@jbrowse/plugin-legacy-jbrowse 2.16.1 → 2.18.0

package/esm/JBrowse1TextSearchAdapter/HttpMap.d.ts

@@ -3,9 +3,6 @@ export default class HttpMap {
     constructor(args: {
         url: string;
     });
-    /**
-     * loads meta.json file from names directory and reads number of hash_bits used
-     */
     readMeta(): Promise<{
         hashHexCharacters: number;
         compress: any;
@@ -14,26 +11,9 @@ export default class HttpMap {
     getHashHexCharacters(): Promise<number>;
     getCompress(): Promise<any>;
     getTrackNames(): Promise<any>;
-    /**
-     * Returns contents of a bucket given a key
-     * @param key - string
-     */
     get(key: string): Promise<any>;
-    /**
-     * Returns a bucket given a key
-     * @param key - string
-     */
     getBucket(key: string): Promise<any>;
-    /**
-     * Loads a file using the url and provided id.
-     * Returns response object with contents of the file
-     * @param id - string
-     */
     loadFile(id: string): Promise<any>;
-    /**
-     * Returns the corresponding path of the file given a hex string
-     * @param hex - hex string
-     */
     hexToDirPath(hex: string): Promise<string>;
     hash(data: string): string;
 }

package/esm/JBrowse1TextSearchAdapter/HttpMap.js

@@ -1,17 +1,9 @@
-/**
- * Helper class allows reading names index generated in JBrowse1
- * Adapted from https://github.com/GMOD/jbrowse/blob/master/src/JBrowse/Store/Hash.js
- */
-import crc32 from 'crc/crc32';
 import { Buffer } from 'buffer';
+import crc32 from 'crc/crc32';
 export default class HttpMap {
     constructor(args) {
-        // make sure url has a trailing slash
         this.url = args.url.endsWith('/') ? args.url : `${args.url}/`;
     }
-    /**
-     * loads meta.json file from names directory and reads number of hash_bits used
-     */
     async readMeta() {
         const meta = await this.loadFile('meta.json');
         const { compress, track_names: tracks } = meta;
@@ -30,28 +22,15 @@ export default class HttpMap {
         const meta = await this.readMeta();
         return meta.tracks;
     }
-    /**
-     * Returns contents of a bucket given a key
-     * @param key - string
-     */
     async get(key) {
         const bucket = await this.getBucket(key);
         return bucket[key];
     }
-    /**
-     * Returns a bucket given a key
-     * @param key - string
-     */
     async getBucket(key) {
         const bucketIdent = this.hash(key);
         const hexToDirPath = await this.hexToDirPath(bucketIdent);
         return this.loadFile(hexToDirPath);
     }
-    /**
-     * Loads a file using the url and provided id.
-     * Returns response object with contents of the file
-     * @param id - string
-     */
     async loadFile(id) {
         const response = await fetch(`${this.url}${id}`);
         if (!response.ok) {
@@ -59,12 +38,7 @@ export default class HttpMap {
         }
         return response.json();
     }
-    /**
-     * Returns the corresponding path of the file given a hex string
-     * @param hex - hex string
-     */
     async hexToDirPath(hex) {
-        // zero-pad the hex string to be 8 chars if necessary
         const hashHexCharacters = await this.getHashHexCharacters();
         if (hashHexCharacters) {
             const compress = await this.getCompress();

package/esm/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.d.ts

@@ -1,9 +1,10 @@
-import { BaseTextSearchAdapter, BaseTextSearchArgs, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import { BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import HttpMap from './HttpMap';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { BaseTextSearchAdapter, BaseTextSearchArgs } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
 export interface TooManyHits {
     name: string;
     hitLimit: number;
@@ -20,11 +21,6 @@ export default class JBrowse1TextSearchAdapter extends BaseAdapter implements Ba
     httpMap: HttpMap;
     tracksNames?: string[];
     constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
-    /**
-     * Returns the contents of the file containing the query if it exists
-     * else it returns empty
-     * @param query - string query
-     */
     loadIndexFile(query: string): Promise<IndexFile>;
     searchIndex(args: BaseTextSearchArgs): Promise<BaseResult[]>;
     formatResults(results: SearchResults, tracks: string[], searchType?: string): BaseResult[];

package/esm/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.js

@@ -1,8 +1,7 @@
-import { BaseAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
 import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
-import { readConfObject, } from '@jbrowse/core/configuration';
+import { readConfObject } from '@jbrowse/core/configuration';
+import { BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import HttpMap from './HttpMap';
-// Uses index built by generate-names.pl
 export default class JBrowse1TextSearchAdapter extends BaseAdapter {
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
@@ -12,11 +11,6 @@ export default class JBrowse1TextSearchAdapter extends BaseAdapter {
             url: baseUri ? new URL(uri, baseUri).href : uri,
         });
     }
-    /**
-     * Returns the contents of the file containing the query if it exists
-     * else it returns empty
-     * @param query - string query
-     */
     async loadIndexFile(query) {
         return this.httpMap.getBucket(query);
     }

