@manuscripts/transform 4.3.52 → 4.4.0

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

@@ -0,0 +1,2090 @@
+/*!
+ * © 2019 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.
+ */
+
+import * as Citeproc from 'citeproc'
+import {
+  DOMOutputSpec,
+  DOMParser as ProsemirrorDOMParser,
+  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'
+import { generateFootnoteLabels } from '../../lib/footnotes'
+import { nodeFromHTML } from '../../lib/html'
+import {
+  sanitizeXmlString,
+  XLINK_NAMESPACE,
+  XML_NAMESPACE,
+} from '../../lib/xml'
+import {
+  AffiliationNode,
+  AuthorNotesNode,
+  AwardNode,
+  CitationNode,
+  ContributorNode,
+  CorrespNode,
+  CrossReferenceNode,
+  FootnoteNode,
+  isBibliographyItemNode,
+  isCitationNode,
+  isNodeOfType,
+  ManuscriptMark,
+  ManuscriptNode,
+  ManuscriptNodeType,
+  Marks,
+  Nodes,
+  ParagraphNode,
+  QuoteImageNode,
+  schema,
+  TableElementFooterNode,
+  TableElementNode,
+} from '../../schema'
+import { isExecutableNodeType, isNodeType } from '../../transformer'
+import { IDGenerator } from '../types'
+import { initJats, jatsVariableWrapper } from './citeproc'
+import { selectVersionIds, Version } from './jats-versions'
+import { buildTargets, Target } from './labels'
+
+interface Attrs {
+  [key: string]: string
+}
+
+type NodeSpecs = { [key in Nodes]: (node: ManuscriptNode) => DOMOutputSpec }
+
+type MarkSpecs = {
+  [key in Marks]: (mark: ManuscriptMark, inline: boolean) => DOMOutputSpec
+}
+
+const normalizeID = (id: string) => id.replace(/:/g, '_')
+
+const parser = ProsemirrorDOMParser.fromSchema(schema)
+// siblings from https://jats.nlm.nih.gov/archiving/tag-library/1.2/element/article-meta.html
+const insertAbstractNode = (front: Element, abstractNode: Element) => {
+  const articleMeta = front.querySelector(':scope > article-meta')
+  if (!articleMeta) {
+    return
+  }
+  const insertBeforeElement = articleMeta.querySelector(
+    'kwd-group, funding-group, support-group, conference, counts, custom-meta-group'
+  )
+
+  if (insertBeforeElement) {
+    articleMeta.insertBefore(abstractNode, insertBeforeElement)
+  } else {
+    articleMeta.appendChild(abstractNode)
+  }
+}
+
+export const createCounter = () => {
+  const counts = new Map<string, number>()
+
+  return {
+    increment: (field: string) => {
+      const value = counts.get(field)
+      const newValue = value === undefined ? 1 : value + 1
+      counts.set(field, newValue)
+      return newValue
+    },
+  }
+}
+
+const createDefaultIdGenerator = (): IDGenerator => {
+  const counter = createCounter()
+
+  return async (element: Element) => {
+    const value = String(counter.increment(element.nodeName))
+
+    return `${element.localName}-${value}`
+  }
+}
+
+const chooseRefType = (type: ManuscriptNodeType): string | undefined => {
+  switch (type) {
+    case schema.nodes.figure:
+    case schema.nodes.figure_element:
+      return 'fig'
+
+    case schema.nodes.footnote:
+      return 'fn'
+
+    case schema.nodes.table:
+    case schema.nodes.table_element:
+      return 'table'
+
+    case schema.nodes.section:
+      return 'sec'
+
+    case schema.nodes.equation:
+    case schema.nodes.equation_element:
+      return 'disp-formula'
+  }
+}
+
+const sortContributors = (a: ContributorNode, b: ContributorNode) =>
+  Number(a.attrs.priority) - Number(b.attrs.priority)
+
+export type CSLOptions = {
+  style: string
+  locale: string
+}
+export type ExportOptions = {
+  version?: Version
+  csl: CSLOptions
+}
+
+export class JATSExporter {
+  protected document: Document
+  protected serializer: DOMSerializer
