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re-implement re-embeddings (#1679)

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* fix mispelling

* re-implement re-embedding

* always load base embedding to fetch counts

* format

* lint

* fix tests

* lint

* fix accept handling

* test log

* more debug

* more

* more

* more

* more

* remove logging

* logging

* jsonify

* remove debugging logs

* lint

* clean up errors a bit

* fix issue found in PR review

* PR review changes
This commit is contained in:
Bruce Martin
2020-07-30 12:31:36 -07:00
committed by GitHub
parent bd147abb3f
commit 75cb513dd9
18 changed files with 225 additions and 179 deletions
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server/test/test_anndata_adaptor.py
+5 -5
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@@ -237,14 +237,14 @@ class AdaptorTest(unittest.TestCase):
self.data.compute_embedding("umap", filter)
return
(schema, fbs) = self.data.compute_embedding("umap", filter)
schema = self.data.compute_embedding("umap", filter)
self.assertIsInstance(schema["name"], str)
name = schema["name"]
self.assertEqual(schema["type"], "float32")
self.assertEqual(schema["dims"], [f"{name}_0", f"{name}_1"])
emb = decode_fbs.decode_matrix_FBS(fbs)
self.assertEqual(emb["n_rows"], 100)
self.assertEqual(emb["n_cols"], 2)
self.assertEqual(emb["col_idx"], [f"{name}_0", f"{name}_1"])
emb = self.data.data.obsm[f"X_{name}"]
self.assertEqual(emb.shape, (2638, 2))
self.assertTrue(np.isfinite(emb[0:100]).all())
self.assertTrue(np.isnan(emb[100:]).all())