@jbrowse/core 2.3.4 → 2.4.1

package/util/map-obj.js

@@ -0,0 +1,33 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+// adapted from map-obj (MIT), with modifications to pass the "whole object"
+// from an array of objects into itself
+const isObject = (value) => typeof value === 'object' && value !== null;
+// Customized for this use-case
+const isObjectCustom = (value) => isObject(value) &&
+    !(value instanceof RegExp) &&
+    !(value instanceof Error) &&
+    !(value instanceof Date) &&
+    !(globalThis.Blob && value instanceof globalThis.Blob);
+function map(object, mapper, isSeen = new WeakSet()) {
+    if (isSeen.has(object)) {
+        return;
+    }
+    isSeen.add(object);
+    const mapArray = (array) => array.forEach(element => {
+        mapper(element);
+        if (isObject(element)) {
+            map(element, mapper, isSeen);
+        }
+    });
+    if (Array.isArray(object)) {
+        mapArray(object);
+    }
+    for (const value of Object.values(object)) {
+        mapper(value);
+        if (isObjectCustom(value)) {
+            Array.isArray(value) ? mapArray(value) : map(value, mapper, isSeen);
+        }
+    }
+}
+exports.default = map;

package/util/offscreenCanvasPonyfill.js

@@ -33,19 +33,20 @@ if (weHave.realOffscreenCanvas) {
 else if (weHave.node) {
     // use node-canvas if we are running in node (i.e. automated tests)
     exports.createCanvas = (...args) => {
-        // @ts-ignore
+        // @ts-expect-error
         // eslint-disable-next-line no-undef
         return nodeCreateCanvas(...args);
     };
     exports.createImageBitmap = async (canvas, ...otherargs) => {
-        if (otherargs.length) {
+        if (otherargs.length > 0) {
             throw new Error('only one-argument uses of createImageBitmap are supported by the node offscreencanvas ponyfill');
         }
         const dataUri = canvas.toDataURL();
-        // @ts-ignore
+        // @ts-expect-error
         // eslint-disable-next-line no-undef
         const img = new nodeImage();
         return new Promise((resolve, reject) => {
+            // need onload for jest
             img.onload = () => resolve(img);
             img.onerror = reject;
             img.src = dataUri;

package/util/offscreenCanvasUtils.d.ts

@@ -1,14 +1,28 @@
-/// <reference types="react" />
-export type RenderReturn = Record<string, unknown>;
+import React from 'react';
+export type RenderReturn = Record<string, unknown> | void;
+type RendererRet = Promise<RenderReturn> | RenderReturn;
 export declare function renderToAbstractCanvas(width: number, height: number, opts: {
     exportSVG?: {
         rasterizeLayers?: boolean;
+        scale?: number;
     };
-    highResolutionScaling: number;
-}, cb: (ctx: CanvasRenderingContext2D) => Promise<RenderReturn | void> | RenderReturn | void): Promise<{
+    highResolutionScaling?: number;
+}, cb: (ctx: CanvasRenderingContext2D) => RendererRet): Promise<{
     canvasRecordedData: any;
 } | {
     reactElement: JSX.Element;
 } | {
     imageData: any;
 }>;
+export declare function getSerializedSvg(results: {
+    width: number;
+    height: number;
+    canvasRecordedData: unknown;
+}): Promise<string>;
+export declare function ReactRendering({ rendering, }: {
+    rendering: {
+        reactElement?: React.ReactNode;
+        html?: string;
+    };
+}): JSX.Element;
+export {};