+  protected labelTargets: Map<string, Target>
+  protected footnoteLabels: Map<string, string>
+  protected manuscriptNode: ManuscriptNode
+  private engine: Citeproc.Engine
+  private renderedCitations: Map<string, string>
+  private nodesMap: Map<NodeType, ManuscriptNode[]> = new Map()
+
+  private populateNodesMap = () => {
+    this.manuscriptNode.descendants((node) => {
+      const type = node.type
+      const nodes = this.nodesMap.get(type) ?? []
+      nodes.push(node)
+      this.nodesMap.set(type, nodes)
+    })
+  }
+
+  protected getFirstChildOfType<T extends ManuscriptNode>(
+    type: NodeType,
+    node?: ManuscriptNode
+  ): T | undefined {
+    return this.getChildrenOfType<T>(type, node)[0]
+  }
+
+  protected getChildrenOfType<T extends ManuscriptNode>(
+    type: NodeType,
+    node?: ManuscriptNode
+  ): T[] {
+    const nodes = node
+      ? findChildrenByType(node, type).map(({ node }) => node)
+      : this.nodesMap.get(type)
+    return (nodes ?? []).filter((n): n is T => isNodeOfType<T>(n, type))
+  }
+
+  public serializeToJATS = async (
+    manuscriptNode: ManuscriptNode,
+    options: ExportOptions
+  ): Promise<string> => {
+    this.manuscriptNode = manuscriptNode
+    this.populateNodesMap()
+    this.initCiteprocEngine(options.csl)
+    this.createSerializer()
+    const versionIds = 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
+    )
+    const front = this.buildFront()
+    article.appendChild(front)
+    article.setAttribute(
+      'article-type',
+      manuscriptNode.attrs.articleType || 'other'
+    )
+    article.setAttributeNS(
+      XML_NAMESPACE,
+      'lang',
+      manuscriptNode.attrs.primaryLanguageCode || 'en'
+    )
+    this.labelTargets = buildTargets(
+      manuscriptNode.descendants.bind(manuscriptNode)
+    )
+    this.footnoteLabels = generateFootnoteLabels(manuscriptNode)
+    const body = this.buildBody()
+    article.appendChild(body)
+    this.addParagraphsToSections(article)
+    const back = this.buildBack(body)
+    this.moveCoiStatementToAuthorNotes(back, front)
+    article.appendChild(back)
+    this.unwrapBody(body)
+    this.moveAbstracts(front, body)
+    this.removeBackContainer(body)
+    this.updateFootnoteTypes(front, back)
+    this.fillEmptyTableFooters(article)
+    this.fillEmptyFootnotes(article)
+    this.fillEmptyListItem(article)
+    this.moveAwards(front, body)
+    this.moveFloatsGroup(article)
+    await this.rewriteIDs()
+    return serializeToXML(this.document)
+  }
+
+  private appendChildNodeOfType = (
+    element: HTMLElement,
+    node: ManuscriptNode,
+    type: ManuscriptNodeType
+  ) => {
+    const childNode = this.getFirstChildOfType(type, node)
+    if (childNode) {
+      element.appendChild(this.serializeNode(childNode))
+    }
+  }
+
+  private appendChildrenNodeOfType = (
+    element: HTMLElement,
+    node: ManuscriptNode,
+    type: ManuscriptNodeType
+  ) => {
+    const children = this.getChildrenOfType(type, node)
+    children.map((childNode) =>
+      element.appendChild(this.serializeNode(childNode))
+    )
+  }
+
+  protected appendCaption = (element: HTMLElement, node: ManuscriptNode) => {
+    const caption = this.createElement('caption')
+    this.appendChildNodeOfType(caption, node, schema.nodes.caption_title)
+    const captionNode = this.getChildrenOfType(schema.nodes.caption, node)[0]
+    if (captionNode && captionNode.content.size > 2) {
+      this.appendChildrenNodeOfType(
+        caption,
+        captionNode,
+        schema.nodes.text_block
+      )
+    }
+    if (caption.children.length > 0) {
