@jbrowse/core 1.7.2 → 1.7.5

package/BaseFeatureWidget/SequenceFeatureDetails.js

@@ -334,11 +334,11 @@ function SequenceFeatureDetails(_ref6) {
                 return rpcManager.call(sessionId, 'CoreGetFeatures', {
                   adapterConfig: (0, _configuration.getConf)(assembly, ['sequence', 'adapter']),
                   sessionId: sessionId,
-                  region: {
+                  regions: [{
                     start: start,
                     end: end,
                     refName: assembly.getCanonicalRefName(refName)
-                  }
+                  }]
                 });
 
               case 8:

package/TextSearch/TextSearchManager.d.ts

@@ -27,12 +27,11 @@ export default class TextSearchManager {
      * Returns list of relevant text search adapters to use
      * @param args - search options/arguments include: search query
      */
-    relevantAdapters(searchScope: SearchScope): (import("mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
-        setSubschema(slotName: string, data: unknown): any;
-    } & import("mobx-state-tree").IStateTreeNode<import("../configuration").AnyConfigurationSchemaType>)[];
+    relevantAdapters(searchScope: SearchScope): any[];
     getAdaptersWithAssembly(asmName: string, adapterConfs: AnyConfigurationModel[]): (import("mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
         setSubschema(slotName: string, data: unknown): any;
     } & import("mobx-state-tree").IStateTreeNode<import("../configuration").AnyConfigurationSchemaType>)[];
+    getTrackAdaptersWithAssembly(asmName: string, adapterConfs: AnyConfigurationModel[]): any[];
     /**
      * Returns list of relevant results given a search query and options
      * @param args - search options/arguments include: search query

package/TextSearch/TextSearchManager.js

@@ -75,9 +75,8 @@ var TextSearchManager = /*#__PURE__*/function () {
           tracks = _ref.tracks;
 
       var assemblyName = searchScope.assemblyName;
-      return [].concat((0, _toConsumableArray2.default)(this.getAdaptersWithAssembly(assemblyName, aggregateTextSearchAdapters)), (0, _toConsumableArray2.default)(this.getAdaptersWithAssembly(assemblyName, tracks.map(function (track) {
-        return (0, _configuration.readConfObject)(track, ['textSearching', 'textSearchAdapter']);
-      }))));
+      var relevant = [].concat((0, _toConsumableArray2.default)(this.getAdaptersWithAssembly(assemblyName, aggregateTextSearchAdapters)), (0, _toConsumableArray2.default)(this.getTrackAdaptersWithAssembly(assemblyName, tracks)));
+      return relevant;
     }
   }, {
     key: "getAdaptersWithAssembly",
@@ -88,6 +87,21 @@ var TextSearchManager = /*#__PURE__*/function () {
         return (_readConfObject = (0, _configuration.readConfObject)(conf, 'assemblyNames')) === null || _readConfObject === void 0 ? void 0 : _readConfObject.includes(asmName);
       });
     }
+  }, {
+    key: "getTrackAdaptersWithAssembly",
+    value: function getTrackAdaptersWithAssembly(asmName, adapterConfs) {
+      var tracksConfs = adapterConfs.filter(function (conf) {
+        var _readConfObject2;
+
+        return (_readConfObject2 = (0, _configuration.readConfObject)(conf, ['textSearching', 'textSearchAdapter', 'assemblyNames'])) === null || _readConfObject2 === void 0 ? void 0 : _readConfObject2.includes(asmName);
+      });
+      var trackAdapters = tracksConfs.map(function (trackConf) {
+        var textSearching = trackConf.textSearching;
+        var textSearchAdapter = textSearching.textSearchAdapter;
+        return textSearchAdapter;
+      });
+      return trackAdapters;
+    }
     /**
      * Returns list of relevant results given a search query and options
      * @param args - search options/arguments include: search query

