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https://github.com/chanzuckerberg/cellxgene.git
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9c6273eb94
* move app creation to function * create engine without load * flake 8 fixes * cleanup original scanpy test * add default config * handle missing data * test data changes * unify update * load data isn't static anymore * make app a class
51 lines
1.6 KiB
Python
51 lines
1.6 KiB
Python
import unittest
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import json
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from server.app.scanpy_engine.scanpy_engine import ScanpyEngine
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from server.app.util.errors import DriverError
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class DataLoadEngineTest(unittest.TestCase):
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def setUp(self):
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self.data_file = "example-dataset/pbmc3k.h5ad"
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self.data = ScanpyEngine()
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def test_init(self):
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self.assertIsNone(self.data.data)
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def test_delayed_load_args(self):
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args = {
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"layout": "tsne",
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"diffexp": "ttest",
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"max_category_items": 1000,
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"obs_names": "foo",
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"var_names": "bar",
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"diffexp_lfc_cutoff": 0.1,
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}
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self.data.update(args=args)
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self.assertEqual(args, self.data.config)
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def test_requires_data(self):
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with self.assertRaises(DriverError):
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self.data._create_schema()
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def test_delayed_load_data(self):
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self.data.update(data=self.data_file)
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self.data._create_schema()
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self.assertEqual(self.data.cell_count, 2638)
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self.assertEqual(self.data.gene_count, 1838)
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epsilon = 0.000_005
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self.assertTrue(self.data.data.X[0, 0] - -0.171_469_51 < epsilon)
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def test_diffexp_topN(self):
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self.data.update(data=self.data_file)
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f1 = {"filter": {"obs": {"index": [[0, 500]]}}}
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f2 = {"filter": {"obs": {"index": [[500, 1000]]}}}
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result = json.loads(self.data.diffexp_topN(f1["filter"], f2["filter"]))
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self.assertEqual(len(result), 10)
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result = json.loads(self.data.diffexp_topN(f1["filter"], f2["filter"], 20))
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self.assertEqual(len(result), 20)
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if __name__ == "__main__":
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unittest.main()
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