@jbrowse/core 1.7.7 → 1.7.10

package/assemblyManager/assemblyManager.js

@@ -148,33 +148,30 @@ function assemblyManagerFactory(assemblyConfigType, pluginManager) {
         }))();
       },
       getRefNameMapForAdapter: function getRefNameMapForAdapter(adapterConf, assemblyName, opts) {
-        return (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-          var _self$get;
+        var _this = this;
 
+        return (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
+          var asm;
           return _regenerator.default.wrap(function _callee2$(_context2) {
             while (1) {
               switch (_context2.prev = _context2.next) {
                 case 0:
                   if (!assemblyName) {
-                    _context2.next = 4;
+                    _context2.next = 5;
                     break;
                   }
 
                   _context2.next = 3;
-                  return (0, _util.when)(function () {
-                    return Boolean(self.get(assemblyName));
-                  }, {
-                    signal: opts.signal,
-                    name: 'when assembly ready'
-                  });
+                  return _this.waitForAssembly(assemblyName);
 
                 case 3:
-                  return _context2.abrupt("return", (_self$get = self.get(assemblyName)) === null || _self$get === void 0 ? void 0 : _self$get.getRefNameMapForAdapter(adapterConf, opts));
+                  asm = _context2.sent;
+                  return _context2.abrupt("return", asm === null || asm === void 0 ? void 0 : asm.getRefNameMapForAdapter(adapterConf, opts));
 
-                case 4:
+                case 5:
                   return _context2.abrupt("return", {});
 
-                case 5:
+                case 6:
                 case "end":
                   return _context2.stop();
               }
@@ -183,33 +180,30 @@ function assemblyManagerFactory(assemblyConfigType, pluginManager) {
         }))();
       },
       getReverseRefNameMapForAdapter: function getReverseRefNameMapForAdapter(adapterConf, assemblyName, opts) {
-        return (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
-          var _self$get2;
+        var _this2 = this;
 
+        return (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
+          var asm;
           return _regenerator.default.wrap(function _callee3$(_context3) {
             while (1) {
               switch (_context3.prev = _context3.next) {
                 case 0:
                   if (!assemblyName) {
-                    _context3.next = 4;
+                    _context3.next = 5;
                     break;
                   }
 
                   _context3.next = 3;
-                  return (0, _util.when)(function () {
-                    return Boolean(self.get(assemblyName));
-                  }, {
-                    signal: opts.signal,
-                    name: 'when assembly ready'
-                  });
+                  return _this2.waitForAssembly(assemblyName);
 
                 case 3:
-                  return _context3.abrupt("return", (_self$get2 = self.get(assemblyName)) === null || _self$get2 === void 0 ? void 0 : _self$get2.getReverseRefNameMapForAdapter(adapterConf, opts));
+                  asm = _context3.sent;
+                  return _context3.abrupt("return", asm === null || asm === void 0 ? void 0 : asm.getReverseRefNameMapForAdapter(adapterConf, opts));
 
-                case 4:
+                case 5:
                   return _context3.abrupt("return", {});
 
-                case 5:
+                case 6:
                 case "end":
                   return _context3.stop();
               }
@@ -241,7 +235,7 @@ function assemblyManagerFactory(assemblyConfigType, pluginManager) {
         self.assemblies.remove(asm);
       },
       afterAttach: function afterAttach() {
-        var _this = this;
+        var _this3 = this;
 
         (0, _mobxStateTree.addDisposer)(self, (0, _mobx.reaction)( // have to slice it to be properly reacted to
         function () {
@@ -249,7 +243,7 @@ function assemblyManagerFactory(assemblyConfigType, pluginManager) {
         }, function (assemblyConfigs) {
           self.assemblies.forEach(function (asm) {
             if (!asm.configuration) {
-              _this.removeAssembly(asm);
+              _this3.removeAssembly(asm);
             }
           });
           assemblyConfigs.forEach(function (assemblyConfig) {
@@ -258,7 +252,7 @@ function assemblyManagerFactory(assemblyConfigType, pluginManager) {
             });
 
