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-rw-r--r--wqflask/tests/base/test_data_set.py71
-rw-r--r--wqflask/tests/base/test_general_object.py9
-rw-r--r--wqflask/tests/base/test_trait.py15
3 files changed, 67 insertions, 28 deletions
diff --git a/wqflask/tests/base/test_data_set.py b/wqflask/tests/base/test_data_set.py
index dd7f5051..96563a16 100644
--- a/wqflask/tests/base/test_data_set.py
+++ b/wqflask/tests/base/test_data_set.py
@@ -1,10 +1,10 @@
"""Tests for wqflask/base/data_set.py"""
import unittest
-import mock
+from unittest import mock
from wqflask import app
-from data import gen_menu_json
+from .data import gen_menu_json
from base.data_set import DatasetType
@@ -59,9 +59,14 @@ class TestDataSetTypes(unittest.TestCase):
self.assertEqual(data_set("BXDGeno"), "Geno")
self.assertEqual(data_set("BXDPublish"), "Publish")
self.assertEqual(data_set("HLC_0311"), "ProbeSet")
+
redis_mock.set.assert_called_once_with(
"dataset_structure",
- '{"BXDGeno": "Geno", "BXDPublish": "Publish", "HLCPublish": "Publish", "HLC_0311": "ProbeSet", "HC_M2_0606_P": "ProbeSet"}')
+ ('{"HLC_0311": "ProbeSet", '
+ '"HLCPublish": "Publish", '
+ '"BXDGeno": "Geno", '
+ '"HC_M2_0606_P": "ProbeSet", '
+ '"BXDPublish": "Publish"}'))
@mock.patch('base.data_set.g')
def test_set_dataset_key_mrna(self, db_mock):
@@ -74,8 +79,17 @@ class TestDataSetTypes(unittest.TestCase):
self.assertEqual(data_set("Test"), "ProbeSet")
redis_mock.set.assert_called_once_with(
"dataset_structure",
- '{"Aging-Brain-UCIPublish": "Publish", "AKXDGeno": "Geno", "B139_K_1206_M": "ProbeSet", "AD-cases-controls-MyersGeno": "Geno", "AD-cases-controls-MyersPublish": "Publish", "All Phenotypes": "Publish", "Test": "ProbeSet", "AXBXAPublish": "Publish", "B139_K_1206_R": "ProbeSet", "AXBXAGeno": "Geno"}')
- expected_db_call = """"""
+ ('{"AD-cases-controls-MyersGeno": "Geno", '
+ '"AD-cases-controls-MyersPublish": "Publish", '
+ '"AKXDGeno": "Geno", '
+ '"AXBXAGeno": "Geno", '
+ '"AXBXAPublish": "Publish", '
+ '"Aging-Brain-UCIPublish": "Publish", '
+ '"All Phenotypes": "Publish", '
+ '"B139_K_1206_M": "ProbeSet", '
+ '"B139_K_1206_R": "ProbeSet", '
+ '"Test": "ProbeSet"}'))
+
db_mock.db.execute.assert_called_with(
("SELECT ProbeSetFreeze.Id FROM ProbeSetFreeze " +
"WHERE ProbeSetFreeze.Name = \"Test\" ")
@@ -92,12 +106,21 @@ class TestDataSetTypes(unittest.TestCase):
self.assertEqual(data_set("Test"), "Publish")
redis_mock.set.assert_called_once_with(
"dataset_structure",
- '{"Aging-Brain-UCIPublish": "Publish", "AKXDGeno": "Geno", "B139_K_1206_M": "ProbeSet", "AD-cases-controls-MyersGeno": "Geno", "AD-cases-controls-MyersPublish": "Publish", "All Phenotypes": "Publish", "Test": "Publish", "AXBXAPublish": "Publish", "B139_K_1206_R": "ProbeSet", "AXBXAGeno": "Geno"}')
+ ('{"AD-cases-controls-MyersGeno": "Geno", '
