Add Endpoint to get menu items for use in UI

1 files changed, 442 insertions, 0 deletions

diff --git a/tests/unit/db/test_gen_menu.py b/tests/unit/db/test_gen_menu.py
new file mode 100644
index 0000000..e6b5711
--- /dev/null
+++ b/tests/unit/db/test_gen_menu.py
@@ -0,0 +1,442 @@
+"""Test cases for gn3.db.menu"""
+import unittest
+from unittest import mock
+
+import pytest
+
+from gn3.db.menu import gen_dropdown_json
+from gn3.db.menu import get_groups
+from gn3.db.menu import get_types
+from gn3.db.menu import get_datasets
+from gn3.db.menu import phenotypes_exist
+from gn3.db.menu import genotypes_exist
+from gn3.db.menu import build_datasets
+from gn3.db.menu import build_types
+
+
+class TestGenMenu(unittest.TestCase):
+    """Tests for the gen_menu module"""
+
+    def setUp(self):
+        self.test_group = {
+            'mouse': [
+                ['H_T1',
+                 'H_T',
+                 'Family:DescriptionA'
+                 ],
+                ['H_T2', "H_T'", 'Family:None']
+            ],
+            'human': [
+                ['BXD', 'BXD', 'Family:None'],
+                ['HLC', 'Liver: Normal Gene Expression with Genotypes (Merck)',
+                 'Family:Test']
+            ]
+        }
+
+        self.test_type = {
+            'mouse': {
+                'H_T2': [('Phenotypes',
+                          'Traits and Cofactors',
+                          'Phenotypes'),
+                         ('Genotypes',
+                          'DNA Markers and SNPs',
+                          'Genotypes'),
+                         ['M', 'M', 'Molecular Trait Datasets']],
+                'H_T1': [('Phenotypes',
+                          'Traits and Cofactors',
+                          'Phenotypes'),
+                         ('Genotypes',
+                          'DNA Markers and SNPs',
+                          'Genotypes'),
+                         ['M', 'M', 'Molecular Trait Datasets']]
+            },
+            'human': {
+                'HLC': [('Phenotypes',
+                         'Traits and Cofactors',
+                         'Phenotypes'),
+                        ('Genotypes',
+                         'DNA Markers and SNPs',
+                         'Genotypes'),
+                        ['M', 'M', 'Molecular Trait Datasets']],
+                'BXD': [('Phenotypes',
+                         'Traits and Cofactors',
+                         'Phenotypes'),
+                        ('Genotypes',
+                         'DNA Markers and SNPs',
+                         'Genotypes'),
+                        ['M', 'M', 'Molecular Trait Datasets']]
+            }
+        }
+
+    @pytest.mark.unit_test
+    def test_get_groups(self):
+        """Test that species groups are grouped correctly"""
+        db_mock = mock.MagicMock()
+        with db_mock.cursor() as cursor:
+            cursor.fetchall.side_effect = [(
+                # Human
+                ('BXD', 'BXD', None, "human"),
+                (
+                    'HLC',
+                    ('Liver: Normal Gene Expression with Genotypes (Merck)'),
+                    'Test',
+                    "human"),
+                # Mouse
+                ('H_T1', "H_T", "DescriptionA", "mouse"),
+                ('H_T2', "H_T'", None, "mouse")
+            )]
+
+            self.assertEqual(
+                get_groups(db_mock, ["human", "mouse"]), self.test_group)
+
+            cursor.execute.assert_called_once_with(
+                ("SELECT InbredSet.Name, InbredSet.FullName, "
+                 "IFNULL(InbredSet.Family, 'None'), Species.Name AS "
+                 "species_name FROM Species INNER JOIN InbredSet "
+                 "ON InbredSet.SpeciesId = Species.Id "
+                 "WHERE "
+                 "Species.Name IN (%s, %s) "
+                 "GROUP BY "
