@jbrowse/app-core 2.6.1

package/esm/JBrowseConfig/index.js

@@ -0,0 +1,148 @@
+import { ConfigurationSchema, } from '@jbrowse/core/configuration';
+import RpcManager from '@jbrowse/core/rpc/RpcManager';
+import { types } from 'mobx-state-tree';
+/**
+ * #config JBrowseRootConfig
+ * #category root
+ * configuration in a config.json/file.jbrowse
+ */
+export function JBrowseConfigF({ pluginManager, assemblyConfigSchema, }) {
+    return types.model('JBrowseConfig', {
+        configuration: ConfigurationSchema('Root', {
+            /**
+             * #slot configuration.rpc
+             */
+            rpc: RpcManager.configSchema,
+            /**
+             * #slot configuration.highResolutionScaling
+             */
+            highResolutionScaling: {
+                type: 'number',
+                defaultValue: 2,
+            },
+            formatDetails: ConfigurationSchema('FormatDetails', {
+                /**
+                 * #slot configuration.formatDetails.feature
+                 */
+                feature: {
+                    type: 'frozen',
+                    description: 'adds extra fields to the feature details',
+                    defaultValue: {},
+                    contextVariable: ['feature'],
+                },
+                /**
+                 * #slot configuration.formatDetails.subfeatures
+                 */
+                subfeatures: {
+                    type: 'frozen',
+                    description: 'adds extra fields to the subfeatures of a feature',
+                    defaultValue: {},
+                    contextVariable: ['feature'],
+                },
+                /**
+                 * #slot configuration.formatDetails.depth
+                 */
+                depth: {
+                    type: 'number',
+                    defaultValue: 2,
+                    description: 'depth to iterate on subfeatures',
+                },
+            }),
+            formatAbout: ConfigurationSchema('FormatAbout', {
+                /**
+                 * #slot configuration.formatAbout.config
+                 */
+                config: {
+                    type: 'frozen',
+                    description: 'formats configuration object in about dialog',
+                    defaultValue: {},
+                    contextVariable: ['config'],
+                },
+                /**
+                 * #slot configuration.formatAbout.hideUris
+                 */
+                hideUris: {
+                    type: 'boolean',
+                    defaultValue: false,
+                },
+            }),
+            /*
+             * #slot configuration.shareURL
+             */
+            shareURL: {
+                type: 'string',
+                defaultValue: 'https://share.jbrowse.org/api/v1/',
+            },
+            /**
+             * #slot configuration.disableAnalytics
+             */
+            disableAnalytics: {
+                type: 'boolean',
+                defaultValue: false,
+            },
+            /**
+             * #slot configuration.theme
+             */
+            theme: {
+                type: 'frozen',
+                defaultValue: {},
+            },
+            /**
+             * #slot configuration.extraThemes
+             */
+            extraThemes: { type: 'frozen', defaultValue: {} },
+            /**
+             * #slot configuration.logoPath
+             */
+            logoPath: {
+                type: 'fileLocation',
+                defaultValue: { uri: '', locationType: 'UriLocation' },
+            },
+            ...pluginManager.pluginConfigurationSchemas(),
+        }),
+        /**
+         * #slot
+         * defines plugins of the format
+         * ```typescript
+         * type PluginDefinition=
+         *    { umdUrl: string, name:string } |
+         *    { url: string, name: string } |
+         *    { esmUrl: string } |
+         *    { cjsUrl: string } |
+         *    { umdLoc: { uri: string } } |
+         *    { esmLoc: { uri: string } } |
+         * ```
+         */
+        plugins: types.array(types.frozen()),
+        /**
+         * #slot
+         * configuration of the assemblies in the instance, see BaseAssembly
+         */
+        assemblies: types.array(assemblyConfigSchema),
+        /**
+         * #slot
+         * track configuration is an array of track config schemas. multiple
+         * instances of a track can exist that use the same configuration
+         */
+        tracks: types.array(pluginManager.pluggableConfigSchemaType('track')),
+        /**
+         * #slot
+         * configuration for internet accounts, see InternetAccounts
+         */
+        internetAccounts: types.array(pluginManager.pluggableConfigSchemaType('internet account')),
+        /**
+         * #slot
+         */
+        aggregateTextSearchAdapters: types.array(pluginManager.pluggableConfigSchemaType('text search adapter')),
+        /**
+         * #slot
+         */
+        connections: types.array(pluginManager.pluggableConfigSchemaType('connection')),
+        /**
+         * #slot
+         */
+        defaultSession: types.optional(types.frozen(), {
+            name: `New Session`,
+        }),
+    });
+}

