nodejs-nomer 1.3.4 → 1.3.7

package/DEVELOPMENT.md

@@ -0,0 +1,26 @@
+# DEVELOPMENT
+
+Build:
+`npm run build`
+
+Link:
+
+`npm link`
+
+Use package for testing:
+`npm link nodejs-nomer`
+
+Run `script.js`
+`node script.js`
+
+# PUBLISH
+
+Update minor version:
+`npm version minor`
+
+Publish
+`npm publish`
+
+Push to git
+`npm push`
+

package/dist/index.js

@@ -0,0 +1,138 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.Nomer = void 0;
+var _utils = require("./utils");
+var _result = _interopRequireDefault(require("./result"));
+var _propertiesFile = require("properties-file");
+function _interopRequireDefault(e) { return e && e.__esModule ? e : { "default": e }; }
+function _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); }
+function _toConsumableArray(r) { return _arrayWithoutHoles(r) || _iterableToArray(r) || _unsupportedIterableToArray(r) || _nonIterableSpread(); }
+function _nonIterableSpread() { throw new TypeError("Invalid attempt to spread non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method."); }
+function _unsupportedIterableToArray(r, a) { if (r) { if ("string" == typeof r) return _arrayLikeToArray(r, a); var t = {}.toString.call(r).slice(8, -1); return "Object" === t && r.constructor && (t = r.constructor.name), "Map" === t || "Set" === t ? Array.from(r) : "Arguments" === t || /^(?:Ui|I)nt(?:8|16|32)(?:Clamped)?Array$/.test(t) ? _arrayLikeToArray(r, a) : void 0; } }
+function _iterableToArray(r) { if ("undefined" != typeof Symbol && null != r[Symbol.iterator] || null != r["@@iterator"]) return Array.from(r); }
+function _arrayWithoutHoles(r) { if (Array.isArray(r)) return _arrayLikeToArray(r); }
+function _arrayLikeToArray(r, a) { (null == a || a > r.length) && (a = r.length); for (var e = 0, n = Array(a); e < a; e++) n[e] = r[e]; return n; }
+function _classCallCheck(a, n) { if (!(a instanceof n)) throw new TypeError("Cannot call a class as a function"); }
+function _defineProperties(e, r) { for (var t = 0; t < r.length; t++) { var o = r[t]; o.enumerable = o.enumerable || !1, o.configurable = !0, "value" in o && (o.writable = !0), Object.defineProperty(e, _toPropertyKey(o.key), o); } }
+function _createClass(e, r, t) { return r && _defineProperties(e.prototype, r), t && _defineProperties(e, t), Object.defineProperty(e, "prototype", { writable: !1 }), e; }
+function _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; }
+function _toPropertyKey(t) { var i = _toPrimitive(t, "string"); return "symbol" == _typeof(i) ? i : i + ""; }
+function _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); }
+var Nomer = exports.Nomer = /*#__PURE__*/function () {
+  function Nomer() {
+    var propertiesPath = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : null;
+    var echoOpt = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : "";
+    _classCallCheck(this, Nomer);
+    _defineProperty(this, "propertiesPath", null);
+    _defineProperty(this, "echoOpt", "");
+    this.propertiesPath = propertiesPath;
+    this.echoOpt = echoOpt;
+  }
+
+  /**
+   * Show version
+   * @returns string
+   */
+  return _createClass(Nomer, [{
+    key: "version",
+    value: function version() {
+      var res = (0, _utils.runNomer)((0, _utils.getNomerSimpleCmd)());
+      return res;
+    }
+  }, {
+    key: "clean",
+    value: function clean() {
+      var res = (0, _utils.runNomer)((0, _utils.getNomerSimpleCmd)("clean", false, this.getPropertiesPath()));
+      return res;
+    }
+  }, {
+    key: "inputSchema",
+    value: function inputSchema() {
+      var res = (0, _utils.runNomer)((0, _utils.getNomerSimpleCmd)("input-schema", false, this.getPropertiesPath()));
+      return res;
+    }
+  }, {
+    key: "outputSchema",
+    value: function outputSchema() {
+      var res = (0, _utils.runNomer)((0, _utils.getNomerSimpleCmd)("output-schema", false, this.getPropertiesPath()));
+      return res;
+    }
+  }, {
+    key: "properties",
+    value: function properties() {
+      var res = (0, _utils.runNomer)((0, _utils.getNomerSimpleCmd)("properties", false, this.getPropertiesPath()));
+      return res;
+    }
+  }, {
+    key: "matcher",
+    value: function matcher() {
+      var outputFormat = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : "tsv";
+      var verbose = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : false;
+      var res = (0, _utils.runNomer)((0, _utils.getNomerSimpleCmd)("matchers", verbose, null, outputFormat));
+      return res;
+    }
+  }, {
+    key: "validateTerm",
+    value: function validateTerm() {
+      var filepath = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : "";
+      var res = (0, _utils.runNomer)((0, _utils.getNomerValidateCmd)(filepath, "validate-term-link", this.getPropertiesPath()));
+      return res;
+    }
+  }, {
+    key: "replace",
+    value: function replace() {
+      var query = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : "";
+      var matcher = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : "globi-taxon-cache";
+      var res = (0, _utils.runNomer)((0, _utils.getNomerMatchCmd)(query, "replace", matcher, this.getPropertiesPath(), null, this.echoOpt));
+      return res;
+    }
+  }, {
+    key: "append",
+    value: function append() {
+      var query = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : "";
+      var matcher = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : "globi-taxon-cache";
+      var outputFormat = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : "tsv";
+      var res = (0, _utils.runNomer)((0, _utils.getNomerMatchCmd)(query, "append", matcher, this.getPropertiesPath(), outputFormat, this.echoOpt), query);
+      return res;
+    }
+  }, {
+    key: "appendAsync",
+    value: function appendAsync() {
+      var matcher = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : "globi-taxon-cache";
+      var outputFormat = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : "tsv";
+      return (0, _utils.runNomerAsync)("nomer append ".concat(matcher, " -o ").concat(outputFormat));
+    }
+  }, {
+    key: "getPropertiesPath",
+    value: function getPropertiesPath() {
+      return this.propertiesPath;
+    }
+  }, {
+    key: "toJson",
+    value: function toJson(result) {
+      return _result["default"].json(result);
+    }
+  }, {
+    key: "toArray",
+    value: function toArray(result) {
+      var columns = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : null;
+      return _result["default"].tsv(result, columns);
+    }
+  }, {
+    key: "toObject",
+    value: function toObject(result) {
+      var content = this.properties(this.getPropertiesPath());
+      var properties = (0, _propertiesFile.getProperties)(content);
+      var schemaInput = JSON.parse(properties["nomer.schema.input"]).map(function (i) {
+        return i.type + 'Input';
+      });
+      var schemaAppend = JSON.parse(properties["nomer.append.schema.output"]).map(function (i) {
+        return i.type;
+      });
+      return _result["default"].tsv(result, [].concat(_toConsumableArray(schemaInput), ["matchType"], _toConsumableArray(schemaAppend)));
+    }
+  }]);
+}();

