@jbrowse/core 1.7.10 → 2.0.1

package/util/index.d.ts

@@ -1,7 +1,8 @@
-import { IAnyStateTreeNode } from 'mobx-state-tree';
+import { IAnyStateTreeNode, IStateTreeNode } from 'mobx-state-tree';
 import { IReactionPublic, IReactionOptions } from 'mobx';
 import SimpleFeature, { Feature, isFeature } from './simpleFeature';
 import { AssemblyManager, Region, TypeTestedByPredicate } from './types';
+import { BaseBlock } from './blockTypes';
 export type { Feature };
 export * from './types';
 export * from './aborting';
@@ -24,7 +25,7 @@ export declare function getSession(node: IAnyStateTreeNode): import("./types").A
 /** get the state model of the view in the state tree that contains the given node */
 export declare function getContainingView(node: IAnyStateTreeNode): import("./types").AbstractViewModel & IAnyStateTreeNode;
 /** get the state model of the view in the state tree that contains the given node */
-export declare function getContainingTrack(node: IAnyStateTreeNode): IAnyStateTreeNode;
+export declare function getContainingTrack(node: IAnyStateTreeNode): import("./types").AbstractTrackModel & IAnyStateTreeNode;
 export declare function getContainingDisplay(node: IAnyStateTreeNode): import("./types").AbstractDisplayModel & IAnyStateTreeNode;
 /**
  * Assemble a 1-based "locString" from an interbase genomic location
@@ -149,12 +150,6 @@ export declare function bpSpanPx(leftBp: number, rightBp: number, region: {
     end: number;
     reversed?: boolean;
 }, bpPerPx: number): [number, number];
-export declare const objectFromEntries: {
-    <T = any>(entries: Iterable<readonly [PropertyKey, T]>): {
-        [k: string]: T;
-    };
-    (entries: Iterable<readonly any[]>): any;
-};
 export declare function iterMap<T, U>(iterable: Iterable<T>, func: (item: T) => U, sizeHint?: number): U[];
 interface Assembly {
     name: string;
@@ -222,7 +217,7 @@ export declare function renameRegionsIfNeeded<ARGTYPE extends {
 export declare function minmax(a: number, b: number): number[];
 export declare function stringify({ refName, coord, oob, }: {
     coord: number;
-    refName: string;
+    refName?: string;
     oob?: boolean;
 }): string;
 export declare const isElectron: boolean;
@@ -324,27 +319,23 @@ export declare type ViewSnap = {
     interRegionPaddingWidth: number;
     minimumBlockWidth: number;
     width: number;
-    displayedRegions: {
+    offsetPx: number;
+    staticBlocks: {
+        contentBlocks: BaseBlock[];
+        blocks: BaseBlock[];
+    };
+    displayedRegions: (IStateTreeNode & {
         start: number;
         end: number;
         refName: string;
         reversed: boolean;
-    }[];
+        assemblyName: string;
+    })[];
 };
-export declare function viewBpToPx({ refName, coord, regionNumber, self, }: {
-    refName: string;
-    coord: number;
-    regionNumber?: number;
-    self: ViewSnap;
-}): {
-    index: number;
-    offsetPx: number;
-} | undefined;
 export declare function supportedIndexingAdapters(type: string): boolean;
 export declare function getBpDisplayStr(totalBp: number): string;
 export declare function toLocale(n: number): string;
 export declare function getTickDisplayStr(totalBp: number, bpPerPx: number): string;
-export declare function getTickDisplayStr2(totalBp: number, bpPerPx: number): string;
 export declare function getViewParams(model: IAnyStateTreeNode, exportSVG?: boolean): {
     offsetPx: number;
     offsetPx1: number;

