Merge github.com:genenetwork/genenetwork2 into acenteno

8 files changed, 435 insertions, 0 deletions

diff --git a/wqflask/tests/unit/utility/__init__.py b/wqflask/tests/unit/utility/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/tests/unit/utility/__init__.py
diff --git a/wqflask/tests/unit/utility/test_authentication_tools.py b/wqflask/tests/unit/utility/test_authentication_tools.py
new file mode 100644
index 00000000..024ab43f
--- /dev/null
+++ b/wqflask/tests/unit/utility/test_authentication_tools.py
@@ -0,0 +1,190 @@
+"""Tests for authentication tools"""
+import unittest
+from unittest import mock
+
+from utility.authentication_tools import check_resource_availability
+from utility.authentication_tools import add_new_resource
+
+
+class TestResponse:
+    """Mock Test Response after a request"""
+    @property
+    def content(self):
+        """Mock the content from Requests.get(params).content"""
+        return '["foo"]'
+
+
+class TestUser:
+    """Mock user"""
+    @property
+    def user_id(self):
+        """Mockes user id. Used in Flask.g.user_session.user_id"""
+        return b"Jane"
+
+
+class TestUserSession:
+    """Mock user session"""
+    @property
+    def user_session(self):
+        """Mock user session. Mocks Flask.g.user_session object"""
+        return TestUser()
+
+
+def mock_add_resource(resource_ob, update=False):
+    return resource_ob
+
+
+class TestCheckResourceAvailability(unittest.TestCase):
+    """Test methods related to checking the resource availability"""
+    @mock.patch('utility.authentication_tools.add_new_resource')
+    @mock.patch('utility.authentication_tools.Redis')
+    @mock.patch('utility.authentication_tools.g', TestUserSession())
+    @mock.patch('utility.authentication_tools.get_resource_id')
+    def test_check_resource_availability_default_mask(
+            self,
+            resource_id_mock,
+            redis_mock,
+            add_new_resource_mock):
+        """Test the resource availability with default mask"""
+
+        resource_id_mock.return_value = 1
+        redis_mock.smembers.return_value = []
+        test_dataset = mock.MagicMock()
+        type(test_dataset).type = mock.PropertyMock(return_value="Test")
+        add_new_resource_mock.return_value = {"default_mask": 2}
+        self.assertEqual(check_resource_availability(test_dataset), 2)
+
+    @mock.patch('utility.authentication_tools.requests.get')
+    @mock.patch('utility.authentication_tools.add_new_resource')
+    @mock.patch('utility.authentication_tools.Redis')
+    @mock.patch('utility.authentication_tools.g', TestUserSession())
+    @mock.patch('utility.authentication_tools.get_resource_id')
+    def test_check_resource_availability_non_default_mask(
+            self,
+            resource_id_mock,
+            redis_mock,
+            add_new_resource_mock,
+            requests_mock):
+        """Test the resource availability with non-default mask"""
+        resource_id_mock.return_value = 1
+        redis_mock.smembers.return_value = []
+        add_new_resource_mock.return_value = {"default_mask": 2}
+        requests_mock.return_value = TestResponse()
+        test_dataset = mock.MagicMock()
+        type(test_dataset).type = mock.PropertyMock(return_value="Test")
+        self.assertEqual(check_resource_availability(test_dataset),
+                         ['foo'])
+
+    @mock.patch('utility.authentication_tools.webqtlConfig.SUPER_PRIVILEGES',
+                "SUPERUSER")
+    @mock.patch('utility.authentication_tools.requests.get')
+    @mock.patch('utility.authentication_tools.add_new_resource')
+    @mock.patch('utility.authentication_tools.Redis')
+    @mock.patch('utility.authentication_tools.g', TestUserSession())
+    @mock.patch('utility.authentication_tools.get_resource_id')
+    def test_check_resource_availability_of_super_user(
+            self,
+            resource_id_mock,
