mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-10-02 06:38:12 +08:00
binary wire format with flatbuffers (#509)
* 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
@@ -25,17 +25,18 @@ export function catchErrorsWrap(fn, dispatchToUser = false) {
|
||||
}
|
||||
|
||||
/*
|
||||
Wrapper to perform an async fetch and JSON decode response.
|
||||
Wrapper to perform async fetch with some modest error handling
|
||||
and decoding.
|
||||
*/
|
||||
export const doJsonRequest = async url => {
|
||||
const doFetch = async (url, acceptType) => {
|
||||
const res = await fetch(url, {
|
||||
method: "get",
|
||||
headers: new Headers({
|
||||
"Content-Type": "application/json"
|
||||
Accept: acceptType
|
||||
})
|
||||
});
|
||||
if (res.ok && res.headers.get("Content-Type") === "application/json") {
|
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return res.json();
|
||||
if (res.ok && res.headers.get("Content-Type") === acceptType) {
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return res;
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}
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// else an error
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let msg = `Unexpected HTTP response ${res.status}, ${res.statusText}`;
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@@ -47,6 +48,22 @@ export const doJsonRequest = async url => {
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throw new Error(msg);
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};
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|
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/*
|
||||
Wrapper to perform an async fetch and JSON decode response.
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||||
*/
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||||
export const doJsonRequest = async url => {
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const res = await doFetch(url, "application/json");
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return res.json();
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};
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|
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/*
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Wrapper to perform an async fetch for binary data.
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*/
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export const doBinaryRequest = async url => {
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const res = await doFetch(url, "application/octet-stream");
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return res.arrayBuffer();
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};
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|
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/*
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This function "packs" filter index lists into the more efficient
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"range" form specified in the REST 0.2 spec.
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@@ -0,0 +1,33 @@
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/*
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Return the [minimum, maximum] extent, of the given typed array, ignoring
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non-finite values (ie, +Infinity, -Infinity).
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If undefined or empty array, or array contains only non-finite numbers,
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will return [undefined, undefined]
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*/
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function finiteExtent(tarr) {
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let min;
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let max;
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let i;
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for (i = 0; i < tarr.length; i += 1) {
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const val = tarr[i];
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if (Number.isFinite(val)) {
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min = val;
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max = val;
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i += 1;
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break;
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}
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}
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for (; i < tarr.length; i += 1) {
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const val = tarr[i];
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if (Number.isFinite(val)) {
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if (min > val) min = val;
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if (max < val) max = val;
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}
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}
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return [min, max];
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}
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export default finiteExtent;
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@@ -3,7 +3,7 @@
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/*
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Model manager providing an abstraction for the use of the reducer code.
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This module provides several buckets of functionality:
