@jbrowse/plugin-grid-bookmark 3.7.0 → 4.0.0

package/dist/GridBookmarkWidget/sessionSharing.d.ts

@@ -1,6 +0,0 @@
-export declare function shareSessionToDynamo(session: unknown, url: string, referer: string): Promise<{
-    json: any;
-    encryptedSession: string;
-    password: string;
-}>;
-export declare function readSessionFromDynamo(baseUrl: string, sessionQueryParam: string, password: string): Promise<string>;

package/dist/GridBookmarkWidget/sessionSharing.js

@@ -1,99 +0,0 @@
-"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 () {
-    var ownKeys = function(o) {
-        ownKeys = Object.getOwnPropertyNames || function (o) {
-            var ar = [];
-            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
-            return ar;
-        };
-        return ownKeys(o);
-    };
-    return function (mod) {
-        if (mod && mod.__esModule) return mod;
-        var result = {};
-        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
-        __setModuleDefault(result, mod);
-        return result;
-    };
-})();
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.shareSessionToDynamo = shareSessionToDynamo;
-exports.readSessionFromDynamo = readSessionFromDynamo;
-const utils_1 = require("./utils");
-function generateUID(length) {
-    return window
-        .btoa([...window.crypto.getRandomValues(new Uint8Array(length * 2))]
-        .map(b => String.fromCharCode(b))
-        .join(''))
-        .replaceAll(/[+/]/g, '')
-        .slice(0, length);
-}
-const encrypt = async (text, password) => {
-    const AES = await Promise.resolve().then(() => __importStar(require('crypto-js/aes')));
-    return AES.encrypt(text, password).toString();
-};
-const decrypt = async (text, password) => {
-    const AES = await Promise.resolve().then(() => __importStar(require('crypto-js/aes')));
-    const Utf8 = await Promise.resolve().then(() => __importStar(require('crypto-js/enc-utf8')));
-    const bytes = AES.decrypt(text, password);
-    return bytes.toString(Utf8);
-};
-function getErrorMsg(err) {
-    try {
-        const obj = JSON.parse(err);
-        return obj.message;
-    }
-    catch (e) {
-        return err;
-    }
-}
-async function shareSessionToDynamo(session, url, referer) {
-    const sess = await (0, utils_1.toUrlSafeB64)(JSON.stringify(session));
-    const password = generateUID(5);
-    const encryptedSession = await encrypt(sess, password);
-    const data = new FormData();
-    data.append('session', encryptedSession);
-    data.append('dateShared', `${Date.now()}`);
-    data.append('referer', referer);
-    const response = await fetch(`${url}share`, {
-        method: 'POST',
-        mode: 'cors',
-        body: data,
-    });
-    if (!response.ok) {
-        const err = await response.text();
-        throw new Error(getErrorMsg(err));
-    }
-    const json = await response.json();
-    return {
-        json,
-        encryptedSession,
-        password,
-    };
-}
-async function readSessionFromDynamo(baseUrl, sessionQueryParam, password) {
-    const sessionId = sessionQueryParam.split('share-')[1];
-    const url = `${baseUrl}?sessionId=${encodeURIComponent(sessionId)}`;
-    const response = await fetch(url);
-    if (!response.ok) {
-        throw new Error(getErrorMsg(await response.text()));
-    }
-    const json = await response.json();
-    return decrypt(json.session, password);
-}

package/dist/GridBookmarkWidget/types.d.ts

@@ -1,4 +0,0 @@
-import type { Region } from '@jbrowse/core/util/types';
-export interface LabeledRegion extends Region {
-    label: string;
-}

package/dist/GridBookmarkWidget/types.js

@@ -1,2 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });

package/dist/GridBookmarkWidget/utils.d.ts

@@ -1,7 +0,0 @@
-import type { GridBookmarkModel } from './model';
-import type { AbstractViewModel } from '@jbrowse/core/util/types';
-export declare function navToBookmark(locString: string, assembly: string, views: AbstractViewModel[], model: GridBookmarkModel): Promise<void>;
-export declare function downloadBookmarkFile(fileFormat: string, model: GridBookmarkModel): void;
-export declare function b64PadSuffix(b64: string): string;
-export declare function fromUrlSafeB64(b64: string): Promise<string>;
-export declare function toUrlSafeB64(str: string): Promise<string>;

