, 2.37, 3, 4, 5], # trait_qtl = g.db.execute(query).fetchone()
+ [2.7333, 2.1204] # 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,
+ "2.4")
+
+ @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")
+
+ @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")
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 18:06:07 +0000