fork/cellxgene
1
0
Fork 0
mirror of https://github.com/chanzuckerberg/cellxgene.git synced 2026-09-23 23:48:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

diffexp performance & UX improvements (#431)

Browse Source 
* new diffexp REST API spec

* new diffexp REST API; faster diffexp and dataframe slicing

* first draft of fast diffexp

* convert variance calculation to two-pass method

* lint

* update front-end use of API

* fix typo in spec

* disable content compression

* catch index filter format errors

* clean up of dead code

* resolve PR review comments
This commit is contained in:
Bruce Martin
2018-11-14 12:51:24 -08:00
committed by GitHub
parent bc0cecbd1c
commit 00a68276a2
11 changed files with 237 additions and 227 deletions
Download Patch File Download Diff File Expand all files Collapse all files
server/app/rest_api/rest.py
+16 -14
View File
@@ -555,11 +555,11 @@ class DiffExpObsAPI(Resource):
"responses": {
"200": {
"description": "Statistics are encoded as an array of arrays, with fields ordered as: "
"varIndex, avgDiff, pVal, pValAdj, set1AvgExp, set2AvgExp",
"varIndex, logfoldchange, pVal, pValAdj",
"examples": {
"application/json": [
[328, -2.569489, 2.655706e-63, 3.642036e-57, 383.393, 583.9],
[1250, -2.569489, 2.655706e-63, 3.642036e-57, 383.393, 583.9],
[328, -2.569489, 2.655706e-63, 3.642036e-57],
[1250, -2.569489, 2.655706e-63, 3.642036e-57],
]
}
},
@@ -584,11 +584,12 @@ class DiffExpObsAPI(Resource):
except ValueError:
return make_response(f"Error: invalid mode option {args['mode']}", HTTPStatus.BAD_REQUEST)
# Validate filters
if mode == DiffExpMode.VAR_FILTER:
if "varFilter" not in args:
return make_response("varFilter is required when mode is set to varFilter ", HTTPStatus.BAD_REQUEST)
if Axis.OBS in args["varFilter"]["filter"]:
return make_response("Obs filter not allowed in varFilter", HTTPStatus.BAD_REQUEST)
if mode == DiffExpMode.VAR_FILTER or "varFilter" in args:
# not NOT_IMPLEMENTED
return make_response("mode=varfilter not implemented", HTTPStatus.NOT_IMPLEMENTED)
if mode == DiffExpMode.TOP_N and "count" not in args:
return make_response("mode=topN requires a count parameter", HTTPStatus.BAD_REQUEST)
if "set1" not in args:
return make_response("set1 is required.", HTTPStatus.BAD_REQUEST)
if Axis.VAR in args["set1"]["filter"]:
@@ -598,16 +599,17 @@ class DiffExpObsAPI(Resource):
return make_response("Set2 as inverse of set1 is not implemented", HTTPStatus.NOT_IMPLEMENTED)
if Axis.VAR in args["set2"]["filter"]:
return make_response("Var filter not allowed for set2", HTTPStatus.BAD_REQUEST)
set1_filter = args["set1"]["filter"]
set2_filter = args.get("set2", {"filter": {}})["filter"]
if "varFilter" in args:
set1_filter[Axis.VAR] = args["varFilter"]["filter"][Axis.VAR]
set2_filter[Axis.VAR] = args["varFilter"]["filter"][Axis.VAR]
# mode
# TODO: implement varfilter mode
# mode=topN
count = args.get("count", None)
try:
diffexp = current_app.data.diffexp(set1_filter, set2_filter, count,
current_app.data.features["diffexp"]["interactiveLimit"])
diffexp = current_app.data.diffexp_topN(set1_filter, set2_filter, count,
current_app.data.features["diffexp"]["interactiveLimit"])
except (ValueError, FilterError) as e:
return make_response(e.message, HTTPStatus.BAD_REQUEST)
except InteractiveError: