@iebh/reflib 2.0.0 → 2.0.3

package/README.md

@@ -18,7 +18,7 @@ Compatibility
 | EndNote ENLX           | `.enlx`         | :x:                | :x:                |
 | EndNote XML            | `.xml`          | :heavy_check_mark: | :heavy_check_mark: |
 | JSON                   | `.json`         | :heavy_check_mark: | :heavy_check_mark: |
-| Medline                | `.nbib`         | :x:                | :x:                |
+| Medline                | `.nbib`         | :heavy_check_mark: | :heavy_check_mark: |
 | RIS                    | `.ris` / `.txt` | :heavy_check_mark: | :heavy_check_mark: |
 | Tab Separated Values   | `.tsv`          | :x:                | :x:                |
 

package/lib/default.js

@@ -1,7 +1,10 @@
-export * from './identifyFormat.js';
-export * from './formats.js';
-export * from './getModule.js';
-export * from './readFile.js';
-export * from './readStream.js';
-export * from './writeFile.js';
-export * from './writeStream.js';
+import {identifyFormat} from './identifyFormat.js';
+import {formats} from './formats.js';
+import {getModule} from './getModule.js';
+import {readStream} from './readStream.js';
+import {readFile} from './readFile.js';
+import {writeStream} from './writeStream.js';
+import {writeFile} from './writeFile.js';
+
+export {identifyFormat, formats, getModule, readStream, readFile, writeStream, writeFile};
+export default {identifyFormat, formats, getModule, readStream, readFile, writeStream, writeFile};

package/lib/fields.js

@@ -125,9 +125,6 @@ export let fields = {
 	language: {
 		type: 'string',
 	},
-	researchNotes: {
-		type: 'string',
-	},
 	databaseProvider: {
 		type: 'string',
 	},

package/lib/formats.js

@@ -39,8 +39,8 @@ export let formats = {
 		title: 'MEDLINE / PubMed',
 		titleShort: 'MEDLINE',
 		ext: ['.nbib'],
-		canRead: false,
-		canWrite: false,
+		canRead: true,
+		canWrite: true,
 	},
 	ris: {
 		id: 'ris',

package/modules/endnoteXml.js

@@ -1,6 +1,6 @@
 import camelCase from '../shared/camelCase.js';
 import Emitter from '../shared/emitter.js';
-import {WritableStream as XMLParser} from 'htmlparser2/lib/WritableStream.js';
+import {WritableStream as XMLParser} from 'htmlparser2/lib/WritableStream';
 
 
 /**
@@ -287,12 +287,12 @@ export function xmlEscape(str) {
 */
 export function xmlUnescape(str) {
 	return ('' + str)
-		.replace(/\&/g, '&')
-		.replace(/\
/g, '\r')
-		.replace(/\&lt;/g, '<')
-		.replace(/\&gt;/g, '>')
-		.replace(/\&quot;/g, '"')
-		.replace(/\&apos;/g, "'");
+		.replace(/&amp;/g, '&')
+		.replace(/&#xD;/g, '\r')
+		.replace(/&lt;/g, '<')
+		.replace(/&gt;/g, '>')
+		.replace(/&quot;/g, '"')
+		.replace(/&apos;/g, "'");
 }
 
 

package/modules/medline.js

@@ -47,14 +47,14 @@ export function readStream(stream, options) {
 		from: 'type',
 		to: 'type',
 		delete: false,
-		reformat: (v, ref) => translations.types.rawMap[v] || settings.defaultType,
+		reformat: v => translations.types.rawMap[v] || settings.defaultType,
 	});
 
 	// Reformat authors
 	settings.fieldsReplace.push({
 		to: 'authors',
 		reformat: (authors, ref) => (ref.medlineAuthorsShort || ref.medlineAuthorsFull || []).map(author =>
-			author.replace(/^(?<last>[\w\-]+?) (?<initials>\w+)$/, (match, last, initials) => {
+			author.replace(/^(?<last>[\w-]+?) (?<initials>\w+)$/, (match, last, initials) => {
 				return (
 					last && initials ? last + ', ' + initials.split('').map(i => `${i}.`).join(' ')
 					: last ? last
@@ -90,7 +90,7 @@ export function readStream(stream, options) {
 			from: 'medlineArticleID',
 			to: 'doi',
 			delete: false,
-			reformat: v => /(?<doi>[\w\.\/\_]+) \[doi\]/.exec(v)?.groups.doi || false,
+			reformat: v => /(?<doi>[\w\.\/_]+) \[doi\]/.exec(v)?.groups.doi || false, // eslint-disable-line no-useless-escape
 		});
 
 	// Allow parsing of years
@@ -128,7 +128,8 @@ export function readStream(stream, options) {
 				let bufferSplitter = /(\r\n|\n){2,}/g; // RegExp to use per segment (multiple calls to .exec() stores state because JS is a hellscape)
 
 				let bufferSegment;
-				while (bufferSegment = bufferSplitter.exec(buffer)) {
+
+				while (bufferSegment = bufferSplitter.exec(buffer)) { // eslint-disable-line no-cond-assign
 					let parsedRef = parseRef(buffer.substring(bufferCrop, bufferSegment.index), settings); // Parse the ref from the start+end points
 					emitter.emit('ref', parsedRef);
 
