path: root/tests/unit/db/test_gen_menu.py

"""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",))