@jbrowse/product-core 2.17.0 → 3.0.0

package/dist/RootModel/BaseRootModel.d.ts

@@ -1,38 +1,17 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-import { BaseAssemblyConfigSchema } from '@jbrowse/core/assemblyManager';
-import RpcManager from '@jbrowse/core/rpc/RpcManager';
-import { IAnyType, Instance, SnapshotIn } from 'mobx-state-tree';
 import TextSearchManager from '@jbrowse/core/TextSearch/TextSearchManager';
-/**
- * #stateModel BaseRootModel
- * #category root
- * factory function for the Base-level root model shared by all products
- */
+import RpcManager from '@jbrowse/core/rpc/RpcManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { BaseAssemblyConfigSchema } from '@jbrowse/core/assemblyManager';
+import type { IAnyType, Instance, SnapshotIn } from 'mobx-state-tree';
 export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType, sessionModelType, assemblyConfigSchema, }: {
     pluginManager: PluginManager;
     jbrowseModelType: IAnyType;
     sessionModelType: IAnyType;
     assemblyConfigSchema: BaseAssemblyConfigSchema;
 }): import("mobx-state-tree").IModelType<{
-    /**
-     * #property
-     * `jbrowse` is a mapping of the config.json into the in-memory state
-     * tree
-     */
     jbrowse: IAnyType;
-    /**
-     * #property
-     * `session` encompasses the currently active state of the app, including
-     * views open, tracks open in those views, etc.
-     */
     session: import("mobx-state-tree").IMaybe<IAnyType>;
-    /**
-     * #property
-     */
     sessionPath: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    /**
-     * #property
-     */
     assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
         assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
             configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
@@ -537,7 +516,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
         }, assemblyName: string | undefined, opts: {
-            signal?: AbortSignal;
+            stopToken?: string;
             sessionId: string;
         }): Promise<{
             [x: string]: string;
@@ -545,7 +524,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
         getReverseRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
         }, assemblyName: string | undefined, opts: {
-            signal?: AbortSignal;
+            stopToken?: string;
             sessionId: string;
         }): Promise<{
             [x: string]: string;
@@ -563,28 +542,12 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
     textSearchManager: TextSearchManager;
     pluginManager: PluginManager;
 } & {
-    /**
-     * #action
-     */
     setError(error: unknown): void;
-    /**
-     * #action
-     */
     setSession(sessionSnapshot?: SnapshotIn<IAnyType>): void;
-    /**
-     * #action
-     */
     setDefaultSession(): void;
-    /**
-     * #action
-     */
     setSessionPath(path: string): void;
-    /**
-     * #action
-     */
     renameCurrentSession(newName: string): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export type BaseRootModelType = ReturnType<typeof BaseRootModelFactory>;
 export type BaseRootModel = Instance<BaseRootModelType>;
-/** Type guard for checking if something is a JB root model */
 export declare function isRootModel(thing: unknown): thing is BaseRootModelType;

package/dist/RootModel/BaseRootModel.js

@@ -5,37 +5,16 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.BaseRootModelFactory = BaseRootModelFactory;
 exports.isRootModel = isRootModel;
+const TextSearchManager_1 = __importDefault(require("@jbrowse/core/TextSearch/TextSearchManager"));
 const assemblyManager_1 = __importDefault(require("@jbrowse/core/assemblyManager"));
 const RpcManager_1 = __importDefault(require("@jbrowse/core/rpc/RpcManager"));
 const mobx_state_tree_1 = require("mobx-state-tree");
-const TextSearchManager_1 = __importDefault(require("@jbrowse/core/TextSearch/TextSearchManager"));
-/**
- * #stateModel BaseRootModel
- * #category root
- * factory function for the Base-level root model shared by all products
- */
 function BaseRootModelFactory({ pluginManager, jbrowseModelType, sessionModelType, assemblyConfigSchema, }) {
     return mobx_state_tree_1.types
         .model('BaseRootModel', {
-        /**
-         * #property
-         * `jbrowse` is a mapping of the config.json into the in-memory state
-         * tree
-         */
         jbrowse: jbrowseModelType,
-        /**
-         * #property
-         * `session` encompasses the currently active state of the app, including
-         * views open, tracks open in those views, etc.
-         */
         session: mobx_state_tree_1.types.maybe(sessionModelType),
-        /**
-         * #property
-         */
         sessionPath: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.string, ''),
-        /**
-         * #property
-         */
         assemblyManager: mobx_state_tree_1.types.optional((0, assemblyManager_1.default)(assemblyConfigSchema, pluginManager), {}),
     })
         .volatile(self => ({
@@ -48,43 +27,28 @@ function BaseRootModelFactory({ pluginManager, jbrowseModelType, sessionModelTyp
         pluginManager,
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         setError(error) {
             self.error = error;
         },
-        /**
-         * #action
-         */
         setSession(sessionSnapshot) {
             self.session = (0, mobx_state_tree_1.cast)(sessionSnapshot);
         },
-        /**
-         * #action
-         */
         setDefaultSession() {
             this.setSession(self.jbrowse.defaultSession);
         },
-        /**
-         * #action
-         */
         setSessionPath(path) {
             self.sessionPath = path;
         },
-        /**
-         * #action
-         */
         renameCurrentSession(newName) {
             if (self.session) {
-                const snapshot = JSON.parse(JSON.stringify((0, mobx_state_tree_1.getSnapshot)(self.session)));
-                snapshot.name = newName;
-                this.setSession(snapshot);
+                this.setSession({
+                    ...(0, mobx_state_tree_1.getSnapshot)(self.session),
+                    name: newName,
+                });
             }
         },
     }));
 }
-/** Type guard for checking if something is a JB root model */
 function isRootModel(thing) {
     return ((0, mobx_state_tree_1.isStateTreeNode)(thing) &&
         'session' in thing &&

