fork/cellxgene
1
0
Fork 0
mirror of https://github.com/chanzuckerberg/cellxgene.git synced 2026-10-05 23:48:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

binary wire format with flatbuffers (#509)

Browse Source 
* first flatbuffer schema

* do not lint auto-generated files

* add flatbuffers package

* add flatbuffer module

* wire up /data/X/T route

* use flatbuffers for matrix data fetc

* clarity and comments

* add flatbuffer layout route

* clean up obsolete code

* fix tests

* move flake8 config to setup.cfg

* add comments

* lint

* rework layout routes for fbs

* add more type support to fbs

* lint

* add flatbuffer support for annotations

* function name improvements

* fix botched merge with master

* remove unused import

* route cleanup for flatbuffers

* rename function for clarity

* add missing globals to Jest tests

* fix client JS tests

* fix routes for Python tests

* comments for clarity

* non-finite floating point hardening

* more non-finite number handling

* lint

* fix tests for summarizeAnnotations

* harden diffexp calculation against FP errors

* cleanup unused code

* lint

* add encoding tests for flatbuffers

* application type specified as strings

* fix spelling error

* improve variable names

* add note about documentation gap

* rename FBS DataFrame to Matrix
This commit is contained in:
Bruce Martin
2019-01-09 14:26:05 -08:00
committed by GitHub
parent 42e25a1a1f
commit b90447c387
41 changed files with 2317 additions and 266 deletions
Download Patch File Download Diff File Expand all files Collapse all files
client/__tests__/util/stateManager/universe.test.js
-54
View File
@@ -30,7 +30,6 @@ describe("createUniverseFromRestV02Response", () => {
create a universe from sample data nad validate its shape & contents
*/
const { nObs, nVar } = REST.schema.schema.dataframe;
const universe = Universe.createUniverseFromRestV02Response(
REST.config,
REST.schema,
@@ -66,56 +65,3 @@ describe("createUniverseFromRestV02Response", () => {
expect(_.keys(universe.varNameToIndexMap)).toHaveLength(nVar);
});
});
describe("convertExpressionRESTv02ToObject", () => {
/*
test convertExpressionRESTv02ToObject
convertExpressionRESTv02ToObject(
universe,
response) --> { geneName: Float32Array, geneName: Float32Array, ... }
reponse is a /data/obs response:
{
var: [ varIndices fetched ],
obs: [
[ obsIndex, evalue, ... ],
...
]
}
*/
test("create from response data", () => {
const universe = Universe.createUniverseFromRestV02Response(
REST.config,
REST.schema,
REST.annotationsObs,
REST.annotationsVar,
REST.layoutObs
);
const expression = Universe.convertExpressionRESTv02ToObject(
universe,
REST.dataObs
);
/* Check that the expected keys are present */
const expectedGeneNames = _.map(
REST.dataObs.var,
v => REST.annotationsVar.data[v][5]
);
expect(Object.keys(expression)).toEqual(
expect.arrayContaining(expectedGeneNames)
);
const expectedExpressionValues = _.map(
_.unzip(REST.dataObs.obs),
a => new Float32Array(a)
);
_.forEach(REST.dataObs.var, (varIdx, idx) => {
const varName = universe.varAnnotations[varIdx].name;
expect(varName).toBeDefined();
expect(varIdx).toBe(universe.varNameToIndexMap[varName]);
expect(expression[varName]).toEqual(expectedExpressionValues[idx + 1]);
});
});
});