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"""module contains tests from datasets"""
from unittest import TestCase
from unittest import mock
from gn3.computations.datasets import retrieve_trait_sample_data
from gn3.computations.datasets import get_query_for_dataset_sample
from gn3.computations.datasets import fetch_from_db_sample_data
class TestDatasets(TestCase):
"""class contains tests for datasets"""
@mock.patch("gn3.computations.datasets.fetch_from_db_sample_data")
def test_retrieve_trait_sample_data(self, mock_fetch_sample_results):
"""test retrieving sample data\
for trait from the dataset"""
trait_name = "1419792_at"
dataset_id = "HC_M2_0606_P&"
dataset_type = "Publish"
dataset = {
"id": dataset_id,
"type": dataset_type,
"name": dataset_id
}
fetch_results = [('BXD32', 8.001, None, None, 'BXD32')]
mock_fetch_sample_results.return_value = fetch_results
results = retrieve_trait_sample_data(
dataset, trait_name)
self.assertEqual(mock_fetch_sample_results.call_count, 1)
self.assertEqual(results, fetch_results)
def test_query_for_dataset_sample(self):
"""test for getting query for sample data"""
no_results = get_query_for_dataset_sample("does not exists")
query_exists = get_query_for_dataset_sample("Publish")
self.assertEqual(no_results, None)
self.assertIsInstance(query_exists, str)
def test_fetch_from_db_sample_data(self):
"""test for function that fetches sample\
results from the database"""
database_results = [('BXD31', 8.001, None, None, 'BXD31'),
('BXD32', 7.884, None, None, 'BXD32'),
('BXD42', 7.682, None, None, 'BXD42'),
('BXD42', 7.682, None, None, 'BXD42'),
('BXD40', 7.945, None, None, 'BXD40'),
('BXD43', 7.873, None, None, 'BXD43')
]
database = mock.Mock()
db_cursor = mock.Mock()
db_cursor.execute.return_value = 6
db_cursor.fetchall.return_value = database_results
database.cursor.return_value = db_cursor
mock_pheno_query = """
SELECT
Strain.Name, PublishData.value, PublishSE.error,NStrain.count, Strain.Name2
WHERE
PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
PublishData.Id = PublishXRef.DataId AND PublishXRef.Id = 1419792_at AND
PublishFreeze.Id = '12' AND PublishData.StrainId = Strain.Id
Order BY
Strain.Name
"""
fetch_results = fetch_from_db_sample_data(mock_pheno_query, database)
self.assertEqual(fetch_results, database_results)
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