@jbrowse/cli 3.6.5 → 3.7.0

package/bundle/index.js

@@ -3116,7 +3116,7 @@ eval("{/*!\n * Tmp\n *\n * Copyright (c) 2011-2017 KARASZI Istvan <github@spam.r
 /***/ ((module, __unused_webpack_exports, __webpack_require__) => {
 
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@@ -3306,7 +3306,7 @@ eval("{__webpack_require__.r(__webpack_exports__);\n/* harmony export */ __webpa
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Please add one before adding connections');\n        case 4:\n          configType = type || determineConnectionType(url);\n          id = connectionId || [configType, assemblyNames, +Date.now()].filter(function (f) {\n            return !!f;\n          }).join('-');\n          connectionConfig = _objectSpread(_objectSpread(_objectSpread({\n            type: configType,\n            name: name || id\n          }, configType === 'UCSCTrackHubConnection' ? {\n            hubTxtLocation: {\n              uri: url,\n              locationType: 'UriLocation'\n            }\n          } : {}), configType === 'JBrowse1Connection' ? {\n            dataDirLocation: {\n              uri: url,\n              locationType: 'UriLocation'\n            }\n          } : {}), {}, {\n            connectionId: id,\n            assemblyNames: assemblyNames ? assemblyNames.split(',') : type === 'JBrowse1Connection' ? 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(0,_cigar_utils__WEBPACK_IMPORTED_MODULE_2__.flipCigar)((0,_cigar_utils__WEBPACK_IMPORTED_MODULE_2__.parseCigar)(CIGAR.slice(5))).join('') : (0,_cigar_utils__WEBPACK_IMPORTED_MODULE_2__.swapIndelCigar)(CIGAR.slice(5)));\n          }\n\n          // Write the second line and handle backpressure\n          _context.n = 6;\n          return writeWithBackpressure(\"\".concat([\"q\".concat(c1), l1, s1, e1, strand, c2, l2, s2, e2].concat(_toConsumableArray(rest)).join('\\t'), \"\\n\"));\n        case 6:\n          _iteratorAbruptCompletion = false;\n          _context.n = 3;\n          break;\n        case 7:\n          _context.n = 9;\n          break;\n        case 8:\n          _context.p = 8;\n          _t = _context.v;\n          _didIteratorError = true;\n          _iteratorError = _t;\n        case 9:\n          _context.p = 9;\n          _context.p = 10;\n          if (!(_iteratorAbruptCompletion && _iterator[\"return\"] != null)) {\n            _context.n = 11;\n            break;\n          }\n          _context.n = 11;\n          return _iterator[\"return\"]();\n        case 11:\n          _context.p = 11;\n          if (!_didIteratorError) {\n            _context.n = 12;\n            break;\n          }\n          throw _iteratorError;\n        case 12:\n          return _context.f(11);\n        case 13:\n          return _context.f(9);\n        case 14:\n          _context.n = 16;\n          break;\n        case 15:\n          _context.p = 15;\n          _t2 = _context.v;\n          console.error('Error processing PAF file:', _t2);\n          throw _t2;\n        case 16:\n          _context.p = 16;\n          rl1.close();\n          return _context.f(16);\n        case 17:\n          return _context.a(2);\n      }\n    }, _callee, null, [[10,, 11, 13], [2, 8, 9, 14], [1, 15, 16, 17]]);\n  }));\n  return _createPIF.apply(this, arguments);\n}\nfunction spawnSortProcess(outputFile, useCsi) {\n  // Use a more portable approach to avoid E2BIG errors\n\n  var sortCmd = \"sort -t\\\"`printf '\\\\t'`\\\" -k1,1 -k3,3n\";\n  var bgzipCommand = \"bgzip > \\\"\".concat(outputFile, \"\\\"\");\n  var tabixCommand = \"tabix \".concat(useCsi ? '-C ' : '', \"-s1 -b3 -e4 -0 \\\"\").concat(outputFile, \"\\\"\");\n  var fullCommand = \"\".concat(sortCmd, \" | \").concat(bgzipCommand, \"; \").concat(tabixCommand);\n  var