@jbrowse/core 1.5.1 → 1.5.2

package/ReExports/material-ui-colors.js

@@ -5,118 +5,118 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-Object.defineProperty(exports, "red", {
+Object.defineProperty(exports, "amber", {
   enumerable: true,
   get: function get() {
-    return _red.default;
+    return _amber.default;
   }
 });
-Object.defineProperty(exports, "pink", {
+Object.defineProperty(exports, "blue", {
   enumerable: true,
   get: function get() {
-    return _pink.default;
+    return _blue.default;
   }
 });
-Object.defineProperty(exports, "purple", {
+Object.defineProperty(exports, "blueGrey", {
   enumerable: true,
   get: function get() {
-    return _purple.default;
+    return _blueGrey.default;
   }
 });
-Object.defineProperty(exports, "deepPurple", {
+Object.defineProperty(exports, "brown", {
   enumerable: true,
   get: function get() {
-    return _deepPurple.default;
+    return _brown.default;
   }
 });
-Object.defineProperty(exports, "indigo", {
+Object.defineProperty(exports, "cyan", {
   enumerable: true,
   get: function get() {
-    return _indigo.default;
+    return _cyan.default;
   }
 });
-Object.defineProperty(exports, "blue", {
+Object.defineProperty(exports, "deepOrange", {
   enumerable: true,
   get: function get() {
-    return _blue.default;
+    return _deepOrange.default;
   }
 });
-Object.defineProperty(exports, "lightBlue", {
+Object.defineProperty(exports, "deepPurple", {
   enumerable: true,
   get: function get() {
-    return _lightBlue.default;
+    return _deepPurple.default;
   }
 });
-Object.defineProperty(exports, "cyan", {
+Object.defineProperty(exports, "green", {
   enumerable: true,
   get: function get() {
-    return _cyan.default;
+    return _green.default;
   }
 });
-Object.defineProperty(exports, "teal", {
+Object.defineProperty(exports, "grey", {
   enumerable: true,
   get: function get() {
-    return _teal.default;
+    return _grey.default;
   }
 });
-Object.defineProperty(exports, "green", {
+Object.defineProperty(exports, "indigo", {
   enumerable: true,
   get: function get() {
-    return _green.default;
+    return _indigo.default;
   }
 });
-Object.defineProperty(exports, "lightGreen", {
+Object.defineProperty(exports, "lightBlue", {
   enumerable: true,
   get: function get() {
-    return _lightGreen.default;
+    return _lightBlue.default;
   }
 });
-Object.defineProperty(exports, "lime", {
+Object.defineProperty(exports, "lightGreen", {
   enumerable: true,
   get: function get() {
-    return _lime.default;
+    return _lightGreen.default;
   }
 });
-Object.defineProperty(exports, "yellow", {
+Object.defineProperty(exports, "lime", {
   enumerable: true,
   get: function get() {
-    return _yellow.default;
+    return _lime.default;
   }
 });
-Object.defineProperty(exports, "amber", {
+Object.defineProperty(exports, "orange", {
   enumerable: true,
   get: function get() {
-    return _amber.default;
+    return _orange.default;
   }
 });
-Object.defineProperty(exports, "orange", {
+Object.defineProperty(exports, "pink", {
   enumerable: true,
   get: function get() {
-    return _orange.default;
+    return _pink.default;
   }
 });
-Object.defineProperty(exports, "deepOrange", {
+Object.defineProperty(exports, "purple", {
   enumerable: true,
   get: function get() {
-    return _deepOrange.default;
+    return _purple.default;
   }
 });
-Object.defineProperty(exports, "brown", {
+Object.defineProperty(exports, "red", {
   enumerable: true,
   get: function get() {
-    return _brown.default;
+    return _red.default;
   }
 });
-Object.defineProperty(exports, "grey", {
+Object.defineProperty(exports, "teal", {
   enumerable: true,
   get: function get() {
-    return _grey.default;
+    return _teal.default;
   }
 });
-Object.defineProperty(exports, "blueGrey", {
+Object.defineProperty(exports, "yellow", {
   enumerable: true,
   get: function get() {
-    return _blueGrey.default;
+    return _yellow.default;
   }
 });
 