+                 "InbredSet.Name ORDER BY IFNULL(InbredSet.FamilyOrder, "
+                 "InbredSet.FullName) ASC, IFNULL(InbredSet.Family, "
+                 "InbredSet.FullName) ASC, InbredSet.FullName ASC, "
+                 "InbredSet.MenuOrderId ASC"),
+                ("human", "mouse"))
+
+    @pytest.mark.unit_test
+    def test_phenotypes_exist_with_falsy_values(self):
+        """Test that phenotype check returns correctly when given
+        a None value"""
+        db_mock = mock.MagicMock()
+        with db_mock.cursor() as cursor:
+            for item in [None, False, (), [], ""]:
+                cursor.fetchone.return_value = item
+            self.assertFalse(phenotypes_exist(db_mock, "test"))
+
+    @pytest.mark.unit_test
+    def test_phenotypes_exist_with_truthy_value(self):
+        """Test that phenotype check returns correctly when given Truthy"""
+        db_mock = mock.MagicMock()
+        with db_mock.cursor() as conn:
+            with conn.cursor() as cursor:
+                for item in ["x", ("result"), ["result"], [1]]:
+                    cursor.fetchone.return_value = (item)
+                self.assertTrue(phenotypes_exist(db_mock, "test"))
+
+    @pytest.mark.unit_test
+    def test_genotypes_exist_with_falsy_values(self):
+        """Test that genotype check returns correctly when given a None value
+
+        """
+        db_mock = mock.MagicMock()
+        with db_mock.cursor() as cursor:
+            for item in [None, False, (), [], ""]:
+                cursor.fetchone.return_value = item
+                self.assertFalse(genotypes_exist(db_mock, "test"))
+
+    @pytest.mark.unit_test
+    def test_genotypes_exist_with_truthy_value(self):
+        """Test that genotype check returns correctly when given Truthy """
+        db_mock = mock.MagicMock()
+        with db_mock.cursor() as cursor:
+            for item in ["x", ("result"), ["result"], [1]]:
+                cursor.fetchone.return_value = (item)
+                self.assertTrue(phenotypes_exist(db_mock, "test"))
+
+    @pytest.mark.unit_test
+    def test_build_datasets_with_type_phenotypes(self):
+        """Test that correct dataset is returned for a phenotype type"""
+        db_mock = mock.MagicMock()
+        with db_mock.cursor() as cursor:
+            cursor.fetchall.return_value = (
+                (602, "BXDPublish", "BXD Published Phenotypes"),
+            )
+            self.assertEqual(build_datasets(db_mock, "Mouse", "BXD",
+                                            "Phenotypes"),
+                             [['602', "BXDPublish",
+                               "BXD Published Phenotypes"]])
+            cursor.execute.assert_called_with((
+                "SELECT InfoFiles.GN_AccesionId, PublishFreeze.Name, "
+                "PublishFreeze.FullName FROM InfoFiles, PublishFreeze, "
+                "InbredSet WHERE InbredSet.Name = %s AND "
+                "PublishFreeze.InbredSetId = InbredSet.Id AND "
+                "InfoFiles.InfoPageName = PublishFreeze.Name "
+                "ORDER BY PublishFreeze.CreateTime ASC"
+            ), ("BXD",))
+            self.assertEqual(
+                build_datasets(db_mock, "Mouse", "MDP","Phenotypes"),
+                [['602', "BXDPublish", "Mouse Phenome Database"]])
+
+            cursor.fetchall.return_value = ()
+            cursor.fetchone.return_value = (
+                "BXDPublish", "Mouse Phenome Database"
+            )
+            self.assertEqual(
+                build_datasets(db_mock, "Mouse", "MDP", "Phenotypes"),
+                [["None", "BXDPublish", "Mouse Phenome Database"]])
+
+    @pytest.mark.unit_test
+    def test_build_datasets_with_type_phenotypes_and_no_results(self):
+        """Test that correct dataset is returned for a phenotype type with no
+        results
+
+        """