minimalEnv = _objectSpread(_objectSpread({}, process.env), {}, {\n    LC_ALL: 'C'\n  });\n  return (0,child_process__WEBPACK_IMPORTED_MODULE_0__.spawn)('sh', ['-c', fullCommand], {\n    env: minimalEnv,\n    stdio: ['pipe', process.stdout, process.stderr]\n  });\n}\nfunction getOutputFilename(file, out) {\n  return out || \"\".concat(path__WEBPACK_IMPORTED_MODULE_1___default().basename(file || 'output', '.paf'), \".pif.gz\");\n}\nfunction waitForProcessClose(_x3) {\n  return _waitForProcessClose.apply(this, arguments);\n}\nfunction _waitForProcessClose() {\n  _waitForProcessClose = _asyncToGenerator(/*#__PURE__*/_regenerator().m(function _callee2(child) {\n    return _regenerator().w(function (_context2) {\n      while (1) switch (_context2.n) {\n        case 0:\n          return _context2.a(2, new Promise(function (resolve) {\n            child.on('close', resolve);\n          }));\n      }\n    }, _callee2);\n  }));\n  return _waitForProcessClose.apply(this, arguments);\n}\n\n//# sourceURL=webpack://@jbrowse/cli/./src/commands/make-pif-utils/pif-generator.ts?\n}");
+eval("{__webpack_require__.r(__webpack_exports__);\n/* harmony export */ __webpack_require__.d(__webpack_exports__, {\n/* harmony export */   createPIF: () => (/* binding */ createPIF),\n/* harmony export */   getOutputFilename: () => (/* binding */ getOutputFilename),\n/* harmony export */   spawnSortProcess: () => (/* binding */ spawnSortProcess),\n/* harmony export */   waitForProcessClose: () => (/* binding */ waitForProcessClose)\n/* harmony export */ });\n/* harmony import */ var child_process__WEBPACK_IMPORTED_MODULE_0__ = __webpack_require__(/*! child_process */ \"child_process\");\n/* harmony import */ var child_process__WEBPACK_IMPORTED_MODULE_0___default = /*#__PURE__*/__webpack_require__.n(child_process__WEBPACK_IMPORTED_MODULE_0__);\n/* harmony import */ var path__WEBPACK_IMPORTED_MODULE_1__ = __webpack_require__(/*! path */ \"path\");\n/* harmony import */ var path__WEBPACK_IMPORTED_MODULE_1___default = /*#__PURE__*/__webpack_require__.n(path__WEBPACK_IMPORTED_MODULE_1__);\n/* harmony import */ var _cigar_utils__WEBPACK_IMPORTED_MODULE_2__ = __webpack_require__(/*! ./cigar-utils */ \"./src/commands/make-pif-utils/cigar-utils.ts\");\n/* harmony import */ var _file_utils__WEBPACK_IMPORTED_MODULE_3__ = __webpack_require__(/*! ./file-utils */ \"./src/commands/make-pif-utils/file-utils.ts\");\nfunction _typeof(o) { \"@babel/helpers - typeof\"; return _typeof = \"function\" == typeof Symbol && \"symbol\" == typeof Symbol.iterator ? function (o) { return typeof o; } : function (o) { return o && \"function\" == typeof Symbol && o.constructor === Symbol && o !== Symbol.prototype ? \"symbol\" : typeof o; }, _typeof(o); }\nfunction _regenerator() { /*! regenerator-runtime -- Copyright (c) 2014-present, Facebook, Inc. -- license (MIT): https://github.com/babel/babel/blob/main/packages/babel-helpers/LICENSE */ var e, t, r = \"function\" == typeof Symbol ? 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Object.defineProperties(e, Object.getOwnPropertyDescriptors(t)) : ownKeys(Object(t)).forEach(function (r) { Object.defineProperty(e, r, Object.getOwnPropertyDescriptor(t, r)); }); } return e; }\nfunction _defineProperty(e, r, t) { return (r = _toPropertyKey(r)) in e ? Object.defineProperty(e, r, { value: t, enumerable: !0, configurable: !0, writable: !0 }) : e[r] = t, e; }\nfunction _toPropertyKey(t) { var i = _toPrimitive(t, \"string\"); return \"symbol\" == _typeof(i) ? i : i + \"\"; }\nfunction _toPrimitive(t, r) { if (\"object\" != _typeof(t) || !t) return t; var e = t[Symbol.toPrimitive]; if (void 0 !== e) { var i = e.call(t, r || \"default\"); if (\"object\" != _typeof(i)) return i; throw new TypeError(\"@@toPrimitive must return a primitive value.