package/util/index.js

@@ -32,7 +32,6 @@ var _exportNames = {
   cartesianToPolar: true,
   featureSpanPx: true,
   bpSpanPx: true,
-  objectFromEntries: true,
   iterMap: true,
   mergeConfigs: true,
   findLastIndex: true,
@@ -55,12 +54,10 @@ var _exportNames = {
   hashCode: true,
   objectHash: true,
   bytesForRegions: true,
-  viewBpToPx: true,
   supportedIndexingAdapters: true,
   getBpDisplayStr: true,
   toLocale: true,
   getTickDisplayStr: true,
-  getTickDisplayStr2: true,
   getViewParams: true,
   getLayoutId: true,
   SimpleFeature: true,
@@ -95,7 +92,6 @@ exports.getContainingView = getContainingView;
 exports.getLayoutId = getLayoutId;
 exports.getSession = getSession;
 exports.getTickDisplayStr = getTickDisplayStr;
-exports.getTickDisplayStr2 = getTickDisplayStr2;
 exports.getViewParams = getViewParams;
 exports.hashCode = hashCode;
 exports.isElectron = exports.inProduction = exports.inDevelopment = void 0;
@@ -110,7 +106,6 @@ exports.makeAbortableReaction = makeAbortableReaction;
 exports.measureText = measureText;
 exports.mergeConfigs = mergeConfigs;
 exports.minmax = minmax;
-exports.objectFromEntries = void 0;
 exports.objectHash = objectHash;
 exports.parseLocString = parseLocString;
 exports.parseLocStringOneBased = parseLocStringOneBased;
@@ -127,7 +122,6 @@ exports.toLocale = toLocale;
 exports.updateStatus = updateStatus;
 exports.useDebounce = useDebounce;
 exports.useDebouncedCallback = useDebouncedCallback;
-exports.viewBpToPx = viewBpToPx;
 
 var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
 
@@ -147,8 +141,6 @@ var _mobxStateTree = require("mobx-state-tree");
 
 var _mobx = require("mobx");
 
-var _object = _interopRequireDefault(require("object.fromentries"));
-
 var _deepmerge = _interopRequireDefault(require("deepmerge"));
 
 var _simpleFeature = _interopRequireWildcard(require("./simpleFeature"));
@@ -251,11 +243,6 @@ function _unsupportedIterableToArray(o, minLen) { if (!o) return; if (typeof o =
 
 function _arrayLikeToArray(arr, len) { if (len == null || len > arr.length) len = arr.length; for (var i = 0, arr2 = new Array(len); i < len; i++) { arr2[i] = arr[i]; } return arr2; }
 
-if (!Object.fromEntries) {
-  // @ts-ignore
-  _object.default.shim();
-}
-
 var inDevelopment = (typeof process === "undefined" ? "undefined" : (0, _typeof2.default)(process)) === 'object' && process.env && process.env.NODE_ENV === 'development';
 exports.inDevelopment = inDevelopment;
 var inProduction = !inDevelopment;
@@ -791,11 +778,8 @@ function bpSpanPx(leftBp, rightBp, region, bpPerPx) {
   var start = bpToPx(leftBp, region, bpPerPx);
   var end = bpToPx(rightBp, region, bpPerPx);
   return region.reversed ? [end, start] : [start, end];
-}
+} // do an array map of an iterable
 
-var objectFromEntries = Object.fromEntries.bind(Object); // do an array map of an iterable
-
-exports.objectFromEntries = objectFromEntries;
 
 function iterMap(iterable, func, sizeHint) {
   var results = sizeHint ? new Array(sizeHint) : [];
@@ -873,7 +857,8 @@ function findLastIndex(array, predicate) {
  */
 
 
-function makeAbortableReaction(self, dataFunction, asyncReactionFunction, reactionOptions, startedFunction, successFunction, errorFunction) {
+function makeAbortableReaction(self, dataFunction, asyncReactionFunction, // @ts-ignore
+reactionOptions, startedFunction, successFunction, errorFunction) {
   var inProgress;
 
   function handleError(error) {
@@ -886,7 +871,7 @@ function makeAbortableReaction(self, dataFunction, asyncReactionFunction, reacti
     }
   }
 
