mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-21 19:38:12 +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'
64 lines
2.8 KiB
Python
64 lines
2.8 KiB
Python
import pytest
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import unittest
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import warnings
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import math
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import server.test.decode_fbs as decode_fbs
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from server.data_anndata.anndata_adaptor import AnndataAdaptor
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from server.common.errors import FilterError
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from server.common.data_locator import DataLocator
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from server.test import PROJECT_ROOT, app_config
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class NaNTest(unittest.TestCase):
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def setUp(self):
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self.data_locator = DataLocator(f"{PROJECT_ROOT}/server/test/test_datasets/nan.h5ad")
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self.config = app_config(self.data_locator.path)
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with warnings.catch_warnings():
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warnings.simplefilter("ignore", category=UserWarning)
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self.data = AnndataAdaptor(self.data_locator, self.config)
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self.data._create_schema()
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def test_load(self):
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with self.assertWarns(UserWarning):
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self.data = AnndataAdaptor(self.data_locator, self.config)
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def test_init(self):
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self.assertEqual(self.data.cell_count, 100)
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self.assertEqual(self.data.gene_count, 100)
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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_dataframe(self):
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data_frame_var = decode_fbs.decode_matrix_FBS(self.data.data_frame_to_fbs_matrix(None, "var"))
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self.assertIsNotNone(data_frame_var)
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self.assertEqual(data_frame_var["n_rows"], 100)
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self.assertEqual(data_frame_var["n_cols"], 100)
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self.assertTrue(math.isnan(data_frame_var["columns"][3][3]))
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with pytest.raises(FilterError):
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self.data.data_frame_to_fbs_matrix("an erroneous filter", "var")
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with pytest.raises(FilterError):
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filter_ = {"filter": {"obs": {"index": [1, 99, [200, 300]]}}}
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self.data.data_frame_to_fbs_matrix(filter_["filter"], "var")
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def test_dataframe_obs_not_implemented(self):
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with self.assertRaises(ValueError) as cm:
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decode_fbs.decode_matrix_FBS(self.data.data_frame_to_fbs_matrix(None, "obs"))
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self.assertIsNotNone(cm.exception)
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def test_annotation(self):
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annotations = decode_fbs.decode_matrix_FBS(self.data.annotation_to_fbs_matrix("obs"))
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obs_index_col_name = self.data.schema["annotations"]["obs"]["index"]
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self.assertEqual(annotations["col_idx"], [obs_index_col_name, "n_genes", "percent_mito", "n_counts", "louvain"])
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self.assertEqual(annotations["n_rows"], 100)
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self.assertTrue(math.isnan(annotations["columns"][2][0]))
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annotations = decode_fbs.decode_matrix_FBS(self.data.annotation_to_fbs_matrix("var"))
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var_index_col_name = self.data.schema["annotations"]["var"]["index"]
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self.assertEqual(annotations["col_idx"], [var_index_col_name, "n_cells", "var_with_nans"])
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self.assertEqual(annotations["n_rows"], 100)
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self.assertTrue(math.isnan(annotations["columns"][2][0]))
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