@jbrowse/core 1.5.0 → 1.5.4

package/util/tracks.js

@@ -3,22 +3,25 @@
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.getTrackAssemblyNames = getTrackAssemblyNames;
-exports.getRpcSessionId = getRpcSessionId;
-exports.getParentRenderProps = getParentRenderProps;
+exports.UNSUPPORTED = exports.UNKNOWN = void 0;
+exports.generateUnknownTrackConf = generateUnknownTrackConf;
+exports.generateUnsupportedTrackConf = generateUnsupportedTrackConf;
 exports.getBlob = getBlob;
 exports.getBlobMap = getBlobMap;
-exports.setBlobMap = setBlobMap;
-exports.storeBlobLocation = storeBlobLocation;
+exports.getFileName = getFileName;
+exports.getParentRenderProps = getParentRenderProps;
+exports.getRpcSessionId = getRpcSessionId;
+exports.getTrackAssemblyNames = getTrackAssemblyNames;
 exports.guessAdapter = guessAdapter;
 exports.guessTrackType = guessTrackType;
-exports.generateUnsupportedTrackConf = generateUnsupportedTrackConf;
-exports.generateUnknownTrackConf = generateUnknownTrackConf;
-exports.UNSUPPORTED = exports.UNKNOWN = void 0;
+exports.makeIndex = makeIndex;
+exports.makeIndexType = makeIndexType;
+exports.setBlobMap = setBlobMap;
+exports.storeBlobLocation = storeBlobLocation;
 
 var _mobxStateTree = require("mobx-state-tree");
 
-var _index = require("./index");
+var _index2 = require("./index");
 
 var _configuration = require("../configuration");
 
@@ -112,187 +115,63 @@ function storeBlobLocation(location) {
 
   return location;
 }
+/**
+ * creates a new location from the provided location including the appropriate suffix and location type
+ * @param location - the FileLocation
+ * @param suffix - the file suffix (e.g. .bam)
+ * @returns the constructed location object from the provided prameters
+ */
 
-function guessAdapter(file, index, getFileName, adapterHint) {
-  function makeIndex(location, suffix) {
-    if ('uri' in location) {
-      return {
-        uri: location.uri + suffix,
-        locationType: 'UriLocation'
-      };
-    }
-
-    if ('localPath' in location) {
-      return {
-        localPath: location.localPath + suffix,
-        locationType: 'LocalPathLocation'
-      };
-    }
-
-    return location;
-  }
-
-  var fileName = getFileName(file);
-  var indexName = index && getFileName(index);
-
-  function makeIndexType(name, typeA, typeB) {
-    return name !== null && name !== void 0 && name.toUpperCase().endsWith(typeA) ? typeA : typeB;
-  }
-
-  if (/\.bam$/i.test(fileName) || adapterHint === 'BamAdapter') {
-    return {
-      type: 'BamAdapter',
-      bamLocation: file,
-      index: {
-        location: index || makeIndex(file, '.bai'),
-        indexType: makeIndexType(indexName, 'CSI', 'BAI')
-      }
-    };
-  }
-
-  if (/\.cram$/i.test(fileName) || adapterHint === 'CramAdapter') {
-    return {
-      type: 'CramAdapter',
-      cramLocation: file,
-      craiLocation: index || makeIndex(file, '.crai')
-    };
-  }
-
-  if (/\.gff3?$/i.test(fileName)) {
-    return {
-      type: 'Gff3Adapter',
-      gffLocation: file
-    };
-  }
-
-  if (/\.gff3?\.b?gz$/i.test(fileName) || adapterHint === 'Gff3TabixAdapter') {
-    return {
-      type: 'Gff3TabixAdapter',
-      gffGzLocation: file,
-      index: {
-        location: index || makeIndex(file, '.tbi'),
-        indexType: makeIndexType(indexName, 'CSI', 'TBI')
-      }
-    };
-  }
-
-  if (/\.gtf?$/i.test(fileName)) {
-    return {
-      type: 'UNSUPPORTED'
-    };
-  }
-
-  if (/\.vcf$/i.test(fileName) || adapterHint === 'VcfAdapter') {
-    return {
-      type: 'VcfAdapter',
-      vcfLocation: file
-    };
-  }
-
-  if (/\.vcf\.b?gz$/i.test(fileName) || adapterHint === 'VcfTabixAdapter') {
-    return {
-      type: 'VcfTabixAdapter',
-      vcfGzLocation: file,
-      index: {
-        location: index || makeIndex(file, '.tbi'),
-        indexType: makeIndexType(indexName, 'CSI', 'TBI')
-      }
-    };
-  }
-
-  if (/\.vcf\.idx$/i.test(fileName)) {
-    return {
-      type: 'UNSUPPORTED'
-    };
-  }
-
-  if (/\.bed$/i.test(fileName)) {
-    return {
-      type: 'UNSUPPORTED'
-    };
-  }
-
-  if (/\.bed\.b?gz$/i.test(fileName) || adapterHint === 'BedTabixAdapter') {
-    return {
-      type: 'BedTabixAdapter',
-      bedGzLocation: file,
-      index: {
-        location: index || makeIndex(file, '.tbi'),
-        indexType: makeIndexType(indexName, 'CSI', 'TBI')
-      }
-    };
-  }
-
-  if (/\.(bb|bigbed)$/i.test(fileName) || adapterHint === 'BigBedAdapter') {
-    return {
-      type: 'BigBedAdapter',
-      bigBedLocation: file
-    };
-  }
-
-  if (/\.(bw|bigwig)$/i.test(fileName) || adapterHint === 'BigWigAdapter') {
-    return {
-      type: 'BigWigAdapter',
-      bigWigLocation: file
-    };
-  }
-
-  if (/\.(fa|fasta|fas|fna|mfa)$/i.test(fileName) || adapterHint === 'IndexedFastaAdapter') {
-    return {
-      type: 'IndexedFastaAdapter',
-      fastaLocation: file,
-      faiLocation: index || makeIndex(file, '.fai')
-    };
-  }
 