+        db_mock = mock.MagicMock()
+        with db_mock.cursor() as cursor:
+            cursor.fetchall.return_value = None
+            cursor.fetchone.return_value = (121,
+                                            "text value")
+            self.assertEqual(
+                build_datasets(db_mock, "Mouse", "BXD", "Phenotypes"),
+                [["None", "121", "text value"]])
+            cursor.execute.assert_called_with((
+                "SELECT PublishFreeze.Name, PublishFreeze.FullName "
+                "FROM PublishFreeze, InbredSet "
+                "WHERE InbredSet.Name = %s AND "
+                "PublishFreeze.InbredSetId = InbredSet.Id "
+                "ORDER BY PublishFreeze.CreateTime ASC"
+            ), ("BXD",))
+
+    @pytest.mark.unit_test
+    def test_build_datasets_with_type_genotypes(self):
+        """Test that correct dataset is returned for a phenotype type"""
+        db_mock = mock.MagicMock()
+        with db_mock.cursor() as cursor:
+            cursor.fetchone.return_value = (
+                635, "HLCPublish", "HLC Published Genotypes"
+            )
+            self.assertEqual(
+                build_datasets(db_mock, "Mouse", "HLC", "Genotypes"),
+                [["635", "HLCGeno", "HLC Genotypes"]])
+            cursor.execute.assert_called_with((
+                "SELECT InfoFiles.GN_AccesionId FROM InfoFiles, "
+                "GenoFreeze, InbredSet WHERE InbredSet.Name = %s AND "
+                "GenoFreeze.InbredSetId = InbredSet.Id AND "
+                "InfoFiles.InfoPageName = GenoFreeze.ShortName "
+                "ORDER BY GenoFreeze.CreateTime DESC"
+            ), ("HLC",))
+            cursor.fetchone.return_value = ()
+            self.assertEqual(
+                build_datasets(db_mock, "Mouse", "HLC", "Genotypes"),
+                [["None", "HLCGeno", "HLC Genotypes"]])
+
+    @pytest.mark.unit_test
+    def test_build_datasets_with_type_mrna(self):
+        """Test that correct dataset is returned for a mRNA
+        expression/ Probeset"""
+        db_mock = mock.MagicMock()
+        with db_mock.cursor() as cursor:
+            cursor.fetchall.return_value = (
+                (112, "HC_M2_0606_P",
+                 "Hippocampus Consortium M430v2 (Jun06) PDNN"), )
+            self.assertEqual(
+                build_datasets(db_mock, "Mouse", "HLC", "mRNA"),
+                [["112", 'HC_M2_0606_P',
+                  "Hippocampus Consortium M430v2 (Jun06) PDNN"]])
+            cursor.execute.assert_called_once_with((
+                "SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, "
+                "ProbeSetFreeze.FullName FROM ProbeSetFreeze, "
+                "ProbeFreeze, InbredSet, Tissue, Species WHERE "
+                "Species.Name = %s AND Species.Id = "
+                "InbredSet.SpeciesId AND InbredSet.Name = %s AND "
+                "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND "
+                "Tissue.Name = %s AND ProbeFreeze.TissueId = "
+                "Tissue.Id AND ProbeFreeze.InbredSetId = InbredSet.Id AND "
+                "ProbeSetFreeze.public > 0 "
+                "ORDER BY -ProbeSetFreeze.OrderList DESC, "
+                "ProbeSetFreeze.CreateTime DESC"), ("Mouse", "HLC", "mRNA"))
+
+    @pytest.mark.unit_test
+    @mock.patch('gn3.db.menu.build_datasets')
+    def test_build_types(self, datasets_mock):
+        """Test that correct tissue metadata is returned"""
+        db_mock = mock.MagicMock()
+        datasets_mock.return_value = [
+            ["112", 'HC_M2_0606_P',
+                "Hippocampus Consortium M430v2 (Jun06) PDNN"]
+        ]
+        with db_mock.cursor() as cursor:
+            cursor.fetchall.return_value = (
+                ('Mouse Tissue'), ('Human Tissue'), ('Rat Tissue')
+            )
+            self.assertEqual(
