@jbrowse/core 2.1.5 → 2.1.6

package/assemblyManager/assemblyManager.d.ts

@@ -44,27 +44,20 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         }): void;
         setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
-        setRefNameAliases(refNameAliases: {
+        setRefNameAliases(aliases: {
             [x: string]: string;
-        }, lowerCaseRefNameAliases: {
+        }, lowerCase: {
             [x: string]: string;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
         afterAttach(): void;
     } & {
-        getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<{
-            forwardMap: {
-                [key: string]: string;
-            };
-            reverseMap: {
-                [key: string]: string;
-            };
-        }>;
+        getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<import("./assembly").RefNameMap>;
         getRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
-            [key: string]: string;
+            [x: string]: string;
         }>;
         getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
-            [key: string]: string;
+            [x: string]: string;
         }>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
 }, {
@@ -111,27 +104,20 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         }): void;
         setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
-        setRefNameAliases(refNameAliases: {
+        setRefNameAliases(aliases: {
             [x: string]: string;
-        }, lowerCaseRefNameAliases: {
+        }, lowerCase: {
             [x: string]: string;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
         afterAttach(): void;
     } & {
-        getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<{
-            forwardMap: {
-                [key: string]: string;
-            };
-            reverseMap: {
-                [key: string]: string;
-            };
-        }>;
+        getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<import("./assembly").RefNameMap>;
         getRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
-            [key: string]: string;
+            [x: string]: string;
         }>;
         getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
-            [key: string]: string;
+            [x: string]: string;
         }>;
     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
         configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
@@ -176,27 +162,20 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         }): void;
         setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
-        setRefNameAliases(refNameAliases: {
+        setRefNameAliases(aliases: {
             [x: string]: string;
-        }, lowerCaseRefNameAliases: {
+        }, lowerCase: {
             [x: string]: string;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
         afterAttach(): void;
     } & {
-        getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<{
-            forwardMap: {
-                [key: string]: string;
-            };
-            reverseMap: {
-                [key: string]: string;
-            };
-        }>;
+        getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<import("./assembly").RefNameMap>;
         getRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
-            [key: string]: string;
+            [x: string]: string;
         }>;
         getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
-            [key: string]: string;
+            [x: string]: string;
         }>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
     readonly assemblyNamesList: string[];
@@ -254,27 +233,20 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         }): void;
         setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
-        setRefNameAliases(refNameAliases: {
+        setRefNameAliases(aliases: {
             [x: string]: string;
-        }, lowerCaseRefNameAliases: {
+        }, lowerCase: {
             [x: string]: string;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
         afterAttach(): void;
     } & {
-        getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<{
-            forwardMap: {
-                [key: string]: string;
-            };
-            reverseMap: {
-                [key: string]: string;
-            };
-        }>;
+        getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<import("./assembly").RefNameMap>;
         getRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
-            [key: string]: string;
+            [x: string]: string;
         }>;
         getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
-            [key: string]: string;
+            [x: string]: string;
         }>;
     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
         configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
@@ -319,40 +291,33 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         }): void;
         setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
-        setRefNameAliases(refNameAliases: {
+        setRefNameAliases(aliases: {
             [x: string]: string;
-        }, lowerCaseRefNameAliases: {
+        }, lowerCase: {
             [x: string]: string;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
         afterAttach(): void;
     } & {
-        getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<{
-            forwardMap: {
-                [key: string]: string;
-            };
-            reverseMap: {
-                [key: string]: string;
-            };
-        }>;
+        getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<import("./assembly").RefNameMap>;
         getRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
-            [key: string]: string;
+            [x: string]: string;
         }>;
         getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
-            [key: string]: string;
+            [x: string]: string;
         }>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
     getRefNameMapForAdapter(adapterConf: unknown, assemblyName: string | undefined, opts: {
         signal?: AbortSignal;
         sessionId: string;
     }): Promise<{
-        [key: string]: string;
+        [x: string]: string;
     } | undefined>;
     getReverseRefNameMapForAdapter(adapterConf: unknown, assemblyName: string | undefined, opts: {
         signal?: AbortSignal;
         sessionId: string;
     }): Promise<{
-        [key: string]: string;
+        [x: string]: string;
     } | undefined>;
     isValidRefName(refName: string, assemblyName?: string): boolean;
 } & {
@@ -399,27 +364,20 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         }): void;
         setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
-        setRefNameAliases(refNameAliases: {
+        setRefNameAliases(aliases: {
             [x: string]: string;
-        }, lowerCaseRefNameAliases: {
+        }, lowerCase: {
             [x: string]: string;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
         afterAttach(): void;
     } & {
-        getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<{
-            forwardMap: {
-                [key: string]: string;
-            };
-            reverseMap: {
-                [key: string]: string;
-            };
-        }>;
+        getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<import("./assembly").RefNameMap>;
         getRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
-            [key: string]: string;
+            [x: string]: string;
         }>;
         getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
-            [key: string]: string;
+            [x: string]: string;
         }>;
     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
         configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
@@ -464,27 +422,20 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         }): void;
         setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
-        setRefNameAliases(refNameAliases: {
+        setRefNameAliases(aliases: {
             [x: string]: string;
-        }, lowerCaseRefNameAliases: {
+        }, lowerCase: {
             [x: string]: string;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
         afterAttach(): void;
     } & {
-        getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<{
-            forwardMap: {
-                [key: string]: string;
-            };
-            reverseMap: {
-                [key: string]: string;
-            };
-        }>;
+        getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<import("./assembly").RefNameMap>;
         getRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
-            [key: string]: string;
+            [x: string]: string;
         }>;
         getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
-            [key: string]: string;
+            [x: string]: string;
         }>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>): void;
     afterAttach(): void;