package/esm/JBrowseModel/index.d.ts

@@ -0,0 +1,144 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+import { BaseAssemblyConfigSchema } from '@jbrowse/core/assemblyManager';
+import RpcManager from '@jbrowse/core/rpc/RpcManager';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import { PluginDefinition } from '@jbrowse/core/PluginLoader';
+export declare function JBrowseModelF({ pluginManager, assemblyConfigSchema, }: {
+    pluginManager: PluginManager;
+    assemblyConfigSchema: BaseAssemblyConfigSchema;
+}): import("mobx-state-tree").IModelType<{
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        rpc: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            defaultDriver: {
+                type: string;
+                description: string;
+                defaultValue: string;
+            };
+            drivers: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IMapType<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> | undefined, import("mobx-state-tree").ModelSnapshotType<Record<string, any>>, (Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> & import("mobx-state-tree/dist/internal").NonEmptyObject) | undefined>>, [undefined]>;
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+        highResolutionScaling: {
+            type: string;
+            defaultValue: number;
+        };
+        formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            feature: {
+                type: string;
+                description: string;
+                defaultValue: {};
+                contextVariable: string[];
+            };
+            subfeatures: {
+                type: string;
+                description: string;
+                defaultValue: {};
+                contextVariable: string[];
+            };
+            depth: {
+                type: string;
+                defaultValue: number;
+                description: string;
+            };
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+        formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            config: {
+                type: string;
+                description: string;
+                defaultValue: {};
+                contextVariable: string[];
+            };
+            hideUris: {
+                type: string;
+                defaultValue: boolean;
+            };
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+        shareURL: {
+            type: string;
+            defaultValue: string;
+        };
+        disableAnalytics: {
+            type: string;
+            defaultValue: boolean;
+        };
+        theme: {
+            type: string;
+            defaultValue: {}; /**
+             * #action
+             */
+        };
+        extraThemes: {
+            type: string;
+            defaultValue: {};
+        };
+        logoPath: {
+            type: string;
+            /**
+             * #action
+             */
+            defaultValue: {
+                uri: string;
+                locationType: string;
+            };
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    plugins: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<PluginDefinition, PluginDefinition, PluginDefinition>>;
+    assemblies: import("mobx-state-tree").IArrayType<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
+    tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+    internetAccounts: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+    aggregateTextSearchAdapters: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+    connections: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+    defaultSession: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<any, any, any>, [undefined]>;
+}, {
+    /**
+     * #getter
+     */
+    readonly assemblyNames: string[];
+    /**
+     * #getter
+     */
+    readonly rpcManager: RpcManager;
+} & {
+    /**
+     * #action
+     */
+    addAssemblyConf(conf: AnyConfigurationModel): {
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: unknown): any;
+    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
+    /**
+     * #action
+     */
+    removeAssemblyConf(assemblyName: string): void;
+    /**
+     * #action
+     */
+    addTrackConf(trackConf: AnyConfigurationModel): any;
+    /**
+     * #action
+     */
+    addConnectionConf(connectionConf: AnyConfigurationModel): any;
+    /**
+     * #action
+     */
+    deleteConnectionConf(configuration: AnyConfigurationModel): boolean;
+    /**
+     * #action
+     */
+    deleteTrackConf(trackConf: AnyConfigurationModel): boolean;
+    /**
+     * #action
+     */
+    addPlugin(pluginDefinition: PluginDefinition): void;
+    /**
+     * #action
+     */
+    removePlugin(pluginDefinition: PluginDefinition): void;
+    /**
+     * #action
+     */
+    addInternetAccountConf(internetAccountConf: AnyConfigurationModel): any;
+    /**
+     * #action
+     */
+    deleteInternetAccountConf(configuration: AnyConfigurationModel): boolean;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/esm/JBrowseModel/index.js