+                build_types(db_mock, 'mouse', 'random group'),
+                [['M', 'M', 'Molecular Traits'],
+                 ['H', 'H', 'Molecular Traits'],
+                 ['R', 'R', 'Molecular Traits']])
+            cursor.execute.assert_called_once_with((
+                "SELECT DISTINCT Tissue.Name "
+                "FROM ProbeFreeze, ProbeSetFreeze, InbredSet, "
+                "Tissue, Species WHERE Species.Name = %s "
+                "AND Species.Id = InbredSet.SpeciesId AND "
+                "InbredSet.Name = %s AND "
+                "ProbeFreeze.TissueId = Tissue.Id AND "
+                "ProbeFreeze.InbredSetId = InbredSet.Id AND "
+                "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id "
+                "ORDER BY Tissue.Name"
+            ), ("mouse", "random group"))
+
+    @pytest.mark.unit_test
+    @mock.patch('gn3.db.menu.build_types')
+    @mock.patch('gn3.db.menu.genotypes_exist')
+    @mock.patch('gn3.db.menu.phenotypes_exist')
+    def test_get_types_with_existing_genotype_and_phenotypes(
+            self,
+            phenotypes_exist_mock,
+            genotypes_exist_mock,
+            build_types_mock):
+        """Test that build types are constructed correctly if phenotypes and genotypes
+        exist
+
+        """
+        phenotypes_exist_mock.return_value = True
+        genotypes_exist_mock.return_value = True
+
+        expected_result = self.test_type
+
+        build_types_mock.return_value = [
+            ['M', 'M', 'Molecular Trait Datasets']
+        ]
+        self.assertEqual(
+            get_types(mock.MagicMock(), self.test_group,), expected_result)
+
+    @pytest.mark.unit_test
+    @mock.patch('gn3.db.menu.build_types')
+    @mock.patch('gn3.db.menu.genotypes_exist')
+    @mock.patch('gn3.db.menu.phenotypes_exist')
+    def test_get_types_with_buildtype_and_non_existent_genotype_and_phenotypes(
+            self,
+            phenotypes_exist_mock,
+            genotypes_exist_mock,
+            build_types_mock):
+        """Test that build types are constructed correctly if phenotypes_exist and
+        genotypes_exist are false but build_type is falsy
+
+        """
+        phenotypes_exist_mock.return_value = False
+        genotypes_exist_mock.return_value = False
+
+        build_types_mock.return_value = []
+        self.assertEqual(get_types(mock.MagicMock(), self.test_group),
+                         {'mouse': {}, 'human': {}})
+
+    @pytest.mark.unit_test
+    @mock.patch('gn3.db.menu.build_types')
+    @mock.patch('gn3.db.menu.genotypes_exist')
+    @mock.patch('gn3.db.menu.phenotypes_exist')
+    def test_get_types_with_non_existent_genotype_phenotypes_and_buildtype(
+            self,
+            phenotypes_exist_mock,
+            genotypes_exist_mock,
+            build_types_mock):
+        """Test that build types are constructed correctly if phenotypes_exist,
+        genotypes_exist and build_types are truthy
+
+        """
+        phenotypes_exist_mock.return_value = False
+        genotypes_exist_mock.return_value = False
+
+        build_types_mock.return_value = [
+            ['M', 'M', 'Molecular Trait Datasets']
+        ]
+        expected_result = {
+            'mouse': {
+                'H_T2': [['M', 'M', 'Molecular Trait Datasets']],
+                'H_T1': [['M', 'M', 'Molecular Trait Datasets']]},
+            'human': {
+                'HLC': [['M', 'M', 'Molecular Trait Datasets']],
+                'BXD': [['M', 'M', 'Molecular Trait Datasets']]}}
+        self.assertEqual(get_types(mock.MagicMock(), self.test_group),
+                         expected_result)
+
+    @pytest.mark.unit_test
+    @mock.patch('gn3.db.menu.build_datasets')
+    def test_get_datasets_with_existent_datasets(
+            self, build_datasets_mock):
+        """Test correct dataset is returned with existent build_datasets"""