\"); } return (\"string\" === r ? String : Number)(t); }\nfunction asyncGeneratorStep(n, t, e, r, o, a, c) { try { var i = n[a](c), u = i.value; } catch (n) { return void e(n); } i.done ? t(u) : Promise.resolve(u).then(r, o); }\nfunction _asyncToGenerator(n) { return function () { var t = this, e = arguments; return new Promise(function (r, o) { var a = n.apply(t, e); function _next(n) { asyncGeneratorStep(a, r, o, _next, _throw, \"next\", n); } function _throw(n) { asyncGeneratorStep(a, r, o, _next, _throw, \"throw\", n); } _next(void 0); }); }; }\nfunction _asyncIterator(r) { var n, t, o, e = 2; for (\"undefined\" != typeof Symbol && (t = Symbol.asyncIterator, o = Symbol.iterator); e--;) { if (t && null != (n = r[t])) return n.call(r); if (o && null != (n = r[o])) return new AsyncFromSyncIterator(n.call(r)); t = \"@@asyncIterator\", o = \"@@iterator\"; } throw new TypeError(\"Object is not async iterable\"); }\nfunction AsyncFromSyncIterator(r) { function AsyncFromSyncIteratorContinuation(r) { if (Object(r) !== r) return Promise.reject(new TypeError(r + \" is not an object.\")); var n = r.done; return Promise.resolve(r.value).then(function (r) { return { value: r, done: n }; }); } return AsyncFromSyncIterator = function AsyncFromSyncIterator(r) { this.s = r, this.n = r.next; }, AsyncFromSyncIterator.prototype = { s: null, n: null, next: function next() { return AsyncFromSyncIteratorContinuation(this.n.apply(this.s, arguments)); }, \"return\": function _return(r) { var n = this.s[\"return\"]; return void 0 === n ? Promise.resolve({ value: r, done: !0 }) : AsyncFromSyncIteratorContinuation(n.apply(this.s, arguments)); }, \"throw\": function _throw(r) { var n = this.s[\"return\"]; return void 0 === n ? Promise.reject(r) : AsyncFromSyncIteratorContinuation(n.apply(this.s, arguments)); } }, new AsyncFromSyncIterator(r); }\n\n\n\n\nfunction createPIF(_x, _x2) {\n  return _createPIF.apply(this, arguments);\n}\nfunction _createPIF() {\n  _createPIF = _asyncToGenerator(/*#__PURE__*/_regenerator().m(function _callee(filename, stream) {\n    var rl1, writeWithBackpressure, _iteratorAbruptCompletion, _didIteratorError, _iteratorError, _iterator, _step, line, _line$split, _line$split2, c1, l1, s1, e1, strand, c2, l2, s2, e2, rest, cigarIdx, CIGAR, _t, _t2;\n    return _regenerator().w(function (_context) {\n      while (1) switch (_context.p = _context.n) {\n        case 0:\n          rl1 = filename ? (0,_file_utils__WEBPACK_IMPORTED_MODULE_3__.getReadline)(filename) : (0,_file_utils__WEBPACK_IMPORTED_MODULE_3__.getStdReadline)();\n          writeWithBackpressure = (0,_file_utils__WEBPACK_IMPORTED_MODULE_3__.createWriteWithBackpressure)(stream); // Process the file line by line with backpressure handling\n          _context.p = 1;\n          _iteratorAbruptCompletion = false;\n          _didIteratorError = false;\n          _context.p = 2;\n          _iterator = _asyncIterator(rl1);\n        case 3:\n          _context.n = 4;\n          return _iterator.next();\n        case 4:\n          if (!(_iteratorAbruptCompletion = !(_step = _context.v).done)) {\n            _context.n = 7;\n            break;\n          }\n          line = _step.value;\n          _line$split = line.split('\\t'), _line$split2 = _toArray(_line$split), c1 = _line$split2[0], l1 = _line$split2[1], s1 = _line$split2[2], e1 = _line$split2[3], strand = _line$split2[4], c2 = _line$split2[5], l2 = _line$split2[6], s2 = _line$split2[7], e2 = _line$split2[8], rest = _arrayLikeToArray(_line$split2).slice(9); // Write the first line and handle backpressure\n          _context.n = 5;\n          return writeWithBackpressure(\"\".concat([\"t\".concat(c2), l2, s2, e2, strand, c1, l1, s1, e1].concat(_toConsumableArray(rest)).join('\\t'), \"\\n\"));\n        