@jbrowse/core 2.8.0 → 2.10.0

package/assemblyManager/assemblyManager.d.ts

@@ -2,6 +2,7 @@ import { IAnyType } from 'mobx-state-tree';
 import { Assembly } from './assembly';
 import PluginManager from '../PluginManager';
 import RpcManager from '../rpc/RpcManager';
+type AdapterConf = Record<string, unknown>;
 /**
  * #stateModel AssemblyManager
  */
@@ -32,6 +33,16 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         readonly initialized: boolean;
         readonly name: string;
         readonly regions: import("./assembly").BasicRegion[] | undefined;
+        /**
+         * #action
+         * private: you would generally want to add to manipulate
+         * jbrowse.assemblies, session.sessionAssemblies, or
+         * session.temporaryAssemblies instead of using this directly
+         *
+         * this can take an active instance of an assembly, in which case it is
+         * referred to, or it can take an identifier e.g. assembly name, which is
+         * used as a reference. snapshots cannot be used
+         */
         readonly aliases: string[];
         readonly displayName: string | undefined;
         hasName(name: string): boolean;
@@ -61,11 +72,17 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         load(): Promise<void>;
         loadPre(): Promise<void>;
     } & {
-        getAdapterMapEntry(adapterConf: unknown, options: import("../data_adapters/BaseAdapter").BaseOptions): Promise<import("./assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: unknown, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
+        getAdapterMapEntry(adapterConf: {
+            [x: string]: unknown;
+        }, options: import("../data_adapters/BaseAdapter").BaseOptions): Promise<import("./assembly").RefNameMap>;
+        getRefNameMapForAdapter(adapterConf: {
+            [x: string]: unknown;
+        }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
             [x: string]: string | undefined;
         }>;
-        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
+        getReverseRefNameMapForAdapter(adapterConf: {
+            [x: string]: unknown;
+        }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
             [x: string]: string | undefined;
         }>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -90,6 +107,16 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         readonly initialized: boolean;
         readonly name: string;
         readonly regions: import("./assembly").BasicRegion[] | undefined;
+        /**
+         * #action
+         * private: you would generally want to add to manipulate
+         * jbrowse.assemblies, session.sessionAssemblies, or
+         * session.temporaryAssemblies instead of using this directly
+         *
+         * this can take an active instance of an assembly, in which case it is
+         * referred to, or it can take an identifier e.g. assembly name, which is
+         * used as a reference. snapshots cannot be used
+         */
         readonly aliases: string[];
         readonly displayName: string | undefined;
         hasName(name: string): boolean;
@@ -119,11 +146,17 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         load(): Promise<void>;
         loadPre(): Promise<void>;
     } & {
-        getAdapterMapEntry(adapterConf: unknown, options: import("../data_adapters/BaseAdapter").BaseOptions): Promise<import("./assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: unknown, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
+        getAdapterMapEntry(adapterConf: {
+            [x: string]: unknown;
+        }, options: import("../data_adapters/BaseAdapter").BaseOptions): Promise<import("./assembly").RefNameMap>;
+        getRefNameMapForAdapter(adapterConf: {
+            [x: string]: unknown;
+        }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
             [x: string]: string | undefined;
         }>;
-        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
+        getReverseRefNameMapForAdapter(adapterConf: {
+            [x: string]: unknown;
+        }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
             [x: string]: string | undefined;
         }>;
     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -146,6 +179,16 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         readonly initialized: boolean;
         readonly name: string;
         readonly regions: import("./assembly").BasicRegion[] | undefined;
+        /**
+         * #action
+         * private: you would generally want to add to manipulate
+         * jbrowse.assemblies, session.sessionAssemblies, or
+         * session.temporaryAssemblies instead of using this directly
+         *
+         * this can take an active instance of an assembly, in which case it is
+         * referred to, or it can take an identifier e.g. assembly name, which is
