@jbrowse/core 3.0.5 → 3.2.0

package/CorePlugin.js

@@ -48,9 +48,9 @@ class CorePlugin extends Plugin_1.default {
         this.name = 'CorePlugin';
     }
     install(pluginManager) {
-        Object.values(coreRpcMethods).forEach(RpcMethod => {
+        for (const RpcMethod of Object.values(coreRpcMethods)) {
             pluginManager.addRpcMethod(() => new RpcMethod(pluginManager));
-        });
+        }
         (0, CytobandAdapter_1.default)(pluginManager);
         pluginManager.addWidgetType(() => {
             return new WidgetType_1.default({

package/PluginLoader.js

@@ -63,12 +63,12 @@ function pluginDescriptionString(d) {
     }
 }
 function pluginUrl(d) {
-    var _a, _b, _c;
+    var _a, _b, _c, _d, _e, _f;
     if (isUMDPluginDefinition(d)) {
-        return (_b = (_a = d.url) !== null && _a !== void 0 ? _a : d.esmLoc.uri) !== null && _b !== void 0 ? _b : d.umdUrl;
+        return (_c = (_a = d.url) !== null && _a !== void 0 ? _a : (_b = d.umdLoc) === null || _b === void 0 ? void 0 : _b.uri) !== null && _c !== void 0 ? _c : d.umdUrl;
     }
     else if (isESMPluginDefinition(d)) {
-        return (_c = d.esmUrl) !== null && _c !== void 0 ? _c : d.esmUri;
+        return (_e = (_d = d.esmUrl) !== null && _d !== void 0 ? _d : d.esmUri) !== null && _e !== void 0 ? _e : (_f = d.esmLoc) === null || _f === void 0 ? void 0 : _f.uri;
     }
     else if (isCJSPluginDefinition(d)) {
         return d.cjsUrl || d.cjsLoc.uri;

package/PluginManager.js

@@ -37,10 +37,11 @@ class PhasedScheduler {
         phaseCallbacks.push(callback);
     }
     run() {
-        this.phaseOrder.forEach(phaseName => {
-            var _a;
-            (_a = this.phaseCallbacks.get(phaseName)) === null || _a === void 0 ? void 0 : _a.forEach(callback => callback());
-        });
+        for (const phaseName of this.phaseOrder) {
+            for (const callback of this.phaseCallbacks.get(phaseName) || []) {
+                callback();
+            }
+        }
     }
 }
 class TypeRecord {
@@ -115,17 +116,17 @@ class PluginManager {
                 isCore: true,
             },
         });
-        initialPlugins.forEach(plugin => {
+        for (const plugin of initialPlugins) {
             this.addPlugin(plugin);
-        });
+        }
     }
     pluginConfigurationSchemas() {
         const configurationSchemas = {};
-        this.plugins.forEach(plugin => {
+        for (const plugin of this.plugins) {
             if (plugin.configurationSchema) {
                 configurationSchemas[plugin.name] = plugin.configurationSchema;
             }
-        });
+        }
         return configurationSchemas;
     }
     addPlugin(load) {
@@ -167,9 +168,9 @@ class PluginManager {
         if (this.configured) {
             throw new Error('already configured');
         }
-        this.plugins.forEach(plugin => {
+        for (const plugin of this.plugins) {
             plugin.configure(this);
-        });
+        }
         this.configured = true;
         return this;
     }
@@ -318,12 +319,12 @@ class PluginManager {
         const callback = () => {
             const track = cb(this);
             const displays = this.getElementTypesInGroup('display');
-            displays.forEach(display => {
+            for (const display of displays) {
                 if (display.trackType === track.name &&
                     !track.displayTypes.includes(display)) {
                     track.addDisplayType(display);
                 }
-            });
+            }
             return track;
         };
         return this.addElementType('track', callback);
@@ -335,13 +336,13 @@ class PluginManager {
         const callback = () => {
             const newView = cb(this);
             const displays = this.getElementTypesInGroup('display');
-            displays.forEach(display => {
+            for (const display of displays) {
                 if ((display.viewType === newView.name ||
                     display.viewType === newView.extendedName) &&
                     !newView.displayTypes.includes(display)) {
                     newView.addDisplayType(display);
                 }
-            });
+            }
             return newView;
         };
         return this.addElementType('view', callback);

