@jbrowse/web-core 3.7.0 → 4.0.1

package/dist/BaseWebSession/index.js

@@ -1,257 +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;
-    };
-})();
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.BaseWebSession = BaseWebSession;
-const react_1 = require("react");
-const app_core_1 = require("@jbrowse/app-core");
-const configuration_1 = require("@jbrowse/core/configuration");
-const SnackbarModel_1 = __importDefault(require("@jbrowse/core/ui/SnackbarModel"));
-const util_1 = require("@jbrowse/core/util");
-const product_core_1 = require("@jbrowse/product-core");
-const Delete_1 = __importDefault(require("@mui/icons-material/Delete"));
-const FileCopy_1 = __importDefault(require("@mui/icons-material/FileCopy"));
-const Info_1 = __importDefault(require("@mui/icons-material/Info"));
-const Settings_1 = __importDefault(require("@mui/icons-material/Settings"));
-const mobx_1 = require("mobx");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const SessionConnections_1 = require("../SessionConnections");
-const AboutDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./AboutDialog'))));
-function BaseWebSession({ pluginManager, assemblyConfigSchema, }) {
-    const sessionModel = mobx_state_tree_1.types
-        .compose('WebCoreSessionModel', mobx_state_tree_1.types.compose('WebCoreSessionModelGroupA', (0, product_core_1.ReferenceManagementSessionMixin)(pluginManager), (0, product_core_1.DrawerWidgetSessionMixin)(pluginManager), (0, product_core_1.DialogQueueSessionMixin)(pluginManager), (0, product_core_1.ThemeManagerSessionMixin)(pluginManager), (0, product_core_1.MultipleViewsSessionMixin)(pluginManager)), mobx_state_tree_1.types.compose('WebCoreSessionModelGroupB', (0, product_core_1.SessionTracksManagerSessionMixin)(pluginManager), (0, app_core_1.SessionAssembliesMixin)(pluginManager, assemblyConfigSchema), (0, app_core_1.TemporaryAssembliesMixin)(pluginManager, assemblyConfigSchema), (0, SessionConnections_1.WebSessionConnectionsMixin)(pluginManager), (0, app_core_1.AppFocusMixin)(), (0, SnackbarModel_1.default)()))
-        .props({
-        margin: 0,
-        sessionPlugins: mobx_state_tree_1.types.array(mobx_state_tree_1.types.frozen()),
-    })
-        .volatile(() => ({
-        sessionThemeName: (0, util_1.localStorageGetItem)('themeName') || 'default',
-        task: undefined,
-    }))
-        .views(self => ({
-        get tracks() {
-            return [...self.sessionTracks, ...self.jbrowse.tracks];
-        },
-        get root() {
-            return (0, mobx_state_tree_1.getParent)(self);
-        },
-        get assemblies() {
-            return [...self.jbrowse.assemblies, ...self.sessionAssemblies];
-        },
-        get connections() {
-            return [...self.jbrowse.connections, ...self.sessionConnections];
-        },
-    }))
-        .actions(self => ({
-        setName(str) {
-            self.name = str;
-        },
-    }))
-        .views(self => ({
-        get assemblyNames() {
-            return self.assemblies.map(f => (0, configuration_1.readConfObject)(f, 'name'));
-        },
-        get version() {
-            return self.root.version;
-        },
-        get shareURL() {
-            return (0, configuration_1.getConf)(self.jbrowse, 'shareURL');
-        },
-        get textSearchManager() {
-            return self.root.textSearchManager;
-        },
-        get assemblyManager() {
-            return self.root.assemblyManager;
-        },
-        get savedSessionMetadata() {
-            return self.root.savedSessionMetadata;
-        },
-        get previousAutosaveId() {
-            return self.root.previousAutosaveId;
-        },
-        get history() {
-            return self.root.history;
-        },
-        renderProps() {
-            return {
-                theme: self.theme,
-                highResolutionScaling: (0, configuration_1.getConf)(self, 'highResolutionScaling'),
-            };
-        },
-    }))
-        .actions(self => ({
-        addAssemblyConf(conf) {
-            self.jbrowse.addAssemblyConf(conf);
-        },
-        addSessionPlugin(plugin) {
-            if (self.sessionPlugins.some(p => p.name === plugin.name)) {
-                throw new Error('session plugin cannot be installed twice');
-            }
-            self.sessionPlugins.push(plugin);
-            self.root.setPluginsUpdated(true);
-        },
-        removeSessionPlugin(pluginDefinition) {
-            self.sessionPlugins = (0, mobx_state_tree_1.cast)(self.sessionPlugins.filter(plugin => plugin.url !== pluginDefinition.url ||
-                plugin.umdUrl !== pluginDefinition.umdUrl ||
-                plugin.cjsUrl !== pluginDefinition.cjsUrl ||
-                plugin.esmUrl !== pluginDefinition.esmUrl));
-            (0, mobx_state_tree_1.getParent)(self).setPluginsUpdated(true);
