@jbrowse/text-indexing 2.10.3 → 2.11.0

package/dist/TextIndexing.js

@@ -77,23 +77,18 @@ async function aggregateIndex(tracks, statusCallback, outLocation, attributes, a
 async function indexDriver(tracks, idxLocation, attributes, name, quiet, exclude, assemblyNames, statusCallback, signal) {
     const readable = stream_1.Readable.from(indexFiles(tracks, attributes, idxLocation, quiet, exclude, statusCallback, signal));
     statusCallback('Indexing files.');
-    try {
-        const ixIxxStream = await runIxIxx(readable, idxLocation, name);
-        (0, util_1.checkAbortSignal)(signal);
-        await (0, common_1.generateMeta)({
-            configs: tracks,
-            attributes,
-            outDir: idxLocation,
-            name,
-            exclude,
-            assemblyNames,
-        });
-        (0, util_1.checkAbortSignal)(signal);
-        return ixIxxStream;
-    }
-    catch (e) {
-        throw e;
-    }
+    const ixIxxStream = await runIxIxx(readable, idxLocation, name);
+    (0, util_1.checkAbortSignal)(signal);
+    await (0, common_1.generateMeta)({
+        configs: tracks,
+        attributes,
+        outDir: idxLocation,
+        name,
+        exclude,
+        assemblyNames,
+    });
+    (0, util_1.checkAbortSignal)(signal);
+    return ixIxxStream;
 }
 async function* indexFiles(tracks, attributes, outLocation, quiet, typesToExclude, statusCallback, signal) {
     for (const track of tracks) {

package/dist/types/gff3Adapter.js

@@ -6,8 +6,9 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.indexGff3 = void 0;
 const zlib_1 = require("zlib");
 const readline_1 = __importDefault(require("readline"));
+const util_1 = require("../util");
 const common_1 = require("./common");
-const util_1 = require("@jbrowse/core/util");
+const util_2 = require("@jbrowse/core/util");
 async function* indexGff3(config, attributes, inLocation, outLocation, typesToExclude, quiet, statusCallback, signal) {
     const { trackId } = config;
     let receivedBytes = 0;
@@ -40,7 +41,7 @@ async function* indexGff3(config, attributes, inLocation, outLocation, typesToEx
                 .map(f => f.split('='))
                 .map(([key, val]) => [
                 key.trim(),
-                decodeURIComponent(val).trim().split(',').join(' '),
+                (0, util_1.decodeURIComponentNoThrow)(val).trim().split(',').join(' '),
             ]));
             const attrs = attributes
                 .map(attr => col9attrs[attr])
@@ -52,7 +53,7 @@ async function* indexGff3(config, attributes, inLocation, outLocation, typesToEx
                     ...attrs.map(a => encodeURIComponent(a)),
                 ]).replaceAll(',', '|');
                 // Check abort signal
-                (0, util_1.checkAbortSignal)(signal);
+                (0, util_2.checkAbortSignal)(signal);
                 yield `${record} ${[...new Set(attrs)].join(' ')}\n`;
             }
         }

package/dist/types/vcfAdapter.js

@@ -6,8 +6,9 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.indexVcf = void 0;
 const zlib_1 = require("zlib");
 const readline_1 = __importDefault(require("readline"));
+const util_1 = require("../util");
 const common_1 = require("./common");
-const util_1 = require("@jbrowse/core/util");
+const util_2 = require("@jbrowse/core/util");
 async function* indexVcf(config, attributesToIndex, inLocation, outLocation, typesToExclude, quiet, statusCallback, signal) {
     const { trackId } = config;
     let receivedBytes = 0;
@@ -38,7 +39,9 @@ async function* indexVcf(config, attributesToIndex, inLocation, outLocation, typ
             .map(f => f.split('='))
             .map(([key, val]) => [
             key.trim(),
-            val ? decodeURIComponent(val).trim().split(',').join(' ') : undefined,
+            val
+                ? (0, util_1.decodeURIComponentNoThrow)(val).trim().split(',').join(' ')
+                : undefined,
         ]));
         const end = fields.END;
         const locStr = `${ref}:${pos}..${end || +pos + 1}`;
@@ -58,7 +61,7 @@ async function* indexVcf(config, attributesToIndex, inLocation, outLocation, typ
                 ...infoAttrs.map(a => encodeURIComponent(a || '')),
             ]).replaceAll(',', '|');
             // Check abort signal
-            (0, util_1.checkAbortSignal)(signal);
+            (0, util_2.checkAbortSignal)(signal);
             yield `${record} ${[...new Set(attrs)].join(' ')}\n`;
         }
     }

package/dist/util.d.ts

@@ -113,3 +113,4 @@ export declare function createTextSearchConf(name: string, trackIds: string[], a
     assemblyNames: string[];
 };
 export declare function findTrackConfigsToIndex(tracks: Track[], trackIds: string[], assemblyName?: string): Track[];
+export declare function decodeURIComponentNoThrow(uri: string): string;

