From 6fad112cd334bffd2c5b7e2dc52b3e79e22bfc38 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Fri, 30 Mar 2018 00:31:22 +0200
Subject: [PATCH] Removed computation from mol-util, use mol-task instead
---
.../schema-generator/schema-from-mmcif-dic.ts | 4 +-
src/mol-io/reader/_spec/csv.spec.ts | 7 +-
src/mol-io/reader/csv/parser.ts | 19 +-
src/mol-util/computation.ts | 283 ------------------
src/mol-util/index.ts | 6 +-
src/mol-util/scheduler.ts | 207 -------------
src/mol-util/time.ts | 24 --
src/mol-util/uuid.ts | 2 +-
8 files changed, 18 insertions(+), 534 deletions(-)
delete mode 100644 src/mol-util/computation.ts
delete mode 100644 src/mol-util/scheduler.ts
delete mode 100644 src/mol-util/time.ts
diff --git a/src/apps/schema-generator/schema-from-mmcif-dic.ts b/src/apps/schema-generator/schema-from-mmcif-dic.ts
index 60141f15c..711fa6774 100644
--- a/src/apps/schema-generator/schema-from-mmcif-dic.ts
+++ b/src/apps/schema-generator/schema-from-mmcif-dic.ts
@@ -48,7 +48,7 @@ async function runGenerateSchema(name: string, fieldNamesPath?: string, minCount
async function getFieldNamesFilter(fieldNamesPath: string): Promise<Filter> {
const fieldNamesStr = fs.readFileSync(fieldNamesPath, 'utf8')
- const parsed = await Csv(fieldNamesStr, { noColumnNames: true })();
+ const parsed = await Run(Csv(fieldNamesStr, { noColumnNames: true }));
if (parsed.isError) throw parser.error
const csvFile = parsed.result;
@@ -69,7 +69,7 @@ async function getFieldNamesFilter(fieldNamesPath: string): Promise<Filter> {
async function getUsageCountsFilter(minCount: number): Promise<Filter> {
const usageCountsStr = fs.readFileSync(MMCIF_USAGE_COUNTS_PATH, 'utf8')
- const parsed = await Csv(usageCountsStr, { delimiter: ' ' })();
+ const parsed = await Run(Csv(usageCountsStr, { delimiter: ' ' }));
if (parsed.isError) throw parser.error
const csvFile = parsed.result;
diff --git a/src/mol-io/reader/_spec/csv.spec.ts b/src/mol-io/reader/_spec/csv.spec.ts
index cd14e30e4..b074b5bc7 100644
--- a/src/mol-io/reader/_spec/csv.spec.ts
+++ b/src/mol-io/reader/_spec/csv.spec.ts
@@ -5,6 +5,7 @@
*/
import Csv from '../csv/parser'
+import { Run } from 'mol-task';
const csvStringBasic = `StrCol,IntCol,FloatCol
# comment
@@ -23,7 +24,7 @@ string2\t42\t2.44`
describe('csv reader', () => {
it('basic', async () => {
- const parsed = await Csv(csvStringBasic)();
+ const parsed = await Run(Csv(csvStringBasic));
if (parsed.isError) return;
const csvFile = parsed.result;
@@ -45,7 +46,7 @@ describe('csv reader', () => {
});
it('advanced', async () => {
- const parsed = await Csv(csvStringAdvanced)();
+ const parsed = await Run(Csv(csvStringAdvanced));
if (parsed.isError) return;
const csvFile = parsed.result;
@@ -62,7 +63,7 @@ describe('csv reader', () => {
});
it('tabs', async () => {
- const parsed = await Csv(tabString, { delimiter: '\t' })();
+ const parsed = await Run(Csv(tabString, { delimiter: '\t' }));
if (parsed.isError) return;
const csvFile = parsed.result;
diff --git a/src/mol-io/reader/csv/parser.ts b/src/mol-io/reader/csv/parser.ts
index 3d80e906e..66a7a9e17 100644
--- a/src/mol-io/reader/csv/parser.ts
+++ b/src/mol-io/reader/csv/parser.ts
@@ -9,7 +9,7 @@ import { Tokens, TokenBuilder, Tokenizer } from '../common/text/tokenizer'
import * as Data from './data-model'
import Field from './field'
import Result from '../result'
-import Computation from 'mol-util/computation'
+import { Task, RuntimeContext, chunkedSubtask, } from 'mol-task'
const enum CsvTokenType {
Value = 0,
@@ -22,7 +22,7 @@ interface State {
tokenizer: Tokenizer,
tokenType: CsvTokenType;
- chunker: Computation.Chunker,
+ runtimeCtx: RuntimeContext,
tokens: Tokens[],
fieldCount: number,
@@ -38,7 +38,7 @@ interface State {
noColumnNamesRecord: boolean
}
-function State(data: string, ctx: Computation.Context, opts: CsvOptions): State {
