@jbrowse/core 2.7.0 → 2.7.2

package/ui/MenuButton.d.ts

@@ -0,0 +1,8 @@
+import React from 'react';
+import { MenuItem } from '@jbrowse/core/ui';
+declare const MenuButton: ({ children, menuItems, ...rest }: {
+    [key: string]: unknown;
+    children?: React.ReactElement<any, string | React.JSXElementConstructor<any>> | undefined;
+    menuItems: MenuItem[];
+}) => React.JSX.Element;
+export default MenuButton;

package/ui/MenuButton.js

@@ -0,0 +1,42 @@
+"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 });
+const react_1 = __importStar(require("react"));
+const Menu_1 = __importDefault(require("@jbrowse/core/ui/Menu"));
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
+const MenuButton = (0, mobx_react_1.observer)(function MenuButton({ children, menuItems, ...rest }) {
+    const [anchorEl, setAnchorEl] = (0, react_1.useState)();
+    return (react_1.default.createElement(react_1.default.Fragment, null,
+        react_1.default.createElement(material_1.IconButton, { ...rest, onClick: event => setAnchorEl(event.currentTarget) }, children),
+        react_1.default.createElement(Menu_1.default, { open: !!anchorEl, anchorEl: anchorEl, onClose: () => setAnchorEl(undefined), onMenuItemClick: (_, callback) => {
+                callback();
+                setAnchorEl(undefined);
+            }, menuItems: menuItems })));
+});
+exports.default = MenuButton;

package/ui/SanitizedHTML.d.ts

@@ -1,4 +1,4 @@
 import React from 'react';
-export default function SanitizedHTML({ html }: {
+export default function SanitizedHTML({ html: pre }: {
     html: string;
 }): React.JSX.Element;

package/ui/SanitizedHTML.js

@@ -6,6 +6,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
 const escape_html_1 = __importDefault(require("escape-html"));
 const dompurify_1 = __importDefault(require("dompurify"));
+const util_1 = require("../util");
 // source https://github.com/sindresorhus/html-tags/blob/master/html-tags.json
 // with some random uncommon ones removed. note: we just use this to run the content
 // through dompurify without escaping if we see an htmlTag from this list
@@ -57,7 +58,9 @@ function isHTML(str) {
 // products/jbrowse-web/src/tests/Connection.test.tsx test (can delete mock to
 // see)
 //
-function SanitizedHTML({ html }) {
+function SanitizedHTML({ html: pre }) {
+    // try to add links to the text first
+    const html = (0, util_1.linkify)(pre);
     const value = isHTML(html) ? html : (0, escape_html_1.default)(html);
     if (!added) {
         added = true;

package/util/blobToDataURL.d.ts

@@ -0,0 +1 @@
+export declare function blobToDataURL(blob: Blob): Promise<string>;

package/util/blobToDataURL.js

@@ -0,0 +1,18 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.blobToDataURL = void 0;
+function blobToDataURL(blob) {
+    const a = new FileReader();
+    return new Promise((resolve, reject) => {
+        a.onload = e => {
+            if (e.target) {
+                resolve(e.target.result);
+            }
+            else {
+                reject(new Error('unknown result reading blob from canvas'));
+            }
+        };
+        a.readAsDataURL(blob);
+    });
+}
+exports.blobToDataURL = blobToDataURL;