package/ReExports/modules.d.ts

@@ -22,6 +22,7 @@ import Plugin from '../Plugin';
 import * as coreUi from '../ui';
 import * as coreUtil from '../util';
 import * as coreColor from '../util/color';
+import * as coreLayouts from '../util/layouts';
 import * as trackUtils from '../util/tracks';
 import * as coreIo from '../util/io';
 import * as coreMstReflection from '../util/mst-reflection';
@@ -129,6 +130,7 @@ declare const libs: {
     '@jbrowse/core/ui': typeof coreUi;
     '@jbrowse/core/util': typeof coreUtil;
     '@jbrowse/core/util/color': typeof coreColor;
+    '@jbrowse/core/util/layouts': typeof coreLayouts;
     '@jbrowse/core/util/tracks': typeof trackUtils;
     '@jbrowse/core/util/Base1DViewModel': mst.IModelType<{
         displayedRegions: mst.IArrayType<mst.IModelType<{

package/ReExports/modules.js

@@ -135,6 +135,8 @@ var coreUtil = _interopRequireWildcard(require("../util"));
 
 var coreColor = _interopRequireWildcard(require("../util/color"));
 
+var coreLayouts = _interopRequireWildcard(require("../util/layouts"));
+
 var trackUtils = _interopRequireWildcard(require("../util/tracks"));
 
 var coreIo = _interopRequireWildcard(require("../util/io"));
@@ -225,6 +227,7 @@ var libs = {
   '@jbrowse/core/ui': coreUi,
   '@jbrowse/core/util': coreUtil,
   '@jbrowse/core/util/color': coreColor,
+  '@jbrowse/core/util/layouts': coreLayouts,
   '@jbrowse/core/util/tracks': trackUtils,
   '@jbrowse/core/util/Base1DViewModel': _Base1DViewModel.default,
   '@jbrowse/core/util/io': coreIo,

package/TextSearch/BaseResults.js

@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.RefSequenceResult = exports.default = void 0;
+exports.default = exports.RefSequenceResult = void 0;
 
 var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
 

package/assemblyManager/assembly.js

@@ -11,10 +11,10 @@ var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/sli
 
 var _objectWithoutProperties2 = _interopRequireDefault(require("@babel/runtime/helpers/objectWithoutProperties"));
 
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
 var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
 
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
 var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
 
 var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
@@ -300,7 +300,9 @@ function assemblyFactory(assemblyConfigType, pluginManager) {
           adapterConf: adapterConf,
           self: self,
           options: rest
-        }, signal, statusCallback);
+        }, // signal intentionally not passed here, fixes issues like #2221.
+        // alternative fix #2540 was proposed but non-working currently
+        undefined, statusCallback);
       },
 
       /**

package/assemblyManager/index.js

@@ -5,16 +5,16 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-Object.defineProperty(exports, "default", {
+Object.defineProperty(exports, "assemblyConfigSchemaFactory", {
   enumerable: true,
   get: function get() {
-    return _assemblyManager.default;
+    return _assemblyConfigSchema.default;
   }
 });
-Object.defineProperty(exports, "assemblyConfigSchemaFactory", {
+Object.defineProperty(exports, "default", {
   enumerable: true,
   get: function get() {
-    return _assemblyConfigSchema.default;
+    return _assemblyManager.default;
   }
 });
 

package/configuration/configurationSchema.js

@@ -5,8 +5,8 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.ConfigurationSchema = ConfigurationSchema;
 exports.ConfigurationReference = ConfigurationReference;
+exports.ConfigurationSchema = ConfigurationSchema;
 
 var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
 
@@ -141,7 +141,9 @@ function makeConfigurationSchemaModel(modelName, schemaDefinition, options) {
   });
 
   if (Object.keys(volatileConstants).length) {
-    completeModel = completeModel.volatile(function () {
+    completeModel = completeModel.volatile(function
+      /* self */
+    () {
       return volatileConstants;
     });
   }

package/configuration/configurationSlot.js

@@ -16,7 +16,9 @@ var _jexlStrings = require("../util/jexlStrings");
 var _mst = require("../util/types/mst");
 