package/configuration/configurationSlot.js

@@ -4,6 +4,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const mobx_state_tree_1 = require("mobx-state-tree");
 const jexlStrings_1 = require("../util/jexlStrings");
 const mst_1 = require("../util/types/mst");
+const util_1 = require("../util");
 function isValidColorString( /* str */) {
     // TODO: check all the crazy cases for whether it's a valid HTML/CSS color string
     return true;
@@ -176,7 +177,7 @@ function ConfigSlot(slotName, { description = '', model, type, defaultValue, con
         get expr() {
             if (self.isCallback) {
                 // compile as jexl function
-                const { pluginManager } = (0, mobx_state_tree_1.getEnv)(self);
+                const { pluginManager } = (0, util_1.getEnv)(self);
                 if (!pluginManager && typeof jest === 'undefined') {
                     console.warn('no pluginManager detected on config env (if you dynamically instantiate a config, for example in renderProps for your display model, check that you add the env argument)');
                 }

package/data_adapters/CytobandAdapter.js

@@ -23,7 +23,7 @@ class CytobandAdapter extends BaseAdapter_1.BaseAdapter {
         }
         const data = await (0, io_1.openLocation)(loc).readFile('utf8');
         return data
-            .split('\n')
+            .split(/\n|\r\n|\r/)
             .filter(f => !!f.trim())
             .map(line => {
             const [refName, start, end, name, type] = line.split('\t');

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "2.1.5",
+  "version": "2.1.6",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -52,8 +52,8 @@
     "material-ui-popup-state": "^3.0.0",
     "rbush": "^3.0.1",
     "react-error-boundary": "^3.0.0",
-    "react-intersection-observer": "^9.3.0",
     "react-use-measure": "^2.1.1",
+    "serialize-error": "^8.0.0",
     "shortid": "^2.2.13",
     "svg-path-generator": "^1.1.0"
   },
@@ -73,5 +73,5 @@
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "bc5253ecdddeceeb999fffebf6dc6cf5f444e1c9"
+  "gitHead": "df810d2a4f057adcd8f5345d54972508fba007a7"
 }

package/pluggableElementTypes/models/BaseDisplayModel.d.ts

@@ -56,7 +56,7 @@ export declare const BaseDisplay: import("mobx-state-tree").IModelType<{
      * the pluggable element type object for this display's
      * renderer
      */
-    readonly rendererType: any;
+    readonly rendererType: import("..").RendererType;
     /**
      * if a display-level message should be displayed instead,
      * make this return a react component