+            redis_mock,
+            add_new_resource_mock,
+            requests_mock):
+        """Test the resource availability if the user is the super user"""
+        resource_id_mock.return_value = 1
+        redis_mock.smembers.return_value = [b"Jane"]
+        add_new_resource_mock.return_value = {"default_mask": 2}
+        requests_mock.return_value = TestResponse()
+        test_dataset = mock.MagicMock()
+        type(test_dataset).type = mock.PropertyMock(return_value="Test")
+        self.assertEqual(check_resource_availability(test_dataset),
+                         "SUPERUSER")
+
+    @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+                "John Doe")
+    def test_check_resource_availability_string_dataset(self):
+        """Test the resource availability if the dataset is a string"""
+        self.assertEqual(check_resource_availability("Test"),
+                         "John Doe")
+
+    @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+                "John Doe")
+    def test_check_resource_availability_temp(self):
+        """Test the resource availability if the dataset is a string"""
+        test_dataset = mock.MagicMock()
+        type(test_dataset).type = mock.PropertyMock(return_value="Temp")
+        self.assertEqual(check_resource_availability(test_dataset),
+                         "John Doe")
+
+
+class TestAddNewResource(unittest.TestCase):
+    """Test cases for add_new_resource method"""
+    @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+                "John Doe")
+    @mock.patch('utility.authentication_tools.add_resource', mock_add_resource)
+    @mock.patch('utility.authentication_tools.get_group_code')
+    def test_add_new_resource_if_publish_datatype(self, group_code_mock):
+        """Test add_new_resource if dataset type is 'publish'"""
+        group_code_mock.return_value = "Test"
+        test_dataset = mock.MagicMock()
+        type(test_dataset).type = mock.PropertyMock(return_value="Publish")
+        type(test_dataset).id = mock.PropertyMock(return_value=10)
+        expected_value = {
+            "owner_id": "none",
+            "default_mask": "John Doe",
+            "group_masks": {},
+            "name": "Test_None",
+            "data": {
+                "dataset": 10,
+                "trait": None
+            },
+            "type": "dataset-publish"
+        }
+        self.assertEqual(add_new_resource(test_dataset),
+                         expected_value)
+
+    @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+                "John Doe")
+    @mock.patch('utility.authentication_tools.add_resource', mock_add_resource)
+    @mock.patch('utility.authentication_tools.get_group_code')
+    def test_add_new_resource_if_geno_datatype(self, group_code_mock):
+        """Test add_new_resource if dataset type is 'geno'"""
+        group_code_mock.return_value = "Test"
+        test_dataset = mock.MagicMock()
+        type(test_dataset).name = mock.PropertyMock(return_value="Geno")
+        type(test_dataset).type = mock.PropertyMock(return_value="Geno")
+        type(test_dataset).id = mock.PropertyMock(return_value=20)
+        expected_value = {
+            "owner_id": "none",
+            "default_mask": "John Doe",
+            "group_masks": {},
+            "name": "Geno",
+            "data": {
+                "dataset": 20,
+            },
+            "type": "dataset-geno"
+        }
+        self.assertEqual(add_new_resource(test_dataset),
+                         expected_value)
+
+    @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+                "John Doe")
+    @mock.patch('utility.authentication_tools.add_resource', mock_add_resource)
+    @mock.patch('utility.authentication_tools.get_group_code')
+    def test_add_new_resource_if_other_datatype(self, group_code_mock):
+        """Test add_new_resource if dataset type is not 'geno' or 'publish'"""