-  if (/\.(fa|fasta|fas|fna|mfa)\.b?gz$/i.test(fileName) || adapterHint === 'BgzipFastaAdapter') {
+function makeIndex(location, suffix) {
+  if ('uri' in location) {
     return {
-      type: 'BgzipFastaAdapter',
-      fastaLocation: file,
-      faiLocation: makeIndex(file, '.fai'),
-      gziLocation: makeIndex(file, '.gzi')
+      uri: location.uri + suffix,
+      locationType: 'UriLocation'
     };
   }
 
-  if (/\.2bit$/i.test(fileName) || adapterHint === 'TwoBitAdapter') {
+  if ('localPath' in location) {
     return {
-      type: 'TwoBitAdapter',
-      twoBitLocation: file
+      localPath: location.localPath + suffix,
+      locationType: 'LocalPathLocation'
     };
   }
 
-  if (/\.sizes$/i.test(fileName)) {
-    return {
-      type: 'UNSUPPORTED'
-    };
-  }
+  return location;
+}
+/**
+ * constructs a potential index file (with suffix) from the provided file name
+ * @param name - the name of the index file
+ * @param typeA - one option of a potential two file suffix (e.g. CSI, BAI)
+ * @param typeB - the second option of a potential two file suffix (e.g. CSI, BAI)
+ * @returns a likely name of the index file for a given filename
+ */
 
-  if (/\/trackData.jsonz?$/i.test(fileName) || adapterHint === 'NCListAdapter') {
-    return {
-      type: 'NCListAdapter',
-      rootUrlTemplate: file
-    };
-  }
 
-  if (/\/sparql$/i.test(fileName) || adapterHint === 'SPARQLAdapter') {
-    return {
-      type: 'SPARQLAdapter',
-      endpoint: file
-    };
-  }
+function makeIndexType(name, typeA, typeB) {
+  return name !== null && name !== void 0 && name.toUpperCase().endsWith(typeA) ? typeA : typeB;
+}
 
