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, 0 insertions, 238 deletions

diff --git a/wqflask/tests/unit/base/test_data_set.py b/wqflask/tests/unit/base/test_data_set.py
deleted file mode 100644
index 744c8a94..00000000
--- a/wqflask/tests/unit/base/test_data_set.py
+++ /dev/null
@@ -1,238 +0,0 @@
-"""Tests for wqflask/base/data_set.py"""
-
-import unittest
-from unittest import mock
-from dataclasses import dataclass
-from gn3.monads import MonadicDict
-
-from wqflask import app
-from base.data_set import DatasetType
-from base.data_set.dataset import DataSet
-
-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"
-        ]
-      ]
-    }
-  }
-}
-"""
-
-class MockPhenotypeDataset(DataSet):
-    def setup(self):
-        self.type = "Publish"
-        self.query_for_group = ""
-        self.group = ""
-
-
-    def check_confidentiality(self):
-        pass
-
-    def retrieve_other_names(self):
-        pass
-
-@dataclass
-class MockGroup:
-    name = "Group"
-
-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()
-
-    def test_data_set_type(self):
-        """Test that DatasetType returns correctly if the Redis Instance is not empty
-        and the name variable exists in the dictionary
-
-        """
-        with app.app_context():
-            redis_mock = mock.Mock()
-            cursor_mock = mock.Mock()
-            redis_mock.get.return_value = self.test_dataset
-            self.assertEqual(DatasetType(redis_mock)
-                             ("All Phenotypes", redis_mock, cursor_mock), "Publish")
-            redis_mock.get.assert_called_once_with("dataset_structure")
-
-    @mock.patch('base.data_set.datasettype.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()
-            cursor_mock = mock.Mock()
-            redis_mock.get.return_value = None
-            data_set = DatasetType(redis_mock)
-            self.assertEqual(data_set("BXDGeno", redis_mock, cursor_mock),
-                             "Geno")
-            self.assertEqual(data_set("BXDPublish", redis_mock, cursor_mock),
-                             "Publish")
-            self.assertEqual(data_set("HLC_0311", redis_mock, cursor_mock),
-                             "ProbeSet")
-
-            redis_mock.set.assert_called_once_with(
-                "dataset_structure",
-                ('{"HLC_0311": "ProbeSet", '
-                 '"HLCPublish": "Publish", '
-                 '"BXDGeno": "Geno", '
-                 '"HC_M2_0606_P": "ProbeSet", '
-                 '"BXDPublish": "Publish"}'))
-
-
-class TestDatasetAccessionId(unittest.TestCase):
-    """Tests for the DataSetType class"""
-
-    @mock.patch("base.data_set.dataset.query_sql")
-    @mock.patch("base.data_set.dataset.DatasetGroup")
-    def test_get_accession_id(self, mock_dataset_group, mock_query_sql):
-        def mock_fn():
-            yield MonadicDict({"accession_id": 7})
-        mock_dataset_group.return_value = MockGroup()
-        mock_query_sql.return_value = mock_fn()
-        sample_dataset = MockPhenotypeDataset(
-            name="BXD-LongevityPublish",
-            get_samplelist=False,
-            group_name="BXD",
-            redis_conn=mock.Mock()
-        )
-        sample_dataset\
-            .accession_id\
-            .bind(lambda x: self.assertEqual(7, x))
-
-    @mock.patch("base.data_set.dataset.query_sql")
-    @mock.patch("base.data_set.dataset.DatasetGroup")
-    def test_get_accession_id_empty_return(self, mock_dataset_group,
-                                           mock_query_sql):
-        mock_dataset_group.return_value = MockGroup()
-        mock_query_sql.return_value = None
-        sample_dataset = MockPhenotypeDataset(
-            name="BXD-LongevityPublish",
-            get_samplelist=False,
-            group_name="BXD",
-            redis_conn=mock.Mock()
-        )
-        sample_dataset\
-            .accession_id\
-            .bind(lambda x: self.assertNone(x))