+        group_code_mock.return_value = "Test"
+        test_dataset = mock.MagicMock()
+        type(test_dataset).name = mock.PropertyMock(return_value="Geno")
+        type(test_dataset).type = mock.PropertyMock(return_value="other")
+        type(test_dataset).id = mock.PropertyMock(return_value=20)
+        expected_value = {
+            "owner_id": "none",
+            "default_mask": "John Doe",
+            "group_masks": {},
+            "name": "Geno",
+            "data": {
+                "dataset": 20,
+            },
+            "type": "dataset-probeset"
+        }
+        self.assertEqual(add_new_resource(test_dataset),
+                         expected_value)
diff --git a/wqflask/tests/unit/utility/test_chunks.py b/wqflask/tests/unit/utility/test_chunks.py
new file mode 100644
index 00000000..1d349193
--- /dev/null
+++ b/wqflask/tests/unit/utility/test_chunks.py
@@ -0,0 +1,20 @@
+"""Test chunking"""
+
+import unittest
+
+from utility.chunks import divide_into_chunks
+
+
+class TestChunks(unittest.TestCase):
+    "Test Utility method for chunking"
+
+    def test_divide_into_chunks(self):
+        "Check that a list is chunked correctly"
+        self.assertEqual(divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 3),
+                         [[1, 2, 7], [3, 22, 8], [5, 22, 333]])
+        self.assertEqual(divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 4),
+                         [[1, 2, 7], [3, 22, 8], [5, 22, 333]])
+        self.assertEqual(divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 5),
+                         [[1, 2], [7, 3], [22, 8], [5, 22], [333]])
+        self.assertEqual(divide_into_chunks([], 5),
+                         [[]])
diff --git a/wqflask/tests/unit/utility/test_corestats.py b/wqflask/tests/unit/utility/test_corestats.py
new file mode 100644
index 00000000..cf91a248
--- /dev/null
+++ b/wqflask/tests/unit/utility/test_corestats.py
@@ -0,0 +1,55 @@
+"""Test Core Stats"""
+
+import unittest
+
+from utility.corestats import Stats
+
+
+class TestChunks(unittest.TestCase):
+    "Test Utility method for chunking"
+
+    def setUp(self):
+        self.stat_test = Stats((x for x in range(1, 11)))
+
+    def test_stats_sum(self):
+        """ Test sequence sum """
+        self.assertEqual(self.stat_test.sum(), 55)
+        self.stat_test = Stats([])
+        self.assertEqual(self.stat_test.sum(), None)
+
+    def test_stats_count(self):
+        """ Test sequence count """
+        self.assertEqual(self.stat_test.count(), 10)
+        self.stat_test = Stats([])
+        self.assertEqual(self.stat_test.count(), 0)
+
+    def test_stats_min(self):
+        """ Test min value in sequence"""
+        self.assertEqual(self.stat_test.min(), 1)
+        self.stat_test = Stats([])
+        self.assertEqual(self.stat_test.min(), None)
+
+    def test_stats_max(self):
+        """ Test max value in sequence """
+        self.assertEqual(self.stat_test.max(), 10)
+        self.stat_test = Stats([])
+        self.assertEqual(self.stat_test.max(), None)
+
+    def test_stats_avg(self):
+        """ Test avg of sequence """
+        self.assertEqual(self.stat_test.avg(), 5.5)
+        self.stat_test = Stats([])
+        self.assertEqual(self.stat_test.avg(), None)
+
+    def test_stats_stdev(self):
+        """ Test standard deviation of sequence """
+        self.assertEqual(self.stat_test.stdev(), 3.0276503540974917)
+        self.stat_test = Stats([])
+        self.assertEqual(self.stat_test.stdev(), None)
+
+    def test_stats_percentile(self):
+        """ Test percentile of sequence """
+        self.assertEqual(self.stat_test.percentile(20), 3.0)
+        self.assertEqual(self.stat_test.percentile(101), None)
+        self.stat_test = Stats([])
+        self.assertEqual(self.stat_test.percentile(20), None)
