@jbrowse/core 2.1.0 → 2.1.3

package/ui/AboutDialog.js

@@ -84,7 +84,7 @@ function AboutDialog({ config, handleClose, }) {
     if ((0, configuration_1.readConfObject)(config, 'type') === 'ReferenceSequenceTrack') {
         const asm = session.assemblies.find(a => a.sequence === config.configuration);
         trackName = asm
-            ? `Reference Sequence (${(0, configuration_1.readConfObject)(asm, 'name')})`
+            ? `Reference Sequence (${(0, configuration_1.readConfObject)(asm, 'displayName') || (0, configuration_1.readConfObject)(asm, 'name')})`
             : 'Reference Sequence';
     }
     const details = typeof info === 'string'

package/ui/SanitizedHTML.js

@@ -58,7 +58,7 @@ function SanitizedHTML({ html }) {
         // see https://github.com/cure53/DOMPurify/issues/317
         // only have to add this once, and can't do it globally because dompurify
         // not yet initialized at global scope
-        dompurify_1.default.addHook('afterSanitizeAttributes', node => {
+        dompurify_1.default.addHook('afterSanitizeAttributes', (node) => {
             if (node.tagName === 'A') {
                 node.setAttribute('rel', 'noopener noreferrer');
                 node.setAttribute('target', '_blank');

package/ui/theme.d.ts

@@ -1,4 +1,26 @@
-import { PaletteOptions } from '@mui/material/styles/createPalette';
+import type { PaletteOptions } from '@mui/material/styles/createPalette';
+declare module '@mui/material/styles/createPalette' {
+    interface Palette {
+        tertiary: Palette['primary'];
+        quaternary: Palette['primary'];
+        bases: {
+            A: Palette['primary'];
+            C: Palette['primary'];
+            G: Palette['primary'];
+            T: Palette['primary'];
+        };
+    }
+    interface PaletteOptions {
+        tertiary?: PaletteOptions['primary'];
+        quaternary?: PaletteOptions['primary'];
+        bases?: {
+            A?: PaletteOptions['primary'];
+            C?: PaletteOptions['primary'];
+            G?: PaletteOptions['primary'];
+            T?: PaletteOptions['primary'];
+        };
+    }
+}
 export declare const jbrowseDefaultPalette: {
     primary: {
         main: string;

package/util/QuickLRU.d.ts

@@ -1,24 +1,32 @@
-export default QuickLRU;
-/**
- * Heavily based on [quick-lru](https://www.npmjs.com/package/quick-lru)
- * (quick-lru didn't work for us because the export wouldn't compile in Webpack
- * properly)
- */
-declare class QuickLRU {
+export default class QuickLRU extends Map<any, any> {
     constructor(options?: {});
     maxSize: any;
+    maxAge: any;
+    onEviction: any;
     cache: Map<any, any>;
     oldCache: Map<any, any>;
     _size: number;
+    _emitEvictions(cache: any): void;
+    _deleteIfExpired(key: any, item: any): boolean;
+    _getOrDeleteIfExpired(key: any, item: any): any;
+    _getItemValue(key: any, item: any): any;
+    _peek(key: any, cache: any): any;
     _set(key: any, value: any): void;
+    _moveToRecent(key: any, item: any): void;
+    _entriesAscending(): Generator<[any, any], void, unknown>;
     get(key: any): any;
-    set(key: any, value: any): QuickLRU;
+    set(key: any, value: any, { maxAge }?: {
+        maxAge?: any;
+    }): void;
     has(key: any): boolean;
     peek(key: any): any;
     delete(key: any): boolean;
-    clear(): void;
+    resize(newSize: any): void;
     keys(): Generator<any, void, unknown>;
     values(): Generator<any, void, unknown>;
-    get size(): number;
-    [Symbol.iterator](): Generator<[any, any], void, unknown>;
+    entriesDescending(): Generator<any[], void, unknown>;
+    entriesAscending(): Generator<any[], void, unknown>;
+    entries(): Generator<any[], void, unknown>;
+    forEach(callbackFunction: any, thisArgument?: QuickLRU): void;
+    [Symbol.iterator](): Generator<any[], void, unknown>;
 }