             if (existingAssemblyIdx === -1) {
-              _this.addAssembly(assemblyConfig);
+              _this3.addAssembly(assemblyConfig);
             }
           });
         }, {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "1.7.7",
+  "version": "1.7.10",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -33,6 +33,9 @@
     "@material-ui/icons": "^4.0.1",
     "abortable-promise-cache": "^1.5.0",
     "canvas": "^2.8.0",
+    "canvas-sequencer": "^3.1.0",
+    "canvas2svg": "^1.0.16",
+    "clone": "^2.1.2",
     "clsx": "^1.0.4",
     "color": "^3.1.3",
     "copy-to-clipboard": "^3.3.1",
@@ -48,6 +51,7 @@
     "json-stable-stringify": "^1.0.1",
     "librpc-web-mod": "^1.1.5",
     "load-script2": "^2.0.5",
+    "material-ui-popup-state": "^1.9.3",
     "object.fromentries": "^2.0.0",
     "rbush": "^3.0.1",
     "react-error-boundary": "^3.0.0",
@@ -72,5 +76,5 @@
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "2c26e04ae942c380bf2f5b79ef7a49cc32b7bfed"
+  "gitHead": "02d8c1e88e5603ea5855faed4ccb814e28071b32"
 }

package/pluggableElementTypes/models/InternetAccountModel.d.ts

@@ -69,7 +69,7 @@ export declare const InternetAccount: import("mobx-state-tree").IModelType<{
      * @param location - UriLocation of the resource
      * @returns A promise for the token
      */
-    getToken(location?: UriLocation | undefined): Promise<string>;
+    getToken(location?: UriLocation): Promise<string>;
 } & {
     addAuthHeaderToInit(init: RequestInit | undefined, token: string): {
         headers: Headers;
@@ -107,7 +107,7 @@ export declare const InternetAccount: import("mobx-state-tree").IModelType<{
      * @param location - UriLocation of the resource
      * @returns A function that can be used to fetch
      */
-    getFetcher(location?: UriLocation | undefined): (input: RequestInfo, init?: RequestInit | undefined) => Promise<Response>;
+    getFetcher(location?: UriLocation): (input: RequestInfo, init?: RequestInit) => Promise<Response>;
 } & {
     /**
      * Gets a filehandle that uses a fetch that adds auth headers

package/pluggableElementTypes/models/baseTrackConfig.js

@@ -58,19 +58,26 @@ function createBaseTrackConfig(pluginManager) {
       },
       textSearchAdapter: pluginManager.pluggableConfigSchemaType('text search adapter')
     }),
-    displays: _mobxStateTree.types.array(pluginManager.pluggableConfigSchemaType('display')) // see corresponding entry in circular-view ChordTrack
-    // no config slot editor exists for this at the time being
-    // configRelationships: {
-    //   type: 'configRelationships',
-    //   model: types.array(
-    //     types.model('Relationship', {
-    //       type: types.string,
-    //       target: types.maybe(types.reference(base)),
-    //     }),
-    //   ),
-    //   defaultValue: [],
-    // },
-
+    displays: _mobxStateTree.types.array(pluginManager.pluggableConfigSchemaType('display')),
+    formatDetails: (0, _configuration.ConfigurationSchema)('FormatDetails', {
+      feature: {
+        type: 'frozen',
+        description: 'adds extra fields to the feature details',
+        defaultValue: {},
+        contextVariable: ['feature']
+      },
+      subfeatures: {
+        type: 'frozen',
+        description: 'adds extra fields to the subfeatures of a feature',
+        defaultValue: {},
+        contextVariable: ['feature']
+      },
+      depth: {
+        type: 'number',
+        defaultValue: 2,
+        description: 'depth to iterate on subfeatures'
+      }
+    })
   }, {
     preProcessSnapshot: function preProcessSnapshot(s) {
       var snap = JSON.parse(JSON.stringify(s));

package/pluggableElementTypes/renderers/ComparativeServerSideRendererType.js

@@ -143,11 +143,7 @@ var ComparativeServerSideRenderer = /*#__PURE__*/function (_ServerSideRenderer)
   }, {
     key: "featurePassesFilters",
     value: function featurePassesFilters(renderArgs, feature) {
-      if (!renderArgs.filters) {
-        return true;
-      }
-
-      return renderArgs.filters.passes(feature, renderArgs);
+      return renderArgs.filters ? renderArgs.filters.passes(feature, renderArgs) : true;
     }
   }, {
     key: "getFeatures",
@@ -155,13 +151,13 @@ var ComparativeServerSideRenderer = /*#__PURE__*/function (_ServerSideRenderer)
       var _getFeatures = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3(renderArgs) {
         var _this = this;
 
-        var signal, sessionId, adapterConfig, _yield$getAdapter, dataAdapter, regions, requestRegions, featureObservable;
+        var sessionId, adapterConfig, _yield$getAdapter, dataAdapter, regions, requestRegions;
 
         return _regenerator.default.wrap(function _callee3$(_context3) {
           while (1) {
             switch (_context3.prev = _context3.next) {
               case 0:
-                signal = renderArgs.signal, sessionId = renderArgs.sessionId, adapterConfig = renderArgs.adapterConfig;
+                sessionId = renderArgs.sessionId, adapterConfig = renderArgs.adapterConfig;
                 _context3.next = 3;
                 return (0, _dataAdapterCache.getAdapter)(this.pluginManager, sessionId, adapterConfig);
 