package/esm/JBrowse1TextSearchAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const _default: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     namesIndexLocation: {
         type: string;
         defaultValue: {
@@ -10,17 +7,11 @@ declare const _default: import("@jbrowse/core/configuration/configurationSchema"
         };
         description: string;
     };
-    /**
-     * #slot
-     */
     tracks: {
         type: string;
         defaultValue: never[];
         description: string;
     };
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: string;
         defaultValue: never[];

package/esm/JBrowse1TextSearchAdapter/configSchema.js

@@ -1,29 +1,16 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config JBrowse1TextSearchAdapter
- * note: metadata about tracks and assemblies covered by text search adapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 export default ConfigurationSchema('JBrowse1TextSearchAdapter', {
-    /**
-     * #slot
-     */
     namesIndexLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/volvox/names', locationType: 'UriLocation' },
         description: 'the location of the JBrowse1 names index data directory',
     },
-    /**
-     * #slot
-     */
     tracks: {
         type: 'stringArray',
         defaultValue: [],
         description: 'List of tracks covered by text search adapter',
     },
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: 'stringArray',
         defaultValue: [],
@@ -31,8 +18,5 @@ export default ConfigurationSchema('JBrowse1TextSearchAdapter', {
     },
 }, {
     explicitlyTyped: true,
-    /**
-     * #identifier
-     */
     explicitIdentifier: 'textSearchAdapterId',
 });

package/esm/JBrowse1TextSearchAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function JBrowse1TextSearchAdapterF(pluginManager: PluginManager): void;

package/esm/JBrowse1TextSearchAdapter/index.js

@@ -1,5 +1,4 @@
 import TextSearchAdapterType from '@jbrowse/core/pluggableElementTypes/TextSearchAdapterType';
-// locals
 import configSchema from './configSchema';
 export default function JBrowse1TextSearchAdapterF(pluginManager) {
     pluginManager.addTextSearchAdapterType(() => new TextSearchAdapterType({

package/esm/NCListAdapter/NCListAdapter.d.ts

@@ -1,33 +1,18 @@
-import { Region } from '@jbrowse/core/util/types';
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import NCListFeature from './NCListFeature';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import type { Feature } from '@jbrowse/core/util/simpleFeature';
+import type { Region } from '@jbrowse/core/util/types';
 export default class NCListAdapter extends BaseFeatureDataAdapter {
     private nclist;
     private configRefNames?;
     constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
-    /**
-     * Fetch features for a certain region. Use getFeaturesInRegion() if you also
-     * want to verify that the store has features for the given reference sequence
-     * before fetching.
-     * @param region -
-     * @param opts - [signal] optional signalling object for aborting the fetch
-     * @returns Observable of Feature objects in the region
-     */
     getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     wrapFeature(ncFeature: any): NCListFeature;
     hasDataForRefName(refName: string): Promise<boolean>;
-    /**
-     * NCList is unable to get list of ref names so returns empty
-     */
     getRefNames(): Promise<string[]>;
-    /**
-     * called to provide a hint that data tied to a certain region
-     * will not be needed for the foreseeable future and can be purged
-     * from caches, etc
-     */
     freeResources(): void;
 }

package/esm/NCListAdapter/NCListAdapter.js

@@ -1,7 +1,7 @@
 import NCListStore from '@gmod/nclist';
-import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { checkAbortSignal } from '@jbrowse/core/util';
+import { checkStopToken } from '@jbrowse/core/util/stopToken';
 import { RemoteFile } from 'generic-filehandle';
 import NCListFeature from './NCListFeature';
 export default class NCListAdapter extends BaseFeatureDataAdapter {
@@ -18,19 +18,11 @@ export default class NCListAdapter extends BaseFeatureDataAdapter {
                 : url)).readFile(),
         });
     }
-    /**
-     * Fetch features for a certain region. Use getFeaturesInRegion() if you also
-     * want to verify that the store has features for the given reference sequence
-     * before fetching.
-     * @param region -
-     * @param opts - [signal] optional signalling object for aborting the fetch
-     * @returns Observable of Feature objects in the region
-     */
     getFeatures(region, opts = {}) {
         return ObservableCreate(async (observer) => {
-            const { signal } = opts;
+            const { stopToken } = opts;
             for await (const feature of this.nclist.getFeatures(region, opts)) {
-                checkAbortSignal(signal);
+                checkStopToken(stopToken);
                 observer.next(this.wrapFeature(feature));
             }
             observer.complete();
@@ -44,16 +36,8 @@ export default class NCListAdapter extends BaseFeatureDataAdapter {
         const root = await this.nclist.getDataRoot(refName);
         return !!((_a = root === null || root === void 0 ? void 0 : root.stats) === null || _a === void 0 ? void 0 : _a.featureCount);
     }
-    /**
-     * NCList is unable to get list of ref names so returns empty
-     */
     async getRefNames() {
         return this.configRefNames || [];
     }
-    /**
-     * called to provide a hint that data tied to a certain region
-     * will not be needed for the foreseeable future and can be purged
-     * from caches, etc
-     */
     freeResources() { }
 }