+function State(data: string, runtimeCtx: RuntimeContext, opts: CsvOptions): State {
const tokenizer = Tokenizer(data)
return {
@@ -46,7 +46,7 @@ function State(data: string, ctx: Computation.Context, opts: CsvOptions): State
tokenizer,
tokenType: CsvTokenType.End,
- chunker: Computation.chunker(ctx, 100000),
+ runtimeCtx,
tokens: [],
fieldCount: 0,
@@ -206,7 +206,7 @@ function moveNext(state: State) {
return newRecord
}
-function readRecordsChunk(state: State, chunkSize: number) {
+function readRecordsChunk(chunkSize: number, state: State) {
if (state.tokenType === CsvTokenType.End) return 0
let newRecord = moveNext(state);
@@ -225,9 +225,8 @@ function readRecordsChunk(state: State, chunkSize: number) {
}
function readRecordsChunks(state: State) {
- return state.chunker.process(
- chunkSize => readRecordsChunk(state, chunkSize),
- update => update({ message: 'Parsing...', current: state.tokenizer.position, max: state.data.length }));
+ return chunkedSubtask(state.runtimeCtx, 100000, state, readRecordsChunk,
+ (ctx, state) => ctx.update({ message: 'Parsing...', current: state.tokenizer.position, max: state.data.length }));
}
function addColumn (state: State) {
@@ -261,7 +260,7 @@ async function handleRecords(state: State): Promise<Data.Table> {
return Data.Table(state.recordCount, state.columnNames, columns)
}
-async function parseInternal(data: string, ctx: Computation.Context, opts: CsvOptions): Promise<Result<Data.File>> {
+async function parseInternal(data: string, ctx: RuntimeContext, opts: CsvOptions): Promise<Result<Data.File>> {
const state = State(data, ctx, opts);
ctx.update({ message: 'Parsing...', current: 0, max: data.length });
@@ -279,7 +278,7 @@ interface CsvOptions {
export function parse(data: string, opts?: Partial<CsvOptions>) {
const completeOpts = Object.assign({}, { quote: '"', comment: '#', delimiter: ',', noColumnNames: false }, opts)
- return Computation.create<Result<Data.File>>(async ctx => {
+ return Task.create<Result<Data.File>>('Parse CSV', async ctx => {
return await parseInternal(data, ctx, completeOpts);
});
}
diff --git a/src/mol-util/computation.ts b/src/mol-util/computation.ts
deleted file mode 100644
index 3d956de70..000000000
--- a/src/mol-util/computation.ts
+++ /dev/null
@@ -1,283 +0,0 @@
-/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Adapted from https://github.com/dsehnal/LiteMol
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import Scheduler from './scheduler'
-import timeNow from './time'
-
-interface Computation<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 ComputationImpl(computation);
- }
-
- export function resolve<A>(a: A) {
- return create<A>(_ => Promise.resolve(a));
- }
-
- export function reject<A>(reason: any) {
- return create<A>(_ => Promise.reject(reason));
- }
-
- export interface Params {
- updateRateMs?: number,
- observer?: ProgressObserver
- }
-
- export const Aborted = 'Aborted';
-
- export interface Progress {
- message: string,
- isIndeterminate: boolean,
- current: number,
- max: number,
- elapsedMs: number,
- requestAbort?: () => void
- }
-
- export interface ProgressUpdate {
- message?: string,
- abort?: boolean | (() => void),
- current?: number,
- max?: number
- }
-
- export interface Context {
- readonly isSynchronous: boolean,
- /** 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. */
- update(info: ProgressUpdate): Promise<void> | void
- }
-
- export type ProgressObserver = (progress: Readonly<Progress>) => void;
-
- const emptyDisposer = { dispose: () => { } }
-
- /** A context without updates. */
- export const synchronous: Context = {
- isSynchronous: true,
- requiresUpdate: false,
- requestAbort() { },
- subscribe(onProgress) { return emptyDisposer; },
- update(info) { }
- }
-
