@jbrowse/core 1.6.5 → 1.6.8

package/rpc/RpcManager.js

@@ -25,6 +25,10 @@ var _WebWorkerRpcDriver = _interopRequireDefault(require("./WebWorkerRpcDriver")
 
 var _MainThreadRpcDriver = _interopRequireDefault(require("./MainThreadRpcDriver"));
 
+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; }
+
 var DriverClasses = {
   WebWorkerRpcDriver: _WebWorkerRpcDriver.default,
   MainThreadRpcDriver: _MainThreadRpcDriver.default
@@ -54,21 +58,35 @@ var RpcManager = /*#__PURE__*/function () {
         return driver;
       }
 
-      var backendConfiguration = this.backendConfigurations[backendName];
-      var DriverClassImpl = DriverClasses[backendName];
+      var newDriver;
+      var config = this.mainConfiguration.drivers.get('WebWorkerRpcDriver');
 
-      if (!DriverClassImpl) {
-        throw new Error("requested RPC driver \"".concat(backendName, "\" is not installed"));
-      }
+      if (backendName === 'MainThreadRpcDriver') {
+        var backendConfiguration = this.backendConfigurations.MainThreadRpcDriver;
 
-      if (!backendConfiguration) {
-        throw new Error("requested RPC driver \"".concat(backendName, "\" is missing config"));
-      } // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        if (!backendConfiguration) {
+          throw new Error("requested RPC driver \"".concat(backendName, "\" is missing config"));
+        }
 
+        newDriver = new _MainThreadRpcDriver.default(_objectSpread(_objectSpread({}, backendConfiguration), {}, {
+          config: config
+        }));
+      } else if (backendName === 'WebWorkerRpcDriver') {
+        var _backendConfiguration = this.backendConfigurations.WebWorkerRpcDriver;
+
+        if (!_backendConfiguration) {
+          throw new Error("requested RPC driver \"".concat(backendName, "\" is missing config"));
+        }
+
+        newDriver = new _WebWorkerRpcDriver.default(_objectSpread(_objectSpread({}, _backendConfiguration), {}, {
+          config: config
+        }), {
+          plugins: this.pluginManager.runtimePluginDefinitions
+        });
+      } else {
+        throw new Error("requested RPC driver \"".concat(backendName, "\" is not installed"));
+      }
 
-      var newDriver = new DriverClassImpl(backendConfiguration, {
-        plugins: this.pluginManager.runtimePluginDefinitions
-      });
       this.driverObjects.set(backendName, newDriver);
       return newDriver;
     }

package/rpc/WebWorkerRpcDriver.d.ts

@@ -24,6 +24,6 @@ export default class WebWorkerRpcDriver extends BaseRpcDriver {
     constructor(args: WebWorkerRpcDriverConstructorArgs, workerBootConfiguration: {
         plugins: PluginDefinition[];
     });
-    makeWorker(): WebWorkerHandle;
+    makeWorker(): Promise<WebWorkerHandle>;
 }
 export {};

package/rpc/WebWorkerRpcDriver.js

@@ -123,17 +123,49 @@ var WebWorkerRpcDriver = /*#__PURE__*/function (_BaseRpcDriver) {
 
   (0, _createClass2.default)(WebWorkerRpcDriver, [{
     key: "makeWorker",
-    value: function makeWorker() {
-      // note that we are making a Rpc.Client connection with a worker pool of
-      // one for each worker, because we want to do our own state-group-aware
-      // load balancing rather than using librpc's builtin round-robin
-      var worker = new WebWorkerHandle({
-        workers: [new this.WorkerClass()]
-      }); // send the worker its boot configuration using info from the pluginManager
-
-      worker.workers[0].postMessage(this.workerBootConfiguration);
-      return worker;
-    }
+    value: function () {
+      var _makeWorker = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
+        var _this2 = this;
+
+        var worker, p;
+        return _regenerator.default.wrap(function _callee2$(_context2) {
+          while (1) {
+            switch (_context2.prev = _context2.next) {
+              case 0:
+                // note that we are making a Rpc.Client connection with a worker pool of
+                // one for each worker, because we want to do our own state-group-aware
+                // load balancing rather than using librpc's builtin round-robin
+                worker = new WebWorkerHandle({
+                  workers: [new this.WorkerClass()]
+                }); // send the worker its boot configuration using info from the pluginManager
+
+                p = new Promise(function (resolve, reject) {
+                  worker.workers[0].onmessage = function (e) {
+                    if (e.data === 'ready') {
+                      resolve(worker);
+                    } else if (e.data === 'readyForConfig') {
+                      worker.workers[0].postMessage(_this2.workerBootConfiguration);
+                    } else {
+                      reject();
+                    }
+                  };
+                });
+                return _context2.abrupt("return", p);
+
+              case 3:
+              case "end":
+                return _context2.stop();
+            }
+          }
+        }, _callee2, this);
+      }));
+
+      function makeWorker() {
+        return _makeWorker.apply(this, arguments);
+      }
+
+      return makeWorker;
+    }()
   }]);
   return WebWorkerRpcDriver;
 }(_BaseRpcDriver2.default);