diff --git a/wqflask/tests/unit/utility/test_corr_result_helpers.py b/wqflask/tests/unit/utility/test_corr_result_helpers.py
new file mode 100644
index 00000000..e196fbdf
--- /dev/null
+++ b/wqflask/tests/unit/utility/test_corr_result_helpers.py
@@ -0,0 +1,32 @@
+""" Test correlation helper methods """
+
+import unittest
+from utility.corr_result_helpers import normalize_values, common_keys, normalize_values_with_samples
+
+
+class TestCorrelationHelpers(unittest.TestCase):
+    """Test methods for normalising lists"""
+
+    def test_normalize_values(self):
+        """Test that a list is normalised correctly"""
+        self.assertEqual(
+            normalize_values([2.3, None, None, 3.2, 4.1, 5], [
+                             3.4, 7.2, 1.3, None, 6.2, 4.1]),
+            ([2.3, 4.1, 5], [3.4, 6.2, 4.1], 3)
+        )
+
+    def test_common_keys(self):
+        """Test that common keys are returned as a list"""
+        a = dict(BXD1=9.113, BXD2=9.825, BXD14=8.985, BXD15=9.300)
+        b = dict(BXD1=9.723, BXD3=9.825, BXD14=9.124, BXD16=9.300)
+        self.assertEqual(sorted(common_keys(a, b)), ['BXD1', 'BXD14'])
+
+    def test_normalize_values_with_samples(self):
+        """Test that a sample(dict) is normalised correctly"""
+        self.assertEqual(
+            normalize_values_with_samples(
+                dict(BXD1=9.113, BXD2=9.825, BXD14=8.985,
+                     BXD15=9.300, BXD20=9.300),
+                dict(BXD1=9.723, BXD3=9.825, BXD14=9.124, BXD16=9.300)),
+            (({'BXD1': 9.113, 'BXD14': 8.985}, {'BXD1': 9.723, 'BXD14': 9.124}, 2))
+        )
diff --git a/wqflask/tests/unit/utility/test_formatting.py b/wqflask/tests/unit/utility/test_formatting.py
new file mode 100644
index 00000000..9d3033d1
--- /dev/null
+++ b/wqflask/tests/unit/utility/test_formatting.py
@@ -0,0 +1,33 @@
+import unittest
+from utility.formatting import numify, commify
+
+
+class TestFormatting(unittest.TestCase):
+    """Test formatting numbers by numifying or commifying"""
+
+    def test_numify(self):
+        "Test that a number is correctly converted to a English readable string"
+        self.assertEqual(numify(1, 'item', 'items'),
+                         'one item')
+        self.assertEqual(numify(2, 'book'), 'two')
+        self.assertEqual(numify(2, 'book', 'books'), 'two books')
+        self.assertEqual(numify(0, 'book', 'books'), 'zero books')
+        self.assertEqual(numify(0), 'zero')
+        self.assertEqual(numify(5), 'five')
+        self.assertEqual(numify(14, 'book', 'books'), '14 books')
+        self.assertEqual(numify(999, 'book', 'books'), '999 books')
+        self.assertEqual(numify(1000000, 'book', 'books'), '1,000,000 books')
+        self.assertEqual(numify(1956), '1956')
+
+    def test_commify(self):
+        "Test that commas are added correctly"
+        self.assertEqual(commify(1), '1')
+        self.assertEqual(commify(123), '123')
+        self.assertEqual(commify(1234), '1234')
+        self.assertEqual(commify(12345), '12,345')
+        self.assertEqual(commify(1234567890), '1,234,567,890')
+        self.assertEqual(commify(123.0), '123.0')
+        self.assertEqual(commify(1234.5), '1234.5')
+        self.assertEqual(commify(1234.56789), '1234.56789')
+        self.assertEqual(commify(123456.789), '123,456.789')
+        self.assertEqual(commify(None), None)
diff --git a/wqflask/tests/unit/utility/test_hmac.py b/wqflask/tests/unit/utility/test_hmac.py
new file mode 100644
index 00000000..13d6261d
--- /dev/null
+++ b/wqflask/tests/unit/utility/test_hmac.py
@@ -0,0 +1,51 @@
+"""Test hmac utility functions"""
+
+import unittest
+from unittest import mock
+
+from utility.hmac import data_hmac
+from utility.hmac import url_for_hmac
+from utility.hmac import hmac_creation
+
+
+class TestHmacUtil(unittest.TestCase):
+    """Test Utility method for hmac creation"""
+
+    @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
+    def test_hmac_creation(self):