-  var reactionDisposer = (0, _mobx.reaction)(function () {
+  (0, _mobxStateTree.addDisposer)(self, (0, _mobx.reaction)(function () {
     try {
       return dataFunction(self);
     } catch (e) {
@@ -917,7 +902,8 @@ function makeAbortableReaction(self, dataFunction, asyncReactionFunction, reacti
               startedFunction(thisInProgress);
               _context.prev = 6;
               _context.next = 9;
-              return asyncReactionFunction(data, thisInProgress.signal, self, mobxReactionHandle);
+              return asyncReactionFunction(data, thisInProgress.signal, self, // @ts-ignore
+              mobxReactionHandle);
 
             case 9:
               result = _context.sent;
@@ -951,8 +937,7 @@ function makeAbortableReaction(self, dataFunction, asyncReactionFunction, reacti
     return function (_x, _x2) {
       return _ref2.apply(this, arguments);
     };
-  }(), reactionOptions);
-  (0, _mobxStateTree.addDisposer)(self, reactionDisposer);
+  }(), reactionOptions));
   (0, _mobxStateTree.addDisposer)(self, function () {
     if (inProgress && !inProgress.signal.aborted) {
       inProgress.abort();
@@ -968,6 +953,7 @@ function renameRegionIfNeeded(refNameMap, region) {
   if (region && refNameMap && refNameMap[region.refName]) {
     // clone the region so we don't modify it
     if ((0, _mobxStateTree.isStateTreeNode)(region)) {
+      // @ts-ignore
       region = _objectSpread({}, (0, _mobxStateTree.getSnapshot)(region));
     } else {
       region = _objectSpread({}, region);
@@ -1015,7 +1001,7 @@ function _renameRegionsIfNeeded() {
             _context3.t0 = Object;
             _context3.next = 7;
             return Promise.all(assemblyNames.map( /*#__PURE__*/function () {
-              var _ref6 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(assemblyName) {
+              var _ref5 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(assemblyName) {
                 return _regenerator.default.wrap(function _callee2$(_context2) {
                   while (1) {
                     switch (_context2.prev = _context2.next) {
@@ -1037,7 +1023,7 @@ function _renameRegionsIfNeeded() {
               }));
 
               return function (_x10) {
-                return _ref6.apply(this, arguments);
+                return _ref5.apply(this, arguments);
               };
             }()));
 
@@ -1070,7 +1056,7 @@ function stringify(_ref3) {
   var refName = _ref3.refName,
       coord = _ref3.coord,
       oob = _ref3.oob;
-  return "".concat(refName, ":").concat(coord.toLocaleString('en-US')).concat(oob ? ' (out of bounds)' : '');
+  return refName ? "".concat(refName, ":").concat(coord.toLocaleString('en-US')).concat(oob ? ' (out of bounds)' : '') : '';
 } // this is recommended in a later comment in https://github.com/electron/electron/issues/2288
 // for detecting electron in a renderer process, which is the one that has node enabled for us
 // const isElectron = process.versions.electron
@@ -1158,20 +1144,25 @@ window.requestIdleCallback : function (cb) {
   }, 1);
 } : function (cb) {
   return cb();
-}; // xref https://gist.github.com/tophtucker/62f93a4658387bb61e4510c37e2e97cf
+}; // prettier-ignore
 
 exports.rIC = rIC;
+var widths = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.2796875, 0.2765625, 0.3546875, 0.5546875, 0.5546875, 0.8890625, 0.665625, 0.190625, 0.3328125, 0.3328125, 0.3890625, 0.5828125, 0.2765625, 0.3328125, 0.2765625, 0.3015625, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.2765625, 0.2765625, 0.584375, 0.5828125, 0.584375, 0.5546875, 1.0140625, 0.665625, 0.665625, 0.721875, 0.721875, 0.665625, 0.609375, 0.7765625, 0.721875, 0.2765625, 0.5, 0.665625, 0.5546875, 0.8328125, 0.721875, 0.7765625, 0.665625, 0.7765625, 0.721875, 0.665625, 0.609375, 0.721875, 0.665625, 0.94375, 0.665625, 0.665625, 0.609375, 0.2765625, 0.3546875, 0.2765625, 0.4765625, 0.5546875, 0.3328125, 0.5546875, 0.5546875, 0.5, 0.5546875, 0.5546875, 0.2765625, 0.5546875, 0.5546875, 0.221875, 0.240625, 0.5, 0.221875, 0.8328125, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.3328125, 0.5, 0.2765625, 0.5546875, 0.5, 0.721875, 0.5, 0.5, 0.5, 0.3546875, 0.259375, 0.353125, 0.5890625]; // xref https://gist.github.com/tophtucker/62f93a4658387bb61e4510c37e2e97cf
 
