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do not hard-wire column names in annotations (#785)

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* enforce column name uniqueness for obs and var

* parameterize the column name containing obs and var user-readable names

* use the new annotation index value from schema

* update f/e unit tests

* PR review suggestions

* lint
This commit is contained in:
Bruce Martin
2019-05-24 21:00:54 -07:00
committed by GitHub
parent a8c2e408d1
commit 3dc45d6330
16 changed files with 246 additions and 155 deletions
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server/test/test_nan_scanpy_engine.py
+4 -2
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@@ -58,14 +58,16 @@ class NaNTest(unittest.TestCase):
def test_annotation(self):
annotations = decode_fbs.decode_matrix_FBS(self.data.annotation_to_fbs_matrix("obs"))
obs_index_col_name = self.data.schema["annotations"]["obs"]["index"]
self.assertEqual(
annotations["col_idx"],
["name", "n_genes", "percent_mito", "n_counts", "louvain"]
[obs_index_col_name, "n_genes", "percent_mito", "n_counts", "louvain"]
)
self.assertEqual(annotations["n_rows"], 100)
self.assertTrue(math.isnan(annotations["columns"][2][0]))
annotations = decode_fbs.decode_matrix_FBS(self.data.annotation_to_fbs_matrix("var"))
self.assertEqual(annotations["col_idx"], ["name", "n_cells", "var_with_nans"])
var_index_col_name = self.data.schema["annotations"]["var"]["index"]
self.assertEqual(annotations["col_idx"], [var_index_col_name, "n_cells", "var_with_nans"])
self.assertEqual(annotations["n_rows"], 100)
self.assertTrue(math.isnan(annotations["columns"][2][0]))