@jbrowse/text-indexing 2.6.2 → 2.7.0

package/dist/TextIndexing.js

@@ -11,16 +11,15 @@ const gff3Adapter_1 = require("./types/gff3Adapter");
 const vcfAdapter_1 = require("./types/vcfAdapter");
 const common_1 = require("./types/common");
 const ixixx_1 = require("ixixx");
-const util_1 = require("./util");
-const util_2 = require("@jbrowse/core/util");
+const util_1 = require("@jbrowse/core/util");
 async function indexTracks(args) {
     const { tracks, outLocation, attributes, exclude, assemblies, indexType, statusCallback, signal, } = args;
     const idxType = indexType || 'perTrack';
-    (0, util_2.checkAbortSignal)(signal);
+    (0, util_1.checkAbortSignal)(signal);
     await (idxType === 'perTrack'
         ? perTrackIndex(tracks, statusCallback, outLocation, attributes, exclude, signal)
         : aggregateIndex(tracks, statusCallback, outLocation, attributes, assemblies, exclude, signal));
-    (0, util_2.checkAbortSignal)(signal);
+    (0, util_1.checkAbortSignal)(signal);
     return [];
 }
 exports.indexTracks = indexTracks;
@@ -37,7 +36,7 @@ async function perTrackIndex(tracks, statusCallback, outLocation, attributes, ex
     const attrs = attributes || ['Name', 'ID'];
     const excludeTypes = exclude || ['exon', 'CDS'];
     const force = true;
-    const supportedTracks = tracks.filter(track => { var _a; return (0, util_1.supportedIndexingAdapters)((_a = track.adapter) === null || _a === void 0 ? void 0 : _a.type); });
+    const supportedTracks = tracks.filter(track => { var _a; return (0, util_1.isSupportedIndexingAdapter)((_a = track.adapter) === null || _a === void 0 ? void 0 : _a.type); });
     for (const trackConfig of supportedTracks) {
         const { textSearching, trackId, assemblyNames } = trackConfig;
         const id = `${trackId}-index`;
@@ -70,7 +69,7 @@ async function aggregateIndex(tracks, statusCallback, outLocation, attributes, a
         const quiet = true;
         // supported tracks for given assembly
         const supportedTracks = tracks
-            .filter(track => { var _a; return (0, util_1.supportedIndexingAdapters)((_a = track.adapter) === null || _a === void 0 ? void 0 : _a.type); })
+            .filter(track => { var _a; return (0, util_1.isSupportedIndexingAdapter)((_a = track.adapter) === null || _a === void 0 ? void 0 : _a.type); })
             .filter(track => (asm ? track.assemblyNames.includes(asm) : true));
         await indexDriver(supportedTracks, outDir, attrs, id, quiet, excludeTypes, [asm], statusCallback, signal);
     }
@@ -80,7 +79,7 @@ async function indexDriver(tracks, idxLocation, attributes, name, quiet, exclude
     statusCallback('Indexing files.');
     try {
         const ixIxxStream = await runIxIxx(readable, idxLocation, name);
-        (0, util_2.checkAbortSignal)(signal);
+        (0, util_1.checkAbortSignal)(signal);
         await (0, common_1.generateMeta)({
             configs: tracks,
             attributes,
@@ -89,7 +88,7 @@ async function indexDriver(tracks, idxLocation, attributes, name, quiet, exclude
             exclude,
             assemblyNames,
         });
-        (0, util_2.checkAbortSignal)(signal);
+        (0, util_1.checkAbortSignal)(signal);
         return ixIxxStream;
     }
     catch (e) {

package/dist/types/vcfAdapter.js

@@ -49,8 +49,7 @@ async function* indexVcf(config, attributesToIndex, inLocation, outLocation, typ
             .map(attr => fields[attr])
             .filter((f) => !!f);
         const ids = id.split(',');
-        for (let i = 0; i < ids.length; i++) {
-            const id = ids[i];
+        for (const id of ids) {
             const attrs = [id];
             const record = JSON.stringify([
                 encodeURIComponent(locStr),