 function measureText(str) {
   var fontSize = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : 10;
-  // prettier-ignore
-  var widths = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.2796875, 0.2765625, 0.3546875, 0.5546875, 0.5546875, 0.8890625, 0.665625, 0.190625, 0.3328125, 0.3328125, 0.3890625, 0.5828125, 0.2765625, 0.3328125, 0.2765625, 0.3015625, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.2765625, 0.2765625, 0.584375, 0.5828125, 0.584375, 0.5546875, 1.0140625, 0.665625, 0.665625, 0.721875, 0.721875, 0.665625, 0.609375, 0.7765625, 0.721875, 0.2765625, 0.5, 0.665625, 0.5546875, 0.8328125, 0.721875, 0.7765625, 0.665625, 0.7765625, 0.721875, 0.665625, 0.609375, 0.721875, 0.665625, 0.94375, 0.665625, 0.665625, 0.609375, 0.2765625, 0.3546875, 0.2765625, 0.4765625, 0.5546875, 0.3328125, 0.5546875, 0.5546875, 0.5, 0.5546875, 0.5546875, 0.2765625, 0.5546875, 0.5546875, 0.221875, 0.240625, 0.5, 0.221875, 0.8328125, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.3328125, 0.5, 0.2765625, 0.5546875, 0.5, 0.721875, 0.5, 0.5, 0.5, 0.3546875, 0.259375, 0.353125, 0.5890625];
   var avg = 0.5279276315789471;
-  return String(str).split('').map(function (c) {
-    return c.charCodeAt(0) < widths.length ? widths[c.charCodeAt(0)] : avg;
-  }).reduce(function (cur, acc) {
-    return acc + cur;
-  }, 0) * fontSize;
+  var s = String(str);
+  var total = 0;
+
+  for (var i = 0; i < s.length; i++) {
+    var _widths$code;
+
+    var code = s.charCodeAt(i);
+    total += (_widths$code = widths[code]) !== null && _widths$code !== void 0 ? _widths$code : avg;
+  }
+
+  return total * fontSize;
 }
 
 var defaultStarts = ['ATG'];
@@ -1369,48 +1360,8 @@ function _bytesForRegions() {
   return _bytesForRegions.apply(this, arguments);
 }
 
