Add caching back in (#312)

* Add caching back in

Works now against filter instead of dataframe view

* Layout cache and move post->put

* Fix tests

docs/REST_API.md

@@ -461,7 +461,7 @@ Get the _default_ layout for all observations or (_future_) all variables. Retur
 }
 ```
 
-### POST /layout/obs, (_future_) POST /layout/var
+### PUT /layout/obs, (_future_) PUT /layout/var
 
 Generate layout for the caller-specified subset of data, as indicated by the filter. This operation implicitly requests a re-layout operation to be performed on the specified data.
 

server/app/rest_api/rest.py

@@ -670,17 +670,12 @@ class LayoutObsAPI(Resource):
             },
         }
     })
-    def post(self):
+    def put(self):
         try:
-            return make_response(
+            filter = request.get_json()["filter"]
-                jsonify({
+            interactive_limit = current_app.data.features["layout"]["obs"]["interactiveLimit"]
-                    "layout": current_app.data.layout(
+            layout = current_app.data.layout(filter, interactive_limit=interactive_limit)
-                        request.get_json()["filter"],
+            return make_response(jsonify({"layout": layout}), HTTPStatus.OK)
-                        interactive_limit=current_app.data.features["layout"]["obs"]["interactiveLimit"]
-                    )
-                }),
-                HTTPStatus.OK
-            )
         except FilterError as e:
             return make_response(e.message, HTTPStatus.BAD_REQUEST)
         except InteractiveError:

server/app/scanpy_engine/scanpy_engine.py

@@ -6,8 +6,7 @@ from pandas import DataFrame, Series
 import scanpy.api as sc
 from scipy import stats
 
-# TODO fix memoization so that it correctly identifies the same request
+from server.app.app import cache
-# from server.app.app import cache
 from server.app.driver.driver import CXGDriver
 from server.app.util.constants import Axis, DEFAULT_TOP_N, DiffExpMode
 from server.app.util.utils import FilterError, InteractiveError
@@ -201,7 +200,7 @@ class ScanpyEngine(CXGDriver):
                     index = np.logical_and(index, key_idx)
         return index
 
-    # @cache.memoize()
+    @cache.memoize()
     def annotation(self, filter, axis, fields=None):
         """
          Gets annotation value for each observation
@@ -224,7 +223,7 @@ class ScanpyEngine(CXGDriver):
             "data": annotations.reset_index().values.tolist()
         }
 
-    # @cache.memoize()
+    @cache.memoize()
     def data_frame(self, filter, axis):
         """
         Retrieves data for each variable for observations in data frame
@@ -261,7 +260,6 @@ class ScanpyEngine(CXGDriver):
             }
         return result
 
-    # @cache.memoize()
     def diffexp(self, filter1, filter2, top_n=None, interactive_limit=None):
         """
         Computes the top differentially expressed variables between two observation sets. If dataframes
@@ -321,7 +319,7 @@ class ScanpyEngine(CXGDriver):
         # Results need to be returned in var index order
         return sorted(result, key=lambda gene: gene[0])
 
-    # @cache.memoize()
+    @cache.memoize()
     def layout(self, filter, interactive_limit=None):
         """
         Computes a n-d layout for cells through dimensionality reduction.

server/test/test_api.py

@@ -84,22 +84,16 @@ class EndPoints(unittest.TestCase):
                 }
             }
         }
-        result = self.session.post(url, json=obs_filter)
+        result = self.session.put(url, json=obs_filter)
         self.assertEqual(result.status_code, HTTPStatus.OK)
         result_data = result.json()
         self.assertEqual(len(result_data["layout"]["coordinates"]), 15)
 
     def test_bad_filter(self):
-        endpoints = {
+        endpoints = ["layout/obs", "annotations/obs", "annotations/var", "data/obs", "data/var"]
-            "layout/obs": "post",
+        for endpoint in endpoints:
-            "annotations/obs": "put",
-            "annotations/var": "put",
-            "data/obs": "put",
-            "data/var": "put"
-        }
-        for endpoint, method in endpoints.items():
             url = f"{URL_BASE}{endpoint}"
-            result = getattr(self.session, method)(url, json=BAD_FILTER)
+            result = self.session.put(url, json=BAD_FILTER)
             self.assertEqual(result.status_code, HTTPStatus.BAD_REQUEST)
 
     def test_get_annotations_obs(self):
@@ -373,6 +367,39 @@ class EndPoints(unittest.TestCase):
                 self.assertEqual(len(result_data["obs"]), 2638)
                 self.assertEqual(len(result_data["var"][0]), 2639)
 
+    def test_cache(self):
+        endpoint = "annotations/var"
+        url = f"{URL_BASE}{endpoint}"
+        f1 = {"filter": {"var": {"annotation_value": [{"name": "name",
+                                                       "values": ["HLA-DRB1", "HLA-DQA1", "HLA-DQB1", "HLA-DPA1",
+                                                                  "HLA-DPB1", "MS4A1", "IL32", "CCL5", "CD79B",
+                                                                  "CD79A"]}]}}}
+        result = self.session.put(url, json=f1)
+        self.assertEqual(result.status_code, HTTPStatus.OK)
+        result_data1 = result.json()
+        f2 = {"filter": {"var": {"annotation_value": [{"name": "name",
+                                                       "values": ["FGFBP2", "GZMA", "LTB", "PRF1", "CTSW", "GZMH",
+                                                                  "CCL5", "CCL4", "CST7", "NKG7"]}]}}}
+        result = self.session.put(url, json=f2)
+        self.assertEqual(result.status_code, HTTPStatus.OK)
+        result_data2 = result.json()
+        self.assertNotEqual(result_data1, result_data2)
+
+    def test_cache_nofilter(self):
+        endpoint = "annotations/var"
+        url = f"{URL_BASE}{endpoint}"
+        f1 = {"filter": {}}
+        result = self.session.put(url, json=f1)
+        self.assertEqual(result.status_code, HTTPStatus.OK)
+        result_data1 = result.json()
+        f2 = {"filter": {"var": {"annotation_value": [{"name": "name",
+                                                       "values": ["FGFBP2", "GZMA", "LTB", "PRF1", "CTSW", "GZMH",
+                                                                  "CCL5", "CCL4", "CST7", "NKG7"]}]}}}
+        result = self.session.put(url, json=f2)
+        self.assertEqual(result.status_code, HTTPStatus.OK)
+        result_data2 = result.json()
+        self.assertNotEqual(result_data1, result_data2)
+
     def test_static(self):
         endpoint = "static"
         file = "js/service-worker.js"