package/dist/RootModel/FormatAbout.d.ts

@@ -1,20 +1,10 @@
-/**
- * #config FormatAbout
- * generally exists on the config.json or root config as configuration.formatAbout
- */
 export declare function FormatAboutConfigSchemaFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot configuration.formatAbout.config
-     */
     config: {
         type: string;
         description: string;
         defaultValue: {};
         contextVariable: string[];
     };
-    /**
-     * #slot configuration.formatAbout.hideUris
-     */
     hideUris: {
         type: string;
         defaultValue: boolean;

package/dist/RootModel/FormatAbout.js

@@ -2,24 +2,14 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.FormatAboutConfigSchemaFactory = FormatAboutConfigSchemaFactory;
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config FormatAbout
- * generally exists on the config.json or root config as configuration.formatAbout
- */
 function FormatAboutConfigSchemaFactory() {
     return (0, configuration_1.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,

package/dist/RootModel/FormatDetails.d.ts

@@ -1,38 +1,21 @@
-/**
- * #config FormatDetails
- * generally exists on the tracks in the config.json or as a 'session' config as
- * configuration.formatDetails
- */
 export declare function FormatDetailsConfigSchemaFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot configuration.formatDetails.feature
-     */
     feature: {
         type: string;
         description: string;
         defaultValue: {};
         contextVariable: string[];
     };
-    /**
-     * #slot configuration.formatDetails.subfeatures
-     */
     subfeatures: {
         type: string;
         description: string;
         defaultValue: {};
         contextVariable: string[];
     };
-    /**
-     * #slot configuration.formatDetails.depth
-     */
     depth: {
         type: string;
         defaultValue: number;
         description: string;
     };
-    /**
-     * #slot configuration.formatDetails.maxDepth
-     */
     maxDepth: {
         type: string;
         defaultValue: number;

package/dist/RootModel/FormatDetails.js

@@ -2,42 +2,25 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.FormatDetailsConfigSchemaFactory = FormatDetailsConfigSchemaFactory;
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config FormatDetails
- * generally exists on the tracks in the config.json or as a 'session' config as
- * configuration.formatDetails
- */
 function FormatDetailsConfigSchemaFactory() {
     return (0, configuration_1.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 the formatDetails->subfeatures callback on subfeatures (used for example to only apply the callback to the first layer of subfeatures)',
         },
-        /**
-         * #slot configuration.formatDetails.maxDepth
-         */
         maxDepth: {
             type: 'number',
             defaultValue: 10000,

package/dist/RootModel/HierarchicalConfig.d.ts

@@ -1,42 +1,23 @@
-/**
- * #config HierarchicalConfigSchema
- * generally exists on the config.json or root config as configuration.hierarchical
- */
 export declare function HierarchicalConfigSchemaFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     sort: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        /**
-         * #slot configuration.hierarchical.sort.trackNames
-         */
         trackNames: {
             type: string;
             defaultValue: boolean;
         };
-        /**
-         * #slot configuration.hierarchical.sort.categories
-         */
         categories: {
             type: string;
             defaultValue: boolean;
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
     defaultCollapsed: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        /**
-         * #slot configuration.hierarchical.defaultCollapsed.categoryNames
-         */
         categoryNames: {
             type: string;
             defaultValue: never[];
         };
-        /**
-         * #slot configuration.hierarchical.defaultCollapsed.topLevelCategories
-         */
         topLevelCategories: {
             type: string;
             defaultValue: boolean;
         };
-        /**
-         * #slot configuration.hierarchical.defaultCollapsed.subCategories
-         */
         subCategories: {
             type: string;
             defaultValue: boolean;

