mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-17 13:58:00 +08:00
57c4e9ff33
* dead code and route removal * more dead code cleanup * fix scanpy_engine tests * lint * add missing catch in filter parsing * update scanpy NaN tests * more fbs tests and dead test removal * remove forced default for content type negotiation * bit of cleanup * more fbs test cleanup * lint * remove swagger * swagger cleanup * lint * correctly handle lack of templates * more dead code removal * remove unused files * fix dev build * lint
72 lines
2.7 KiB
Python
72 lines
2.7 KiB
Python
import pytest
|
|
import unittest
|
|
import warnings
|
|
import math
|
|
|
|
import decode_fbs
|
|
|
|
from server.app.scanpy_engine.scanpy_engine import ScanpyEngine
|
|
from server.app.util.errors import FilterError
|
|
|
|
|
|
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,
|
|
}
|
|
with warnings.catch_warnings():
|
|
warnings.simplefilter("ignore", category=UserWarning)
|
|
self.data = ScanpyEngine("server/test/test_datasets/nan.h5ad", self.args)
|
|
self.data._create_schema()
|
|
|
|
def test_load(self):
|
|
with self.assertWarns(UserWarning):
|
|
ScanpyEngine("server/test/test_datasets/nan.h5ad", self.args)
|
|
|
|
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)
|
|
|
|
def test_dataframe(self):
|
|
data_frame_var = decode_fbs.decode_matrix_FBS(self.data.data_frame_to_fbs_matrix(None, "var"))
|
|
self.assertIsNotNone(data_frame_var)
|
|
self.assertEqual(data_frame_var["n_rows"], 100)
|
|
self.assertEqual(data_frame_var["n_cols"], 100)
|
|
self.assertTrue(math.isnan(data_frame_var["columns"][3][3]))
|
|
|
|
with pytest.raises(FilterError):
|
|
self.data.data_frame_to_fbs_matrix("an erroneous filter", "var")
|
|
with pytest.raises(FilterError):
|
|
filter_ = {
|
|
"filter": {
|
|
"obs": {"index": [1, 99, [200, 300]]}
|
|
}
|
|
}
|
|
self.data.data_frame_to_fbs_matrix(filter_["filter"], "var")
|
|
|
|
def test_dataframe_obs_not_implemented(self):
|
|
with self.assertRaises(ValueError) as cm:
|
|
decode_fbs.decode_matrix_FBS(self.data.data_frame_to_fbs_matrix(None, "obs"))
|
|
self.assertIsNotNone(cm.exception)
|
|
|
|
def test_annotation(self):
|
|
annotations = decode_fbs.decode_matrix_FBS(self.data.annotation_to_fbs_matrix("obs"))
|
|
self.assertEqual(
|
|
annotations["col_idx"],
|
|
["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"])
|
|
self.assertEqual(annotations["n_rows"], 100)
|
|
self.assertTrue(math.isnan(annotations["columns"][2][0]))
|