package/rpc/configSchema.d.ts

@@ -1,2 +1,2 @@
-declare const _default: import("../configuration/configurationSchema").AnyConfigurationSchemaType;
+declare const _default: import("../configuration").AnyConfigurationSchemaType;
 export default _default;

package/rpc/configSchema.js

@@ -9,14 +9,22 @@ var _mobxStateTree = require("mobx-state-tree");
 
 var _configuration = require("../configuration");
 
-var MainThreadRpcDriverConfigSchema = (0, _configuration.ConfigurationSchema)('MainThreadRpcDriver', {}, {
+var BaseRpcDriverConfigSchema = (0, _configuration.ConfigurationSchema)('BaseRpcDriver', {
+  workerCount: {
+    type: 'number',
+    description: 'The number of workers to use. If 0 (the default) JBrowse will decide how many workers to use.',
+    defaultValue: 0
+  }
+}, {
   explicitlyTyped: true
 });
-var WebWorkerRpcDriverConfigSchema = (0, _configuration.ConfigurationSchema)('WebWorkerRpcDriver', {}, {
-  explicitlyTyped: true
+var MainThreadRpcDriverConfigSchema = (0, _configuration.ConfigurationSchema)('MainThreadRpcDriver', {}, {
+  explicitlyTyped: true,
+  baseConfiguration: BaseRpcDriverConfigSchema
 });
-var ElectronRpcDriverConfigSchema = (0, _configuration.ConfigurationSchema)('ElectronRpcDriver', {}, {
-  explicitlyTyped: true
+var WebWorkerRpcDriverConfigSchema = (0, _configuration.ConfigurationSchema)('WebWorkerRpcDriver', {}, {
+  explicitlyTyped: true,
+  baseConfiguration: BaseRpcDriverConfigSchema
 });
 
 var _default = (0, _configuration.ConfigurationSchema)('RpcOptions', {
@@ -25,7 +33,7 @@ var _default = (0, _configuration.ConfigurationSchema)('RpcOptions', {
     description: 'the RPC driver to use for tracks and tasks that are not configured to use a specific RPC backend',
     defaultValue: 'MainThreadRpcDriver'
   },
-  drivers: _mobxStateTree.types.optional(_mobxStateTree.types.map(_mobxStateTree.types.union(MainThreadRpcDriverConfigSchema, WebWorkerRpcDriverConfigSchema, ElectronRpcDriverConfigSchema)), {
+  drivers: _mobxStateTree.types.optional(_mobxStateTree.types.map(_mobxStateTree.types.union(MainThreadRpcDriverConfigSchema, WebWorkerRpcDriverConfigSchema)), {
     MainThreadRpcDriver: {
       type: 'MainThreadRpcDriver'
     }

package/ui/ErrorMessage.js

@@ -32,22 +32,37 @@ var useStyles = (0, _core.makeStyles)(function (theme) {
 var ErrorMessage = function ErrorMessage(_ref) {
   var error = _ref.error;
   var classes = useStyles();
+  var snapshotError = '';
   var str = "".concat(error);
-  var snapshotError = ''; // best effort to make a better error message than the default
-  // mobx-state-tree
+  var findStr = 'is not assignable';
+  var idx = str.indexOf(findStr);
 
-  var match = str.match(/.*at path "(.*)" snapshot `(.*)` is not assignable/);
+  if (idx !== -1) {
+    var trim = str.slice(0, idx + findStr.length); // best effort to make a better error message than the default
+    // mobx-state-tree
+    // case 1. element has a path
 
