Removed computation from mol-util, use mol-task instead

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;
 

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;
 

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);
     });
 }

src/mol-util/computation.ts

@@ -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;

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

src/mol-util/scheduler.ts

@@ -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); }
-};

src/mol-util/time.ts

@@ -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;

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' }