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Code Issues Packages Projects Releases Wiki Activity

Flatbuffer cleanup (#598)

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* 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
This commit is contained in:
Bruce Martin
2019-02-19 08:50:29 -08:00
committed by GitHub
parent 4e67c645f8
commit 57c4e9ff33
16 changed files with 210 additions and 1663 deletions
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server/test/test_nan_scanpy_engine.py
+10 -11
View File
@@ -1,4 +1,3 @@
import json
import pytest
import unittest
import warnings
@@ -7,7 +6,7 @@ import math
import decode_fbs
from server.app.scanpy_engine.scanpy_engine import ScanpyEngine
from server.app.util.errors import JSONEncodingValueError
from server.app.util.errors import FilterError
class NaNTest(unittest.TestCase):
@@ -42,10 +41,15 @@ class NaNTest(unittest.TestCase):
self.assertEqual(data_frame_var["n_cols"], 100)
self.assertTrue(math.isnan(data_frame_var["columns"][3][3]))
with pytest.raises(JSONEncodingValueError):
json.loads(self.data.data_frame(None, "obs"))
with pytest.raises(JSONEncodingValueError):
json.loads(self.data.data_frame(None, "var"))
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:
@@ -65,8 +69,3 @@ class NaNTest(unittest.TestCase):
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]))
with pytest.raises(JSONEncodingValueError):
json.loads(self.data.annotation(None, "obs"))
with pytest.raises(JSONEncodingValueError):
json.loads(self.data.annotation(None, "var"))