@manuscripts/transform 4.2.9 → 4.2.11

package/dist/cjs/jats/exporter/jats-exporter.js

@@ -50,13 +50,12 @@ const citeproc_1 = require("../../lib/citeproc");
 const credit_roles_1 = require("../../lib/credit-roles");
 const footnotes_1 = require("../../lib/footnotes");
 const html_1 = require("../../lib/html");
+const xml_1 = require("../../lib/xml");
 const schema_1 = require("../../schema");
 const transformer_1 = require("../../transformer");
 const citeproc_2 = require("./citeproc");
 const jats_versions_1 = require("./jats-versions");
 const labels_1 = require("./labels");
-const XLINK_NAMESPACE = 'http://www.w3.org/1999/xlink';
-const XML_NAMESPACE = 'http://www.w3.org/XML/1998/namespace';
 const normalizeID = (id) => id.replace(/:/g, '_');
 const parser = prosemirror_model_1.DOMParser.fromSchema(schema_1.schema);
 const insertAbstractNode = (front, abstractNode) => {
@@ -128,10 +127,11 @@ class JATSExporter {
             const versionIds = (0, jats_versions_1.selectVersionIds)(options.version ?? '1.2');
             this.document = document.implementation.createDocument(null, 'article', document.implementation.createDocumentType('article', versionIds.publicId, versionIds.systemId));
             const article = this.document.documentElement;
-            article.setAttributeNS('http://www.w3.org/2000/xmlns/', 'xmlns:xlink', XLINK_NAMESPACE);
+            article.setAttributeNS('http://www.w3.org/2000/xmlns/', 'xmlns:xlink', xml_1.XLINK_NAMESPACE);
             const front = this.buildFront(options.journal);
             article.appendChild(front);
             article.setAttribute('article-type', manuscriptNode.attrs.articleType || 'other');
+            article.setAttributeNS(xml_1.XML_NAMESPACE, 'lang', manuscriptNode.attrs.primaryLanguageCode || 'en');
             this.labelTargets = (0, labels_1.buildTargets)(manuscriptNode);
             this.footnoteLabels = (0, footnotes_1.generateFootnoteLabels)(manuscriptNode);
             const body = this.buildBody();
@@ -315,7 +315,7 @@ class JATSExporter {
             supplementsNodes.forEach((node) => {
                 const supplementaryMaterial = this.createElement('supplementary-material');
                 supplementaryMaterial.setAttribute('id', normalizeID(node.attrs.id));
-                supplementaryMaterial.setAttributeNS(XLINK_NAMESPACE, 'href', node.attrs.href ?? '');
+                supplementaryMaterial.setAttributeNS(xml_1.XLINK_NAMESPACE, 'href', node.attrs.href ?? '');
                 supplementaryMaterial.setAttribute('mimetype', node.attrs.mimeType ?? '');
                 supplementaryMaterial.setAttribute('mime-subtype', node.attrs.mimeSubType ?? '');
                 const caption = this.createElement('caption');
@@ -378,7 +378,7 @@ class JATSExporter {
             selfUriAttachments.forEach((attachment) => {
                 const selfUriElement = this.createElement('self-uri');
                 selfUriElement.setAttribute('content-type', attachment.attrs.type);
-                selfUriElement.setAttributeNS(XLINK_NAMESPACE, 'href', attachment.attrs.href);
+                selfUriElement.setAttributeNS(xml_1.XLINK_NAMESPACE, 'href', attachment.attrs.href);
                 const insertBeforeElements = articleMeta.querySelector('related-article, related-object, abstract, trans-abstract, kwd-group, funding-group, support-group, conference, counts, custom-meta-group');
                 insertBeforeElements
                     ? articleMeta.insertBefore(selfUriElement, insertBeforeElements)
@@ -443,7 +443,7 @@ class JATSExporter {
             const parser = new DOMParser();
             const [_, bibliography] = this.engine.makeBibliography();
             for (let i = 0; i < bibliography.length; i++) {
-                const item = `<template xmlns:xlink="${XLINK_NAMESPACE}">${bibliography[i]}</template>`;
+                const item = `<template xmlns:xlink="${xml_1.XLINK_NAMESPACE}">${bibliography[i]}</template>`;
                 const ref = parser.parseFromString(item, 'text/xml').querySelector('ref');
                 if (ref) {
                     refList.appendChild(ref);
@@ -473,7 +473,7 @@ class JATSExporter {
                         id: normalizeID(node.attrs.id),
                     };
                     if (node.attrs.lang) {
-                        attrs[`${XML_NAMESPACE} lang`] = node.attrs.lang;
+                        attrs[`${xml_1.XML_NAMESPACE} lang`] = node.attrs.lang;
                     }
                     if (node.attrs.category) {
                         attrs['sec-type'] = node.attrs.category;
@@ -501,13 +501,14 @@ class JATSExporter {
                 attachments: () => '',
                 image_element: (node) => createImage(node),
                 embed: (node) => {
-                    const mediaElement = this.createElement('media');
                     const { id, href, mimetype, mimeSubtype } = node.attrs;
-                    mediaElement.setAttribute('id', normalizeID(id));
-                    mediaElement.setAttributeNS(XLINK_NAMESPACE, 'show', 'embed');
-                    if (href) {
-                        mediaElement.setAttributeNS(XLINK_NAMESPACE, 'href', node.attrs.href);
+                    if (!href) {
+                        return '';
                     }
+                    const mediaElement = this.createElement('media');
+                    mediaElement.setAttribute('id', normalizeID(id));
+                    mediaElement.setAttributeNS(xml_1.XLINK_NAMESPACE, 'show', 'embed');
+                    mediaElement.setAttributeNS(xml_1.XLINK_NAMESPACE, 'href', href);
                     if (mimetype) {
                         mediaElement.setAttribute('mimetype', node.attrs.mimetype);
                     }
@@ -685,10 +686,10 @@ class JATSExporter {
                     }
                     const linkNode = this.createElement('ext-link');
                     linkNode.setAttribute('ext-link-type', 'uri');
-                    linkNode.setAttributeNS(XLINK_NAMESPACE, 'href', node.attrs.href);
+                    linkNode.setAttributeNS(xml_1.XLINK_NAMESPACE, 'href', node.attrs.href);
                     linkNode.textContent = text;
                     if (node.attrs.title) {
-                        linkNode.setAttributeNS(XLINK_NAMESPACE, 'xlink:title', node.attrs.title);
+                        linkNode.setAttributeNS(xml_1.XLINK_NAMESPACE, 'xlink:title', node.attrs.title);
                     }
                     return linkNode;
                 },
@@ -705,7 +706,7 @@ class JATSExporter {
                 missing_figure: () => {
                     const graphic = this.createElement('graphic');
                     graphic.setAttribute('specific-use', 'MISSING');
-                    graphic.setAttributeNS(XLINK_NAMESPACE, 'xlink:href', '');
+                    graphic.setAttributeNS(xml_1.XLINK_NAMESPACE, 'xlink:href', '');
                     return graphic;
                 },
                 paragraph: (node) => {
@@ -908,7 +909,7 @@ class JATSExporter {
                 const graphicElement = createGraphic(graphicNode);
                 if (node.attrs.extLink) {
                     const extLink = this.appendElement(graphicElement, 'ext-link');
-                    extLink.setAttributeNS(XLINK_NAMESPACE, 'href', node.attrs.extLink);
+                    extLink.setAttributeNS(xml_1.XLINK_NAMESPACE, 'href', node.attrs.extLink);
                 }
                 appendChildNodeOfType(graphicElement, node, schema_1.schema.nodes.alt_text);
                 appendChildNodeOfType(graphicElement, node, schema_1.schema.nodes.long_desc);
@@ -916,7 +917,7 @@ class JATSExporter {
             };
             const createGraphic = (node) => {
                 const graphic = this.createElement('graphic');
-                graphic.setAttributeNS(XLINK_NAMESPACE, 'xlink:href', node.attrs.src);
+                graphic.setAttributeNS(xml_1.XLINK_NAMESPACE, 'xlink:href', node.attrs.src);
                 if (isChildOfNodeType(node.attrs.id, schema_1.schema.nodes.hero_image)) {
                     graphic.setAttribute('content-type', 'leading');
                 }
@@ -1133,7 +1134,7 @@ class JATSExporter {
                         }
                         if (affiliation.attrs.email) {
                             const email = this.createElement('email');
-                            email.setAttributeNS(XLINK_NAMESPACE, 'href', affiliation.attrs.email.href ?? '');
+                            email.setAttributeNS(xml_1.XLINK_NAMESPACE, 'href', affiliation.attrs.email.href ?? '');
                             email.textContent = affiliation.attrs.email.text ?? '';
                             aff.appendChild(email);
                         }
@@ -1530,7 +1531,7 @@ class JATSExporter {
     }
     createTransAbstractNode(transAbstract) {
         const transAbstractNode = this.createElement('trans-abstract');
-        transAbstractNode.setAttributeNS(XML_NAMESPACE, 'lang', transAbstract.getAttributeNS(XML_NAMESPACE, 'lang') ?? '');
+        transAbstractNode.setAttributeNS(xml_1.XML_NAMESPACE, 'lang', transAbstract.getAttributeNS(xml_1.XML_NAMESPACE, 'lang') ?? '');
         this.setAbstractType(transAbstractNode, transAbstract);
         transAbstractNode.append(...transAbstract.childNodes);
         return transAbstractNode;