+ '"AD-cases-controls-MyersPublish": "Publish", '
+ '"AKXDGeno": "Geno", '
+ '"AXBXAGeno": "Geno", '
+ '"AXBXAPublish": "Publish", '
+ '"Aging-Brain-UCIPublish": "Publish", '
+ '"All Phenotypes": "Publish", '
+ '"B139_K_1206_M": "ProbeSet", '
+ '"B139_K_1206_R": "ProbeSet", '
+ '"Test": "Publish"}'))
db_mock.db.execute.assert_called_with(
- ("SELECT InfoFiles.GN_AccesionId " +
- "FROM InfoFiles, PublishFreeze, InbredSet " +
+ ("SELECT InfoFiles.GN_AccesionId "
+ "FROM InfoFiles, PublishFreeze, InbredSet "
"WHERE InbredSet.Name = 'Test' AND "
- "PublishFreeze.InbredSetId = InbredSet.Id AND " +
+ "PublishFreeze.InbredSetId = InbredSet.Id AND "
"InfoFiles.InfoPageName = PublishFreeze.Name")
)
@@ -110,9 +133,20 @@ class TestDataSetTypes(unittest.TestCase):
data_set = DatasetType(redis_mock)
data_set.set_dataset_key("other_pheno", "Test")
self.assertEqual(data_set("Test"), "Publish")
+
redis_mock.set.assert_called_once_with(
"dataset_structure",
- '{"Aging-Brain-UCIPublish": "Publish", "AKXDGeno": "Geno", "B139_K_1206_M": "ProbeSet", "AD-cases-controls-MyersGeno": "Geno", "AD-cases-controls-MyersPublish": "Publish", "All Phenotypes": "Publish", "Test": "Publish", "AXBXAPublish": "Publish", "B139_K_1206_R": "ProbeSet", "AXBXAGeno": "Geno"}')
+ ('{"AD-cases-controls-MyersGeno": "Geno", '
+ '"AD-cases-controls-MyersPublish": "Publish", '
+ '"AKXDGeno": "Geno", '
+ '"AXBXAGeno": "Geno", '
+ '"AXBXAPublish": "Publish", '
+ '"Aging-Brain-UCIPublish": "Publish", '
+ '"All Phenotypes": "Publish", '
+ '"B139_K_1206_M": "ProbeSet", '
+ '"B139_K_1206_R": "ProbeSet", '
+ '"Test": "Publish"}'))
+
db_mock.db.execute.assert_called_with(
("SELECT PublishFreeze.Name " +
"FROM PublishFreeze, InbredSet " +
@@ -131,8 +165,17 @@ class TestDataSetTypes(unittest.TestCase):
self.assertEqual(data_set("Test"), "Geno")
redis_mock.set.assert_called_once_with(
"dataset_structure",
- '{"Aging-Brain-UCIPublish": "Publish", "AKXDGeno": "Geno", "B139_K_1206_M": "ProbeSet", "AD-cases-controls-MyersGeno": "Geno", "AD-cases-controls-MyersPublish": "Publish", "All Phenotypes": "Publish", "Test": "Geno", "AXBXAPublish": "Publish", "B139_K_1206_R": "ProbeSet", "AXBXAGeno": "Geno"}')
- expected_db_call = """"""
+ ('{"AD-cases-controls-MyersGeno": "Geno", '
+ '"AD-cases-controls-MyersPublish": "Publish", '
+ '"AKXDGeno": "Geno", '
+ '"AXBXAGeno": "Geno", '
+ '"AXBXAPublish": "Publish", '
+ '"Aging-Brain-UCIPublish": "Publish", '
+ '"All Phenotypes": "Publish", '
+ '"B139_K_1206_M": "ProbeSet", '
+ '"B139_K_1206_R": "ProbeSet", '
+ '"Test": "Geno"}'))
+
db_mock.db.execute.assert_called_with(
- ("SELECT GenoFreeze.Id FROM GenoFreeze WHERE GenoFreeze.Name = \"Test\" ")
- )
+ ("SELECT GenoFreeze.Id FROM "
+ "GenoFreeze WHERE GenoFreeze.Name = \"Test\" "))
diff --git a/wqflask/tests/base/test_general_object.py b/wqflask/tests/base/test_general_object.py
