@jbrowse/text-indexing 2.16.0 → 2.17.0

package/dist/types/common.d.ts

@@ -3,13 +3,12 @@ import fetch from 'node-fetch';
 import { LocalPathLocation, UriLocation, Track } from '../util';
 export declare function createRemoteStream(urlIn: string): Promise<fetch.Response>;
 export declare function isURL(FileName: string): boolean;
-export declare function getLocalOrRemoteStream(uri: string, out: string): Promise<{
-    totalBytes: number;
-    stream: NodeJS.ReadableStream;
-} | {
-    totalBytes: number;
-    stream: fs.ReadStream;
-}>;
+export declare function getLocalOrRemoteStream({ file, out, onBytesReceived, onTotalBytes, }: {
+    file: string;
+    out: string;
+    onBytesReceived: (totalBytesReceived: number) => void;
+    onTotalBytes: (totalBytes: number) => void;
+}): Promise<NodeJS.ReadableStream | fs.ReadStream>;
 export declare function makeLocation(location: string, protocol: string): UriLocation | LocalPathLocation;
 export declare function guessAdapterFromFileName(filePath: string): Track;
 /**

package/dist/types/common.js

@@ -33,20 +33,26 @@ function isURL(FileName) {
     }
     return url.protocol === 'http:' || url.protocol === 'https:';
 }
-async function getLocalOrRemoteStream(uri, out) {
-    if (isURL(uri)) {
-        const result = await createRemoteStream(uri);
-        return {
-            totalBytes: +(result.headers.get('Content-Length') || 0),
-            stream: result.body,
-        };
+async function getLocalOrRemoteStream({ file, out, onBytesReceived, onTotalBytes, }) {
+    let receivedBytes = 0;
+    if (isURL(file)) {
+        const result = await createRemoteStream(file);
+        result.body.on('data', chunk => {
+            receivedBytes += chunk.length;
+            onBytesReceived(receivedBytes);
+        });
+        onTotalBytes(+(result.headers.get('Content-Length') || 0));
+        return result.body;
     }
     else {
-        const filename = path_1.default.isAbsolute(uri) ? uri : path_1.default.join(out, uri);
-        return {
-            totalBytes: fs_1.default.statSync(filename).size,
-            stream: fs_1.default.createReadStream(filename),
-        };
+        const filename = path_1.default.isAbsolute(file) ? file : path_1.default.join(out, file);
+        const stream = fs_1.default.createReadStream(filename);
+        stream.on('data', chunk => {
+            receivedBytes += chunk.length;
+            onBytesReceived(receivedBytes);
+        });
+        onTotalBytes(fs_1.default.statSync(filename).size);
+        return stream;
     }
 }
 function makeLocation(location, protocol) {

package/dist/types/gff3Adapter.js

@@ -11,12 +11,11 @@ const util_1 = require("../util");
 const common_1 = require("./common");
 async function* indexGff3({ config, attributesToIndex, inLocation, outDir, featureTypesToExclude, onStart, onUpdate, }) {
     const { trackId } = config;
-    let receivedBytes = 0;
-    const { totalBytes, stream } = await (0, common_1.getLocalOrRemoteStream)(inLocation, outDir);
-    onStart(totalBytes);
-    stream.on('data', chunk => {
-        receivedBytes += chunk.length;
-        onUpdate(receivedBytes);
+    const stream = await (0, common_1.getLocalOrRemoteStream)({
+        file: inLocation,
+        out: outDir,
+        onTotalBytes: onStart,
+        onBytesReceived: onUpdate,
     });
     const rl = readline_1.default.createInterface({
         input: /.b?gz$/.exec(inLocation) ? stream.pipe((0, zlib_1.createGunzip)()) : stream,

package/dist/types/vcfAdapter.js

@@ -11,12 +11,11 @@ const util_1 = require("../util");
 const common_1 = require("./common");
 async function* indexVcf({ config, attributesToIndex, inLocation, outDir, onStart, onUpdate, }) {
     const { trackId } = config;
-    let receivedBytes = 0;
-    const { totalBytes, stream } = await (0, common_1.getLocalOrRemoteStream)(inLocation, outDir);
-    onStart(totalBytes);
-    stream.on('data', chunk => {
-        receivedBytes += chunk.length;
-        onUpdate(receivedBytes);
+    const stream = await (0, common_1.getLocalOrRemoteStream)({
+        file: inLocation,
+        out: outDir,
+        onTotalBytes: onStart,
+        onBytesReceived: onUpdate,
     });
     const gzStream = /.b?gz$/.exec(inLocation)
         ? stream.pipe((0, zlib_1.createGunzip)())