package/dist/cjs/jats/importer/jats-dom-parser.js

@@ -19,12 +19,12 @@ exports.JATSDOMParser = void 0;
 const json_schema_1 = require("@manuscripts/json-schema");
 const prosemirror_model_1 = require("prosemirror-model");
 const utils_1 = require("../../lib/utils");
+const xml_1 = require("../../lib/xml");
 const jats_comments_1 = require("./jats-comments");
 class JATSDOMParser {
     constructor(sectionCategories, schema) {
         this.sectionCategories = sectionCategories;
         this.schema = schema;
-        this.XLINK_NAMESPACE = 'http://www.w3.org/1999/xlink';
         this.parsePriority = (priority) => {
             if (!priority) {
                 return undefined;
@@ -92,7 +92,7 @@ class JATSDOMParser {
             const email = element.querySelector('email');
             if (email) {
                 return {
-                    href: email.getAttributeNS(this.XLINK_NAMESPACE, 'href') ?? '',
+                    href: email.getAttributeNS(xml_1.XLINK_NAMESPACE, 'href') ?? '',
                     text: (0, utils_1.getTrimmedTextContent)(email) ?? '',
                 };
             }
@@ -106,8 +106,8 @@ class JATSDOMParser {
                 type: parentElement?.getAttribute('fig-type') ??
                     element.getAttribute('content-type') ??
                     '',
-                src: element.getAttributeNS(this.XLINK_NAMESPACE, 'href'),
-                extLink: extLink?.getAttributeNS(this.XLINK_NAMESPACE, 'href'),
+                src: element.getAttributeNS(xml_1.XLINK_NAMESPACE, 'href'),
+                extLink: extLink?.getAttributeNS(xml_1.XLINK_NAMESPACE, 'href'),
             };
         };
         this.getInstitutionDetails = (element) => {
@@ -220,7 +220,7 @@ class JATSDOMParser {
                     const element = node;
                     return {
                         id: element.getAttribute('id'),
-                        href: element.getAttributeNS(this.XLINK_NAMESPACE, 'href') || '',
+                        href: element.getAttributeNS(xml_1.XLINK_NAMESPACE, 'href') || '',
                         type: element.getAttribute('content-type') || '',
                     };
                 },
@@ -236,7 +236,7 @@ class JATSDOMParser {
                     return {
                         doi: (0, utils_1.getTrimmedTextContent)(doi),
                         articleType: element.getAttribute('article-type') || '',
-                        primaryLanguageCode: element.getAttribute('lang') ?? '',
+                        primaryLanguageCode: element.getAttributeNS(xml_1.XML_NAMESPACE, 'lang'),
                         ...dates,
                     };
                 },
@@ -576,8 +576,8 @@ class JATSDOMParser {
                 getAttrs: (node) => {
                     const element = node;
                     return {
-                        href: element.getAttributeNS(this.XLINK_NAMESPACE, 'href') || '',
-                        title: element.getAttributeNS(this.XLINK_NAMESPACE, 'title') || '',
+                        href: element.getAttributeNS(xml_1.XLINK_NAMESPACE, 'href') || '',
+                        title: element.getAttributeNS(xml_1.XLINK_NAMESPACE, 'title') || '',
                     };
                 },
             },
@@ -598,7 +598,7 @@ class JATSDOMParser {
                     const element = node;
                     return {
                         id: element.getAttribute('id'),
-                        href: element.getAttributeNS(this.XLINK_NAMESPACE, 'href'),
+                        href: element.getAttributeNS(xml_1.XLINK_NAMESPACE, 'href'),
                         mimetype: element.getAttribute('mimetype'),
                         mimeSubtype: element.getAttribute('mime-subtype'),
                     };
@@ -773,7 +773,7 @@ class JATSDOMParser {
                     const element = node;
                     return {
                         id: element.getAttribute('id'),
-                        href: element.getAttributeNS(this.XLINK_NAMESPACE, 'href'),
+                        href: element.getAttributeNS(xml_1.XLINK_NAMESPACE, 'href'),
                         mimeType: element.getAttribute('mimetype'),
                         mimeSubType: element.getAttribute('mime-subtype'),
                         title: (0, utils_1.getTrimmedTextContent)(element, 'title'),

