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"""module contains unittests for pca"""
import unittest
from unittest.mock import patch
from unittest.mock import Mock
import numpy as np
import pytest
from gn3.computations.pca import cache_pca_dataset
from gn3.computations.pca import generate_pca_temp_traits
from gn3.computations.pca import generate_scree_plot_data
from gn3.computations.pca import process_factor_loadings_tdata
class TestPCA(unittest.TestCase):
"""pca testcase class"""
@pytest.mark.unit_test
def test_process_factor_loadings(self):
"""test for processing factor loadings"""
test_array = np.array([
[-0.23511749, -0.61483617, -0.26872797, 0.70319381],
[-0.71057342, 0.4623377, -0.52921008, -0.0355803],
[-0.60977093, -0.02877103, 0.78874096, 0.07238328],
[0.26073856, 0.63827311, 0.16003023, 0.70640864]
])
expected_results = [[-0.23511749, -0.71057342, -0.60977093],
[-0.61483617, 0.4623377, -0.02877103],
[-0.26872797, -0.52921008, 0.78874096],
[0.70319381, -0.0355803, 0.07238328]]
self.assertEqual(process_factor_loadings_tdata(
test_array, 3), expected_results)
@pytest.mark.unit_test
@patch("gn3.computations.pca.generate_pca_traits_vals")
def test_generate_pca_datasets(self, mock_pca_data):
"""test for generating temp pca dataset"""
mock_pca_data.return_value = np.array([[21, 10, 17, 15, 13],
[21, 11, 18,
9, 1],
[22, 16, 0,
0.22667229, -1],
[31, 12, 10, 17, 11]])
shared_samples = ["BXD1", "BXD2", "BXD", "BXD4", "Unkown"]
dataset_samples = ["BXD1", "BXD5", "BXD4", "BXD"]
expected_results = {
"PCA1_mouse_G1_now": ["21.0", "x", "10.0", "17.0"],
"PCA2_mouse_G1_now": ["21.0", "x", "11.0", "18.0"],
"PCA3_mouse_G1_now": ["22.0", "x", "16.0", "0.0"],
"PCA4_mouse_G1_now": ["31.0", "x", "12.0", "10.0"]
}
results = generate_pca_temp_traits(species="mouse", group="G1",
traits_data=[],
dataset_samples=dataset_samples,
corr_array=[],
shared_samples=shared_samples,
create_time="now")
self.assertEqual(results, expected_results)
@pytest.mark.unit_test
def test_generate_scree_plot(self):
"""test scree plot data is generated"""
variance = [0.9271, 0.06232, 0.031]
self.assertEqual(generate_scree_plot_data(variance),
(['PC1', 'PC2', 'PC3'], [92.7, 6.2, 3.1]))
@pytest.mark.unit_test
def test_cache_pca_datasets(self):
"""test for caching pca datasets"""
pca_traits = {
"PCA_1": ["11.0", "x", "9.0", "7.0"],
"PCA_2": ["x", "x", "1.2", "3.1"]
}
self.assertEqual(cache_pca_dataset(redis_conn={}, exp_days=30,
pca_trait_dict=pca_traits), False)
mock_redis = Mock()
mock_redis.set.return_value = True
test_data = [({}, 30, pca_traits, False),
(mock_redis, 30, pca_traits, True)]
for (test_redis, exp_day, test_traits, expected) in test_data:
with self.subTest(redis_conn=test_redis,
exp_days=exp_day, pca_trait_dict=test_traits):
self.assertEqual(cache_pca_dataset(
test_redis, exp_day, test_traits), expected)
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