@jbrowse/core 2.3.2 → 2.3.4

package/PluginLoader.d.ts

@@ -40,24 +40,23 @@ export interface PluginRecord {
 export interface LoadedPlugin {
     default: PluginConstructor;
 }
-export declare function getWindowPath(windowHref: string): string;
 export default class PluginLoader {
     definitions: PluginDefinition[];
-    fetchESM?: (url: string) => Promise<unknown>;
+    fetchESM?: (url: string) => Promise<LoadedPlugin>;
     fetchCJS?: (url: string) => Promise<LoadedPlugin>;
     constructor(defs?: PluginDefinition[], args?: {
-        fetchESM?: (url: string) => Promise<unknown>;
+        fetchESM?: (url: string) => Promise<LoadedPlugin>;
         fetchCJS?: (url: string) => Promise<LoadedPlugin>;
     });
     loadScript(scriptUrl: string): Promise<void>;
-    loadCJSPlugin(def: CJSPluginDefinition, windowHref: string): Promise<LoadedPlugin>;
-    loadESMPlugin(def: ESMPluginDefinition, windowHref: string): Promise<LoadedPlugin>;
-    loadUMDPlugin(def: UMDPluginDefinition | LegacyUMDPluginDefinition, windowHref: string): Promise<{
+    loadCJSPlugin(def: CJSPluginDefinition, baseUri?: string): Promise<LoadedPlugin>;
+    loadESMPlugin(def: ESMPluginDefinition, baseUri?: string): Promise<LoadedPlugin>;
+    loadUMDPlugin(def: UMDPluginDefinition | LegacyUMDPluginDefinition, baseUri?: string): Promise<{
         default: PluginConstructor;
     }>;
-    loadPlugin(def: PluginDefinition, windowHref: string): Promise<PluginConstructor>;
+    loadPlugin(def: PluginDefinition, baseUri?: string): Promise<PluginConstructor>;
     installGlobalReExports(target: WindowOrWorkerGlobalScope): void;
-    load(windowHref?: string): Promise<{
+    load(baseUri?: string): Promise<{
         plugin: PluginConstructor;
         definition: PluginDefinition;
     }[]>;

package/PluginLoader.js

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getWindowPath = exports.isCJSPluginDefinition = exports.isESMPluginDefinition = exports.isUMDPluginDefinition = void 0;
+exports.isCJSPluginDefinition = exports.isESMPluginDefinition = exports.isUMDPluginDefinition = void 0;
 const load_script2_1 = __importDefault(require("load-script2"));
 const ReExports_1 = __importDefault(require("./ReExports"));
 const util_1 = require("./util");
@@ -23,10 +23,6 @@ function isCJSPluginDefinition(def) {
     return def.cjsUrl !== undefined;
 }
 exports.isCJSPluginDefinition = isCJSPluginDefinition;
-function getWindowPath(windowHref) {
-    return window.location.href + windowHref;
-}
-exports.getWindowPath = getWindowPath;
 function getGlobalObject() {
     // Based on window-or-global
     // https://github.com/purposeindustries/window-or-global/blob/322abc71de0010c9e5d9d0729df40959e1ef8775/lib/index.js
@@ -60,8 +56,8 @@ class PluginLoader {
         }
         throw new Error('cannot figure out how to load external JS scripts in this environment');
     }
-    async loadCJSPlugin(def, windowHref) {
-        const parsedUrl = new URL(def.cjsUrl, windowHref);
+    async loadCJSPlugin(def, baseUri) {
+        const parsedUrl = new URL(def.cjsUrl, baseUri);
         if (parsedUrl.protocol !== 'http:' && parsedUrl.protocol !== 'https:') {
             throw new Error(`Cannot load plugins using protocol "${parsedUrl.protocol}"`);
         }
@@ -70,25 +66,27 @@ class PluginLoader {
         }
         return this.fetchCJS(parsedUrl.href);
     }
-    async loadESMPlugin(def, windowHref) {
-        var _a;
+    async loadESMPlugin(def, baseUri) {
         const parsedUrl = 'esmUrl' in def
-            ? new URL(def.esmUrl, windowHref)
+            ? new URL(def.esmUrl, baseUri)
             : new URL(def.esmLoc.uri, def.esmLoc.baseUri);
         if (parsedUrl.protocol !== 'http:' && parsedUrl.protocol !== 'https:') {
             throw new Error(`cannot load plugins using protocol "${parsedUrl.protocol}"`);
         }
-        const plugin = (await ((_a = this.fetchESM) === null || _a === void 0 ? void 0 : _a.call(this, parsedUrl.href)));
+        if (!this.fetchESM) {
+            throw new Error(`No ESM fetcher installed`);
+        }
+        const plugin = await this.fetchESM(parsedUrl.href);
         if (!plugin) {
             throw new Error(`Could not load ESM plugin: ${parsedUrl}`);
         }
         return plugin;
     }
-    async loadUMDPlugin(def, windowHref) {
+    async loadUMDPlugin(def, baseUri) {
         const parsedUrl = 'url' in def
-            ? new URL(def.url, windowHref)
+            ? new URL(def.url, baseUri)
             : 'umdUrl' in def
-                ? new URL(def.umdUrl, windowHref)
+                ? new URL(def.umdUrl, baseUri)
                 : new URL(def.umdLoc.uri, def.umdLoc.baseUri);
         if (parsedUrl.protocol !== 'http:' && parsedUrl.protocol !== 'https:') {
             throw new Error(`cannot load plugins using protocol "${parsedUrl.protocol}"`);
@@ -104,16 +102,16 @@ class PluginLoader {
         }
         return plugin;
     }
-    async loadPlugin(def, windowHref) {
+    async loadPlugin(def, baseUri) {
         let plugin;
         if (util_1.isElectron && isCJSPluginDefinition(def)) {
-            plugin = await this.loadCJSPlugin(def, windowHref);
+            plugin = await this.loadCJSPlugin(def, baseUri);
         }
         else if (isESMPluginDefinition(def)) {
-            plugin = await this.loadESMPlugin(def, windowHref);
+            plugin = await this.loadESMPlugin(def, baseUri);
         }
         else if (isUMDPluginDefinition(def)) {
-            plugin = await this.loadUMDPlugin(def, windowHref);
+            plugin = await this.loadUMDPlugin(def, baseUri);
         }
         else if (!util_1.isElectron && isCJSPluginDefinition(def)) {
             throw new Error(`CommonJS plugin found, but not in a NodeJS environment: ${JSON.stringify(def)}`);
@@ -129,9 +127,9 @@ class PluginLoader {
             return [moduleName, module];
         }));
     }
-    async load(windowHref = '') {
+    async load(baseUri) {
         return Promise.all(this.definitions.map(async (definition) => ({
-            plugin: await this.loadPlugin(definition, windowHref),
+            plugin: await this.loadPlugin(definition, baseUri),
             definition,
         })));
     }

