@jbrowse/core 1.7.11 → 2.1.0

package/util/tracks.js

@@ -1,145 +1,108 @@
 "use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.UNSUPPORTED = exports.UNKNOWN = void 0;
-exports.generateUnknownTrackConf = generateUnknownTrackConf;
-exports.generateUnsupportedTrackConf = generateUnsupportedTrackConf;
-exports.getBlob = getBlob;
-exports.getBlobMap = getBlobMap;
-exports.getFileName = getFileName;
-exports.getParentRenderProps = getParentRenderProps;
-exports.getRpcSessionId = getRpcSessionId;
-exports.getTrackAssemblyNames = getTrackAssemblyNames;
-exports.guessAdapter = guessAdapter;
-exports.guessTrackType = guessTrackType;
-exports.makeIndex = makeIndex;
-exports.makeIndexType = makeIndexType;
-exports.setBlobMap = setBlobMap;
-exports.storeBlobLocation = storeBlobLocation;
-
-var _mobxStateTree = require("mobx-state-tree");
-
-var _index2 = require("./index");
-
-var _configuration = require("../configuration");
-
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.generateUnknownTrackConf = exports.generateUnsupportedTrackConf = exports.guessTrackType = exports.guessAdapter = exports.getFileName = exports.makeIndexType = exports.makeIndex = exports.storeBlobLocation = exports.setBlobMap = exports.getBlobMap = exports.getBlob = exports.UNSUPPORTED = exports.UNKNOWN = exports.getParentRenderProps = exports.getRpcSessionId = exports.getTrackAssemblyNames = void 0;
+const mobx_state_tree_1 = require("mobx-state-tree");
+const index_1 = require("./index");
+const configuration_1 = require("../configuration");
 /* utility functions for use by track models and so forth */
 function getTrackAssemblyNames(track) {
-  var trackConf = track.configuration;
-  var trackAssemblyNames = (0, _configuration.readConfObject)(trackConf, 'assemblyNames');
-
-  if (!trackAssemblyNames) {
-    // Check if it's an assembly sequence track
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    var parent = (0, _mobxStateTree.getParent)(track.configuration);
-
-    if ('sequence' in parent) {
-      return [(0, _configuration.readConfObject)(parent, 'name')];
+    const trackConf = track.configuration;
+    const trackAssemblyNames = (0, configuration_1.readConfObject)(trackConf, 'assemblyNames');
+    if (!trackAssemblyNames) {
+        // Check if it's an assembly sequence track
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        const parent = (0, mobx_state_tree_1.getParent)(track.configuration);
+        if ('sequence' in parent) {
+            return [(0, configuration_1.readConfObject)(parent, 'name')];
+        }
     }
-  }
-
-  return trackAssemblyNames;
+    return trackAssemblyNames;
 }
+exports.getTrackAssemblyNames = getTrackAssemblyNames;
 /** return the rpcSessionId of the highest parent node in the tree that has an rpcSessionId */
-
-
 function getRpcSessionId(thisNode) {
-  var highestRpcSessionId;
-
-  for (var node = thisNode; !(0, _mobxStateTree.isRoot)(node); node = (0, _mobxStateTree.getParent)(node)) {
-    if ('rpcSessionId' in node) {
-      highestRpcSessionId = node.rpcSessionId;
+    let highestRpcSessionId;
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    for (let node = thisNode; !(0, mobx_state_tree_1.isRoot)(node); node = (0, mobx_state_tree_1.getParent)(node)) {
+        if ('rpcSessionId' in node) {
+            highestRpcSessionId = node.rpcSessionId;
+        }
+    }
+    if (!highestRpcSessionId) {
+        throw new Error('getRpcSessionId failed, no parent node in the state tree has an `rpcSessionId` attribute');
     }
-  }
-
-  if (!highestRpcSessionId) {
-    throw new Error('getRpcSessionId failed, no parent node in the state tree has an `rpcSessionId` attribute');
-  }
-
-  return highestRpcSessionId;