@@ -187,7 +188,7 @@ export function writeStream(stream, options) {
 							? [
 								'TI  - ' + ref.title,
 								...(ref.authors || []).flatMap((a, i) => [
-									ref.medlineAuthorsFull?.[i] ? `FAU - ${ref.medlineAuthorsFull[i]}` : `FAU - ${authors[i]}`,
+									ref.medlineAuthorsFull?.[i] ? `FAU - ${ref.medlineAuthorsFull[i]}` : `FAU - ${ref.authors[i]}`,
 									ref.medlineAuthorsShort?.[i] && `AU  - ${ref.medlineAuthorsShort[i]}`,
 									ref.medlineAuthorsAffiliation?.[i] && `AD  - ${ref.medlineAuthorsAffiliation[i]}`,
 									ref.medlineAuthorsId?.[i] && `AUID- ${ref.medlineAuthorsId[i]}`,
@@ -224,7 +225,6 @@ export function writeStream(stream, options) {
 export function parseRef(refString, settings) {
 	let ref = {}; // Reference under construction
 	let lastField; // Last field object we saw, used to append values if they don't match the default RIS key=val one-liner
-	let didWrap = false; // Whether the input was taken over multiple lines - if so obey `trimDotSuffix` before accepting
 
 	refString
 		.split(/[\r\n|\n]/) // Split into lines
@@ -237,7 +237,6 @@ export function parseRef(refString, settings) {
 					if (lastField.inputArray) { // Treat each line feed like an array entry
 						ref[lastField.rl].push(line);
 					} else { // Assume we append each line entry as a single-line string
-						didWrap = true;
 						ref[lastField.rl] += ' ' + line;
 					}
 				}
@@ -246,10 +245,8 @@ export function parseRef(refString, settings) {
 
 			let fieldLookup = translations.fields.rawMap.get(parsedLine.key);
 
-			if (lastField?.trimDotSuffix) {
+			if (lastField?.trimDotSuffix)
 				ref[lastField.rl] = ref[lastField.rl].replace(/\.$/, '');
-				didWrap = false;
-			}
 
 			if (!fieldLookup) { // Skip unknown field translations
 				lastField = null;
@@ -286,6 +283,7 @@ export function parseRef(refString, settings) {
 			if (replacement.from && (replacement.delete ?? true))
 				delete ref[replacement.from];
 		})
+	// }}}
 
 	return ref;
 }

package/modules/ris.js

@@ -27,7 +27,7 @@ export function readStream(stream, options) {
 				let bufferSplitter = /(\r\n|\n)ER\s+-\s*(\r\n|\n)/g; // RegExp to use per segment (multiple calls to .exec() stores state because JS is a hellscape)
 
 				let bufferSegment;
-				while (bufferSegment = bufferSplitter.exec(buffer)) {
+				while (bufferSegment = bufferSplitter.exec(buffer)) { // eslint-disable-line no-cond-assign
 					let parsedRef = parseRef(buffer.substring(bufferCrop, bufferSegment.index), settings); // Parse the ref from the start+end points
 
 					emitter.emit('ref', parsedRef);
@@ -85,9 +85,8 @@ export function writeStream(stream, options) {
 				delete ref.pages;
 			}
 
-			let a ;
 			stream.write(
-				a = translations.fields.collectionOutput
+				translations.fields.collectionOutput
 					.filter(f => ref[f.rl]) // Has field?
 					.flatMap(f =>
 						f.rl == 'type' // Translate type field

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@iebh/reflib",
-  "version": "2.0.0",
+  "version": "2.0.3",
   "description": "Reference / Citation reference library utilities",
   "scripts": {
     "lint": "eslint lib modules shared test",
@@ -36,16 +36,28 @@
     "./*": "./lib/*.js"
   },
   "devDependencies": {
-    "chai": "^4.3.4",
-    "eslint": "^8.7.0",
-    "mocha": "^9.1.3",
-    "mocha-logger": "^1.0.7",
+    "chai": "^4.3.6",
+    "eslint": "^8.15.0",
+    "mocha": "^10.0.0",
+    "mocha-logger": "^1.0.8",
     "temp": "^0.9.4"
   },
   "dependencies": {
-    "htmlparser2": "^7.2.0",
+    "htmlparser2": "^8.0.1",
     "JSONStream": "^1.3.5",
     "mitt": "^3.0.0",
     "vite-plugin-replace": "^0.1.1"
+  },
+  "eslintConfig": {
+    "extends": "eslint:recommended",
+    "env": {
+      "browser": true,
+      "es2021": true,
+      "mocha": true
+    },
+    "parserOptions": {
+      "ecmaVersion": 13,
+      "sourceType": "module"
+    }
   }
 }

package/.eslintrc.cjs

@@ -1,14 +0,0 @@
-module.exports = {
-    "env": {
-        "browser": true,
-        "es2021": true,
-		"mocha": true
-    },
-    "extends": "eslint:recommended",
-    "parserOptions": {
-        "ecmaVersion": 13,
-        "sourceType": "module"
-    },
-    "rules": {
-    }
-};