package/util/QuickLRU.js

@@ -1,67 +1,140 @@
 "use strict";
+// vendored from quick-lru@6.1.1, didn't like being compiled as a 'pure-esm' nodejs dependency
+// the license is reproduced below https://github.com/sindresorhus/quick-lru/blob/main/license
+// MIT License
 Object.defineProperty(exports, "__esModule", { value: true });
-/* eslint-disable no-underscore-dangle */
-/**
- * Heavily based on [quick-lru](https://www.npmjs.com/package/quick-lru)
- * (quick-lru didn't work for us because the export wouldn't compile in Webpack
- * properly)
- */
-class QuickLRU {
+// Copyright (c) Sindre Sorhus <sindresorhus@gmail.com> (https://sindresorhus.com)
+// Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+// The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+class QuickLRU extends Map {
     constructor(options = {}) {
+        super();
         if (!(options.maxSize && options.maxSize > 0)) {
             throw new TypeError('`maxSize` must be a number greater than 0');
         }
+        if (typeof options.maxAge === 'number' && options.maxAge === 0) {
+            throw new TypeError('`maxAge` must be a number greater than 0');
+        }
+        // TODO: Use private class fields when ESLint supports them.
         this.maxSize = options.maxSize;
+        this.maxAge = options.maxAge || Number.POSITIVE_INFINITY;
+        this.onEviction = options.onEviction;
         this.cache = new Map();
         this.oldCache = new Map();
         this._size = 0;
     }
+    // TODO: Use private class methods when targeting Node.js 16.
+    _emitEvictions(cache) {
+        if (typeof this.onEviction !== 'function') {
+            return;
+        }
+        for (const [key, item] of cache) {
+            this.onEviction(key, item.value);
+        }
+    }
+    _deleteIfExpired(key, item) {
+        if (typeof item.expiry === 'number' && item.expiry <= Date.now()) {
+            if (typeof this.onEviction === 'function') {
+                this.onEviction(key, item.value);
+            }
+            return this.delete(key);
+        }
+        return false;
+    }
+    _getOrDeleteIfExpired(key, item) {
+        const deleted = this._deleteIfExpired(key, item);
+        if (deleted === false) {
+            return item.value;
+        }
+    }
+    _getItemValue(key, item) {
+        return item.expiry ? this._getOrDeleteIfExpired(key, item) : item.value;
+    }
+    _peek(key, cache) {
+        const item = cache.get(key);
+        return this._getItemValue(key, item);
+    }
     _set(key, value) {
         this.cache.set(key, value);
-        this._size += 1;
+        this._size++;
         if (this._size >= this.maxSize) {
             this._size = 0;
+            this._emitEvictions(this.oldCache);
             this.oldCache = this.cache;
             this.cache = new Map();
         }
     }
+    _moveToRecent(key, item) {
+        this.oldCache.delete(key);
+        this._set(key, item);
+    }
+    *_entriesAscending() {
+        for (const item of this.oldCache) {
+            const [key, value] = item;
+            if (!this.cache.has(key)) {
+                const deleted = this._deleteIfExpired(key, value);
+                if (deleted === false) {
+                    yield item;
+                }
+            }
+        }
+        for (const item of this.cache) {
+            const [key, value] = item;
+            const deleted = this._deleteIfExpired(key, value);
+            if (deleted === false) {
+                yield item;
+            }
+        }
+    }
     get(key) {
         if (this.cache.has(key)) {
-            return this.cache.get(key);
+            const item = this.cache.get(key);
+            return this._getItemValue(key, item);
         }
         if (this.oldCache.has(key)) {
-            const value = this.oldCache.get(key);
-            this.oldCache.delete(key);
-            this._set(key, value);
-            return value;
+            const item = this.oldCache.get(key);
+            if (this._deleteIfExpired(key, item) === false) {
+                this._moveToRecent(key, item);
+                return item.value;
+            }
         }
-        return undefined;
     }
-    set(key, value) {
+    set(key, value, { maxAge = this.maxAge } = {}) {
+        const expiry = typeof maxAge === 'number' && maxAge !== Number.POSITIVE_INFINITY
+            ? Date.now() + maxAge
+            : undefined;
         if (this.cache.has(key)) {
-            this.cache.set(key, value);
+            this.cache.set(key, {
+                value,