+         * used as a reference. snapshots cannot be used
+         */
         readonly aliases: string[];
         readonly displayName: string | undefined;
         hasName(name: string): boolean;
@@ -175,11 +218,17 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         load(): Promise<void>;
         loadPre(): Promise<void>;
     } & {
-        getAdapterMapEntry(adapterConf: unknown, options: import("../data_adapters/BaseAdapter").BaseOptions): Promise<import("./assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: unknown, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
+        getAdapterMapEntry(adapterConf: {
+            [x: string]: unknown;
+        }, options: import("../data_adapters/BaseAdapter").BaseOptions): Promise<import("./assembly").RefNameMap>;
+        getRefNameMapForAdapter(adapterConf: {
+            [x: string]: unknown;
+        }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
             [x: string]: string | undefined;
         }>;
-        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
+        getReverseRefNameMapForAdapter(adapterConf: {
+            [x: string]: unknown;
+        }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
             [x: string]: string | undefined;
         }>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
@@ -207,6 +256,16 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         readonly initialized: boolean;
         readonly name: string;
         readonly regions: import("./assembly").BasicRegion[] | undefined;
+        /**
+         * #action
+         * private: you would generally want to add to manipulate
+         * jbrowse.assemblies, session.sessionAssemblies, or
+         * session.temporaryAssemblies instead of using this directly
+         *
+         * this can take an active instance of an assembly, in which case it is
+         * referred to, or it can take an identifier e.g. assembly name, which is
+         * used as a reference. snapshots cannot be used
+         */
         readonly aliases: string[];
         readonly displayName: string | undefined;
         hasName(name: string): boolean;
@@ -236,11 +295,17 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         load(): Promise<void>;
         loadPre(): Promise<void>;
     } & {
-        getAdapterMapEntry(adapterConf: unknown, options: import("../data_adapters/BaseAdapter").BaseOptions): Promise<import("./assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: unknown, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
+        getAdapterMapEntry(adapterConf: {
+            [x: string]: unknown;
+        }, options: import("../data_adapters/BaseAdapter").BaseOptions): Promise<import("./assembly").RefNameMap>;
+        getRefNameMapForAdapter(adapterConf: {
+            [x: string]: unknown;
+        }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
             [x: string]: string | undefined;
         }>;
-        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
+        getReverseRefNameMapForAdapter(adapterConf: {
+            [x: string]: unknown;
+        }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
             [x: string]: string | undefined;
         }>;
     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -263,6 +328,16 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         readonly initialized: boolean;
         readonly name: string;
         readonly regions: import("./assembly").BasicRegion[] | undefined;
+        /**
+         * #action
+         * private: you would generally want to add to manipulate
+         * jbrowse.assemblies, session.sessionAssemblies, or
+         * session.temporaryAssemblies instead of using this directly
+         *
+         * this can take an active instance of an assembly, in which case it is
+         * referred to, or it can take an identifier e.g. assembly name, which is
+         * used as a reference. snapshots cannot be used
+         */
         readonly aliases: string[];
         readonly displayName: string | undefined;
         hasName(name: string): boolean;
@@ -292,11 +367,17 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         load(): Promise<void>;
         loadPre(): Promise<void>;
     } & {
-        getAdapterMapEntry(adapterConf: unknown, options: import("../data_adapters/BaseAdapter").BaseOptions): Promise<import("./assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: unknown, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
+        getAdapterMapEntry(adapterConf: {
+            [x: string]: unknown;
+        }, options: import("../data_adapters/BaseAdapter").BaseOptions): Promise<import("./assembly").RefNameMap>;
+        getRefNameMapForAdapter(adapterConf: {
+            [x: string]: unknown;
+        }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
             [x: string]: string | undefined;
         }>;
