@jbrowse/plugin-legacy-jbrowse 4.3.0 → 5.0.0-beta.10

package/esm/JBrowse1TextSearchAdapter/configSchema.js

@@ -1,22 +1,45 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-function x() { }
+/**
+ * #config JBrowse1TextSearchAdapter
+ * #trackType TextSearchAdapter
+ * #fileFormat textsearch | JBrowse 1 names index | From JBrowse 1 `generate-names.pl`
+ * note: metadata about tracks and assemblies covered by text search adapter
+ *
+ * #example
+ * An entry in `aggregateTextSearchAdapters`, pointing at the `names/`
+ * directory JBrowse 1's `generate-names.pl` wrote — so an existing instance's
+ * search index is reused rather than rebuilt with `jbrowse text-index`:
+ * ```js
+ * {
+ *   type: 'JBrowse1TextSearchAdapter',
+ *   namesIndexLocation: { uri: 'https://example.com/jbrowse1/data/names/' },
+ *   assemblyNames: ['hg19'],
+ * }
+ * ```
+ */
 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: [],
         description: 'List of assemblies covered by text search adapter',
     },
-}, {
-    explicitlyTyped: true,
-    explicitIdentifier: 'textSearchAdapterId',
-});
+}, { explicitlyTyped: true });

package/esm/JBrowse1TextSearchAdapter/index.js

@@ -1,10 +1,10 @@
 import TextSearchAdapterType from '@jbrowse/core/pluggableElementTypes/TextSearchAdapterType';
-import configSchema from "./configSchema.js";
+import configSchema from './configSchema.js';
 export default function JBrowse1TextSearchAdapterF(pluginManager) {
     pluginManager.addTextSearchAdapterType(() => new TextSearchAdapterType({
         name: 'JBrowse1TextSearchAdapter',
         configSchema,
         description: 'A JBrowse 1 text search adapter',
-        getAdapterClass: () => import("./JBrowse1TextSearchAdapter.js").then(t => t.default),
+        getAdapterClass: () => import('./JBrowse1TextSearchAdapter.js').then(t => t.default),
     }));
 }

package/esm/NCListAdapter/NCListAdapter.d.ts

@@ -1,5 +1,6 @@
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import NCListFeature from './NCListFeature.ts';
+import type { NCListRawFeature } from './NCListFeature.ts';
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
@@ -10,8 +11,17 @@ export default class NCListAdapter extends BaseFeatureDataAdapter {
     private nclist;
     private configRefNames?;
     constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+    /**
+     * Fetch features for a certain region.
+     * @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;
+    wrapFeature(ncFeature: NCListRawFeature): NCListFeature;
     hasDataForRefName(refName: string): Promise<boolean>;
+    /**
+     * NCList is unable to get list of ref names so returns empty
+     */
     getRefNames(): Promise<string[]>;
 }

package/esm/NCListAdapter/NCListAdapter.js

@@ -1,9 +1,9 @@
 import NCListStore from '@gmod/nclist';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { checkAbortSignal } from '@jbrowse/core/util/aborting';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { checkStopToken } from '@jbrowse/core/util/stopToken';
 import { RemoteFile } from 'generic-filehandle2';
-import NCListFeature from "./NCListFeature.js";
+import NCListFeature from './NCListFeature.js';
 export default class NCListAdapter extends BaseFeatureDataAdapter {
     nclist;
     configRefNames;
@@ -20,15 +20,21 @@ export default class NCListAdapter extends BaseFeatureDataAdapter {
                 : url).readFile(),
         });
     }
+    /**
+     * Fetch features for a certain region.
+     * @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 { stopToken } = opts;
-            for await (const feature of this.nclist.getFeatures(region, opts)) {
-                checkStopToken(stopToken);
+            const { signal } = opts;
+            for await (const feature of this.nclist.getFeatures(region)) {
+                checkAbortSignal(signal);
                 observer.next(this.wrapFeature(feature));
             }
             observer.complete();
-        });
+        }, opts.signal);
     }
     wrapFeature(ncFeature) {
         return new NCListFeature(ncFeature, undefined, `${this.id}-${ncFeature.id()}`);
@@ -37,7 +43,10 @@ export default class NCListAdapter extends BaseFeatureDataAdapter {
         const root = await this.nclist.getDataRoot(refName);
         return !!root?.stats?.featureCount;
     }
+    /**
+     * NCList is unable to get list of ref names so returns empty
+     */
     async getRefNames() {
-        return this.configRefNames || [];
+        return this.configRefNames ?? [];
     }
 }