package/pluggableElementTypes/models/BaseDisplayModel.js

@@ -5,6 +5,7 @@ exports.BaseDisplay = void 0;
 const mobx_state_tree_1 = require("mobx-state-tree");
 const configuration_1 = require("../../configuration");
 const tracks_1 = require("../../util/tracks");
+const util_1 = require("../../util");
 const mst_1 = require("../../util/types/mst");
 exports.BaseDisplay = mobx_state_tree_1.types
     .model('BaseDisplay', {
@@ -18,7 +19,7 @@ exports.BaseDisplay = mobx_state_tree_1.types
 }))
     .views(self => ({
     get RenderingComponent() {
-        const { pluginManager } = (0, mobx_state_tree_1.getEnv)(self);
+        const { pluginManager } = (0, util_1.getEnv)(self);
         const displayType = pluginManager.getDisplayType(self.type);
         return displayType.ReactComponent;
     },
@@ -54,7 +55,7 @@ exports.BaseDisplay = mobx_state_tree_1.types
      * renderer
      */
     get rendererType() {
-        const { pluginManager } = (0, mobx_state_tree_1.getEnv)(self);
+        const { pluginManager } = (0, util_1.getEnv)(self);
         const RendererType = pluginManager.getRendererType(self.rendererTypeName);
         if (!RendererType) {
             throw new Error(`renderer "${self.rendererTypeName}" not found`);

package/pluggableElementTypes/models/BaseTrackModel.d.ts

@@ -14,7 +14,7 @@ export declare function createBaseTrackModel(pluginManager: PluginManager, track
     /**
      * the PluggableElementType for the currently defined adapter
      */
-    readonly adapterType: any;
+    readonly adapterType: import("..").AdapterType;
     readonly viewMenuActions: MenuItem[];
     readonly canConfigure: any;
 } & {

package/pluggableElementTypes/models/BaseTrackModel.js

@@ -35,7 +35,7 @@ function createBaseTrackModel(pluginManager, trackType, baseTrackConfig) {
          */
         get adapterType() {
             const adapterConfig = (0, configuration_1.getConf)(self, 'adapter');
-            const { pluginManager: pm } = (0, mobx_state_tree_1.getEnv)(self);
+            const { pluginManager: pm } = (0, util_1.getEnv)(self);
             if (!adapterConfig) {
                 throw new Error(`no adapter configuration provided for ${self.type}`);
             }

package/pluggableElementTypes/models/baseTrackConfig.js

@@ -65,6 +65,18 @@ function createBaseTrackConfig(pluginManager) {
                 description: 'depth to iterate on subfeatures',
             },
         }),
+        formatAbout: (0, configuration_1.ConfigurationSchema)('FormatAbout', {
+            config: {
+                type: 'frozen',
+                description: 'formats configuration object in about dialog',
+                defaultValue: {},
+                contextVariable: ['config'],
+            },
+            hideUris: {
+                type: 'boolean',
+                defaultValue: false,
+            },
+        }),
     }, {
         preProcessSnapshot: s => {
             const snap = JSON.parse(JSON.stringify(s));
@@ -90,16 +102,16 @@ function createBaseTrackConfig(pluginManager) {
         explicitIdentifier: 'trackId',
         explicitlyTyped: true,
         actions: (self) => ({
-            addDisplayConf(displayConf) {
-                const { type } = displayConf;
+            addDisplayConf(conf) {
+                const { type } = conf;
                 if (!type) {
                     throw new Error(`unknown display type ${type}`);
                 }
-                const display = self.displays.find((d) => d && d.displayId === displayConf.displayId);
+                const display = self.displays.find((d) => d && d.displayId === conf.displayId);
                 if (display) {
                     return display;
                 }
-                const length = self.displays.push(displayConf);
+                const length = self.displays.push(conf);
                 return self.displays[length - 1];
             },
         }),

package/rpc/RpcManager.d.ts

@@ -1,7 +1,7 @@
 import PluginManager from '../PluginManager';
+import { AnyConfigurationModel } from '../configuration';
 import WebWorkerRpcDriver from './WebWorkerRpcDriver';
 import MainThreadRpcDriver from './MainThreadRpcDriver';
-import { AnyConfigurationModel } from '../configuration/configurationSchema';
 declare type DriverClass = WebWorkerRpcDriver | MainThreadRpcDriver;
 declare type BackendConfigurations = {
     WebWorkerRpcDriver?: Omit<ConstructorParameters<typeof WebWorkerRpcDriver>[0], 'config'>;

package/rpc/RpcManager.js

@@ -40,7 +40,10 @@ class RpcManager {
             if (!backendConfiguration) {
                 throw new Error(`requested RPC driver "${backendName}" is missing config`);
             }
-            newDriver = new WebWorkerRpcDriver_1.default({ ...backendConfiguration, config }, { plugins: this.pluginManager.runtimePluginDefinitions });
+            newDriver = new WebWorkerRpcDriver_1.default({ ...backendConfiguration, config }, {
+                plugins: this.pluginManager.runtimePluginDefinitions,
+                windowHref: window.location.href,
+            });
         }
         else {
             throw new Error(`requested RPC driver "${backendName}" is not installed`);