+    return highestRpcSessionId;
 }
+exports.getRpcSessionId = getRpcSessionId;
 /**
  * given an MST node, get the renderprops of the first parent container that has
  * renderProps
  * @param node -
  * @returns renderprops, or empty object if none found
  */
-
-
 function getParentRenderProps(node) {
-  for (var currentNode = (0, _mobxStateTree.getParent)(node); !(0, _mobxStateTree.isRoot)(currentNode); currentNode = (0, _mobxStateTree.getParent)(currentNode)) {
-    if ('renderProps' in currentNode) {
-      return currentNode.renderProps();
+    for (
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    let currentNode = (0, mobx_state_tree_1.getParent)(node); !(0, mobx_state_tree_1.isRoot)(currentNode); 
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    currentNode = (0, mobx_state_tree_1.getParent)(currentNode)) {
+        if ('renderProps' in currentNode) {
+            return currentNode.renderProps();
+        }
     }
-  }
-
-  return {};
+    return {};
 }
-
-var UNKNOWN = 'UNKNOWN';
-exports.UNKNOWN = UNKNOWN;
-var UNSUPPORTED = 'UNSUPPORTED';
-exports.UNSUPPORTED = UNSUPPORTED;
-var blobMap = {}; // get a specific blob
-
+exports.getParentRenderProps = getParentRenderProps;
+exports.UNKNOWN = 'UNKNOWN';
+exports.UNSUPPORTED = 'UNSUPPORTED';
+let blobMap = {};
+// get a specific blob
 function getBlob(id) {
-  return blobMap[id];
-} // used to export entire context to webworker
-
-
+    return blobMap[id];
+}
+exports.getBlob = getBlob;
+// used to export entire context to webworker
 function getBlobMap() {
-  return blobMap;
-} // used in new contexts like webworkers
-
-
+    return blobMap;
+}
+exports.getBlobMap = getBlobMap;
+// used in new contexts like webworkers
 function setBlobMap(map) {
-  blobMap = map;
-} // blob files are stored in a global map
-
-
+    blobMap = map;
+}
+exports.setBlobMap = setBlobMap;
+let counter = 0;
+// blob files are stored in a global map. the blobId is based on a combination
+// of timestamp plus counter to be unique across sessions and fast repeated
+// calls
 function storeBlobLocation(location) {
-  if (location && 'blob' in location) {
-    // possibly we should be more clear about when this is not undefined, and
-    // also allow mix of blob and url for index and file
-    // @ts-ignore
-    var blobId = "b".concat(+Date.now());
-    blobMap[blobId] = location.blob;
-    return {
-      name: location === null || location === void 0 ? void 0 : location.blob.name,
-      blobId: blobId,
-      locationType: 'BlobLocation'
-    };
-  }
-
-  return location;
+    if (location && 'blob' in location) {
+        const blobId = `b${+Date.now()}-${counter++}`;
+        blobMap[blobId] = location.blob;
+        return { name: location === null || location === void 0 ? void 0 : location.blob.name, blobId, locationType: 'BlobLocation' };
+    }
+    return location;
 }
+exports.storeBlobLocation = storeBlobLocation;
 /**
  * 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 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;
+    if ('uri' in location) {
+        return { uri: location.uri + suffix, locationType: 'UriLocation' };
+    }
+    if ('localPath' in location) {
+        return {
+            localPath: location.localPath + suffix,
+            locationType: 'LocalPathLocation',
+        };
+    }
+    return location;
 }
+exports.makeIndex = makeIndex;
 /**
  * constructs a potential index file (with suffix) from the provided file name
  * @param name - the name of the index file
@@ -147,76 +110,72 @@ function makeIndex(location, suffix) {
  * @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
  */
-
-
 function makeIndexType(name, typeA, typeB) {