-        },
-        addSavedSession(sessionSnapshot) {
-            return self.root.addSavedSession(sessionSnapshot);
-        },
-        deleteSavedSession(id) {
-            return self.root.deleteSavedSession(id);
-        },
-        favoriteSavedSession(id) {
-            return self.root.favoriteSavedSession(id);
-        },
-        unfavoriteSavedSession(id) {
-            return self.root.unfavoriteSavedSession(id);
-        },
-        renameCurrentSession(sessionName) {
-            return self.root.renameCurrentSession(sessionName);
-        },
-        duplicateCurrentSession() {
-            return self.root.duplicateCurrentSession();
-        },
-        activateSession(sessionName) {
-            return self.root.activateSession(sessionName);
-        },
-        setDefaultSession() {
-            return self.root.setDefaultSession();
-        },
-        saveSessionToLocalStorage() {
-            return self.root.saveSessionToLocalStorage();
-        },
-        loadAutosaveSession() {
-            return self.root.loadAutosaveSession();
-        },
-        setSession(sessionSnapshot) {
-            return self.root.setSession(sessionSnapshot);
-        },
-    }))
-        .actions(self => ({
-        editTrackConfiguration(configuration) {
-            const { adminMode, sessionTracks } = self;
-            if (!adminMode && !sessionTracks.includes(configuration)) {
-                throw new Error("Can't edit the configuration of a non-session track");
-            }
-            self.editConfiguration(configuration);
-        },
-    }))
-        .views(self => ({
-        getTrackActionMenuItems(config) {
-            const { adminMode, sessionTracks } = self;
-            const canEdit = adminMode || sessionTracks.find(t => t.trackId === config.trackId);
-            const isRefSeq = config.type === 'ReferenceSequenceTrack';
-            return [
-                {
-                    label: 'About track',
-                    priority: 1002,
-                    onClick: () => {
-                        self.queueDialog(handleClose => [
-                            AboutDialog,
-                            {
-                                config,
-                                handleClose,
-                            },
-                        ]);
-                    },
-                    icon: Info_1.default,
-                },
-                {
-                    label: 'Settings',
-                    priority: 1001,
-                    disabled: !canEdit,
-                    icon: Settings_1.default,
-                    onClick: () => {
-                        self.editTrackConfiguration(config);
-                    },
-                },
-                {
-                    label: 'Delete track',
-                    priority: 1000,
-                    disabled: !canEdit || isRefSeq,
-                    icon: Delete_1.default,
-                    onClick: () => {
-                        self.deleteTrackConf(config);
-                    },
-                },
-                {
-                    label: 'Copy track',
-                    priority: 999,
-                    disabled: isRefSeq,
-                    onClick: () => {
-                        const snap = structuredClone((0, mobx_state_tree_1.getSnapshot)(config));
-                        const now = Date.now();
-                        snap.trackId += `-${now}`;
-                        for (const display of snap.displays) {
-                            display.displayId += `-${now}`;
-                        }
-                        if (!self.adminMode) {
-                            snap.trackId += '-sessionTrack';
-                            snap.category = undefined;
-                        }
-                        snap.name += ' (copy)';
-                        self.addTrackConf(snap);
-                    },
-                    icon: FileCopy_1.default,
-                },
-                { type: 'divider' },
-            ];
-        },
-        menus() {
-            return self.root.menus();
-        },
-    }))
-        .actions(self => ({
-        afterAttach() {
-            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
-                (0, util_1.localStorageSetItem)('drawerPosition', self.drawerPosition);
-                (0, util_1.localStorageSetItem)('themeName', self.themeName);
-            }));
-        },
-    }));
-    const extendedSessionModel = pluginManager.evaluateExtensionPoint('Core-extendSession', sessionModel);
-    return mobx_state_tree_1.types.snapshotProcessor(extendedSessionModel, {
-        preProcessor(snapshot) {
-            const { connectionInstances, ...rest } = snapshot || {};
-            return !Array.isArray(connectionInstances) ? rest : snapshot;
-        },
-    });
-}

