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-rw-r--r--wqflask/tests/unit/base/__init__.py0
-rw-r--r--wqflask/tests/unit/base/data.py110
-rw-r--r--wqflask/tests/unit/base/test_data_set.py181
-rw-r--r--wqflask/tests/unit/base/test_general_object.py40
-rw-r--r--wqflask/tests/unit/base/test_trait.py241
-rw-r--r--wqflask/tests/unit/base/test_webqtl_case_data.py39
6 files changed, 611 insertions, 0 deletions
diff --git a/wqflask/tests/unit/base/__init__.py b/wqflask/tests/unit/base/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/tests/unit/base/__init__.py
diff --git a/wqflask/tests/unit/base/data.py b/wqflask/tests/unit/base/data.py
new file mode 100644
index 00000000..06a5a989
--- /dev/null
+++ b/wqflask/tests/unit/base/data.py
@@ -0,0 +1,110 @@
+gen_menu_json = """
+{
+ "datasets": {
+ "human": {
+ "HLC": {
+ "Liver mRNA": [
+ [
+ "320",
+ "HLC_0311",
+ "GSE9588 Human Liver Normal (Mar11) Both Sexes"
+ ]
+ ],
+ "Phenotypes": [
+ [
+ "635",
+ "HLCPublish",
+ "HLC Published Phenotypes"
+ ]
+ ]
+ }
+ },
+ "mouse": {
+ "BXD": {
+ "Genotypes": [
+ [
+ "600",
+ "BXDGeno",
+ "BXD Genotypes"
+ ]
+ ],
+ "Hippocampus mRNA": [
+ [
+ "112",
+ "HC_M2_0606_P",
+ "Hippocampus Consortium M430v2 (Jun06) PDNN"
+ ]
+ ],
+ "Phenotypes": [
+ [
+ "602",
+ "BXDPublish",
+ "BXD Published Phenotypes"
+ ]
+ ]
+ }
+ }
+ },
+ "groups": {
+ "human": [
+ [
+ "HLC",
+ "Liver: Normal Gene Expression with Genotypes (Merck)",
+ "Family:None"
+ ]
+ ],
+ "mouse": [
+ [
+ "BXD",
+ "BXD",
+ "Family:None"
+ ]
+ ]
+ },
+ "species": [
+ [
+ "human",
+ "Human"
+ ],
+ [
+ "mouse",
+ "Mouse"
+ ]
+ ],
+ "types": {
+ "human": {
+ "HLC": [
+ [
+ "Phenotypes",
+ "Traits and Cofactors",
+ "Phenotypes"
+ ],
+ [
+ "Liver mRNA",
+ "Liver mRNA",
+ "Molecular Trait Datasets"
+ ]
+ ]
+ },
+ "mouse": {
+ "BXD": [
+ [
+ "Phenotypes",
+ "Traits and Cofactors",
+ "Phenotypes"
+ ],
+ [
+ "Genotypes",
+ "DNA Markers and SNPs",
+ "Genotypes"
+ ],
+ [
+ "Hippocampus mRNA",
+ "Hippocampus mRNA",
+ "Molecular Trait Datasets"
+ ]
+ ]
+ }
+ }
+}
+"""
diff --git a/wqflask/tests/unit/base/test_data_set.py b/wqflask/tests/unit/base/test_data_set.py
new file mode 100644
index 00000000..96563a16
--- /dev/null
+++ b/wqflask/tests/unit/base/test_data_set.py
@@ -0,0 +1,181 @@
+"""Tests for wqflask/base/data_set.py"""
+
+import unittest
+from unittest import mock
+
+from wqflask import app
+from .data import gen_menu_json
+from base.data_set import DatasetType
+
+
+class TestDataSetTypes(unittest.TestCase):
+ """Tests for the DataSetType class"""
+
+ def setUp(self):
+ self.test_dataset = """
+ {
+ "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"
+ }
+ """
+ self.app_context = app.app_context()
+ self.app_context.push()
+
+ def tearDown(self):
+ self.app_context.pop()
+
+ @mock.patch('base.data_set.g')
+ def test_data_set_type(self, db_mock):
+ """Test that DatasetType returns correctly if the Redis Instance is not empty
+ and the name variable exists in the dictionary
+
+ """
+ with app.app_context():
+ db_mock.get = mock.Mock()
+ redis_mock = mock.Mock()
+ redis_mock.get.return_value = self.test_dataset
+ self.assertEqual(DatasetType(redis_mock)
+ ("All Phenotypes"), "Publish")
+ redis_mock.get.assert_called_once_with("dataset_structure")
