@jbrowse/core 2.13.1 → 2.15.0

package/ui/SnackbarModel.js

@@ -42,7 +42,18 @@ function SnackbarModel() {
     return mobx_state_tree_1.types
         .model({})
         .volatile(() => ({
+        /**
+         * #volatile
+         */
         snackbarMessages: mobx_1.observable.array(),
+    }))
+        .views(self => ({
+        /**
+         * #getter
+         */
+        get snackbarMessageSet() {
+            return new Map(self.snackbarMessages.map(s => [s.message, s]));
+        },
     }))
         .actions(self => ({
         /**
@@ -56,6 +67,9 @@ function SnackbarModel() {
                 }, 5000);
             }
         },
+        /**
+         * #action
+         */
         notifyError(errorMessage, error, extra) {
             this.notify(errorMessage, 'error', {
                 name: react_1.default.createElement(Report_1.default, null),
@@ -76,7 +90,9 @@ function SnackbarModel() {
          * #action
          */
         pushSnackbarMessage(message, level, action) {
-            return self.snackbarMessages.push({ message, level, action });
+            if (action || !self.snackbarMessageSet.has(message)) {
+                self.snackbarMessages.push({ message, level, action });
+            }
         },
         /**
          * #action
@@ -88,8 +104,8 @@ function SnackbarModel() {
          * #action
          */
         removeSnackbarMessage(message) {
-            const element = self.snackbarMessages.find(f => f.message === message);
-            if (element) {
+            const element = self.snackbarMessageSet.get(message);
+            if (element !== undefined) {
                 self.snackbarMessages.remove(element);
             }
         },

package/ui/theme.js

@@ -186,8 +186,11 @@ function createJBrowseBaseTheme(theme) {
             MuiAccordion: {
                 defaultProps: {
                     disableGutters: true,
-                    TransitionProps: {
-                        timeout: 150,
+                    slotProps: {
+                        transition: {
+                            timeout: 150,
+                            unmountOnExit: true,
+                        },
                     },
                 },
             },
@@ -372,11 +375,11 @@ function createJBrowseTheme(configTheme = {}, themes = exports.defaultThemes, th
         ? (0, deepmerge_1.default)(themes.default, augmentTheme(configTheme), {
             arrayMerge: overwriteArrayMerge,
         })
-        : augmentThemePlus(themes[themeName]) || themes.default));
+        : augmentThemePlus(themes[themeName])));
 }
 function augmentTheme(theme = {}) {
     var _a, _b;
-    if ((_a = theme === null || theme === void 0 ? void 0 : theme.palette) === null || _a === void 0 ? void 0 : _a.tertiary) {
+    if ((_a = theme.palette) === null || _a === void 0 ? void 0 : _a.tertiary) {
         theme = (0, deepmerge_1.default)(theme, {
             palette: {
                 tertiary: refTheme.palette.augmentColor('color' in theme.palette.tertiary
@@ -385,7 +388,7 @@ function augmentTheme(theme = {}) {
             },
         });
     }
-    if ((_b = theme === null || theme === void 0 ? void 0 : theme.palette) === null || _b === void 0 ? void 0 : _b.quaternary) {
+    if ((_b = theme.palette) === null || _b === void 0 ? void 0 : _b.quaternary) {
         theme = (0, deepmerge_1.default)(theme, {
             palette: {
                 quaternary: refTheme.palette.augmentColor('color' in theme.palette.quaternary
@@ -400,7 +403,7 @@ function augmentTheme(theme = {}) {
 function augmentThemePlus(theme = {}) {
     var _a, _b;
     theme = augmentTheme(theme);
-    if (!((_a = theme === null || theme === void 0 ? void 0 : theme.palette) === null || _a === void 0 ? void 0 : _a.quaternary)) {
+    if (!((_a = theme.palette) === null || _a === void 0 ? void 0 : _a.quaternary)) {
         theme = (0, deepmerge_1.default)(theme, {
             palette: {
                 quaternary: refTheme.palette.augmentColor({
@@ -411,7 +414,7 @@ function augmentThemePlus(theme = {}) {
             },
         });
     }
-    if (!((_b = theme === null || theme === void 0 ? void 0 : theme.palette) === null || _b === void 0 ? void 0 : _b.tertiary)) {
+    if (!((_b = theme.palette) === null || _b === void 0 ? void 0 : _b.tertiary)) {
         theme = (0, deepmerge_1.default)(theme, {
             palette: {
                 tertiary: refTheme.palette.augmentColor({