package/assemblyManager/assemblyManager.js

@@ -149,7 +149,8 @@ function assemblyManagerFactory(assemblyConfigType, pluginManager) {
       },
       getRefNameMapForAdapter: function getRefNameMapForAdapter(adapterConf, assemblyName, opts) {
         return (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-          var assembly;
+          var _self$get;
+
           return _regenerator.default.wrap(function _callee2$(_context2) {
             while (1) {
               switch (_context2.prev = _context2.next) {
@@ -163,19 +164,9 @@ function assemblyManagerFactory(assemblyConfigType, pluginManager) {
                   });
 
                 case 2:
-                  assembly = self.get(assemblyName);
-
-                  if (!assembly) {
-                    _context2.next = 5;
-                    break;
-                  }
-
-                  return _context2.abrupt("return", assembly.getRefNameMapForAdapter(adapterConf, opts));
+                  return _context2.abrupt("return", (_self$get = self.get(assemblyName)) === null || _self$get === void 0 ? void 0 : _self$get.getRefNameMapForAdapter(adapterConf, opts));
 
-                case 5:
-                  return _context2.abrupt("return", undefined);
-
-                case 6:
+                case 3:
                 case "end":
                   return _context2.stop();
               }
@@ -185,7 +176,8 @@ function assemblyManagerFactory(assemblyConfigType, pluginManager) {
       },
       getReverseRefNameMapForAdapter: function getReverseRefNameMapForAdapter(adapterConf, assemblyName, opts) {
         return (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
-          var assembly;
+          var _self$get2;
+
           return _regenerator.default.wrap(function _callee3$(_context3) {
             while (1) {
               switch (_context3.prev = _context3.next) {
@@ -199,19 +191,9 @@ function assemblyManagerFactory(assemblyConfigType, pluginManager) {
                   });
 
                 case 2:
-                  assembly = self.get(assemblyName);
-
-                  if (!assembly) {
-                    _context3.next = 5;
-                    break;
-                  }
-
-                  return _context3.abrupt("return", assembly.getReverseRefNameMapForAdapter(adapterConf, opts));
+                  return _context3.abrupt("return", (_self$get2 = self.get(assemblyName)) === null || _self$get2 === void 0 ? void 0 : _self$get2.getReverseRefNameMapForAdapter(adapterConf, opts));
 
-                case 5:
-                  return _context3.abrupt("return", undefined);
-
-                case 6:
+                case 3:
                 case "end":
                   return _context3.stop();
               }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "1.7.2",
+  "version": "1.7.5",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -29,9 +29,9 @@
     "postbuild": "tsc -b tsconfig.build.json"
   },
   "dependencies": {
+    "@babel/runtime": "^7.17.9",
     "@material-ui/icons": "^4.0.1",
     "abortable-promise-cache": "^1.5.0",
-    "base64-js": "^1.3.0",
     "canvas": "^2.8.0",
     "clsx": "^1.0.4",
     "color": "^3.1.3",
@@ -41,7 +41,6 @@
     "dompurify": "^2.3.4",
     "escape-html": "^1.0.3",
     "fast-deep-equal": "^3.1.3",
-    "file-uri-to-path": "^1.0.0",
     "generic-filehandle": "^2.2.2",
     "http-range-fetcher": "^1.4.0",
     "is-object": "^1.0.1",
@@ -55,9 +54,7 @@
     "react-intersection-observer": "^8.32.5",
     "react-use-measure": "^2.1.1",
     "shortid": "^2.2.13",
-    "svg-path-generator": "^1.1.0",
-    "tenacious-fetch": "^2.1.0",
-    "util.promisify": "^1.1.1"
+    "svg-path-generator": "^1.1.0"
   },
   "peerDependencies": {
     "@material-ui/core": "^4.12.2",
@@ -75,5 +72,5 @@
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "8710d5770cfebb7351f0a802da2d0c5a0b9e42ba"
+  "gitHead": "2c3a1f0c95a47b24eba790eaeb49274caf297aeb"
 }

package/pluggableElementTypes/models/BaseTrackModel.d.ts

@@ -1,5 +1,5 @@
 import { Instance } from 'mobx-state-tree';
-import { AnyConfigurationSchemaType } from '../../configuration/configurationSchema';
+import { AnyConfigurationSchemaType } from '../../configuration';
 import PluginManager from '../../PluginManager';
 import { MenuItem } from '../../ui';
 export declare function createBaseTrackModel(pluginManager: PluginManager, trackType: string, baseTrackConfig: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{

package/pluggableElementTypes/models/BaseTrackModel.js

@@ -17,8 +17,6 @@ var _mobxStateTree = require("mobx-state-tree");
 
 var _configuration = require("../../configuration");
 
