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-rw-r--r--wqflask/tests/unit/base/test_trait.py262
1 files changed, 0 insertions, 262 deletions
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")
generated by cgit v1.2.3 (git 2.44.0) at 2024-12-01 23:04:06 +0000