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- schema and config driven tranformation of the dataframe wire protocol
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- schema and config driven tranformation of the wire protocol
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into a format that is easy for the UI code to use.
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- manage the universe/world abstraction:
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+ universe: all of the server-provided, read-only data
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@@ -0,0 +1,75 @@
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import { flatbuffers } from "flatbuffers";
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import { NetEncoding } from "./matrix_generated";
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const utf8Decoder = new TextDecoder("utf-8");
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/*
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Matrix flatbuffer decoding support. See fbs/matrix.fbs
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*/
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/*
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Decode NetEncoding.TypedArray
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*/
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function decodeTypedArray(uType, uValF, inplace = false) {
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if (uType === NetEncoding.TypedArray.NONE) {
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return null;
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}
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// Convert to a JS class that supports this type
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const TypeClass = NetEncoding[NetEncoding.TypedArray[uType]];
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// Create a TypedArray that references the underlying buffer
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let arr = uValF(new TypeClass()).dataArray();
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if (uType === NetEncoding.TypedArray.JSONEncodedArray) {
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const json = utf8Decoder.decode(arr);
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arr = JSON.parse(json);
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} else if (!inplace) {
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/* force copy to release underlying FBS buffer */
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arr = new arr.constructor(arr);
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}
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return arr;
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}
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/*
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Parameter: Uint8Array or ArrayBuffer containing raw flatbuffer Matrix
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Returns: object containing decoded Matrix:
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{
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nRows: num,
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nCols: num,
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columns: [
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each column, which will be a TypedArray or Array
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]
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colIdx: []|null
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}
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*/
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function decodeMatrixFBS(arrayBuffer, inplace = false) {
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const bb = new flatbuffers.ByteBuffer(new Uint8Array(arrayBuffer));
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const df = NetEncoding.Matrix.getRootAsMatrix(bb);
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const nRows = df.nRows();
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const nCols = df.nCols();
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|
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/* decode columns */
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||||
const columnsLength = df.columnsLength();
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const columns = Array(columnsLength).fill(null);
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for (let c = 0; c < columnsLength; c += 1) {
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const col = df.columns(c);
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columns[c] = decodeTypedArray(col.uType(), col.u.bind(col), inplace);
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}
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||||
|
||||
/* decode col_idx */
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const colIdx = decodeTypedArray(
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df.colIndexType(),
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df.colIndex.bind(df),
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inplace
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);
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||||
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return {
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nRows,
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nCols,
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columns,
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colIdx,