case 5:\n          cigarIdx = rest.findIndex(function (f) {\n            return f.startsWith('cg:Z');\n          });\n          CIGAR = rest[cigarIdx];\n          if (CIGAR) {\n            rest[cigarIdx] = \"cg:Z:\".concat(strand === '-' ? (0,_cigar_utils__WEBPACK_IMPORTED_MODULE_2__.flipCigar)((0,_cigar_utils__WEBPACK_IMPORTED_MODULE_2__.parseCigar)(CIGAR.slice(5))).join('') : (0,_cigar_utils__WEBPACK_IMPORTED_MODULE_2__.swapIndelCigar)(CIGAR.slice(5)));\n          }\n\n          // Write the second line and handle backpressure\n          _context.n = 6;\n          return writeWithBackpressure(\"\".concat([\"q\".concat(c1), l1, s1, e1, strand, c2, l2, s2, e2].concat(_toConsumableArray(rest)).join('\\t'), \"\\n\"));\n        case 6:\n          _iteratorAbruptCompletion = false;\n          _context.n = 3;\n          break;\n        case 7:\n          _context.n = 9;\n          break;\n        case 8:\n          _context.p = 8;\n          _t = _context.v;\n          _didIteratorError = true;\n          _iteratorError = _t;\n        case 9:\n          _context.p = 9;\n          _context.p = 10;\n          if (!(_iteratorAbruptCompletion && _iterator[\"return\"] != null)) {\n            _context.n = 11;\n            break;\n          }\n          _context.n = 11;\n          return _iterator[\"return\"]();\n        case 11:\n          _context.p = 11;\n          if (!_didIteratorError) {\n            _context.n = 12;\n            break;\n          }\n          throw _iteratorError;\n        case 12:\n          return _context.f(11);\n        case 13:\n          return _context.f(9);\n        case 14:\n          _context.n = 16;\n          break;\n        case 15:\n          _context.p = 15;\n          _t2 = _context.v;\n          console.error('Error processing PAF file:', _t2);\n          throw _t2;\n        case 16:\n          _context.p = 16;\n          rl1.close();\n          return _context.f(16);\n        case 17:\n          return _context.a(2);\n      }\n    }, _callee, null, [[10,, 11, 13], [2, 8, 9, 14], [1, 15, 16, 17]]);\n  }));\n  return _createPIF.apply(this, arguments);\n}\nfunction spawnSortProcess(outputFile, useCsi) {\n  // Use a more portable approach to avoid E2BIG errors\n\n  var sortCmd = \"sort -t\\\"`printf '\\\\t'`\\\" -k1,1 -k3,3n\";\n  var bgzipCommand = \"bgzip > \\\"\".concat(outputFile, \"\\\"\");\n  var tabixCommand = \"tabix \".concat(useCsi ? '-C ' : '', \"-s1 -b3 -e4 -0 \\\"\").concat(outputFile, \"\\\"\");\n  var fullCommand = \"\".concat(sortCmd, \" | \").concat(bgzipCommand, \"; \").concat(tabixCommand);\n  var minimalEnv = _objectSpread(_objectSpread({}, process.env), {}, {\n    LC_ALL: 'C'\n  });\n  return (0,child_process__WEBPACK_IMPORTED_MODULE_0__.spawn)('sh', ['-c', fullCommand], {\n    env: minimalEnv,\n    stdio: ['pipe', process.stdout, process.stderr]\n  });\n}\nfunction getOutputFilename(file, out) {\n  return out || \"\".concat(path__WEBPACK_IMPORTED_MODULE_1___default().basename(file || 'output', '.paf'), \".pif.gz\");\n}\nfunction waitForProcessClose(_x3) {\n  return _waitForProcessClose.apply(this, arguments);\n}\nfunction _waitForProcessClose() {\n  _waitForProcessClose = _asyncToGenerator(/*#__PURE__*/_regenerator().m(function _callee2(child) {\n    return _regenerator().w(function (_context2) {\n      while (1) switch (_context2.n) {\n        case 0:\n          return _context2.a(2, new Promise(function (resolve) {\n            child.on('close', resolve);\n          }));\n      }\n    }, _callee2);\n  }));\n  return _waitForProcessClose.apply(this, arguments);\n}\n\n//# sourceURL=webpack://@jbrowse/cli/./src/commands/make-pif-utils/pif-generator.ts?\n}");
 
