@jbrowse/cli 4.1.1 → 4.1.3

package/dist/cliFetch.js

@@ -0,0 +1,3 @@
+export default function cliFetch(url, options = {}) {
+    return fetch(url, options);
+}

package/dist/commands/add-connection.js

@@ -1,7 +1,7 @@
 import path from 'path';
 import { parseArgs } from 'util';
 import parseJSON from 'json-parse-better-errors';
-import fetch from "../fetchWithProxy.js";
+import fetch from "../cliFetch.js";
 import { debug, printHelp, readJsonFile, resolveConfigPath, writeJsonFile, } from "../utils.js";
 async function resolveURL(location, check = true) {
     let locationUrl;

package/dist/commands/add-track-utils/file-operations.js

@@ -12,7 +12,7 @@ export async function loadFile({ src, destDir, mode, subDir = '', force = false,
             await unlink(dest);
         }
         catch (e) {
-            if (e.code !== 'ENOENT') {
+            if (e && typeof e === 'object' && 'code' in e && e.code !== 'ENOENT') {
                 throw e;
             }
         }

package/dist/commands/admin-server/index.js

@@ -76,7 +76,7 @@ export async function run(args) {
         debug(`Admin key stored at ${keyPath}`);
     }
     catch (error) {
-        console.error(`Failed to write admin key to ${keyPath}:`, error.message);
+        console.error(`Failed to write admin key to ${keyPath}:`, error instanceof Error ? error.message : error);
         // Continue anyway, as this is not critical
     }
     // Create server reference for shutdown route

package/dist/commands/create.js

@@ -1,7 +1,7 @@
 import fs from 'fs';
 import { parseArgs } from 'util';
 import decompress from 'decompress';
-import fetch from "../fetchWithProxy.js";
+import fetch from "../cliFetch.js";
 import { fetchGithubVersions, getBranch, getLatest, getTag, printHelp, } from "../utils.js";
 const fsPromises = fs.promises;
 const description = 'Downloads and installs the latest JBrowse 2 release';

package/dist/commands/text-index/config-utils.js

@@ -91,7 +91,9 @@ export function getTrackConfigs(config, trackIds, assemblyName, excludeTrackIds)
     if (!tracks) {
         return [];
     }
-    const trackIdsToIndex = trackIds || tracks.map(track => track.trackId);
+    const trackIdsToIndex = trackIds?.length
+        ? trackIds
+        : tracks.map(track => track.trackId);
     const excludeSet = new Set(excludeTrackIds || []);
     return trackIdsToIndex
         .map(trackId => {
@@ -103,11 +105,10 @@ export function getTrackConfigs(config, trackIds, assemblyName, excludeTrackIds)
     })
         .filter(track => {
         if (excludeSet.has(track.trackId)) {
-            console.log(`Skipping ${track.trackId}: excluded via --exclude-tracks`);
+            // console.log(`Skipping ${track.trackId}: excluded via --exclude-tracks`)
             return false;
         }
         if (!supported(track.adapter?.type)) {
-            console.log(`Skipping ${track.trackId}: unsupported adapter type '${track.adapter?.type}'`);
             return false;
         }
         if (assemblyName && !track.assemblyNames.includes(assemblyName)) {

package/dist/commands/upgrade.js

@@ -2,7 +2,7 @@ import fs from 'fs';
 import path from 'path';
 import { parseArgs } from 'util';
 import decompress from 'decompress';
-import fetch from "../fetchWithProxy.js";
+import fetch from "../cliFetch.js";
 import { fetchGithubVersions, getBranch, getLatest, getTag, printHelp, } from "../utils.js";
 const description = 'Upgrades JBrowse 2 to latest version';
 const examples = [

package/dist/types/common.js

@@ -1,4 +1,4 @@
-import fetch from "../fetchWithProxy.js";
+import fetch from "../cliFetch.js";
 export async function createRemoteStream(urlIn) {
     const res = await fetch(urlIn);
     if (!res.ok) {