-  if (match) {
-    str = "Failed to load element at ".concat(match[1]);
-    snapshotError = match[2];
+    var match = trim.match(/.*at path "(.*)" snapshot `(.*)` is not assignable/m);
+
+    if (match) {
+      str = "Failed to load element at ".concat(match[1], "...Failed element had snapshot");
+      snapshotError = match[2];
+    } // case 2. element has no path
+
+
+    var match2 = trim.match(/.*snapshot `(.*)` is not assignable/);
+
+    if (match2) {
+      str = "Failed to load element...Failed element had snapshot";
+      snapshotError = match2[1];
+    }
   }
 
   return /*#__PURE__*/_react.default.createElement("div", {
     className: classes.message
-  }, str.slice(0, 10000), snapshotError ? /*#__PURE__*/_react.default.createElement("div", null, "... Failed element had snapshot:", /*#__PURE__*/_react.default.createElement("pre", {
+  }, str.slice(0, 10000), snapshotError ? /*#__PURE__*/_react.default.createElement("pre", {
     className: classes.errorBox
-  }, JSON.stringify(JSON.parse(snapshotError), null, 2))) : null);
+  }, JSON.stringify(JSON.parse(snapshotError), null, 2)) : null);
 };
 
 var _default = ErrorMessage;

package/ui/FileSelector/FileSelector.js

@@ -159,7 +159,7 @@ var FileSelector = (0, _mobxReact.observer)(function (props) {
       value: internetAccountId,
       "aria-label": name,
       title: name
-    }, shorten(toggleContents || name, 5));
+    }, typeof toggleContents === 'string' ? shorten(toggleContents, 5) : toggleContents || shorten(name, 5));
   }), hiddenAccts.length ? /*#__PURE__*/_react.default.createElement(_lab.ToggleButton, {
     onClick: function onClick(event) {
       return setAnchorEl(event.target);

package/ui/ReturnToImportFormDialog.d.ts

@@ -0,0 +1,9 @@
+/// <reference types="react" />
+declare function ReturnToImportFormDialog({ model, handleClose, }: {
+    model: {
+        clearView: Function;
+    };
+    handleClose: () => void;
+}): JSX.Element;
+declare const _default: typeof ReturnToImportFormDialog;
+export default _default;

package/ui/ReturnToImportFormDialog.js

@@ -0,0 +1,63 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.default = void 0;
+
+var _react = _interopRequireDefault(require("react"));
+
+var _mobxReact = require("mobx-react");
+
+var _styles = require("@material-ui/core/styles");
+
+var _core = require("@material-ui/core");
+
+var _Close = _interopRequireDefault(require("@material-ui/icons/Close"));
+
+var useStyles = (0, _styles.makeStyles)(function (theme) {
+  return {
+    closeButton: {
+      position: 'absolute',
+      right: theme.spacing(1),
+      top: theme.spacing(1),
+      color: theme.palette.grey[500]
+    }
+  };
+});
+
+function ReturnToImportFormDialog(_ref) {
+  var model = _ref.model,
+      handleClose = _ref.handleClose;
+  var classes = useStyles();
+  return /*#__PURE__*/_react.default.createElement(_core.Dialog, {
+    maxWidth: "xl",
+    open: true,
+    onClose: handleClose
+  }, /*#__PURE__*/_react.default.createElement(_core.DialogTitle, null, "Reference sequence", handleClose ? /*#__PURE__*/_react.default.createElement(_core.IconButton, {
+    className: classes.closeButton,
+    onClick: function onClick() {
+      return handleClose();
+    }
+  }, /*#__PURE__*/_react.default.createElement(_Close.default, null)) : null), /*#__PURE__*/_react.default.createElement(_core.Divider, null), /*#__PURE__*/_react.default.createElement(_core.DialogContent, null, /*#__PURE__*/_react.default.createElement(_core.Typography, null, "Are you sure you want to return to the import form? This will lose your current view")), /*#__PURE__*/_react.default.createElement(_core.DialogActions, null, /*#__PURE__*/_react.default.createElement(_core.Button, {
+    onClick: function onClick() {
+      model.clearView();
+      handleClose();
+    },
+    variant: "contained",
+    color: "primary",
+    autoFocus: true
+  }, "OK"), /*#__PURE__*/_react.default.createElement(_core.Button, {
+    onClick: function onClick() {
+      return handleClose();
+    },
+    color: "secondary",
+    variant: "contained"
+  }, "Cancel")));
+}
+
+var _default = (0, _mobxReact.observer)(ReturnToImportFormDialog);
+
+exports.default = _default;