 /* eslint-disable @typescript-eslint/no-explicit-any */
-function isValidColorString() {
+function
+  /* str */
+isValidColorString() {
   // TODO: check all the crazy cases for whether it's a valid HTML/CSS color string
   return true;
 }

package/configuration/index.js

@@ -7,16 +7,16 @@ var _exportNames = {
   ConfigurationSchema: true,
   ConfigurationReference: true
 };
-Object.defineProperty(exports, "ConfigurationSchema", {
+Object.defineProperty(exports, "ConfigurationReference", {
   enumerable: true,
   get: function get() {
-    return _configurationSchema.ConfigurationSchema;
+    return _configurationSchema.ConfigurationReference;
   }
 });
-Object.defineProperty(exports, "ConfigurationReference", {
+Object.defineProperty(exports, "ConfigurationSchema", {
   enumerable: true,
   get: function get() {
-    return _configurationSchema.ConfigurationReference;
+    return _configurationSchema.ConfigurationSchema;
   }
 });
 

package/configuration/util.js

@@ -5,13 +5,13 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.readConfObject = readConfObject;
 exports.getConf = getConf;
 exports.getTypeNamesFromExplicitlyTypedUnion = getTypeNamesFromExplicitlyTypedUnion;
 exports.isBareConfigurationSchemaType = isBareConfigurationSchemaType;
-exports.isConfigurationSchemaType = isConfigurationSchemaType;
 exports.isConfigurationModel = isConfigurationModel;
+exports.isConfigurationSchemaType = isConfigurationSchemaType;
 exports.isConfigurationSlotType = isConfigurationSlotType;
+exports.readConfObject = readConfObject;
 
 var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
 

package/data_adapters/BaseAdapter.d.ts

@@ -2,7 +2,7 @@ import { Observable } from 'rxjs';
 import { Feature } from '../util/simpleFeature';
 import { AnyConfigurationModel } from '../configuration/configurationSchema';
 import { getSubAdapterType } from './dataAdapterCache';
-import { Region, NoAssemblyRegion } from '../util/types';
+import { AugmentedRegion as Region, NoAssemblyRegion } from '../util/types';
 import BaseResult from '../TextSearch/BaseResults';
 import PluginManager from '../PluginManager';
 export interface BaseOptions {

package/data_adapters/BaseAdapter.js

@@ -5,17 +5,17 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.isSequenceAdapter = isSequenceAdapter;
-exports.isRegionsAdapter = isRegionsAdapter;
+exports.BaseFeatureDataAdapter = exports.BaseAdapter = void 0;
 exports.isFeatureAdapter = isFeatureAdapter;
 exports.isRefNameAliasAdapter = isRefNameAliasAdapter;
+exports.isRegionsAdapter = isRegionsAdapter;
+exports.isSequenceAdapter = isSequenceAdapter;
 exports.isTextSearchAdapter = isTextSearchAdapter;
-exports.BaseFeatureDataAdapter = exports.BaseAdapter = void 0;
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
 
 var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
 
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
 var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
 
 var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));

package/data_adapters/CytobandAdapter.js

@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.DataAdapter = exports.configSchema = void 0;
+exports.configSchema = exports.DataAdapter = void 0;
 
 var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
 
@@ -118,7 +118,9 @@ var CytobandAdapter = /*#__PURE__*/function (_BaseAdapter) {
     }()
   }, {
     key: "freeResources",
-    value: function freeResources() {}
+    value: function
+      /* { region } */
+    freeResources() {}
   }]);
   return CytobandAdapter;
 }(_BaseAdapter2.BaseAdapter);

package/data_adapters/dataAdapterCache.js

@@ -5,9 +5,9 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.getAdapter = getAdapter;
-exports.freeAdapterResources = freeAdapterResources;
 exports.clearAdapterCache = clearAdapterCache;
+exports.freeAdapterResources = freeAdapterResources;
+exports.getAdapter = getAdapter;
 