-  if (/\.hic/i.test(fileName) || adapterHint === 'HicAdapter') {
-    return {
-      type: 'HicAdapter',
-      hicLocation: file
-    };
-  }
+function getFileName(track) {
+  var uri = 'uri' in track ? track.uri : undefined;
+  var localPath = 'localPath' in track ? track.localPath : undefined;
+  var blob = 'blobId' in track ? track : undefined;
+  return (blob === null || blob === void 0 ? void 0 : blob.name) || (uri === null || uri === void 0 ? void 0 : uri.slice(uri.lastIndexOf('/') + 1)) || (localPath === null || localPath === void 0 ? void 0 : localPath.slice(localPath.lastIndexOf('/') + 1)) || '';
+}
 
-  if (/\.paf/i.test(fileName) || adapterHint === 'PAFAdapter') {
-    return {
-      type: 'PAFAdapter',
-      pafLocation: file
-    };
+function guessAdapter(file, index, adapterHint, model) {
+  if (model) {
+    // @ts-ignore
+    var session = (0, _index2.getSession)(model);
+    var adapterGuesser = (0, _mobxStateTree.getEnv)(session).pluginManager.evaluateExtensionPoint('Core-guessAdapterForLocation', function (_file, _index, _adapterHint) {
+      return undefined;
+    });
+    var adapter = adapterGuesser(file, index, adapterHint);
+
+    if (adapter) {
+      return adapter;
+    }
   }
 
   return {
@@ -300,20 +179,21 @@ function guessAdapter(file, index, getFileName, adapterHint) {
   };
 }
 
-function guessTrackType(adapterType) {
-  var known = {
-    BamAdapter: 'AlignmentsTrack',
-    CramAdapter: 'AlignmentsTrack',
-    BgzipFastaAdapter: 'ReferenceSequenceTrack',
-    BigWigAdapter: 'QuantitativeTrack',
-    IndexedFastaAdapter: 'ReferenceSequenceTrack',
-    TwoBitAdapter: 'ReferenceSequenceTrack',
-    VcfAdapter: 'VariantTrack',
-    VcfTabixAdapter: 'VariantTrack',
-    HicAdapter: 'HicTrack',
-    PAFAdapter: 'SyntenyTrack'
-  };
-  return known[adapterType] || 'FeatureTrack';
+function guessTrackType(adapterType, model) {
+  if (model) {
+    // @ts-ignore
+    var session = (0, _index2.getSession)(model);
+    var trackTypeGuesser = (0, _mobxStateTree.getEnv)(session).pluginManager.evaluateExtensionPoint('Core-guessTrackTypeForLocation', function (_adapterName) {
+      return undefined;
+    });
+    var trackType = trackTypeGuesser(adapterType);
+
+    if (trackType) {
+      return trackType;
+    }
+  }
+
+  return 'FeatureTrack';
 }
 
 function generateUnsupportedTrackConf(trackName, trackUrl, categories) {
@@ -324,7 +204,7 @@ function generateUnsupportedTrackConf(trackName, trackUrl, categories) {
     category: categories,
     trackId: ''
   };
-  conf.trackId = (0, _index.objectHash)(conf);
+  conf.trackId = (0, _index2.objectHash)(conf);
   return conf;
 }
 
@@ -336,6 +216,6 @@ function generateUnknownTrackConf(trackName, trackUrl, categories) {
     category: categories,
     trackId: ''
   };
-  conf.trackId = (0, _index.objectHash)(conf);
+  conf.trackId = (0, _index2.objectHash)(conf);
   return conf;
 }