-        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
+        getReverseRefNameMapForAdapter(adapterConf: {
+            [x: string]: unknown;
+        }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
             [x: string]: string | undefined;
         }>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
@@ -341,6 +422,16 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         readonly initialized: boolean;
         readonly name: string;
         readonly regions: import("./assembly").BasicRegion[] | undefined;
+        /**
+         * #action
+         * private: you would generally want to add to manipulate
+         * jbrowse.assemblies, session.sessionAssemblies, or
+         * session.temporaryAssemblies instead of using this directly
+         *
+         * this can take an active instance of an assembly, in which case it is
+         * referred to, or it can take an identifier e.g. assembly name, which is
+         * used as a reference. snapshots cannot be used
+         */
         readonly aliases: string[];
         readonly displayName: string | undefined;
         hasName(name: string): boolean;
@@ -370,11 +461,17 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         load(): Promise<void>;
         loadPre(): Promise<void>;
     } & {
-        getAdapterMapEntry(adapterConf: unknown, options: import("../data_adapters/BaseAdapter").BaseOptions): Promise<import("./assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: unknown, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
+        getAdapterMapEntry(adapterConf: {
+            [x: string]: unknown;
+        }, options: import("../data_adapters/BaseAdapter").BaseOptions): Promise<import("./assembly").RefNameMap>;
+        getRefNameMapForAdapter(adapterConf: {
+            [x: string]: unknown;
+        }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
             [x: string]: string | undefined;
         }>;
-        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
+        getReverseRefNameMapForAdapter(adapterConf: {
+            [x: string]: unknown;
+        }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
             [x: string]: string | undefined;
         }>;
     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -397,6 +494,16 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         readonly initialized: boolean;
         readonly name: string;
         readonly regions: import("./assembly").BasicRegion[] | undefined;
+        /**
+         * #action
+         * private: you would generally want to add to manipulate
+         * jbrowse.assemblies, session.sessionAssemblies, or
+         * session.temporaryAssemblies instead of using this directly
+         *
+         * this can take an active instance of an assembly, in which case it is
+         * referred to, or it can take an identifier e.g. assembly name, which is
+         * used as a reference. snapshots cannot be used
+         */
         readonly aliases: string[];
         readonly displayName: string | undefined;
         hasName(name: string): boolean;
@@ -426,18 +533,24 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         load(): Promise<void>;
         loadPre(): Promise<void>;
     } & {
-        getAdapterMapEntry(adapterConf: unknown, options: import("../data_adapters/BaseAdapter").BaseOptions): Promise<import("./assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: unknown, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
+        getAdapterMapEntry(adapterConf: {
+            [x: string]: unknown;
+        }, options: import("../data_adapters/BaseAdapter").BaseOptions): Promise<import("./assembly").RefNameMap>;
+        getRefNameMapForAdapter(adapterConf: {
+            [x: string]: unknown;
+        }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
             [x: string]: string | undefined;
         }>;
-        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
+        getReverseRefNameMapForAdapter(adapterConf: {
+            [x: string]: unknown;
+        }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
             [x: string]: string | undefined;
         }>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
     /**
      * #method
      */
-    getRefNameMapForAdapter(adapterConf: unknown, assemblyName: string | undefined, opts: {
+    getRefNameMapForAdapter(adapterConf: AdapterConf, assemblyName: string | undefined, opts: {
         signal?: AbortSignal;
         sessionId: string;
     }): Promise<{
@@ -446,7 +559,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
     /**
      * #method
      */
-    getReverseRefNameMapForAdapter(adapterConf: unknown, assemblyName: string | undefined, opts: {
+    getReverseRefNameMapForAdapter(adapterConf: AdapterConf, assemblyName: string | undefined, opts: {
         signal?: AbortSignal;
         sessionId: string;
     }): Promise<{

