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"""Tests for wqflask/base/data_set.py"""
import unittest
from unittest import mock
from dataclasses import dataclass
from gn3.monads import MonadicDict
from gn2.wqflask import app
from gn2.base.data_set import DatasetType
from gn2.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('gn2.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("gn2.base.data_set.dataset.query_sql")
@mock.patch("gn2.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("gn2.base.data_set.dataset.query_sql")
@mock.patch("gn2.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))
|