-var _configurationSchema = require("../../configuration/configurationSchema");
-
 var _util = require("../../util");
 
 var _types = require("../../util/types");
@@ -38,7 +36,7 @@ function createBaseTrackModel(pluginManager, trackType, baseTrackConfig) {
   return _mobxStateTree.types.model(trackType, {
     id: _mst.ElementId,
     type: _mobxStateTree.types.literal(trackType),
-    configuration: (0, _configurationSchema.ConfigurationReference)(baseTrackConfig),
+    configuration: (0, _configuration.ConfigurationReference)(baseTrackConfig),
     displays: _mobxStateTree.types.array(pluginManager.pluggableMstType('display', 'stateModel'))
   }).views(function (self) {
     return {
@@ -194,11 +192,11 @@ function createBaseTrackModel(pluginManager, trackType, baseTrackConfig) {
           compatibleDisplays.forEach(function (displayConf) {
             displayChoices.push({
               type: 'radio',
-              label: "".concat(displayConf.type),
+              label: displayConf.type,
+              checked: displayConf.displayId === shownId,
               onClick: function onClick() {
-                self.replaceDisplay(shownId, displayConf.displayId);
-              },
-              checked: displayConf.displayId === shownId
+                return self.replaceDisplay(shownId, displayConf.displayId);
+              }
             });
           });
         }

package/pluggableElementTypes/renderers/BoxRendererType.d.ts

@@ -1,11 +1,10 @@
-import { AnyConfigurationModel } from '../../configuration/configurationSchema';
 import GranularRectLayout from '../../util/layouts/GranularRectLayout';
 import MultiLayout from '../../util/layouts/MultiLayout';
 import PrecomputedLayout from '../../util/layouts/PrecomputedLayout';
 import FeatureRendererType, { RenderArgs as FeatureRenderArgs, RenderArgsSerialized as FeatureRenderArgsSerialized, RenderArgsDeserialized as FeatureRenderArgsDeserialized, RenderResults as FeatureRenderResults, ResultsSerialized as FeatureResultsSerialized, ResultsDeserialized as FeatureResultsDeserialized } from './FeatureRendererType';
-import { Region } from '../../util/types';
-import { Feature } from '../../util/simpleFeature';
+import { Region, Feature } from '../../util';
 import { SerializedLayout, BaseLayout } from '../../util/layouts/BaseLayout';
+import { AnyConfigurationModel } from '../../configuration';
 import SerializableFilterChain from './util/serializableFilterChain';
 import RpcManager from '../../rpc/RpcManager';
 export interface LayoutSessionProps {
@@ -36,12 +35,14 @@ export declare class LayoutSession implements LayoutSessionProps {
 }
 export interface RenderArgs extends FeatureRenderArgs {
     bpPerPx: number;
+    layoutId: string;
 }
 export interface RenderArgsSerialized extends FeatureRenderArgsSerialized {
     bpPerPx: number;
 }
 export interface RenderArgsDeserialized extends FeatureRenderArgsDeserialized {
     bpPerPx: number;
+    layoutId: string;
 }
 export interface RenderResults extends FeatureRenderResults {
     layout: BaseLayout<Feature>;
@@ -56,10 +57,11 @@ export interface ResultsDeserialized extends FeatureResultsDeserialized {
 }
 export default class BoxRendererType extends FeatureRendererType {
     sessions: {
-        [sessionId: string]: LayoutSession;
+        [key: string]: LayoutSession;
     };
     getWorkerSession(props: LayoutSessionProps & {
         sessionId: string;
+        layoutId: string;
     }): LayoutSession;
     getExpandedRegion(region: Region, renderArgs: RenderArgsDeserialized): Region;
     createSession(props: LayoutSessionProps): LayoutSession;

package/pluggableElementTypes/renderers/BoxRendererType.js

@@ -39,6 +39,8 @@ var _PrecomputedLayout = _interopRequireDefault(require("../../util/layouts/Prec
 
 var _FeatureRendererType2 = _interopRequireDefault(require("./FeatureRendererType"));
 