- export function observable(params?: Partial<Params>) {
- const ret = new ObservableContext(params && params.updateRateMs);
- if (params && params.observer) ret.subscribe(params.observer);
- return ret;
- }
-
- export const now = timeNow;
-
- /** A utility for splitting large computations into smaller parts. */
- export interface Chunker {
- setNextChunkSize(size: number): void,
- /** nextChunk must return the number of actually processed chunks. */
- process(nextChunk: (chunkSize: number) => number, update: (updater: Context['update']) => void, nextChunkSize?: number): Promise<void>
- }
-
- export function chunker(ctx: Context, nextChunkSize: number): Chunker {
- return new ChunkerImpl(ctx, nextChunkSize);
- }
-}
-
-const DefaulUpdateRateMs = 150;
-
-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();
- }
- });
- }
-}
-
-class ObservableContext implements Computation.Context {
- readonly updateRate: number;
- readonly isSynchronous: boolean = false;
- private level = 0;
- private startedTime = 0;
- private abortRequested = false;
- private lastUpdated = 0;
- private observers: Computation.ProgressObserver[] | undefined = void 0;
- private progress: Computation.Progress = { message: 'Working...', current: 0, max: 0, elapsedMs: 0, isIndeterminate: true, requestAbort: void 0 };
-
- private checkAborted() {
- if (this.abortRequested) throw Computation.Aborted;
- }
-
- private abortRequester = () => { this.abortRequested = true };
-
- 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() {
- try {
- if (this.abortRequester) {
- this.abortRequester.call(null);
- }
- } catch (e) { }
- }
-
- update({ message, abort, current, max }: Computation.ProgressUpdate): Promise<void> | void {
- this.checkAborted();
-
- const time = Computation.now();
-
- if (typeof abort === 'boolean') {
- this.progress.requestAbort = abort ? this.abortRequester : void 0;
- } else {
- if (abort) this.abortRequester = abort;
- this.progress.requestAbort = abort ? this.abortRequester : void 0;
- }
-
- if (typeof message !== 'undefined') this.progress.message = message;
- this.progress.elapsedMs = time - this.startedTime;
- if (isNaN(current!)) {
- this.progress.isIndeterminate = true;
- } else {
- this.progress.isIndeterminate = false;
- this.progress.current = current!;
- if (!isNaN(max!)) this.progress.max = max!;
- }
-
- if (this.observers) {
- const p = { ...this.progress };
- for (let i = 0, _i = this.observers.length; i < _i; i++) {
- Scheduler.immediate(this.observers[i], p);
- }
- }
-
- this.lastUpdated = time;
-
- return Scheduler.immediatePromise();
- }
-
- get requiresUpdate() {
- this.checkAborted();
- if (this.isSynchronous) return false;
- return Computation.now() - this.lastUpdated > this.updateRate;
- }
-
- started() {
- if (!this.level) {
- this.startedTime = Computation.now();
- this.lastUpdated = this.startedTime;
- }
- this.level++;
- }
-
- finished() {
- this.level--;
- if (this.level < 0) {
- throw new Error('Bug in code somewhere, Computation.resolve/reject called too many times.');
- }
- if (!this.level) this.observers = void 0;
- }
-
- constructor(updateRate?: number) {
- this.updateRate = updateRate || DefaulUpdateRateMs;
- }
-}
-
-class ChunkerImpl implements Computation.Chunker {
- private processedSinceUpdate = 0;
- private updater: Computation.Context['update'];
-
- private computeChunkSize(delta: number) {
- if (!delta) {
- this.processedSinceUpdate = 0;
- return this.nextChunkSize;
- }
- const rate = (this.context as ObservableContext).updateRate || DefaulUpdateRateMs;
- const ret = Math.round(this.processedSinceUpdate * rate / delta + 1);
- this.processedSinceUpdate = 0;
- return ret;
- }
-
- private getNextChunkSize() {
- const ctx = this.context as ObservableContext;
- // be smart if the computation is synchronous and process the whole chunk at once.