+        build_datasets_mock.return_value = "Test"
+        expected_result = {
+            'mouse': {
+                'H_T2': {'Genotypes': 'Test',
+                         'M': 'Test',
+                         'Phenotypes': 'Test'},
+                'H_T1': {'Genotypes': 'Test',
+                         'M': 'Test',
+                         'Phenotypes': 'Test'}},
+            'human': {'HLC': {'Genotypes': 'Test',
+                              'M': 'Test',
+                              'Phenotypes': 'Test'},
+                      'BXD': {'Genotypes': 'Test',
+                              'M': 'Test',
+                              'Phenotypes': 'Test'}}}
+        self.assertEqual(
+            get_datasets(mock.MagicMock(), self.test_type), expected_result)
+
+    @pytest.mark.unit_test
+    @mock.patch('gn3.db.menu.build_datasets')
+    def test_get_datasets_with_non_existent_datasets(self,
+                                                     build_datasets_mock):
+        """Test correct dataset is returned with non-existent build_datasets"""
+        build_datasets_mock.return_value = None
+        expected_result = {
+            'mouse': {
+                'H_T2': {},
+                'H_T1': {}},
+            'human': {'HLC': {},
+                      'BXD': {}}}
+        self.assertEqual(
+            get_datasets(mock.MagicMock(), self.test_type), expected_result)
+
+    @pytest.mark.unit_test
+    @mock.patch('gn3.db.menu.get_datasets')
+    @mock.patch('gn3.db.menu.get_types')
+    @mock.patch('gn3.db.menu.get_groups')
+    @mock.patch('gn3.db.menu.get_all_species')
+    def test_gen_dropdown_json(self,
+                               species_mock,
+                               groups_mock,
+                               types_mock,
+                               datasets_mock):
+        "Test that the correct dictionary is constructed properly"
+        species_mock.return_value = ("speciesA speciesB speciesC speciesD"
+                                     .split(" "))
+        datasets_mock.return_value = ("datasetA datasetB datasetC datasetD"
+                                      .split(" "))
+        groups_mock.return_value = ("groupA groupB groupC groupD"
+                                    .split(" "))
+        types_mock.return_value = ("typeA typeB typeC typeD"
+                                   .split(" "))
+        datasets_mock.return_value = ("datasetA datasetB datasetC datasetD"
+                                      .split(" "))
+
+        expected_result = {
+            'datasets': ['datasetA', 'datasetB', 'datasetC', 'datasetD'],
+            'types': ['typeA', 'typeB', 'typeC', 'typeD'],
+            'groups': ['groupA', 'groupB', 'groupC', 'groupD'],
+            'species': ['speciesA', 'speciesB', 'speciesC', 'speciesD']}
+
+        self.assertEqual(gen_dropdown_json(mock.MagicMock()), expected_result)
+
+@pytest.mark.unit_test
+def test_phenotypes_exist_called_with_correct_query():
+    """Test that phenotypes_exist is called with the correct query"""
+    db_mock = mock.MagicMock()
+    with db_mock.cursor() as cursor:
+        cursor.fetchone.return_value = None
+        phenotypes_exist(db_mock, "test")
+        cursor.execute.assert_called_with((
+            "SELECT Name FROM PublishFreeze "
+            "WHERE PublishFreeze.Name = %s"
+        ), ("testPublish",))
+
+@pytest.mark.unit_test
+def test_genotypes_exist_called_with_correct_query():
+    """Test that genotypes_exist is called with the correct query"""
+    db_mock = mock.MagicMock()
+    with db_mock.cursor() as cursor:
+        cursor.fetchone.return_value = None
+        genotypes_exist(db_mock, "test")
+        cursor.execute.assert_called_with((
+            "SELECT Name FROM GenoFreeze WHERE "
+            "GenoFreeze.Name = %s"
+        ), ("testGeno",))