package/esm/NCListAdapter/NCListFeature.d.ts

@@ -1,16 +1,47 @@
 import type { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
+/**
+ * the duck-typed shape of a raw @gmod/nclist feature (which the library types
+ * only as `any`)
+ */
+export interface NCListRawFeature {
+    id(): string;
+    get(attr: string): unknown;
+    tags(): string[];
+}
+/**
+ * wrapper to adapt nclist features to act like jbrowse 2 features
+ */
 export default class NCListFeature implements Feature {
-    private ncFeature;
     private parentHandle?;
     private uniqueId;
-    constructor(ncFeature: any, parent?: Feature, id?: string);
+    private ncFeature;
+    constructor(ncFeature: NCListRawFeature, parent?: Feature, id?: string);
     set(): void;
     jb2TagToJb1Tag(tag: string): string;
     jb1TagToJb2Tag(tag: string): string;
-    get(attrName: string): any;
+    get(name: 'refName'): string;
+    get(name: 'name' | 'type' | 'id' | 'source'): string | undefined;
+    get(name: 'start' | 'end'): number;
+    get(name: 'phase'): 0 | 1 | 2 | undefined;
+    get(name: 'strand'): -1 | 0 | 1 | undefined;
+    get(name: 'score'): number | undefined;
+    get(name: 'subfeatures'): Feature[] | undefined;
+    get(name: string): unknown;
+    /**
+     * 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

@@ -1,9 +1,12 @@
 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 {
-    ncFeature;
     parentHandle;
     uniqueId;
+    ncFeature;
     constructor(ncFeature, parent, id) {
         this.ncFeature = ncFeature;
         this.uniqueId = id || ncFeature.id();
@@ -13,29 +16,40 @@ export default class NCListFeature {
         throw new Error('not implemented');
     }
     jb2TagToJb1Tag(tag) {
-        const mapped = jb2ToJb1[tag] || tag;
-        return mapped.toLowerCase();
+        return (jb2ToJb1[tag] ?? tag).toLowerCase();
     }
     jb1TagToJb2Tag(tag) {
         const t = tag.toLowerCase();
-        return jb1ToJb2[t] || t;
+        return jb1ToJb2[t] ?? t;
     }
     get(attrName) {
         const attr = this.ncFeature.get(this.jb2TagToJb1Tag(attrName));
         if (attr && attrName === 'subfeatures') {
-            return attr.map((subfeature) => new NCListFeature(subfeature, this));
+            return attr.map(subfeature => new NCListFeature(subfeature, this));
         }
         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');
     }
@@ -45,9 +59,9 @@ export default class NCListFeature {
             const mappedTag = this.jb1TagToJb2Tag(tag);
             const value = this.ncFeature.get(tag);
             if (mappedTag === 'subfeatures') {
-                data.subfeatures = (value || []).map((f) => {
-                    return new NCListFeature(f, this).toJSON();
-                });
+                data.subfeatures = (value ?? []).map(
+                // note: was new NCListFeature(f, `${this.id()}-${i}`, this).toJSON()
+                f => new NCListFeature(f, this).toJSON());
             }
             else {
                 data[mappedTag] = value;

package/esm/NCListAdapter/configSchema.d.ts

@@ -1,15 +1,35 @@
+/**
+ * #config NCListAdapter
+ * #trackType FeatureTrack
+ *
+ * #example
+ * Reads a JBrowse 1 NCList store in place, so an existing JBrowse 1 instance's
+ * data serves JBrowse 2 without re-processing. `{refseq}` in the URL template
+ * is substituted per sequence, which is how the store is laid out on disk:
+ * ```js
+ * {
+ *   type: 'NCListAdapter',
+ *   rootUrlTemplate: {
+ *     uri: 'https://example.com/jbrowse1/data/tracks/genes/{refseq}/trackData.json',
+ *   },
+ * }
+ * ```
+ */
 declare const NCListAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    rootUrlTemplate: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
+    type: {
+        type: "string";
+    } & {
+        defaultValue: string;
     };
-    refNames: {
-        type: string;
-        defaultValue: never[];
-        description: string;
+    readonly rootUrlTemplate: {
+        type: "fileLocation";
+    } & {
+        defaultValue: unknown;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    readonly refNames: {
+        type: "stringArray";
+    } & {
+        defaultValue: unknown;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, true, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
 export default NCListAdapter;

package/esm/NCListAdapter/configSchema.js

@@ -1,6 +1,28 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-function x() { }
+/**
+ * #config NCListAdapter
+ * #trackType FeatureTrack
+ *
+ * #example
+ * Reads a JBrowse 1 NCList store in place, so an existing JBrowse 1 instance's
+ * data serves JBrowse 2 without re-processing. `{refseq}` in the URL template
+ * is substituted per sequence, which is how the store is laid out on disk:
+ * ```js
+ * {
+ *   type: 'NCListAdapter',
+ *   rootUrlTemplate: {
+ *     uri: 'https://example.com/jbrowse1/data/tracks/genes/{refseq}/trackData.json',
+ *   },
+ * }
+ * ```
+ */
 const NCListAdapter = ConfigurationSchema('NCListAdapter', {
+    /**
+     * #slot
+     * URL of a JBrowse 1 NCList `trackData.json`, with `{refseq}` standing in
+     * for the reference sequence name — the per-reference directory layout
+     * `flatfile-to-json.pl` and `biodb-to-json.pl` write.
+     */
     rootUrlTemplate: {
         type: 'fileLocation',
         defaultValue: {
@@ -8,6 +30,9 @@ const NCListAdapter = ConfigurationSchema('NCListAdapter', {
             locationType: 'UriLocation',
         },
     },
+    /**
+     * #slot
+     */
     refNames: {
         type: 'stringArray',
         defaultValue: [],