-function viewBpToPx(_ref4) {
-  var refName = _ref4.refName,
-      coord = _ref4.coord,
-      regionNumber = _ref4.regionNumber,
-      self = _ref4.self;
-  var offsetBp = 0;
-  var interRegionPaddingBp = self.interRegionPaddingWidth * self.bpPerPx;
-  var minimumBlockBp = self.minimumBlockWidth * self.bpPerPx;
-  var index = self.displayedRegions.findIndex(function (region, idx) {
-    var len = region.end - region.start;
-
-    if (refName === region.refName && coord >= region.start && coord <= region.end) {
-      if (regionNumber ? regionNumber === idx : true) {
-        offsetBp += region.reversed ? region.end - coord : coord - region.start;
-        return true;
-      }
-    } // add the interRegionPaddingWidth if the boundary is in the screen
-    // e.g. offset>=0 && offset<width
-
-
-    if (len > minimumBlockBp && offsetBp / self.bpPerPx >= 0 && offsetBp / self.bpPerPx < self.width) {
-      offsetBp += len + interRegionPaddingBp;
-    } else {
-      offsetBp += len;
-    }
-
-    return false;
-  });
-  var found = self.displayedRegions[index];
-
-  if (found) {
-    return {
-      index: index,
-      offsetPx: Math.round(offsetBp / self.bpPerPx)
-    };
-  }
-
-  return undefined;
-} // supported adapter types by text indexer
+// supported adapter types by text indexer
 //  ensure that this matches the method found in @jbrowse/text-indexing/util
-
-
 function supportedIndexingAdapters(type) {
   return ['Gff3TabixAdapter', 'VcfTabixAdapter', 'Gff3Adapter', 'VcfAdapter'].includes(type);
 }
@@ -1423,7 +1374,7 @@ function getBpDisplayStr(totalBp) {
   } else if (Math.floor(totalBp / 1000) > 0) {
     str = "".concat(parseFloat((totalBp / 1000).toPrecision(3)), "Kbp");
   } else {
-    str = "".concat(Math.floor(totalBp).toLocaleString('en-US'), "bp");
+    str = "".concat(toLocale(Math.floor(totalBp)), "bp");
   }
 
   return str;
@@ -1445,18 +1396,6 @@ function getTickDisplayStr(totalBp, bpPerPx) {
   return str;
 }
 
-function getTickDisplayStr2(totalBp, bpPerPx) {
-  var str;
-
-  if (Math.floor(bpPerPx / 1000) > 0) {
-    str = "".concat(toLocale(parseFloat((totalBp / 1000000).toFixed(2))), "Mbp");
-  } else {
-    str = "".concat(toLocale(Math.floor(totalBp)), "bp");
-  }
-
-  return str;
-}
-
 function getViewParams(model, exportSVG) {
   // @ts-ignore
   var _getContainingView = getContainingView(model),
@@ -1475,8 +1414,8 @@ function getViewParams(model, exportSVG) {
   };
 }
 
-function getLayoutId(_ref5) {
-  var sessionId = _ref5.sessionId,
-      layoutId = _ref5.layoutId;
+function getLayoutId(_ref4) {
+  var sessionId = _ref4.sessionId,
+      layoutId = _ref4.layoutId;
   return sessionId + '-' + layoutId;
 }

package/util/layouts/GranularRectLayout.js

@@ -15,8 +15,6 @@ var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/creat
 
 var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
 
-var _index = require("../index");
-
 function _createForOfIteratorHelper(o, allowArrayLike) { var it = typeof Symbol !== "undefined" && o[Symbol.iterator] || o["@@iterator"]; if (!it) { if (Array.isArray(o) || (it = _unsupportedIterableToArray(o)) || allowArrayLike && o && typeof o.length === "number") { if (it) o = it; var i = 0; var F = function F() {}; return { s: F, n: function n() { if (i >= o.length) return { done: true }; return { done: false, value: o[i++] }; }, e: function e(_e) { throw _e; }, f: F }; } throw new TypeError("Invalid attempt to iterate non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method."); } var normalCompletion = true, didErr = false, err; return { s: function s() { it = it.call(o); }, n: function n() { var step = it.next(); normalCompletion = step.done; return step; }, e: function e(_e2) { didErr = true; err = _e2; }, f: function f() { try { if (!normalCompletion && it.return != null) it.return(); } finally { if (didErr) throw err; } } }; }
 
 function _unsupportedIterableToArray(o, minLen) { if (!o) return; if (typeof o === "string") return _arrayLikeToArray(o, minLen); var n = Object.prototype.toString.call(o).slice(8, -1); if (n === "Object" && o.constructor) n = o.constructor.name; if (n === "Map" || n === "Set") return Array.from(o); if (n === "Arguments" || /^(?:Ui|I)nt(?:8|16|32)(?:Clamped)?Array$/.test(n)) return _arrayLikeToArray(o, minLen); }
@@ -588,7 +586,7 @@ var GranularRectLayout = /*#__PURE__*/function () {
   }, {
     key: "toJSON",
     value: function toJSON() {
-      var rectangles = (0, _index.objectFromEntries)(this.getRectangles());
+      var rectangles = Object.fromEntries(this.getRectangles());
       return {
         rectangles: rectangles,
         containsNoTransferables: true,