index c7701021..00fd3c72 100644
--- a/wqflask/tests/base/test_general_object.py
+++ b/wqflask/tests/base/test_general_object.py
@@ -17,9 +17,9 @@ class TestGeneralObjectTests(unittest.TestCase):
def test_object_dict(self):
"""Test whether the base class is printed properly"""
test_obj = GeneralObject("a", name="test", value=1)
- self.assertEqual(str(test_obj), "value = 1\nname = test\n")
+ self.assertEqual(str(test_obj), "name = test\nvalue = 1\n")
self.assertEqual(
- repr(test_obj), "value = 1\nname = test\ncontents = ['a']\n")
+ repr(test_obj), "contents = ['a']\nname = test\nvalue = 1\n")
self.assertEqual(len(test_obj), 2)
self.assertEqual(test_obj["value"], 1)
test_obj["test"] = 1
@@ -36,6 +36,5 @@ class TestGeneralObjectTests(unittest.TestCase):
test_obj1 = GeneralObject("a", name="test", value=1)
test_obj2 = GeneralObject("b", name="test2", value=2)
test_obj3 = GeneralObject("a", name="test", x=1, y=2)
- self.assertTrue(test_obj1 == test_obj2 )
- self.assertFalse(test_obj1 == test_obj3 )
-
+ self.assertTrue(test_obj1 == test_obj2)
+ self.assertFalse(test_obj1 == test_obj3)
diff --git a/wqflask/tests/base/test_trait.py b/wqflask/tests/base/test_trait.py
index 1a3820f2..60ebaee0 100644
--- a/wqflask/tests/base/test_trait.py
+++ b/wqflask/tests/base/test_trait.py
@@ -1,7 +1,7 @@
# -*- coding: utf-8 -*-
"""Tests wqflask/base/trait.py"""
import unittest
-import mock
+from unittest import mock
from base.trait import GeneralTrait
from base.trait import retrieve_trait_info
@@ -38,9 +38,8 @@ class TestRetrieveTraitInfo(unittest.TestCase):
dataset={})
@mock.patch('base.trait.requests.get')
- @mock.patch('base.trait.g')
+ @mock.patch('base.trait.g', mock.Mock())
def test_retrieve_trait_info_with_empty_trait_info(self,
- g_mock,
requests_mock):
"""Empty trait info"""
requests_mock.return_value = TestNilResponse()
@@ -49,9 +48,8 @@ class TestRetrieveTraitInfo(unittest.TestCase):
dataset=mock.MagicMock())
@mock.patch('base.trait.requests.get')
- @mock.patch('base.trait.g')
+ @mock.patch('base.trait.g', mock.Mock())
def test_retrieve_trait_info_with_non_empty_trait_info(self,
- g_mock,
requests_mock):
"""Test that attributes are set"""
mock_dataset = mock.MagicMock()
@@ -66,9 +64,8 @@ class TestRetrieveTraitInfo(unittest.TestCase):
self.assertEqual(test_trait.d, 4)
@mock.patch('base.trait.requests.get')
- @mock.patch('base.trait.g')
+ @mock.patch('base.trait.g', mock.Mock())
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"
@@ -96,9 +93,9 @@ class TestRetrieveTraitInfo(unittest.TestCase):
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'))
+ "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".decode('utf-8'))
+ "Jane Doe かいと")
@mock.patch('base.trait.requests.get')
@mock.patch('base.trait.g')
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-21 18:48:25 +0000