package/util/index.d.ts

@@ -13,23 +13,40 @@ export * from './range';
 export * from './dedupe';
 export * from './offscreenCanvasPonyfill';
 export * from './offscreenCanvasUtils';
-export declare const inDevelopment: boolean;
-export declare const inProduction: boolean;
 export declare function useDebounce<T>(value: T, delay: number): T;
 export declare function useWidthSetter(view: {
     setWidth: (arg: number) => void;
 }, padding: string): import("react").RefObject<HTMLDivElement>;
 export declare function useDebouncedCallback<T>(callback: (...args: T[]) => void, wait?: number): (...args: T[]) => void;
-/** find the first node in the hierarchy that matches the given predicate */
+/**
+ * find the first node in the hierarchy that matches the given predicate
+ */
 export declare function findParentThat(node: IAnyStateTreeNode, predicate: (thing: IAnyStateTreeNode) => boolean): IAnyStateTreeNode;
 export declare function springAnimate(fromValue: number, toValue: number, setValue: (value: number) => void, onFinish?: () => void, precision?: number, tension?: number, friction?: number): (() => void)[];
+/**
+ * find the first node in the hierarchy that matches the given 'is' typescript
+ * type guard predicate
+ */
 export declare function findParentThatIs<T extends (a: IAnyStateTreeNode) => boolean>(node: IAnyStateTreeNode, predicate: T): TypeTestedByPredicate<T>;
-/** get the current JBrowse session model, starting at any node in the state tree */
+/**
+ * get the current JBrowse session model, starting at any node in the state
+ * tree
+ */
 export declare function getSession(node: IAnyStateTreeNode): import("./types").AbstractSessionModel;
-/** get the state model of the view in the state tree that contains the given node */
+/**
+ * get the state model of the view in the state tree that contains the given
+ * node
+ */
 export declare function getContainingView(node: IAnyStateTreeNode): import("./types").AbstractViewModel;
-/** get the state model of the view in the state tree that contains the given node */
+/**
+ * get the state model of the view in the state tree that contains the given
+ * node
+ */
 export declare function getContainingTrack(node: IAnyStateTreeNode): import("./types").AbstractTrackModel;
+/**
+ * get the state model of the display in the state tree that contains the given
+ * node
+ */
 export declare function getContainingDisplay(node: IAnyStateTreeNode): import("./types").AbstractDisplayModel;
 /**
  * Assemble a 1-based "locString" from an interbase genomic location
@@ -159,10 +176,14 @@ export declare function iterMap<T, U>(iter: Iterable<T>, func: (arg: T) => U, si
 /**
  * Returns the index of the last element in the array where predicate is true,
  * and -1 otherwise.
+ * Based on https://stackoverflow.com/a/53187807
+ *
  * @param array - The source array to search in
+ *
  * @param predicate - find calls predicate once for each element of the array, in
- * descending order, until it finds one where predicate returns true. If such an
- * element is found, findLastIndex immediately returns that element index.
+ * descending order, until it finds one where predicate returns true.
+ *
+ * @returns findLastIndex returns element index where predicate is true.
  * Otherwise, findLastIndex returns -1.
  */
 export declare function findLastIndex<T>(array: T[], predicate: (value: T, index: number, obj: T[]) => boolean): number;
@@ -212,7 +233,6 @@ 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);
 export declare function measureText(str: unknown, fontSize?: number): number;
 export declare const defaultStarts: string[];
@@ -339,6 +359,8 @@ export declare function getUriLink(value: {
     baseUri?: string;
 }): string;
 export declare function getStr(obj: unknown): string;
+export declare function coarseStripHTML(s: string): string;
+export declare function linkify(s: string): string;
 export declare function measureGridWidth(elements: unknown[], args?: {
     minWidth?: number;
     fontSize?: number;
@@ -355,7 +377,7 @@ 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: T[], predicate: (v: T) => string): Record<string, T[]>;
+export declare function groupBy<T>(array: Iterable<T>, predicate: (v: T) => string): Record<string, T[] | undefined>;
 export declare function notEmpty<T>(value: T | null | undefined): value is T;
 export declare function mergeIntervals<T extends {
     start: number;
@@ -369,3 +391,4 @@ interface BasicFeature {
 export declare function gatherOverlaps(regions: BasicFeature[]): BasicFeature[];
 export { default as SimpleFeature, type Feature, type SimpleFeatureSerialized, isFeature, } from './simpleFeature';
 export declare function stripAlpha(str: string): string;
+export { blobToDataURL } from './blobToDataURL';