 var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "1.5.1",
+  "version": "1.5.2",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -44,18 +44,19 @@
     "escape-html": "^1.0.3",
     "fast-deep-equal": "^3.1.3",
     "file-uri-to-path": "^1.0.0",
-    "generic-filehandle": "^2.2.0",
+    "generic-filehandle": "^2.2.2",
     "http-range-fetcher": "^1.2.2",
     "is-object": "^1.0.1",
     "jexl": "^2.3.0",
     "json-stable-stringify": "^1.0.1",
-    "librpc-web-mod": "^1.1.2",
+    "librpc-web-mod": "^1.1.4",
     "load-script2": "^2.0.5",
     "object.fromentries": "^2.0.0",
     "rbush": "^3.0.1",
     "react-error-boundary": "^3.0.0",
     "react-intersection-observer": "^8.31.0",
     "react-measure": "^2.3.0",
+    "sanitize-filename": "^1.6.3",
     "shortid": "^2.2.13",
     "svg-path-generator": "^1.1.0",
     "tenacious-fetch": "^2.1.0",
@@ -77,5 +78,5 @@
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "284e408c72a3d4d7a0d603197501a8fc8f68c4bc"
+  "gitHead": "94fdfbc34787ab8f12a87e00038da74b247b42fa"
 }

package/pluggableElementTypes/RpcMethodType.js

@@ -7,12 +7,12 @@ Object.defineProperty(exports, "__esModule", {
 });
 exports.default = void 0;
 
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
 var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
 
 var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
 
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
 var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
 
 var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));

package/pluggableElementTypes/index.d.ts

@@ -9,6 +9,7 @@ import RpcMethodType from './RpcMethodType';
 import InternetAccountType from './InternetAccountType';
 import TextSearchAdapterType from './TextSearchAdapterType';
 export * from './renderers';
-export { AdapterType, ConnectionType, RendererType, WidgetType, TrackType, DisplayType, ViewType, RpcMethodType, TextSearchAdapterType, };
+export * from './models';
+export { AdapterType, ConnectionType, RendererType, WidgetType, TrackType, DisplayType, ViewType, RpcMethodType, InternetAccountType, TextSearchAdapterType, };
 export declare type PluggableElementType = AdapterType | ConnectionType | RendererType | WidgetType | TrackType | DisplayType | ViewType | RpcMethodType | InternetAccountType | TextSearchAdapterType;
 export declare type PluggableElementMember = keyof AdapterType | keyof ConnectionType | keyof RendererType | keyof WidgetType | keyof TrackType | keyof DisplayType | keyof ViewType | keyof RpcMethodType | keyof InternetAccountType | keyof TextSearchAdapterType;

package/pluggableElementTypes/index.js

@@ -14,6 +14,7 @@ var _exportNames = {
   DisplayType: true,
   ViewType: true,
   RpcMethodType: true,
+  InternetAccountType: true,
   TextSearchAdapterType: true
 };
 Object.defineProperty(exports, "AdapterType", {
@@ -28,46 +29,52 @@ Object.defineProperty(exports, "ConnectionType", {
     return _ConnectionType.default;
   }
 });
-Object.defineProperty(exports, "RendererType", {
+Object.defineProperty(exports, "DisplayType", {
   enumerable: true,
   get: function get() {
-    return _RendererType.default;
+    return _DisplayType.default;
   }
 });
-Object.defineProperty(exports, "WidgetType", {
+Object.defineProperty(exports, "InternetAccountType", {
   enumerable: true,
   get: function get() {
-    return _WidgetType.default;
+    return _InternetAccountType.default;
   }
 });
-Object.defineProperty(exports, "TrackType", {
+Object.defineProperty(exports, "RendererType", {
   enumerable: true,
   get: function get() {
-    return _TrackType.default;
+    return _RendererType.default;
   }
 });
-Object.defineProperty(exports, "DisplayType", {
+Object.defineProperty(exports, "RpcMethodType", {
   enumerable: true,
   get: function get() {
-    return _DisplayType.default;
+    return _RpcMethodType.default;
   }
 });
-Object.defineProperty(exports, "ViewType", {
+Object.defineProperty(exports, "TextSearchAdapterType", {
   enumerable: true,
   get: function get() {
-    return _ViewType.default;
+    return _TextSearchAdapterType.default;
   }
 });
-Object.defineProperty(exports, "RpcMethodType", {
+Object.defineProperty(exports, "TrackType", {
   enumerable: true,
   get: function get() {
-    return _RpcMethodType.default;
+    return _TrackType.default;
   }
 });
-Object.defineProperty(exports, "TextSearchAdapterType", {
+Object.defineProperty(exports, "ViewType", {
   enumerable: true,
   get: function get() {
-    return _TextSearchAdapterType.default;
+    return _ViewType.default;
+  }
+});
+Object.defineProperty(exports, "WidgetType", {
+  enumerable: true,
+  get: function get() {
+    return _WidgetType.default;
   }
 });
 
