@jbrowse/core 1.7.10 → 2.0.1

package/pluggableElementTypes/models/BaseTrackModel.js

@@ -112,55 +112,54 @@ function createBaseTrackModel(pluginManager, trackType, baseTrackConfig) {
       },
       showDisplay: function showDisplay(displayId) {
         var initialSnapshot = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
-        var displayTypeConfigSchema = pluginManager.pluggableConfigSchemaType('display');
-        var configuration = (0, _mobxStateTree.resolveIdentifier)(displayTypeConfigSchema, (0, _mobxStateTree.getRoot)(self), displayId);
-        var displayType = pluginManager.getDisplayType(configuration.type);
+        var schema = pluginManager.pluggableConfigSchemaType('display');
+        var conf = (0, _mobxStateTree.resolveIdentifier)(schema, (0, _mobxStateTree.getRoot)(self), displayId);
+        var displayType = pluginManager.getDisplayType(conf.type);
 
         if (!displayType) {
-          throw new Error("unknown display type ".concat(configuration.type));
+          throw new Error("unknown display type ".concat(conf.type));
         }
 
         var display = displayType.stateModel.create(_objectSpread(_objectSpread({}, initialSnapshot), {}, {
-          type: configuration.type,
-          configuration: configuration
+          type: conf.type,
+          configuration: conf
         }));
         self.displays.push(display);
       },
       hideDisplay: function hideDisplay(displayId) {
-        var displayTypeConfigSchema = pluginManager.pluggableConfigSchemaType('display');
-        var configuration = (0, _mobxStateTree.resolveIdentifier)(displayTypeConfigSchema, (0, _mobxStateTree.getRoot)(self), displayId); // if we have any displays with that configuration, turn them off
-
-        var shownDisplays = self.displays.filter(function (d) {
-          return d.configuration === configuration;
+        var schema = pluginManager.pluggableConfigSchemaType('display');
+        var conf = (0, _mobxStateTree.resolveIdentifier)(schema, (0, _mobxStateTree.getRoot)(self), displayId);
+        var t = self.displays.filter(function (d) {
+          return d.conf === conf;
         });
         (0, _mobx.transaction)(function () {
-          return shownDisplays.forEach(function (d) {
+          return t.forEach(function (d) {
             return self.displays.remove(d);
           });
         });
-        return shownDisplays.length;
+        return t.length;
       },
-      replaceDisplay: function replaceDisplay(oldDisplayId, newDisplayId) {
+      replaceDisplay: function replaceDisplay(oldId, newId) {
         var initialSnapshot = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : {};
-        var displayIdx = self.displays.findIndex(function (d) {
-          return d.configuration.displayId === oldDisplayId;
+        var idx = self.displays.findIndex(function (d) {
+          return d.conf.displayId === oldId;
         });
 
-        if (displayIdx === -1) {
-          throw new Error("could not find display id ".concat(oldDisplayId, " to replace"));
+        if (idx === -1) {
+          throw new Error("could not find display id ".concat(oldId, " to replace"));
         }
 
-        var displayTypeConfigSchema = pluginManager.pluggableConfigSchemaType('display');
-        var configuration = (0, _mobxStateTree.resolveIdentifier)(displayTypeConfigSchema, (0, _mobxStateTree.getRoot)(self), newDisplayId);
-        var displayType = pluginManager.getDisplayType(configuration.type);
+        var schema = pluginManager.pluggableConfigSchemaType('display');
+        var conf = (0, _mobxStateTree.resolveIdentifier)(schema, (0, _mobxStateTree.getRoot)(self), newId);
+        var displayType = pluginManager.getDisplayType(conf.type);
 
         if (!displayType) {
-          throw new Error("unknown display type ".concat(configuration.type));
+          throw new Error("unknown display type ".concat(conf.type));
         }
 
-        self.displays.splice(displayIdx, 1, _objectSpread(_objectSpread({}, initialSnapshot), {}, {
-          type: configuration.type,
-          configuration: configuration
+        self.displays.splice(idx, 1, _objectSpread(_objectSpread({}, initialSnapshot), {}, {
+          type: conf.type,
+          configuration: conf
         }));
       }
     };

package/pluggableElementTypes/renderers/FeatureRendererType.js

@@ -35,6 +35,8 @@ var _dataAdapterCache = require("../../data_adapters/dataAdapterCache");
 
 var _ServerSideRendererType = _interopRequireDefault(require("./ServerSideRendererType"));
 
+var _BaseAdapter = require("../../data_adapters/BaseAdapter");
+
 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; }
@@ -159,16 +161,25 @@ var FeatureRendererType = /*#__PURE__*/function (_ServerSideRendererTy) {
               case 3:
                 _yield$getAdapter = _context.sent;
                 dataAdapter = _yield$getAdapter.dataAdapter;
+
+                if ((0, _BaseAdapter.isFeatureAdapter)(dataAdapter)) {
+                  _context.next = 7;
+                  break;
+                }
+
+                throw new Error('Adapter does not support retrieving features');
+
+              case 7:
                 features = new Map();
 
                 if (!(!regions || regions.length === 0)) {
-                  _context.next = 8;
+                  _context.next = 10;
                   break;
                 }
 
                 return _context.abrupt("return", features);
 