+                expiry,
+            });
         }
         else {
-            this._set(key, value);
+            this._set(key, { value, expiry });
         }
-        return this;
     }
     has(key) {
-        return this.cache.has(key) || this.oldCache.has(key);
+        if (this.cache.has(key)) {
+            return !this._deleteIfExpired(key, this.cache.get(key));
+        }
+        if (this.oldCache.has(key)) {
+            return !this._deleteIfExpired(key, this.oldCache.get(key));
+        }
+        return false;
     }
     peek(key) {
         if (this.cache.has(key)) {
-            return this.cache.get(key);
+            return this._peek(key, this.cache);
         }
         if (this.oldCache.has(key)) {
-            return this.oldCache.get(key);
+            return this._peek(key, this.oldCache);
         }
-        return undefined;
     }
     delete(key) {
         const deleted = this.cache.delete(key);
         if (deleted) {
-            this._size -= 1;
+            this._size--;
         }
         return this.oldCache.delete(key) || deleted;
     }
@@ -70,6 +143,27 @@ class QuickLRU {
         this.oldCache.clear();
         this._size = 0;
     }
+    resize(newSize) {
+        if (!(newSize && newSize > 0)) {
+            throw new TypeError('`maxSize` must be a number greater than 0');
+        }
+        const items = [...this._entriesAscending()];
+        const removeCount = items.length - newSize;
+        if (removeCount < 0) {
+            this.cache = new Map(items);
+            this.oldCache = new Map();
+            this._size = items.length;
+        }
+        else {
+            if (removeCount > 0) {
+                this._emitEvictions(items.slice(0, removeCount));
+            }
+            this.oldCache = new Map(items.slice(removeCount));
+            this.cache = new Map();
+            this._size = 0;
+        }
+        this.maxSize = newSize;
+    }
     *keys() {
         for (const [key] of this) {
             yield key;
@@ -82,23 +176,71 @@ class QuickLRU {
     }
     *[Symbol.iterator]() {
         for (const item of this.cache) {
-            yield item;
+            const [key, value] = item;
+            const deleted = this._deleteIfExpired(key, value);
+            if (deleted === false) {
+                yield [key, value.value];
+            }
         }
         for (const item of this.oldCache) {
-            const [key] = item;
+            const [key, value] = item;
             if (!this.cache.has(key)) {
-                yield item;
+                const deleted = this._deleteIfExpired(key, value);
+                if (deleted === false) {
+                    yield [key, value.value];
+                }
             }
         }
     }
+    *entriesDescending() {
+        let items = [...this.cache];
+        for (let i = items.length - 1; i >= 0; --i) {
+            const item = items[i];
+            const [key, value] = item;
+            const deleted = this._deleteIfExpired(key, value);
+            if (deleted === false) {
+                yield [key, value.value];
+            }
+        }
+        items = [...this.oldCache];
+        for (let i = items.length - 1; i >= 0; --i) {
+            const item = items[i];
+            const [key, value] = item;
+            if (!this.cache.has(key)) {
+                const deleted = this._deleteIfExpired(key, value);
+                if (deleted === false) {
+                    yield [key, value.value];
+                }
+            }
+        }
+    }
+    *entriesAscending() {
+        for (const [key, value] of this._entriesAscending()) {
+            yield [key, value.value];
+        }
+    }
     get size() {
+        if (!this._size) {
+            return this.oldCache.size;
+        }
         let oldCacheSize = 0;
         for (const key of this.oldCache.keys()) {
             if (!this.cache.has(key)) {
-                oldCacheSize += 1;
+                oldCacheSize++;
             }
         }
-        return this._size + oldCacheSize;
+        return Math.min(this._size + oldCacheSize, this.maxSize);
+    }
+    entries() {
+        return this.entriesAscending();
+    }
+    forEach(callbackFunction, thisArgument = this) {
+        for (const [key, value] of this.entriesAscending()) {
+            callbackFunction.call(thisArgument, value, key, this);
+        }
+    }
+    get [Symbol.toStringTag]() {
+        return JSON.stringify([...this.entriesAscending()]);
     }
 }
 exports.default = QuickLRU;

