mirror of
https://github.com/chanzuckerberg/cellxgene.git
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fb61bd6e9c
This splits the backend into two parts: the local backend for desktop cellxgene and the AWS backend for hosted cellxgene. The local backend is in local_server while the hosted remains in server. The general idea is to copy everything from server to local_server, pull unneeded stuff out of local_server, and keep server as-is for this PR. Not touching server means all the infra and deployment code will continue working just as it did before so we can make those changes incrementally.
63 lines
2.7 KiB
Python
63 lines
2.7 KiB
Python
import unittest
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import numpy as np
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from local_server.data_common.matrix_loader import MatrixDataLoader
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from local_server.test import PROJECT_ROOT, app_config
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class DiffExpTest(unittest.TestCase):
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"""Tests the diffexp returns the expected results for one test case, using different
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adaptor types and different algorithms."""
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def load_dataset(self, path, extra_server_config={}, extra_dataset_config={}):
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config = app_config(path, extra_server_config=extra_server_config, extra_dataset_config=extra_dataset_config)
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loader = MatrixDataLoader(path)
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adaptor = loader.open(config)
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return adaptor
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def get_mask(self, adaptor, start, stride):
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"""Simple function to return a mask or rows"""
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rows = adaptor.get_shape()[0]
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sel = list(range(start, rows, stride))
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mask = np.zeros(rows, dtype=bool)
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mask[sel] = True
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return mask
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def compare_diffexp_results(self, results, expects):
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self.assertEqual(len(results), len(expects))
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for result, expect in zip(results, expects):
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self.assertEqual(result[0], expect[0])
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self.assertTrue(np.isclose(result[1], expect[1], 1e-6, 1e-4))
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self.assertTrue(np.isclose(result[2], expect[2], 1e-6, 1e-4))
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self.assertTrue(np.isclose(result[3], expect[3], 1e-6, 1e-4))
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def check_1_10_2_10(self, results):
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"""Checks the results for a specific set of rows selections"""
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expects = [
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[956, 0.016060986, 0.0008649321884808977, 1.0],
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[1124, 0.96602094, 0.0011717216548271284, 1.0],
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[1809, 1.1110606, 0.0019304405196777848, 1.0],
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[1712, -0.5525154, 0.0051788902660723345, 1.0],
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[1754, 0.5201581, 0.005691734062127954, 1.0],
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[948, 1.6390722, 0.006622111055981219, 1.0],
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[1810, 0.78618884, 0.007055917428377063, 1.0],
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[779, 1.5241305, 0.007202934422407284, 1.0],
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[1575, 1.0317602, 0.007830310753043345, 1.0],
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[576, 0.97873515, 0.008272092578813124, 1.0],
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]
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self.compare_diffexp_results(results, expects)
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def get_X_col(self, adaptor, cols):
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varmask = np.zeros(adaptor.get_shape()[1], dtype=bool)
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varmask[cols] = True
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return adaptor.get_X_array(None, varmask)
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def test_anndata_default(self):
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"""Test an anndata adaptor with its default diffexp algorithm (diffexp_generic)"""
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adaptor = self.load_dataset(f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad")
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maskA = self.get_mask(adaptor, 1, 10)
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maskB = self.get_mask(adaptor, 2, 10)
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results = adaptor.compute_diffexp_ttest(maskA, maskB, 10)
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self.check_1_10_2_10(results)
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