@manuscripts/transform 4.5.6 → 4.5.8

package/src/jats/__tests__/jats-roundtrip.test.ts

@@ -15,6 +15,7 @@
  */
 
 import { parseXml } from 'libxmljs2'
+import serializeToXML from 'w3c-xmlserializer'
 
 import { JATSExporter } from '../exporter/jats-exporter'
 import { parseJATSArticle } from '../importer/parse-jats-article'
@@ -36,9 +37,10 @@ const roundtrip = async (filename: string) => {
   const node = parseJATSArticle(doc, sectionCategories)
 
   const exporter = new JATSExporter()
-  return await exporter.serializeToJATS(node, {
+  const document = await exporter.export(node, {
     csl: DEFAULT_CSL_OPTIONS,
   })
+  return serializeToXML(document)
 }
 
 describe('JATS roundtrip', () => {

package/src/jats/exporter/jats-exporter.ts

@@ -17,7 +17,6 @@
 import * as Citeproc from 'citeproc'
 import { DOMOutputSpec, DOMSerializer, type NodeType } from 'prosemirror-model'
 import { findChildrenByAttr, findChildrenByType } from 'prosemirror-utils'
-import serializeToXML from 'w3c-xmlserializer'
 
 import { buildCiteprocCitation } from '../../lib/citeproc'
 import { CreditRoleUrls } from '../../lib/credit-roles'
@@ -33,6 +32,7 @@ import {
   AffiliationNode,
   AuthorNotesNode,
   AwardNode,
+  ExtLink,
   CitationNode,
   ContributorNode,
   CorrespNode,
@@ -162,10 +162,10 @@ export class JATSExporter {
     return (nodes ?? []).filter((n): n is T => isNodeOfType<T>(n, type))
   }
 
-  public serializeToJATS = async (
+  public export = async (
     manuscriptNode: ActualManuscriptNode,
     options: ExportOptions
-  ): Promise<string> => {
+  ): Promise<Document> => {
     this.manuscriptNode = manuscriptNode
     this.populateNodesMap()
     this.initCiteprocEngine(options)
@@ -222,7 +222,7 @@ export class JATSExporter {
       $article.appendChild($floatsGroup)
     }
     await this.rewriteIDs()
-    return serializeToXML(this.document)
+    return this.document
   }
 
   private appendChildNodeOfType = (
@@ -615,9 +615,9 @@ export class JATSExporter {
     const [, bibliography] = this.engine.makeBibliography()
     const parser = new DOMParser()
     bibliography.forEach((item) => {
-      const fragment = `<template xmlns:xlink="${XLINK_NAMESPACE}">${sanitizeXmlString(
+      const fragment = `<wrapper xmlns:xlink="${XLINK_NAMESPACE}">${sanitizeXmlString(
         item
-      )}</template>`
+      )}</wrapper>`
       const $ref = parser
         .parseFromString(fragment, 'text/xml')
         .querySelector('ref')
@@ -691,7 +691,7 @@ export class JATSExporter {
       attachments: () => '',
       image_element: (node) => createImage(node),
       embed: (node) => {
-        const { id, href, mimetype, mimeSubtype } = node.attrs
+        const { id, href, mimetype, mimeSubtype, extLinks } = node.attrs
         if (!href) {
           return ''
         }
@@ -709,6 +709,22 @@ export class JATSExporter {
         this.appendChildNodeOfType($media, node, schema.nodes.alt_text)
         this.appendChildNodeOfType($media, node, schema.nodes.long_desc)
         this.appendCaption($media, node)
+        if (extLinks && extLinks.length > 0) {
+          extLinks.forEach((extLink: ExtLink) => {
+            if (extLink.href) {
+              const extLinkElement = this.createElement('ext-link')
+              extLinkElement.setAttribute('ext-link-type', extLink.type)
+              extLinkElement.setAttributeNS(XLINK_NAMESPACE, 'href', extLink.href)
+              if (extLink.lang) {
+                extLinkElement.setAttributeNS(XML_NAMESPACE, 'lang', extLink.lang)
+              }
+              if (extLink.label) {
+                extLinkElement.textContent = extLink.label
+              }
+              $media.appendChild(extLinkElement)
+            }
+          })
+        }
         return $media
       },
       awards: () => ['funding-group', 0],

package/src/jats/importer/jats-dom-parser.ts

@@ -730,6 +730,11 @@ export class JATSDOMParser {
       context: 'pullquote_element/',
       getAttrs: this.getFigAttrs,
     },
+    {
+      tag: 'ext-link',
+      context: 'embed/',
+      ignore: true, // ext-links within media are handled via extLinks attribute
+    },
     {
       tag: 'ext-link',
       node: 'link',
@@ -758,11 +763,22 @@ export class JATSDOMParser {
       node: 'embed',
       getAttrs: (node) => {
         const element = node as HTMLElement
+        const extLinkElements = element.querySelectorAll('ext-link')
+        const extLinks = Array.from(extLinkElements)
+          .map((extLinkElement) => ({
+            type: extLinkElement.getAttribute('ext-link-type') || '',
+            href: extLinkElement.getAttributeNS(XLINK_NAMESPACE, 'href') || '',
+            lang: extLinkElement.getAttributeNS(XML_NAMESPACE, 'lang') || '',
+            label: getTrimmedTextContent(extLinkElement) || undefined,
+          }))
+          .filter((extLink) => extLink.href) // Filter out entries without href
+        
         return {
           id: element.getAttribute('id'),
           href: element.getAttributeNS(XLINK_NAMESPACE, 'href'),
           mimetype: element.getAttribute('mimetype'),
           mimeSubtype: element.getAttribute('mime-subtype'),
+          extLinks: extLinks.length > 0 ? extLinks : undefined,
         }
       },
     },

package/src/schema/nodes/embed.ts

@@ -18,11 +18,19 @@ import { NodeSpec } from 'prosemirror-model'
 
 import { ManuscriptNode } from '../types'
 
+export interface ExtLink {
+  type: string
+  href: string
+  lang: string
+  label?: string
+}
+
 export interface EmbedAttrs {
   id: string
   href: string
   mimetype: string
   mimeSubtype: string
+  extLinks?: ExtLink[]
 }
 
 export interface EmbedNode extends ManuscriptNode {
@@ -38,6 +46,7 @@ export const embed: NodeSpec = {
     mimetype: { default: undefined },
     mimeSubtype: { default: undefined },
     longDesc: { default: '' },
+    extLinks: { default: [] },
   },
   group: 'block element',
   toDOM: (node) => {

package/src/version.ts

@@ -1 +1 @@
-export const VERSION = "4.5.6";
+export const VERSION = "4.5.8";