package/util/calculateDynamicBlocks.js

@@ -1,5 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
+const mobx_state_tree_1 = require("mobx-state-tree");
 const range_1 = require("./range");
 const _1 = require(".");
 const blockTypes_1 = require("./blockTypes");
@@ -35,6 +36,7 @@ function calculateDynamicBlocks(model, padding = true, elision = true) {
         const { assemblyName, refName, start: regionStart, end: regionEnd, reversed, } = region;
         const displayedRegionRightPx = displayedRegionLeftPx + (regionEnd - regionStart) / bpPerPx;
         const regionWidthPx = (regionEnd - regionStart) / bpPerPx;
+        const parentRegion = (0, mobx_state_tree_1.isStateTreeNode)(region) ? (0, mobx_state_tree_1.getSnapshot)(region) : region;
         if (displayedRegionLeftPx < windowRightPx &&
             displayedRegionRightPx > windowLeftPx) {
             // this displayed region overlaps the view, so make a record for it
@@ -66,7 +68,7 @@ function calculateDynamicBlocks(model, padding = true, elision = true) {
                 end,
                 reversed,
                 offsetPx: blockOffsetPx,
-                parentRegion: region,
+                parentRegion,
                 regionNumber,
                 widthPx,
                 isLeftEndOfDisplayedRegion,

package/util/calculateStaticBlocks.d.ts

@@ -1,9 +1,11 @@
+import { Instance } from 'mobx-state-tree';
 import { BlockSet } from './blockTypes';
 import { Region } from './types';
+import { Region as RegionModel } from './types/mst';
 export interface Base1DViewModel {
     offsetPx: number;
     width: number;
-    displayedRegions: Region[];
+    displayedRegions: (Region | Instance<typeof RegionModel>)[];
     bpPerPx: number;
     minimumBlockWidth: number;
     interRegionPaddingWidth: number;

package/util/calculateStaticBlocks.js

@@ -1,5 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
+const mobx_state_tree_1 = require("mobx-state-tree");
 const _1 = require(".");
 const blockTypes_1 = require("./blockTypes");
 function calculateStaticBlocks(model, padding = true, elision = true, extra = 0, 
@@ -21,6 +22,7 @@ width = (typeof window !== 'undefined' && window.innerWidth) || model.width) {
         // clamp those to the region range, and then make blocks for that range
         const { assemblyName, refName, start: regionStart, end: regionEnd, reversed, } = region;
         const regionBlockCount = Math.ceil((regionEnd - regionStart) / blockSizeBp);
+        const parentRegion = (0, mobx_state_tree_1.isStateTreeNode)(region) ? (0, mobx_state_tree_1.getSnapshot)(region) : region;
         let windowRightBlockNum = Math.floor((windowRightBp - regionBpOffset) / blockSizeBp) + extra;
         if (windowRightBlockNum >= regionBlockCount) {
             windowRightBlockNum = regionBlockCount - 1;
@@ -55,7 +57,7 @@ width = (typeof window !== 'undefined' && window.innerWidth) || model.width) {
                 end,
                 reversed,
                 offsetPx: (regionBpOffset + blockNum * blockSizeBp) / bpPerPx,
-                parentRegion: region,
+                parentRegion,
                 regionNumber,
                 widthPx,
                 isLeftEndOfDisplayedRegion,