@@ -0,0 +1,128 @@
+import { cast, getParent } from 'mobx-state-tree';
+import { readConfObject, } from '@jbrowse/core/configuration';
+// locals
+import { JBrowseConfigF } from '../JBrowseConfig';
+export function JBrowseModelF({ pluginManager, assemblyConfigSchema, }) {
+    return JBrowseConfigF({ pluginManager, assemblyConfigSchema })
+        .views(self => ({
+        /**
+         * #getter
+         */
+        get assemblyNames() {
+            return self.assemblies.map(assembly => readConfObject(assembly, 'name'));
+        },
+        /**
+         * #getter
+         */
+        get rpcManager() {
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            return getParent(self).rpcManager;
+        },
+    }))
+        .actions(self => ({
+        /**
+         * #action
+         */
+        addAssemblyConf(conf) {
+            const { name } = conf;
+            if (!name) {
+                throw new Error('Can\'t add assembly with no "name"');
+            }
+            if (self.assemblyNames.includes(name)) {
+                throw new Error(`Can't add assembly with name "${name}", an assembly with that name already exists`);
+            }
+            const length = self.assemblies.push({
+                ...conf,
+                sequence: {
+                    type: 'ReferenceSequenceTrack',
+                    trackId: `${name}-${Date.now()}`,
+                    ...conf.sequence,
+                },
+            });
+            return self.assemblies[length - 1];
+        },
+        /**
+         * #action
+         */
+        removeAssemblyConf(assemblyName) {
+            const toRemove = self.assemblies.find(a => a.name === assemblyName);
+            if (toRemove) {
+                self.assemblies.remove(toRemove);
+            }
+        },
+        /**
+         * #action
+         */
+        addTrackConf(trackConf) {
+            const { type } = trackConf;
+            if (!type) {
+                throw new Error(`unknown track type ${type}`);
+            }
+            const length = self.tracks.push(trackConf);
+            return self.tracks[length - 1];
+        },
+        /**
+         * #action
+         */
+        addConnectionConf(connectionConf) {
+            const { type } = connectionConf;
+            if (!type) {
+                throw new Error(`unknown connection type ${type}`);
+            }
+            const length = self.connections.push(connectionConf);
+            return self.connections[length - 1];
+        },
+        /**
+         * #action
+         */
+        deleteConnectionConf(configuration) {
+            const elt = self.connections.find(conn => conn.id === configuration.id);
+            return self.connections.remove(elt);
+        },
+        /**
+         * #action
+         */
+        deleteTrackConf(trackConf) {
+            const elt = self.tracks.find(t => t.trackId === trackConf.trackId);
+            return self.tracks.remove(elt);
+        },
+        /**
+         * #action
+         */
+        addPlugin(pluginDefinition) {
+            self.plugins.push(pluginDefinition);
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            const rootModel = getParent(self);
+            rootModel.setPluginsUpdated(true);
+        },
+        /**
+         * #action
+         */
+        removePlugin(pluginDefinition) {
+            self.plugins = cast(self.plugins.filter(plugin => plugin.url !== pluginDefinition.url ||
+                plugin.umdUrl !== pluginDefinition.umdUrl ||
+                plugin.cjsUrl !== pluginDefinition.cjsUrl ||
+                plugin.esmUrl !== pluginDefinition.esmUrl));
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            getParent(self).setPluginsUpdated(true);
+        },
+        /**
+         * #action
+         */
+        addInternetAccountConf(internetAccountConf) {
+            const { type } = internetAccountConf;
+            if (!type) {
+                throw new Error(`unknown internetAccount type ${type}`);
+            }
+            const length = self.internetAccounts.push(internetAccountConf);
+            return self.internetAccounts[length - 1];
+        },
+        /**
+         * #action
+         */
+        deleteInternetAccountConf(configuration) {
+            const elt = self.internetAccounts.find(a => a.id === configuration.id);
+            return self.internetAccounts.remove(elt);
+        },
+    }));
+}