package/dist/GridBookmarkWidget/utils.js

@@ -1,144 +0,0 @@
-"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 () {
-    var ownKeys = function(o) {
-        ownKeys = Object.getOwnPropertyNames || function (o) {
-            var ar = [];
-            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
-            return ar;
-        };
-        return ownKeys(o);
-    };
-    return function (mod) {
-        if (mod && mod.__esModule) return mod;
-        var result = {};
-        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
-        __setModuleDefault(result, mod);
-        return result;
-    };
-})();
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.navToBookmark = navToBookmark;
-exports.downloadBookmarkFile = downloadBookmarkFile;
-exports.b64PadSuffix = b64PadSuffix;
-exports.fromUrlSafeB64 = fromUrlSafeB64;
-exports.toUrlSafeB64 = toUrlSafeB64;
-const util_1 = require("@jbrowse/core/util");
-const file_saver_1 = require("file-saver");
-async function navToBookmark(locString, assembly, views, model) {
-    const session = (0, util_1.getSession)(model);
-    try {
-        let view = views.find(view => view.id === session.focusedViewId);
-        if ((view === null || view === void 0 ? void 0 : view.assemblyNames[0]) !== assembly) {
-            view = views.find(elt => elt.type === 'LinearGenomeView' && elt.assemblyNames[0] === assembly);
-        }
-        if (!view) {
-            const newViewId = `${model.id}_${assembly}`;
-            view = session.addView('LinearGenomeView', {
-                id: newViewId,
-            });
-        }
-        await view.navToLocString(locString, assembly);
-    }
-    catch (e) {
-        console.error(e);
-        session.notifyError(`${e}`, e);
-    }
-}
-function downloadBookmarkFile(fileFormat, model) {
-    const { selectedBookmarks, bookmarksWithValidAssemblies } = model;
-    const bookmarksToDownload = selectedBookmarks.length === 0
-        ? bookmarksWithValidAssemblies
-        : selectedBookmarks;
-    if (fileFormat === 'BED') {
-        const fileHeader = '';
-        const fileContents = {};
-        for (const bookmark of bookmarksToDownload) {
-            const { label } = bookmark;
-            const labelVal = label === '' ? '.' : label;
-            const line = `${bookmark.refName}\t${bookmark.start}\t${bookmark.end}\t${labelVal}\n`;
-            if (fileContents[bookmark.assemblyName]) {
-                fileContents[bookmark.assemblyName].push(line);
-            }
-            else {
-                fileContents[bookmark.assemblyName] = [line];
-            }
-        }
-        for (const assembly in fileContents) {
-            const fileContent = fileContents[assembly].reduce((a, b) => a + b, fileHeader);
-            const blob = new Blob([fileContent || ''], {
-                type: 'text/x-bed;charset=utf-8',
-            });
-            const fileName = `jbrowse_bookmarks_${assembly}.bed`;
-            (0, file_saver_1.saveAs)(blob, fileName);
-        }
-    }
-    else {
-        const fileHeader = 'chrom\tstart\tend\tlabel\tassembly_name\tcoord_range\n';
-        const fileContents = bookmarksToDownload
-            .map(bookmark => {
-            const { label } = bookmark;
-            const labelVal = label === '' ? '.' : label;
-            const locString = (0, util_1.assembleLocString)(bookmark);
-            return `${bookmark.refName}\t${bookmark.start + 1}\t${bookmark.end}\t${labelVal}\t${bookmark.assemblyName}\t${locString}\n`;
-        })
-            .reduce((a, b) => a + b, fileHeader);
-        const blob = new Blob([fileContents || ''], {
-            type: 'text/tab-separated-values;charset=utf-8',
-        });
-        const fileName = 'jbrowse_bookmarks.tsv';
-        (0, file_saver_1.saveAs)(blob, fileName);
-    }
-}
-function b64PadSuffix(b64) {
-    let num = 0;
-    const mo = b64.length % 4;
-    switch (mo) {
-        case 3:
-            num = 1;
-            break;
-        case 2:
-            num = 2;
-            break;
-        case 0:
-            num = 0;
-            break;
-        default:
-            throw new Error('base64 not a valid length');
-    }
-    return b64 + '='.repeat(num);
-}
-async function fromUrlSafeB64(b64) {
-    const originalB64 = b64PadSuffix(b64.replaceAll('-', '+').replaceAll('_', '/'));
-    const { toByteArray } = await Promise.resolve().then(() => __importStar(require('base64-js')));
-    const { inflate } = await Promise.resolve().then(() => __importStar(require('pako')));
-    const bytes = toByteArray(originalB64);
-    const inflated = inflate(bytes);
-    return new TextDecoder().decode(inflated);
-}
-async function toUrlSafeB64(str) {
-    const bytes = new TextEncoder().encode(str);
-    const { deflate } = await Promise.resolve().then(() => __importStar(require('pako')));
-    const { fromByteArray } = await Promise.resolve().then(() => __importStar(require('base64-js')));
-    const deflated = deflate(bytes);
-    const encoded = fromByteArray(deflated);
-    const pos = encoded.indexOf('=');
-    return pos > 0
-        ? encoded.slice(0, pos).replaceAll('+', '-').replaceAll('/', '_')
-        : encoded.replaceAll('+', '-').replaceAll('/', '_');
-}