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rowIdx: null
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||||
};
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||||
}
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||||
|
||||
export default decodeMatrixFBS;
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@@ -0,0 +1,835 @@
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// automatically generated by the FlatBuffers compiler, do not modify
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||||
|
||||
/**
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||||
* @const
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||||
* @namespace
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||||
*/
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||||
var NetEncoding = NetEncoding || {};
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||||
|
||||
/**
|
||||
* @enum
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||||
*/
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||||
NetEncoding.TypedArray = {
|
||||
NONE: 0, 0: 'NONE',
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Float32Array: 1, 1: 'Float32Array',
|
||||
Int32Array: 2, 2: 'Int32Array',
|
||||
Uint32Array: 3, 3: 'Uint32Array',
|
||||
Float64Array: 4, 4: 'Float64Array',
|
||||
JSONEncodedArray: 5, 5: 'JSONEncodedArray'
|
||||
};
|
||||
|
||||
/**
|
||||
* @constructor
|
||||
*/
|
||||
NetEncoding.Float32Array = function() {
|
||||
/**
|
||||
* @type {flatbuffers.ByteBuffer}
|
||||
*/
|
||||
this.bb = null;
|
||||
|
||||
/**
|
||||
* @type {number}
|
||||
*/
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||||
this.bb_pos = 0;
|
||||
};
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||||
|
||||
/**
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||||
* @param {number} i
|
||||
* @param {flatbuffers.ByteBuffer} bb
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||||
* @returns {NetEncoding.Float32Array}
|
||||
*/
|
||||
NetEncoding.Float32Array.prototype.__init = function(i, bb) {
|
||||
this.bb_pos = i;
|
||||
this.bb = bb;
|
||||
return this;
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.ByteBuffer} bb
|
||||
* @param {NetEncoding.Float32Array=} obj
|
||||
* @returns {NetEncoding.Float32Array}
|
||||
*/
|
||||
NetEncoding.Float32Array.getRootAsFloat32Array = function(bb, obj) {
|
||||
return (obj || new NetEncoding.Float32Array).__init(bb.readInt32(bb.position()) + bb.position(), bb);
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {number} index
|
||||
* @returns {number}
|
||||
*/
|
||||
NetEncoding.Float32Array.prototype.data = function(index) {
|
||||
var offset = this.bb.__offset(this.bb_pos, 4);
|
||||
return offset ? this.bb.readFloat32(this.bb.__vector(this.bb_pos + offset) + index * 4) : 0;
|
||||
};
|
||||
|
||||
/**
|
||||
* @returns {number}
|
||||
*/
|
||||
NetEncoding.Float32Array.prototype.dataLength = function() {
|
||||
var offset = this.bb.__offset(this.bb_pos, 4);
|
||||
return offset ? this.bb.__vector_len(this.bb_pos + offset) : 0;
|
||||
};
|
||||
|
||||
/**
|
||||
* @returns {Float32Array}
|
||||
*/
|
||||
NetEncoding.Float32Array.prototype.dataArray = function() {
|
||||
var offset = this.bb.__offset(this.bb_pos, 4);
|
||||
return offset ? new Float32Array(this.bb.bytes().buffer, this.bb.bytes().byteOffset + this.bb.__vector(this.bb_pos + offset), this.bb.__vector_len(this.bb_pos + offset)) : null;
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
*/
|
||||
NetEncoding.Float32Array.startFloat32Array = function(builder) {
|
||||
builder.startObject(1);
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @param {flatbuffers.Offset} dataOffset
|
||||
*/
|
||||
NetEncoding.Float32Array.addData = function(builder, dataOffset) {
|
||||
builder.addFieldOffset(0, dataOffset, 0);
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @param {Array.<number>} data
|
||||
* @returns {flatbuffers.Offset}
|
||||
*/
|
||||
NetEncoding.Float32Array.createDataVector = function(builder, data) {
|
||||
builder.startVector(4, data.length, 4);
|
||||
for (var i = data.length - 1; i >= 0; i--) {
|
||||
builder.addFloat32(data[i]);
|
||||
}
|
||||
return builder.endVector();
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @param {number} numElems
|
||||
*/
|
||||
NetEncoding.Float32Array.startDataVector = function(builder, numElems) {
|
||||
builder.startVector(4, numElems, 4);
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @returns {flatbuffers.Offset}
|
||||
*/
|
||||
NetEncoding.Float32Array.endFloat32Array = function(builder) {
|
||||
var offset = builder.endObject();
|
||||
return offset;
|
||||
};
|
||||
|
||||
/**
|
||||
* @constructor
|
||||
*/
|
||||
NetEncoding.Uint32Array = function() {
|
||||
/**
|
||||
* @type {flatbuffers.ByteBuffer}
|
||||
*/
|
||||
this.bb = null;
|
||||
|
||||
/**
|
||||
* @type {number}
|
||||
*/
|
||||
this.bb_pos = 0;
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {number} i
|
||||
* @param {flatbuffers.ByteBuffer} bb
|
||||
* @returns {NetEncoding.Uint32Array}
|
||||
*/
|
||||
NetEncoding.Uint32Array.prototype.__init = function(i, bb) {
|
||||
this.bb_pos = i;
|
||||
this.bb = bb;
|
||||
return this;
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.ByteBuffer} bb
|
||||
* @param {NetEncoding.Uint32Array=} obj
|
||||
* @returns {NetEncoding.Uint32Array}
|
||||
*/
|
||||
NetEncoding.Uint32Array.getRootAsUint32Array = function(bb, obj) {
|
||||
return (obj || new NetEncoding.Uint32Array).__init(bb.readInt32(bb.position()) + bb.position(), bb);
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {number} index
|
||||
* @returns {number}
|
