diff --git a/server/app/app.py b/server/app/app.py index d9e8e2ce..547a9db5 100644 --- a/server/app/app.py +++ b/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) diff --git a/server/app/rest_api/rest.py b/server/app/rest_api/rest.py index 40742dc3..f5892125 100644 --- a/server/app/rest_api/rest.py +++ b/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): diff --git a/server/app/scanpy_engine/scanpy_engine.py b/server/app/scanpy_engine/scanpy_engine.py index 405003f5..9ede3b45 100644 --- a/server/app/scanpy_engine/scanpy_engine.py +++ b/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 diff --git a/server/requirements.txt b/server/requirements.txt index 7ab96abb..a881e310 100644 --- a/server/requirements.txt +++ b/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