class DataLoadEngineTest(unittest.TestCase):
"""
Test file loading, including deferred loading/update.
"""
def setUp(self):
self.data_file = DataLocator("example-dataset/pbmc3k.h5ad")
self.data = ScanpyEngine()
def test_init(self):
self.assertIsNone(self.data.data)
def test_delayed_load_args(self):
args = {
"layout": ["tsne"],
"max_category_items": 1000,
"obs_names": "foo",
"var_names": "bar",
"diffexp_lfc_cutoff": 0.1,
"annotations": False,
"annotations_file": None,
"annotations_output_dir": None,
"backed": False,
"diffexp_may_be_slow": False,
"disable_diffexp": False
}
self.data.update(args=args)
self.assertEqual(args, self.data.config)
def test_requires_data(self):
with self.assertRaises(DriverError):
self.data._create_schema()
def test_delayed_load_data(self):
self.data.update(data_locator=self.data_file)
self.data._create_schema()
self.assertEqual(self.data.cell_count, 2638)
self.assertEqual(self.data.gene_count, 1838)
epsilon = 0.000_005
self.assertTrue(self.data.data.X[0, 0] - -0.171_469_51 < epsilon)
def test_diffexp_topN(self):
self.data.update(data_locator=self.data_file)
f1 = {"filter": {"obs": {"index": [[0, 500]]}}}
f2 = {"filter": {"obs": {"index": [[500, 1000]]}}}
result = json.loads(self.data.diffexp_topN(f1["filter"], f2["filter"]))
self.assertEqual(len(result), 10)
result = json.loads(
self.data.diffexp_topN(f1["filter"], f2["filter"], 20))
self.assertEqual(len(result), 20)
class DataLoadEngineTest(unittest.TestCase):
def setUp(self):
self.data_file = "example-dataset/pbmc3k.h5ad"
self.data = ScanpyEngine()
def test_init(self):
self.assertIsNone(self.data.data)
def test_delayed_load_args(self):
args = {
"layout": ["tsne"],
"max_category_items": 1000,
"obs_names": "foo",
"var_names": "bar",
"diffexp_lfc_cutoff": 0.1,
}
self.data.update(args=args)
self.assertEqual(args, self.data.config)
def test_requires_data(self):
with self.assertRaises(DriverError):
self.data._create_schema()
def test_delayed_load_data(self):
self.data.update(data=self.data_file)
self.data._create_schema()
self.assertEqual(self.data.cell_count, 2638)
self.assertEqual(self.data.gene_count, 1838)
epsilon = 0.000_005
self.assertTrue(self.data.data.X[0, 0] - -0.171_469_51 < epsilon)
def test_diffexp_topN(self):
self.data.update(data=self.data_file)
f1 = {"filter": {"obs": {"index": [[0, 500]]}}}
f2 = {"filter": {"obs": {"index": [[500, 1000]]}}}
result = json.loads(self.data.diffexp_topN(f1["filter"], f2["filter"]))
self.assertEqual(len(result), 10)
result = json.loads(
self.data.diffexp_topN(f1["filter"], f2["filter"], 20))
self.assertEqual(len(result), 20)
if __name__ == "__main__":
unittest.main()