package/dist/result.js

@@ -0,0 +1,48 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+function _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); }
+function _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; }
+function _toConsumableArray(r) { return _arrayWithoutHoles(r) || _iterableToArray(r) || _unsupportedIterableToArray(r) || _nonIterableSpread(); }
+function _nonIterableSpread() { throw new TypeError("Invalid attempt to spread non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method."); }
+function _unsupportedIterableToArray(r, a) { if (r) { if ("string" == typeof r) return _arrayLikeToArray(r, a); var t = {}.toString.call(r).slice(8, -1); return "Object" === t && r.constructor && (t = r.constructor.name), "Map" === t || "Set" === t ? Array.from(r) : "Arguments" === t || /^(?:Ui|I)nt(?:8|16|32)(?:Clamped)?Array$/.test(t) ? _arrayLikeToArray(r, a) : void 0; } }
+function _iterableToArray(r) { if ("undefined" != typeof Symbol && null != r[Symbol.iterator] || null != r["@@iterator"]) return Array.from(r); }
+function _arrayWithoutHoles(r) { if (Array.isArray(r)) return _arrayLikeToArray(r); }
+function _arrayLikeToArray(r, a) { (null == a || a > r.length) && (a = r.length); for (var e = 0, n = Array(a); e < a; e++) n[e] = r[e]; return n; }
+function _classCallCheck(a, n) { if (!(a instanceof n)) throw new TypeError("Cannot call a class as a function"); }
+function _defineProperties(e, r) { for (var t = 0; t < r.length; t++) { var o = r[t]; o.enumerable = o.enumerable || !1, o.configurable = !0, "value" in o && (o.writable = !0), Object.defineProperty(e, _toPropertyKey(o.key), o); } }
+function _createClass(e, r, t) { return r && _defineProperties(e.prototype, r), t && _defineProperties(e, t), Object.defineProperty(e, "prototype", { writable: !1 }), e; }
+function _toPropertyKey(t) { var i = _toPrimitive(t, "string"); return "symbol" == _typeof(i) ? i : i + ""; }
+function _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); }
+var Result = exports["default"] = /*#__PURE__*/function () {
+  function Result() {
+    _classCallCheck(this, Result);
+  }
+  return _createClass(Result, null, [{
+    key: "json",
+    value: function json(result) {
+      var arr = [];
+      result.split("\n").forEach(function (e) {
+        return arr.push(JSON.parse(e));
+      });
+      return arr;
+    }
+  }, {
+    key: "tsv",
+    value: function tsv(result) {
+      var columns = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : null;
+      var arr = [];
+      result.split('\n').forEach(function (line) {
+        arr.push(line.split('\t'));
+      });
+      return columns ? arr.map(function (v) {
+        return Object.assign.apply(Object, _toConsumableArray(columns.map(function (k, i) {
+          return _defineProperty({}, k, v[i]);
+        })));
+      }) : arr;
+    }
+  }]);
+}();