-              case 8:
+              case 10:
                 requestRegions = regions.map(function (r) {
                   // make sure the requested region's start and end are integers, if
                   // there is a region specification.
@@ -185,13 +196,11 @@ var FeatureRendererType = /*#__PURE__*/function (_ServerSideRendererTy) {
                   return requestRegion;
                 });
                 region = requestRegions[0];
-                featureObservable = requestRegions.length === 1 ? dataAdapter.getFeatures(this.getExpandedRegion(region, renderArgs), // @ts-ignore
-                renderArgs) : // @ts-ignore
-                dataAdapter.getFeaturesInMultipleRegions(requestRegions, renderArgs);
-                _context.next = 13;
+                featureObservable = requestRegions.length === 1 ? dataAdapter.getFeatures(this.getExpandedRegion(region, renderArgs), renderArgs) : dataAdapter.getFeaturesInMultipleRegions(requestRegions, renderArgs);
+                _context.next = 15;
                 return featureObservable.pipe((0, _operators.toArray)()).toPromise();
 
-              case 13:
+              case 15:
                 feats = _context.sent;
                 (0, _util.checkAbortSignal)(signal);
                 return _context.abrupt("return", new Map(feats.filter(function (feat) {
@@ -200,7 +209,7 @@ var FeatureRendererType = /*#__PURE__*/function (_ServerSideRendererTy) {
                   return [feat.id(), feat];
                 })));
 
-              case 16:
+              case 18:
               case "end":
                 return _context.stop();
             }

package/pluggableElementTypes/renderers/ServerSideRenderedContent.js

@@ -11,10 +11,10 @@ exports.default = ServerSideRenderedContent;
 
 var _objectWithoutProperties2 = _interopRequireDefault(require("@babel/runtime/helpers/objectWithoutProperties"));
 
-var _styles = require("@material-ui/core/styles");
-
 var _react = _interopRequireWildcard(require("react"));
 
+var _styles = require("@mui/material/styles");
+
 var _reactDom = require("react-dom");
 
 var _ui = require("../../ui");

package/pluggableElementTypes/renderers/ServerSideRendererType.d.ts

@@ -1,4 +1,4 @@
-import { ThemeOptions } from '@material-ui/core';
+import { DeprecatedThemeOptions } from '@mui/material';
 import { SnapshotOrInstance, SnapshotIn } from 'mobx-state-tree';
 import RendererType, { RenderProps, RenderResults } from './RendererType';
 import SerializableFilterChain, { SerializedFilterChain } from './util/serializableFilterChain';
@@ -7,7 +7,7 @@ import RpcManager from '../../rpc/RpcManager';
 interface BaseRenderArgs extends RenderProps {
     sessionId: string;
     signal?: AbortSignal;
-    theme: ThemeOptions;
+    theme: DeprecatedThemeOptions;
     exportSVG: {
         rasterizeLayers?: boolean;
     };

package/pluggableElementTypes/renderers/ServerSideRendererType.js

@@ -31,7 +31,7 @@ var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/ge
 
 var _react = _interopRequireDefault(require("react"));
 
-var _styles = require("@material-ui/core/styles");
+var _styles = require("@mui/material/styles");
 
 var _canvasSequencer = require("canvas-sequencer");
 

package/rpc/BaseRpcDriver.js

@@ -214,7 +214,7 @@ var BaseRpcDriver = /*#__PURE__*/function () {
           return thing;
         }
 
-        return (0, _util.objectFromEntries)(Object.entries(thing).filter(function (e) {
+        return Object.fromEntries(Object.entries(thing).filter(function (e) {
           return isClonable(e[1]);
         }).map(function (_ref) {
           var _ref2 = (0, _slicedToArray2.default)(_ref, 2),

package/rpc/coreRpcMethods.d.ts

@@ -72,9 +72,7 @@ export declare class CoreEstimateRegionStats extends RpcMethodType {
         signal?: RemoteAbortSignal;
         headers?: Record<string, string>;
         sessionId: string;
-    }, rpcDriverClassName: string): Promise<import("../data_adapters/BaseAdapter").Stats | {
-        featureDensity: number;
-    }>;
+    }, rpcDriverClassName: string): Promise<import("../data_adapters/BaseAdapter").Stats>;
 }
 /**
  * fetches features from an adapter and call a renderer with them

package/rpc/coreRpcMethods.js

@@ -91,7 +91,7 @@ var CoreGetRefNames = /*#__PURE__*/function (_RpcMethodType) {
                 _yield$getAdapter = _context.sent;
                 dataAdapter = _yield$getAdapter.dataAdapter;
 
-                if (!(dataAdapter instanceof _BaseAdapter.BaseFeatureDataAdapter)) {
+                if (!(0, _BaseAdapter.isFeatureAdapter)(dataAdapter)) {
                   _context.next = 10;
                   break;
                 }
@@ -378,7 +378,7 @@ var CoreGetFeatures = /*#__PURE__*/function (_RpcMethodType4) {
                   break;
                 }
 
-                return _context6.abrupt("return", []);
+                throw new Error('Adapter does not support retrieving features');
 
               case 10:
                 ret = dataAdapter.getFeaturesInMultipleRegions(regions, _objectSpread(_objectSpread({}, opts), {}, {
@@ -590,15 +590,15 @@ var CoreEstimateRegionStats = /*#__PURE__*/function (_RpcMethodType6) {
                 _yield$getAdapter5 = _context10.sent;
                 dataAdapter = _yield$getAdapter5.dataAdapter;
 
-                if (!(dataAdapter instanceof _BaseAdapter.BaseFeatureDataAdapter)) {
+                if ((0, _BaseAdapter.isFeatureAdapter)(dataAdapter)) {
                   _context10.next = 10;
                   break;
                 }
 
-                return _context10.abrupt("return", dataAdapter.estimateRegionsStats(regions, deserializedArgs));
+                throw new Error('Adapter does not support retrieving features');
 
               case 10:
-                throw new Error('Data adapter not found');
+                return _context10.abrupt("return", dataAdapter.estimateRegionsStats(regions, deserializedArgs));
 
               case 11:
               case "end":