+
+ @mock.patch('base.data_set.requests.get')
+ def test_data_set_type_with_empty_redis(self, request_mock):
+ """Test that DatasetType returns correctly if the Redis Instance is empty and
+ the name variable exists in the dictionary
+
+ """
+ with app.app_context():
+ request_mock.return_value.content = gen_menu_json
+ redis_mock = mock.Mock()
+ redis_mock.get.return_value = None
+ data_set = DatasetType(redis_mock)
+ 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",
+ ('{"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):
+ with app.app_context():
+ db_mock.db.execute.return_value.fetchone.return_value = [1, 2, 3]
+ redis_mock = mock.Mock()
+ redis_mock.get.return_value = self.test_dataset
+ data_set = DatasetType(redis_mock)
+ data_set.set_dataset_key("mrna_expr", "Test")
+ self.assertEqual(data_set("Test"), "ProbeSet")
+ redis_mock.set.assert_called_once_with(
+ "dataset_structure",
+ ('{"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\" ")
+ )
+
+ @mock.patch('base.data_set.g')
+ def test_set_dataset_key_pheno(self, db_mock):
+ with app.app_context():
+ db_mock.db.execute.return_value.fetchone.return_value = [1, 2, 3]
+ redis_mock = mock.Mock()
+ redis_mock.get.return_value = self.test_dataset
+ data_set = DatasetType(redis_mock)
+ data_set.set_dataset_key("pheno", "Test")
+ self.assertEqual(data_set("Test"), "Publish")
+ redis_mock.set.assert_called_once_with(
+ "dataset_structure",
+ ('{"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 "
+ "WHERE InbredSet.Name = 'Test' AND "
+ "PublishFreeze.InbredSetId = InbredSet.Id AND "
+ "InfoFiles.InfoPageName = PublishFreeze.Name")
+ )
+
+ @mock.patch('base.data_set.g')
+ def test_set_dataset_other_pheno(self, db_mock):
+ with app.app_context():
+ db_mock.db.execute.return_value.fetchone.return_value = [1, 2, 3]
+ redis_mock = mock.Mock()
+ redis_mock.get.return_value = self.test_dataset
+ 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",
+ ('{"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 " +
+ "WHERE InbredSet.Name = 'Test' AND "
+ "PublishFreeze.InbredSetId = InbredSet.Id")
+ )
+
+ @mock.patch('base.data_set.g')
+ def test_set_dataset_geno(self, db_mock):
+ with app.app_context():
+ db_mock.db.execute.return_value.fetchone.return_value = [1, 2, 3]
+ redis_mock = mock.Mock()
+ redis_mock.get.return_value = self.test_dataset
+ data_set = DatasetType(redis_mock)
+ data_set.set_dataset_key("geno", "Test")
+ self.assertEqual(data_set("Test"), "Geno")
+ redis_mock.set.assert_called_once_with(
+ "dataset_structure",
+ ('{"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\" "))
diff --git a/wqflask/tests/unit/base/test_general_object.py b/wqflask/tests/unit/base/test_general_object.py
new file mode 100644
index 00000000..00fd3c72
--- /dev/null
+++ b/wqflask/tests/unit/base/test_general_object.py
@@ -0,0 +1,40 @@
+import unittest
+
+from base.GeneralObject import GeneralObject
+
+
+class TestGeneralObjectTests(unittest.TestCase):
+ """
+ Test the GeneralObject base class
+ """
+
+ def test_object_contents(self):
+ """Test whether base contents are stored properly"""
+ test_obj = GeneralObject("a", "b", "c")
+ self.assertEqual("abc", ''.join(test_obj.contents))
+ self.assertEqual(len(test_obj), 0)