package/dist/utils.js

@@ -0,0 +1,76 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.runNomerAsync = exports.runNomer = exports.getNomerValidateCmd = exports.getNomerSimpleCmd = exports.getNomerMatchCmd = void 0;
+var _require = require('child_process'),
+  execSync = _require.execSync,
+  spawn = _require.spawn;
+var getNomerValidateCmd = exports.getNomerValidateCmd = function getNomerValidateCmd() {
+  var filepath = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : "";
+  var cmd = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : "validate-term";
+  var properties = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : null;
+  if (filepath === "") {
+    throw new Exception("Filepath cannot be empty string");
+  }
+  var nomerCmd = "curl -L ".concat(filepath, " | nomer ").concat(cmd);
+  if (properties) {
+    nomerCmd = "".concat(nomerCmd, " -p ").concat(properties);
+  }
+  return nomerCmd;
+};
+var getNomerMatchCmd = exports.getNomerMatchCmd = function getNomerMatchCmd() {
+  var query = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : "";
+  var cmd = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : "append";
+  var matcher = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : "globi-taxon-cache";
+  var properties = arguments.length > 3 && arguments[3] !== undefined ? arguments[3] : null;
+  var outputFormat = arguments.length > 4 && arguments[4] !== undefined ? arguments[4] : null;
+  var echoOpt = arguments.length > 5 && arguments[5] !== undefined ? arguments[5] : "-e";
+  var nomerCmd = "echo ".concat(echoOpt, " '").concat(query, "' | nomer ").concat(cmd, " ").concat(matcher);
+  if (properties) {
+    nomerCmd = "".concat(nomerCmd, " -p ").concat(properties);
+  }
+  if (outputFormat) {
+    nomerCmd = "".concat(nomerCmd, " -o ").concat(outputFormat);
+  }
+  return nomerCmd;
+};
+var getNomerSimpleCmd = exports.getNomerSimpleCmd = function getNomerSimpleCmd() {
+  var cmd = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : "version";
+  var verbose = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : false;
+  var properties = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : null;
+  var outputFormat = arguments.length > 3 && arguments[3] !== undefined ? arguments[3] : null;
+  var nomerCmd = "nomer ".concat(cmd);
+  if (properties) {
+    nomerCmd = "".concat(nomerCmd, " -p ").concat(properties);
+  }
+  if (outputFormat) {
+    nomerCmd = "".concat(nomerCmd, " -o ").concat(outputFormat);
+  }
+  if (verbose) {
+    nomerCmd = "".concat(nomerCmd, " -v");
+  }
+  return nomerCmd;
+};
+var runNomer = exports.runNomer = function runNomer(nomerCmd) {
+  try {
+    var result = execSync(nomerCmd, {
+      maxBuffer: 4096 * 4096
+    }).toString();
+    if (result) {
+      return result.trimEnd();
+    }
+  } catch (error) {
+    console.log("Error running nomer cmd: " + error.message);
+    return null;
+  }
+};
+var runNomerAsync = exports.runNomerAsync = function runNomerAsync(nomerCmd) {
+  var nomerCmdArr = nomerCmd.split(/\s+/);
+  var p = spawn(nomerCmdArr[0], nomerCmdArr.slice(1), {
+    // maxBuffer: 4096 * 4096
+    shell: true
+  });
+  return p;
+};

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "nodejs-nomer",
-  "version": "1.3.4",
+  "version": "1.3.7",
   "description": "NodeJS wrapper for nomer",
   "bin": {
     "nomer": "./bin/nomer"

package/src/index.js

@@ -93,8 +93,8 @@ export class Nomer {
         return Result.json(result);
     }
 
-    toArray(result) {
-        return Result.tsv(result);
+    toArray(result, columns = null) {
+        return Result.tsv(result, columns);
     }
 
     toObject(result) {

package/test/script.js

@@ -0,0 +1,46 @@
+const Nomer = require("nodejs-nomer")
+
+const nomer = new Nomer.Nomer();
+
+console.time("version")
+console.log(nomer.version());
+console.timeEnd("version")
+
+
+console.time("append async")
+const process = nomer.appendAsync("col")
+const resultsAsync = []
+
+const result = (stdout) => new Promise(resolve => {
+    stdout.on('data', async (data) => {
+        console.log(data.toString())
+        return nomer.toObject(data).filter((obj) => obj.matchType !== "NONE")
+
+    })
+    stdout.on('end', () => {
+        resolve('end')
+    })
+})
+
+p = result(process.stdout)
+for (let index = 0; index < 1000; index++) {
+    process.stdin.write("\tBauhinia rufa\t\n")
+}
+process.stdin.end()
+
+result.then((v) => console.log(v))
+
+
+// console.time("append")
+// const results = []
+// for (let index = 0; index < 100; index++) {
+//     results.push(nomer.append("\tBauhinia rufa\t", "gbif"))
+// }
+// console.timeEnd("append")
+
+// console.time("toObject")
+// for (let index = 0; index < results.length; index++) {
+//     const element = results[index];
+//     nomer.toObject(element)
+// }
+// console.timeEnd("toObject")