package/configuration/configurationSchema.js

@@ -75,7 +75,7 @@ function makeConfigurationSchemaModel(modelName, schemaDefinition, options) {
             options,
         },
     };
-    Object.entries(schemaDefinition).forEach(([slotName, slotDefinition]) => {
+    for (const [slotName, slotDefinition] of Object.entries(schemaDefinition)) {
         if (((0, mobx_state_tree_1.isType)(slotDefinition) && (0, mobx_state_tree_1.isLateType)(slotDefinition)) ||
             (0, util_1.isConfigurationSchemaType)(slotDefinition)) {
             modelDefinition[slotName] = slotDefinition;
@@ -98,7 +98,7 @@ function makeConfigurationSchemaModel(modelName, schemaDefinition, options) {
         else {
             throw new Error(`invalid configuration schema definition, "${slotName}" must be either a valid configuration slot definition, a constant, or a nested configuration schema`);
         }
-    });
+    }
     let completeModel = mobx_state_tree_1.types
         .model(`${modelName}ConfigurationSchema`, modelDefinition)
         .actions(self => ({

package/configuration/util.js

@@ -58,7 +58,7 @@ function getTypeNamesFromExplicitlyTypedUnion(maybeUnionType) {
         maybeUnionType = (0, mst_reflection_1.resolveLateType)(maybeUnionType);
         if ((0, mobx_state_tree_1.isUnionType)(maybeUnionType)) {
             const typeNames = [];
-            (0, mst_reflection_1.getUnionSubTypes)(maybeUnionType).forEach(type => {
+            for (let type of (0, mst_reflection_1.getUnionSubTypes)(maybeUnionType)) {
                 type = (0, mst_reflection_1.resolveLateType)(type);
                 let typeName = getTypeNamesFromExplicitlyTypedUnion(type);
                 if (!typeName.length) {
@@ -69,7 +69,7 @@ function getTypeNamesFromExplicitlyTypedUnion(maybeUnionType) {
                     throw new Error(`invalid config schema type ${type}`);
                 }
                 typeNames.push(...typeName);
-            });
+            }
             return typeNames;
         }
     }

package/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js

@@ -68,9 +68,16 @@ class BaseFeatureDataAdapter extends BaseAdapter_1.BaseAdapter {
                 start: Math.max(0, Math.round(sampleCenter - length / 2)),
                 end: Math.min(Math.round(sampleCenter + length / 2), end),
             }, opts).pipe((0, operators_1.toArray)()));
-            return maybeRecordStats(length, { featureDensity: features.length / length }, features.length, expansionTime);
+            return maybeRecordStats({
+                interval: length,
+                statsSampleFeatures: features.length,
+                expansionTime,
+                stats: {
+                    featureDensity: features.length / length,
+                },
+            });
         };
-        const maybeRecordStats = async (interval, stats, statsSampleFeatures, expansionTime) => {
+        const maybeRecordStats = async ({ interval, stats, statsSampleFeatures, expansionTime, }) => {
             const refLen = region.end - region.start;
             if (statsSampleFeatures >= 70 || interval * 2 > refLen) {
                 return stats;

package/data_adapters/BaseAdapter/BaseOptions.d.ts

@@ -4,7 +4,6 @@ export interface BaseOptions {
     sessionId?: string;
     statusCallback?: (message: string) => void;
     headers?: Record<string, string>;
-    [key: string]: unknown;
 }
 export type SearchType = 'full' | 'prefix' | 'exact';
 export interface BaseTextSearchArgs {

package/data_adapters/BaseAdapter/types.d.ts

@@ -2,9 +2,9 @@ export interface BaseOptions {
     stopToken?: string;
     bpPerPx?: number;
     sessionId?: string;
+    signal?: AbortSignal;
     statusCallback?: (message: string) => void;
     headers?: Record<string, string>;
-    [key: string]: unknown;
 }
 export type SearchType = 'full' | 'prefix' | 'exact';
 export interface BaseTextSearchArgs {

package/data_adapters/CytobandAdapter/configSchema.js

@@ -5,7 +5,22 @@ function x() { }
 const configSchema = (0, configuration_1.ConfigurationSchema)('CytobandAdapter', {
     cytobandLocation: {
         type: 'fileLocation',
-        defaultValue: { uri: '/path/to/cytoband.txt.gz' },
+        defaultValue: {
+            uri: '/path/to/cytoband.txt.gz',
+        },
     },
-}, { explicitlyTyped: true });
+}, {
+    explicitlyTyped: true,
+    preProcessSnapshot: snap => {
+        return snap.uri
+            ? {
+                ...snap,
+                cytobandLocation: {
+                    uri: snap.uri,
+                    baseUri: snap.baseUri,
+                },
+            }
+            : snap;
+    },
+});
 exports.default = configSchema;

