mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-21 16:18:12 +08:00
bmccandless
907cc634f5
This PR contains a refactoring to make adding new features easier. The new features include supporting the tiledb format, and the multi dataset application. The refactoring includes Simplifying the directory structure and files. a class structure to handle annotations (currently one type: AnnotationsLocalFile). a class to handle application configuration a class structure to handle matrix data (currently AnndataAdaptor and CxgAdaptor). CxgAdaptor uses tiledb. Algorithms that were previously dependent on the scanpy anndata object are now generalized to work with an abstract interface. The multi dataset option is not fully supported yet, and so the option to use it is hidden. Use "cli launch --dataroot ..." To access this feature. All combinations of app single dataset/ app multi dataset and AnndataAdaptor/CxgAdaptor work with all the features, such as annotations, ontologies, diffexp.
69 lines
2.3 KiB
Python
69 lines
2.3 KiB
Python
import unittest
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import json
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from server.data_anndata.anndata_adaptor import AnndataAdaptor
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from server.common.data_locator import DataLocator
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class DataLoadAdaptorTest(unittest.TestCase):
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"""
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Test file loading, including deferred loading/update.
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"""
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def setUp(self):
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self.data_file = DataLocator("../example-dataset/pbmc3k.h5ad")
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self.data = AnndataAdaptor(self.data_file)
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def test_delayed_load_data(self):
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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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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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class DataLocatorAdaptorTest(unittest.TestCase):
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"""
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Test various types of data locators we expect to consume
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"""
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def setUp(self):
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self.args = {
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"layout": ["umap"],
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"max_category_items": 100,
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"obs_names": None,
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"var_names": None,
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"diffexp_lfc_cutoff": 0.01,
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}
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def stdAsserts(self, data):
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""" run these each time we load the data """
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self.assertIsNotNone(data)
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self.assertEqual(data.cell_count, 2638)
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self.assertEqual(data.gene_count, 1838)
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def test_posix_file(self):
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locator = DataLocator("../example-dataset/pbmc3k.h5ad")
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data = AnndataAdaptor(locator, self.args)
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self.stdAsserts(data)
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def test_url_https(self):
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url = "https://raw.githubusercontent.com/chanzuckerberg/cellxgene/master/example-dataset/pbmc3k.h5ad"
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locator = DataLocator(url)
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data = AnndataAdaptor(locator, self.args)
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self.stdAsserts(data)
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def test_url_http(self):
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url = "http://raw.githubusercontent.com/chanzuckerberg/cellxgene/master/example-dataset/pbmc3k.h5ad"
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locator = DataLocator(url)
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data = AnndataAdaptor(locator, self.args)
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self.stdAsserts(data)
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