- if (ctx.isSynchronous) return Number.MAX_SAFE_INTEGER;
- return this.nextChunkSize;
- }
-
- setNextChunkSize(size: number) {
- this.nextChunkSize = size;
- }
-
- async process(nextChunk: (size: number) => number, update: (updater: Computation.Context['update']) => Promise<void> | void, nextChunkSize?: number) {
- if (typeof nextChunkSize !== 'undefined') this.setNextChunkSize(nextChunkSize);
- this.processedSinceUpdate = 0;
-
- // track time for the actual computation and exclude the "update time"
- let chunkStart = Computation.now();
- let lastChunkSize: number;
- let chunkCount = 0;
- let totalSize = 0;
- let updateCount = 0;
- while ((lastChunkSize = nextChunk(this.getNextChunkSize())) > 0) {
- chunkCount++;
- this.processedSinceUpdate += lastChunkSize;
- totalSize += lastChunkSize;
- if (this.context.requiresUpdate) {
- let time = Computation.now();
- await update(this.updater);
- this.nextChunkSize = updateCount > 0
- ? Math.round((totalSize + this.computeChunkSize(time - chunkStart)) / (chunkCount + 1))
- : this.computeChunkSize(time - chunkStart)
- updateCount++;
- chunkStart = Computation.now();
- }
- }
- if (this.context.requiresUpdate) {
- let time = Computation.now();
- await update(this.updater);
- this.nextChunkSize = updateCount > 0
- ? Math.round((totalSize + this.computeChunkSize(time - chunkStart)) / (chunkCount + 1))
- : this.computeChunkSize(time - chunkStart)
- }
- }
-
- constructor(public context: Computation.Context, private nextChunkSize: number) {
- this.updater = this.context.update.bind(this.context);
- }
-}
-
-export default Computation;
\ No newline at end of file
diff --git a/src/mol-util/index.ts b/src/mol-util/index.ts
index 191fddd92..4d540010c 100644
--- a/src/mol-util/index.ts
+++ b/src/mol-util/index.ts
@@ -6,13 +6,11 @@
*/
import BitFlags from './bit-flags'
-import Computation from './computation'
-import Scheduler from './scheduler'
import StringBuilder from './string-builder'
-import Time from './time'
import UUID from './uuid'
+import Mask from './mask'
-export { BitFlags, Computation, Scheduler, StringBuilder, Time, UUID }
+export { BitFlags, StringBuilder, UUID, Mask }
export function arrayEqual<T>(arr1: T[], arr2: T[]) {
const length = arr1.length
diff --git a/src/mol-util/scheduler.ts b/src/mol-util/scheduler.ts
deleted file mode 100644
index e118ec97c..000000000
--- a/src/mol-util/scheduler.ts
+++ /dev/null
@@ -1,207 +0,0 @@
-/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-/**
- * setImmediate polyfill adapted from https://github.com/YuzuJS/setImmediate
- * Copyright (c) 2012 Barnesandnoble.com, llc, Donavon West, and Domenic Denicola
- * MIT license.
- */
-
-function createImmediateActions() {
- type Callback = (...args: any[]) => void;
- type Task = { callback: Callback, args: any[] }
-
- const tasksByHandle: { [handle: number]: Task } = { };
- const doc = typeof document !== 'undefined' ? document : void 0;
-
- let currentlyRunningATask = false;
- let nextHandle = 1; // Spec says greater than zero
- let registerImmediate: ((handle: number) => void);
-
- function setImmediate(callback: Callback, ...args: any[]) {
- // Callback can either be a function or a string
- if (typeof callback !== 'function') {
- callback = new Function('' + callback) as Callback;
- }
- // Store and register the task
- const task = { callback: callback, args: args };
- tasksByHandle[nextHandle] = task;
- registerImmediate(nextHandle);
- return nextHandle++;
- }
-
- function clearImmediate(handle: number) {
- delete tasksByHandle[handle];
- }
-
- function run(task: Task) {
- const callback = task.callback;
- const args = task.args;
- switch (args.length) {
- case 0:
- callback();
- break;
- case 1:
- callback(args[0]);
- break;
- case 2:
- callback(args[0], args[1]);
- break;
- case 3:
- callback(args[0], args[1], args[2]);
- break;
- default:
- callback.apply(undefined, args);
- break;
- }
- }
-
- function runIfPresent(handle: number) {
- // From the spec: 'Wait until any invocations of this algorithm started before this one have completed.'
- // So if we're currently running a task, we'll need to delay this invocation.
- if (currentlyRunningATask) {
- // Delay by doing a setTimeout. setImmediate was tried instead, but in Firefox 7 it generated a
- // 'too much recursion' error.
- setTimeout(runIfPresent, 0, handle);
- } else {
- const task = tasksByHandle[handle];
- if (task) {
- currentlyRunningATask = true;
- try {
- run(task);
- } finally {
- clearImmediate(handle);
- currentlyRunningATask = false;
- }
- }
- }
- }
-
- function installNextTickImplementation() {
- registerImmediate = function(handle) {
- process.nextTick(function () { runIfPresent(handle); });
- };
- }
-
- function canUsePostMessage() {
- // The test against `importScripts` prevents this implementation from being installed inside a web worker,
- // where `global.postMessage` means something completely different and can't be used for this purpose.