package/util/types/index.d.ts

@@ -29,7 +29,10 @@ export interface JBrowsePlugin {
     authors: string[];
     description: string;
     location: string;
-    url: string;
+    url?: string;
+    umdUrl?: string;
+    esmUrl?: string;
+    cjsUrl?: string;
     license: string;
     image?: string;
 }
@@ -61,7 +64,6 @@ export interface AbstractSessionModel extends AbstractViewContainer {
     adminMode?: boolean;
     showWidget?: Function;
     addWidget?: Function;
-    addTrackConf?: Function;
     DialogComponent?: DialogComponentType;
     DialogProps: any;
     queueDialog: (callback: (doneCallback: Function) => [DialogComponentType, any]) => void;
@@ -74,6 +76,11 @@ export interface SessionWithConfigEditing extends AbstractSessionModel {
     editConfiguration(configuration: AnyConfigurationModel): void;
 }
 export declare function isSessionModelWithConfigEditing(thing: unknown): thing is SessionWithConfigEditing;
+/** abstract interface for a session allows adding tracks */
+export interface SessionWithConfigEditing extends AbstractSessionModel {
+    addTrackConf(configuration: AnyConfigurationModel | SnapshotIn<AnyConfigurationModel>): void;
+}
+export declare function isSessionWithAddTracks(thing: unknown): thing is SessionWithConfigEditing;
 export interface Widget {
     type: string;
     id: string;
@@ -169,16 +176,21 @@ export interface NoAssemblyRegion extends SnapshotIn<typeof MUNoAssemblyRegion>
 }
 export interface Region extends SnapshotIn<typeof MUIRegion> {
 }
+export interface AugmentedRegion extends Region {
+    originalRefName?: string;
+}
 export interface LocalPathLocation extends SnapshotIn<typeof MULocalPathLocation> {
 }
 export interface UriLocation extends SnapshotIn<typeof MUUriLocation> {
 }
 export declare function isUriLocation(location: unknown): location is UriLocation;
 export declare class AuthNeededError extends Error {
+    message: string;
     location: UriLocation;
     constructor(message: string, location: UriLocation);
 }
 export declare class RetryError extends Error {
+    message: string;
     internetAccountId: string;
     constructor(message: string, internetAccountId: string);
 }

package/util/types/index.js

@@ -9,6 +9,7 @@ var _exportNames = {
   isViewContainer: true,
   isSessionModel: true,
   isSessionModelWithConfigEditing: true,
+  isSessionWithAddTracks: true,
   isSessionModelWithWidgets: true,
   isSessionWithSessionPlugins: true,
   isSelectionContainer: true,
@@ -24,22 +25,25 @@ var _exportNames = {
   isAuthNeededException: true,
   isRetryException: true
 };
-exports.isViewContainer = isViewContainer;
+exports.RetryError = exports.AuthNeededError = void 0;
+exports.isAbstractMenuManager = isAbstractMenuManager;
+exports.isAppRootModel = isAppRootModel;
+exports.isAuthNeededException = isAuthNeededException;
+exports.isDisplayModel = isDisplayModel;
+exports.isRetryException = isRetryException;
+exports.isSelectionContainer = isSelectionContainer;
 exports.isSessionModel = isSessionModel;
 exports.isSessionModelWithConfigEditing = isSessionModelWithConfigEditing;
 exports.isSessionModelWithWidgets = isSessionModelWithWidgets;
+exports.isSessionWithAddTracks = isSessionWithAddTracks;
 exports.isSessionWithSessionPlugins = isSessionWithSessionPlugins;
-exports.isSelectionContainer = isSelectionContainer;
-exports.isViewModel = isViewModel;
 exports.isTrackModel = isTrackModel;
-exports.isDisplayModel = isDisplayModel;
 exports.isTrackViewModel = isTrackViewModel;
-exports.isAppRootModel = isAppRootModel;
-exports.isAbstractMenuManager = isAbstractMenuManager;
 exports.isUriLocation = isUriLocation;
-exports.isAuthNeededException = isAuthNeededException;
-exports.isRetryException = isRetryException;
-exports.RetryError = exports.AuthNeededError = void 0;
+exports.isViewContainer = isViewContainer;
+exports.isViewModel = isViewModel;
+
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
 
 var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
 
@@ -53,8 +57,6 @@ var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/ge
 
 var _wrapNativeSuper2 = _interopRequireDefault(require("@babel/runtime/helpers/wrapNativeSuper"));
 