package/util/layouts/PrecomputedLayout.js

@@ -15,8 +15,6 @@ var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/creat
 
 var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
 
-var _ = require("..");
-
 var _rbush = _interopRequireDefault(require("rbush"));
 
 var PrecomputedLayout = /*#__PURE__*/function () {
@@ -116,7 +114,7 @@ var PrecomputedLayout = /*#__PURE__*/function () {
     key: "toJSON",
     value: function toJSON() {
       return {
-        rectangles: (0, _.objectFromEntries)(this.rectangles),
+        rectangles: Object.fromEntries(this.rectangles),
         totalHeight: this.totalHeight,
         maxHeightReached: false,
         containsNoTransferables: true

package/util/offscreenCanvasPonyfill.js

@@ -31,10 +31,8 @@ imageData, context) {
   if (imageData.serializedCommands) {
     var seq = new _canvasSequencer.CanvasSequence(imageData.serializedCommands);
     seq.execute(context);
-  } else if (imageData instanceof ImageBitmapType) {
+  } else {
     context.drawImage(imageData, 0, 0);
-  } else if (imageData.dataURL) {
-    throw new Error('dataURL deserialization no longer supported');
   }
 }
 
@@ -54,11 +52,11 @@ if (weHave.realOffscreenCanvas) {
   exports.ImageBitmapType = ImageBitmapType = window.ImageBitmap || self.ImageBitmap;
 } else if (weHave.node) {
   // use node-canvas if we are running in node (i.e. automated tests)
-  var _require = require('canvas'),
-      nodeCreateCanvas = _require.createCanvas,
-      Image = _require.Image;
-
-  exports.createCanvas = createCanvas = nodeCreateCanvas;
+  exports.createCanvas = createCanvas = function createCanvas() {
+    // @ts-ignore
+    // eslint-disable-next-line no-undef
+    return nodeCreateCanvas.apply(void 0, arguments);
+  };
 
   exports.createImageBitmap = createImageBitmap = /*#__PURE__*/function () {
     var _ref = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(canvas) {
@@ -77,8 +75,10 @@ if (weHave.realOffscreenCanvas) {
               throw new Error('only one-argument uses of createImageBitmap are supported by the node offscreencanvas ponyfill');
 
             case 2:
-              dataUri = canvas.toDataURL();
-              img = new Image();
+              dataUri = canvas.toDataURL(); // @ts-ignore
+              // eslint-disable-next-line no-undef
+
+              img = new nodeImage();
               return _context.abrupt("return", new Promise(function (resolve, reject) {
                 img.onload = function () {
                   return resolve(img);
@@ -100,8 +100,6 @@ if (weHave.realOffscreenCanvas) {
       return _ref.apply(this, arguments);
     };
   }();
-
-  exports.ImageBitmapType = ImageBitmapType = Image;
 } else {
   exports.createCanvas = createCanvas = function createCanvas(width, height) {
     var context = new _canvasSequencer.CanvasSequence();

package/util/tracks.js

@@ -46,7 +46,7 @@ function getTrackAssemblyNames(track) {
 
 
 function getRpcSessionId(thisNode) {
-  var highestRpcSessionId;
+  var highestRpcSessionId; // eslint-disable-next-line @typescript-eslint/no-explicit-any
 
   for (var node = thisNode; !(0, _mobxStateTree.isRoot)(node); node = (0, _mobxStateTree.getParent)(node)) {
     if ('rpcSessionId' in node) {
@@ -69,7 +69,9 @@ function getRpcSessionId(thisNode) {
 