package/dist/util.d.ts

@@ -70,9 +70,7 @@ export interface VcfAdapter {
     type: 'VcfAdapter';
     vcfLocation: UriLocation | LocalPathLocation;
 }
-export interface Track {
-    [key: string]: any;
-}
+export type Track = Record<string, any>;
 export interface TextSearching {
     indexingFeatureTypesToExclude?: string[];
     indexingAttributes?: string[];
@@ -96,7 +94,6 @@ export interface Config {
     tracks?: Track[];
 }
 export type indexType = 'aggregate' | 'perTrack';
-export declare function supportedIndexingAdapters(type: string): boolean;
 export declare function createTextSearchConf(name: string, trackIds: string[], assemblyNames: string[], locationPath: string): {
     type: string;
     textSearchAdapterId: string;

package/dist/util.js

@@ -1,17 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.findTrackConfigsToIndex = exports.createTextSearchConf = exports.supportedIndexingAdapters = void 0;
-// supported adapter types by text indexer
-//  ensure that this matches the method found in @jbrowse/core/util
-function supportedIndexingAdapters(type) {
-    return [
-        'Gff3TabixAdapter',
-        'VcfTabixAdapter',
-        'Gff3Adapter',
-        'VcfAdapter',
-    ].includes(type);
-}
-exports.supportedIndexingAdapters = supportedIndexingAdapters;
+exports.findTrackConfigsToIndex = exports.createTextSearchConf = void 0;
+const util_1 = require("@jbrowse/core/util");
 function createTextSearchConf(name, trackIds, assemblyNames, locationPath) {
     // const locationPath = self.sessionPath.substring(
     //   0,
@@ -47,6 +37,6 @@ function findTrackConfigsToIndex(tracks, trackIds, assemblyName) {
         return currentTrack;
     })
         .filter(track => assemblyName ? track.assemblyNames.includes(assemblyName) : true)
-        .filter(track => supportedIndexingAdapters(track.adapter.type));
+        .filter(track => { var _a; return (0, util_1.isSupportedIndexingAdapter)((_a = track.adapter) === null || _a === void 0 ? void 0 : _a.type); });
 }
 exports.findTrackConfigsToIndex = findTrackConfigsToIndex;

package/esm/TextIndexing.js

@@ -5,8 +5,7 @@ import { indexGff3 } from './types/gff3Adapter';
 import { indexVcf } from './types/vcfAdapter';
 import { generateMeta } from './types/common';
 import { ixIxxStream } from 'ixixx';
-import { supportedIndexingAdapters } from './util';
-import { checkAbortSignal } from '@jbrowse/core/util';
+import { checkAbortSignal, isSupportedIndexingAdapter, } from '@jbrowse/core/util';
 export async function indexTracks(args) {
     const { tracks, outLocation, attributes, exclude, assemblies, indexType, statusCallback, signal, } = args;
     const idxType = indexType || 'perTrack';
@@ -30,7 +29,7 @@ async function perTrackIndex(tracks, statusCallback, outLocation, attributes, ex
     const attrs = attributes || ['Name', 'ID'];
     const excludeTypes = exclude || ['exon', 'CDS'];
     const force = true;
-    const supportedTracks = tracks.filter(track => { var _a; return supportedIndexingAdapters((_a = track.adapter) === null || _a === void 0 ? void 0 : _a.type); });
+    const supportedTracks = tracks.filter(track => { var _a; return isSupportedIndexingAdapter((_a = track.adapter) === null || _a === void 0 ? void 0 : _a.type); });
     for (const trackConfig of supportedTracks) {
         const { textSearching, trackId, assemblyNames } = trackConfig;
         const id = `${trackId}-index`;
@@ -63,7 +62,7 @@ async function aggregateIndex(tracks, statusCallback, outLocation, attributes, a
         const quiet = true;
         // supported tracks for given assembly
         const supportedTracks = tracks
-            .filter(track => { var _a; return supportedIndexingAdapters((_a = track.adapter) === null || _a === void 0 ? void 0 : _a.type); })
+            .filter(track => { var _a; return isSupportedIndexingAdapter((_a = track.adapter) === null || _a === void 0 ? void 0 : _a.type); })
             .filter(track => (asm ? track.assemblyNames.includes(asm) : true));
         await indexDriver(supportedTracks, outDir, attrs, id, quiet, excludeTypes, [asm], statusCallback, signal);
     }