package/dist/utils.js

@@ -1,7 +1,7 @@
 import { promises as fsPromises } from 'fs';
 import path from 'path';
 import parseJSON from 'json-parse-better-errors';
-import fetch from "./fetchWithProxy.js";
+import fetch from "./cliFetch.js";
 export function debug(message) {
     if (process.env.DEBUG) {
         console.log(`DEBUG: ${message}`);
@@ -80,12 +80,12 @@ export async function getLatest() {
     for await (const versions of fetchVersions()) {
         // if a release was just uploaded, or an erroneous build was made then it
         // might have no build asset
-        const nonprereleases = versions
+        const nonprerelease = versions
             .filter(release => !release.prerelease)
-            .filter(release => release.assets?.length);
-        if (nonprereleases.length > 0) {
-            // @ts-expect-error
-            const file = nonprereleases[0].assets.find(f => f.name.includes('jbrowse-web'))?.browser_download_url;
+            .find(release => release.assets?.length);
+        const first = nonprerelease;
+        if (first?.assets) {
+            const file = first.assets.find(f => f.name.includes('jbrowse-web'))?.browser_download_url;
             if (!file) {
                 throw new Error('no jbrowse-web download found');
             }

package/dist/version.js

@@ -1 +1 @@
-export const version = '4.1.1';
+export const version = '4.1.3';

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/cli",
-  "version": "4.1.1",
+  "version": "4.1.3",
   "type": "module",
   "description": "A command line tool for working with JBrowse 2",
   "keywords": [
@@ -31,14 +31,13 @@
   "dependencies": {
     "cli-progress": "^3.12.0",
     "command-exists": "^1.2.9",
-    "cors": "^2.8.5",
+    "cors": "^2.8.6",
     "decompress": "^4.2.1",
     "express": "^5.2.1",
     "ixixx": "^3.0.3",
     "json-parse-better-errors": "^1.0.2",
-    "node-fetch-native": "^1.6.7",
     "tmp": "^0.2.5",
-    "@jbrowse/text-indexing-core": "^4.1.1"
+    "@jbrowse/text-indexing-core": "^4.1.3"
   },
   "publishConfig": {
     "access": "public"

package/dist/fetchWithProxy.js

@@ -1,9 +0,0 @@
-import { fetch } from 'node-fetch-native/node';
-import { createProxy } from 'node-fetch-native/proxy';
-const proxy = createProxy();
-// The correct proxy `Agent` implementation to use will be determined
-// via the `http_proxy` / `https_proxy` / `no_proxy` / etc. env vars
-// https://github.com/unjs/node-fetch-native?tab=readme-ov-file#proxy-support
-export default function fetchWithProxy(url, options = {}) {
-    return fetch(url, { ...options, ...proxy });
-}

package/dist/types/gff3Adapter.js

@@ -1,42 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.indexGff3 = indexGff3;
-const util_ts_1 = require("../util.js");
-const streamUtils_ts_1 = require("./streamUtils.js");
-async function* indexGff3({ config, attributesToIndex, inLocation, outLocation, typesToExclude, quiet, }) {
-    const { trackId } = config;
-    const { rl, progressBar } = await (0, streamUtils_ts_1.createIndexingStream)({
-        inLocation,
-        outLocation,
-        trackId,
-        quiet,
-    });
-    const excludeSet = new Set(typesToExclude);
-    const encodedTrackId = encodeURIComponent(trackId);
-    for await (const line of rl) {
-        if (!line.trim()) {
-            continue;
-        }
-        else if (line.startsWith('#')) {
-            continue;
-        }
-        else if (line.startsWith('>')) {
-            break;
-        }
-        const [seq_id, , type, start, end, , , , col9] = line.split('\t');
-        if (!excludeSet.has(type)) {
-            const col9attrs = (0, streamUtils_ts_1.parseAttributes)(col9, util_ts_1.decodeURIComponentNoThrow);
-            const attrs = attributesToIndex
-                .map(attr => col9attrs[attr])
-                .filter((f) => !!f);
-            if (attrs.length > 0) {
-                const locStr = `${seq_id}:${start}..${end}`;
-                const encodedAttrs = attrs.map(a => `"${encodeURIComponent(a)}"`);
-                const record = `["${encodeURIComponent(locStr)}"|"${encodedTrackId}"|${encodedAttrs.join('|')}]`;
-                const uniqueAttrs = [...new Set(attrs)];
-                yield `${record} ${uniqueAttrs.join(' ')}\n`;
-            }
-        }
-    }
-    progressBar.stop();
-}

