@jbrowse/plugin-trix 5.0.0-beta.8 → 5.0.0-beta.9

package/esm/TrixTextSearchAdapter/TrixTextSearchAdapter.js

@@ -2,8 +2,8 @@ import Trix from '@gmod/trix';
 import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
 import { readConfObject } from '@jbrowse/core/configuration';
 import { BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { checkAbortSignal } from '@jbrowse/core/util/aborting';
 import { openLocation } from '@jbrowse/core/util/io';
-import { checkStopToken } from '@jbrowse/core/util/stopToken';
 function decodeURIComponentNoThrow(uri) {
     try {
         return decodeURIComponent(uri);
@@ -57,7 +57,7 @@ export default class TrixTextSearchAdapter extends BaseAdapter {
         // the index read has landed but nothing below it has run yet; a broad
         // prefix returns thousands of records to JSON-parse, decode and snippet,
         // and the keystroke that asked for them is 50ms stale by now
-        checkStopToken(args.stopToken);
+        checkAbortSignal(args.signal);
         const formatted = results
             .map(([term, data]) => {
             // record is ["loc"|"trackId"|"attr1"|...] with commas pre-encoded as

package/esm/TrixTextSearchAdapter/configSchema.d.ts

@@ -8,7 +8,9 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  * `jbrowse text-index` writes this entry into `aggregateTextSearchAdapters` for
  * you. The `uri` shorthand points at the `.ix` and the sibling `.ixx` is derived
  * from it, so the pair only needs spelling out when they are named against
- * convention.
+ * convention. Written by hand, `{ uri: 'trix/hg38.ix' }` is the whole entry: a
+ * `.ix` implies this type, the id is generated, and `assemblyNames` defaults to
+ * the track's own for a per-track index or to the config's one assembly.
  * ```js
  * {
  *   type: 'TrixTextSearchAdapter',
@@ -19,38 +21,25 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  * ```
  */
 declare const TrixTextSearchAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     * location of the Trix `.ix` index written by `jbrowse text-index`: the
-     * sorted term-to-feature table the search box reads.
-     */
+    type: {
+        type: "string";
+    } & {
+        defaultValue: string;
+    };
     readonly ixFilePath: {
-        readonly type: "fileLocation";
-        readonly defaultValue: {
-            readonly uri: "out.ix";
-            readonly locationType: "UriLocation";
-        };
+        type: "fileLocation";
+    } & {
+        defaultValue: unknown;
     };
-    /**
-     * #slot
-     * location of the `.ixx` prefix index, which records where in the `.ix`
-     * each prefix begins. It is what makes a lookup a couple of range requests
-     * instead of a download of the whole index.
-     */
     readonly ixxFilePath: {
-        readonly type: "fileLocation";
-        readonly defaultValue: {
-            readonly uri: "out.ixx";
-            readonly locationType: "UriLocation";
-        };
+        type: "fileLocation";
+    } & {
+        defaultValue: unknown;
     };
-    /**
-     * #slot
-     */
     readonly assemblyNames: {
-        readonly type: "stringArray";
-        readonly defaultValue: readonly [];
-        readonly description: "List of assemblies covered by text search adapter";
+        type: "stringArray";
+    } & {
+        defaultValue: unknown;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, true, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
 export default TrixTextSearchAdapter;

package/esm/TrixTextSearchAdapter/configSchema.js

@@ -24,7 +24,9 @@ export function normalizeSnapshot(snap) {
  * `jbrowse text-index` writes this entry into `aggregateTextSearchAdapters` for
  * you. The `uri` shorthand points at the `.ix` and the sibling `.ixx` is derived
  * from it, so the pair only needs spelling out when they are named against
- * convention.
+ * convention. Written by hand, `{ uri: 'trix/hg38.ix' }` is the whole entry: a
+ * `.ix` implies this type, the id is generated, and `assemblyNames` defaults to
+ * the track's own for a per-track index or to the config's one assembly.
  * ```js
  * {
  *   type: 'TrixTextSearchAdapter',
@@ -50,8 +52,8 @@ const TrixTextSearchAdapter = ConfigurationSchema('TrixTextSearchAdapter', {
     /**
      * #slot
      * location of the `.ixx` prefix index, which records where in the `.ix`
-     * each prefix begins. It is what makes a lookup a couple of range requests
-     * instead of a download of the whole index.
+     * each prefix begins, so a lookup takes a couple of range requests instead
+     * of a download of the whole index.
      */
     ixxFilePath: {
         type: 'fileLocation',

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-trix",
-  "version": "5.0.0-beta.8",
+  "version": "5.0.0-beta.9",
   "type": "module",
   "description": "JBrowse 2 trix text search adapter",
   "keywords": [
@@ -25,7 +25,7 @@
   },
   "dependencies": {
     "@gmod/trix": "^3.0.22",
-    "@jbrowse/core": "^5.0.0-beta.8"
+    "@jbrowse/core": "^5.0.0-beta.9"
   },
   "publishConfig": {
     "access": "public"