||||
*/
|
||||
NetEncoding.Uint32Array.prototype.data = function(index) {
|
||||
var offset = this.bb.__offset(this.bb_pos, 4);
|
||||
return offset ? this.bb.readUint32(this.bb.__vector(this.bb_pos + offset) + index * 4) : 0;
|
||||
};
|
||||
|
||||
/**
|
||||
* @returns {number}
|
||||
*/
|
||||
NetEncoding.Uint32Array.prototype.dataLength = function() {
|
||||
var offset = this.bb.__offset(this.bb_pos, 4);
|
||||
return offset ? this.bb.__vector_len(this.bb_pos + offset) : 0;
|
||||
};
|
||||
|
||||
/**
|
||||
* @returns {Uint32Array}
|
||||
*/
|
||||
NetEncoding.Uint32Array.prototype.dataArray = function() {
|
||||
var offset = this.bb.__offset(this.bb_pos, 4);
|
||||
return offset ? new Uint32Array(this.bb.bytes().buffer, this.bb.bytes().byteOffset + this.bb.__vector(this.bb_pos + offset), this.bb.__vector_len(this.bb_pos + offset)) : null;
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
*/
|
||||
NetEncoding.Uint32Array.startUint32Array = function(builder) {
|
||||
builder.startObject(1);
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @param {flatbuffers.Offset} dataOffset
|
||||
*/
|
||||
NetEncoding.Uint32Array.addData = function(builder, dataOffset) {
|
||||
builder.addFieldOffset(0, dataOffset, 0);
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @param {Array.<number>} data
|
||||
* @returns {flatbuffers.Offset}
|
||||
*/
|
||||
NetEncoding.Uint32Array.createDataVector = function(builder, data) {
|
||||
builder.startVector(4, data.length, 4);
|
||||
for (var i = data.length - 1; i >= 0; i--) {
|
||||
builder.addInt32(data[i]);
|
||||
}
|
||||
return builder.endVector();
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @param {number} numElems
|
||||
*/
|
||||
NetEncoding.Uint32Array.startDataVector = function(builder, numElems) {
|
||||
builder.startVector(4, numElems, 4);
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @returns {flatbuffers.Offset}
|
||||
*/
|
||||
NetEncoding.Uint32Array.endUint32Array = function(builder) {
|
||||
var offset = builder.endObject();
|
||||
return offset;
|
||||
};
|
||||
|
||||
/**
|
||||
* @constructor
|
||||
*/
|
||||
NetEncoding.Int32Array = function() {
|
||||
/**
|
||||
* @type {flatbuffers.ByteBuffer}
|
||||
*/
|
||||
this.bb = null;
|
||||
|
||||
/**
|
||||
* @type {number}
|
||||
*/
|
||||
this.bb_pos = 0;
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {number} i
|
||||
* @param {flatbuffers.ByteBuffer} bb
|
||||
* @returns {NetEncoding.Int32Array}
|
||||
*/
|
||||
NetEncoding.Int32Array.prototype.__init = function(i, bb) {
|
||||
this.bb_pos = i;
|
||||
this.bb = bb;
|
||||
return this;
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.ByteBuffer} bb
|
||||
* @param {NetEncoding.Int32Array=} obj
|
||||
* @returns {NetEncoding.Int32Array}
|
||||
*/
|
||||
NetEncoding.Int32Array.getRootAsInt32Array = function(bb, obj) {
|
||||
return (obj || new NetEncoding.Int32Array).__init(bb.readInt32(bb.position()) + bb.position(), bb);
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {number} index
|
||||
* @returns {number}
|
||||
*/
|
||||
NetEncoding.Int32Array.prototype.data = function(index) {
|
||||
var offset = this.bb.__offset(this.bb_pos, 4);
|
||||
return offset ? this.bb.readInt32(this.bb.__vector(this.bb_pos + offset) + index * 4) : 0;
|
||||
};
|
||||
|
||||
/**
|
||||
* @returns {number}
|
||||
*/
|
||||
NetEncoding.Int32Array.prototype.dataLength = function() {
|
||||
var offset = this.bb.__offset(this.bb_pos, 4);
|
||||
return offset ? this.bb.__vector_len(this.bb_pos + offset) : 0;
|
||||
};
|
||||
|
||||
/**
|
||||
* @returns {Int32Array}
|
||||
*/
|
||||
NetEncoding.Int32Array.prototype.dataArray = function() {
|
||||
var offset = this.bb.__offset(this.bb_pos, 4);
|
||||
return offset ? new Int32Array(this.bb.bytes().buffer, this.bb.bytes().byteOffset + this.bb.__vector(this.bb_pos + offset), this.bb.__vector_len(this.bb_pos + offset)) : null;
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
*/
|
||||
NetEncoding.Int32Array.startInt32Array = function(builder) {
|
||||
builder.startObject(1);
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @param {flatbuffers.Offset} dataOffset
|
||||
*/
|
||||
NetEncoding.Int32Array.addData = function(builder, dataOffset) {
|
||||
builder.addFieldOffset(0, dataOffset, 0);
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @param {Array.<number>} data
|
||||
* @returns {flatbuffers.Offset}
|
||||
*/
|
||||
NetEncoding.Int32Array.createDataVector = function(builder, data) {
|
||||
builder.startVector(4, data.length, 4);
|
||||
for (var i = data.length - 1; i >= 0; i--) {
|
||||
builder.addInt32(data[i]);
|
||||
}
|
||||
return builder.endVector();
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @param {number} numElems
|
||||
*/
|
||||
NetEncoding.Int32Array.startDataVector = function(builder, numElems) {
|
||||
builder.startVector(4, numElems, 4);
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @returns {flatbuffers.Offset}
|
||||
*/
|
||||
NetEncoding.Int32Array.endInt32Array = function(builder) {
|
||||
var offset = builder.endObject();
|
||||
return offset;
|
||||
};
|
||||
|
||||
/**
|
||||
* @constructor
|
||||
*/
|
||||
NetEncoding.Float64Array = function() {
|
||||
/**
|
||||
* @type {flatbuffers.ByteBuffer}
|
||||
*/
|
||||
this.bb = null;
|
||||
|
||||
/**
|
||||
* @type {number}
|
||||
*/
|
||||
this.bb_pos = 0;
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {number} i
|
||||
* @param {flatbuffers.ByteBuffer} bb
|
||||
* @returns {NetEncoding.Float64Array}
|
||||
*/
|
||||
NetEncoding.Float64Array.prototype.__init = function(i, bb) {
|
||||
this.bb_pos = i;
|
||||