package/util/Base1DViewModel.js

@@ -175,7 +175,9 @@ const Base1DView = mobx_state_tree_1.types
      * #action
      */
     zoomTo(bpPerPx, offset = self.width / 2) {
-        const newBpPerPx = (0, index_1.clamp)(bpPerPx, 'minBpPerPx' in self ? self.minBpPerPx : 0, 'maxBpPerPx' in self ? self.maxBpPerPx : Infinity);
+        const newBpPerPx = (0, index_1.clamp)(bpPerPx, 'minBpPerPx' in self ? self.minBpPerPx : 0, 'maxBpPerPx' in self
+            ? self.maxBpPerPx
+            : Number.POSITIVE_INFINITY);
         const oldBpPerPx = self.bpPerPx;
         if (Math.abs(oldBpPerPx - newBpPerPx) < 0.000001) {
             return oldBpPerPx;

package/util/QuickLRU.js

@@ -44,7 +44,7 @@ class QuickLRU extends Map {
     }
     _getOrDeleteIfExpired(key, item) {
         const deleted = this._deleteIfExpired(key, item);
-        if (deleted === false) {
+        if (!deleted) {
             return item.value;
         }
     }
@@ -74,7 +74,7 @@ class QuickLRU extends Map {
             const [key, value] = item;
             if (!this.cache.has(key)) {
                 const deleted = this._deleteIfExpired(key, value);
-                if (deleted === false) {
+                if (!deleted) {
                     yield item;
                 }
             }
@@ -82,7 +82,7 @@ class QuickLRU extends Map {
         for (const item of this.cache) {
             const [key, value] = item;
             const deleted = this._deleteIfExpired(key, value);
-            if (deleted === false) {
+            if (!deleted) {
                 yield item;
             }
         }
@@ -94,7 +94,7 @@ class QuickLRU extends Map {
         }
         if (this.oldCache.has(key)) {
             const item = this.oldCache.get(key);
-            if (this._deleteIfExpired(key, item) === false) {
+            if (!this._deleteIfExpired(key, item)) {
                 this._moveToRecent(key, item);
                 return item.value;
             }
@@ -178,7 +178,7 @@ class QuickLRU extends Map {
         for (const item of this.cache) {
             const [key, value] = item;
             const deleted = this._deleteIfExpired(key, value);
-            if (deleted === false) {
+            if (!deleted) {
                 yield [key, value.value];
             }
         }
@@ -186,7 +186,7 @@ class QuickLRU extends Map {
             const [key, value] = item;
             if (!this.cache.has(key)) {
                 const deleted = this._deleteIfExpired(key, value);
-                if (deleted === false) {
+                if (!deleted) {
                     yield [key, value.value];
                 }
             }
@@ -198,7 +198,7 @@ class QuickLRU extends Map {
             const item = items[i];
             const [key, value] = item;
             const deleted = this._deleteIfExpired(key, value);
-            if (deleted === false) {
+            if (!deleted) {
                 yield [key, value.value];
             }
         }
@@ -208,7 +208,7 @@ class QuickLRU extends Map {
             const [key, value] = item;
             if (!this.cache.has(key)) {
                 const deleted = this._deleteIfExpired(key, value);
-                if (deleted === false) {
+                if (!deleted) {
                     yield [key, value.value];
                 }
             }

package/util/TimeTraveller.js

@@ -7,7 +7,9 @@ function debounce(func, timeout = 300) {
     let timer;
     return (...args) => {
         clearTimeout(timer);
-        timer = setTimeout(() => func(...args), timeout);
+        timer = setTimeout(() => {
+            func(...args);
+        }, timeout);
     };
 }
 const TimeTraveller = mobx_state_tree_1.types
@@ -66,7 +68,9 @@ const TimeTraveller = mobx_state_tree_1.types
             if (!targetStore) {
                 throw new Error('Failed to find target store for TimeTraveller. Please provide `targetPath` property, or a `targetStore` in the environment');
             }
-            snapshotDisposer = (0, mobx_state_tree_1.onSnapshot)(targetStore, debounce((snapshot) => this.addUndoState(snapshot), 300));
+            snapshotDisposer = (0, mobx_state_tree_1.onSnapshot)(targetStore, debounce((snapshot) => {
+                this.addUndoState(snapshot);
+            }, 300));
             if (self.history.length === 0) {
                 this.addUndoState((0, mobx_state_tree_1.getSnapshot)(targetStore));
             }
@@ -74,12 +78,16 @@ const TimeTraveller = mobx_state_tree_1.types
         undo() {
             self.undoIdx--;
             skipNextUndoState = true;
-            (0, mobx_state_tree_1.applySnapshot)(targetStore, self.history[self.undoIdx]);
+            if (targetStore) {
+                (0, mobx_state_tree_1.applySnapshot)(targetStore, self.history[self.undoIdx]);
+            }
         },
         redo() {
             self.undoIdx++;
             skipNextUndoState = true;
-            (0, mobx_state_tree_1.applySnapshot)(targetStore, self.history[self.undoIdx]);
+            if (targetStore) {
+                (0, mobx_state_tree_1.applySnapshot)(targetStore, self.history[self.undoIdx]);
+            }
         },
     };
 });