package/data_adapters/dataAdapterCache.js

@@ -33,22 +33,22 @@ function freeAdapterResources(args) {
     const specKeys = Object.keys(args);
     if (specKeys.length === 1 && specKeys[0] === 'sessionId') {
         const { sessionId } = args;
-        Object.entries(adapterCache).forEach(([cacheKey, cacheEntry]) => {
+        for (const [cacheKey, cacheEntry] of Object.entries(adapterCache)) {
             cacheEntry.sessionIds.delete(sessionId);
             if (cacheEntry.sessionIds.size === 0) {
                 delete adapterCache[cacheKey];
             }
-        });
+        }
     }
     else {
-        Object.values(adapterCache).forEach(cacheEntry => {
+        for (const cacheEntry of Object.values(adapterCache)) {
             const regions = args.regions || (args.region ? [args.region] : []);
             for (const region of regions) {
                 if (region.refName !== undefined) {
                     cacheEntry.dataAdapter.freeResources(region);
                 }
             }
-        });
+        }
     }
 }
 function clearAdapterCache() {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "3.0.5",
+  "version": "3.2.0",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -69,5 +69,5 @@
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "a03749efe19e51609922272b845a331897346789"
+  "gitHead": "c750e3f56706a490c19ba75abd807fec5e38aebf"
 }

package/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.d.ts

@@ -1,7 +1,9 @@
 import RpcMethodType from './RpcMethodType';
 import type { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods';
 export default abstract class RpcMethodTypeWithFiltersAndRenameRegions extends RpcMethodType {
-    deserializeArguments(args: any, rpcDriverClassName: string): Promise<any>;
+    deserializeArguments<T>(args: T & {
+        filters?: any;
+    }, rpcDriverClassName: string): Promise<T>;
     serializeArguments(args: RenderArgs & {
         stopToken?: string;
         statusCallback?: (arg: string) => void;

package/pluggableElementTypes/models/BaseTrackModel.d.ts

@@ -14,6 +14,7 @@ export declare function createBaseTrackModel(pm: PluginManager, trackType: strin
     type: import("mobx-state-tree").ISimpleType<string>;
     configuration: AnyConfigurationSchemaType;
     minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    pinned: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
 }, {
     readonly rpcSessionId: any;
@@ -30,6 +31,7 @@ export declare function createBaseTrackModel(pm: PluginManager, trackType: strin
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>) | undefined;
 } & {
+    setPinned(flag: boolean): void;
     setMinimized(flag: boolean): void;
     showDisplay(displayId: string, initialSnapshot?: {}): void;
     hideDisplay(displayId: string): number;

package/pluggableElementTypes/models/BaseTrackModel.js

@@ -24,6 +24,7 @@ function createBaseTrackModel(pm, trackType, baseTrackConfig) {
         type: mobx_state_tree_1.types.literal(trackType),
         configuration: (0, configuration_1.ConfigurationReference)(baseTrackConfig),
         minimized: false,
+        pinned: false,
         displays: mobx_state_tree_1.types.array(pm.pluggableMstType('display', 'stateModel')),
     })
         .views(self => ({
@@ -65,6 +66,9 @@ function createBaseTrackModel(pm, trackType, baseTrackConfig) {
         },
     }))
         .actions(self => ({
+        setPinned(flag) {
+            self.pinned = flag;
+        },
         setMinimized(flag) {
             self.minimized = flag;
         },
@@ -87,7 +91,9 @@ function createBaseTrackModel(pm, trackType, baseTrackConfig) {
             const conf = (0, mobx_state_tree_1.resolveIdentifier)(schema, (0, mobx_state_tree_1.getRoot)(self), displayId);
             const t = self.displays.filter(d => d.configuration === conf);
             (0, mobx_1.transaction)(() => {
-                t.forEach(d => self.displays.remove(d));
+                for (const d of t) {
+                    self.displays.remove(d);
+                }
             });
             return t.length;
         },