package/ui/Tooltip.d.ts

@@ -5,7 +5,7 @@ declare const _default: ({ offsetX, offsetY, configuration, feature, timeout, }:
     offsetY: number;
     configuration: import("mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
         setSubschema(slotName: string, data: unknown): any;
-    } & import("mobx-state-tree").IStateTreeNode<import("../configuration/configurationSchema").AnyConfigurationSchemaType>;
+    } & import("mobx-state-tree").IStateTreeNode<import("../configuration").AnyConfigurationSchemaType>;
     feature?: Feature | undefined;
     timeout?: number | undefined;
 }) => JSX.Element | null;

package/ui/Tooltip.js

@@ -13,7 +13,7 @@ var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/sli
 
 var _react = _interopRequireWildcard(require("react"));
 
-var _styles = require("@material-ui/core/styles");
+var _core = require("@material-ui/core");
 
 var _mobxReact = require("mobx-react");
 
@@ -23,7 +23,7 @@ function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "functio
 
 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; }
 
-var useStyles = (0, _styles.makeStyles)({
+var useStyles = (0, _core.makeStyles)({
   hoverLabel: {
     border: '1px solid black',
     position: 'absolute',

package/ui/index.d.ts

@@ -1,7 +1,9 @@
 export * from './theme';
 export { LogoFull, Logomark } from './Logo';
 export { default as App } from './App';
+export { default as ReturnToImportFormDialog } from './ReturnToImportFormDialog';
 export { default as ErrorMessage } from './ErrorMessage';
+export { default as AssemblySelector } from './AssemblySelector';
 export { default as FileSelector } from './FileSelector';
 export { default as PrerenderedCanvas } from './PrerenderedCanvas';
 export { default as ResizeHandle } from './ResizeHandle';

package/ui/index.js

@@ -11,7 +11,9 @@ var _exportNames = {
   LogoFull: true,
   Logomark: true,
   App: true,
+  ReturnToImportFormDialog: true,
   ErrorMessage: true,
+  AssemblySelector: true,
   FileSelector: true,
   PrerenderedCanvas: true,
   ResizeHandle: true,
@@ -28,6 +30,12 @@ Object.defineProperty(exports, "App", {
     return _App.default;
   }
 });
+Object.defineProperty(exports, "AssemblySelector", {
+  enumerable: true,
+  get: function get() {
+    return _AssemblySelector.default;
+  }
+});
 Object.defineProperty(exports, "EditableTypography", {
   enumerable: true,
   get: function get() {
@@ -88,6 +96,12 @@ Object.defineProperty(exports, "ResizeHandle", {
     return _ResizeHandle.default;
   }
 });
+Object.defineProperty(exports, "ReturnToImportFormDialog", {
+  enumerable: true,
+  get: function get() {
+    return _ReturnToImportFormDialog.default;
+  }
+});
 Object.defineProperty(exports, "SanitizedHTML", {
   enumerable: true,
   get: function get() {
@@ -119,8 +133,12 @@ var _Logo = require("./Logo");
 
 var _App = _interopRequireDefault(require("./App"));
 
+var _ReturnToImportFormDialog = _interopRequireDefault(require("./ReturnToImportFormDialog"));
+
 var _ErrorMessage = _interopRequireDefault(require("./ErrorMessage"));
 
+var _AssemblySelector = _interopRequireDefault(require("./AssemblySelector"));
+
 var _FileSelector = _interopRequireDefault(require("./FileSelector"));
 
 var _PrerenderedCanvas = _interopRequireDefault(require("./PrerenderedCanvas"));

package/ui/theme.d.ts

@@ -115,6 +115,14 @@ export declare function createJBrowseDefaultOverrides(palette?: PaletteOptions):
             color: string;
         };
     };
+    MuiAccordion: {
+        root: {
+            margin: number;
+            '&$expanded': {
+                margin: number;
+            };
+        };
+    };
     MuiAccordionSummary: {
         root: {
             backgroundColor: string;

package/ui/theme.js

@@ -137,6 +137,15 @@ function createJBrowseDefaultOverrides() {
         color: generatedPalette.tertiary.main
       }
     },
+    MuiAccordion: {
+      root: {
+        // avoid extra padding around accordion element
+        margin: 0,
+        '&$expanded': {
+          margin: 0
+        }
+      }
+    },
     MuiAccordionSummary: {
       root: {
         // !important needed to combat the MuiButton being applied to