 
 function getParentRenderProps(node) {
-  for (var currentNode = (0, _mobxStateTree.getParent)(node); !(0, _mobxStateTree.isRoot)(currentNode); currentNode = (0, _mobxStateTree.getParent)(currentNode)) {
+  for ( // eslint-disable-next-line @typescript-eslint/no-explicit-any
+  var currentNode = (0, _mobxStateTree.getParent)(node); !(0, _mobxStateTree.isRoot)(currentNode); // eslint-disable-next-line @typescript-eslint/no-explicit-any
+  currentNode = (0, _mobxStateTree.getParent)(currentNode)) {
     if ('renderProps' in currentNode) {
       return currentNode.renderProps();
     }

package/util/types/index.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { Instance, SnapshotIn, IAnyStateTreeNode } from 'mobx-state-tree';
+import { Instance, SnapshotIn, IAnyStateTreeNode, IStateTreeNode, IType } from 'mobx-state-tree';
 import { AnyConfigurationModel } from '../../configuration/configurationSchema';
 import assemblyManager from '../../assemblyManager';
 import TextSearchManager from '../../TextSearch/TextSearchManager';
@@ -10,10 +10,10 @@ import { Feature } from '../simpleFeature';
 import { BaseInternetAccountModel } from '../../pluggableElementTypes/models';
 export * from './util';
 /** abstract type for a model that contains multiple views */
-export interface AbstractViewContainer extends IAnyStateTreeNode {
+export interface AbstractViewContainer extends IStateTreeNode<IType<any, unknown, any>> {
     views: AbstractViewModel[];
     removeView(view: AbstractViewModel): void;
-    addView(typeName: string, initialState?: Record<string, unknown>): void | AbstractViewModel;
+    addView(typeName: string, initialState?: Record<string, unknown>): AbstractViewModel;
 }
 export declare function isViewContainer(thing: unknown): thing is AbstractViewContainer;
 export declare type NotificationLevel = 'error' | 'info' | 'warning' | 'success';
@@ -43,6 +43,7 @@ export interface JBrowsePlugin {
 export declare type DialogComponentType = React.LazyExoticComponent<React.FC<any>> | React.FC<any>;
 /** minimum interface that all session state models must implement */
 export interface AbstractSessionModel extends AbstractViewContainer {
+    drawerPosition?: string;
     setSelection(feature: Feature): void;
     clearSelection(): void;
     configuration: AnyConfigurationModel;
@@ -63,6 +64,8 @@ export interface AbstractSessionModel extends AbstractViewContainer {
     sessionConnections?: AnyConfigurationModel[];
     connectionInstances?: {
         name: string;
+        connectionId: string;
+        tracks: AnyConfigurationModel[];
     }[];
     makeConnection?: Function;
     adminMode?: boolean;
@@ -73,6 +76,7 @@ export interface AbstractSessionModel extends AbstractViewContainer {
     queueDialog: (callback: (doneCallback: Function) => [DialogComponentType, any]) => void;
     name: string;
     id?: string;
+    tracks: AnyConfigurationModel[];
 }
 export declare function isSessionModel(thing: unknown): thing is AbstractSessionModel;
 /** abstract interface for a session allows editing configurations */
@@ -110,6 +114,10 @@ export interface SessionWithDrawerWidgets extends SessionWithWidgets {
     setDrawerPosition(arg: string): void;
 }
 export declare function isSessionModelWithWidgets(thing: unknown): thing is SessionWithWidgets;
+interface SessionWithConnections {
+    addConnectionConf: (arg: AnyConfigurationModel) => void;
+}
+export declare function isSessionModelWithConnections(thing: unknown): thing is SessionWithConnections;
 export interface SessionWithSessionPlugins extends AbstractSessionModel {
     sessionPlugins: JBrowsePlugin[];
     addSessionPlugin: Function;
@@ -133,7 +141,9 @@ export interface AbstractViewModel {
     menuItems: () => MenuItem[];
 }
 export declare function isViewModel(thing: unknown): thing is AbstractViewModel;
-declare type AbstractTrackModel = {};
+export interface AbstractTrackModel {
+    displays: AbstractDisplayModel[];
+}
 export declare function isTrackModel(thing: unknown): thing is AbstractTrackModel;
 export interface AbstractDisplayModel {
     id: string;