package/PluginManager.js

@@ -258,7 +258,7 @@ class PluginManager {
             .filter(t => (0, mobx_state_tree_1.isType)(t) && (0, mobx_state_tree_1.isModelType)(t));
         // try to smooth over the case when no types are registered, mostly
         // encountered in tests
-        if (pluggableTypes.length === 0) {
+        if (pluggableTypes.length === 0 && typeof jest === 'undefined') {
             console.warn(`No pluggable types found matching ('${groupName}','${fieldName}')`);
             return fallback;
         }

package/data_adapters/BaseAdapter.d.ts

@@ -96,6 +96,7 @@ export declare abstract class BaseFeatureDataAdapter extends BaseAdapter {
      * Currently this just calls getFeatureInRegion for each region. Adapters that
      * are frequently called on multiple regions simultaneously may want to
      * implement a more efficient custom version of this method.
+     *
      * @param regions - Regions
      * @param opts - Feature adapter options
      * @returns Observable of Feature objects in the regions

package/data_adapters/BaseAdapter.js

@@ -7,6 +7,7 @@ exports.isTextSearchAdapter = exports.isRefNameAliasAdapter = exports.isFeatureA
 const rxjs_1 = require("rxjs");
 const operators_1 = require("rxjs/operators");
 const mobx_state_tree_1 = require("mobx-state-tree");
+// locals
 const rxjs_2 = require("../util/rxjs");
 const util_1 = require("../util");
 const configuration_1 = require("../configuration");
@@ -95,6 +96,7 @@ class BaseFeatureDataAdapter extends BaseAdapter {
      * Currently this just calls getFeatureInRegion for each region. Adapters that
      * are frequently called on multiple regions simultaneously may want to
      * implement a more efficient custom version of this method.
+     *
      * @param regions - Regions
      * @param opts - Feature adapter options
      * @returns Observable of Feature objects in the regions
@@ -122,12 +124,12 @@ class BaseFeatureDataAdapter extends BaseAdapter {
             return (0, stats_1.blankStats)();
         }
         const feats = await Promise.all(regions.map(region => this.getRegionStats(region, opts)));
-        const scoreMax = feats.map(a => a.scoreMax).reduce((a, b) => Math.max(a, b));
-        const scoreMin = feats.map(a => a.scoreMin).reduce((a, b) => Math.min(a, b));
-        const scoreSum = feats.reduce((a, b) => a + b.scoreSum, 0);
-        const scoreSumSquares = feats.reduce((a, b) => a + b.scoreSumSquares, 0);
-        const featureCount = feats.reduce((a, b) => a + b.featureCount, 0);
-        const basesCovered = feats.reduce((a, b) => a + b.basesCovered, 0);
+        const scoreMax = (0, util_1.max)(feats.map(a => a.scoreMax));
+        const scoreMin = (0, util_1.min)(feats.map(a => a.scoreMin));
+        const scoreSum = (0, util_1.sum)(feats.map(a => a.scoreSum));
+        const scoreSumSquares = (0, util_1.sum)(feats.map(a => a.scoreSumSquares));
+        const featureCount = (0, util_1.sum)(feats.map(a => a.featureCount));
+        const basesCovered = (0, util_1.sum)(feats.map(a => a.basesCovered));
         return (0, stats_1.rectifyStats)({
             scoreMin,
             scoreMax,
@@ -151,9 +153,7 @@ class BaseFeatureDataAdapter extends BaseAdapter {
                 start: Math.max(0, Math.round(sampleCenter - length / 2)),
                 end: Math.min(Math.round(sampleCenter + length / 2), end),
             };
-            const features = await this.getFeatures(query, opts)
-                .pipe((0, operators_1.toArray)())
-                .toPromise();
+            const features = await (0, rxjs_1.firstValueFrom)(this.getFeatures(query, opts).pipe((0, operators_1.toArray)()));
             return maybeRecordStats(length, { featureDensity: features.length / length }, features.length, expansionTime);
         };
         const maybeRecordStats = async (interval, stats, statsSampleFeatures, expansionTime) => {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "2.3.2",
+  "version": "2.3.4",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -30,6 +30,7 @@
   "dependencies": {
     "@babel/runtime": "^7.17.9",
     "@mui/icons-material": "^5.0.1",
+    "@types/clone": "^2.0.0",
     "abortable-promise-cache": "^1.5.0",
     "canvas-sequencer": "^3.1.0",
     "canvas2svg": "^1.0.16",
@@ -66,12 +67,12 @@
     "prop-types": "^15.0.0",
     "react": ">=16.8.0",
     "react-dom": ">=16.8.0",
-    "rxjs": "^6.0.0",
+    "rxjs": "^7.0.0",
     "tss-react": "^4.0.0"
   },
   "publishConfig": {
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "467d973535bb7b2664e9f66311fb0dc21c1ce5ba"
+  "gitHead": "98ae48be91ee2371e1b2768a907b4997995e9915"
 }