package/esm/types/vcfAdapter.js

@@ -43,8 +43,7 @@ export async function* indexVcf(config, attributesToIndex, inLocation, outLocati
             .map(attr => fields[attr])
             .filter((f) => !!f);
         const ids = id.split(',');
-        for (let i = 0; i < ids.length; i++) {
-            const id = ids[i];
+        for (const id of ids) {
             const attrs = [id];
             const record = JSON.stringify([
                 encodeURIComponent(locStr),

package/esm/util.d.ts

@@ -70,9 +70,7 @@ export interface VcfAdapter {
     type: 'VcfAdapter';
     vcfLocation: UriLocation | LocalPathLocation;
 }
-export interface Track {
-    [key: string]: any;
-}
+export type Track = Record<string, any>;
 export interface TextSearching {
     indexingFeatureTypesToExclude?: string[];
     indexingAttributes?: string[];
@@ -96,7 +94,6 @@ export interface Config {
     tracks?: Track[];
 }
 export type indexType = 'aggregate' | 'perTrack';
-export declare function supportedIndexingAdapters(type: string): boolean;
 export declare function createTextSearchConf(name: string, trackIds: string[], assemblyNames: string[], locationPath: string): {
     type: string;
     textSearchAdapterId: string;

package/esm/util.js

@@ -1,13 +1,4 @@
-// supported adapter types by text indexer
-//  ensure that this matches the method found in @jbrowse/core/util
-export function supportedIndexingAdapters(type) {
-    return [
-        'Gff3TabixAdapter',
-        'VcfTabixAdapter',
-        'Gff3Adapter',
-        'VcfAdapter',
-    ].includes(type);
-}
+import { isSupportedIndexingAdapter } from '@jbrowse/core/util';
 export function createTextSearchConf(name, trackIds, assemblyNames, locationPath) {
     // const locationPath = self.sessionPath.substring(
     //   0,
@@ -42,5 +33,5 @@ export function findTrackConfigsToIndex(tracks, trackIds, assemblyName) {
         return currentTrack;
     })
         .filter(track => assemblyName ? track.assemblyNames.includes(assemblyName) : true)
-        .filter(track => supportedIndexingAdapters(track.adapter.type));
+        .filter(track => { var _a; return isSupportedIndexingAdapter((_a = track.adapter) === null || _a === void 0 ? void 0 : _a.type); });
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/text-indexing",
-  "version": "2.6.2",
+  "version": "2.7.0",
   "description": "JBrowse 2 text indexing for desktop",
   "keywords": [
     "jbrowse",
@@ -47,14 +47,14 @@
   },
   "peerDependencies": {
     "mobx": "^6.0.0",
-    "mobx-react": "^7.0.0",
+    "mobx-react": "^9.0.0",
     "mobx-state-tree": "^5.0.0",
-    "react": "^17.0.0",
-    "react-dom": "^17.0.0",
+    "react": ">=16.8.0",
+    "react-dom": ">=16.8.0",
     "rxjs": "^7.0.0"
   },
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "bbea587a402d9974acdd804a33f4b77f31a2fd5f"
+  "gitHead": "dbe7fb1af01fc89f833d2744635eb44a17365b41"
 }