package/dist/index.d.ts

@@ -1,7 +0,0 @@
-import Plugin from '@jbrowse/core/Plugin';
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default class GridBookmarkPlugin extends Plugin {
-    name: string;
-    install(pluginManager: PluginManager): void;
-    configure(pluginManager: PluginManager): void;
-}

package/dist/index.js

@@ -1,185 +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 Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-const util_1 = require("@jbrowse/core/util");
-const Bookmark_1 = __importDefault(require("@mui/icons-material/Bookmark"));
-const Bookmarks_1 = __importDefault(require("@mui/icons-material/Bookmarks"));
-const Highlight_1 = __importDefault(require("@mui/icons-material/Highlight"));
-const Label_1 = __importDefault(require("@mui/icons-material/Label"));
-const GridBookmarkWidget_1 = __importDefault(require("./GridBookmarkWidget"));
-class GridBookmarkPlugin extends Plugin_1.default {
-    constructor() {
-        super(...arguments);
-        this.name = 'GridBookmarkPlugin';
-    }
-    install(pluginManager) {
-        (0, GridBookmarkWidget_1.default)(pluginManager);
-        pluginManager.addToExtensionPoint('Core-extendPluggableElement', (pluggableElement) => {
-            if (pluggableElement.name === 'LinearGenomeView') {
-                const { stateModel } = pluggableElement;
-                const lgv = stateModel;
-                const newStateModel = lgv
-                    .props({
-                    bookmarkHighlightsVisible: true,
-                    bookmarkLabelsVisible: true,
-                })
-                    .actions(self => ({
-                    setBookmarkHighlightsVisible(arg) {
-                        self.bookmarkHighlightsVisible = arg;
-                    },
-                    setBookmarkLabelsVisible(arg) {
-                        self.bookmarkLabelsVisible = arg;
-                    },
-                    activateBookmarkWidget() {
-                        const session = (0, util_1.getSession)(self);
-                        if ((0, util_1.isSessionModelWithWidgets)(session)) {
-                            let bookmarkWidget = session.widgets.get('GridBookmark');
-                            if (!bookmarkWidget) {
-                                bookmarkWidget = session.addWidget('GridBookmarkWidget', 'GridBookmark');
-                            }
-                            session.showWidget(bookmarkWidget);
-                            return session.widgets.get('GridBookmark');
-                        }
-                        throw new Error('Could not open bookmark widget');
-                    },
-                }))
-                    .actions(self => ({
-                    navigateNewestBookmark() {
-                        const session = (0, util_1.getSession)(self);
-                        const bookmarkWidget = self.activateBookmarkWidget();
-                        if (bookmarkWidget.bookmarks.length) {
-                            self.navTo(bookmarkWidget.bookmarks.at(-1));
-                        }
-                        else {
-                            session.notify('There are no recent bookmarks to navigate to.', 'info');
-                        }
-                    },
-                    bookmarkCurrentRegion() {
-                        if (self.id === (0, util_1.getSession)(self).focusedViewId) {
-                            const selectedRegions = self.getSelectedRegions(undefined, undefined);
-                            const bookmarkWidget = self.activateBookmarkWidget();
-                            if (!selectedRegions.length) {
-                                throw new Error('no region selected');
-                            }
-                            else {
-                                bookmarkWidget.addBookmark(selectedRegions[0]);
-                            }
-                        }
-                    },
-                }))
-                    .views(self => {
-                    const superMenuItems = self.menuItems;
-                    const superRubberBandMenuItems = self.rubberBandMenuItems;
-                    return {
-                        menuItems() {
-                            return [
-                                ...superMenuItems(),
-                                { type: 'divider' },
-                                {
-                                    label: 'Bookmarks',
-                                    icon: Bookmarks_1.default,
-                                    subMenu: [
-                                        {
-                                            label: 'Open bookmark widget',
-                                            icon: Bookmarks_1.default,
-                                            onClick: () => self.activateBookmarkWidget(),
-                                        },
-                                        {