package/util/index.d.ts

@@ -188,7 +188,7 @@ export declare function renameRegionsIfNeeded<ARGTYPE extends {
     signal?: AbortSignal;
     adapterConfig: unknown;
     sessionId: string;
-    statusCallback?: Function;
+    statusCallback?: (arg: string) => void;
 }>(assemblyManager: AssemblyManager, args: ARGTYPE): Promise<ARGTYPE & {
     regions: (Region & {
         originalRefName?: string | undefined;
@@ -202,6 +202,7 @@ export declare function stringify({ refName, coord, oob, }: {
 }): string;
 export declare const isElectron: boolean;
 export declare function revcom(seqString: string): string;
+export declare function reverse(seqString: string): string;
 export declare const complement: (seqString: string) => string;
 export declare function blobToDataURL(blob: Blob): Promise<string>;
 export declare const rIC: (((callback: IdleRequestCallback, options?: IdleRequestOptions | undefined) => number) & typeof requestIdleCallback) | ((cb: Function) => any);

package/util/index.js

@@ -29,8 +29,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.toLocale = exports.getBpDisplayStr = exports.supportedIndexingAdapters = exports.bytesForRegions = exports.objectHash = exports.hashCode = exports.updateStatus = exports.generateCodonTable = exports.defaultCodonTable = exports.defaultStops = exports.defaultStarts = exports.measureText = exports.rIC = exports.blobToDataURL = exports.complement = exports.revcom = exports.isElectron = exports.stringify = exports.minmax = exports.renameRegionsIfNeeded = exports.renameRegionIfNeeded = exports.makeAbortableReaction = exports.findLastIndex = exports.iterMap = exports.bpSpanPx = exports.featureSpanPx = exports.cartesianToPolar = exports.polarToCartesian = exports.degToRad = exports.radToDeg = exports.bpToPx = exports.clamp = exports.compareLocStrings = exports.compareLocs = exports.parseLocString = exports.parseLocStringOneBased = exports.assembleLocString = exports.getContainingDisplay = exports.getContainingTrack = exports.getContainingView = exports.getSession = exports.findParentThatIs = exports.springAnimate = exports.findParentThat = exports.useDebouncedCallback = exports.useDebounce = exports.inProduction = exports.inDevelopment = exports.isFeature = exports.SimpleFeature = void 0;
-exports.measureGridWidth = exports.getStr = exports.getUriLink = exports.useLocalStorage = exports.getLayoutId = exports.getViewParams = exports.getTickDisplayStr = void 0;
+exports.getBpDisplayStr = exports.supportedIndexingAdapters = exports.bytesForRegions = exports.objectHash = exports.hashCode = exports.updateStatus = exports.generateCodonTable = exports.defaultCodonTable = exports.defaultStops = exports.defaultStarts = exports.measureText = exports.rIC = exports.blobToDataURL = exports.complement = exports.reverse = exports.revcom = exports.isElectron = exports.stringify = exports.minmax = exports.renameRegionsIfNeeded = exports.renameRegionIfNeeded = exports.makeAbortableReaction = exports.findLastIndex = exports.iterMap = exports.bpSpanPx = exports.featureSpanPx = exports.cartesianToPolar = exports.polarToCartesian = exports.degToRad = exports.radToDeg = exports.bpToPx = exports.clamp = exports.compareLocStrings = exports.compareLocs = exports.parseLocString = exports.parseLocStringOneBased = exports.assembleLocString = exports.getContainingDisplay = exports.getContainingTrack = exports.getContainingView = exports.getSession = exports.findParentThatIs = exports.springAnimate = exports.findParentThat = exports.useDebouncedCallback = exports.useDebounce = exports.inProduction = exports.inDevelopment = exports.isFeature = exports.SimpleFeature = void 0;
+exports.measureGridWidth = exports.getStr = exports.getUriLink = exports.useLocalStorage = exports.getLayoutId = exports.getViewParams = exports.getTickDisplayStr = exports.toLocale = void 0;
 /* eslint-disable @typescript-eslint/no-explicit-any */
 const react_1 = require("react");
 const is_object_1 = __importDefault(require("is-object"));
@@ -659,9 +659,13 @@ exports.stringify = stringify;
 // const i2 = process.versions.hasOwnProperty('electron')
 exports.isElectron = /electron/i.test(typeof navigator !== 'undefined' ? navigator.userAgent : '');
 function revcom(seqString) {
-    return (0, exports.complement)(seqString).split('').reverse().join('');
+    return reverse((0, exports.complement)(seqString));
 }
 exports.revcom = revcom;
+function reverse(seqString) {
+    return seqString.split('').reverse().join('');
+}
+exports.reverse = reverse;
 exports.complement = (() => {
     const complementRegex = /[ACGT]/gi;
     // from bioperl: tr/acgtrymkswhbvdnxACGTRYMKSWHBVDNX/tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX/

