mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-21 06:58:12 +08:00
Matt Weiden
546e272a60
* Add user-defined category-label colors Fixes https://github.com/chanzuckerberg/cellxgene/issues/1152 As described in https://github.com/chanzuckerberg/cellxgene/issues/1307 * Respond to feedback from @bkmartinjr in nodejs * Respond to feedback from @bkmartinjr in python * Add tests to the server module * Autoformat python, run linter * Make colors_get error handling specific * Respond to feedback from @bkmartinjr * Respond to feedback from @bkmartinjr * Fix whitespace * Fix python lint errrors * Update documentation * Add --disable-user-colors option to launch and cxgtool.py * Fix python formatting * Rename '--disable-user-colors' to '--disable-custom-colors'
82 lines
2.8 KiB
Python
82 lines
2.8 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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from server.common.app_config import AppConfig
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from server.test import PROJECT_ROOT
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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(f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad")
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config = AppConfig()
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config.update(single_dataset__datapath=self.data_file.path)
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config.complete_config()
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self.data = AnndataAdaptor(self.data_file, config)
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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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"embeddings__names": ["umap"],
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"presentation__max_categories": 100,
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"single_dataset__obs_names": None,
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"single_dataset__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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config = AppConfig()
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config.update(**self.args)
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config.update(single_dataset__datapath=locator.path)
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config.complete_config()
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data = AnndataAdaptor(locator, config)
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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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config = AppConfig()
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config.update(**self.args)
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data = AnndataAdaptor(locator, config)
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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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config = AppConfig()
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config.update(**self.args)
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data = AnndataAdaptor(locator, config)
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self.stdAsserts(data)
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