-                                            label: 'Bookmark current region',
-                                            icon: Bookmark_1.default,
-                                            onClick: () => {
-                                                self.bookmarkCurrentRegion();
-                                            },
-                                        },
-                                        {
-                                            label: 'Toggle bookmark highlights',
-                                            icon: Highlight_1.default,
-                                            type: 'checkbox',
-                                            checked: self.bookmarkHighlightsVisible,
-                                            onClick: () => {
-                                                self.setBookmarkHighlightsVisible(!self.bookmarkHighlightsVisible);
-                                            },
-                                        },
-                                        {
-                                            label: 'Toggle bookmark labels',
-                                            icon: Label_1.default,
-                                            type: 'checkbox',
-                                            checked: self.bookmarkLabelsVisible,
-                                            onClick: () => {
-                                                self.setBookmarkLabelsVisible(!self.bookmarkLabelsVisible);
-                                            },
-                                        },
-                                    ],
-                                },
-                            ];
-                        },
-                        rubberBandMenuItems() {
-                            return [
-                                ...superRubberBandMenuItems(),
-                                {
-                                    label: 'Bookmark region',
-                                    icon: Bookmark_1.default,
-                                    onClick: () => {
-                                        const { leftOffset, rightOffset } = self;
-                                        const selectedRegions = self.getSelectedRegions(leftOffset, rightOffset);
-                                        const bookmarkWidget = self.activateBookmarkWidget();
-                                        if (!selectedRegions.length) {
-                                            throw new Error('no regions selected');
-                                        }
-                                        else {
-                                            bookmarkWidget.addBookmark(selectedRegions[0]);
-                                        }
-                                    },
-                                },
-                            ];
-                        },
-                    };
-                })
-                    .actions(self => {
-                    const keydownListener = (e) => {
-                        const activationSequence = (e.ctrlKey || e.metaKey) && e.shiftKey;
-                        if (activationSequence && e.code === 'KeyD') {
-                            e.preventDefault();
-                            self.activateBookmarkWidget();
-                            self.bookmarkCurrentRegion();
-                            (0, util_1.getSession)(self).notify('Bookmark created.', 'success');
-                        }
-                        if (activationSequence && e.code === 'KeyM') {
-                            e.preventDefault();
-                            self.navigateNewestBookmark();
-                        }
-                    };
-                    return {
-                        afterCreate() {
-                            document.addEventListener('keydown', keydownListener);
-                        },
-                        beforeDestroy() {
-                            document.removeEventListener('keydown', keydownListener);
-                        },
-                    };
-                });
-                pluggableElement.stateModel = newStateModel;
-            }
-            return pluggableElement;
-        });
-    }
-    configure(pluginManager) {
-        if ((0, util_1.isAbstractMenuManager)(pluginManager.rootModel)) {
-            pluginManager.rootModel.appendToMenu('Tools', {
-                label: 'Bookmarks',
-                icon: Bookmarks_1.default,
-                onClick: (session) => {
-                    let bookmarkWidget = session.widgets.get('GridBookmark');
-                    if (!bookmarkWidget) {
-                        bookmarkWidget = session.addWidget('GridBookmarkWidget', 'GridBookmark');
-                    }
-                    session.showWidget(bookmarkWidget);
-                },
-            });
-        }
-    }
-}
-exports.default = GridBookmarkPlugin;