this.bb = bb;
|
||||
return this;
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.ByteBuffer} bb
|
||||
* @param {NetEncoding.Float64Array=} obj
|
||||
* @returns {NetEncoding.Float64Array}
|
||||
*/
|
||||
NetEncoding.Float64Array.getRootAsFloat64Array = function(bb, obj) {
|
||||
return (obj || new NetEncoding.Float64Array).__init(bb.readInt32(bb.position()) + bb.position(), bb);
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {number} index
|
||||
* @returns {number}
|
||||
*/
|
||||
NetEncoding.Float64Array.prototype.data = function(index) {
|
||||
var offset = this.bb.__offset(this.bb_pos, 4);
|
||||
return offset ? this.bb.readFloat64(this.bb.__vector(this.bb_pos + offset) + index * 8) : 0;
|
||||
};
|
||||
|
||||
/**
|
||||
* @returns {number}
|
||||
*/
|
||||
NetEncoding.Float64Array.prototype.dataLength = function() {
|
||||
var offset = this.bb.__offset(this.bb_pos, 4);
|
||||
return offset ? this.bb.__vector_len(this.bb_pos + offset) : 0;
|
||||
};
|
||||
|
||||
/**
|
||||
* @returns {Float64Array}
|
||||
*/
|
||||
NetEncoding.Float64Array.prototype.dataArray = function() {
|
||||
var offset = this.bb.__offset(this.bb_pos, 4);
|
||||
return offset ? new Float64Array(this.bb.bytes().buffer, this.bb.bytes().byteOffset + this.bb.__vector(this.bb_pos + offset), this.bb.__vector_len(this.bb_pos + offset)) : null;
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
*/
|
||||
NetEncoding.Float64Array.startFloat64Array = function(builder) {
|
||||
builder.startObject(1);
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @param {flatbuffers.Offset} dataOffset
|
||||
*/
|
||||
NetEncoding.Float64Array.addData = function(builder, dataOffset) {
|
||||
builder.addFieldOffset(0, dataOffset, 0);
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @param {Array.<number>} data
|
||||
* @returns {flatbuffers.Offset}
|
||||
*/
|
||||
NetEncoding.Float64Array.createDataVector = function(builder, data) {
|
||||
builder.startVector(8, data.length, 8);
|
||||
for (var i = data.length - 1; i >= 0; i--) {
|
||||
builder.addFloat64(data[i]);
|
||||
}
|
||||
return builder.endVector();
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @param {number} numElems
|
||||
*/
|
||||
NetEncoding.Float64Array.startDataVector = function(builder, numElems) {
|
||||
builder.startVector(8, numElems, 8);
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @returns {flatbuffers.Offset}
|
||||
*/
|
||||
NetEncoding.Float64Array.endFloat64Array = function(builder) {
|
||||
var offset = builder.endObject();
|
||||
return offset;
|
||||
};
|
||||
|
||||
/**
|
||||
* @constructor
|
||||
*/
|
||||
NetEncoding.JSONEncodedArray = function() {
|
||||
/**
|
||||
* @type {flatbuffers.ByteBuffer}
|
||||
*/
|
||||
this.bb = null;
|
||||
|
||||
/**
|
||||
* @type {number}
|
||||
*/
|
||||
this.bb_pos = 0;
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {number} i
|
||||
* @param {flatbuffers.ByteBuffer} bb
|
||||
* @returns {NetEncoding.JSONEncodedArray}
|
||||
*/
|
||||
NetEncoding.JSONEncodedArray.prototype.__init = function(i, bb) {
|
||||
this.bb_pos = i;
|
||||
this.bb = bb;
|
||||
return this;
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.ByteBuffer} bb
|
||||
* @param {NetEncoding.JSONEncodedArray=} obj
|
||||
* @returns {NetEncoding.JSONEncodedArray}
|
||||
*/
|
||||
NetEncoding.JSONEncodedArray.getRootAsJSONEncodedArray = function(bb, obj) {
|
||||
return (obj || new NetEncoding.JSONEncodedArray).__init(bb.readInt32(bb.position()) + bb.position(), bb);
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {number} index
|
||||
* @returns {number}
|
||||
*/
|
||||
NetEncoding.JSONEncodedArray.prototype.data = function(index) {
|
||||
var offset = this.bb.__offset(this.bb_pos, 4);
|
||||
return offset ? this.bb.readUint8(this.bb.__vector(this.bb_pos + offset) + index) : 0;
|
||||
};
|
||||
|
||||
/**
|
||||
* @returns {number}
|
||||
*/
|
||||
NetEncoding.JSONEncodedArray.prototype.dataLength = function() {
|
||||
var offset = this.bb.__offset(this.bb_pos, 4);
|
||||
return offset ? this.bb.__vector_len(this.bb_pos + offset) : 0;
|
||||
};
|
||||
|
||||
/**
|
||||
* @returns {Uint8Array}
|
||||
*/
|
||||
NetEncoding.JSONEncodedArray.prototype.dataArray = function() {
|
||||
var offset = this.bb.__offset(this.bb_pos, 4);
|
||||
return offset ? new Uint8Array(this.bb.bytes().buffer, this.bb.bytes().byteOffset + this.bb.__vector(this.bb_pos + offset), this.bb.__vector_len(this.bb_pos + offset)) : null;
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
*/
|
||||
NetEncoding.JSONEncodedArray.startJSONEncodedArray = function(builder) {
|
||||
builder.startObject(1);
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @param {flatbuffers.Offset} dataOffset
|
||||
*/
|
||||
NetEncoding.JSONEncodedArray.addData = function(builder, dataOffset) {
|
||||
builder.addFieldOffset(0, dataOffset, 0);
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @param {Array.<number>} data
|
||||
* @returns {flatbuffers.Offset}
|
||||
*/
|
||||
NetEncoding.JSONEncodedArray.createDataVector = function(builder, data) {
|
||||
builder.startVector(1, data.length, 1);
|
||||
for (var i = data.length - 1; i >= 0; i--) {
|
||||
builder.addInt8(data[i]);
|
||||
}
|
||||
return builder.endVector();
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @param {number} numElems
|
||||
*/
|
||||
NetEncoding.JSONEncodedArray.startDataVector = function(builder, numElems) {
|
||||
builder.startVector(1, numElems, 1);
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @returns {flatbuffers.Offset}
|
||||
*/
|
||||
NetEncoding.JSONEncodedArray.endJSONEncodedArray = function(builder) {