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
 var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
 
 var _mobxStateTree = require("mobx-state-tree");
@@ -90,6 +92,12 @@ function isSessionModel(thing) {
 function isSessionModelWithConfigEditing(thing) {
   return isSessionModel(thing) && 'editConfiguration' in thing;
 }
+/** abstract interface for a session allows adding tracks */
+
+
+function isSessionWithAddTracks(thing) {
+  return isSessionModel(thing) && 'addTrackConf' in thing;
+}
 
 function isSessionModelWithWidgets(thing) {
   return isSessionModel(thing) && 'widgets' in thing;
@@ -155,14 +163,12 @@ var AuthNeededError = /*#__PURE__*/function (_Error) {
 
     (0, _classCallCheck2.default)(this, AuthNeededError);
     _this = _super.call(this, message);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "location", void 0);
-    _this.location = location;
     _this.name = 'AuthNeededError';
     Object.setPrototypeOf((0, _assertThisInitialized2.default)(_this), AuthNeededError.prototype);
     return _this;
   }
 
-  return AuthNeededError;
+  return (0, _createClass2.default)(AuthNeededError);
 }( /*#__PURE__*/(0, _wrapNativeSuper2.default)(Error));
 
 exports.AuthNeededError = AuthNeededError;
@@ -177,14 +183,11 @@ var RetryError = /*#__PURE__*/function (_Error2) {
 
     (0, _classCallCheck2.default)(this, RetryError);
     _this2 = _super2.call(this, message);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this2), "internetAccountId", void 0);
-    _this2.message = message;
-    _this2.internetAccountId = internetAccountId;
     _this2.name = 'RetryError';
     return _this2;
   }
 
-  return RetryError;
+  return (0, _createClass2.default)(RetryError);
 }( /*#__PURE__*/(0, _wrapNativeSuper2.default)(Error));
 
 exports.RetryError = RetryError;

package/util/types/mst.js

@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.FileLocation = exports.UriLocation = exports.UriLocationRaw = exports.BlobLocation = exports.LocalPathLocation = exports.Region = exports.NoAssemblyRegion = exports.PropTypes = exports.ElementId = void 0;
+exports.UriLocationRaw = exports.UriLocation = exports.Region = exports.PropTypes = exports.NoAssemblyRegion = exports.LocalPathLocation = exports.FileLocation = exports.ElementId = exports.BlobLocation = void 0;
 
 var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
 
@@ -22,9 +22,9 @@ var _mobxReact = require("mobx-react");
 var _excluded = ["baseUri"],
     _excluded2 = ["locationType"];
 
-function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); if (enumerableOnly) { symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; }); } keys.push.apply(keys, symbols); } return keys; }
+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 = arguments[i] != null ? arguments[i] : {}; if (i % 2) { ownKeys(Object(source), true).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }); } else if (Object.getOwnPropertyDescriptors) { Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)); } else { ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } } return target; }
+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 ElementId = _mobxStateTree.types.optional(_mobxStateTree.types.identifier, _shortid.default.generate); // PropTypes that are useful when working with instances of these in react components
 
@@ -129,11 +129,11 @@ var FileLocation = _mobxStateTree.types.snapshotProcessor(_mobxStateTree.types.u
           blob = rest.blob;
       var _locationType = '';
 
-      if (uri) {
+      if (uri !== undefined) {
         _locationType = 'UriLocation';
-      } else if (localPath) {
+      } else if (localPath !== undefined) {
         _locationType = 'LocalPathLocation';
-      } else if (blob) {
+      } else if (blob !== undefined) {
         _locationType = 'BlobLocation';
       }
 

package/assemblyManager/assemblyConfigSchemas.d.ts

@@ -1,7 +0,0 @@
-import { SnapshotIn } from 'mobx-state-tree';
-import PluginManager from '../PluginManager';
-declare const _default: (pluginManager: PluginManager) => {
-    assemblyConfigSchemas: import("../configuration/configurationSchema").AnyConfigurationSchemaType[];
-    dispatcher: (snapshot: import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> | undefined) => import("../configuration/configurationSchema").AnyConfigurationSchemaType;
-};
-export default _default;

package/value.d.ts

@@ -1 +0,0 @@
-export default function (): number;

package/value.js

@@ -1,10 +0,0 @@
-"use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = _default;
-
-function _default() {
-  return 43;
-}