Merge pull request #138 from chanzuckerberg/csweaver/cache

Add simple cache to backend

server/app/app.py

@@ -2,16 +2,18 @@ import argparse
 import os
 
 from flask import Flask
+from flask_caching import Cache
 from flask_compress import Compress
 from flask_cors import CORS
 from flask_restful_swagger_2 import get_swagger_blueprint
 
-from .web import webapp
 from .rest_api.rest import get_api_resources
+from .web import webapp
 
 REACTIVE_LIMIT = 1_000_000
 
 app = Flask(__name__)
+cache = Cache(app, config={"CACHE_TYPE": "simple", "CACHE_DEFAULT_TIMEOUT": 860000})
 Compress(app)
 CORS(app)
 

server/app/rest_api/rest.py

@@ -3,8 +3,8 @@ from flask import (
 )
 from flask_restful_swagger_2 import Api, swagger, Resource
 
-from ..util.utils import make_payload
-from ..util.filter import parse_filter
+from server.app.util.utils import make_payload
+from server.app.util.filter import parse_filter
 
 
 class InitializeAPI(Resource):

server/app/scanpy_engine/scanpy_engine.py

@@ -4,8 +4,9 @@ import numpy as np
 import scanpy.api as sc
 from scipy import stats
 
-from ..util.schema_parse import parse_schema
-from ..driver.driver import CXGDriver
+from server.app.app import cache
+from server.app.driver.driver import CXGDriver
+from server.app.util.schema_parse import parse_schema
 
 
 class ScanpyEngine(CXGDriver):
@@ -41,6 +42,7 @@ class ScanpyEngine(CXGDriver):
     def genes(self):
         return self.data.var.index.tolist()
 
+    # Can't seem to cache a view of a dataframe, need to investigate why
     def filter_cells(self, filter):
         """
         Filter cells from data and return a subset of the data
@@ -69,6 +71,7 @@ class ScanpyEngine(CXGDriver):
                     cell_idx = np.logical_and(cell_idx, key_idx)
         return self.data[cell_idx, :]
 
+    @cache.memoize()
     def metadata_ranges(self, df=None):
         metadata_ranges = {}
         if not df:
@@ -88,6 +91,7 @@ class ScanpyEngine(CXGDriver):
                 }
         return metadata_ranges
 
+    @cache.memoize()
     def metadata(self, df, fields=None):
         """
          Gets metadata key:value for each cells
@@ -101,6 +105,7 @@ class ScanpyEngine(CXGDriver):
             metadata[idx]["CellName"] = metadata[idx].pop("cell_name", None)
         return metadata
 
+    @cache.memoize()
     def create_graph(self, df):
         """
         Computes a n-d layout for cells through dimensionality reduction.
@@ -112,6 +117,7 @@ class ScanpyEngine(CXGDriver):
         normalized_graph = (graph - graph.min()) / (graph.max() - graph.min())
         return np.hstack((df.obs["cell_name"].values.reshape(len(df.obs.index), 1), normalized_graph)).tolist()
 
+    @cache.memoize()
     def diffexp(self, cell_list_1, cell_list_2, pval, num_genes):
         """
         Computes the top differentially expressed genes between two clusters
@@ -158,6 +164,7 @@ class ScanpyEngine(CXGDriver):
             },
         }
 
+    @cache.memoize()
     def expression(self, cells=None, genes=None):
         """
         Retrieves expression for each gene for cells in data frame

server/requirements.txt

@@ -6,6 +6,7 @@ click==6.7
 cycler==0.10.0
 decorator==4.3.0
 Flask==0.12.4
+Flask-Caching==1.4.0
 Flask-Compress==1.4.0
 Flask-Cors==3.0.6
 Flask-RESTful==0.3.6