@jbrowse/core 2.1.3 → 2.1.5

package/BaseFeatureWidget/types.d.ts

@@ -1,9 +1,9 @@
 import React from 'react';
 import { IAnyStateTreeNode } from 'mobx-state-tree';
-import { SimpleFeatureSerialized } from '../util/simpleFeature';
+import { SimpleFeatureSerializedNoId } from '../util/simpleFeature';
 import { AbstractViewModel } from '../util';
 export interface BaseProps extends BaseCardProps {
-    feature: SimpleFeatureSerialized;
+    feature: SimpleFeatureSerializedNoId;
     formatter?: (val: unknown, key: string) => React.ReactNode;
     descriptions?: Record<string, React.ReactNode>;
     model?: IAnyStateTreeNode & {

package/BaseFeatureWidget/util.d.ts

@@ -11,8 +11,8 @@ export interface ParentFeat extends Feat {
 }
 export interface SeqState {
     seq: string;
-    upstream: string;
-    downstream: string;
+    upstream?: string;
+    downstream?: string;
 }
 export declare function stitch(subfeats: Feat[], sequence: string): string;
 export declare function dedupe(list: Feat[]): Feat[];

package/PluginManager.d.ts

@@ -279,8 +279,8 @@ export default class PluginManager {
     addRpcMethod(cb: (pm: PluginManager) => RpcMethodType): this;
     addInternetAccountType(cb: (pm: PluginManager) => InternetAccountType): this;
     addAddTrackWorkflowType(cb: (pm: PluginManager) => AddTrackWorkflowType): this;
-    addToExtensionPoint<T>(extensionPointName: string, callback: (extendee: T) => T): void;
-    evaluateExtensionPoint(extensionPointName: string, extendee: unknown): unknown;
-    evaluateAsyncExtensionPoint(extensionPointName: string, extendee: unknown): Promise<unknown>;
+    addToExtensionPoint<T>(extensionPointName: string, callback: (extendee: T, props: Record<string, unknown>) => T): void;
+    evaluateExtensionPoint(extensionPointName: string, extendee: unknown, props?: Record<string, unknown>): unknown;
+    evaluateAsyncExtensionPoint(extensionPointName: string, extendee: unknown, props?: Record<string, unknown>): Promise<unknown>;
 }
 export {};

package/PluginManager.js

@@ -329,7 +329,9 @@ class PluginManager {
             const displays = this.getElementTypesInGroup('display');
             displays.forEach(display => {
                 // view may have already added the displayType in its callback
-                if (display.viewType === newView.name &&
+                // see ViewType for description of extendedName
+                if ((display.viewType === newView.name ||
+                    display.viewType === newView.extendedName) &&
                     !newView.displayTypes.includes(display)) {
                     newView.addDisplayType(display);
                 }
@@ -361,13 +363,13 @@ class PluginManager {
         }
         callbacks.push(callback);
     }
-    evaluateExtensionPoint(extensionPointName, extendee) {
+    evaluateExtensionPoint(extensionPointName, extendee, props) {
         const callbacks = this.extensionPoints.get(extensionPointName);
         let accumulator = extendee;
         if (callbacks) {
             for (const callback of callbacks) {
                 try {
-                    accumulator = callback(accumulator);
+                    accumulator = callback(accumulator, props);
                 }
                 catch (error) {
                     console.error(error);
@@ -376,13 +378,13 @@ class PluginManager {
         }
         return accumulator;
     }
-    async evaluateAsyncExtensionPoint(extensionPointName, extendee) {
+    async evaluateAsyncExtensionPoint(extensionPointName, extendee, props) {
         const callbacks = this.extensionPoints.get(extensionPointName);
         let accumulator = extendee;
         if (callbacks) {
             for (const callback of callbacks) {
                 try {
-                    accumulator = await callback(accumulator);
+                    accumulator = await callback(accumulator, props);
                 }
                 catch (error) {
                     console.error(error);

