nodejs-nomer 1.1.0 → 1.2.0

package/.github/workflows/npm-publish.yml

@@ -0,0 +1,25 @@
+# This workflow will run tests using node and then publish a package to GitHub Packages when a release is created
+# For more information see: https://docs.github.com/en/actions/publishing-packages/publishing-nodejs-packages
+
+name: Node.js Package
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-node@v3
+        with:
+          node-version: '21.x'           
+          registry-url: 'https://registry.npmjs.org'
+      - run: npm ci
+      - run: npm publish      
+        env:
+          NODE_AUTH_TOKEN: ${{secrets.NPM_TOKEN}}

package/install_nomer.sh

@@ -1,6 +1,6 @@
 #!/bin/sh
 
-NOMER_VERSION=$1
+NOMER_VERSION="0.5.13"
 
 mkdir -p ./bin
 echo "https://github.com/globalbioticinteractions/nomer/releases/download/${NOMER_VERSION}/nomer.jar)"

package/package.json

@@ -1,18 +1,15 @@
 {
   "name": "nodejs-nomer",
-  "version": "1.1.0",
+  "version": "1.2.0",
   "description": "NodeJS wrapper for nomer",
   "bin": {
     "nomer": "./bin/nomer"
   },
-  "config": {
-    "nomerVersion": "0.5.7"
-  },
   "main": "index.js",
   "scripts": {
     "test": "npm run test",
     "build": "babel src -d dist",
-    "preinstall": "./install_nomer.sh ${npm_package_config_nomerVersion}"
+    "preinstall": "./install_nomer.sh"
   },
   "repository": {
     "type": "git",

package/DEVELOPMENT.md

@@ -1,17 +0,0 @@
-# DEVELOPMENT
-
-Build:
-`npm run build`
-
-Link:
-
-`npm link`
-
-Use package for testing:
-`npm link nodejs-nomer`
-
-Run `script.js`
-`node script.js`
-
-# PUBLISH
-

package/dist/index.js

@@ -1,135 +0,0 @@
-"use strict";
-
-var _utils = require("./utils");
-var _result = _interopRequireDefault(require("./result"));
-var _propertiesFile = require("properties-file");
-function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { "default": obj }; }
-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(arr) { return _arrayWithoutHoles(arr) || _iterableToArray(arr) || _unsupportedIterableToArray(arr) || _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(o, minLen) { if (!o) return; if (typeof o === "string") return _arrayLikeToArray(o, minLen); var n = Object.prototype.toString.call(o).slice(8, -1); if (n === "Object" && o.constructor) n = o.constructor.name; if (n === "Map" || n === "Set") return Array.from(o); if (n === "Arguments" || /^(?:Ui|I)nt(?:8|16|32)(?:Clamped)?Array$/.test(n)) return _arrayLikeToArray(o, minLen); }
-function _iterableToArray(iter) { if (typeof Symbol !== "undefined" && iter[Symbol.iterator] != null || iter["@@iterator"] != null) return Array.from(iter); }
-function _arrayWithoutHoles(arr) { if (Array.isArray(arr)) return _arrayLikeToArray(arr); }
-function _arrayLikeToArray(arr, len) { if (len == null || len > arr.length) len = arr.length; for (var i = 0, arr2 = new Array(len); i < len; i++) arr2[i] = arr[i]; return arr2; }
-function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } }
-function _defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, _toPropertyKey(descriptor.key), descriptor); } }
-function _createClass(Constructor, protoProps, staticProps) { if (protoProps) _defineProperties(Constructor.prototype, protoProps); if (staticProps) _defineProperties(Constructor, staticProps); Object.defineProperty(Constructor, "prototype", { writable: false }); return Constructor; }
-function _defineProperty(obj, key, value) { key = _toPropertyKey(key); if (key in obj) { Object.defineProperty(obj, key, { value: value, enumerable: true, configurable: true, writable: true }); } else { obj[key] = value; } return obj; }
-function _toPropertyKey(t) { var i = _toPrimitive(t, "string"); return "symbol" == _typeof(i) ? i : String(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 = /*#__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
-   */
-  _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) {
-      return _result["default"].tsv(result);
-    }
-  }, {
-    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)));
-    }
-  }]);
-  return Nomer;
-}();
-module.exports = Nomer;

package/dist/result.js

@@ -1,46 +0,0 @@
-"use strict";
-
-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(obj, key, value) { key = _toPropertyKey(key); if (key in obj) { Object.defineProperty(obj, key, { value: value, enumerable: true, configurable: true, writable: true }); } else { obj[key] = value; } return obj; }
-function _toConsumableArray(arr) { return _arrayWithoutHoles(arr) || _iterableToArray(arr) || _unsupportedIterableToArray(arr) || _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(o, minLen) { if (!o) return; if (typeof o === "string") return _arrayLikeToArray(o, minLen); var n = Object.prototype.toString.call(o).slice(8, -1); if (n === "Object" && o.constructor) n = o.constructor.name; if (n === "Map" || n === "Set") return Array.from(o); if (n === "Arguments" || /^(?:Ui|I)nt(?:8|16|32)(?:Clamped)?Array$/.test(n)) return _arrayLikeToArray(o, minLen); }
-function _iterableToArray(iter) { if (typeof Symbol !== "undefined" && iter[Symbol.iterator] != null || iter["@@iterator"] != null) return Array.from(iter); }
-function _arrayWithoutHoles(arr) { if (Array.isArray(arr)) return _arrayLikeToArray(arr); }
-function _arrayLikeToArray(arr, len) { if (len == null || len > arr.length) len = arr.length; for (var i = 0, arr2 = new Array(len); i < len; i++) arr2[i] = arr[i]; return arr2; }
-function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } }
-function _defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, _toPropertyKey(descriptor.key), descriptor); } }
-function _createClass(Constructor, protoProps, staticProps) { if (protoProps) _defineProperties(Constructor.prototype, protoProps); if (staticProps) _defineProperties(Constructor, staticProps); Object.defineProperty(Constructor, "prototype", { writable: false }); return Constructor; }
-function _toPropertyKey(t) { var i = _toPrimitive(t, "string"); return "symbol" == _typeof(i) ? i : String(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 = /*#__PURE__*/function () {
-  function Result() {
-    _classCallCheck(this, Result);
-  }
-  _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;
-    }
-  }]);
-  return Result;
-}();
-module.exports = Result;

package/dist/utils.js

@@ -1,80 +0,0 @@
-"use strict";
-
-var _require = require('child_process'),
-  execSync = _require.execSync,
-  exec = _require.exec,
-  spawn = _require.spawn;
-var 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 = 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 = 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 = 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 = function runNomerAsync(nomerCmd) {
-  var nomerCmdArr = nomerCmd.split(/\s+/);
-  var p = spawn(nomerCmdArr[0], nomerCmdArr.slice(1), {
-    // maxBuffer: 4096 * 4096
-    shell: true
-  });
-  return p;
-};
-module.exports = {
-  getNomerValidateCmd: getNomerValidateCmd,
-  getNomerMatchCmd: getNomerMatchCmd,
-  getNomerSimpleCmd: getNomerSimpleCmd,
-  runNomer: runNomer,
-  runNomerAsync: runNomerAsync
-};

package/test/script.js

@@ -1,23 +0,0 @@
-const Nomer = require("nodejs-nomer")
-
-const nomer = new Nomer();
-
-console.time("version")
-console.log(nomer.version());
-console.timeEnd("version")
-
-
-
-// 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")