Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing

9 files changed, 215 insertions, 0 deletions

diff --git a/wqflask/tests/__init__.py b/wqflask/tests/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/tests/__init__.py
diff --git a/wqflask/tests/base/__init__.py b/wqflask/tests/base/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/tests/base/__init__.py
diff --git a/wqflask/tests/base/test_data_set.py b/wqflask/tests/base/test_data_set.py
new file mode 100644
index 00000000..44a54c7e
--- /dev/null
+++ b/wqflask/tests/base/test_data_set.py
@@ -0,0 +1,35 @@
+import unittest
+import mock
+
+from wqflask import app
+
+from base.data_set import DatasetType
+
+    
+class TestDataSetTypes(unittest.TestCase):
+    def setUp(self):
+        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):
+        with app.app_context():
+            db_mock.get = mock.Mock()
+            r = mock.Mock()
+            r.get.return_value = """
+            {
+                "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.assertEqual(DatasetType(r)("All Phenotypes"), "Publish")
diff --git a/wqflask/tests/base/test_general_object.py b/wqflask/tests/base/test_general_object.py
new file mode 100644
index 00000000..c7701021
--- /dev/null
+++ b/wqflask/tests/base/test_general_object.py
@@ -0,0 +1,41 @@
+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), "value = 1\nname = test\n")
+        self.assertEqual(
+            repr(test_obj), "value = 1\nname = test\ncontents = ['a']\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/utility/__init__.py b/wqflask/tests/utility/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/tests/utility/__init__.py
diff --git a/wqflask/tests/utility/test_chunks.py b/wqflask/tests/utility/test_chunks.py
new file mode 100644
index 00000000..8d90a1ec
--- /dev/null
+++ b/wqflask/tests/utility/test_chunks.py
@@ -0,0 +1,19 @@
+"""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/utility/test_corestats.py b/wqflask/tests/utility/test_corestats.py
new file mode 100644
index 00000000..cf91a248
--- /dev/null
+++ b/wqflask/tests/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/utility/test_corr_result_helpers.py b/wqflask/tests/utility/test_corr_result_helpers.py
new file mode 100644
index 00000000..e196fbdf
--- /dev/null
+++ b/wqflask/tests/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/utility/test_formatting.py b/wqflask/tests/utility/test_formatting.py
new file mode 100644
index 00000000..9d3033d1
--- /dev/null
+++ b/wqflask/tests/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)