package/rpc/WebWorkerRpcDriver.d.ts

@@ -14,11 +14,13 @@ declare class WebWorkerHandle extends Rpc.Client {
 export default class WebWorkerRpcDriver extends BaseRpcDriver {
     workerBootConfiguration: {
         plugins: PluginDefinition[];
+        windowHref: string;
     };
     name: string;
     makeWorkerInstance: () => Worker;
     constructor(args: WebWorkerRpcDriverConstructorArgs, workerBootConfiguration: {
         plugins: PluginDefinition[];
+        windowHref: string;
     });
     makeWorker(): Promise<WebWorkerHandle>;
 }

package/rpc/WebWorkerRpcDriver.js

@@ -5,6 +5,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const librpc_web_mod_1 = __importDefault(require("librpc-web-mod"));
 const shortid_1 = __importDefault(require("shortid"));
+const serialize_error_1 = require("serialize-error");
+// locals
 const BaseRpcDriver_1 = __importDefault(require("./BaseRpcDriver"));
 class WebWorkerHandle extends librpc_web_mod_1.default.Client {
     destroy() {
@@ -14,9 +16,7 @@ class WebWorkerHandle extends librpc_web_mod_1.default.Client {
         const { statusCallback, rpcDriverClassName } = opts;
         const channel = `message-${shortid_1.default.generate()}`;
         const listener = (message) => {
-            if (statusCallback) {
-                statusCallback(message);
-            }
+            statusCallback === null || statusCallback === void 0 ? void 0 : statusCallback(message);
         };
         this.on(channel, listener);
         const result = await super.call(functionName, { ...args, channel, rpcDriverClassName }, opts);
@@ -37,21 +37,31 @@ class WebWorkerRpcDriver extends BaseRpcDriver_1.default {
         // load balancing rather than using librpc's builtin round-robin
         const instance = this.makeWorkerInstance();
         const worker = new WebWorkerHandle({ workers: [instance] });
+        const isSafari = /^((?!chrome|android).)*safari/i.test(navigator.userAgent);
+        if (isSafari) {
+            // xref https://github.com/GMOD/jbrowse-components/issues/3245
+            // eslint-disable-next-line no-console
+            console.log('console logging the webworker handle avoids the track going into an infinite loading state, this is a hacky workaround for safari', instance);
+        }
         // send the worker its boot configuration using info from the pluginManager
-        const p = new Promise((resolve, reject) => {
-            worker.workers[0].onmessage = e => {
-                if (e.data === 'ready') {
+        return new Promise((resolve, reject) => {
+            const listener = (e) => {
+                if (e.data.message === 'ready') {
                     resolve(worker);
+                    worker.workers[0].removeEventListener('message', listener);
                 }
-                else if (e.data === 'readyForConfig') {
-                    worker.workers[0].postMessage(this.workerBootConfiguration);
+                else if (e.data.message === 'readyForConfig') {
+                    worker.workers[0].postMessage({
+                        message: 'config',
+                        config: this.workerBootConfiguration,
+                    });
                 }
-                else {
-                    reject();
+                else if (e.data.message === 'error') {
+                    reject((0, serialize_error_1.deserializeError)(e.data.error));
                 }
             };
+            worker.workers[0].addEventListener('message', listener);
         });
-        return p;
     }
 }
 exports.default = WebWorkerRpcDriver;

package/rpc/configSchema.js

@@ -17,7 +17,10 @@ exports.default = (0, configuration_1.ConfigurationSchema)('RpcOptions', {
         description: 'the RPC driver to use for tracks and tasks that are not configured to use a specific RPC backend',
         defaultValue: 'MainThreadRpcDriver',
     },
-    drivers: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.map(mobx_state_tree_1.types.union(MainThreadRpcDriverConfigSchema, WebWorkerRpcDriverConfigSchema)), { MainThreadRpcDriver: { type: 'MainThreadRpcDriver' } }),
+    drivers: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.map(mobx_state_tree_1.types.union(MainThreadRpcDriverConfigSchema, WebWorkerRpcDriverConfigSchema)), {
+        MainThreadRpcDriver: { type: 'MainThreadRpcDriver' },
+        WebWorkerRpcDriver: { type: 'WebWorkerRpcDriver' },
+    }),
 }, {
     // eslint-disable-next-line @typescript-eslint/no-explicit-any
     actions: (self) => ({