From f03e0b6736e68dfcc0aa745e4dd3aa4076e97ee1 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Wed, 4 Oct 2017 16:42:17 +0200
Subject: [PATCH] simplified computation API
---
src/reader/cif/text/parser.ts | 2 +-
src/reader/common/text/tokenizer.ts | 1 -
src/reader/gro/parser.ts | 5 +-
src/reader/spec/gro.spec.ts | 6 +-
src/script.ts | 28 +++++----
src/utils/computation.ts | 98 +++++++++++++++--------------
6 files changed, 71 insertions(+), 69 deletions(-)
diff --git a/src/reader/cif/text/parser.ts b/src/reader/cif/text/parser.ts
index b7f593f86..d27dcd240 100644
--- a/src/reader/cif/text/parser.ts
+++ b/src/reader/cif/text/parser.ts
@@ -555,7 +555,7 @@ async function parseInternal(data: string, ctx: Computation.Context) {
//inSaveFrame = false,
//blockSaveFrames: any;
- ctx.updateProgress({ message: 'Parsing...' });
+ ctx.update({ message: 'Parsing...', current: 0, max: data.length });
moveNext(tokenizer);
while (tokenizer.tokenType !== CifTokenType.End) {
diff --git a/src/reader/common/text/tokenizer.ts b/src/reader/common/text/tokenizer.ts
index a21f90c21..17991fbdb 100644
--- a/src/reader/common/text/tokenizer.ts
+++ b/src/reader/common/text/tokenizer.ts
@@ -37,7 +37,6 @@ export function Tokenizer(data: string): Tokenizer {
}
export namespace Tokenizer {
-
export function getTokenString(state: Tokenizer) {
return state.data.substring(state.tokenStart, state.tokenEnd);
}
diff --git a/src/reader/gro/parser.ts b/src/reader/gro/parser.ts
index 60d3dcddb..7ec1c994b 100644
--- a/src/reader/gro/parser.ts
+++ b/src/reader/gro/parser.ts
@@ -34,7 +34,7 @@ function State(tokenizer: Tokenizer, ctx: Computation.Context): State {
tokenizer,
header: createEmptyHeader(),
numberOfAtoms: 0,
- chunker: Computation.chunker(ctx, 100000)
+ chunker: Computation.chunker(ctx, 100000) // 100000 lines is the default chunk size for this reader
};
}
@@ -140,8 +140,7 @@ function handleBoxVectors(state: State) {
async function parseInternal(data: string, ctx: Computation.Context): Promise<Result<Schema.File>> {
const tokenizer = Tokenizer(data);
- // 100000 lines is the default chunk size for this reader
-
+ ctx.update({ message: 'Parsing...', current: 0, max: data.length });
const structures: Schema.Structure[] = [];
while (tokenizer.position < data.length) {
const state = State(tokenizer, ctx);
diff --git a/src/reader/spec/gro.spec.ts b/src/reader/spec/gro.spec.ts
index ba2e48aef..8f78668d5 100644
--- a/src/reader/spec/gro.spec.ts
+++ b/src/reader/spec/gro.spec.ts
@@ -26,8 +26,7 @@ const groStringHighPrecision = `Generated by trjconv : 2168 system t= 15.00000
describe('gro reader', () => {
it('basic', async () => {
- const comp = Gro(groString)
- const parsed = await comp.run()
+ const parsed = await Gro(groString)();
if (parsed.isError) {
console.log(parsed)
@@ -59,8 +58,7 @@ describe('gro reader', () => {
});
it('high precision', async () => {
- const comp = Gro(groStringHighPrecision)
- const parsed = await comp.run()
+ const parsed = await Gro(groStringHighPrecision)()
if (parsed.isError) {
console.log(parsed)
diff --git a/src/script.ts b/src/script.ts
index b6df67554..f4cf5a07a 100644
--- a/src/script.ts
+++ b/src/script.ts
@@ -11,17 +11,21 @@ import * as fs from 'fs'
import Gro from './reader/gro/parser'
import CIF from './reader/cif/index'
-// const file = '1crn.gro'
+const file = '1crn.gro'
// const file = 'water.gro'
// const file = 'test.gro'
-const file = 'md_1u19_trj.gro'
+// const file = 'md_1u19_trj.gro'
+
+function showProgress(tag: string, p: Computation.Progress) {
+ console.log(`[${tag}] ${p.message} ${p.isIndeterminate ? '' : (p.current / p.max * 100).toFixed(2) + '% '}(${p.elapsedMs | 0}ms)`)
+}
async function runGro(input: string) {
console.time('parseGro');
const comp = Gro(input);
- const running = comp.runObservable(Computation.observable({ updateRateMs: 150 }));
- running.subscribe(p => console.log(`[Gro] ${(p.current / p.max * 100).toFixed(2)} (${p.elapsedMs | 0}ms)`));
- const parsed = await running.result;
+
+ const ctx = Computation.observable({ updateRateMs: 150, observer: p => showProgress('GRO', p) });
+ const parsed = await comp(ctx);
console.timeEnd('parseGro');