- const global = typeof window !== 'undefined' ? window as any : void 0;
- if (global && global.postMessage && !global.importScripts) {
- let postMessageIsAsynchronous = true;
- const oldOnMessage = global.onmessage;
- global.onmessage = function() {
- postMessageIsAsynchronous = false;
- };
- global.postMessage('', '*');
- global.onmessage = oldOnMessage;
- return postMessageIsAsynchronous;
- }
- }
-
- function installPostMessageImplementation() {
- // Installs an event handler on `global` for the `message` event: see
- // * https://developer.mozilla.org/en/DOM/window.postMessage
- // * http://www.whatwg.org/specs/web-apps/current-work/multipage/comms.html#crossDocumentMessages
-
- const messagePrefix = 'setImmediate$' + Math.random() + '$';
- const global = typeof window !== 'undefined' ? window as any : void 0;
- const onGlobalMessage = function(event: any) {
- if (event.source === global &&
- typeof event.data === 'string' &&
- event.data.indexOf(messagePrefix) === 0) {
- runIfPresent(+event.data.slice(messagePrefix.length));
- }
- };
-
- if (window.addEventListener) {
- window.addEventListener('message', onGlobalMessage, false);
- } else {
- (window as any).attachEvent('onmessage', onGlobalMessage);
- }
-
- registerImmediate = function(handle) {
- window.postMessage(messagePrefix + handle, '*');
- };
- }
-
- function installMessageChannelImplementation() {
- const channel = new MessageChannel();
- channel.port1.onmessage = function(event) {
- const handle = event.data;
- runIfPresent(handle);
- };
-
- registerImmediate = function(handle) {
- channel.port2.postMessage(handle);
- };
- }
-
- function installReadyStateChangeImplementation() {
- const html = doc!.documentElement;
- registerImmediate = function(handle) {
- // Create a <script> element; its readystatechange event will be fired asynchronously once it is inserted
- // into the document. Do so, thus queuing up the task. Remember to clean up once it's been called.
- let script = doc!.createElement('script') as any;
- script.onreadystatechange = function () {
- runIfPresent(handle);
- script.onreadystatechange = null;
- html.removeChild(script);
- script = null;
- };
- html.appendChild(script);
- };
- }
-
- function installSetTimeoutImplementation() {
- registerImmediate = function(handle) {
- setTimeout(runIfPresent, 0, handle);
- };
- }
-
- // Don't get fooled by e.g. browserify environments.
- if (typeof process !== 'undefined' && {}.toString.call(process) === '[object process]') {
- // For Node.js before 0.9
- installNextTickImplementation();
- } else if (canUsePostMessage()) {
- // For non-IE10 modern browsers
- installPostMessageImplementation();
- } else if (typeof MessageChannel !== 'undefined') {
- // For web workers, where supported
- installMessageChannelImplementation();
- } else if (doc && 'onreadystatechange' in doc.createElement('script')) {
- // For IE 6–8
- installReadyStateChangeImplementation();
- } else {
- // For older browsers
- installSetTimeoutImplementation();
- }
-
- return {
- setImmediate,
- clearImmediate
- };
-}
-
-const immediateActions = (function () {
- if (typeof setImmediate !== 'undefined') {
- if (typeof window !== 'undefined') {
- return { setImmediate: (handler: any, ...args: any[]) => window.setImmediate(handler, ...args as any), clearImmediate: (handle: any) => window.clearImmediate(handle) };
- } else return { setImmediate, clearImmediate }
- }
- return createImmediateActions();
-}());
-
-function resolveImmediate(res: () => void) {
- immediateActions.setImmediate(res);
-}
-
-export default {
- immediate: immediateActions.setImmediate,
- clearImmediate: immediateActions.clearImmediate,
-
- immediatePromise() { return new Promise<void>(resolveImmediate); }
-};
diff --git a/src/mol-util/time.ts b/src/mol-util/time.ts
deleted file mode 100644
index a0ee3abfd..000000000
--- a/src/mol-util/time.ts
+++ /dev/null
@@ -1,24 +0,0 @@
-/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-declare var process: any;
-declare var window: any;
-
-const now: () => number = (function () {
- if (typeof window !== 'undefined' && window.performance) {
- const perf = window.performance;
- return () => perf.now();
- } else if (typeof process !== 'undefined' && process.hrtime !== 'undefined') {
- return () => {
- let t = process.hrtime();
- return t[0] * 1000 + t[1] / 1000000;
- };
- } else {
- return () => +new Date();
- }
-}());
-
-export default now;
\ No newline at end of file
diff --git a/src/mol-util/uuid.ts b/src/mol-util/uuid.ts
index 471d34969..b3dc51a34 100644
--- a/src/mol-util/uuid.ts
+++ b/src/mol-util/uuid.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import now from './time'
+import { now } from 'mol-task'
interface UUID extends String { '@type': 'uuid' }
--
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