package/dist/util.js

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.findTrackConfigsToIndex = exports.createTextSearchConf = void 0;
+exports.decodeURIComponentNoThrow = exports.findTrackConfigsToIndex = exports.createTextSearchConf = void 0;
 const util_1 = require("@jbrowse/core/util");
 const sanitize_filename_1 = __importDefault(require("sanitize-filename"));
 const path_1 = __importDefault(require("path"));
@@ -43,3 +43,13 @@ function findTrackConfigsToIndex(tracks, trackIds, assemblyName) {
         .filter(track => { var _a; return (0, util_1.isSupportedIndexingAdapter)((_a = track.adapter) === null || _a === void 0 ? void 0 : _a.type); });
 }
 exports.findTrackConfigsToIndex = findTrackConfigsToIndex;
+function decodeURIComponentNoThrow(uri) {
+    try {
+        return decodeURIComponent(uri);
+    }
+    catch (e) {
+        // avoid throwing exception on a failure to decode URI component
+        return uri;
+    }
+}
+exports.decodeURIComponentNoThrow = decodeURIComponentNoThrow;

package/esm/TextIndexing.js

@@ -70,23 +70,18 @@ async function aggregateIndex(tracks, statusCallback, outLocation, attributes, a
 async function indexDriver(tracks, idxLocation, attributes, name, quiet, exclude, assemblyNames, statusCallback, signal) {
     const readable = Readable.from(indexFiles(tracks, attributes, idxLocation, quiet, exclude, statusCallback, signal));
     statusCallback('Indexing files.');
-    try {
-        const ixIxxStream = await runIxIxx(readable, idxLocation, name);
-        checkAbortSignal(signal);
-        await generateMeta({
-            configs: tracks,
-            attributes,
-            outDir: idxLocation,
-            name,
-            exclude,
-            assemblyNames,
-        });
-        checkAbortSignal(signal);
-        return ixIxxStream;
-    }
-    catch (e) {
-        throw e;
-    }
+    const ixIxxStream = await runIxIxx(readable, idxLocation, name);
+    checkAbortSignal(signal);
+    await generateMeta({
+        configs: tracks,
+        attributes,
+        outDir: idxLocation,
+        name,
+        exclude,
+        assemblyNames,
+    });
+    checkAbortSignal(signal);
+    return ixIxxStream;
 }
 async function* indexFiles(tracks, attributes, outLocation, quiet, typesToExclude, statusCallback, signal) {
     for (const track of tracks) {

package/esm/types/gff3Adapter.js

@@ -1,5 +1,6 @@
 import { createGunzip } from 'zlib';
 import readline from 'readline';
+import { decodeURIComponentNoThrow } from '../util';
 import { getLocalOrRemoteStream } from './common';
 import { checkAbortSignal } from '@jbrowse/core/util';
 export async function* indexGff3(config, attributes, inLocation, outLocation, typesToExclude, quiet, statusCallback, signal) {
@@ -34,7 +35,7 @@ export async function* indexGff3(config, attributes, inLocation, outLocation, ty
                 .map(f => f.split('='))
                 .map(([key, val]) => [
                 key.trim(),
-                decodeURIComponent(val).trim().split(',').join(' '),
+                decodeURIComponentNoThrow(val).trim().split(',').join(' '),
             ]));
             const attrs = attributes
                 .map(attr => col9attrs[attr])

package/esm/types/vcfAdapter.js

@@ -1,5 +1,6 @@
 import { createGunzip } from 'zlib';
 import readline from 'readline';
+import { decodeURIComponentNoThrow } from '../util';
 import { getLocalOrRemoteStream } from './common';
 import { checkAbortSignal } from '@jbrowse/core/util';
 export async function* indexVcf(config, attributesToIndex, inLocation, outLocation, typesToExclude, quiet, statusCallback, signal) {
@@ -32,7 +33,9 @@ export async function* indexVcf(config, attributesToIndex, inLocation, outLocati
             .map(f => f.split('='))
             .map(([key, val]) => [
             key.trim(),
-            val ? decodeURIComponent(val).trim().split(',').join(' ') : undefined,
+            val
+                ? decodeURIComponentNoThrow(val).trim().split(',').join(' ')
+                : undefined,
         ]));
         const end = fields.END;
         const locStr = `${ref}:${pos}..${end || +pos + 1}`;

package/esm/util.d.ts

@@ -113,3 +113,4 @@ export declare function createTextSearchConf(name: string, trackIds: string[], a
     assemblyNames: string[];
 };
 export declare function findTrackConfigsToIndex(tracks: Track[], trackIds: string[], assemblyName?: string): Track[];
+export declare function decodeURIComponentNoThrow(uri: string): string;

package/esm/util.js

@@ -35,3 +35,12 @@ export function findTrackConfigsToIndex(tracks, trackIds, assemblyName) {
         .filter(track => assemblyName ? track.assemblyNames.includes(assemblyName) : true)
         .filter(track => { var _a; return isSupportedIndexingAdapter((_a = track.adapter) === null || _a === void 0 ? void 0 : _a.type); });
 }
+export function decodeURIComponentNoThrow(uri) {
+    try {
+        return decodeURIComponent(uri);
+    }
+    catch (e) {
+        // avoid throwing exception on a failure to decode URI component
+        return uri;
+    }
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/text-indexing",
-  "version": "2.10.3",
+  "version": "2.11.0",
   "description": "JBrowse 2 text indexing for desktop",
   "keywords": [
     "jbrowse",
@@ -57,5 +57,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "c8fc800cd17decd72b2e971c7a6add3b95214e72"
+  "gitHead": "3d43a820b9274a6160aa4dc15616147f390d9094"
 }