package/assemblyManager/assemblyManager.js

@@ -24,12 +24,13 @@ function assemblyManagerFactory(assemblyConfigType, pluginManager) {
         get assemblyList() {
             // name is the explicit identifier and can be accessed without getConf,
             // hence the union with {name:string}
-            const { jbrowse: { assemblies }, session: { sessionAssemblies = [] } = {},
+            const { jbrowse: { assemblies }, session: { sessionAssemblies = [], temporaryAssemblies = [] } = {},
             // eslint-disable-next-line @typescript-eslint/no-explicit-any
              } = (0, mobx_state_tree_1.getParent)(self);
             return [
                 ...assemblies,
                 ...sessionAssemblies,
+                ...temporaryAssemblies,
             ];
         },
         get rpcManager() {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "2.1.3",
+  "version": "2.1.5",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -73,5 +73,5 @@
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "ebd548ceb52adb36cf6ab437082b5b5feac1338e"
+  "gitHead": "bc5253ecdddeceeb999fffebf6dc6cf5f444e1c9"
 }

package/pluggableElementTypes/ViewType.d.ts

@@ -11,10 +11,12 @@ export default class ViewType extends PluggableElementBase {
     ReactComponent: ViewReactComponent;
     stateModel: IAnyModelType;
     displayTypes: DisplayType[];
+    extendedName?: string;
     constructor(stuff: {
         name: string;
         ReactComponent: ViewReactComponent;
         stateModel: IAnyModelType;
+        extendedName?: string;
     });
     addDisplayType(display: DisplayType): void;
 }

package/pluggableElementTypes/ViewType.js

@@ -10,6 +10,7 @@ class ViewType extends PluggableElementBase_1.default {
         this.displayTypes = [];
         this.ReactComponent = stuff.ReactComponent;
         this.stateModel = stuff.stateModel;
+        this.extendedName = stuff.extendedName;
         if (!this.ReactComponent) {
             throw new Error(`no ReactComponent defined for view ${this.name}`);
         }

package/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts

@@ -1,11 +1,13 @@
-declare function _default(pluginManager: any): import("mobx-state-tree").IModelType<{
+import { AnyConfigurationModel } from '../../configuration';
+import PluginManager from '../../PluginManager';
+declare const _default: (pluginManager: PluginManager) => import("mobx-state-tree").IModelType<{
     name: import("mobx-state-tree").ISimpleType<string>;
-    tracks: import("mobx-state-tree").IArrayType<any>;
+    tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
 }, {
     afterAttach(): void;
-    addTrackConf(trackConf: any): any;
-    addTrackConfs(trackConfs: any): any[];
-    setTrackConfs(trackConfs: any): import("mobx-state-tree").IMSTArray<any> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<any>>;
+    addTrackConf(trackConf: AnyConfigurationModel): any;
+    addTrackConfs(trackConfs: AnyConfigurationModel[]): any[];
+    setTrackConfs(trackConfs: AnyConfigurationModel[]): 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>>;
     clear(): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export default _default;

package/pluggableElementTypes/models/BaseConnectionModelFactory.js

@@ -1,7 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const mobx_state_tree_1 = require("mobx-state-tree");
-exports.default = pluginManager => {
+exports.default = (pluginManager) => {
     return mobx_state_tree_1.types
         .model('Connection', {
         name: mobx_state_tree_1.types.identifier,
@@ -10,6 +10,7 @@ exports.default = pluginManager => {
         .actions(self => ({
         afterAttach() {
             if (!self.tracks.length) {
+                // @ts-ignore
                 self.connect(self.configuration);
             }
         },
@@ -22,7 +23,7 @@ exports.default = pluginManager => {
             return self.tracks.slice(length - 1 - trackConfs.length, length - 1);
         },
         setTrackConfs(trackConfs) {
-            self.tracks = trackConfs;
+            self.tracks = (0, mobx_state_tree_1.cast)(trackConfs);
             return self.tracks;
         },
         clear() { },