package/util/offscreenCanvasUtils.js

@@ -1,16 +1,39 @@
 "use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.renderToAbstractCanvas = void 0;
+exports.ReactRendering = exports.getSerializedSvg = exports.renderToAbstractCanvas = void 0;
 const react_1 = __importDefault(require("react"));
 const canvas_sequencer_1 = require("canvas-sequencer");
 // locals
 const offscreenCanvasPonyfill_1 = require("./offscreenCanvasPonyfill");
 const index_1 = require("./index");
 async function renderToAbstractCanvas(width, height, opts, cb) {
-    const { exportSVG, highResolutionScaling: scaling = 1 } = opts;
+    const { exportSVG, highResolutionScaling = 1 } = opts;
     if (exportSVG) {
         if (!exportSVG.rasterizeLayers) {
             const fakeCtx = new canvas_sequencer_1.CanvasSequence();
@@ -21,13 +44,13 @@ async function renderToAbstractCanvas(width, height, opts, cb) {
             };
         }
         else {
-            const scale = 4;
-            const canvas = (0, offscreenCanvasPonyfill_1.createCanvas)(Math.ceil(width * scale), height * scale);
+            const s = exportSVG.scale || highResolutionScaling;
+            const canvas = (0, offscreenCanvasPonyfill_1.createCanvas)(Math.ceil(width * s), height * s);
             const ctx = canvas.getContext('2d');
             if (!ctx) {
                 throw new Error('2d canvas rendering not supported on this platform');
             }
-            ctx.scale(scale, scale);
+            ctx.scale(s, s);
             const result = await cb(ctx);
             // two methods needed for converting canvas to PNG, one for webworker
             // offscreen canvas, one for main thread
@@ -42,14 +65,33 @@ async function renderToAbstractCanvas(width, height, opts, cb) {
         }
     }
     else {
-        const canvas = (0, offscreenCanvasPonyfill_1.createCanvas)(Math.ceil(width * scaling), height * scaling);
+        const s = highResolutionScaling;
+        const canvas = (0, offscreenCanvasPonyfill_1.createCanvas)(Math.ceil(width * s), height * s);
         const ctx = canvas.getContext('2d');
         if (!ctx) {
             throw new Error('2d canvas rendering not supported on this platform');
         }
-        ctx.scale(scaling, scaling);
+        ctx.scale(s, s);
         const result = await cb(ctx);
         return { ...result, imageData: await (0, offscreenCanvasPonyfill_1.createImageBitmap)(canvas) };
     }
 }
 exports.renderToAbstractCanvas = renderToAbstractCanvas;
+async function getSerializedSvg(results) {
+    const { width, height, canvasRecordedData } = results;
+    // @ts-ignore needs to be ignore not expect error, produces error in build step
+    const C2S = await Promise.resolve().then(() => __importStar(require('canvas2svg')));
+    const ctx = new C2S.default(width, height);
+    const seq = new canvas_sequencer_1.CanvasSequence(canvasRecordedData);
+    seq.execute(ctx);
+    // innerHTML strips the outer <svg> element from returned data, we add
+    // our own <svg> element in the view's SVG export
+    return ctx.getSvg().innerHTML;
+}
+exports.getSerializedSvg = getSerializedSvg;
+function ReactRendering({ rendering, }) {
+    return (react_1.default.createElement(react_1.default.Fragment, null, react_1.default.isValidElement(rendering.reactElement) ? (rendering.reactElement) : (react_1.default.createElement("g", { 
+        /* eslint-disable-next-line react/no-danger */
+        dangerouslySetInnerHTML: { __html: rendering.html || '' } }))));
+}
+exports.ReactRendering = ReactRendering;

package/util/tracks.d.ts

@@ -75,4 +75,4 @@ export declare function generateUnknownTrackConf(trackName: string, trackUrl: st
 };
 export declare function getTrackName(conf: AnyConfigurationModel, session: {
     assemblies: AnyConfigurationModel[];
-}): any;
+}): string;

package/util/tracks.js

@@ -141,7 +141,6 @@ function guessAdapter(file, index, adapterHint, model) {
 exports.guessAdapter = guessAdapter;
 function guessTrackType(adapterType, model) {
     if (model) {
-        // @ts-ignore
         const session = (0, index_1.getSession)(model);
         const trackTypeGuesser = (0, index_1.getEnv)(session).pluginManager.evaluateExtensionPoint('Core-guessTrackTypeForLocation', (_adapterName) => {
             return undefined;

package/util/types/index.d.ts

@@ -22,7 +22,6 @@ export interface SnackAction {
     onClick: () => void;
 }
 export type AssemblyManager = Instance<ReturnType<typeof assemblyManager>>;
-export type { TextSearchManager };
 export interface BasePlugin {
     version?: string;
     name: string;
@@ -230,3 +229,4 @@ export type PreBlobLocation = {
     blob: File;
 };
 export type PreFileLocation = PreUriLocation | PreLocalPathLocation | PreBlobLocation;
+export { type default as TextSearchManager } from '../../TextSearch/TextSearchManager';