 /***/ }),
 

package/dist/commands/add-connection.js

@@ -128,7 +128,7 @@ async function run(args) {
     }
     const configType = type || determineConnectionType(url);
     const id = connectionId ||
-        [configType, assemblyNames, +Date.now()].filter(f => !!f).join('-');
+        [configType, assemblyNames, Date.now()].filter(f => !!f).join('-');
     const connectionConfig = {
         type: configType,
         name: name || id,

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

@@ -8,14 +8,10 @@ exports.parsePort = parsePort;
 exports.generateKey = generateKey;
 exports.setupConfigFile = setupConfigFile;
 exports.setupRoutes = setupRoutes;
-exports.setupServer = setupServer;
 exports.startServer = startServer;
 const crypto_1 = __importDefault(require("crypto"));
 const fs_1 = __importDefault(require("fs"));
-const os_1 = __importDefault(require("os"));
 const path_1 = __importDefault(require("path"));
-const cors_1 = __importDefault(require("cors"));
-const express_1 = __importDefault(require("express"));
 const utils_1 = require("../utils");
 /**
  * Validates if a port number is in the valid range
@@ -176,44 +172,6 @@ function setupRoutes({ app, baseDir, outFile, key, serverRef, }) {
         });
     });
 }
-/**
- * Sets up the Express server with routes
- */
-function setupServer({ baseDir, outFile, bodySizeLimit, }) {
-    // Create Express application
-    const app = (0, express_1.default)();
-    // Configure middleware
-    app.use(express_1.default.static(baseDir));
-    app.use((0, cors_1.default)());
-    app.use(express_1.default.json({ limit: bodySizeLimit }));
-    // Add error handling middleware
-    app.use((err, _req, res, next) => {
-        if (err) {
-            console.error('Server error:', err);
-            res.status(500).setHeader('Content-Type', 'text/plain');
-            res.send('Internal Server Error');
-        }
-        else {
-            next();
-        }
-    });
-    // Generate admin key and store it
-    const key = generateKey();
-    const keyPath = path_1.default.join(os_1.default.tmpdir(), `jbrowse-admin-${key}`);
-    try {
-        fs_1.default.writeFileSync(keyPath, key);
-        (0, utils_1.debug)(`Admin key stored at ${keyPath}`);
-    }
-    catch (error) {
-        console.error(`Failed to write admin key to ${keyPath}:`, error.message);
-        // Continue anyway, as this is not critical
-    }
-    // Create server reference for shutdown route
-    const serverRef = { current: null };
-    // Set up routes
-    setupRoutes({ app, baseDir, outFile, key, serverRef });
-    return { app, key, keyPath, serverRef };
-}
 /**
  * Starts the server and sets up shutdown handlers
  */