package/esm/types/common.d.ts

@@ -3,13 +3,12 @@ import fetch from 'node-fetch';
 import { LocalPathLocation, UriLocation, Track } from '../util';
 export declare function createRemoteStream(urlIn: string): Promise<fetch.Response>;
 export declare function isURL(FileName: string): boolean;
-export declare function getLocalOrRemoteStream(uri: string, out: string): Promise<{
-    totalBytes: number;
-    stream: NodeJS.ReadableStream;
-} | {
-    totalBytes: number;
-    stream: fs.ReadStream;
-}>;
+export declare function getLocalOrRemoteStream({ file, out, onBytesReceived, onTotalBytes, }: {
+    file: string;
+    out: string;
+    onBytesReceived: (totalBytesReceived: number) => void;
+    onTotalBytes: (totalBytes: number) => void;
+}): Promise<NodeJS.ReadableStream | fs.ReadStream>;
 export declare function makeLocation(location: string, protocol: string): UriLocation | LocalPathLocation;
 export declare function guessAdapterFromFileName(filePath: string): Track;
 /**

package/esm/types/common.js

@@ -22,20 +22,26 @@ export function isURL(FileName) {
     }
     return url.protocol === 'http:' || url.protocol === 'https:';
 }
-export async function getLocalOrRemoteStream(uri, out) {
-    if (isURL(uri)) {
-        const result = await createRemoteStream(uri);
-        return {
-            totalBytes: +(result.headers.get('Content-Length') || 0),
-            stream: result.body,
-        };
+export async function getLocalOrRemoteStream({ file, out, onBytesReceived, onTotalBytes, }) {
+    let receivedBytes = 0;
+    if (isURL(file)) {
+        const result = await createRemoteStream(file);
+        result.body.on('data', chunk => {
+            receivedBytes += chunk.length;
+            onBytesReceived(receivedBytes);
+        });
+        onTotalBytes(+(result.headers.get('Content-Length') || 0));
+        return result.body;
     }
     else {
-        const filename = path.isAbsolute(uri) ? uri : path.join(out, uri);
-        return {
-            totalBytes: fs.statSync(filename).size,
-            stream: fs.createReadStream(filename),
-        };
+        const filename = path.isAbsolute(file) ? file : path.join(out, file);
+        const stream = fs.createReadStream(filename);
+        stream.on('data', chunk => {
+            receivedBytes += chunk.length;
+            onBytesReceived(receivedBytes);
+        });
+        onTotalBytes(fs.statSync(filename).size);
+        return stream;
     }
 }
 export function makeLocation(location, protocol) {

package/esm/types/gff3Adapter.js

@@ -5,12 +5,11 @@ import { decodeURIComponentNoThrow } from '../util';
 import { getLocalOrRemoteStream } from './common';
 export async function* indexGff3({ config, attributesToIndex, inLocation, outDir, featureTypesToExclude, onStart, onUpdate, }) {
     const { trackId } = config;
-    let receivedBytes = 0;
-    const { totalBytes, stream } = await getLocalOrRemoteStream(inLocation, outDir);
-    onStart(totalBytes);
-    stream.on('data', chunk => {
-        receivedBytes += chunk.length;
-        onUpdate(receivedBytes);
+    const stream = await getLocalOrRemoteStream({
+        file: inLocation,
+        out: outDir,
+        onTotalBytes: onStart,
+        onBytesReceived: onUpdate,
     });
     const rl = readline.createInterface({
         input: /.b?gz$/.exec(inLocation) ? stream.pipe(createGunzip()) : stream,

package/esm/types/vcfAdapter.js

@@ -5,12 +5,11 @@ import { decodeURIComponentNoThrow } from '../util';
 import { getLocalOrRemoteStream } from './common';
 export async function* indexVcf({ config, attributesToIndex, inLocation, outDir, onStart, onUpdate, }) {
     const { trackId } = config;
-    let receivedBytes = 0;
-    const { totalBytes, stream } = await getLocalOrRemoteStream(inLocation, outDir);
-    onStart(totalBytes);
-    stream.on('data', chunk => {
-        receivedBytes += chunk.length;
-        onUpdate(receivedBytes);
+    const stream = await getLocalOrRemoteStream({
+        file: inLocation,
+        out: outDir,
+        onTotalBytes: onStart,
+        onBytesReceived: onUpdate,
     });
     const gzStream = /.b?gz$/.exec(inLocation)
         ? stream.pipe(createGunzip())

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/text-indexing",
-  "version": "2.16.0",
+  "version": "2.17.0",
   "description": "JBrowse 2 text indexing for desktop",
   "keywords": [
     "jbrowse",
@@ -42,7 +42,7 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.16.3",
-    "@jbrowse/core": "^2.16.0",
+    "@jbrowse/core": "^2.17.0",
     "ixixx": "^2.0.1",
     "node-fetch": "^2.6.0",
     "sanitize-filename": "^1.6.3"
@@ -58,5 +58,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "1e6d4fbc27ce684eed19e3c217f34bd2da24ab75"
+  "gitHead": "eed30b5e671f8f7823652d7cecc51aa89226de46"
 }