nodejs-nomer 1.0.3 → 1.0.4

package/dist/index.js

@@ -2,18 +2,30 @@
 
 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 properties = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : null;
+    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;
   }
 
   /**
@@ -29,29 +41,25 @@ var Nomer = /*#__PURE__*/function () {
   }, {
     key: "clean",
     value: function clean() {
-      var properties = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : null;
-      var res = (0, _utils.runNomer)((0, _utils.getNomerSimpleCmd)("clean", this.getProperties(properties)));
+      var res = (0, _utils.runNomer)((0, _utils.getNomerSimpleCmd)("clean", this.getPropertiesPath()));
       return res;
     }
   }, {
     key: "inputSchema",
     value: function inputSchema() {
-      var properties = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : null;
-      var res = (0, _utils.runNomer)((0, _utils.getNomerSimpleCmd)("input-schema", this.getProperties(properties)));
+      var res = (0, _utils.runNomer)((0, _utils.getNomerSimpleCmd)("input-schema", this.getPropertiesPath()));
       return res;
     }
   }, {
     key: "outputSchema",
     value: function outputSchema() {
-      var properties = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : null;
-      var res = (0, _utils.runNomer)((0, _utils.getNomerSimpleCmd)("output-schema", this.getProperties(properties)));
+      var res = (0, _utils.runNomer)((0, _utils.getNomerSimpleCmd)("output-schema", this.getPropertiesPath()));
       return res;
     }
   }, {
     key: "properties",
     value: function properties() {
-      var _properties = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : null;
-      var res = (0, _utils.runNomer)((0, _utils.getNomerSimpleCmd)("properties", this.getProperties(_properties)));
+      var res = (0, _utils.runNomer)((0, _utils.getNomerSimpleCmd)("properties", this.getPropertiesPath()));
       return res;
     }
   }, {
@@ -66,8 +74,7 @@ var Nomer = /*#__PURE__*/function () {
     key: "validateTerm",
     value: function validateTerm() {
       var filepath = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : "";
-      var properties = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : null;
-      var res = (0, _utils.runNomer)((0, _utils.getNomerValidateCmd)(filepath, "validate-term-link", this.getProperties(properties)));
+      var res = (0, _utils.runNomer)((0, _utils.getNomerValidateCmd)(filepath, "validate-term-link", this.getPropertiesPath()));
       return res;
     }
   }, {
@@ -75,9 +82,7 @@ var Nomer = /*#__PURE__*/function () {
     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 properties = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : null;
-      var echoOpt = arguments.length > 3 && arguments[3] !== undefined ? arguments[3] : "";
-      var res = (0, _utils.runNomer)((0, _utils.getNomerMatchCmd)(query, "replace", matcher, this.getProperties(properties), null, echoOpt));
+      var res = (0, _utils.runNomer)((0, _utils.getNomerMatchCmd)(query, "replace", matcher, this.getPropertiesPath(), null, this.echoOpt));
       return res;
     }
   }, {
@@ -85,16 +90,14 @@ var Nomer = /*#__PURE__*/function () {
     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 properties = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : null;
-      var outputFormat = arguments.length > 3 && arguments[3] !== undefined ? arguments[3] : "tsv";
-      var echoOpt = arguments.length > 4 && arguments[4] !== undefined ? arguments[4] : "";
-      var res = (0, _utils.runNomer)((0, _utils.getNomerMatchCmd)(query, "append", matcher, this.getProperties(properties), outputFormat, echoOpt));
+      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));
       return res;
     }
   }, {
-    key: "getProperties",
-    value: function getProperties(p) {
-      return p;
+    key: "getPropertiesPath",
+    value: function getPropertiesPath() {
+      return this.propertiesPath;
     }
   }, {
     key: "toJson",
@@ -109,7 +112,15 @@ var Nomer = /*#__PURE__*/function () {
   }, {
     key: "toObject",
     value: function toObject(result) {
-      return _result["default"].tsv(result, true);
+      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), _toConsumableArray(schemaAppend)));
     }
   }]);
   return Nomer;

package/dist/result.js

@@ -13,7 +13,7 @@ function _defineProperties(target, props) { for (var i = 0; i < props.length; i+
 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 TSV_COLUMNS = ['match', 'externalId', 'name', 'authorship', 'rank', 'commonNames', 'path', 'pathIds', 'pathNames', 'pathAuthorship', 'externalUrl'];
+var TSV_COLUMNS = ['inputId', 'inputName', 'match', 'externalId', 'name', 'authorship', 'rank', 'commonNames', 'path', 'pathIds', 'pathNames', 'pathAuthorship', 'externalUrl'];
 var Result = /*#__PURE__*/function () {
   function Result() {
     _classCallCheck(this, Result);
@@ -21,16 +21,25 @@ var Result = /*#__PURE__*/function () {
   _createClass(Result, null, [{
     key: "json",
     value: function json(result) {
-      return JSON.parse(result);
+      var arr = [];
+      result.split("\n").forEach(function (e) {
+        return arr.push(JSON.parse(e));
+      });
+      return arr;
     }
   }, {
     key: "tsv",
     value: function tsv(result) {
-      var toObject = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : false;
-      var values = result.split('\t').slice(1);
-      return toObject ? Object.assign.apply(Object, _toConsumableArray(TSV_COLUMNS.map(function (k, i) {
-        return _defineProperty({}, k, values[i]);
-      }))) : values;
+      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;

