@jbrowse/plugin-trix 5.0.0-beta.1 → 5.0.0-beta.10

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);
@@ -53,11 +53,11 @@ export default class TrixTextSearchAdapter extends BaseAdapter {
         // any run of whitespace separates words; splitting on a single ' ' let a
         // double space or a tab produce an empty word that matches everything
         const words = query.split(/\s+/);
-        const results = await this.trixJs.search(query);
+        const results = await this.trixJs.search(query, { signal: args.signal });
         // 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

@@ -6,71 +6,40 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  *
  * #example
  * `jbrowse text-index` writes this entry into `aggregateTextSearchAdapters` for
- * you. The `uri` shorthand points at the `.ix`; the sibling `.ixx` and
- * `_meta.json` are derived from it, so all three only need spelling out when
- * they are named against convention.
+ * 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. Written by hand, the string `'trix/hg38.ix'` is the whole entry,
+ * the same as `{ uri: 'trix/hg38.ix' }`: a `.ix` implies this type, and
+ * `assemblyNames` defaults to the track's own for a per-track index or to the
+ * config's one assembly.
  * ```js
  * {
  *   type: 'TrixTextSearchAdapter',
- *   textSearchAdapterId: 'hg38-index',
  *   uri: 'trix/hg38.ix',
  *   assemblyNames: ['hg38'],
  * }
  * ```
  */
 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";
-        };
-    };
-    /**
-     * #slot
-     * location of the `_meta.json` written beside the index, recording which
-     * tracks and assemblies it covers and the attributes it was built from.
-     */
-    readonly metaFilePath: {
-        readonly type: "fileLocation";
-        readonly defaultValue: {
-            readonly uri: "meta.json";
-            readonly locationType: "UriLocation";
-        };
-    };
-    /**
-     * #slot
-     */
-    readonly tracks: {
-        readonly type: "stringArray";
-        readonly defaultValue: readonly [];
-        readonly description: "List of tracks covered by text search adapter";
+        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>, any>>;
 export default TrixTextSearchAdapter;

package/esm/TrixTextSearchAdapter/configSchema.js

@@ -1,10 +1,9 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { ConfigurationSchema, fillLocations } from '@jbrowse/core/configuration';
 export function normalizeSnapshot(snap) {
     return typeof snap.uri === 'string'
-        ? {
-            ...snap,
-            // `uri` points at the `.ix` file; `.ixx` and `_meta.json` sit beside it
-            // (the `jbrowse text-index` naming convention), so derive all three
+        ? fillLocations(snap, {
+            // `uri` points at the `.ix` file and the `.ixx` sits beside it (the
+            // `jbrowse text-index` naming convention), so derive the pair
             ixFilePath: {
                 uri: snap.uri,
                 baseUri: snap.baseUri,
@@ -13,11 +12,7 @@ export function normalizeSnapshot(snap) {
                 uri: `${snap.uri}x`,
                 baseUri: snap.baseUri,
             },
-            metaFilePath: {
-                uri: `${snap.uri.replace(/\.ix$/, '')}_meta.json`,
-                baseUri: snap.baseUri,
-            },
-        }
+        })
         : snap;
 }
 /**
@@ -27,13 +22,15 @@ export function normalizeSnapshot(snap) {
  *
  * #example
  * `jbrowse text-index` writes this entry into `aggregateTextSearchAdapters` for
- * you. The `uri` shorthand points at the `.ix`; the sibling `.ixx` and
- * `_meta.json` are derived from it, so all three only need spelling out when
- * they are named against convention.
+ * 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. Written by hand, the string `'trix/hg38.ix'` is the whole entry,
+ * the same as `{ uri: 'trix/hg38.ix' }`: a `.ix` implies this type, and
+ * `assemblyNames` defaults to the track's own for a per-track index or to the
+ * config's one assembly.
  * ```js
  * {
  *   type: 'TrixTextSearchAdapter',
- *   textSearchAdapterId: 'hg38-index',
  *   uri: 'trix/hg38.ix',
  *   assemblyNames: ['hg38'],
  * }
@@ -55,8 +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',
@@ -65,26 +62,6 @@ const TrixTextSearchAdapter = ConfigurationSchema('TrixTextSearchAdapter', {
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     * location of the `_meta.json` written beside the index, recording which
-     * tracks and assemblies it covers and the attributes it was built from.
-     */
-    metaFilePath: {
-        type: 'fileLocation',
-        defaultValue: {
-            uri: 'meta.json',
-            locationType: 'UriLocation',
-        },
-    },
-    /**
-     * #slot
-     */
-    tracks: {
-        type: 'stringArray',
-        defaultValue: [],
-        description: 'List of tracks covered by text search adapter',
-    },
     /**
      * #slot
      */
@@ -95,24 +72,18 @@ const TrixTextSearchAdapter = ConfigurationSchema('TrixTextSearchAdapter', {
     },
 }, {
     explicitlyTyped: true,
-    /**
-     * #identifier
-     * an explicit `textSearchAdapterId` is still honored when given
-     */
-    implicitIdentifier: 'textSearchAdapterId',
     /**
      * #preProcessSnapshot
      *
      *
      * preprocessor to allow minimal config: `uri` points at the `.ix` file and
-     * the sibling `.ixx` and `_meta.json` are derived from it (the
-     * `jbrowse text-index` naming convention):
+     * the sibling `.ixx` is derived from it (the `jbrowse text-index` naming
+     * convention):
      * ```json
      * {
      *   "type": "TrixTextSearchAdapter",
      *   "uri": "file.ix",
-     *   "assemblyNames": ["hg19"],
-     *   "textSearchAdapterId": "hg19SearchIndex"
+     *   "assemblyNames": ["hg19"]
      * }
      * ```
      */

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-trix",
-  "version": "5.0.0-beta.1",
+  "version": "5.0.0-beta.10",
   "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.1"
+    "@jbrowse/core": "^5.0.0-beta.10"
   },
   "publishConfig": {
     "access": "public"