package/esm/NCListAdapter/NCListFeature.d.ts

@@ -1,7 +1,4 @@
-import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
-/**
- * wrapper to adapt nclist features to act like jbrowse 2 features
- */
+import type { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
 export default class NCListFeature implements Feature {
     private ncFeature;
     private parentHandle?;
@@ -11,21 +8,9 @@ export default class NCListFeature implements Feature {
     jb2TagToJb1Tag(tag: string): string;
     jb1TagToJb2Tag(tag: string): string;
     get(attrName: string): any;
-    /**
-     * Get an array listing which data keys are present in this feature.
-     */
     tags(): string[];
-    /**
-     * Get the unique ID of this feature.
-     */
     id(): string;
-    /**
-     * Get this feature's parent feature, or undefined if none.
-     */
     parent(): Feature | undefined;
-    /**
-     * Get an array of child features, or undefined if none.
-     */
     children(): Feature[] | undefined;
     toJSON(): SimpleFeatureSerialized;
 }

package/esm/NCListAdapter/NCListFeature.js

@@ -1,8 +1,5 @@
 const jb2ToJb1 = { refName: 'seq_id' };
 const jb1ToJb2 = { seq_id: 'refName' };
-/**
- * wrapper to adapt nclist features to act like jbrowse 2 features
- */
 export default class NCListFeature {
     constructor(ncFeature, parent, id) {
         this.ncFeature = ncFeature;
@@ -13,13 +10,11 @@ export default class NCListFeature {
         throw new Error('not implemented');
     }
     jb2TagToJb1Tag(tag) {
-        // @ts-expect-error
         const mapped = jb2ToJb1[tag] || tag;
         return mapped.toLowerCase();
     }
     jb1TagToJb2Tag(tag) {
         const t = tag.toLowerCase();
-        // @ts-expect-error
         return jb1ToJb2[t] || t;
     }
     get(attrName) {
@@ -29,39 +24,25 @@ export default class NCListFeature {
         }
         return attr;
     }
-    /**
-     * Get an array listing which data keys are present in this feature.
-     */
     tags() {
         return this.ncFeature.tags().map((t) => this.jb1TagToJb2Tag(t));
     }
-    /**
-     * Get the unique ID of this feature.
-     */
     id() {
         return this.uniqueId;
     }
-    /**
-     * Get this feature's parent feature, or undefined if none.
-     */
     parent() {
         return this.parentHandle;
     }
-    /**
-     * Get an array of child features, or undefined if none.
-     */
     children() {
         return this.get('subfeatures');
     }
     toJSON() {
-        // @ts-expect-error
         const data = { uniqueId: this.id() };
         this.ncFeature.tags().forEach((tag) => {
             const mappedTag = this.jb1TagToJb2Tag(tag);
             const value = this.ncFeature.get(tag);
             if (mappedTag === 'subfeatures') {
                 data.subfeatures = (value || []).map((f) => {
-                    // note: was new NCListFeature(f, `${this.id()}-${i}`, this).toJSON()
                     return new NCListFeature(f, this).toJSON();
                 });
             }

package/esm/NCListAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const NCListAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     rootUrlTemplate: {
         type: string;
         defaultValue: {
@@ -9,9 +6,6 @@ declare const NCListAdapter: import("@jbrowse/core/configuration/configurationSc
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     refNames: {
         type: string;
         defaultValue: never[];

package/esm/NCListAdapter/configSchema.js

@@ -1,12 +1,6 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config NCListAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const NCListAdapter = ConfigurationSchema('NCListAdapter', {
-    /**
-     * #slot
-     */
     rootUrlTemplate: {
         type: 'fileLocation',
         defaultValue: {
@@ -14,9 +8,6 @@ const NCListAdapter = ConfigurationSchema('NCListAdapter', {
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     refNames: {
         type: 'stringArray',
         defaultValue: [],

package/esm/NCListAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function NCListAdapterF(pluginManager: PluginManager): void;

package/esm/index.d.ts

@@ -1,5 +1,5 @@
 import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default class LegacyJBrowsePlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/esm/index.js

@@ -1,8 +1,8 @@
 import Plugin from '@jbrowse/core/Plugin';
-import NCListAdapterF from './NCListAdapter';
-import JBrowse1TextSearchAdapterF from './JBrowse1TextSearchAdapter';
-import JBrowse1ConnectionF from './JBrowse1Connection';
 import GuessNCListF from './GuessNCList';
+import JBrowse1ConnectionF from './JBrowse1Connection';
+import JBrowse1TextSearchAdapterF from './JBrowse1TextSearchAdapter';
+import NCListAdapterF from './NCListAdapter';
 export default class LegacyJBrowsePlugin extends Plugin {
     constructor() {
         super(...arguments);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-legacy-jbrowse",
-  "version": "2.16.1",
+  "version": "2.18.0",
   "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data",
   "keywords": [
     "jbrowse",
@@ -55,5 +55,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "c6a658d2344989895543f0456b1cf7dd3b937769"
+  "gitHead": "c344ea60099cb7e460b77f15808946b24a7eee74"
 }