package/dist/types/streamUtils.js

@@ -1,66 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.createIndexingStream = createIndexingStream;
-exports.parseAttributes = parseAttributes;
-const cli_progress_1 = require("cli-progress");
-const util_ts_1 = require("../util.js");
-async function* readLines(reader, progressBar) {
-    const decoder = new TextDecoder();
-    let buffer = '';
-    let receivedBytes = 0;
-    try {
-        let result = await reader.read();
-        while (!result.done) {
-            receivedBytes += result.value.length;
-            progressBar.update(receivedBytes);
-            buffer += decoder.decode(result.value, { stream: true });
-            const lines = buffer.split('\n');
-            buffer = lines.pop();
-            for (const line of lines) {
-                yield line;
-            }
-            result = await reader.read();
-        }
-    }
-    finally {
-        reader.releaseLock();
-    }
-    buffer += decoder.decode();
-    if (buffer) {
-        yield buffer;
-    }
-}
-async function createIndexingStream({ inLocation, outLocation, trackId, quiet, }) {
-    const progressBar = new cli_progress_1.SingleBar({
-        format: `{bar} ${trackId} {percentage}% | ETA: {eta}s`,
-        etaBuffer: 2000,
-    }, cli_progress_1.Presets.shades_classic);
-    const { totalBytes, stream } = await (0, util_ts_1.getLocalOrRemoteStream)(inLocation, outLocation);
-    if (!quiet) {
-        progressBar.start(totalBytes, 0);
-    }
-    if (!stream) {
-        throw new Error(`Failed to fetch ${inLocation}: no response body`);
-    }
-    const inputStream = /.b?gz$/.exec(inLocation)
-        ? // @ts-ignore root tsconfig includes DOM lib which has incompatible stream types
-            stream.pipeThrough(new DecompressionStream('gzip'))
-        : stream;
-    const rl = readLines(inputStream.getReader(), progressBar);
-    return { rl, progressBar };
-}
-function parseAttributes(infoString, decodeFunc) {
-    const result = {};
-    for (const field of infoString.split(';')) {
-        const trimmed = field.trim();
-        if (trimmed) {
-            const eqIdx = trimmed.indexOf('=');
-            if (eqIdx !== -1) {
-                const key = trimmed.slice(0, eqIdx).trim();
-                const val = trimmed.slice(eqIdx + 1);
-                result[key] = decodeFunc(val).trim().replaceAll(',', ' ');
-            }
-        }
-    }
-    return result;
-}

package/dist/types/vcfAdapter.js

@@ -1,39 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.indexVcf = indexVcf;
-const util_ts_1 = require("../util.js");
-const streamUtils_ts_1 = require("./streamUtils.js");
-async function* indexVcf({ config, attributesToIndex, inLocation, outLocation, quiet, }) {
-    const { trackId } = config;
-    const { rl, progressBar } = await (0, streamUtils_ts_1.createIndexingStream)({
-        inLocation,
-        outLocation,
-        trackId,
-        quiet,
-    });
-    const encodedTrackId = encodeURIComponent(trackId);
-    for await (const line of rl) {
-        if (line.startsWith('#')) {
-            continue;
-        }
-        // eslint-disable-next-line @typescript-eslint/no-unused-vars
-        const [ref, pos, id, _ref, _alt, _qual, _filter, info] = line.split('\t');
-        if (id === '.') {
-            continue;
-        }
-        const fields = (0, streamUtils_ts_1.parseAttributes)(info, util_ts_1.decodeURIComponentNoThrow);
-        const end = fields.END;
-        const locStr = `${ref}:${pos}..${end || +pos + 1}`;
-        const encodedLocStr = encodeURIComponent(locStr);
-        const infoAttrs = attributesToIndex
-            .map(attr => fields[attr])
-            .filter((f) => !!f);
-        const encodedInfoAttrs = infoAttrs.map(a => `"${encodeURIComponent(a)}"`);
-        for (const variantId of id.split(',')) {
-            const encodedId = encodeURIComponent(variantId);
-            const record = `["${encodedLocStr}"|"${encodedTrackId}"|"${encodedId}"${encodedInfoAttrs.length > 0 ? `|${encodedInfoAttrs.join('|')}` : ''}]`;
-            yield `${record} ${variantId}\n`;
-        }
-    }
-    progressBar.stop();
-}