@jbrowse/core 2.13.0 → 2.14.0

package/util/simpleFeature.d.ts

@@ -7,8 +7,7 @@ export interface Feature {
      * 'start' and 'end', but everything else is optional.
      */
     get(name: 'refName'): string;
-    get(name: 'start'): number;
-    get(name: 'end'): number;
+    get(name: 'start' | 'end'): number;
     get(name: 'subfeatures'): Feature[] | undefined;
     get(name: string): any;
     /**
@@ -39,7 +38,7 @@ export interface Feature {
 export declare function isFeature(thing: unknown): thing is Feature;
 export interface SimpleFeatureArgs {
     /** key-value data, must include 'start' and 'end' */
-    data: {};
+    data: Record<string, unknown>;
     /** optional parent feature */
     parent?: Feature;
     /** unique identifier. can also be in data.uniqueId */

package/util/simpleFeature.js

@@ -26,15 +26,17 @@ class SimpleFeature {
             this.data = args;
         }
         else {
-            this.data = args.data || {};
-            // load handle from args.parent (not args.data.parent)
-            // this reason is because if args is an object, it likely isn't properly loaded with
-            // parent as a Feature reference (probably a raw parent ID or something instead)
+            this.data = args.data;
+            // load handle from args.parent (not args.data.parent) this reason is
+            // because if args is an object, it likely isn't properly loaded with
+            // parent as a Feature reference (probably a raw parent ID or something
+            // instead)
             this.parentHandle = args.parent;
         }
-        // the feature id comes from
-        // args.id, args.data.uniqueId, or args.uniqueId due to this initialization
+        // the feature id comes from args.id, args.data.uniqueId, or args.uniqueId
+        // due to this initialization
         const id = isSimpleFeatureSerialized(args) ? args.uniqueId : args.id;
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         if (id === undefined || id === null) {
             throw new Error('SimpleFeature requires a unique `id` or `data.uniqueId` attribute');
         }
@@ -43,15 +45,12 @@ class SimpleFeature {
             throw new Error(`invalid feature data, end less than start. end: ${this.data.end} start: ${this.data.start}`);
         }
         if (this.data.subfeatures) {
-            this.subfeatures = (_a = this.data.subfeatures) === null || _a === void 0 ? void 0 : _a.map(
-            // eslint-disable-next-line @typescript-eslint/no-explicit-any
-            (f, i) => typeof f.get !== 'function'
+            this.subfeatures = (_a = this.data.subfeatures) === null || _a === void 0 ? void 0 : _a.map((f, i) => typeof f.get !== 'function'
                 ? new SimpleFeature({
                     id: f.uniqueId || `${id}-${i}`,
                     data: {
                         strand: this.data.strand,
                         ...f,
-                        // eslint-disable-next-line @typescript-eslint/no-explicit-any
                     },
                     parent: this,
                 })
@@ -62,7 +61,6 @@ class SimpleFeature {
      * Get a piece of data about the feature.  All features must have
      * 'start' and 'end', but everything else is optional.
      */
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     get(name) {
         return name === 'subfeatures'
             ? this.subfeatures
@@ -73,7 +71,6 @@ class SimpleFeature {
     /**
      * Set an item of data.
      */
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     set(name, val) {
         this.data[name] = val;
     }

package/util/stats.js

@@ -63,7 +63,8 @@ function calcPerBaseStats(region, features) {
     let currentFeat = 0;
     let i = 0;
     while (pos < end) {
-        while (currentFeat < feats.length && pos >= feats[currentFeat].get('end')) {
+        while (currentFeat < feats.length &&
+            pos >= feats[currentFeat].get('end')) {
             currentFeat += 1;
         }
         const f = feats[currentFeat];
@@ -110,6 +111,7 @@ async function scoresToStats(region, feats) {
         found = true;
         return acc;
     }, seed)));
+    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
     return found
         ? rectifyStats({
             scoreMax,

