Move jsonification to engine level (#511)

2026-10-03 06:48:12 +08:00 · 2018-12-18 21:14:24 -08:00
parent 6af7708d62
commit f0f7200f0b
10 changed files with 657 additions and 133 deletions
@@ -0,0 +1,85 @@
+import json
+import pytest
+import unittest
+import warnings
+
+from server.app.scanpy_engine.scanpy_engine import ScanpyEngine
+from server.app.util.errors import JSONEncodingValueError
+
+
+class NaNTest(unittest.TestCase):
+    def setUp(self):
+        self.args = {
+            "layout": "umap",
+            "diffexp": "ttest",
+            "max_category_items": 100,
+            "obs_names": None,
+            "var_names": None,
+            "diffexp_lfc_cutoff": 0.01,
+            "nan_to_num": False,
+        }
+        with warnings.catch_warnings():
+            warnings.simplefilter("ignore", category=UserWarning)
+            self.data = ScanpyEngine("server/test/test_datasets/nan.h5ad", self.args)
+            self.data._create_schema()
+        self.args_nan = dict(self.args)
+        self.args_nan["nan_to_num"] = True
+        with warnings.catch_warnings():
+            warnings.simplefilter("ignore", category=UserWarning)
+            self.data_nan = ScanpyEngine(
+                "server/test/test_datasets/nan.h5ad", self.args_nan
+            )
+            self.data_nan._create_schema()
+
+    def test_load(self):
+        with self.assertWarns(UserWarning):
+            ScanpyEngine("server/test/test_datasets/nan.h5ad", self.args_nan)
+
+    def test_init(self):
+        self.assertEqual(self.data.cell_count, 100)
+        self.assertEqual(self.data.gene_count, 100)
+        epsilon = 0.000_005
+        self.assertTrue(self.data.data.X[0, 0] - -0.171_469_51 < epsilon)
+
+        self.assertEqual(self.data_nan.cell_count, 100)
+        self.assertEqual(self.data_nan.gene_count, 100)
+        epsilon = 0.000_005
+        self.assertTrue(self.data_nan.data.X[0, 0] - -0.171_469_51 < epsilon)
+
+    def test_dataframe(self):
+        data_frame_obs = json.loads(self.data_nan.data_frame(None, "obs"))
+        self.assertEqual(len(data_frame_obs["var"]), 100)
+        self.assertEqual(len(data_frame_obs["obs"]), 100)
+        data_frame_var = json.loads(self.data_nan.data_frame(None, "var"))
+        self.assertEqual(len(data_frame_var["var"]), 100)
+        self.assertEqual(len(data_frame_var["obs"]), 100)
+        with pytest.raises(JSONEncodingValueError):
+            data_frame_obs = json.loads(self.data.data_frame(None, "obs"))
+        with pytest.raises(JSONEncodingValueError):
+            data_frame_var = json.loads(self.data.data_frame(None, "var"))
+
+    def test_dataframe_nan_to_0(self):
+        data_frame_obs = json.loads(self.data_nan.data_frame(None, "obs"))
+        self.assertEqual(data_frame_obs["obs"][1][3], 0.0)
+        data_frame_var = json.loads(self.data_nan.data_frame(None, "var"))
+        self.assertEqual(data_frame_var["var"][1][5], 0.0)
+
+    def test_annotation_nan_to_0(self):
+        annotations_obs = json.loads(self.data_nan.annotation(None, "obs"))
+        self.assertEqual(annotations_obs["data"][0][3], 0.0)
+        annotations_var = json.loads(self.data_nan.annotation(None, "var"))
+        self.assertEqual(annotations_var["data"][0][3], 0.0)
+
+    def test_annotation(self):
+        annotations = json.loads(self.data_nan.annotation(None, "obs"))
+        self.assertEqual(
+            annotations["names"],
+            ["name", "n_genes", "percent_mito", "n_counts", "louvain"],
+        )
+        annotations = json.loads(self.data_nan.annotation(None, "var"))
+        self.assertEqual(annotations["names"], ["name", "n_cells", "var_with_nans"])
+        self.assertEqual(len(annotations["data"]), 100)
+        with pytest.raises(JSONEncodingValueError):
+            annotations = json.loads(self.data.annotation(None, "obs"))
+        with pytest.raises(JSONEncodingValueError):
+            annotations = json.loads(self.data.annotation(None, "var"))