package/pluggableElementTypes/renderers/ComparativeServerSideRendererType.js

@@ -8,6 +8,7 @@ const operators_1 = require("rxjs/operators");
 const ServerSideRendererType_1 = __importDefault(require("./ServerSideRendererType"));
 const dataAdapterCache_1 = require("../../data_adapters/dataAdapterCache");
 const util_1 = require("../../util");
+const rxjs_1 = require("rxjs");
 class ComparativeServerSideRenderer extends ServerSideRendererType_1.default {
     /**
      * directly modifies the render arguments to prepare
@@ -78,10 +79,9 @@ class ComparativeServerSideRenderer extends ServerSideRendererType_1.default {
             return requestRegion;
         });
         // note that getFeaturesInMultipleRegions does not do glyph expansion
-        const res = await dataAdapter
+        const res = await (0, rxjs_1.firstValueFrom)(dataAdapter
             .getFeaturesInMultipleRegions(requestRegions, renderArgs)
-            .pipe((0, operators_1.filter)(f => this.featurePassesFilters(renderArgs, f)), (0, operators_1.toArray)())
-            .toPromise();
+            .pipe((0, operators_1.filter)(f => this.featurePassesFilters(renderArgs, f)), (0, operators_1.toArray)()));
         // dedupe needed xref https://github.com/GMOD/jbrowse-components/pull/3404/
         return (0, util_1.dedupe)(res, f => f.id());
     }

package/pluggableElementTypes/renderers/FeatureRendererType.js

@@ -5,6 +5,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const operators_1 = require("rxjs/operators");
 const clone_1 = __importDefault(require("clone"));
+const rxjs_1 = require("rxjs");
+// locals
 const util_1 = require("../../util");
 const simpleFeature_1 = __importDefault(require("../../util/simpleFeature"));
 const dataAdapterCache_1 = require("../../data_adapters/dataAdapterCache");
@@ -106,7 +108,7 @@ class FeatureRendererType extends ServerSideRendererType_1.default {
         const featureObservable = requestRegions.length === 1
             ? dataAdapter.getFeatures(this.getExpandedRegion(region, renderArgs), renderArgs)
             : dataAdapter.getFeaturesInMultipleRegions(requestRegions, renderArgs);
-        const feats = await featureObservable.pipe((0, operators_1.toArray)()).toPromise();
+        const feats = await (0, rxjs_1.firstValueFrom)(featureObservable.pipe((0, operators_1.toArray)()));
         (0, util_1.checkAbortSignal)(signal);
         return new Map(feats
             .filter(feat => this.featurePassesFilters(renderArgs, feat))

package/rpc/methods/CoreGetFeatures.js

@@ -5,6 +5,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 /* eslint-disable @typescript-eslint/no-non-null-assertion */
 const operators_1 = require("rxjs/operators");
+const rxjs_1 = require("rxjs");
+// locals
 const dataAdapterCache_1 = require("../../data_adapters/dataAdapterCache");
 const RpcMethodType_1 = __importDefault(require("../../pluggableElementTypes/RpcMethodType"));
 const BaseAdapter_1 = require("../../data_adapters/BaseAdapter");
@@ -37,7 +39,7 @@ class CoreGetFeatures extends RpcMethodType_1.default {
             ...opts,
             signal,
         });
-        const r = await ret.pipe((0, operators_1.toArray)()).toPromise();
+        const r = await (0, rxjs_1.firstValueFrom)(ret.pipe((0, operators_1.toArray)()));
         return r.map(f => f.toJSON());
     }
 }