package/dist/RootModel/HierarchicalConfig.js

@@ -2,46 +2,27 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.HierarchicalConfigSchemaFactory = HierarchicalConfigSchemaFactory;
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config HierarchicalConfigSchema
- * generally exists on the config.json or root config as configuration.hierarchical
- */
 function HierarchicalConfigSchemaFactory() {
     return (0, configuration_1.ConfigurationSchema)('hierarchical', {
         sort: (0, configuration_1.ConfigurationSchema)('hierarchicalSort', {
-            /**
-             * #slot configuration.hierarchical.sort.trackNames
-             */
             trackNames: {
                 type: 'boolean',
                 defaultValue: false,
             },
-            /**
-             * #slot configuration.hierarchical.sort.categories
-             */
             categories: {
                 type: 'boolean',
                 defaultValue: false,
             },
         }),
         defaultCollapsed: (0, configuration_1.ConfigurationSchema)('defaultCollapsed', {
-            /**
-             * #slot configuration.hierarchical.defaultCollapsed.categoryNames
-             */
             categoryNames: {
                 type: 'stringArray',
                 defaultValue: [],
             },
-            /**
-             * #slot configuration.hierarchical.defaultCollapsed.topLevelCategories
-             */
             topLevelCategories: {
                 type: 'boolean',
                 defaultValue: false,
             },
-            /**
-             * #slot configuration.hierarchical.defaultCollapsed.subCategories
-             */
             subCategories: {
                 type: 'boolean',
                 defaultValue: false,

package/dist/RootModel/InternetAccounts.d.ts

@@ -1,28 +1,12 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { UriLocation } from '@jbrowse/core/util';
-import { Instance } from 'mobx-state-tree';
-/**
- * #stateModel InternetAccountsMixin
- * #category root
- */
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { UriLocation } from '@jbrowse/core/util';
+import type { Instance } from 'mobx-state-tree';
 export declare function InternetAccountsRootModelMixin(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
-    /**
-     * #property
-     */
     internetAccounts: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
 }, {
-    /**
-     * #action
-     */
     initializeInternetAccount(internetAccountConfig: AnyConfigurationModel, initialSnapshot?: {}): any;
-    /**
-     * #action
-     */
     createEphemeralInternetAccount(internetAccountId: string, initialSnapshot: Record<string, unknown>, url: string): any;
-    /**
-     * #action
-     */
     findAppropriateInternetAccount(location: UriLocation): any;
 } & {
     afterCreate(): void;

package/dist/RootModel/InternetAccounts.js

@@ -3,22 +3,12 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.InternetAccountsRootModelMixin = InternetAccountsRootModelMixin;
 const mobx_1 = require("mobx");
 const mobx_state_tree_1 = require("mobx-state-tree");
-/**
- * #stateModel InternetAccountsMixin
- * #category root
- */
 function InternetAccountsRootModelMixin(pluginManager) {
     return mobx_state_tree_1.types
         .model({
-        /**
-         * #property
-         */
         internetAccounts: mobx_state_tree_1.types.array(pluginManager.pluggableMstType('internet account', 'stateModel')),
     })
         .actions(self => ({
-        /**
-         * #action
-         */
         initializeInternetAccount(internetAccountConfig, initialSnapshot = {}) {
             const internetAccountType = pluginManager.getInternetAccountType(internetAccountConfig.type);
             if (!internetAccountType) {
@@ -31,16 +21,12 @@ function InternetAccountsRootModelMixin(pluginManager) {
             });
             return self.internetAccounts[length - 1];
         },
-        /**
-         * #action
-         */
         createEphemeralInternetAccount(internetAccountId, initialSnapshot, url) {
             let hostUri;
             try {
                 hostUri = new URL(url).origin;
             }
             catch (e) {
-                // ignore
             }
             const internetAccountSplit = internetAccountId.split('-');
             const configuration = {
@@ -59,11 +45,7 @@ function InternetAccountsRootModelMixin(pluginManager) {
             self.internetAccounts.push(internetAccount);
             return internetAccount;
         },
-        /**
-         * #action
-         */
         findAppropriateInternetAccount(location) {
-            // find the existing account selected from menu
             const selectedId = location.internetAccountId;
             if (selectedId) {
                 const selectedAccount = self.internetAccounts.find(account => {
@@ -73,14 +55,12 @@ function InternetAccountsRootModelMixin(pluginManager) {
                     return selectedAccount;
                 }
             }
-            // if no existing account or not found, try to find working account
             for (const account of self.internetAccounts) {
                 const handleResult = account.handlesLocation(location);
                 if (handleResult) {
                     return account;
                 }
             }
-            // if still no existing account, create ephemeral config to use
             return selectedId
                 ? this.createEphemeralInternetAccount(selectedId, {}, location.uri)
                 : null;