package/util/index.js

@@ -17,8 +17,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-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.shorten = exports.minmax = exports.renameRegionsIfNeeded = exports.renameRegionIfNeeded = exports.makeAbortableReaction = exports.findLast = 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.assembleLocStringFast = exports.assembleLocString = exports.getContainingDisplay = exports.getContainingTrack = exports.getContainingView = exports.getSession = exports.findParentThatIs = exports.springAnimate = exports.findParentThat = exports.useDebouncedCallback = exports.useWidthSetter = exports.useDebounce = exports.inProduction = exports.inDevelopment = void 0;
-exports.stripAlpha = exports.isFeature = exports.SimpleFeature = exports.gatherOverlaps = exports.mergeIntervals = exports.notEmpty = exports.groupBy = exports.avg = exports.sum = exports.min = exports.max = exports.localStorageSetItem = exports.localStorageGetItem = exports.getEnv = exports.measureGridWidth = exports.getStr = exports.getUriLink = exports.useLocalStorage = exports.getLayoutId = exports.getViewParams = exports.getTickDisplayStr = exports.toLocale = exports.getBpDisplayStr = exports.isSupportedIndexingAdapter = void 0;
+exports.toLocale = exports.getBpDisplayStr = exports.isSupportedIndexingAdapter = exports.bytesForRegions = exports.objectHash = exports.hashCode = exports.updateStatus = exports.generateCodonTable = exports.defaultCodonTable = exports.defaultStops = exports.defaultStarts = exports.measureText = exports.rIC = exports.complement = exports.reverse = exports.revcom = exports.isElectron = exports.stringify = exports.shorten = exports.minmax = exports.renameRegionsIfNeeded = exports.renameRegionIfNeeded = exports.makeAbortableReaction = exports.findLast = 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.assembleLocStringFast = exports.assembleLocString = exports.getContainingDisplay = exports.getContainingTrack = exports.getContainingView = exports.getSession = exports.findParentThatIs = exports.springAnimate = exports.findParentThat = exports.useDebouncedCallback = exports.useWidthSetter = exports.useDebounce = void 0;
+exports.blobToDataURL = exports.stripAlpha = exports.isFeature = exports.SimpleFeature = exports.gatherOverlaps = exports.mergeIntervals = exports.notEmpty = exports.groupBy = exports.avg = exports.sum = exports.min = exports.max = exports.localStorageSetItem = exports.localStorageGetItem = exports.getEnv = exports.measureGridWidth = exports.linkify = exports.coarseStripHTML = exports.getStr = exports.getUriLink = exports.useLocalStorage = exports.getLayoutId = exports.getViewParams = exports.getTickDisplayStr = void 0;
 /* eslint-disable @typescript-eslint/no-explicit-any */
 const react_1 = require("react");
 const is_object_1 = __importDefault(require("is-object"));
@@ -37,10 +37,6 @@ __exportStar(require("./range"), exports);
 __exportStar(require("./dedupe"), exports);
 __exportStar(require("./offscreenCanvasPonyfill"), exports);
 __exportStar(require("./offscreenCanvasUtils"), exports);
-exports.inDevelopment = typeof process === 'object' &&
-    process.env &&
-    process.env.NODE_ENV === 'development';
-exports.inProduction = !exports.inDevelopment;
 function useDebounce(value, delay) {
     const [debouncedValue, setDebouncedValue] = (0, react_1.useState)(value);
     (0, react_1.useEffect)(() => {
@@ -78,7 +74,8 @@ function useDebouncedCallback(callback, wait = 400) {
             clearTimeout(timeout.current);
         }
     }
-    // make sure our timeout gets cleared if our consuming component gets unmounted
+    // make sure our timeout gets cleared if our consuming component gets
+    // unmounted
     (0, react_1.useEffect)(() => cleanup, []);
     return function debouncedCallback(...args) {
         // capture latest args
@@ -94,7 +91,9 @@ function useDebouncedCallback(callback, wait = 400) {
     };
 }
 exports.useDebouncedCallback = useDebouncedCallback;
-/** find the first node in the hierarchy that matches the given predicate */
+/**
+ * find the first node in the hierarchy that matches the given predicate
+ */
 function findParentThat(node, predicate) {
     if (!(0, mobx_state_tree_1.hasParent)(node)) {
         throw new Error('node does not have parent');
@@ -161,12 +160,18 @@ function springAnimate(fromValue, toValue, setValue, onFinish = () => { }, preci
     ];
 }
 exports.springAnimate = springAnimate;