package/dist/cjs/lib/xml.js

@@ -0,0 +1,20 @@
+"use strict";
+/*!
+ * © 2025 Atypon Systems LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.XML_NAMESPACE = exports.XLINK_NAMESPACE = void 0;
+exports.XLINK_NAMESPACE = 'http://www.w3.org/1999/xlink';
+exports.XML_NAMESPACE = 'http://www.w3.org/XML/1998/namespace';

package/dist/cjs/version.js

@@ -1,4 +1,4 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.VERSION = void 0;
-exports.VERSION = "4.2.9";
+exports.VERSION = "4.2.11";

package/dist/es/jats/exporter/jats-exporter.js

@@ -21,13 +21,12 @@ import { buildCiteprocCitation } from '../../lib/citeproc';
 import { CreditRoleUrls } from '../../lib/credit-roles';
 import { generateFootnoteLabels } from '../../lib/footnotes';
 import { nodeFromHTML } from '../../lib/html';
+import { XLINK_NAMESPACE, XML_NAMESPACE } from '../../lib/xml';
 import { isBibliographyItemNode, isCitationNode, isNodeOfType, schema, } from '../../schema';
 import { isExecutableNodeType, isNodeType } from '../../transformer';
 import { initJats, jatsVariableWrapper } from './citeproc';
 import { selectVersionIds } from './jats-versions';
 import { buildTargets } from './labels';
-const XLINK_NAMESPACE = 'http://www.w3.org/1999/xlink';
-const XML_NAMESPACE = 'http://www.w3.org/XML/1998/namespace';
 const normalizeID = (id) => id.replace(/:/g, '_');
 const parser = ProsemirrorDOMParser.fromSchema(schema);
 const insertAbstractNode = (front, abstractNode) => {
@@ -102,6 +101,7 @@ export class JATSExporter {
             const front = this.buildFront(options.journal);
             article.appendChild(front);
             article.setAttribute('article-type', manuscriptNode.attrs.articleType || 'other');
+            article.setAttributeNS(XML_NAMESPACE, 'lang', manuscriptNode.attrs.primaryLanguageCode || 'en');
             this.labelTargets = buildTargets(manuscriptNode);
             this.footnoteLabels = generateFootnoteLabels(manuscriptNode);
             const body = this.buildBody();
@@ -471,13 +471,14 @@ export class JATSExporter {
                 attachments: () => '',
                 image_element: (node) => createImage(node),
                 embed: (node) => {
-                    const mediaElement = this.createElement('media');
                     const { id, href, mimetype, mimeSubtype } = node.attrs;
+                    if (!href) {
+                        return '';
+                    }
+                    const mediaElement = this.createElement('media');
                     mediaElement.setAttribute('id', normalizeID(id));
                     mediaElement.setAttributeNS(XLINK_NAMESPACE, 'show', 'embed');
-                    if (href) {
-                        mediaElement.setAttributeNS(XLINK_NAMESPACE, 'href', node.attrs.href);
-                    }
+                    mediaElement.setAttributeNS(XLINK_NAMESPACE, 'href', href);
                     if (mimetype) {
                         mediaElement.setAttribute('mimetype', node.attrs.mimetype);
                     }

