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Apply yapf to python files

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This commit is contained in:
Matt Weiden
2019-12-19 15:20:41 -08:00
parent 42a8d45bd7
commit cdca128a01
43 changed files with 1143 additions and 678 deletions
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server/test/test_nan_scanpy_engine.py
+17 -15
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@@ -11,6 +11,7 @@ from server.app.util.data_locator import DataLocator
class NaNTest(unittest.TestCase):
def setUp(self):
self.args = {
"layout": ["umap"],
@@ -21,7 +22,8 @@ class NaNTest(unittest.TestCase):
}
with warnings.catch_warnings():
warnings.simplefilter("ignore", category=UserWarning)
self.data = ScanpyEngine(DataLocator("test/test_datasets/nan.h5ad"), self.args)
self.data = ScanpyEngine(DataLocator("test/test_datasets/nan.h5ad"),
self.args)
self.data._create_schema()
def test_load(self):
@@ -35,7 +37,8 @@ class NaNTest(unittest.TestCase):
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"))
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)
@@ -44,30 +47,29 @@ class NaNTest(unittest.TestCase):
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]]}
}
}
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"))
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"))
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"],
[obs_index_col_name, "n_genes", "percent_mito", "n_counts", "louvain"]
)
self.assertEqual(annotations["col_idx"], [
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"))
annotations = decode_fbs.decode_matrix_FBS(
self.data.annotation_to_fbs_matrix("var"))
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["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]))