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Return empty colors for .cxg v0.0 files (#1441)
* Return empty colors for .cxg v0.0 files Fixes https://github.com/chanzuckerberg/cellxgene/issues/1440 The CxgAdaptor.get_colors method currently assumes that the .cxg file has cxg_group_metadata. As a result, the /api/v0.2/colors endpoint always fails for .cxg v0.0 files. * Add test fixture
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@@ -195,6 +195,8 @@ class CxgAdaptor(DataAdaptor):
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return diffexp_cxg.diffexp_ttest(self, maskA, maskB, top_n, lfc_cutoff)
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def get_colors(self):
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if self.cxg_version == "0.0":
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return dict()
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meta = self.open_array("cxg_group_metadata").meta
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return json.loads(meta["cxg_category_colors"]) if "cxg_category_colors" in meta else dict()
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@@ -7,10 +7,14 @@ from server.test.test_datasets.fixtures import pbmc3k_colors
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class TestCxgAdaptor(unittest.TestCase):
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def setUp(self):
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data_locator = f"{PROJECT_ROOT}/server/test/test_datasets/pbmc3k.cxg"
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config = app_config(data_locator)
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self.data = CxgAdaptor(DataLocator(data_locator), config)
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def test_get_colors(self):
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self.assertEqual(self.data.get_colors(), pbmc3k_colors)
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data = self.get_data("pbmc3k.cxg")
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self.assertDictEqual(data.get_colors(), pbmc3k_colors)
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data = self.get_data("pbmc3k_v0.cxg")
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self.assertDictEqual(data.get_colors(), dict())
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def get_data(self, fixture):
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data_locator = f"{PROJECT_ROOT}/server/test/test_datasets/{fixture}"
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config = app_config(data_locator)
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return CxgAdaptor(DataLocator(data_locator), config)
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