package/util/io/index.d.ts

@@ -4,4 +4,4 @@ import { FileLocation } from '../types';
 import PluginManager from '../../PluginManager';
 export { RemoteFileWithRangeCache };
 export declare function openLocation(location: FileLocation, pluginManager?: PluginManager): GenericFilehandle;
-export declare function getFetcher(location: FileLocation, pluginManager: PluginManager): Fetcher;
+export declare function getFetcher(location: FileLocation, pluginManager?: PluginManager): Fetcher;

package/util/io/index.js

@@ -70,9 +70,11 @@ function getFetcher(location, pluginManager) {
     if (!(0, types_1.isUriLocation)(location)) {
         throw new Error(`Not a valid UriLocation: ${JSON.stringify(location)}`);
     }
-    const internetAccount = getInternetAccount(location, pluginManager);
-    if (internetAccount) {
-        return internetAccount.getFetcher(location);
+    if (pluginManager) {
+        const internetAccount = getInternetAccount(location, pluginManager);
+        if (internetAccount) {
+            return internetAccount.getFetcher(location);
+        }
     }
     return checkAuthNeededFetch;
 }

package/util/types/index.js

@@ -13,13 +13,9 @@ var __createBinding = (this && this.__createBinding) || (Object.create ? (functi
 var __exportStar = (this && this.__exportStar) || function(m, exports) {
     for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
 };
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.isRetryException = exports.isAuthNeededException = exports.RetryError = exports.AuthNeededError = exports.isUriLocation = exports.isAbstractMenuManager = exports.isAppRootModel = exports.isTrackViewModel = exports.isDisplayModel = exports.isTrackModel = exports.isViewModel = exports.isSelectionContainer = exports.isSessionWithSessionPlugins = exports.isSessionModelWithConnections = exports.isSessionModelWithWidgets = exports.isSessionWithAddTracks = exports.isSessionModelWithConfigEditing = exports.isSessionModel = exports.isViewContainer = void 0;
 const mobx_state_tree_1 = require("mobx-state-tree");
-const TextSearchManager_1 = __importDefault(require("../../TextSearch/TextSearchManager"));
 __exportStar(require("./util"), exports);
 function isViewContainer(thing) {
     return ((0, mobx_state_tree_1.isStateTreeNode)(thing) &&

package/util/when.d.ts

@@ -1,7 +1,6 @@
-interface WhenOpts {
-    timeout?: number;
+import { IWhenOptions } from 'mobx';
+interface WhenOpts extends IWhenOptions {
     signal?: AbortSignal;
-    name?: string;
 }
 /**
  * Wrapper for mobx `when` that adds timeout and aborting support.