+var _util = require("../../util");
+
 var _configuration = require("../../configuration");
 
 function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
@@ -57,11 +59,6 @@ var LayoutSession = /*#__PURE__*/function () {
     (0, _defineProperty2.default)(this, "filters", void 0);
     (0, _defineProperty2.default)(this, "cachedLayout", void 0);
     this.config = args.config;
-
-    if (!(0, _configuration.isConfigurationModel)(this.config)) {
-      throw new Error('configuration required');
-    }
-
     this.bpPerPx = args.bpPerPx;
     this.filters = args.filters;
     this.update(args);
@@ -133,13 +130,13 @@ var BoxRendererType = /*#__PURE__*/function (_FeatureRendererType) {
   (0, _createClass2.default)(BoxRendererType, [{
     key: "getWorkerSession",
     value: function getWorkerSession(props) {
-      var sessionId = props.sessionId;
+      var key = (0, _util.getLayoutId)(props);
 
-      if (!this.sessions[sessionId]) {
-        this.sessions[sessionId] = this.createSession(props);
+      if (!this.sessions[key]) {
+        this.sessions[key] = this.createSession(props);
       }
 
-      var session = this.sessions[sessionId];
+      var session = this.sessions[key];
       session.update(props);
       return session;
     } // expands region for glyphs to use
@@ -174,17 +171,18 @@ var BoxRendererType = /*#__PURE__*/function (_FeatureRendererType) {
     key: "freeResourcesInClient",
     value: function () {
       var _freeResourcesInClient = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(rpcManager, args) {
-        var sessionId, regions, freed, session;
+        var regions, key, freed, session;
         return _regenerator.default.wrap(function _callee$(_context) {
           while (1) {
             switch (_context.prev = _context.next) {
               case 0:
-                sessionId = args.sessionId, regions = args.regions;
+                regions = args.regions;
+                key = (0, _util.getLayoutId)(args);
                 freed = 0;
-                session = this.sessions[sessionId];
+                session = this.sessions[key];
 
                 if (!regions && session) {
-                  delete this.sessions[sessionId];
+                  delete this.sessions[key];
                   freed = 1;
                 }
 
@@ -193,14 +191,14 @@ var BoxRendererType = /*#__PURE__*/function (_FeatureRendererType) {
                 }
 
                 _context.t0 = freed;
-                _context.next = 8;
+                _context.next = 9;
                 return (0, _get2.default)((0, _getPrototypeOf2.default)(BoxRendererType.prototype), "freeResourcesInClient", this).call(this, rpcManager, args);
 
-              case 8:
+              case 9:
                 _context.t1 = _context.sent;
                 return _context.abrupt("return", _context.t0 + _context.t1);
 
-              case 10:
+              case 11:
               case "end":
                 return _context.stop();
             }

package/pluggableElementTypes/renderers/FeatureRendererType.d.ts

@@ -57,7 +57,7 @@ export default class FeatureRendererType extends ServerSideRendererType {
     /**
      * Adds feature serialization to base server-side result serialization
      *
-     * @param results - object containing the results of calling the `render`
+     * @param result - object containing the results of calling the `render`
      * method
      * @param args - deserialized render args
      */

package/pluggableElementTypes/renderers/FeatureRendererType.js

@@ -105,7 +105,7 @@ var FeatureRendererType = /*#__PURE__*/function (_ServerSideRendererTy) {
     /**
      * Adds feature serialization to base server-side result serialization
      *
-     * @param results - object containing the results of calling the `render`
+     * @param result - object containing the results of calling the `render`
      * method
      * @param args - deserialized render args
      */

package/pluggableElementTypes/renderers/ServerSideRendererType.js

@@ -197,37 +197,30 @@ var ServerSideRenderer = /*#__PURE__*/function (_RendererType) {
       var _renderInWorker = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(args) {
         var _this = this;
 
