Add tests for scanpy engine

server/app/scanpy_engine/scanpy_engine.py

@@ -61,11 +61,11 @@ class ScanpyEngine(CXGDriver):
             else:
                 min_ = value["query"]["min"]
                 max_ = value["query"]["max"]
-                if min_:
+                if min_ is not None:
                     key_idx = np.array((getattr(self.data.obs, key) >= min_).data)
                     cell_idx = np.logical_and(cell_idx, key_idx)
-                if max_:
+                if max_ is not None:
-                    key_idx = np.array((getattr(self.data.obs, key) <= min_).data)
+                    key_idx = np.array((getattr(self.data.obs, key) <= max_).data)
                     cell_idx = np.logical_and(cell_idx, key_idx)
         return self.data[cell_idx, :]
 

server/test/test_scanpy_engine.py

@@ -0,0 +1,49 @@
+import unittest
+
+from server.app.scanpy_engine.scanpy_engine import ScanpyEngine
+
+
+class UtilTest(unittest.TestCase):
+    def setUp(self):
+        self.data = ScanpyEngine("example-dataset/", schema="data_schema.json")
+
+    def test_init(self):
+        assert self.data.cell_count == 2638
+        assert self.data.gene_count == 1838
+        epsilon = 0.000005
+        assert self.data.data.X[0,0] - -0.17146951 < epsilon
+
+    def test_schema(self):
+        assert self.data.schema == {'CellName': {'type': 'string', 'variabletype': 'categorical', 'displayname': 'Name', 'include': True}, 'n_genes': {'type': 'int', 'variabletype': 'continuous', 'displayname': 'Num Genes', 'include': True}, 'percent_mito': {'type': 'float', 'variabletype': 'continuous', 'displayname': 'Mitochondrial Percentage', 'include': True}, 'n_counts': {'type': 'float', 'variabletype': 'continuous', 'displayname': 'Num Counts', 'include': True}, 'louvain': {'type': 'string', 'variabletype': 'categorical', 'displayname': 'Louvain Cluster', 'include': True}}
+
+    def test_cells(self):
+        cells = self.data.cells()
+        assert "AAACATACAACCAC-1" in cells
+        assert len(cells) == 2638
+
+    def test_genes(self):
+        genes = self.data.genes()
+        assert "SEPT4" in genes
+        assert len(genes) == 1838
+
+    def test_filter_categorical(self):
+        filter = {"louvain": {"variable_type": "categorical", "value_type": "string", "query": ["B cells"]}}
+        filtered_data = self.data.filter_cells(filter)
+        assert filtered_data.shape == (342, 1838)
+        louvain_vals = filtered_data.obs['louvain'].tolist()
+        assert "B cells" in louvain_vals
+        assert "NK cells" not in louvain_vals
+
+    def test_filter_continuous(self):
+        # print(self.data.data.obs["n_genes"].tolist())
+        filter = {"n_genes": {"variable_type": "continuous", "value_type": "int", "query": {"min": 300, "max": 400}}}
+        filtered_data = self.data.filter_cells(filter)
+        assert filtered_data.shape == (71, 1838)
+        n_genes_vals = filtered_data.obs['n_genes'].tolist()
+        for val in n_genes_vals:
+            assert 300 <= val <= 400
+
+
+
+if __name__ == '__main__':
+    unittest.main()