-// find the first node in the hierarchy that matches the given 'is' typescript type guard predicate
+/**
+ * find the first node in the hierarchy that matches the given 'is' typescript
+ * type guard predicate
+ */
 function findParentThatIs(node, predicate) {
     return findParentThat(node, predicate);
 }
 exports.findParentThatIs = findParentThatIs;
-/** get the current JBrowse session model, starting at any node in the state tree */
+/**
+ * get the current JBrowse session model, starting at any node in the state
+ * tree
+ */
 function getSession(node) {
     try {
         return findParentThatIs(node, types_1.isSessionModel);
@@ -176,7 +181,10 @@ function getSession(node) {
     }
 }
 exports.getSession = getSession;
-/** get the state model of the view in the state tree that contains the given node */
+/**
+ * get the state model of the view in the state tree that contains the given
+ * node
+ */
 function getContainingView(node) {
     try {
         return findParentThatIs(node, types_1.isViewModel);
@@ -186,7 +194,10 @@ function getContainingView(node) {
     }
 }
 exports.getContainingView = getContainingView;
-/** get the state model of the view in the state tree that contains the given node */
+/**
+ * get the state model of the view in the state tree that contains the given
+ * node
+ */
 function getContainingTrack(node) {
     try {
         return findParentThatIs(node, types_1.isTrackModel);
@@ -196,6 +207,10 @@ function getContainingTrack(node) {
     }
 }
 exports.getContainingTrack = getContainingTrack;
+/**
+ * get the state model of the display in the state tree that contains the given
+ * node
+ */
 function getContainingDisplay(node) {
     try {
         return findParentThatIs(node, types_1.isDisplayModel);
@@ -516,14 +531,17 @@ function iterMap(iter, func, sizeHint) {
     return results;
 }
 exports.iterMap = iterMap;
-// https://stackoverflow.com/a/53187807
 /**
  * Returns the index of the last element in the array where predicate is true,
  * and -1 otherwise.
+ * Based on https://stackoverflow.com/a/53187807
+ *
  * @param array - The source array to search in
+ *
  * @param predicate - find calls predicate once for each element of the array, in
- * descending order, until it finds one where predicate returns true. If such an
- * element is found, findLastIndex immediately returns that element index.
+ * descending order, until it finds one where predicate returns true.
+ *
+ * @returns findLastIndex returns element index where predicate is true.
  * Otherwise, findLastIndex returns -1.
  */
 function findLastIndex(array, predicate) {
@@ -733,21 +751,6 @@ exports.complement = (() => {
         return seqString.replaceAll(complementRegex, m => complementTable[m] || '');
     };
 })();
-function blobToDataURL(blob) {
-    const a = new FileReader();
-    return new Promise((resolve, reject) => {
-        a.onload = e => {
-            if (e.target) {
-                resolve(e.target.result);
-            }
-            else {
-                reject(new Error('unknown result reading blob from canvas'));
-            }
-        };
-        a.readAsDataURL(blob);
-    });
-}
-exports.blobToDataURL = blobToDataURL;
 // requires immediate execution in jest environment, because (hypothesis) it
 // otherwise listens for prerendered_canvas but reads empty pixels, and doesn't
 // get the contents of the canvas
@@ -1012,6 +1015,13 @@ exports.getStr = getStr;
 function coarseStripHTML(s) {
     return s.replaceAll(/(<([^>]+)>)/gi, '');
 }
+exports.coarseStripHTML = coarseStripHTML;
+// based on autolink-js, license MIT
+function linkify(s) {
+    const pattern = /(^|[\s\n]|<[A-Za-z]*\/?>)((?:https?|ftp):\/\/[\-A-Z0-9+\u0026\u2019@#\/%?=()~_|!:,.;]*[\-A-Z0-9+\u0026@#\/%=~()_|])/gi;
+    return s.replaceAll(pattern, '$1<a href=\'$2\' target="_blank">$2</a>');
+}
+exports.linkify = linkify;
 // heuristic measurement for a column of a @mui/x-data-grid, pass in values from a column
 function measureGridWidth(elements, args) {
     const { padding = 30, minWidth = 80, fontSize = 12, maxWidth = 1000, stripHTML = false, } = args || {};
@@ -1130,3 +1140,5 @@ function stripAlpha(str) {
     return c.alpha(1).toHex();
 }
 exports.stripAlpha = stripAlpha;
+var blobToDataURL_1 = require("./blobToDataURL");
+Object.defineProperty(exports, "blobToDataURL", { enumerable: true, get: function () { return blobToDataURL_1.blobToDataURL; } });