package/esm/RootMenu/index.d.ts

@@ -0,0 +1,68 @@
+import { MenuItem } from '@jbrowse/core/ui/Menu';
+export interface Menu {
+    label: string;
+    menuItems: MenuItem[];
+}
+export declare function RootAppMenuMixin(): import("mobx-state-tree").IModelType<{}, {
+    /**
+     * #action
+     */
+    setMenus(newMenus: Menu[]): void;
+    /**
+     * #action
+     * Add a top-level menu
+     * @param menuName - Name of the menu to insert.
+     * @returns The new length of the top-level menus array
+     */
+    appendMenu(menuName: string): number;
+    /**
+     * #action
+     * Insert a top-level menu
+     * @param menuName - Name of the menu to insert.
+     * @param position - Position to insert menu. If negative, counts from th
+     * end, e.g. `insertMenu('My Menu', -1)` will insert the menu as the
+     * second-to-last one.
+     * @returns The new length of the top-level menus array
+     */
+    insertMenu(menuName: string, position: number): number;
+    /**
+     * #action
+     * Add a menu item to a top-level menu
+     * @param menuName - Name of the top-level menu to append to.
+     * @param menuItem - Menu item to append.
+     * @returns The new length of the menu
+     */
+    appendToMenu(menuName: string, menuItem: MenuItem): number;
+    /**
+     * #action
+     * Insert a menu item into a top-level menu
+     * @param menuName - Name of the top-level menu to insert into
+     * @param menuItem - Menu item to insert
+     * @param position - Position to insert menu item. If negative, counts
+     * from the end, e.g. `insertMenu('My Menu', -1)` will insert the menu as
+     * the second-to-last one.
+     * @returns The new length of the menu
+     */
+    insertInMenu(menuName: string, menuItem: MenuItem, position: number): number;
+    /**
+     * #action
+     * Add a menu item to a sub-menu
+     * @param menuPath - Path to the sub-menu to add to, starting with the
+     * top-level menu (e.g. `['File', 'Insert']`).
+     * @param menuItem - Menu item to append.
+     * @returns The new length of the sub-menu
+     */
+    appendToSubMenu(menuPath: string[], menuItem: MenuItem): number;
+    /**
+     * #action
+     * Insert a menu item into a sub-menu
+     * @param menuPath - Path to the sub-menu to add to, starting with the
+     * top-level menu (e.g. `['File', 'Insert']`).
+     * @param menuItem - Menu item to insert.
+     * @param position - Position to insert menu item. If negative, counts
+     * from the end, e.g. `insertMenu('My Menu', -1)` will insert the menu as
+     * the second-to-last one.
+     * @returns The new length of the sub-menu
+     */
+    insertInSubMenu(menuPath: string[], menuItem: MenuItem, position: number): number;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/esm/RootMenu/index.js