package/util/tracks.d.ts

@@ -5,7 +5,9 @@ export declare function getTrackAssemblyNames(track: IAnyStateTreeNode & {
     configuration: AnyConfigurationModel;
 }): string[];
 export declare function getConfAssemblyNames(conf: AnyConfigurationModel): string[];
-/** return the rpcSessionId of the highest parent node in the tree that has an rpcSessionId */
+/**
+ * return the rpcSessionId of the highest parent node in the tree that has an
+ * rpcSessionId */
 export declare function getRpcSessionId(thisNode: IAnyStateTreeNode): string;
 /**
  * given an MST node, get the renderprops of the first parent container that
@@ -16,7 +18,7 @@ export declare function getRpcSessionId(thisNode: IAnyStateTreeNode): string;
 export declare function getParentRenderProps(node: IAnyStateTreeNode): any;
 export declare const UNKNOWN = "UNKNOWN";
 export declare const UNSUPPORTED = "UNSUPPORTED";
-export declare function getBlob(id: string): File;
+export declare function getBlob(id: string): File | undefined;
 export declare function getBlobMap(): Record<string, File>;
 export declare function setBlobMap(map: Record<string, File>): void;
 export declare function storeBlobLocation(location: PreFileLocation): import("./types").PreUriLocation | import("./types").PreLocalPathLocation | {

package/util/tracks.js

@@ -28,18 +28,21 @@ function getConfAssemblyNames(conf) {
     const trackAssemblyNames = (0, configuration_1.readConfObject)(conf, '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)(conf);
         if ('sequence' in parent) {
             return [(0, configuration_1.readConfObject)(parent, 'name')];
         }
+        else {
+            throw new Error('unknown assembly names');
+        }
     }
     return trackAssemblyNames;
 }
-/** return the rpcSessionId of the highest parent node in the tree that has an rpcSessionId */
+/**
+ * return the rpcSessionId of the highest parent node in the tree that has an
+ * rpcSessionId */
 function getRpcSessionId(thisNode) {
     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;
@@ -57,11 +60,7 @@ function getRpcSessionId(thisNode) {
  * @returns renderprops, or empty object if none found
  */
 function getParentRenderProps(node) {
-    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)) {
+    for (let currentNode = (0, mobx_state_tree_1.getParent)(node); !(0, mobx_state_tree_1.isRoot)(currentNode); currentNode = (0, mobx_state_tree_1.getParent)(currentNode)) {
         if ('renderProps' in currentNode) {
             return currentNode.renderProps();
         }
@@ -88,10 +87,10 @@ let counter = 0;
 // of timestamp plus counter to be unique across sessions and fast repeated
 // calls
 function storeBlobLocation(location) {
-    if (location && 'blob' in location) {
+    if ('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 { name: location.blob.name, blobId, locationType: 'BlobLocation' };
     }
     return location;
 }
@@ -129,7 +128,7 @@ function getFileName(track) {
     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 === null || localPath === void 0 ? void 0 : localPath.replace(/\\/g, '/').lastIndexOf('/')) + 1)) ||
+        (localPath === null || localPath === void 0 ? void 0 : localPath.slice(localPath.replace(/\\/g, '/').lastIndexOf('/') + 1)) ||
         '');
 }
 function guessAdapter(file, index, adapterHint, model) {