+        """Test hmac creation with a utf-8 string"""
+        self.assertEqual(hmac_creation("ファイ"), "7410466338cfe109e946")
+
+    @mock.patch("utility.hmac.app.config",
+                {'SECRET_HMAC_CODE': ('\x08\xdf\xfa\x93N\x80'
+                                      '\xd9\\H@\\\x9f`\x98d^'
+                                      '\xb4a;\xc6OM\x946a\xbc'
+                                      '\xfc\x80:*\xebc')})
+    def test_hmac_creation_with_cookie(self):
+        """Test hmac creation with a cookie"""
+        cookie = "3f4c1dbf-5b56-4260-87d6-f35445bda37e:af4fcf5eace9e7c864ce"
+        uuid_, _, signature = cookie.partition(":")
+        self.assertEqual(
+            hmac_creation(uuid_),
+            "af4fcf5eace9e7c864ce")
+
+    @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
+    def test_data_hmac(self):
+        """Test data_hmac fn with a utf-8 string"""
+        self.assertEqual(data_hmac("ファイ"), "ファイ:7410466338cfe109e946")
+
+    @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
+    @mock.patch("utility.hmac.url_for")
+    def test_url_for_hmac_with_plain_url(self, mock_url):
+        """Test url_for_hmac without params"""
+        mock_url.return_value = "https://mock_url.com/ファイ/"
+        self.assertEqual(url_for_hmac("ファイ"),
+                         "https://mock_url.com/ファイ/?hm=05bc39e659b1948f41e7")
+
+    @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
+    @mock.patch("utility.hmac.url_for")
+    def test_url_for_hmac_with_param_in_url(self, mock_url):
+        """Test url_for_hmac with params"""
+        mock_url.return_value = "https://mock_url.com/?ファイ=1"
+        self.assertEqual(url_for_hmac("ファイ"),
+                         "https://mock_url.com/?ファイ=1&hm=4709c1708270644aed79")
diff --git a/wqflask/tests/unit/utility/test_type_checking.py b/wqflask/tests/unit/utility/test_type_checking.py
new file mode 100644
index 00000000..48d110c7
--- /dev/null
+++ b/wqflask/tests/unit/utility/test_type_checking.py
@@ -0,0 +1,54 @@
+import unittest
+from utility.type_checking import is_float
+from utility.type_checking import is_int
+from utility.type_checking import is_str
+from utility.type_checking import get_float
+from utility.type_checking import get_int
+from utility.type_checking import get_string
+
+
+class TestTypeChecking(unittest.TestCase):
+    def test_is_float(self):
+        floats = [2, 1.2, '3.1']
+        not_floats = ["String", None, [], ()]
+        for flt in floats:
+            results = is_float(flt)
+            self.assertTrue(results)
+        for nflt in not_floats:
+            results = is_float(nflt)
+            self.assertFalse(results)
+
+    def test_is_int(self):
+        int_values = [1, 1.1]
+        not_int_values = ["string", None, [], "1.1"]
+        for int_val in int_values:
+            results = is_int(int_val)
+            self.assertTrue(results)
+        for not_int in not_int_values:
+            results = is_int(not_int)
+            self.assertFalse(results)
+
+    def test_is_str(self):
+        string_values = [1, False, [], {}, "string_value"]
+        falsey_values = [None]
+        for string_val in string_values:
+            results = is_str(string_val)
+            self.assertTrue(results)
+        for non_string in falsey_values:
+            results = is_str(non_string)
+            self.assertFalse(results)
+
+    def test_get_float(self):
+        vars_object = {"min_value": "12"}
+        results = get_float(vars_object, "min_value")
+        self.assertEqual(results, 12.0)
+
+    def test_get_int(self):
+        vars_object = {"lx_value": "1"}
+        results = get_int(vars_object, "lx_value")
+        self.assertEqual(results, 1)
+
+    def test_get_string(self):
+        string_object = {"mx_value": 1}
+        results = get_string(string_object, "mx_value")
+        self.assertEqual(results, "1")
\ No newline at end of file