package/esm/NCListAdapter/index.js

@@ -1,5 +1,5 @@
 import { AdapterType } from '@jbrowse/core/pluggableElementTypes';
-import configSchema from "./configSchema.js";
+import configSchema from './configSchema.js';
 export default function NCListAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'NCListAdapter',
@@ -8,6 +8,6 @@ export default function NCListAdapterF(pluginManager) {
         adapterMetadata: {
             category: 'Uncommon',
         },
-        getAdapterClass: () => import("./NCListAdapter.js").then(r => r.default),
+        getAdapterClass: () => import('./NCListAdapter.js').then(r => r.default),
     }));
 }

package/esm/index.js

@@ -1,13 +1,11 @@
 import Plugin from '@jbrowse/core/Plugin';
-import GuessNCListF from "./GuessNCList/index.js";
-import JBrowse1ConnectionF from "./JBrowse1Connection/index.js";
-import JBrowse1TextSearchAdapterF from "./JBrowse1TextSearchAdapter/index.js";
-import NCListAdapterF from "./NCListAdapter/index.js";
+import JBrowse1ConnectionF from './JBrowse1Connection/index.js';
+import JBrowse1TextSearchAdapterF from './JBrowse1TextSearchAdapter/index.js';
+import NCListAdapterF from './NCListAdapter/index.js';
 export default class LegacyJBrowsePlugin extends Plugin {
     name = 'LegacyJBrowsePlugin';
     install(pluginManager) {
         NCListAdapterF(pluginManager);
-        GuessNCListF(pluginManager);
         JBrowse1TextSearchAdapterF(pluginManager);
         JBrowse1ConnectionF(pluginManager);
     }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-legacy-jbrowse",
-  "version": "4.3.0",
+  "version": "5.0.0-beta.10",
   "type": "module",
   "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data",
   "keywords": [
@@ -21,13 +21,13 @@
     "esm"
   ],
   "dependencies": {
-    "@gmod/nclist": "^3.0.7",
-    "@jbrowse/mobx-state-tree": "^5.6.0",
-    "generic-filehandle2": "^2.1.7",
-    "mobx": "^6.15.3",
+    "@gmod/nclist": "^3.0.14",
+    "@jbrowse/mobx-state-tree": "^6.6.1",
+    "generic-filehandle2": "^2.4.0",
+    "mobx": "^7.0.5",
     "rxjs": "^7.8.2",
-    "set-value": "^4.1.0",
-    "@jbrowse/core": "^4.3.0"
+    "@jbrowse/add-track-core": "^5.0.0-beta.10",
+    "@jbrowse/core": "^5.0.0-beta.10"
   },
   "publishConfig": {
     "access": "public"
@@ -37,14 +37,11 @@
     "build": "pnpm run /^build:/",
     "test": "cd ../..; jest --passWithNoTests plugins/legacy-jbrowse",
     "prebuild": "pnpm clean",
-    "build:esm": "tsc -p tsconfig.build.esm.json",
+    "build:esm": "node ../../node_modules/typescript7/bin/tsc --build tsconfig.build.esm.json",
     "clean": "rimraf esm *.tsbuildinfo"
   },
   "types": "esm/index.d.ts",
   "exports": {
-    ".": {
-      "types": "./esm/index.d.ts",
-      "import": "./esm/index.js"
-    }
+    ".": "./esm/index.js"
   }
 }

package/esm/GuessNCList/index.d.ts

@@ -1,2 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function GuessNCListF(pluginManager: PluginManager): void;

package/esm/GuessNCList/index.js

@@ -1,15 +0,0 @@
-import { getFileName } from '@jbrowse/core/util/tracks';
-export default function GuessNCListF(pluginManager) {
-    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-        return (file, index, adapterHint) => {
-            const fileName = getFileName(file);
-            return (/trackData.jsonz?$/i.test(fileName) && !adapterHint) ||
-                adapterHint === 'NCListAdapter'
-                ? {
-                    type: 'NCListAdapter',
-                    rootUrlTemplate: file,
-                }
-                : adapterGuesser(file, index, adapterHint);
-        };
-    });
-}