-  return name !== null && name !== void 0 && name.toUpperCase().endsWith(typeA) ? typeA : typeB;
+    return (name === null || name === void 0 ? void 0 : name.toUpperCase().endsWith(typeA)) ? typeA : typeB;
 }
-
+exports.makeIndexType = makeIndexType;
 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)) || '';
+    const uri = 'uri' in track ? track.uri : undefined;
+    const localPath = 'localPath' in track ? track.localPath : undefined;
+    const 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)) ||
+        '');
 }
-
+exports.getFileName = getFileName;
 function guessAdapter(file, index, adapterHint, model) {
-  if (model) {
-    var _getEnv = (0, _mobxStateTree.getEnv)(model),
-        pluginManager = _getEnv.pluginManager;
-
-    var adapterGuesser = pluginManager.evaluateExtensionPoint('Core-guessAdapterForLocation', function (_file, _index, _adapterHint) {
-      return undefined;
-    });
-    var adapter = adapterGuesser(file, index, adapterHint);
-
-    if (adapter) {
-      return adapter;
+    if (model) {
+        const { pluginManager } = (0, mobx_state_tree_1.getEnv)(model);
+        const adapterGuesser = pluginManager.evaluateExtensionPoint('Core-guessAdapterForLocation', (_file, _index, _adapterHint) => {
+            return undefined;
+        });
+        const adapter = adapterGuesser(file, index, adapterHint);
+        if (adapter) {
+            return adapter;
+        }
     }
-  }
-
-  return {
-    type: UNKNOWN
-  };
+    return {
+        type: exports.UNKNOWN,
+    };
 }
-
+exports.guessAdapter = guessAdapter;
 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;
+    if (model) {
+        // @ts-ignore
+        const session = (0, index_1.getSession)(model);
+        const trackTypeGuesser = (0, mobx_state_tree_1.getEnv)(session).pluginManager.evaluateExtensionPoint('Core-guessTrackTypeForLocation', (_adapterName) => {
+            return undefined;
+        });
+        const trackType = trackTypeGuesser(adapterType);
+        if (trackType) {
+            return trackType;
+        }
     }
-  }
-
-  return 'FeatureTrack';
+    return 'FeatureTrack';
 }
-
+exports.guessTrackType = guessTrackType;
 function generateUnsupportedTrackConf(trackName, trackUrl, categories) {
-  var conf = {
-    type: 'FeatureTrack',
-    name: "".concat(trackName, " (Unsupported)"),
-    description: "Support not yet implemented for \"".concat(trackUrl, "\""),
-    category: categories,
-    trackId: ''
-  };
-  conf.trackId = (0, _index2.objectHash)(conf);
-  return conf;
+    const conf = {
+        type: 'FeatureTrack',
+        name: `${trackName} (Unsupported)`,
+        description: `Support not yet implemented for "${trackUrl}"`,
+        category: categories,
+        trackId: '',
+    };
+    conf.trackId = (0, index_1.objectHash)(conf);
+    return conf;
 }
-
+exports.generateUnsupportedTrackConf = generateUnsupportedTrackConf;
 function generateUnknownTrackConf(trackName, trackUrl, categories) {
-  var conf = {
-    type: 'FeatureTrack',
-    name: "".concat(trackName, " (Unknown)"),
-    description: "Could not determine track type for \"".concat(trackUrl, "\""),
-    category: categories,
-    trackId: ''
-  };
-  conf.trackId = (0, _index2.objectHash)(conf);
-  return conf;
-}
+    const conf = {
+        type: 'FeatureTrack',
+        name: `${trackName} (Unknown)`,
+        description: `Could not determine track type for "${trackUrl}"`,
+        category: categories,
+        trackId: '',
+    };
+    conf.trackId = (0, index_1.objectHash)(conf);
+    return conf;
+}
+exports.generateUnknownTrackConf = generateUnknownTrackConf;

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';