|
||||
var offset = builder.endObject();
|
||||
return offset;
|
||||
};
|
||||
|
||||
/**
|
||||
* @constructor
|
||||
*/
|
||||
NetEncoding.Column = function() {
|
||||
/**
|
||||
* @type {flatbuffers.ByteBuffer}
|
||||
*/
|
||||
this.bb = null;
|
||||
|
||||
/**
|
||||
* @type {number}
|
||||
*/
|
||||
this.bb_pos = 0;
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {number} i
|
||||
* @param {flatbuffers.ByteBuffer} bb
|
||||
* @returns {NetEncoding.Column}
|
||||
*/
|
||||
NetEncoding.Column.prototype.__init = function(i, bb) {
|
||||
this.bb_pos = i;
|
||||
this.bb = bb;
|
||||
return this;
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.ByteBuffer} bb
|
||||
* @param {NetEncoding.Column=} obj
|
||||
* @returns {NetEncoding.Column}
|
||||
*/
|
||||
NetEncoding.Column.getRootAsColumn = function(bb, obj) {
|
||||
return (obj || new NetEncoding.Column).__init(bb.readInt32(bb.position()) + bb.position(), bb);
|
||||
};
|
||||
|
||||
/**
|
||||
* @returns {NetEncoding.TypedArray}
|
||||
*/
|
||||
NetEncoding.Column.prototype.uType = function() {
|
||||
var offset = this.bb.__offset(this.bb_pos, 4);
|
||||
return offset ? /** @type {NetEncoding.TypedArray} */ (this.bb.readUint8(this.bb_pos + offset)) : NetEncoding.TypedArray.NONE;
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Table} obj
|
||||
* @returns {?flatbuffers.Table}
|
||||
*/
|
||||
NetEncoding.Column.prototype.u = function(obj) {
|
||||
var offset = this.bb.__offset(this.bb_pos, 6);
|
||||
return offset ? this.bb.__union(obj, this.bb_pos + offset) : null;
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
*/
|
||||
NetEncoding.Column.startColumn = function(builder) {
|
||||
builder.startObject(2);
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @param {NetEncoding.TypedArray} uType
|
||||
*/
|
||||
NetEncoding.Column.addUType = function(builder, uType) {
|
||||
builder.addFieldInt8(0, uType, NetEncoding.TypedArray.NONE);
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @param {flatbuffers.Offset} uOffset
|
||||
*/
|
||||
NetEncoding.Column.addU = function(builder, uOffset) {
|
||||
builder.addFieldOffset(1, uOffset, 0);
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @returns {flatbuffers.Offset}
|
||||
*/
|
||||
NetEncoding.Column.endColumn = function(builder) {
|
||||
var offset = builder.endObject();
|
||||
return offset;
|
||||
};
|
||||
|
||||
/**
|
||||
* @constructor
|
||||
*/
|
||||
NetEncoding.Matrix = function() {
|
||||
/**
|
||||
* @type {flatbuffers.ByteBuffer}
|
||||
*/
|
||||
this.bb = null;
|
||||
|
||||
/**
|
||||
* @type {number}
|
||||
*/
|
||||
this.bb_pos = 0;
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {number} i
|
||||
* @param {flatbuffers.ByteBuffer} bb
|
||||
* @returns {NetEncoding.Matrix}
|
||||
*/
|
||||
NetEncoding.Matrix.prototype.__init = function(i, bb) {
|
||||
this.bb_pos = i;
|
||||
this.bb = bb;
|
||||
return this;
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.ByteBuffer} bb
|
||||
* @param {NetEncoding.Matrix=} obj
|
||||
* @returns {NetEncoding.Matrix}
|
||||
*/
|
||||
NetEncoding.Matrix.getRootAsMatrix = function(bb, obj) {
|
||||
return (obj || new NetEncoding.Matrix).__init(bb.readInt32(bb.position()) + bb.position(), bb);
|
||||
};
|
||||
|
||||
/**
|
||||
* @returns {number}
|
||||
*/
|
||||
NetEncoding.Matrix.prototype.nRows = function() {
|
||||
var offset = this.bb.__offset(this.bb_pos, 4);
|
||||
return offset ? this.bb.readUint32(this.bb_pos + offset) : 0;
|
||||
};
|
||||
|
||||
/**
|
||||
* @returns {number}
|
||||
*/
|
||||
NetEncoding.Matrix.prototype.nCols = function() {
|
||||
var offset = this.bb.__offset(this.bb_pos, 6);
|
||||
return offset ? this.bb.readUint32(this.bb_pos + offset) : 0;
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {number} index
|
||||
* @param {NetEncoding.Column=} obj
|
||||
* @returns {NetEncoding.Column}
|
||||
*/
|
||||
NetEncoding.Matrix.prototype.columns = function(index, obj) {
|
||||
var offset = this.bb.__offset(this.bb_pos, 8);
|
||||
return offset ? (obj || new NetEncoding.Column).__init(this.bb.__indirect(this.bb.__vector(this.bb_pos + offset) + index * 4), this.bb) : null;
|
||||
};
|
||||
|
||||
/**
|
||||
* @returns {number}
|
||||
*/
|
||||
NetEncoding.Matrix.prototype.columnsLength = function() {
|
||||
var offset = this.bb.__offset(this.bb_pos, 8);
|
||||
return offset ? this.bb.__vector_len(this.bb_pos + offset) : 0;
|
||||
};
|
||||
|
||||
/**
|
||||
* @returns {NetEncoding.TypedArray}
|
||||
*/
|
||||
NetEncoding.Matrix.prototype.colIndexType = function() {
|
||||
var offset = this.bb.__offset(this.bb_pos, 10);
|
||||
return offset ? /** @type {NetEncoding.TypedArray} */ (this.bb.readUint8(this.bb_pos + offset)) : NetEncoding.TypedArray.NONE;
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Table} obj
|
||||
* @returns {?flatbuffers.Table}
|
||||
*/
|
||||
NetEncoding.Matrix.prototype.colIndex = function(obj) {
|
||||
var offset = this.bb.__offset(this.bb_pos, 12);
|
||||
return offset ? this.bb.__union(obj, this.bb_pos + offset) : null;
|
||||
};
|
||||
|
||||
/**
|
||||
* @returns {NetEncoding.TypedArray}
|
||||
*/
|
||||
NetEncoding.Matrix.prototype.rowIndexType = function() {
|
||||
var offset = this.bb.__offset(this.bb_pos, 14);
|
||||
return offset ? /** @type {NetEncoding.TypedArray} */ (this.bb.readUint8(this.bb_pos + offset)) : NetEncoding.TypedArray.NONE;
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Table} obj
|
||||
* @returns {?flatbuffers.Table}
|
||||
*/
|
||||
NetEncoding.Matrix.prototype.rowIndex = function(obj) {
|
||||
var offset = this.bb.__offset(this.bb_pos, 16);
|
||||
