@jbrowse/plugin-bed 5.0.0-beta.10 → 5.0.0-beta.13

package/esm/BedGraphTabixAdapter/BedGraphTabixAdapter.js

@@ -14,9 +14,9 @@ export default class BedGraphTabixAdapter extends BaseFeatureDataAdapter {
     // getFeatures/byte-estimate awaits it) doesn't re-flash "Downloading index"
     configure = cachedSetup({
         label: 'Downloading index',
-        setup: () => this.configurePre(),
+        setup: opts => this.configurePre(opts),
     });
-    async configurePre() {
+    async configurePre(opts) {
         const pm = this.pluginManager;
         const bedGraphGzLocation = this.getConf('bedGraphGzLocation');
         const location = this.getConf(['index', 'location']);
@@ -31,7 +31,7 @@ export default class BedGraphTabixAdapter extends BaseFeatureDataAdapter {
         // Not bedGraph.getHeader(): that returns only a `#`-commented header, so a
         // file whose header is a plain row skipped via `tabix -S 1` reported none
         // and quietly lost the names of its value columns.
-        const header = (await readTabixHeaderLines(bedGraph)).join('\n');
+        const header = (await readTabixHeaderLines(bedGraph, { signal: opts.signal })).join('\n');
         return {
             columnNames,
             bedGraph,

package/esm/BedTabixAdapter/BedTabixAdapter.js

@@ -26,14 +26,14 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
     // re-entry (every getFeatures awaits it) doesn't re-flash "Downloading index"
     getMetadata = cachedSetup({
         label: 'Downloading index',
-        setup: () => this.bed.getMetadata(),
+        setup: opts => this.bed.getMetadata({ signal: opts.signal }),
     });
     // Memoized: getFeatures needs the names on every query, and reading them goes
     // to the file's leading blocks — a fetch and a decompress that was being
     // repeated on every pan and zoom. Resolves undefined when the file declares
     // no column names — parseNamesFromHeader's answer for a header it can't read
     // names out of.
-    getNames = cachedSetup({ setup: () => this.readNames() });
+    getNames = cachedSetup({ setup: opts => this.readNames(opts.signal) });
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
         this.bedGzLoc = readConfObject(this.config, 'bedGzLocation');
@@ -61,7 +61,7 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
     async getRegionByteSize(regions, opts) {
         return this.bed.bytesForRegions(regions, opts);
     }
-    async readNames() {
+    async readNames(signal) {
         const columnNames = readConfObject(this.config, 'columnNames');
         if (columnNames.length) {
             return columnNames;
@@ -69,7 +69,7 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
         // readTabixHeaderLines covers both ways a tabix file keeps a header: a
         // `#`-commented block, which getHeader() returns, and a plain row skipped
         // via `tabix -S N`, which it does not.
-        return parseNamesFromHeader((await readTabixHeaderLines(this.bed)).join('\n'));
+        return parseNamesFromHeader((await readTabixHeaderLines(this.bed, { signal })).join('\n'));
     }
     getFeatures(query, opts) {
         const { signal, statusCallback } = opts ?? {};

package/esm/BigBedTextSearchAdapter/BigBedTextSearchAdapter.js

@@ -10,13 +10,6 @@ import { openLocation } from '@jbrowse/core/util/io';
 const MAX_EXACT_NAMES = 50;
 const MAX_PREFIX_NAMES = 50;
 const MAX_TRIX_HITS = 500;
-function isSet(location) {
-    return 'uri' in location
-        ? !!location.uri
-        : 'localPath' in location
-            ? !!location.localPath
-            : true;
-}
 // the column that matched is the name the hit goes by: a gene symbol for a
 // search by symbol, the accession for a search by accession
 function hitFor({ refName, start, end, rest = '', }, word) {
@@ -69,7 +62,7 @@ export default class BigBedTextSearchAdapter extends BaseAdapter {
         });
         const ix = this.getConf('ixFilePath');
         const ixx = this.getConf('ixxFilePath');
-        if (isSet(ix) && isSet(ixx)) {
+        if (ix && ixx) {
             this.trix = new Trix(openLocation(ixx, pluginManager), openLocation(ix, pluginManager), MAX_TRIX_HITS);
         }
     }

package/esm/BigBedTextSearchAdapter/configSchema.d.ts

@@ -31,14 +31,10 @@ declare const BigBedTextSearchAdapter: import("@jbrowse/core/configuration/confi
         defaultValue: unknown;
     };
     readonly ixFilePath: {
-        type: "fileLocation";
-    } & {
-        defaultValue: unknown;
+        type: "maybeFileLocation";
     };
     readonly ixxFilePath: {
-        type: "fileLocation";
-    } & {
-        defaultValue: unknown;
+        type: "maybeFileLocation";
     };
     readonly assemblyNames: {
         type: "stringArray";

package/esm/BigBedTextSearchAdapter/configSchema.js

@@ -34,16 +34,14 @@ const BigBedTextSearchAdapter = ConfigurationSchema('BigBedTextSearchAdapter', {
      * indexes hold. Unset, a search matches a name exactly as typed
      */
     ixFilePath: {
-        type: 'fileLocation',
-        defaultValue: { uri: '', locationType: 'UriLocation' },
+        type: 'maybeFileLocation',
     },
     /**
      * #slot
      * the `.ixx` beside `ixFilePath`
      */
     ixxFilePath: {
-        type: 'fileLocation',
-        defaultValue: { uri: '', locationType: 'UriLocation' },
+        type: 'maybeFileLocation',
     },
     /**
      * #slot

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-bed",
-  "version": "5.0.0-beta.10",
+  "version": "5.0.0-beta.13",
   "type": "module",
   "description": "JBrowse 2 bed adapters, tracks, etc.",
   "keywords": [
@@ -23,12 +23,16 @@
   "dependencies": {
     "@gmod/bbi": "^11.3.0",
     "@gmod/bed": "^2.3.1",
-    "@gmod/tabix": "^3.8.3",
+    "@gmod/tabix": "^3.9.1",
     "@gmod/trix": "^3.0.22",
-    "@jbrowse/mobx-state-tree": "^6.6.1",
-    "mobx": "^7.0.5",
+    "@jbrowse/mobx-state-tree": "^6.7.0",
+    "mobx": "^7.0.6",
     "rxjs": "^7.8.2",
-    "@jbrowse/core": "^5.0.0-beta.10"
+    "@jbrowse/core": "^5.0.0-beta.13"
+  },
+  "peerDependencies": {
+    "react": ">=19.0.0",
+    "react-dom": ">=19.0.0"
   },
   "publishConfig": {
     "access": "public"