package/dist/utils.js

@@ -52,7 +52,7 @@ var runNomer = function runNomer(nomerCmd) {
   try {
     var result = execSync(nomerCmd).toString();
     if (result) {
-      return result.trim();
+      return result.trimEnd();
     }
   } catch (error) {
     console.log("Error running nomer cmd: " + error.message);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "nodejs-nomer",
-  "version": "1.0.3",
+  "version": "1.0.4",
   "description": "NodeJS wrapper for nomer",
   "config": {
     "nomerVersion": "0.5.6"
@@ -29,5 +29,8 @@
     "@babel/cli": "^7.23.9",
     "@babel/core": "^7.24.0",
     "@babel/preset-env": "^7.24.0"
+  },
+  "dependencies": {
+    "properties-file": "^3.5.1"
   }
 }

package/src/index.js

@@ -1,10 +1,16 @@
 import { runNomer, getNomerSimpleCmd, getNomerValidateCmd, getNomerMatchCmd } from "./utils";
 import Result from './result'
+import { getProperties } from "properties-file";
+
 
 class Nomer {
 
-    constructor(properties = null, echoOpt = "") {
+    propertiesPath = null;
+    echoOpt = "";
 
+    constructor(propertiesPath = null, echoOpt = "") {
+        this.propertiesPath = propertiesPath;
+        this.echoOpt = echoOpt;
     }
 
     /**
@@ -16,23 +22,23 @@ class Nomer {
         return res;
     }
 
-    clean(properties = null) {
-        const res = runNomer(getNomerSimpleCmd("clean", this.getProperties(properties)))
+    clean() {
+        const res = runNomer(getNomerSimpleCmd("clean", this.getPropertiesPath()))
         return res;
     }
 
-    inputSchema(properties = null) {
-        const res = runNomer(getNomerSimpleCmd("input-schema", this.getProperties(properties)))
+    inputSchema() {
+        const res = runNomer(getNomerSimpleCmd("input-schema", this.getPropertiesPath()))
         return res;
     }
 
-    outputSchema(properties = null) {
-        const res = runNomer(getNomerSimpleCmd("output-schema", this.getProperties(properties)))
+    outputSchema() {
+        const res = runNomer(getNomerSimpleCmd("output-schema", this.getPropertiesPath()))
         return res;
     }
 
-    properties(properties = null) {
-        const res = runNomer(getNomerSimpleCmd("properties", this.getProperties(properties)))
+    properties() {
+        const res = runNomer(getNomerSimpleCmd("properties", this.getPropertiesPath()))
         return res;
     }
 
@@ -41,41 +47,41 @@ class Nomer {
         return res;
     }
 
-    validateTerm(filepath = "", properties = null) {
-        const res = runNomer(getNomerValidateCmd(filepath, "validate-term-link", this.getProperties(properties)))
+    validateTerm(filepath = "") {
+        const res = runNomer(getNomerValidateCmd(filepath, "validate-term-link", this.getPropertiesPath()))
         return res;
     }
 
-    replace(query = "", matcher = "globi-taxon-cache", properties = null, echoOpt = "") {
+    replace(query = "", matcher = "globi-taxon-cache") {
         const res = runNomer(
             getNomerMatchCmd(
                 query,
                 "replace",
                 matcher,
-                this.getProperties(properties),
+                this.getPropertiesPath(),
                 null,
-                echoOpt
+                this.echoOpt
             )
         );
         return res;
     }
 
-    append(query = "", matcher = "globi-taxon-cache", properties = null, outputFormat = "tsv", echoOpt = "") {
+    append(query = "", matcher = "globi-taxon-cache", outputFormat = "tsv") {
         const res = runNomer(
             getNomerMatchCmd(
                 query,
                 "append",
                 matcher,
-                this.getProperties(properties),
+                this.getPropertiesPath(),
                 outputFormat,
-                echoOpt
+                this.echoOpt
             )
         );
         return res;
     }
 
-    getProperties(p) {
-        return p;
+    getPropertiesPath() {
+        return this.propertiesPath;
     }
 
     toJson(result) {
@@ -87,7 +93,11 @@ class Nomer {
     }
 
     toObject(result) {
-        return Result.tsv(result, true)
+        const content = this.properties(this.getPropertiesPath())
+        const properties = getProperties(content)
+        const schemaInput = JSON.parse(properties["nomer.schema.input"]).map((i) => i.type + 'Input')
+        const schemaAppend = JSON.parse(properties["nomer.append.schema.output"]).map((i) => i.type)
+        return Result.tsv(result, [...schemaInput, ...schemaAppend])
     }
 
 

package/src/result.js

@@ -1,4 +1,6 @@
 const TSV_COLUMNS = [
+    'inputId',
+    'inputName',
     'match',
     'externalId',
     'name',
@@ -15,12 +17,18 @@ const TSV_COLUMNS = [
 class Result {
 
     static json(result) {
-        return JSON.parse(result)
+        const arr = [];
+        result.split("\n").forEach((e) => arr.push(JSON.parse(e)))
+        return arr;
     }
 
-    static tsv(result, toObject = false) {
-        const values = result.split('\t').slice(1);
-        return toObject ? Object.assign(...TSV_COLUMNS.map((k, i) => ({ [k]: values[i] }))) : values
+    static tsv(result, columns = null) {
+        const arr = [];
+        result.split('\n').forEach((line) => {
+            arr.push(line.split('\t'));
+        });
+
+        return columns ? arr.map((v) => Object.assign(...columns.map((k, i) => ({ [k]: v[i] })))) : arr
     }
 }
 

package/src/utils.js

@@ -43,7 +43,7 @@ const runNomer = (nomerCmd) => {
     try {
         const result = execSync(nomerCmd).toString();
         if (result) {
-            return result.trim();
+            return result.trimEnd();
         }
     } catch (error) {
         console.log("Error running nomer cmd: " + error.message);