package/util/aborting.js

@@ -56,7 +56,7 @@ function makeAbortError() {
 }
 function observeAbortSignal(signal) {
     if (!signal) {
-        return rxjs_1.Observable.create();
+        return new rxjs_1.Observable();
     }
     return (0, rxjs_1.fromEvent)(signal, 'abort');
 }

package/util/analytics.js

@@ -3,7 +3,6 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.writeAWSAnalytics = writeAWSAnalytics;
 exports.writeGAAnalytics = writeGAAnalytics;
 exports.doAnalytics = doAnalytics;
-/* eslint-disable @typescript-eslint/no-explicit-any */
 const configuration_1 = require("../configuration");
 const util_1 = require("../util");
 async function writeAWSAnalytics(rootModel, initialTimeStamp, sessionQuery) {

package/util/blockTypes.js

@@ -29,7 +29,7 @@ class BlockSet {
     }
     forEach(func, thisarg) {
         // eslint-disable-next-line unicorn/no-array-method-this-argument
-        return this.blocks.forEach(func, thisarg);
+        this.blocks.forEach(func, thisarg);
     }
     get length() {
         return this.blocks.length;
@@ -61,7 +61,6 @@ class BaseBlock {
     /**
      * a block that should be shown as filled with data
      */
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     constructor(data) {
         this.type = 'BaseBlock';
         this.widthPx = 0;
@@ -96,7 +95,6 @@ exports.ContentBlock = ContentBlock;
  * too small to be shown at the current zoom level
  */
 class ElidedBlock extends BaseBlock {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     constructor(data) {
         super(data);
         this.type = 'ElidedBlock';
@@ -105,12 +103,10 @@ class ElidedBlock extends BaseBlock {
     }
     push(otherBlock) {
         this.elidedBlockCount += 1;
-        if (otherBlock) {
-            this.refName = '';
-            this.start = 0;
-            this.end = 0;
-            this.widthPx += otherBlock.widthPx;
-        }
+        this.refName = '';
+        this.start = 0;
+        this.end = 0;
+        this.widthPx += otherBlock.widthPx;
     }
 }
 exports.ElidedBlock = ElidedBlock;

package/util/calculateStaticBlocks.d.ts

@@ -1,7 +1,7 @@
 import { Instance } from 'mobx-state-tree';
 import { BlockSet } from './blockTypes';
 import { Region } from './types';
-import { Region as RegionModel } from './types/mst';
+import type { Region as RegionModel } from './types/mst';
 export interface Base1DViewModel {
     offsetPx: number;
     width: number;

package/util/compositeMap.js

@@ -1,7 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-// takes an array or Map or Set (anything iterable with values()) of Maps
-// and lets you query them as one Map
+// takes an array or Map or Set (anything iterable with values()) of Maps and
+// lets you query them as one Map
 class CompositeMap {
     constructor(submaps) {
         this.submaps = submaps;

package/util/idMaker.js

@@ -5,7 +5,6 @@ const _1 = require("./");
 // generates a short "id fingerprint" from the config passed to the base
 // feature adapter by recursively enumerating props, but if config is too big
 // does not process entire config (FromConfigAdapter for example can be large)
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
 function idMaker(args, id = '') {
     const keys = Object.keys(args);
     for (const key of keys) {

