core library (#711)

* move app creation to function

* create engine without load

* flake 8 fixes

* cleanup original scanpy test

* add default config

* handle missing data

* test data changes

* unify update

* load data isn't static anymore

* make app a class

server/test/test_scanpy_engine_data_load.py

@@ -0,0 +1,50 @@
+import unittest
+import json
+
+from server.app.scanpy_engine.scanpy_engine import ScanpyEngine
+from server.app.util.errors import DriverError
+
+
+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",
+            "diffexp": "ttest",
+            "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()