package/dist/es/jats/importer/jats-dom-parser.js

@@ -16,12 +16,12 @@
 import { buildContribution, ObjectTypes } from '@manuscripts/json-schema';
 import { DOMParser, Fragment } from 'prosemirror-model';
 import { dateToTimestamp, getCreditRole, getHTMLContent, getTrimmedTextContent, } from '../../lib/utils';
+import { XLINK_NAMESPACE, XML_NAMESPACE } from '../../lib/xml';
 import { DEFAULT_PROFILE_ID } from './jats-comments';
 export class JATSDOMParser {
     constructor(sectionCategories, schema) {
         this.sectionCategories = sectionCategories;
         this.schema = schema;
-        this.XLINK_NAMESPACE = 'http://www.w3.org/1999/xlink';
         this.parsePriority = (priority) => {
             if (!priority) {
                 return undefined;
@@ -89,7 +89,7 @@ export class JATSDOMParser {
             const email = element.querySelector('email');
             if (email) {
                 return {
-                    href: email.getAttributeNS(this.XLINK_NAMESPACE, 'href') ?? '',
+                    href: email.getAttributeNS(XLINK_NAMESPACE, 'href') ?? '',
                     text: getTrimmedTextContent(email) ?? '',
                 };
             }
@@ -103,8 +103,8 @@ export class JATSDOMParser {
                 type: parentElement?.getAttribute('fig-type') ??
                     element.getAttribute('content-type') ??
                     '',
-                src: element.getAttributeNS(this.XLINK_NAMESPACE, 'href'),
-                extLink: extLink?.getAttributeNS(this.XLINK_NAMESPACE, 'href'),
+                src: element.getAttributeNS(XLINK_NAMESPACE, 'href'),
+                extLink: extLink?.getAttributeNS(XLINK_NAMESPACE, 'href'),
             };
         };
         this.getInstitutionDetails = (element) => {
@@ -217,7 +217,7 @@ export class JATSDOMParser {
                     const element = node;
                     return {
                         id: element.getAttribute('id'),
-                        href: element.getAttributeNS(this.XLINK_NAMESPACE, 'href') || '',
+                        href: element.getAttributeNS(XLINK_NAMESPACE, 'href') || '',
                         type: element.getAttribute('content-type') || '',
                     };
                 },
@@ -233,7 +233,7 @@ export class JATSDOMParser {
                     return {
                         doi: getTrimmedTextContent(doi),
                         articleType: element.getAttribute('article-type') || '',
-                        primaryLanguageCode: element.getAttribute('lang') ?? '',
+                        primaryLanguageCode: element.getAttributeNS(XML_NAMESPACE, 'lang'),
                         ...dates,
                     };
                 },
@@ -573,8 +573,8 @@ export class JATSDOMParser {
                 getAttrs: (node) => {
                     const element = node;
                     return {
-                        href: element.getAttributeNS(this.XLINK_NAMESPACE, 'href') || '',
-                        title: element.getAttributeNS(this.XLINK_NAMESPACE, 'title') || '',
+                        href: element.getAttributeNS(XLINK_NAMESPACE, 'href') || '',
+                        title: element.getAttributeNS(XLINK_NAMESPACE, 'title') || '',
                     };
                 },
             },
@@ -595,7 +595,7 @@ export class JATSDOMParser {
                     const element = node;
                     return {
                         id: element.getAttribute('id'),
-                        href: element.getAttributeNS(this.XLINK_NAMESPACE, 'href'),
+                        href: element.getAttributeNS(XLINK_NAMESPACE, 'href'),
                         mimetype: element.getAttribute('mimetype'),
                         mimeSubtype: element.getAttribute('mime-subtype'),
                     };
@@ -770,7 +770,7 @@ export class JATSDOMParser {
                     const element = node;
                     return {
                         id: element.getAttribute('id'),
-                        href: element.getAttributeNS(this.XLINK_NAMESPACE, 'href'),
+                        href: element.getAttributeNS(XLINK_NAMESPACE, 'href'),
                         mimeType: element.getAttribute('mimetype'),
                         mimeSubType: element.getAttribute('mime-subtype'),
                         title: getTrimmedTextContent(element, 'title'),

package/dist/es/lib/xml.js

@@ -0,0 +1,17 @@
+/*!
+ * © 2025 Atypon Systems LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+export const XLINK_NAMESPACE = 'http://www.w3.org/1999/xlink';
+export const XML_NAMESPACE = 'http://www.w3.org/XML/1998/namespace';

package/dist/es/version.js

@@ -1 +1 @@
-export const VERSION = "4.2.9";
+export const VERSION = "4.2.11";

package/dist/types/jats/importer/jats-dom-parser.d.ts

@@ -18,7 +18,6 @@ import { SectionCategory } from '../../schema';
 export declare class JATSDOMParser {
     private sectionCategories;
     private schema;
-    private XLINK_NAMESPACE;
     private parser;
     constructor(sectionCategories: SectionCategory[], schema: Schema);
     parse(doc: Node, options?: ParseOptions): import("prosemirror-model").Node;

package/dist/types/lib/xml.d.ts

@@ -0,0 +1,17 @@
+/*!
+ * © 2025 Atypon Systems LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+export declare const XLINK_NAMESPACE = "http://www.w3.org/1999/xlink";
+export declare const XML_NAMESPACE = "http://www.w3.org/XML/1998/namespace";

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const VERSION = "4.2.9";
+export declare const VERSION = "4.2.11";

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@manuscripts/transform",
   "description": "ProseMirror transformer for Manuscripts applications",
-  "version": "4.2.9",
+  "version": "4.2.11",
   "repository": "github:Atypon-OpenSource/manuscripts-transform",
   "license": "Apache-2.0",
   "main": "dist/cjs",