package/util/types/index.js

@@ -11,6 +11,7 @@ var _exportNames = {
   isSessionModelWithConfigEditing: true,
   isSessionWithAddTracks: true,
   isSessionModelWithWidgets: true,
+  isSessionModelWithConnections: true,
   isSessionWithSessionPlugins: true,
   isSelectionContainer: true,
   isViewModel: true,
@@ -34,6 +35,7 @@ exports.isRetryException = isRetryException;
 exports.isSelectionContainer = isSelectionContainer;
 exports.isSessionModel = isSessionModel;
 exports.isSessionModelWithConfigEditing = isSessionModelWithConfigEditing;
+exports.isSessionModelWithConnections = isSessionModelWithConnections;
 exports.isSessionModelWithWidgets = isSessionModelWithWidgets;
 exports.isSessionWithAddTracks = isSessionWithAddTracks;
 exports.isSessionWithSessionPlugins = isSessionWithSessionPlugins;
@@ -103,6 +105,10 @@ function isSessionModelWithWidgets(thing) {
   return isSessionModel(thing) && 'widgets' in thing;
 }
 
+function isSessionModelWithConnections(thing) {
+  return isSessionModel(thing) && 'addConnectionConf' in thing;
+}
+
 function isSessionWithSessionPlugins(thing) {
   return isSessionModel(thing) && 'sessionPlugins' in thing;
 }

package/util/types/mst.d.ts

@@ -108,11 +108,11 @@ export declare const FileLocation: import("mobx-state-tree").ISnapshotProcessor<
         internetAccountType: import("mobx-state-tree").ISimpleType<string>;
         authInfo: import("mobx-state-tree").IType<any, any, any>;
     }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-}>> | import("mobx-state-tree").ModelInstanceTypeProps<{
+}>> | import("mobx-state-tree").ModelInstanceType<{
     locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
     name: import("mobx-state-tree").ISimpleType<string>;
     blobId: import("mobx-state-tree").ISimpleType<string>;
-}> | import("mobx-state-tree").ModelInstanceTypeProps<{
+}, {}> | import("mobx-state-tree").ModelInstanceType<{
     locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
     localPath: import("mobx-state-tree").ISimpleType<string>;
-}>>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+}, {}>>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/util/types/mst.js

@@ -98,8 +98,10 @@ exports.UriLocationRaw = UriLocationRaw;
 
 var UriLocation = _mobxStateTree.types.snapshotProcessor(UriLocationRaw, {
   postProcessor: function postProcessor(snap) {
-    var baseUri = snap.baseUri,
-        rest = (0, _objectWithoutProperties2.default)(snap, _excluded);
+    // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
+    var _ref = snap,
+        baseUri = _ref.baseUri,
+        rest = (0, _objectWithoutProperties2.default)(_ref, _excluded);
 
     if (!baseUri) {
       return rest;
@@ -113,14 +115,16 @@ exports.UriLocation = UriLocation;
 
 var FileLocation = _mobxStateTree.types.snapshotProcessor(_mobxStateTree.types.union(LocalPathLocation, UriLocation, BlobLocation), {
   // @ts-ignore
-  preProcessor: function preProcessor(snapshot) {
-    if (!snapshot) {
+  preProcessor: function preProcessor(snap) {
+    if (!snap) {
       return undefined;
     } // @ts-ignore
+    // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
 
 
-    var locationType = snapshot.locationType,
-        rest = (0, _objectWithoutProperties2.default)(snapshot, _excluded2);
+    var _ref2 = snap,
+        locationType = _ref2.locationType,
+        rest = (0, _objectWithoutProperties2.default)(_ref2, _excluded2);
 
     if (!locationType) {
       // @ts-ignore
@@ -142,7 +146,7 @@ var FileLocation = _mobxStateTree.types.snapshotProcessor(_mobxStateTree.types.u
       });
     }
 
-    return snapshot;
+    return snap;
   }
 });