@@ -0,0 +1,138 @@
+import { types } from 'mobx-state-tree';
+export function RootAppMenuMixin() {
+    return types.model({}).actions(s => {
+        const self = s;
+        return {
+            /**
+             * #action
+             */
+            setMenus(newMenus) {
+                self.menus = newMenus;
+            },
+            /**
+             * #action
+             * Add a top-level menu
+             * @param menuName - Name of the menu to insert.
+             * @returns The new length of the top-level menus array
+             */
+            appendMenu(menuName) {
+                return self.menus.push({ label: menuName, menuItems: [] });
+            },
+            /**
+             * #action
+             * Insert a top-level menu
+             * @param menuName - Name of the menu to insert.
+             * @param position - Position to insert menu. If negative, counts from th
+             * end, e.g. `insertMenu('My Menu', -1)` will insert the menu as the
+             * second-to-last one.
+             * @returns The new length of the top-level menus array
+             */
+            insertMenu(menuName, position) {
+                self.menus.splice((position < 0 ? self.menus.length : 0) + position, 0, {
+                    label: menuName,
+                    menuItems: [],
+                });
+                return self.menus.length;
+            },
+            /**
+             * #action
+             * Add a menu item to a top-level menu
+             * @param menuName - Name of the top-level menu to append to.
+             * @param menuItem - Menu item to append.
+             * @returns The new length of the menu
+             */
+            appendToMenu(menuName, menuItem) {
+                const menu = self.menus.find(m => m.label === menuName);
+                if (!menu) {
+                    self.menus.push({ label: menuName, menuItems: [menuItem] });
+                    return 1;
+                }
+                return menu.menuItems.push(menuItem);
+            },
+            /**
+             * #action
+             * Insert a menu item into a top-level menu
+             * @param menuName - Name of the top-level menu to insert into
+             * @param menuItem - Menu item to insert
+             * @param position - Position to insert menu item. If negative, counts
+             * from the end, e.g. `insertMenu('My Menu', -1)` will insert the menu as
+             * the second-to-last one.
+             * @returns The new length of the menu
+             */
+            insertInMenu(menuName, menuItem, position) {
+                const menu = self.menus.find(m => m.label === menuName);
+                if (!menu) {
+                    self.menus.push({ label: menuName, menuItems: [menuItem] });
+                    return 1;
+                }
+                const insertPosition = position < 0 ? menu.menuItems.length + position : position;
+                menu.menuItems.splice(insertPosition, 0, menuItem);
+                return menu.menuItems.length;
+            },
+            /**
+             * #action
+             * Add a menu item to a sub-menu
+             * @param menuPath - Path to the sub-menu to add to, starting with the
+             * top-level menu (e.g. `['File', 'Insert']`).
+             * @param menuItem - Menu item to append.
+             * @returns The new length of the sub-menu
+             */
+            appendToSubMenu(menuPath, menuItem) {
+                let topMenu = self.menus.find(m => m.label === menuPath[0]);
+                if (!topMenu) {
+                    const idx = this.appendMenu(menuPath[0]);
+                    topMenu = self.menus[idx - 1];
+                }
+                let { menuItems: subMenu } = topMenu;
+                const pathSoFar = [menuPath[0]];
+                menuPath.slice(1).forEach(menuName => {
+                    pathSoFar.push(menuName);
+                    let sm = subMenu.find(mi => 'label' in mi && mi.label === menuName);
+                    if (!sm) {
+                        const idx = subMenu.push({ label: menuName, subMenu: [] });
+                        sm = subMenu[idx - 1];
+                    }
+                    if (!('subMenu' in sm)) {
+                        throw new Error(`"${menuName}" in path "${pathSoFar}" is not a subMenu`);
+                    }
+                    subMenu = sm.subMenu;
+                });
+                return subMenu.push(menuItem);
+            },
+            /**
+             * #action
+             * Insert a menu item into a sub-menu
+             * @param menuPath - Path to the sub-menu to add to, starting with the
+             * top-level menu (e.g. `['File', 'Insert']`).
+             * @param menuItem - Menu item to insert.
+             * @param position - Position to insert menu item. If negative, counts
+             * from the end, e.g. `insertMenu('My Menu', -1)` will insert the menu as
+             * the second-to-last one.
+             * @returns The new length of the sub-menu
+             */
+            insertInSubMenu(menuPath, menuItem, position) {
+                let topMenu = self.menus.find(m => m.label === menuPath[0]);
+                if (!topMenu) {
+                    const idx = this.appendMenu(menuPath[0]);
+                    topMenu = self.menus[idx - 1];
+                }
+                let { menuItems: subMenu } = topMenu;
+                const pathSoFar = [menuPath[0]];
+                menuPath.slice(1).forEach(menuName => {
+                    pathSoFar.push(menuName);
+                    let sm = subMenu.find(mi => 'label' in mi && mi.label === menuName);
+                    if (!sm) {
+                        const idx = subMenu.push({ label: menuName, subMenu: [] });
+                        sm = subMenu[idx - 1];
+                    }
+                    if (!('subMenu' in sm)) {
+                        throw new Error(`"${menuName}" in path "${pathSoFar}" is not a subMenu`);
+                    }
+                    subMenu = sm.subMenu;
+                });
+                subMenu.splice(position, 0, menuItem);
+                return subMenu.length;
+            },
+        };
+    });
+}

package/esm/index.d.ts

@@ -0,0 +1,6 @@
+export * from './ui';
+export * from './HistoryManagement';
+export * from './JBrowseConfig';
+export * from './JBrowseModel';
+export * from './Assemblies';
+export * from './RootMenu';

package/esm/index.js

@@ -0,0 +1,6 @@
+export * from './ui';
+export * from './HistoryManagement';
+export * from './JBrowseConfig';
+export * from './JBrowseModel';
+export * from './Assemblies';
+export * from './RootMenu';

package/esm/ui/App/App.d.ts

@@ -0,0 +1,19 @@
+import React from 'react';
+import { SessionWithDrawerWidgets } from '@jbrowse/core/util';
+import { SnackbarMessage } from '@jbrowse/core/ui/SnackbarModel';
+import { MenuItem as JBMenuItem } from '@jbrowse/core/ui/Menu';
+type Props = {
+    HeaderButtons?: React.ReactElement;
+    session: SessionWithDrawerWidgets & {
+        savedSessionNames: string[];
+        menus: {
+            label: string;
+            menuItems: JBMenuItem[];
+        }[];
+        renameCurrentSession: (arg: string) => void;
+        snackbarMessages: SnackbarMessage[];
+        popSnackbarMessage: () => unknown;
+    };
+};
+declare const App: (props: Props) => React.JSX.Element;
+export { App };