package/util/types/index.d.ts

@@ -1,14 +1,14 @@
 import React from 'react';
 import { Instance, SnapshotIn, IAnyStateTreeNode, IStateTreeNode, IType } from 'mobx-state-tree';
+import { ThemeOptions } from '@mui/material';
 import { AnyConfigurationModel } from '../../configuration';
-import assemblyManager from '../../assemblyManager';
 import TextSearchManager from '../../TextSearch/TextSearchManager';
 import { MenuItem } from '../../ui';
-import { NoAssemblyRegion as MUNoAssemblyRegion, Region as MUIRegion, LocalPathLocation as MULocalPathLocation, UriLocation as MUUriLocation, BlobLocation as MUBlobLocation } from './mst';
 import RpcManager from '../../rpc/RpcManager';
 import { Feature } from '../simpleFeature';
 import { BaseInternetAccountModel } from '../../pluggableElementTypes/models';
-import { ThemeOptions } from '@mui/material';
+import type assemblyManager from '../../assemblyManager';
+import type { NoAssemblyRegion as MUNoAssemblyRegion, Region as MUIRegion, LocalPathLocation as MULocalPathLocation, UriLocation as MUUriLocation, BlobLocation as MUBlobLocation } from './mst';
 export * from './util';
 /** abstract type for a model that contains multiple views */
 export interface AbstractViewContainer extends IStateTreeNode<IType<any, unknown, any>> {
@@ -55,7 +55,7 @@ export interface AbstractSessionModel extends AbstractViewContainer {
     hovered: unknown;
     setHovered: (arg: unknown) => void;
     setFocusedViewId?: (id: string) => void;
-    allThemes?: () => Record<string, ThemeOptions | undefined>;
+    allThemes?: () => Record<string, ThemeOptions>;
     setSelection: (feature: Feature) => void;
     setSession?: (arg: {
         name: string;
@@ -266,4 +266,4 @@ export interface PreBlobLocation {
     blob: File;
 }
 export type PreFileLocation = PreUriLocation | PreLocalPathLocation | PreBlobLocation;
-export { type default as TextSearchManager } from '../../TextSearch/TextSearchManager';
+export { default as TextSearchManager } from '../../TextSearch/TextSearchManager';

package/util/types/index.js

@@ -13,8 +13,11 @@ var __createBinding = (this && this.__createBinding) || (Object.create ? (functi
 var __exportStar = (this && this.__exportStar) || function(m, exports) {
     for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
 };
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.RetryError = exports.AuthNeededError = void 0;
+exports.TextSearchManager = exports.RetryError = exports.AuthNeededError = void 0;
 exports.isViewContainer = isViewContainer;
 exports.isSessionModel = isSessionModel;
 exports.isSessionModelWithConfigEditing = isSessionModelWithConfigEditing;
@@ -164,11 +167,15 @@ function isAuthNeededException(exception) {
     return (exception instanceof Error &&
         // DOMException
         (exception.name === 'AuthNeededError' ||
+            // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
             exception.url !== undefined));
 }
 function isRetryException(exception) {
     return (
     // DOMException
     exception.name === 'RetryError' ||
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         exception.internetAccountId !== undefined);
 }
+var TextSearchManager_1 = require("../../TextSearch/TextSearchManager");
+Object.defineProperty(exports, "TextSearchManager", { enumerable: true, get: function () { return __importDefault(TextSearchManager_1).default; } });

package/util/types/mst.js

@@ -54,6 +54,7 @@ exports.UriLocation = mobx_state_tree_1.types.snapshotProcessor(exports.UriLocat
 exports.FileLocation = mobx_state_tree_1.types.snapshotProcessor(mobx_state_tree_1.types.union(exports.LocalPathLocation, exports.UriLocation, exports.BlobLocation), {
     // @ts-expect-error
     preProcessor(snap) {
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         if (!snap) {
             return undefined;
         }

package/util/when.js

@@ -22,7 +22,11 @@ function when(getter, { timeout, signal, name } = {}) {
                     reject(new Error(`timed out waiting for ${name || 'whenPresent'}`));
                 }
             }, timeout);
-            finishTimeout = () => timeoutId && clearTimeout(timeoutId);
+            finishTimeout = () => {
+                if (timeoutId) {
+                    clearTimeout(timeoutId);
+                }
+            };
         }
         // set up aborting
         if (signal) {
@@ -44,10 +48,11 @@ function when(getter, { timeout, signal, name } = {}) {
                 resolve(true);
             }
         })
-            .catch(err => {
+            .catch((err) => {
             if (!finished) {
                 finished = true;
                 finishTimeout();
+                // eslint-disable-next-line @typescript-eslint/prefer-promise-reject-errors
                 reject(err);
             }
         });