+
+ 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), "name = test\nvalue = 1\n")
+ self.assertEqual(
+ 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
+ self.assertEqual(test_obj["test"], 1)
+
+ def test_get_attribute(self):
+ "Test that getattr works"
+ test_obj = GeneralObject("a", name="test", value=1)
+ self.assertEqual(getattr(test_obj, "value", None), 1)
+ self.assertEqual(getattr(test_obj, "non-existent", None), None)
+
+ def test_object_comparisons(self):
+ "Test that 2 objects of the same length are equal"
+ 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)
diff --git a/wqflask/tests/unit/base/test_trait.py b/wqflask/tests/unit/base/test_trait.py
new file mode 100644
index 00000000..826ccefd
--- /dev/null
+++ b/wqflask/tests/unit/base/test_trait.py
@@ -0,0 +1,241 @@
+# -*- coding: utf-8 -*-
+"""Tests wqflask/base/trait.py"""
+import unittest
+from unittest import mock
+
+from wqflask import app
+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 setUp(self):
+ self.app_context = app.app_context()
+ self.app_context.push()
+
+ def tearDown(self):
+ self.app_context.pop()
+
+ 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', mock.Mock())
+ def test_retrieve_trait_info_with_empty_trait_info(self,
+ 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', mock.Mock())
+ def test_retrieve_trait_info_with_non_empty_trait_info(self,
+ 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', mock.Mock())
+ def test_retrieve_trait_info_utf8_parsing(self,
+ 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。")
+ self.assertEqual(test_trait.authors,
+ "Jane Doe かいと")
+
+ @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 retrieve trait info when lrs has a value"""
+ 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")
diff --git a/wqflask/tests/unit/base/test_webqtl_case_data.py b/wqflask/tests/unit/base/test_webqtl_case_data.py
new file mode 100644
index 00000000..8e8ba482
--- /dev/null
+++ b/wqflask/tests/unit/base/test_webqtl_case_data.py
@@ -0,0 +1,39 @@
+"""Tests for wqflask/base/webqtlCaseData.py"""
+import unittest
+
+from wqflask import app # Required because of utility.tools in webqtlCaseData.py
+from base.webqtlCaseData import webqtlCaseData
+
+class TestWebqtlCaseData(unittest.TestCase):
+ """Tests for WebqtlCaseData class"""
+
+ def setUp(self):
+ self.w = webqtlCaseData(name="Test",
+ value=0,
+ variance=0.0,
+ num_cases=10,
+ name2="Test2")
+
+ def test_webqtl_case_data_repr(self):
+ self.assertEqual(
+ repr(self.w),
+ "<webqtlCaseData> value=0.000 variance=0.000 ndata=10 name=Test name2=Test2"
+ )
+
+ def test_class_outlier(self):
+ self.assertEqual(self.w.class_outlier, "")
+
+ def test_display_value(self):
+ self.assertEqual(self.w.display_value, "0.000")
+ self.w.value = None
+ self.assertEqual(self.w.display_value, "x")
+
+ def test_display_variance(self):
+ self.assertEqual(self.w.display_variance, "0.000")
+ self.w.variance = None
+ self.assertEqual(self.w.display_variance, "x")
+
+ def test_display_num_cases(self):
+ self.assertEqual(self.w.display_num_cases, "10")
+ self.w.num_cases = None
+ self.assertEqual(self.w.display_num_cases, "x")
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 13:44:01 +0000