package/assemblyManager/assemblyManager.js

@@ -92,7 +92,7 @@ function assemblyManagerFactory(conf, pm) {
                 return undefined;
             }
             await assembly.load();
-            await (0, util_1.when)(() => Boolean((assembly === null || assembly === void 0 ? void 0 : assembly.regions) && assembly.refNameAliases) ||
+            await (0, util_1.when)(() => !!((assembly === null || assembly === void 0 ? void 0 : assembly.regions) && assembly.refNameAliases) ||
                 !!(assembly === null || assembly === void 0 ? void 0 : assembly.error));
             if (assembly.error) {
                 throw assembly.error;

package/data_adapters/dataAdapterCache.d.ts

@@ -3,6 +3,7 @@ import PluginManager from '../PluginManager';
 import { AnyConfigurationSchemaType } from '../configuration';
 import { AnyDataAdapter } from './BaseAdapter';
 type ConfigSnap = SnapshotIn<AnyConfigurationSchemaType>;
+export declare function adapterConfigCacheKey(conf?: Record<string, unknown>): string;
 interface AdapterCacheEntry {
     dataAdapter: AnyDataAdapter;
     sessionIds: Set<string>;

package/data_adapters/dataAdapterCache.js

@@ -3,11 +3,12 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.clearAdapterCache = exports.freeAdapterResources = exports.getAdapter = void 0;
+exports.clearAdapterCache = exports.freeAdapterResources = exports.getAdapter = exports.adapterConfigCacheKey = void 0;
 const idMaker_1 = __importDefault(require("../util/idMaker"));
-function adapterConfigCacheKey(adapterConfig) {
-    return `${(0, idMaker_1.default)(adapterConfig)}`;
+function adapterConfigCacheKey(conf = {}) {
+    return `${(0, idMaker_1.default)(conf)}`;
 }
+exports.adapterConfigCacheKey = adapterConfigCacheKey;
 let adapterCache = {};
 /**
  * instantiate a data adapter, or return an already-instantiated one if we have one with the same

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "2.8.0",
+  "version": "2.10.0",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -36,7 +36,6 @@
     "canvas-sequencer": "^3.1.0",
     "canvas2svg": "^1.0.16",
     "clone": "^2.1.2",
-    "clsx": "^2.0.0",
     "colord": "^2.9.3",
     "copy-to-clipboard": "^3.3.1",
     "deepmerge": "^4.2.2",
@@ -48,7 +47,6 @@
     "http-range-fetcher": "^2.0.0",
     "is-object": "^1.0.1",
     "jexl": "^2.3.0",
-    "json-stable-stringify": "^1.0.1",
     "librpc-web-mod": "^1.1.5",
     "load-script": "^2.0.0",
     "material-ui-popup-state": "^5.0.0",
@@ -73,5 +71,5 @@
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "ee8c2bdc8bd4f1a70b1eefda984f04a2830d9ca0"
+  "gitHead": "223d8bfb68fd1bacaf22852639ad5920f1b7f43b"
 }

package/pluggableElementTypes/models/baseTrackConfig.d.ts

@@ -101,6 +101,14 @@ export declare function createBaseTrackConfig(pluginManager: PluginManager): imp
             defaultValue: number;
             description: string;
         };
+        /**
+         * #slot formatDetails.maxDepth
+         */
+        maxDepth: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
     }, import("../../configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
     formatAbout: import("../../configuration/configurationSchema").ConfigurationSchemaType<{
         /**

package/pluggableElementTypes/models/baseTrackConfig.js

@@ -105,6 +105,14 @@ function createBaseTrackConfig(pluginManager) {
                 defaultValue: 2,
                 description: 'depth of subfeatures to iterate the formatter on formatDetails.subfeatures (e.g. you may not want to format the exon/cds subfeatures, so limited to 2',
             },
+            /**
+             * #slot formatDetails.maxDepth
+             */
+            maxDepth: {
+                type: 'number',
+                defaultValue: 99999,
+                description: 'Maximum depth to render subfeatures',
+            },
         }),
         formatAbout: (0, configuration_1.ConfigurationSchema)('FormatAbout', {
             /**

package/rpc/BaseRpcDriver.js

@@ -138,7 +138,7 @@ class BaseRpcDriver {
         // now actually call the worker
         const callP = worker
             .call(functionName, filteredAndSerializedArgs, {
-            timeout: 5 * 60 * 1000,
+            timeout: 5 * 60 * 1000, // 5 minutes
             statusCallback: args.statusCallback,
             rpcDriverClassName: this.name,
             ...options,

package/rpc/WebWorkerRpcDriver.d.ts

@@ -1,3 +1,4 @@
+/// <reference path="../../rpc/declaration.d.ts" />
 import Rpc from 'librpc-web-mod';
 import BaseRpcDriver, { RpcDriverConstructorArgs } from './BaseRpcDriver';
 import { PluginDefinition } from '../PluginLoader';