return offset ? this.bb.__union(obj, this.bb_pos + offset) : null;
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
*/
|
||||
NetEncoding.Matrix.startMatrix = function(builder) {
|
||||
builder.startObject(7);
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @param {number} nRows
|
||||
*/
|
||||
NetEncoding.Matrix.addNRows = function(builder, nRows) {
|
||||
builder.addFieldInt32(0, nRows, 0);
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @param {number} nCols
|
||||
*/
|
||||
NetEncoding.Matrix.addNCols = function(builder, nCols) {
|
||||
builder.addFieldInt32(1, nCols, 0);
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @param {flatbuffers.Offset} columnsOffset
|
||||
*/
|
||||
NetEncoding.Matrix.addColumns = function(builder, columnsOffset) {
|
||||
builder.addFieldOffset(2, columnsOffset, 0);
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @param {Array.<flatbuffers.Offset>} data
|
||||
* @returns {flatbuffers.Offset}
|
||||
*/
|
||||
NetEncoding.Matrix.createColumnsVector = function(builder, data) {
|
||||
builder.startVector(4, data.length, 4);
|
||||
for (var i = data.length - 1; i >= 0; i--) {
|
||||
builder.addOffset(data[i]);
|
||||
}
|
||||
return builder.endVector();
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @param {number} numElems
|
||||
*/
|
||||
NetEncoding.Matrix.startColumnsVector = function(builder, numElems) {
|
||||
builder.startVector(4, numElems, 4);
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @param {NetEncoding.TypedArray} colIndexType
|
||||
*/
|
||||
NetEncoding.Matrix.addColIndexType = function(builder, colIndexType) {
|
||||
builder.addFieldInt8(3, colIndexType, NetEncoding.TypedArray.NONE);
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @param {flatbuffers.Offset} colIndexOffset
|
||||
*/
|
||||
NetEncoding.Matrix.addColIndex = function(builder, colIndexOffset) {
|
||||
builder.addFieldOffset(4, colIndexOffset, 0);
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @param {NetEncoding.TypedArray} rowIndexType
|
||||
*/
|
||||
NetEncoding.Matrix.addRowIndexType = function(builder, rowIndexType) {
|
||||
builder.addFieldInt8(5, rowIndexType, NetEncoding.TypedArray.NONE);
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @param {flatbuffers.Offset} rowIndexOffset
|
||||
*/
|
||||
NetEncoding.Matrix.addRowIndex = function(builder, rowIndexOffset) {
|
||||
builder.addFieldOffset(6, rowIndexOffset, 0);
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @returns {flatbuffers.Offset}
|
||||
*/
|
||||
NetEncoding.Matrix.endMatrix = function(builder) {
|
||||
var offset = builder.endObject();
|
||||
return offset;
|
||||
};
|
||||
|
||||
/**
|
||||
* @param {flatbuffers.Builder} builder
|
||||
* @param {flatbuffers.Offset} offset
|
||||
*/
|
||||
NetEncoding.Matrix.finishMatrixBuffer = function(builder, offset) {
|
||||
builder.finish(offset);
|
||||
};
|
||||
|
||||
// Exports for ECMAScript6 Modules
|
||||
export {NetEncoding};
|
||||
@@ -1,4 +1,5 @@
|
||||
import _ from "lodash";
|
||||
import finiteExtent from "../finiteExtent";
|
||||
|
||||
/*
|
||||
Build and return obs/var summary using any annotation in the schema
|
||||
@@ -61,16 +62,32 @@ function _summarizeAnnotations(_schema, annotations) {
|
||||
const continuous = type === "int32" || type === "float32";
|
||||
|
||||
if (continuous) {
|
||||
let min = Number.POSITIVE_INFINITY;
|
||||
let max = Number.NEGATIVE_INFINITY;
|
||||
let min;
|
||||
let max;
|
||||
let nan = 0;
|
||||
let pinf = 0;
|
||||
let ninf = 0;
|
||||
for (let r = 0; r < annotations.length; r += 1) {
|
||||
const val = Number(annotations[r][name]);
|
||||
min = val < min ? val : min;
|
||||
max = val > max ? val : max;
|
||||
if (Number.isFinite(val)) {
|
||||
if (min === undefined) {
|
||||
min = val;
|
||||
max = val;
|
||||
} else {
|
||||
min = val < min ? val : min;
|
||||
max = val > max ? val : max;
|
||||
}
|
||||
} else if (Number.isNaN(val)) {
|
||||
nan += 1;
|
||||
} else if (val > 0) {
|
||||
pinf += 1;
|
||||
} else {
|
||||
ninf += 1;
|
||||
}
|
||||
}
|
||||
return {
|
||||
categorical: false,
|
||||
range: { min, max }
|
||||
range: { min, max, nan, pinf, ninf }
|
||||
};
|
||||
}
|
||||
|
||||
|
||||
@@ -1,8 +1,10 @@
|
||||
// jshint esversion: 6
|
||||
|
||||
import _ from "lodash";
|
||||
|
||||
import * as kvCache from "./keyvalcache";
|
||||
import summarizeAnnotations from "./summarizeAnnotations";
|
||||
import decodeMatrixFBS from "./matrix";
|
||||
|
||||
/*
|
||||
Private helper function - create and return a template Universe
|
||||
@@ -92,73 +94,40 @@ function finalize(universe) {
|
||||
return universe;
|
||||
}
|
||||
|
||||
function RESTv02AnnotationsResponseToInternal(response) {
|
||||
function RESTv02AnotationsFBSResponseToInternal(arrayBuffer) {
|
||||
/*
|
||||
Source per the spec:
|
||||
{
|
||||
names: [
|
||||
'tissue_type', 'sex', 'num_reads', 'clusters'
|
||||
],
|
||||
data: [
|
||||
[ 0, 'lung', 'F', 39844, 99 ],
|
||||
[ 1, 'heart', 'M', 83, 1 ],
|
||||
[ 49, 'spleen', null, 2, "unknown cluster" ],
|
||||
// [ obsOrVarIndex, value, value, value, value ],
|
||||
// ...
|
||||
]
|
||||
}
|
||||
Convert a Matrix FBS to our internal format -- row-major array of
|
||||
observations/cells, stored as an object. Each obs has a key for each
|
||||
annotation, plus __index__ containing its obsIndex.
|
||||
|
||||
Internal (target) format:
|
||||
Example:
|
||||
[
|
||||
{ __index__: 0, tissue_type: "lung", sex: "F", ... },
|
||||
...
|
||||
]
|
||||
|
||||
XXX TODO: we could make use of the columns in building crossfilter
|
||||
dimensions (they have to be recreated). Future optimization.