-        var signal, _args$statusCallback, statusCallback, deserializedArgs, results, serialized;
+        var signal, _args$statusCallback, statusCallback, deserializedArgs, results;
 
         return _regenerator.default.wrap(function _callee2$(_context2) {
           while (1) {
             switch (_context2.prev = _context2.next) {
               case 0:
                 signal = args.signal, _args$statusCallback = args.statusCallback, statusCallback = _args$statusCallback === void 0 ? function () {} : _args$statusCallback;
-                (0, _util.checkAbortSignal)(signal);
                 deserializedArgs = this.deserializeArgsInWorker(args);
-                (0, _util.checkAbortSignal)(signal);
-                _context2.next = 6;
+                _context2.next = 4;
                 return (0, _util.updateStatus)('Rendering plot', statusCallback, function () {
                   return _this.render(deserializedArgs);
                 });
 
-              case 6:
+              case 4:
                 results = _context2.sent;
                 (0, _util.checkAbortSignal)(signal); // serialize the results for passing back to the main thread.
                 // these will be transmitted to the main process, and will come out
                 // as the result of renderRegionWithWorker.
 
-                _context2.next = 10;
-                return (0, _util.updateStatus)('Serializing results', statusCallback, function () {
+                return _context2.abrupt("return", (0, _util.updateStatus)('Serializing results', statusCallback, function () {
                   return _this.serializeResultsInWorker(results, deserializedArgs);
-                });
-
-              case 10:
-                serialized = _context2.sent;
-                return _context2.abrupt("return", serialized);
+                }));
 
-              case 12:
+              case 7:
               case "end":
                 return _context2.stop();
             }

package/rpc/BaseRpcDriver.js

@@ -147,6 +147,9 @@ var LazyWorker = /*#__PURE__*/function () {
                       }
                     });
                     return worker;
+                  }).catch(function (e) {
+                    _this.workerP = undefined;
+                    throw e;
                   });
                 }
 

package/rpc/coreRpcMethods.d.ts

@@ -1,7 +1,7 @@
 import RpcMethodType from '../pluggableElementTypes/RpcMethodType';
 import { RenderArgs as ServerSideRenderArgs, RenderArgsSerialized as ServerSideRenderArgsSerialized, RenderResults, ResultsSerialized } from '../pluggableElementTypes/renderers/ServerSideRendererType';
 import { RemoteAbortSignal } from './remoteAbortSignals';
-import { Region } from '../util/types';
+import { Region } from '../util';
 import SimpleFeature, { SimpleFeatureSerialized } from '../util/simpleFeature';
 export declare class CoreGetRefNames extends RpcMethodType {
     name: string;
@@ -30,9 +30,10 @@ export declare class CoreGetMetadata extends RpcMethodType {
 export declare class CoreGetFeatures extends RpcMethodType {
     name: string;
     deserializeReturn(feats: SimpleFeatureSerialized[], args: unknown, rpcDriverClassName: string): Promise<SimpleFeature[]>;
+    serializeArguments(args: RenderArgs, rpcDriverClassName: string): Promise<RenderArgs>;
     execute(args: {
         sessionId: string;
-        region: Region;
+        regions: Region[];
         adapterConfig: {};
         signal?: RemoteAbortSignal;
         opts?: any;
@@ -86,3 +87,15 @@ export declare class CoreRender extends RpcMethodType {
     }, rpcDriverClassName: string): Promise<ResultsSerialized | RenderResults>;
     deserializeReturn(serializedReturn: RenderResults | ResultsSerialized, args: RenderArgs, rpcDriverClassName: string): Promise<unknown>;
 }
+/**
+ * fetches features from an adapter and call a renderer with them
+ */
+export declare class CoreGetFeatureDetails extends RpcMethodType {
+    name: string;
+    serializeArguments(args: RenderArgs, rpcDriverClassName: string): Promise<ServerSideRenderArgsSerialized | RenderArgs>;
+    execute(args: RenderArgsSerialized & {
+        signal?: RemoteAbortSignal;
+    }, rpcDriverClassName: string): Promise<{
+        feature: any;
+    }>;
+}