package/ui/theme.test.js

@@ -62,7 +62,7 @@ describe('theme utils', function () {
       }
     });
     expect((_theme$overrides = theme.overrides) === null || _theme$overrides === void 0 ? void 0 : _theme$overrides.MuiPaper).toEqual(muiPaperStyle);
-    expect(Object.keys(theme.overrides || {}).length).toBe(9);
+    expect(Object.keys(theme.overrides || {}).length).toBe(10);
   });
   it('allows modifying a default override', function () {
     var _theme$overrides2;
@@ -78,7 +78,7 @@ describe('theme utils', function () {
       }
     });
     expect((_theme$overrides2 = theme.overrides) === null || _theme$overrides2 === void 0 ? void 0 : _theme$overrides2.MuiButton).toEqual(muiButtonStyle);
-    expect(Object.keys(theme.overrides || {}).length).toBe(8);
+    expect(Object.keys(theme.overrides || {}).length).toBe(9);
   });
   it('allows adding a custom prop', function () {
     var _theme$props;

package/util/Base1DViewModel.d.ts

@@ -9,6 +9,7 @@ export interface BpOffset {
     end?: number;
 }
 declare const Base1DView: import("mobx-state-tree").IModelType<{
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
         refName: import("mobx-state-tree").ISimpleType<string>;
         start: import("mobx-state-tree").ISimpleType<number>;
@@ -32,6 +33,7 @@ declare const Base1DView: import("mobx-state-tree").IModelType<{
     setVolatileWidth(width: number): void;
 } & {
     readonly width: number;
+    readonly assemblyNames: string[];
     readonly displayedRegionsTotalPx: number;
     readonly maxOffset: number;
     readonly minOffset: number;

package/util/Base1DViewModel.js

@@ -9,6 +9,8 @@ exports.default = void 0;
 
 var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
 
+var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
+
 var _mobxStateTree = require("mobx-state-tree");
 
 var _index = require("./index");
@@ -24,6 +26,7 @@ function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (O
 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; }
 
 var Base1DView = _mobxStateTree.types.model('Base1DView', {
+  id: _mst.ElementId,
   displayedRegions: _mobxStateTree.types.array(_mst.Region),
   bpPerPx: 0,
   offsetPx: 0,
@@ -52,6 +55,12 @@ var Base1DView = _mobxStateTree.types.model('Base1DView', {
       return self.volatileWidth;
     },
 
+    get assemblyNames() {
+      return (0, _toConsumableArray2.default)(new Set(self.displayedRegions.map(function (region) {
+        return region.assemblyName;
+      })));
+    },
+
     get displayedRegionsTotalPx() {
       return this.totalBp / self.bpPerPx;
     },

package/util/index.d.ts

@@ -1,7 +1,8 @@
 import { IAnyStateTreeNode } from 'mobx-state-tree';
 import { IReactionPublic, IReactionOptions } from 'mobx';
 import SimpleFeature, { Feature, isFeature } from './simpleFeature';
-import { TypeTestedByPredicate, Region, AssemblyManager } from './types';
+import { AssemblyManager, Region, TypeTestedByPredicate } from './types';
+export type { Feature };
 export * from './types';
 export * from './aborting';
 export * from './when';
@@ -65,6 +66,7 @@ export interface ParsedLocString {
     refName: string;
     start?: number;
     end?: number;
+    reversed?: boolean;
 }
 export declare function parseLocStringOneBased(locString: string, isValidRefName: (refName: string, assemblyName?: string) => boolean): ParsedLocString;
 /**
@@ -120,9 +122,9 @@ export declare function clamp(num: number, min: number, max: number): number;
  * @param region -
  * @param bpPerPx -
  */
-export declare function bpToPx(bp: number, region: {
-    start: number;
-    end: number;
+export declare function bpToPx(bp: number, { reversed, end, start, }: {
+    start?: number;
+    end?: number;
     reversed?: boolean;
 }, bpPerPx: number): number;
 export declare function radToDeg(radians: number): number;
@@ -338,3 +340,4 @@ export declare function viewBpToPx({ refName, coord, regionNumber, self, }: {
     index: number;
     offsetPx: number;
 } | undefined;
+export declare function getBpDisplayStr(totalBp: number): string;