package/dist/commands/admin-server.js

@@ -1,9 +1,17 @@
 "use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.run = run;
+const fs_1 = __importDefault(require("fs"));
+const os_1 = __importDefault(require("os"));
+const path_1 = __importDefault(require("path"));
 const util_1 = require("util");
-const utils_1 = require("../utils");
+const cors_1 = __importDefault(require("cors"));
+const express_1 = __importDefault(require("express"));
 const admin_server_utils_1 = require("./admin-server-utils");
+const utils_1 = require("../utils");
 async function run(args) {
     const options = {
         help: {
@@ -45,10 +53,47 @@ async function run(args) {
     // Parse and validate port
     const port = (0, admin_server_utils_1.parsePort)({ portStr: flags.port });
     // Set up the Express server
-    const { app, key, keyPath, serverRef } = (0, admin_server_utils_1.setupServer)({
+    // const { app, key, keyPath, serverRef } = setupServer({
+    //   baseDir,
+    //   outFile,
+    //   bodySizeLimit,
+    // })
+    const app = (0, express_1.default)();
+    // Configure middleware
+    app.use(express_1.default.static(baseDir));
+    app.use((0, cors_1.default)());
+    app.use(express_1.default.json({ limit: bodySizeLimit }));
+    // Add error handling middleware
+    app.use((err, _req, res, next) => {
+        if (err) {
+            console.error('Server error:', err);
+            res.status(500).setHeader('Content-Type', 'text/plain');
+            res.send('Internal Server Error');
+        }
+        else {
+            next();
+        }
+    });
+    // Generate admin key and store it
+    const key = (0, admin_server_utils_1.generateKey)();
+    const keyPath = path_1.default.join(os_1.default.tmpdir(), `jbrowse-admin-${key}`);
+    try {
+        fs_1.default.writeFileSync(keyPath, key);
+        (0, utils_1.debug)(`Admin key stored at ${keyPath}`);
+    }
+    catch (error) {
+        console.error(`Failed to write admin key to ${keyPath}:`, error.message);
+        // Continue anyway, as this is not critical
+    }
+    // Create server reference for shutdown route
+    const serverRef = { current: null };
+    // Set up routes
+    (0, admin_server_utils_1.setupRoutes)({
+        app,
         baseDir,
         outFile,
-        bodySizeLimit,
+        key,
+        serverRef,
     });
     // Start the server and set up shutdown handlers
     (0, admin_server_utils_1.startServer)({ app, port, key, outFile, keyPath, serverRef });

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/cli",
-  "version": "3.6.5",
+  "version": "3.7.0",
   "description": "A command line tool for working with JBrowse 2",
   "keywords": [
     "jbrowse",
@@ -43,10 +43,11 @@
     "express": "^5.1.0",
     "ixixx": "^2.0.1",
     "json-parse-better-errors": "^1.0.2",
-    "node-fetch-native": "^1.6.4"
+    "node-fetch-native": "^1.6.4",
+    "tmp": "^0.2.1"
   },
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "354d0a87b757b4d84f824b47507662f6f3a1693f"
+  "gitHead": "85bdd0d58286b7adbfd408146b15847676317635"
 }