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https://github.com/chanzuckerberg/cellxgene.git
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59f989d26f
* initial support for corpora schema conventions * remove debugging print * add corpora util module * tests * lint * PR review edits * PR changes * more PR changes * more PR chnages * PR fixes * formatting * PR updates * lint * PR review
42 lines
1.5 KiB
Python
42 lines
1.5 KiB
Python
import shutil
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import unittest
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import anndata
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from server.common.data_locator import DataLocator
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from server.converters.cxgtool import write_cxg, create_cxg_group_metadata
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from server.data_cxg.cxg_adaptor import CxgAdaptor
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from server.test import PROJECT_ROOT, app_config, random_string
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from server.test.test_datasets.fixtures import pbmc3k_colors
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class TestCxgAdaptor(unittest.TestCase):
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def setUp(self) -> None:
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self.fixtures = []
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def tearDown(self) -> None:
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try:
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for data_locator in self.fixtures:
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print("REMOVING ", data_locator)
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shutil.rmtree(data_locator)
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except FileNotFoundError:
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pass
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def test_cxg_category_colors(self):
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data = self.convert_pbmc3k(extract_colors=True)
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self.assertEqual(data.get_colors(), pbmc3k_colors)
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data = self.convert_pbmc3k(extract_colors=False)
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self.assertEqual(data.get_colors(), {})
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def convert_pbmc3k(self, **kwargs):
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rand_str = random_string(8)
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data_locator = f"/tmp/test_{rand_str}.cxg"
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self.fixtures.append(data_locator)
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source_h5ad = anndata.read_h5ad(f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad")
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cxg_group_metadata = create_cxg_group_metadata(
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adata=source_h5ad, basefname="pbmc3k.h5ad", title="pbmc3k", **kwargs
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)
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write_cxg(adata=source_h5ad, container=data_locator, cxg_group_metadata=cxg_group_metadata)
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config = app_config(data_locator)
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return CxgAdaptor(DataLocator(data_locator), config)
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