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.

1 files changed, 262 insertions, 0 deletions

diff --git a/gn2/tests/unit/base/test_trait.py b/gn2/tests/unit/base/test_trait.py
new file mode 100644
index 00000000..417956ae
--- /dev/null
+++ b/gn2/tests/unit/base/test_trait.py
@@ -0,0 +1,262 @@
+# -*- coding: utf-8 -*-
+"""Tests wqflask/base/trait.py"""
+import unittest
+from unittest import mock
+
+from gn2.base.trait import GeneralTrait
+from gn2.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'"""
+    @mock.patch('base.trait.database_connection')
+    def test_retrieve_trait_info_with_empty_dataset(self, mock_db):
+        """Test that an exception is raised when dataset is empty"""
+        conn = mock.MagicMock()
+        mock_db.return_value.__enter__.return_value = conn
+        with self.assertRaises(ValueError):
+            retrieve_trait_info(trait=mock.MagicMock(),
+                                dataset={})
+
+    @mock.patch('base.trait.requests.get')
+    @mock.patch('base.trait.g', mock.Mock())
+    @mock.patch('base.trait.database_connection')
+    def test_retrieve_trait_info_with_empty_trait_info(self,
+                                                       mock_db,
+                                                       requests_mock):
+        """Empty trait info"""
+        conn = mock.MagicMock()
+        cursor = mock.MagicMock()
+        cursor.fetchone.return_value = {}
+        conn.cursor.return_value.__enter__.return_value = cursor
+        mock_db.return_value.__enter__.return_value = conn
+        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())
+    @mock.patch('base.trait.database_connection')
+    def test_retrieve_trait_info_with_non_empty_trait_info(self,
+                                                           mock_db,
+                                                           requests_mock):
+        """Test that attributes are set"""
+        mock_dataset = mock.MagicMock()
+        conn = mock.MagicMock()
+        cursor = mock.MagicMock()
+        cursor.fetchone.return_value = [1, 2, 3, 4]
+        conn.cursor.return_value.__enter__.return_value = cursor
+        mock_db.return_value.__enter__.return_value = conn
+        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())
+    @mock.patch('base.trait.database_connection')
+    def test_retrieve_trait_info_utf8_parsing(self,
+                                              mock_db,
+                                              requests_mock):
+        """Test that utf-8 strings are parsed correctly"""
+        utf_8_string = "test_string"
+        conn = mock.MagicMock()
+        mock_db.return_value.__enter__.return_value = conn
+        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")
+
+
+    @unittest.skip("Too complicated")
+    @mock.patch('base.trait.requests.get')
+    @mock.patch('base.trait.database_connection')
+    @mock.patch('base.trait.get_resource_id')
+    def test_retrieve_trait_info_with_non_empty_lrs(self,
+                                                    resource_id_mock,
+                                                    mock_db,
+                                                    requests_mock):
+        """Test retrieve trait info when lrs has a value"""
+        resource_id_mock.return_value = 1
+        conn = mock.MagicMock()
+        mock_db.return_value.__enter__.return_value = conn
+        with conn.cursor() as cursor:
+            cursor.fetchone.side_effect = [
+                # trait_info = g.db.execute(query).fetchone()
+                [1, 2, 3, 4],
+                # trait_qtl = g.db.execute(query).fetchone()
+                [1, 2.37, 3, 4, 5],
+                # trait_info = g.db.execute(query).fetchone()
+                [2.7333, 2.1204]
+            ]
+            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")
+
+    @unittest.skip("Too complicated")
+    @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")
+        
+    @unittest.skip("Too complicated")
+    @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")