if (parsed.isError) {
@@ -85,9 +89,8 @@ async function runCIF(input: string | Uint8Array) {
console.time('parseCIF');
const comp = typeof input === 'string' ? CIF.parseText(input) : CIF.parseBinary(input);
- const running = comp.runObservable(Computation.observable({ updateRateMs: 250 })); // Computation.synchronous
- running.subscribe(p => console.log(`[CIF] ${p.message} ${(p.current / p.max * 100).toFixed(2)}% (${p.elapsedMs | 0}ms)`));
- const parsed = await running.result;
+ const ctx = Computation.observable({ updateRateMs: 250, observer: p => showProgress('CIF', p) });
+ const parsed = await comp(ctx);
console.timeEnd('parseCIF');
if (parsed.isError) {
console.log(parsed);
@@ -118,7 +121,7 @@ export function _cif() {
});
path = `./examples/1cbs_full.bcif`;
- //const path = 'c:/test/quick/3j3q.cif';
+ // const path = 'c:/test/quick/3j3q.cif';
fs.readFile(path, function (err, input) {
if (err) {
return console.log(err);
@@ -137,14 +140,13 @@ import Computation from './utils/computation'
const comp = Computation.create(async ctx => {
for (let i = 0; i < 0; i++) {
await new Promise(res => setTimeout(res, 500));
- if (ctx.requiresUpdate) await ctx.updateProgress({ message: 'working', current: i, max: 2 });
+ if (ctx.requiresUpdate) await ctx.update({ message: 'working', current: i, max: 2 });
}
return 42;
});
async function testComp() {
- const running = comp.runObservable();
- running.subscribe(p => console.log(JSON.stringify(p)));
- const ret = await running.result;
+ const ctx = Computation.observable({ observer: p => showProgress('test', p) });
+ const ret = await comp(ctx);
console.log('computation returned', ret);
}
testComp();
\ No newline at end of file
diff --git a/src/utils/computation.ts b/src/utils/computation.ts
index fa91d83f7..efaade355 100644
--- a/src/utils/computation.ts
+++ b/src/utils/computation.ts
@@ -8,15 +8,14 @@
import Scheduler from './scheduler'
interface Computation<A> {
- run(ctx?: Computation.Context): Promise<A>,
- runObservable(ctx?: Computation.Context): Computation.Running<A>
+ (ctx?: Computation.Context): Promise<A>
}
namespace Computation {
export let PRINT_ERRORS_TO_CONSOLE = false;
export function create<A>(computation: (ctx: Context) => Promise<A>) {
- return new ComputationImpl(computation);
+ return ComputationImpl(computation);
}
export function resolve<A>(a: A) {
@@ -28,7 +27,8 @@ namespace Computation {
}
export interface Params {
- updateRateMs: number
+ updateRateMs?: number,
+ observer?: ProgressObserver
}
export const Aborted = 'Aborted';
@@ -54,27 +54,29 @@ namespace Computation {
/** Also checks if the computation was aborted. If so, throws. */
readonly requiresUpdate: boolean,
requestAbort(): void,
+
+ subscribe(onProgress: ProgressObserver): { dispose: () => void },
/** Also checks if the computation was aborted. If so, throws. */
- updateProgress(info: ProgressUpdate): Promise<void> | void
+ update(info: ProgressUpdate): Promise<void> | void
}
export type ProgressObserver = (progress: Readonly<Progress>) => void;
- export interface Running<A> {
- subscribe(onProgress: ProgressObserver): void,
- result: Promise<A>
- }
+ const emptyDisposer = { dispose: () => { } }
/** A context without updates. */
export const synchronous: Context = {
isSynchronous: true,
requiresUpdate: false,
requestAbort() { },
- updateProgress(info) { }
+ subscribe(onProgress) { return emptyDisposer; },
+ update(info) { }
}
export function observable(params?: Partial<Params>) {
- return new ObservableContext(params);
+ const ret = new ObservableContext(params && params.updateRateMs);
+ if (params && params.observer) ret.subscribe(params.observer);
+ return ret;
}
declare var process: any;
@@ -98,7 +100,7 @@ namespace Computation {
export interface Chunker {
setNextChunkSize(size: number): void,
/** nextChunk must return the number of actually processed chunks. */
- process(nextChunk: (chunkSize: number) => number, update: (updater: Context['updateProgress']) => void, nextChunkSize?: number): Promise<void>
+ process(nextChunk: (chunkSize: number) => number, update: (updater: Context['update']) => void, nextChunkSize?: number): Promise<void>