package/pluggableElementTypes/models/baseTrackConfig.js

@@ -87,14 +87,14 @@ function createBaseTrackConfig(pluginManager) {
             const { displays = [] } = snap;
             if (snap.trackId !== 'placeholderId') {
                 const configDisplayTypes = new Set(displays.map(d => d.type));
-                pluginManager.getTrackType(snap.type).displayTypes.forEach(d => {
+                for (const d of pluginManager.getTrackType(snap.type).displayTypes) {
                     if (!configDisplayTypes.has(d.name)) {
                         displays.push({
                             displayId: `${snap.trackId}-${d.name}`,
                             type: d.name,
                         });
                     }
-                });
+                }
             }
             return { ...snap, displays };
         },

package/pluggableElementTypes/renderers/BoxRendererType.js

@@ -81,7 +81,9 @@ class BoxRendererType extends FeatureRendererType_1.default {
             ...rest,
             layout,
             maxHeightReached: layout.maxHeightReached,
-            features: features.filter(f => !!layout.rectangles[f.uniqueId]),
+            features: layout.rectangles !== undefined
+                ? features.filter(f => !!layout.rectangles[f.uniqueId])
+                : features,
         };
     }
     async render(props) {

package/pluggableElementTypes/renderers/FeatureRendererType.js

@@ -49,6 +49,7 @@ class FeatureRendererType extends ServerSideRendererType_1.default {
         if (!(0, BaseAdapter_1.isFeatureAdapter)(dataAdapter)) {
             throw new Error('Adapter does not support retrieving features');
         }
+        (0, stopToken_1.checkStopToken)(stopToken);
         const requestRegions = regions.map(r => ({
             ...r,
             start: Math.floor(r.start),

package/rpc/methods/CoreFreeResources.js

@@ -12,9 +12,9 @@ class CoreFreeResources extends RpcMethodType_1.default {
     }
     async execute(args) {
         (0, dataAdapterCache_1.freeAdapterResources)(args);
-        this.pluginManager.getRendererTypes().forEach(renderer => {
+        for (const renderer of this.pluginManager.getRendererTypes()) {
             renderer.freeResources(args);
-        });
+        }
     }
     async serializeArguments(args, _rpcDriver) {
         return args;

package/rpc/methods/CoreRender.js

@@ -6,7 +6,6 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const util_1 = require("./util");
 const RpcMethodType_1 = __importDefault(require("../../pluggableElementTypes/RpcMethodType"));
 const util_2 = require("../../util");
-const stopToken_1 = require("../../util/stopToken");
 class CoreRender extends RpcMethodType_1.default {
     constructor() {
         super(...arguments);
@@ -20,35 +19,28 @@ class CoreRender extends RpcMethodType_1.default {
         if (rpcDriver === 'MainThreadRpcDriver') {
             return superArgs;
         }
-        const { rendererType } = args;
-        const RendererType = (0, util_1.validateRendererType)(rendererType, this.pluginManager.getRendererType(rendererType));
-        return RendererType.serializeArgsInClient(superArgs);
+        return (0, util_1.validateRendererType)(args.rendererType, this.pluginManager.getRendererType(args.rendererType)).serializeArgsInClient(superArgs);
     }
     async execute(args, rpcDriver) {
         let deserializedArgs = args;
         if (rpcDriver !== 'MainThreadRpcDriver') {
             deserializedArgs = await this.deserializeArguments(args, rpcDriver);
         }
-        const { sessionId, rendererType, stopToken } = deserializedArgs;
+        const { sessionId, rendererType } = deserializedArgs;
         if (!sessionId) {
             throw new Error('must pass a unique session id');
         }
-        (0, stopToken_1.checkStopToken)(stopToken);
         const RendererType = (0, util_1.validateRendererType)(rendererType, this.pluginManager.getRendererType(rendererType));
-        const result = rpcDriver === 'MainThreadRpcDriver'
+        return rpcDriver === 'MainThreadRpcDriver'
             ? await RendererType.render(deserializedArgs)
             : await RendererType.renderInWorker(deserializedArgs);
-        (0, stopToken_1.checkStopToken)(stopToken);
-        return result;
     }
     async deserializeReturn(serializedReturn, args, rpcDriver) {
         const des = await super.deserializeReturn(serializedReturn, args, rpcDriver);
         if (rpcDriver === 'MainThreadRpcDriver') {
             return des;
         }
-        const { rendererType } = args;
-        const RendererType = (0, util_1.validateRendererType)(rendererType, this.pluginManager.getRendererType(rendererType));
-        return RendererType.deserializeResultsInClient(des, args);
+        return (0, util_1.validateRendererType)(args.rendererType, this.pluginManager.getRendererType(args.rendererType)).deserializeResultsInClient(des, args);
     }
 }
 exports.default = CoreRender;