package/util/index.d.ts

@@ -4,7 +4,7 @@ import { IAnyStateTreeNode, IStateTreeNode, Instance } from 'mobx-state-tree';
 import { IReactionPublic, IReactionOptions } from 'mobx';
 import { Feature } from './simpleFeature';
 import { AssemblyManager, Region, TypeTestedByPredicate } from './types';
-import { Region as MUIRegion } from './types/mst';
+import type { Region as MUIRegion } from './types/mst';
 import { BaseBlock } from './blockTypes';
 export * from './types';
 export * from './aborting';
@@ -206,7 +206,7 @@ export declare function findLast<T>(array: T[], predicate: (value: T, index: num
  * @param errorFunction -
  */
 export declare function makeAbortableReaction<T, U, V>(self: T, dataFunction: (arg: T) => U, asyncReactionFunction: (arg: U | undefined, signal: AbortSignal, model: T, handle: IReactionPublic) => Promise<V>, reactionOptions: IReactionOptions, startedFunction: (aborter: AbortController) => void, successFunction: (arg: V) => void, errorFunction: (err: unknown) => void): void;
-export declare function renameRegionIfNeeded(refNameMap: Record<string, string>, region: Region | Instance<typeof MUIRegion>): Region & {
+export declare function renameRegionIfNeeded(refNameMap: Record<string, string> | undefined, region: Region | Instance<typeof MUIRegion>): Region & {
     originalRefName?: string;
 };
 export declare function renameRegionsIfNeeded<ARGTYPE extends {
@@ -221,7 +221,7 @@ export declare function renameRegionsIfNeeded<ARGTYPE extends {
         originalRefName?: string;
     })[];
 }>;
-export declare function minmax(a: number, b: number): number[];
+export declare function minmax(a: number, b: number): readonly [number, number];
 export declare function shorten(name: string, max?: number, short?: number): string;
 export declare function stringify({ refName, coord, assemblyName, oob, }: {
     assemblyName?: string;
@@ -233,7 +233,7 @@ 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 const rIC: (((callback: IdleRequestCallback, options?: IdleRequestOptions) => number) & typeof requestIdleCallback) | ((cb: Function) => any);
+export declare const rIC: (((callback: IdleRequestCallback, options?: IdleRequestOptions) => number) & typeof requestIdleCallback) | ((cb: () => void) => void);
 export declare function measureText(str: unknown, fontSize?: number): number;
 export type Frame = 1 | 2 | 3 | -1 | -2 | -3;
 export declare function getFrame(start: number, end: number, strand: 1 | -1, phase: 0 | 1 | 2): Frame;
@@ -341,7 +341,7 @@ export interface ViewSnap {
         assemblyName: string;
     })[];
 }
-export declare function isSupportedIndexingAdapter(type: string): boolean;
+export declare function isSupportedIndexingAdapter(type?: string): boolean;
 export declare function getBpDisplayStr(totalBp: number): string;
 export declare function toLocale(n: number): string;
 export declare function getTickDisplayStr(totalBp: number, bpPerPx: number): string;
@@ -379,18 +379,18 @@ export declare function max(arr: number[], init?: number): number;
 export declare function min(arr: number[], init?: number): number;
 export declare function sum(arr: number[]): number;
 export declare function avg(arr: number[]): number;
-export declare function groupBy<T>(array: Iterable<T>, predicate: (v: T) => string): Record<string, T[] | undefined>;
+export declare function groupBy<T>(array: Iterable<T>, predicate: (v: T) => string): Record<string, T[]>;
 export declare function notEmpty<T>(value: T | null | undefined): value is T;
 export declare function mergeIntervals<T extends {
     start: number;
     end: number;
-}>(intervals: T[], w?: number): T[];
+}>(intervals: T[], w?: number): (T | undefined)[];
 interface BasicFeature {
     end: number;
     start: number;
     refName: string;
 }
-export declare function gatherOverlaps(regions: BasicFeature[]): BasicFeature[];
+export declare function gatherOverlaps(regions: BasicFeature[]): (BasicFeature | undefined)[];
 export declare function stripAlpha(str: string): string;
 export declare function getStrokeProps(str: string): {
     strokeOpacity: number;
@@ -403,5 +403,6 @@ export declare function getFillProps(str: string): {
 export declare function renderToStaticMarkup(node: React.ReactElement, createRootFn?: (elt: Element | DocumentFragment) => {
     render: (node: React.ReactElement) => unknown;
 }): string;
+export declare function isGzip(buf: Buffer): boolean;
 export { default as SimpleFeature, type Feature, type SimpleFeatureSerialized, isFeature, } from './simpleFeature';
 export { blobToDataURL } from './blobToDataURL';