package/util/types/index.js

@@ -37,7 +37,7 @@ function isSessionModelWithConfigEditing(thing) {
 exports.isSessionModelWithConfigEditing = isSessionModelWithConfigEditing;
 function isSessionWithAddTracks(thing) {
     return (
-    // @ts-ignore
+    // @ts-expect-error
     isSessionModel(thing) && 'addTrackConf' in thing && !thing.disableAddTracks);
 }
 exports.isSessionWithAddTracks = isSessionWithAddTracks;
@@ -71,7 +71,7 @@ function isTrackModel(thing) {
     return (typeof thing === 'object' &&
         thing !== null &&
         'configuration' in thing &&
-        // @ts-ignore
+        // @ts-expect-error
         thing.configuration.trackId);
 }
 exports.isTrackModel = isTrackModel;
@@ -79,7 +79,7 @@ function isDisplayModel(thing) {
     return (typeof thing === 'object' &&
         thing !== null &&
         'configuration' in thing &&
-        // @ts-ignore
+        // @ts-expect-error
         thing.configuration.displayId);
 }
 exports.isDisplayModel = isDisplayModel;

package/util/types/mst.js

@@ -70,16 +70,16 @@ exports.UriLocation = mobx_state_tree_1.types.snapshotProcessor(exports.UriLocat
     },
 });
 exports.FileLocation = mobx_state_tree_1.types.snapshotProcessor(mobx_state_tree_1.types.union(exports.LocalPathLocation, exports.UriLocation, exports.BlobLocation), {
-    // @ts-ignore
+    // @ts-expect-error
     preProcessor(snap) {
         if (!snap) {
             return undefined;
         }
-        // @ts-ignore
+        // @ts-expect-error
         // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
         const { locationType, ...rest } = snap;
         if (!locationType) {
-            // @ts-ignore
+            // @ts-expect-error
             const { uri, localPath, blob } = rest;
             let locationType = '';
             if (uri !== undefined) {

package/data_adapters/CytobandAdapter.d.ts

@@ -1,8 +0,0 @@
-import SimpleFeature from '../util/simpleFeature';
-import { BaseAdapter } from './BaseAdapter';
-declare const configSchema: import("../configuration").AnyConfigurationSchemaType;
-declare class CytobandAdapter extends BaseAdapter {
-    getData(): Promise<SimpleFeature[]>;
-    freeResources(): void;
-}
-export { configSchema, CytobandAdapter as DataAdapter };

package/data_adapters/CytobandAdapter.js

@@ -1,49 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.DataAdapter = exports.configSchema = void 0;
-const simpleFeature_1 = __importDefault(require("../util/simpleFeature"));
-const configuration_1 = require("../configuration");
-const io_1 = require("../util/io");
-const BaseAdapter_1 = require("./BaseAdapter");
-/**
- * #config CytobandAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
-const configSchema = (0, configuration_1.ConfigurationSchema)('CytobandAdapter', {
-    /**
-     * #slot
-     */
-    cytobandLocation: {
-        type: 'fileLocation',
-        defaultValue: { uri: '/path/to/cytoband.txt.gz' },
-    },
-}, { explicitlyTyped: true });
-exports.configSchema = configSchema;
-class CytobandAdapter extends BaseAdapter_1.BaseAdapter {
-    async getData() {
-        const loc = (0, configuration_1.readConfObject)(this.config, 'cytobandLocation');
-        if (loc.uri === '' || loc.uri === '/path/to/cytoband.txt.gz') {
-            return [];
-        }
-        const data = await (0, io_1.openLocation)(loc).readFile('utf8');
-        return data
-            .split(/\n|\r\n|\r/)
-            .filter(f => !!f.trim())
-            .map(line => {
-            const [refName, start, end, name, type] = line.split('\t');
-            return new simpleFeature_1.default({
-                uniqueId: line,
-                refName,
-                start: +start,
-                end: +end,
-                name,
-                type,
-            });
-        });
-    }
-    freeResources( /* { region } */) { }
-}
-exports.DataAdapter = CytobandAdapter;