package/util/layouts/SceneGraph.js

@@ -1,6 +1,5 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-const __1 = require("..");
 class SceneGraph {
     /**
      * note: all coordinates are inter-base or inter-pixel coordinates
@@ -14,18 +13,6 @@ class SceneGraph {
         this.width = width;
         this.height = height;
         this.data = data;
-        if (__1.inDevelopment &&
-            (typeof name !== 'string' ||
-                typeof left !== 'number' ||
-                Number.isNaN(left) ||
-                typeof top !== 'number' ||
-                Number.isNaN(top) ||
-                typeof width !== 'number' ||
-                Number.isNaN(width) ||
-                typeof height !== 'number' ||
-                Number.isNaN(height))) {
-            throw new TypeError('invalid SceneGraph arguments');
-        }
         this.children = new Map();
         this.absoluteCache = { dirty: true };
     }

package/util/offscreenCanvasUtils.js

@@ -32,7 +32,7 @@ const react_1 = __importDefault(require("react"));
 const canvas_sequencer_1 = require("canvas-sequencer");
 // locals
 const offscreenCanvasPonyfill_1 = require("./offscreenCanvasPonyfill");
-const index_1 = require("./index");
+const blobToDataURL_1 = require("./blobToDataURL");
 async function renderToAbstractCanvas(width, height, opts, cb) {
     const { exportSVG, highResolutionScaling = 1 } = opts;
     if (exportSVG) {
@@ -58,7 +58,7 @@ async function renderToAbstractCanvas(width, height, opts, cb) {
             return {
                 ...result,
                 reactElement: (react_1.default.createElement("image", { width: width, height: height, xlinkHref: 'convertToBlob' in canvas
-                        ? await (0, index_1.blobToDataURL)(await canvas.convertToBlob({
+                        ? await (0, blobToDataURL_1.blobToDataURL)(await canvas.convertToBlob({
                             type: 'image/png',
                         }))
                         : canvas.toDataURL('image/png') })),

package/util/types/index.d.ts

@@ -52,6 +52,8 @@ export interface AbstractSessionModel extends AbstractViewContainer {
     selection?: unknown;
     focusedViewId?: string;
     themeName?: string;
+    hovered: unknown;
+    setHovered: (arg: unknown) => void;
     setFocusedViewId?: (id: string) => void;
     allThemes?: () => Record<string, ThemeOptions | undefined>;
     setSelection: (feature: Feature) => void;
@@ -117,9 +119,9 @@ export interface Widget {
 export interface SessionWithWidgets extends AbstractSessionModel {
     minimized: boolean;
     visibleWidget?: Widget;
-    widgets: Map<string, Widget>;
+    widgets: Map<string | number, Widget>;
     hideAllWidgets: () => void;
-    activeWidgets: Map<string, Widget>;
+    activeWidgets: Map<string | number, Widget>;
     addWidget(typeName: string, id: string, initialState?: Record<string, unknown>, configuration?: {
         type: string;
     }): Widget;

package/BaseFeatureWidget/BaseFeatureDetail/UriLink.d.ts

@@ -1,7 +0,0 @@
-import React from 'react';
-export default function UriLink({ value, }: {
-    value: {
-        uri: string;
-        baseUri?: string;
-    };
-}): React.JSX.Element;

package/BaseFeatureWidget/BaseFeatureDetail/UriLink.js

@@ -1,13 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importDefault(require("react"));
-const util_1 = require("../../util");
-const ui_1 = require("../../ui");
-function UriLink({ value, }) {
-    const href = (0, util_1.getUriLink)(value);
-    return react_1.default.createElement(ui_1.SanitizedHTML, { html: `<a href="${href}">${href}</a>` });
-}
-exports.default = UriLink;