package/dist/Session/BaseSession.d.ts

@@ -1,122 +1,31 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-import { IAnyStateTreeNode, Instance } from 'mobx-state-tree';
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import type { BaseRootModelType } from '../RootModel/BaseRootModel';
-/**
- * #stateModel BaseSessionModel
- *
- * base session shared by all JBrowse products. Be careful what you include
- * here, everything will use it.
- */
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { BaseAssemblyConfigSchema } from '@jbrowse/core/assemblyManager';
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import type { IAnyStateTreeNode, Instance } from 'mobx-state-tree';
 export declare function BaseSessionModel<ROOT_MODEL_TYPE extends BaseRootModelType, JB_CONFIG_SCHEMA extends AnyConfigurationSchemaType>(_pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     name: import("mobx-state-tree").ISimpleType<string>;
     margin: import("mobx-state-tree").IType<number | undefined, number, number>;
 }, {
-    /**
-     * #volatile
-     * this is the globally "selected" object. can be anything. code that
-     * wants to deal with this should examine it to see what kind of thing it
-     * is.
-     */
     selection: unknown;
-    /**
-     * #volatile
-     * this is the globally "hovered" object. can be anything. code that
-     * wants to deal with this should examine it to see what kind of thing it
-     * is.
-     */
     hovered: unknown;
 } & {
-    /**
-     * #getter
-     */
     readonly root: import("mobx-state-tree").TypeOrStateTreeNodeToStateTreeNode<ROOT_MODEL_TYPE>;
 } & {
-    /**
-     * #getter
-     */
     readonly jbrowse: any;
-    /**
-     * #getter
-     */
     readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-    /**
-     * #getter
-     */
     readonly configuration: Instance<JB_CONFIG_SCHEMA>;
-    /**
-     * #getter
-     */
     readonly adminMode: boolean;
-    /**
-     * #getter
-     */
     readonly textSearchManager: import("@jbrowse/core/util").TextSearchManager;
 } & {
-    /**
-     * #getter
-     */
-    readonly assemblies: ({
-        [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<AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
-    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        aliases: {
-            type: string;
-            defaultValue: never[];
-            description: string;
-        };
-        sequence: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-        refNameColors: {
-            type: string;
-            defaultValue: never[];
-            description: string;
-        };
-        refNameAliases: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-            adapter: import("mobx-state-tree").IAnyModelType;
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-        cytobands: import("@jbrowse/core/configuration/configurationSchema" /**
-         * #getter
-         */).ConfigurationSchemaType<{
-            adapter: import("mobx-state-tree" /**
-             * #getter
-             */).IAnyModelType;
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-        displayName: {
-            type: string;
-            defaultValue: string;
-            description: string;
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name">>>)[];
+    readonly assemblies: Instance<BaseAssemblyConfigSchema>[];
 } & {
-    /**
-     * #action
-     * set the global selection, i.e. the globally-selected object. can be a
-     * feature, a view, just about anything
-     */
     setSelection(thing: unknown): void;
-    /**
-     * #action
-     * clears the global selection
-     */
     clearSelection(): void;
-    /**
-     * #action
-     */
     setHovered(thing: unknown): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-/** Session mixin MST type for the most basic session */
 export type BaseSessionType = ReturnType<typeof BaseSessionModel>;
-/** Instance of the most basic possible session */
 export type BaseSession = Instance<BaseSessionType>;
-/** Type guard for BaseSession */
 export declare function isBaseSession(thing: IAnyStateTreeNode): thing is BaseSession;
-/** Type guard for whether a thing is JBrowse session */
 export declare function isSession(thing: unknown): thing is BaseSession;