@@ -197,15 +193,11 @@ var ComparativeServerSideRenderer = /*#__PURE__*/function (_ServerSideRenderer)
                   return requestRegion;
                 }); // note that getFeaturesInMultipleRegions does not do glyph expansion
 
-                featureObservable = dataAdapter.getFeaturesInMultipleRegions(requestRegions, {
-                  signal: signal
-                });
-                return _context3.abrupt("return", featureObservable.pipe( // @ts-ignore
-                (0, _operators.filter)(function (feature) {
-                  return _this.featurePassesFilters(renderArgs, feature);
+                return _context3.abrupt("return", dataAdapter.getFeaturesInMultipleRegions(requestRegions, renderArgs).pipe((0, _operators.filter)(function (f) {
+                  return _this.featurePassesFilters(renderArgs, f);
                 }), (0, _operators.toArray)()).toPromise());
 
-              case 13:
+              case 12:
               case "end":
                 return _context3.stop();
             }

package/pluggableElementTypes/renderers/ServerSideRendererType.d.ts

@@ -29,6 +29,12 @@ export type { RenderResults };
 export interface ResultsSerialized extends Omit<RenderResults, 'reactElement'> {
     html: string;
 }
+export interface ResultsSerializedSvgExport extends ResultsSerialized {
+    canvasRecordedData: unknown;
+    width: number;
+    height: number;
+    reactElement: unknown;
+}
 export declare type ResultsDeserialized = RenderResults;
 export default class ServerSideRenderer extends RendererType {
     /**

package/pluggableElementTypes/renderers/ServerSideRendererType.js

@@ -2,6 +2,8 @@
 
 var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
 
+var _typeof = require("@babel/runtime/helpers/typeof");
+
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
@@ -31,6 +33,8 @@ var _react = _interopRequireDefault(require("react"));
 
 var _styles = require("@material-ui/core/styles");
 
+var _canvasSequencer = require("canvas-sequencer");
+
 var _server = require("react-dom/server");
 
 var _mobxStateTree = require("mobx-state-tree");
@@ -47,6 +51,10 @@ var _ServerSideRenderedContent = _interopRequireDefault(require("./ServerSideRen
 
 var _excluded = ["html"];
 
+function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
+
+function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
+
 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; }
 
 function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
@@ -55,6 +63,10 @@ function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflec
 
 function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }
 
+function isSvgExport(elt) {
+  return 'canvasRecordedData' in elt;
+}
+
 var ServerSideRenderer = /*#__PURE__*/function (_RendererType) {
   (0, _inherits2.default)(ServerSideRenderer, _RendererType);
 
@@ -164,13 +176,43 @@ var ServerSideRenderer = /*#__PURE__*/function (_RendererType) {
     key: "renderInClient",
     value: function () {
       var _renderInClient = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(rpcManager, args) {
+        var results, width, height, canvasRecordedData, C2S, ctx, seq, str;
         return _regenerator.default.wrap(function _callee$(_context) {
           while (1) {
             switch (_context.prev = _context.next) {
               case 0:
-                return _context.abrupt("return", rpcManager.call(args.sessionId, 'CoreRender', args));
+                _context.next = 2;
+                return rpcManager.call(args.sessionId, 'CoreRender', args);
+
+              case 2:
+                results = _context.sent;
+
+                if (!isSvgExport(results)) {
+                  _context.next = 14;
+                  break;
+                }
+
+                width = results.width, height = results.height, canvasRecordedData = results.canvasRecordedData;
+                _context.next = 7;
+                return Promise.resolve().then(function () {
+                  return _interopRequireWildcard(require('canvas2svg'));
+                });
+
+              case 7:
+                C2S = _context.sent;
+                ctx = new C2S.default(width, height);
+                seq = new _canvasSequencer.CanvasSequence(canvasRecordedData);
+                seq.execute(ctx);
+                str = ctx.getSvg(); // innerHTML strips the outer <svg> element from returned data, we add
+                // our own <svg> element in the view's SVG export
+
+                results.html = str.innerHTML;
+                delete results.reactElement;
+
+              case 14:
+                return _context.abrupt("return", results);
 
-              case 1:
+              case 15:
               case "end":
                 return _context.stop();
             }

package/pluggableElementTypes/renderers/declare.d.js

@@ -0,0 +1 @@
+"use strict";