@@ -87,6 +94,8 @@ var _ViewType = _interopRequireDefault(require("./ViewType"));
 
 var _RpcMethodType = _interopRequireDefault(require("./RpcMethodType"));
 
+var _InternetAccountType = _interopRequireDefault(require("./InternetAccountType"));
+
 var _TextSearchAdapterType = _interopRequireDefault(require("./TextSearchAdapterType"));
 
 var _renderers = require("./renderers");
@@ -101,4 +110,18 @@ Object.keys(_renderers).forEach(function (key) {
       return _renderers[key];
     }
   });
+});
+
+var _models = require("./models");
+
+Object.keys(_models).forEach(function (key) {
+  if (key === "default" || key === "__esModule") return;
+  if (Object.prototype.hasOwnProperty.call(_exportNames, key)) return;
+  if (key in exports && exports[key] === _models[key]) return;
+  Object.defineProperty(exports, key, {
+    enumerable: true,
+    get: function get() {
+      return _models[key];
+    }
+  });
 });

package/pluggableElementTypes/models/BaseTrackModel.js

@@ -86,7 +86,8 @@ function createBaseTrackModel(pluginManager, trackType, baseTrackConfig) {
 
       get canConfigure() {
         var session = (0, _util.getSession)(self);
-        return (0, _types.isSessionModelWithConfigEditing)(session) && (session.adminMode || // @ts-ignore
+        return (0, _types.isSessionModelWithConfigEditing)(session) && ( // @ts-ignore
+        session.adminMode || // @ts-ignore
         session.sessionTracks.find(function (track) {
           return track.trackId === self.configuration.trackId;
         }));

package/pluggableElementTypes/models/BaseViewModel.js

@@ -12,11 +12,15 @@ var _mst = require("../../util/types/mst");
 var BaseViewModel = _mobxStateTree.types.model('BaseView', {
   id: _mst.ElementId,
   displayName: _mobxStateTree.types.maybe(_mobxStateTree.types.string)
-}).volatile(function () {
+}).volatile(function
+  /* self */
+() {
   return {
     width: 800
   };
-}).views(function () {
+}).views(function
+  /* self */
+() {
   return {
     menuItems: function menuItems() {
       return [];

package/pluggableElementTypes/models/InternetAccountModel.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
 import { Instance } from 'mobx-state-tree';
-import { GenericFilehandle } from 'generic-filehandle';
+import { RemoteFileWithRangeCache } from '../../util/io';
 import { FileLocation, UriLocation, AnyReactComponentType } from '@jbrowse/core/util/types';
 export declare const InternetAccount: import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -15,7 +15,7 @@ export declare const InternetAccount: import("mobx-state-tree").IModelType<{
     readonly selectorLabel: string | undefined;
     handlesLocation(location: FileLocation): boolean;
 } & {
-    openLocation(location: UriLocation): GenericFilehandle;
+    openLocation(location: UriLocation): RemoteFileWithRangeCache;
     getPreAuthorizationInformation(location: UriLocation): Promise<{
         internetAccountType: string;
     }>;