|
||||
*/
|
||||
const { names, data } = response;
|
||||
const keys = ["__index__", ...names];
|
||||
return _(data)
|
||||
.map(obs => _.zipObject(keys, obs))
|
||||
.value();
|
||||
const fbs = decodeMatrixFBS(arrayBuffer);
|
||||
const keys = fbs.colIdx;
|
||||
const result = Array(fbs.nRows);
|
||||
for (let row = 0; row < fbs.nRows; row += 1) {
|
||||
const rec = { __index__: row };
|
||||
for (let col = 0; col < fbs.nCols; col += 1) {
|
||||
rec[keys[col]] = fbs.columns[col][row];
|
||||
}
|
||||
result[row] = rec;
|
||||
}
|
||||
return result;
|
||||
}
|
||||
|
||||
function RESTv02LayoutResponseToInternal(response) {
|
||||
/*
|
||||
Source per the spec:
|
||||
{
|
||||
layout: {
|
||||
ndims: 2,
|
||||
coordinates: [
|
||||
[ 0, 0.284483, 0.983744 ],
|
||||
[ 1, 0.038844, 0.739444 ],
|
||||
// [ obsOrVarIndex, X_coord, Y_coord ],
|
||||
// ...
|
||||
]
|
||||
}
|
||||
}
|
||||
|
||||
Target (internal) format:
|
||||
{
|
||||
X: Float32Array(numObs),
|
||||
Y: Float32Array(numObs)
|
||||
}
|
||||
In the same order as obsAnnotations
|
||||
*/
|
||||
const { ndims, coordinates } = response.layout;
|
||||
if (ndims !== 2) {
|
||||
throw new Error("Unsupported layout dimensionality");
|
||||
}
|
||||
|
||||
const layout = {
|
||||
X: new Float32Array(coordinates.length),
|
||||
Y: new Float32Array(coordinates.length)
|
||||
function RESTv02LayoutFBSResponseToInternal(arrayBuffer) {
|
||||
const fbs = decodeMatrixFBS(arrayBuffer, true);
|
||||
return {
|
||||
X: fbs.columns[0],
|
||||
Y: fbs.columns[1]
|
||||
};
|
||||
|
||||
for (let i = 0; i < coordinates.length; i += 1) {
|
||||
const [idx, x, y] = coordinates[i];
|
||||
layout.X[idx] = x;
|
||||
layout.Y[idx] = y;
|
||||
}
|
||||
return layout;
|
||||
}
|
||||
|
||||
function reconcileSchemaCategoriesWithSummary(universe) {
|
||||
@@ -192,7 +161,7 @@ export function createUniverseFromRestV02Response(
|
||||
schemaResponse,
|
||||
annotationsObsResponse,
|
||||
annotationsVarResponse,
|
||||
layoutObsResponse
|
||||
layoutFBSResponse
|
||||
) {
|
||||
/*
|
||||
build & return universe from a REST 0.2 /config, /schema and /annotations/obs response
|
||||
@@ -209,15 +178,15 @@ export function createUniverseFromRestV02Response(
|
||||
universe.nVar = schema.dataframe.nVar;
|
||||
|
||||
/* annotations */
|
||||
universe.obsAnnotations = RESTv02AnnotationsResponseToInternal(
|
||||
universe.obsAnnotations = RESTv02AnotationsFBSResponseToInternal(
|
||||
annotationsObsResponse
|
||||
);
|
||||
universe.varAnnotations = RESTv02AnnotationsResponseToInternal(
|
||||
universe.varAnnotations = RESTv02AnotationsFBSResponseToInternal(
|
||||
annotationsVarResponse
|
||||
);
|
||||
|
||||
/* layout */
|
||||
universe.obsLayout = RESTv02LayoutResponseToInternal(layoutObsResponse);
|
||||
universe.obsLayout = RESTv02LayoutFBSResponseToInternal(layoutFBSResponse);
|
||||
|
||||
universe.summary = summarizeAnnotations(
|
||||
universe.schema,
|
||||
@@ -229,32 +198,24 @@ export function createUniverseFromRestV02Response(
|
||||
return finalize(universe);
|
||||
}
|
||||
|
||||
export function convertExpressionRESTv02ToObject(universe, response) {
|
||||
export function convertDataFBStoObject(universe, arrayBuffer) {
|
||||
/*
|
||||
/data/obs response looks like:
|
||||
{
|
||||
var: [ varIndices fetched ],
|
||||
obs: [
|
||||
[ obsIndex, evalue, ... ],
|
||||
...
|
||||
]
|
||||
}
|
||||
/data/var returns a flatbuffer (FBS) as described by cellxgene/fbs/matrix.fbs
|
||||
|
||||
convert expression toa simple Float32Array, and return
|
||||
{ geneName: array, geneName: array, ... }
|
||||
NOTE: geneName, not varIndex
|
||||
This routine converts the binary wire encoding into a JS object:
|
||||
|
||||
{
|
||||
gene: Float32Array,
|
||||
...
|
||||
}
|
||||
*/
|
||||
const vars = response.var;
|
||||
const { obs } = response;
|
||||
const fbs = decodeMatrixFBS(arrayBuffer);
|
||||
const { colIdx, columns } = fbs;
|
||||
const result = {};
|
||||
// XXX TODO: could this use _.unzip and have less code?
|
||||
for (let varIdx = 0; varIdx < vars.length; varIdx += 1) {
|
||||
const gene = universe.varAnnotations[vars[varIdx]].name;
|
||||
const data = new Float32Array(universe.nObs);
|
||||
for (let obsIdx = 0; obsIdx < obs.length; obsIdx += 1) {
|
||||
data[obsIdx] = obs[obsIdx][varIdx + 1];
|
||||
}
|
||||
result[gene] = data;
|
||||
|
||||
for (let c = 0; c < colIdx.length; c += 1) {
|
||||
const gene = universe.varAnnotations[colIdx[c]].name;
|
||||
result[gene] = columns[c];
|
||||
}
|
||||
return result;
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user