}
export function chunker(ctx: Context, nextChunkSize: number): Chunker {
@@ -107,35 +109,22 @@ namespace Computation {
}
const DefaulUpdateRateMs = 150;
-const NoOpSubscribe = () => { }
-
-class ComputationImpl<A> implements Computation<A> {
- run(ctx?: Computation.Context) {
- return this.runObservable(ctx).result;
- }
-
- runObservable(ctx?: Computation.Context): Computation.Running<A> {
- const context = ctx ? ctx as ObservableContext : new ObservableContext();
-
- return {
- subscribe: (context as ObservableContext).subscribe || NoOpSubscribe,
- result: new Promise<A>(async (resolve, reject) => {
- try {
- if (context.started) context.started();
- const result = await this.computation(context);
- resolve(result);
- } catch (e) {
- if (Computation.PRINT_ERRORS_TO_CONSOLE) console.error(e);
- reject(e);
- } finally {
- if (context.finished) context.finished();
- }
- })
- };
- }
-
- constructor(private computation: (ctx: Computation.Context) => Promise<A>) {
+function ComputationImpl<A>(computation: (ctx: Computation.Context) => Promise<A>): Computation<A> {
+ return (ctx?: Computation.Context) => {
+ const context: ObservableContext = ctx ? ctx : Computation.synchronous as any;
+ return new Promise<A>(async (resolve, reject) => {
+ try {
+ if (context.started) context.started();
+ const result = await computation(context);
+ resolve(result);
+ } catch (e) {
+ if (Computation.PRINT_ERRORS_TO_CONSOLE) console.error(e);
+ reject(e);
+ } finally {
+ if (context.finished) context.finished();
+ }
+ });
}
}
@@ -160,6 +149,18 @@ class ObservableContext implements Computation.Context {
subscribe = (obs: Computation.ProgressObserver) => {
if (!this.observers) this.observers = [];
this.observers.push(obs);
+ return {
+ dispose: () => {
+ if (!this.observers) return;
+ for (let i = 0; i < this.observers.length; i++) {
+ if (this.observers[i] === obs) {
+ this.observers[i] = this.observers[this.observers.length - 1];
+ this.observers.pop();
+ return;
+ }
+ }
+ }
+ };
}
requestAbort() {
@@ -170,7 +171,7 @@ class ObservableContext implements Computation.Context {
} catch (e) { }
}
- updateProgress({ message, abort, current, max }: Computation.ProgressUpdate): Promise<void> | void {
+ update({ message, abort, current, max }: Computation.ProgressUpdate): Promise<void> | void {
this.checkAborted();
const time = Computation.now();
@@ -210,7 +211,10 @@ class ObservableContext implements Computation.Context {
}
started() {
- if (!this.level) this.startedTime = Computation.now();
+ if (!this.level) {
+ this.startedTime = Computation.now();
+ this.lastUpdated = this.startedTime;
+ }
this.level++;
}
@@ -222,14 +226,14 @@ class ObservableContext implements Computation.Context {
if (!this.level) this.observers = void 0;
}
- constructor(params?: Partial<Computation.Params>) {
- this.updateRate = (params && params.updateRateMs) || DefaulUpdateRateMs;
+ constructor(updateRate?: number) {
+ this.updateRate = updateRate || DefaulUpdateRateMs;
}
}
class ChunkerImpl implements Computation.Chunker {
private processedSinceUpdate = 0;
- private updater: Computation.Context['updateProgress'];
+ private updater: Computation.Context['update'];
private computeChunkSize() {
const lastDelta = (this.context as ObservableContext).lastDelta || 0;
@@ -251,7 +255,7 @@ class ChunkerImpl implements Computation.Chunker {
this.nextChunkSize = size;
}
- async process(nextChunk: (size: number) => number, update: (updater: Computation.Context['updateProgress']) => Promise<void> | void, nextChunkSize?: number) {
+ async process(nextChunk: (size: number) => number, update: (updater: Computation.Context['update']) => Promise<void> | void, nextChunkSize?: number) {
if (typeof nextChunkSize !== 'undefined') this.setNextChunkSize(nextChunkSize);
let lastChunkSize: number;
@@ -269,7 +273,7 @@ class ChunkerImpl implements Computation.Chunker {
}
constructor(public context: Computation.Context, private nextChunkSize: number) {
- this.updater = this.context.updateProgress.bind(this.context);
+ this.updater = this.context.update.bind(this.context);
}
}
--
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