@jbrowse/cli 3.6.0 → 3.6.1

package/dist/utils.js

@@ -0,0 +1,154 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.debug = debug;
+exports.readFile = readFile;
+exports.readJsonFile = readJsonFile;
+exports.writeJsonFile = writeJsonFile;
+exports.resolveFileLocation = resolveFileLocation;
+exports.readInlineOrFileJson = readInlineOrFileJson;
+exports.fetchGithubVersions = fetchGithubVersions;
+exports.getLatest = getLatest;
+exports.fetchVersions = fetchVersions;
+exports.getTag = getTag;
+exports.getBranch = getBranch;
+exports.printHelp = printHelp;
+const fs_1 = require("fs");
+const path_1 = __importDefault(require("path"));
+const json_parse_better_errors_1 = __importDefault(require("json-parse-better-errors"));
+const fetchWithProxy_1 = __importDefault(require("./fetchWithProxy"));
+function debug(message) {
+    if (process.env.DEBUG) {
+        console.log(`DEBUG: ${message}`);
+    }
+}
+async function readFile(location) {
+    return fs_1.promises.readFile(location, { encoding: 'utf8' });
+}
+async function readJsonFile(location) {
+    const contents = await fs_1.promises.readFile(location, { encoding: 'utf8' });
+    return (0, json_parse_better_errors_1.default)(contents);
+}
+async function writeJsonFile(location, contents) {
+    debug(`Writing JSON file to ${process.cwd()} ${location}`);
+    return fs_1.promises.writeFile(location, JSON.stringify(contents, null, 2));
+}
+async function resolveFileLocation(location, check = true, inPlace = false) {
+    let locationUrl;
+    try {
+        locationUrl = new URL(location);
+    }
+    catch (error) {
+        // ignore
+    }
+    if (locationUrl) {
+        if (check) {
+            // @ts-expect-error
+            const response = await (0, fetchWithProxy_1.default)(locationUrl, { method: 'HEAD' });
+            if (!response.ok) {
+                throw new Error(`${locationUrl} result ${response.statusText}`);
+            }
+        }
+        return locationUrl.href;
+    }
+    let locationPath;
+    try {
+        locationPath = check ? await fs_1.promises.realpath(location) : location;
+    }
+    catch (e) {
+        // ignore
+    }
+    if (locationPath) {
+        const filePath = path_1.default.relative(process.cwd(), locationPath);
+        if (inPlace && filePath.startsWith('..')) {
+            console.warn(`Location ${filePath} is not in the JBrowse directory. Make sure it is still in your server directory.`);
+        }
+        return inPlace ? location : filePath;
+    }
+    throw new Error(`Could not resolve to a file or a URL: "${location}"`);
+}
+async function readInlineOrFileJson(inlineOrFileName) {
+    let result;
+    // see if it's inline JSON
+    try {
+        result = (0, json_parse_better_errors_1.default)(inlineOrFileName);
+    }
+    catch (error) {
+        debug(`Not valid inline JSON, attempting to parse as filename: '${inlineOrFileName}'`);
+        // not inline JSON, must be location of a JSON file
+        result = await readJsonFile(inlineOrFileName);
+    }
+    return result;
+}
+async function fetchGithubVersions() {
+    let versions = [];
+    for await (const iter of fetchVersions()) {
+        versions = [...versions, ...iter];
+    }
+    return versions;
+}
+async function getLatest() {
+    for await (const versions of fetchVersions()) {
+        // if a release was just uploaded, or an erroneous build was made then it
+        // might have no build asset
+        const nonprereleases = versions
+            .filter(release => !release.prerelease)
+            .filter(release => release.assets?.length);
+        if (nonprereleases.length > 0) {
+            // @ts-expect-error
+            const file = nonprereleases[0].assets.find(f => f.name.includes('jbrowse-web'))?.browser_download_url;
+            if (!file) {
+                throw new Error('no jbrowse-web download found');
+            }
+            return file;
+        }
+    }
+    throw new Error('no version tags found');
+}
+async function* fetchVersions() {
+    let page = 1;
+    let result;
+    do {
+        const url = `https://api.github.com/repos/GMOD/jbrowse-components/releases?page=${page}`;
+        const response = await (0, fetchWithProxy_1.default)(url);
+        if (response.ok) {
+            result = (await response.json());
+            yield result.filter(release => release.tag_name.startsWith('v'));
+            page++;
+        }
+        else {
+            throw new Error(`HTTP ${response.status} fetching ${url}`);
+        }
+    } while (result.length);
+}
+async function getTag(tag) {
+    const response = await (0, fetchWithProxy_1.default)(`https://api.github.com/repos/GMOD/jbrowse-components/releases/tags/${tag}`);
+    if (response.ok) {
+        const result = (await response.json());
+        const file = result.assets?.find(f => f.name.includes('jbrowse-web'))?.browser_download_url;
+        if (!file) {
+            throw new Error('Could not find version specified. Use --listVersions to see all available versions');
+        }
+        return file;
+    }
+    throw new Error(`Could not find version: ${response.statusText}`);
+}
+async function getBranch(branch) {
+    return `https://s3.amazonaws.com/jbrowse.org/code/jb2/${branch}/jbrowse-web-${branch}.zip`;
+}
+function printHelp({ description, options, examples, usage, }) {
+    console.log(description);
+    console.log(`\nUsage: ${usage || 'jbrowse <command> [options]'}`);
+    console.log('\nOptions:');
+    for (const [name, option] of Object.entries(options)) {
+        const short = 'short' in option && option.short
+            ? `-${option.short}`
+            : '   ';
+        const namePadded = `--${name}`.padEnd(25, ' ');
+        const desc = option.description?.replace(/\n/g, `\n${' '.repeat(29)}`);
+        console.log(`  ${short}, ${namePadded} ${desc}`);
+    }
+    console.log(`\n${examples.join('\n')}`);
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/cli",
-  "version": "3.6.0",
+  "version": "3.6.1",
   "description": "A command line tool for working with JBrowse 2",
   "keywords": [
     "jbrowse",
@@ -17,7 +17,7 @@
   "author": "JBrowse Team",
   "main": "dist/index.js",
   "bin": {
-    "jbrowse": "./bin/run"
+    "jbrowse": "./dist/bin.js"
   },
   "files": [
     "/bin",
@@ -48,5 +48,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "133a68815ab348d156c18d83cffc997356c3cfbb"
+  "gitHead": "3b7ba0005a28fb0903b7b31f15259c2cfccecfa1"
 }