Namespace all modules under gn2.

We move all modules under a gn2 directory. This is important for
"correct" packaging and deployment as a Guix service.

3 files changed, 166 insertions, 0 deletions

diff --git a/gn2/tests/unit/wqflask/show_trait/__init__.py b/gn2/tests/unit/wqflask/show_trait/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/gn2/tests/unit/wqflask/show_trait/__init__.py
diff --git a/gn2/tests/unit/wqflask/show_trait/test_export_trait_data.py b/gn2/tests/unit/wqflask/show_trait/test_export_trait_data.py
new file mode 100644
index 00000000..a933d0bf
--- /dev/null
+++ b/gn2/tests/unit/wqflask/show_trait/test_export_trait_data.py
@@ -0,0 +1,151 @@
+import datetime
+import unittest
+from unittest import mock
+from gn2.wqflask.show_trait.export_trait_data import dict_to_sorted_list
+from gn2.wqflask.show_trait.export_trait_data import cmp_samples
+from gn2.wqflask.show_trait.export_trait_data import export_sample_table
+from gn2.wqflask.show_trait.export_trait_data import get_export_metadata
+
+
+class AttributesSetter:
+    def __init__(self, obj):
+        for key, value in obj.items():
+            setattr(self, key, value)
+
+
+class TestExportTraits(unittest.TestCase):
+    """Test methods for exporting traits and metadata"""
+
+    @mock.patch("wqflask.show_trait.export_trait_data.datetime")
+    @mock.patch("wqflask.show_trait.export_trait_data.create_trait")
+    @mock.patch("wqflask.show_trait.export_trait_data.data_set")
+    def test_get_export_metadata(self, data_mock, trait_mock, date_mock):
+        """test for exporting metadata with dataset.type=Publish"""
+        mock_dataset = AttributesSetter({"type": "Publish",
+                                         "name": "HC_M2_0606_P",
+                                         "dataset_name": "HC_M2_0606_P"})
+
+        mock_dataset.group = AttributesSetter({"name": "C"})
+        data_mock.create_dataset.return_value = mock_dataset
+
+        trait_data = {
+            "symbol": "Nr3c1",
+            "description_display": "nuclear receptor subfamily 3,group C, member 1 (glucocorticoid receptor); distal 3' UTR",
+            "title": "Trait_1 title",
+
+            "authors": "XL_1",
+            "journal": ""
+
+        }
+
+        date_mock.datetime.now.return_value = datetime.datetime(
+            2022, 8, 8, 19, 2, 31, 628813)
+        trait_mock.return_value = AttributesSetter(trait_data)
+
+        results = get_export_metadata({
+            "trait_id": "1460303_at",
+            "trait_display_name": "1460303_at",
+            "dataset": "HC_M2_0606_P",
+            "group": "BXD",
+        })
+
+        expected = [["Phenotype ID:", "1460303_at"],
+                    ["Phenotype URL: ", "http://genenetwork.org/show_trait?trait_id=1460303_at&dataset=HC_M2_0606_P"],
+                    ["Group: ", "C"],
+                    ["Phenotype: ",
+                        'nuclear receptor subfamily 3","group C"," member 1 (glucocorticoid receptor); distal 3\' UTR'],
+                    ["Authors: ", "XL_1"],
+                    ["Title: ", "Trait_1 title"],
+                    ["Journal: ", "N/A"],
+                    ["Dataset Link: ", "http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=HC_M2_0606_P"],
+                    ["Export Date: ", "August 08, 2022"],
+                    ["Export Time: ", "19:02 GMT"]]
+
+        self.assertEqual(results, expected)
+
+    def test_dict_to_sortedlist(self):
+        """test for conversion of dict to sorted list"""
+        sample1 = {
+            "other": "exp1",
+            "name": "exp2"
+        }
+        sample2 = {
+            "se": 1,
+            "num_cases": 4,
+            "value": 6,
+            "name": 3
+
+        }
+        rever = {
+            "name": 3,
+            "value": 6,
+            "num_cases": 4,
+            "se": 1
+        }
+        oneItem = {
+            "item1": "one"
+        }
+
+        self.assertEqual(["exp2", "exp1"], dict_to_sorted_list(sample1))
+        self.assertEqual([3, 6, 1, 4], dict_to_sorted_list(sample2))
+        self.assertEqual([3, 6, 1, 4], dict_to_sorted_list(rever))
+        self.assertEqual(["one"], dict_to_sorted_list(oneItem))
+        """test that the func returns the values not the keys"""
+        self.assertFalse(["other", "name"] == dict_to_sorted_list(sample1))
+
+    def test_cmp_samples(self):
+        """test for comparing samples function"""
+        sampleA = [
+            [
+                ("value", "other"),
+                ("name", "test_name")
+            ]
+        ]
+        sampleB = [
+            [
+                ("value", "other"),
+                ("unknown", "test_name")
+            ]
+        ]
+        sampleC = [
+            [("other", "value"),
+             ("name", "value")
+             ],
+            [
+                ("name", "value"),
+                ("value", "name")
+            ],
+            [
+                ("other", "value"),
+                ("name", "value"
+                 )],
+            [
+                ("name", "name1"),
+                ("se", "valuex")
+            ],
+            [(
+                "value", "name1"),
+                ("se", "valuex")
+             ],
+            [(
+                "other", "name1"),
+                ("se", "valuex"
+                 )
+             ],
+            [(
+                "name", "name_val"),
+                ("num_cases", "num_val")
+             ],
+            [(
+                "other_a", "val_a"),
+                ("other_b", "val"
+                 )
+             ]
+        ]
+        results = [cmp_samples(val[0], val[1]) for val in sampleA]
+        resultB = [cmp_samples(val[0], val[1]) for val in sampleB]
+        resultC = [cmp_samples(val[0], val[1]) for val in sampleC]
+
+        self.assertEqual(1, *results)
+        self.assertEqual(-1, *resultB)
+        self.assertEqual([1, -1, 1, -1, -1, 1, -1, -1], resultC)
diff --git a/gn2/tests/unit/wqflask/show_trait/test_get_max_digits.py b/gn2/tests/unit/wqflask/show_trait/test_get_max_digits.py
new file mode 100644
index 00000000..45484f17
--- /dev/null
+++ b/gn2/tests/unit/wqflask/show_trait/test_get_max_digits.py
@@ -0,0 +1,15 @@
+import pytest
+import unittest
+
+from gn2.wqflask.show_trait.show_trait import get_max_digits
+
+@unittest.skip("Too complicated")
+@pytest.mark.parametrize(
+    "trait_vals,expected",
+    (((
+        (0, 1345, 92, 734),
+        (234253, 33, 153, 5352),
+        (3542, 24, 135)),
+      [3, 5, 3]),))
+def test_get_max_digits(trait_vals, expected):
+    assert get_max_digits(trait_vals) == expected