package/dist/SessionConnections.d.ts

@@ -1,159 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { BaseConnectionConfigModel } from '@jbrowse/core/pluggableElementTypes/models/baseConnectionConfig';
-export declare function WebSessionConnectionsMixin(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
-    connectionInstances: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
-        name: import("mobx-state-tree").ISimpleType<string>;
-        tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
-        configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-            name: {
-                type: string;
-                defaultValue: string;
-                description: string;
-            };
-            assemblyNames: {
-                type: string;
-                defaultValue: never[];
-                description: string;
-            };
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
-    }, {
-        connect(_arg: AnyConfigurationModel): void;
-    } & {
-        afterAttach(): void;
-        addTrackConf(trackConf: ({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                    [x: string]: any;
-                } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-            } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>): any;
-        addTrackConfs(trackConfs: (({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                    [x: string]: any;
-                } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-            } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>)[]): void;
-        setTrackConfs(trackConfs: AnyConfigurationModel[]): void;
-        clear(): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-} & {
-    sessionConnections: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
-}, {
-    readonly connections: BaseConnectionConfigModel[];
-} & {
-    makeConnection(configuration: AnyConfigurationModel, initialSnapshot?: {}): ({
-        name: string;
-        tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyModelType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>>;
-        configuration: {
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                    [x: string]: any;
-                } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-            } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-            name: {
-                type: string;
-                defaultValue: string;
-                description: string;
-            };
-            assemblyNames: {
-                type: string;
-                defaultValue: never[];
-                description: string;
-            };
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>>;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        connect(_arg: AnyConfigurationModel): void;
-    } & {
-        afterAttach(): void;
-        addTrackConf(trackConf: ({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                    [x: string]: any;
-                } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-            } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>): any;
-        addTrackConfs(trackConfs: (({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                    [x: string]: any;
-                } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-            } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>)[]): void;
-        setTrackConfs(trackConfs: AnyConfigurationModel[]): void;
-        clear(): void;
-    } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-        name: import("mobx-state-tree").ISimpleType<string>;
-        tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
-        configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-            name: {
-                type: string;
-                defaultValue: string;
-                description: string;
-            };
-            assemblyNames: {
-                type: string;
-                defaultValue: never[];
-                description: string;
-            };
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
-    }, {
-        connect(_arg: AnyConfigurationModel): void;
-    } & {
-        afterAttach(): void;
-        addTrackConf(trackConf: ({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                    [x: string]: any;
-                } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-            } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>): any;
-        addTrackConfs(trackConfs: (({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                    [x: string]: any;
-                } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-            } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>)[]): void;
-        setTrackConfs(trackConfs: AnyConfigurationModel[]): void;
-        clear(): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
-    prepareToBreakConnection(configuration: AnyConfigurationModel): (Record<string, number> | (() => void))[] | undefined;
-    breakConnection(configuration: AnyConfigurationModel): void;
-    deleteConnection(configuration: AnyConfigurationModel): any;
-    addConnectionConf(connectionConf: AnyConfigurationModel): any;
-    clearConnections(): void;
-} & {
-    addConnectionConf(connectionConf: BaseConnectionConfigModel): any;
-    deleteConnection(configuration: AnyConfigurationModel): any;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/dist/SessionConnections.js

@@ -1,49 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.WebSessionConnectionsMixin = WebSessionConnectionsMixin;
-const product_core_1 = require("@jbrowse/product-core");
-const mobx_state_tree_1 = require("mobx-state-tree");
-function WebSessionConnectionsMixin(pluginManager) {
-    return mobx_state_tree_1.types
-        .compose('SessionConnectionsManagement', (0, product_core_1.ConnectionManagementSessionMixin)(pluginManager), mobx_state_tree_1.types.model({
-        sessionConnections: mobx_state_tree_1.types.array(pluginManager.pluggableConfigSchemaType('connection')),
-    }))
-        .actions(s => {
-        const self = s;
-        const superDeleteConnection = self.deleteConnection;
-        const superAddConnectionConf = self.addConnectionConf;
-        return {
-            addConnectionConf(connectionConf) {
-                if (self.adminMode) {
-                    return superAddConnectionConf(connectionConf);
-                }
-                else {
-                    const { connectionId, type } = connectionConf;
-                    if (!type) {
-                        throw new Error(`unknown connection type "${type}"`);
-                    }
-                    const connection = self.sessionConnections.find(c => c.connectionId === connectionId);
-                    if (connection) {
-                        return connection;
-                    }
-                    else {
-                        const length = self.sessionConnections.push(connectionConf);
-                        return self.sessionConnections[length - 1];
-                    }
-                }
-            },
-            deleteConnection(configuration) {
-                if (self.adminMode) {
-                    return superDeleteConnection(configuration);
-                }
-                else {
-                    const { connectionId } = configuration;
-                    const idx = self.sessionConnections.findIndex(c => c.connectionId === connectionId);
-                    return idx === -1
-                        ? undefined
-                        : self.sessionConnections.splice(idx, 1);
-                }
-            },
-        };
-    });
-}

package/dist/index.d.ts

@@ -1,2 +0,0 @@
-export * from './SessionConnections';
-export * from './BaseWebSession';

package/dist/index.js

@@ -1,18 +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 __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);
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-__exportStar(require("./SessionConnections"), exports);
-__exportStar(require("./BaseWebSession"), exports);