+      element.appendChild(caption)
+    }
+  }
+  private initCiteprocEngine = (csl: CSLOptions) => {
+    const bibitems: Map<string, CSL.Data> = new Map()
+    const citations: Map<string, Citeproc.Citation> = new Map()
+
+    this.manuscriptNode.descendants((n) => {
+      if (isBibliographyItemNode(n)) {
+        bibitems.set(n.attrs.id, n.attrs as CSL.Data)
+      }
+      if (isCitationNode(n)) {
+        citations.set(n.attrs.id, buildCiteprocCitation(n.attrs))
+      }
+    })
+
+    initJats()
+    const engine = new Citeproc.Engine(
+      {
+        retrieveLocale: () => csl.locale,
+        retrieveItem: (id: string) => {
+          const item = bibitems.get(id)
+          if (!item) {
+            throw Error(`Missing bibliography item with id ${id}`)
+          }
+          return item
+        },
+        variableWrapper: jatsVariableWrapper,
+      },
+      csl.style
+    )
+    engine.setOutputFormat('jats')
+
+    const output = engine.rebuildProcessorState([...citations.values()])
+
+    this.engine = engine
+    this.renderedCitations = new Map(output.map((i) => [i[0], i[2]]))
+  }
+
+  private nodeFromJATS = (JATSFragment: string) => {
+    JATSFragment = JATSFragment.trim()
+    JATSFragment = JATSFragment.replace('&nbsp;', ' ')
+
+    if (!JATSFragment.length) {
+      return null
+    }
+
+    const template = this.createElement('template')
+
+    template.innerHTML = JATSFragment
+
+    return template.firstChild
+  }
+
+  protected rewriteIDs = async (
+    generator: IDGenerator = createDefaultIdGenerator()
+  ) => {
+    const ids = new Map<string, string | null>()
+
+    for (const element of this.document.querySelectorAll('[id]')) {
+      const oldID = element.getAttribute('id')
+      const newID = await generator(element)
+
+      if (newID) {
+        element.setAttribute('id', newID)
+      } else {
+        element.removeAttribute('id')
+      }
+
+      if (oldID) {
+        ids.set(oldID, newID)
+      }
+    }
+
+    for (const node of this.document.querySelectorAll('[rid]')) {
+      const rids = node.getAttribute('rid')
+
+      if (rids) {
+        const newRids = rids
+          .split(/\s+/)
+          .filter(Boolean)
+          .map((rid) => ids.get(rid))
+          .filter(Boolean)
+
+        if (newRids.length) {
+          node.setAttribute('rid', newRids.join(' '))
+        }
+      }
+    }
+  }
+
+  protected setTitleContent = (element: HTMLElement, title: string) => {
+    const htmlTitleNode = nodeFromHTML(`<h1>${title}</h1>`)
+
+    if (htmlTitleNode) {
+      // TODO: parse and serialize with title schema
+      const titleNode = parser.parse(htmlTitleNode, {
+        topNode: schema.nodes.section_title.create(),
+      })
+
+      const jatsTitleNode = this.serializeNode(titleNode)
+
+      while (jatsTitleNode.firstChild) {
+        element.appendChild(jatsTitleNode.firstChild)
+      }
+    }
+  }
+
+  protected buildFront = () => {
+    // https://jats.nlm.nih.gov/archiving/tag-library/1.2/element/front.html
+    const front = this.createElement('front')
+
+    // https://jats.nlm.nih.gov/archiving/tag-library/1.2/element/article-meta.html
+    const articleMeta = this.createElement('article-meta')
+    front.appendChild(articleMeta)
+
+    if (this.manuscriptNode.attrs.doi) {
+      const articleID = this.createElement('article-id')
+      articleID.setAttribute('pub-id-type', 'doi')
+      // @ts-ignore
+      articleID.textContent = this.manuscriptNode.attrs.doi
+      articleMeta.appendChild(articleID)
+    }
+
+    const titleGroup = this.createElement('title-group')
+
+    const titleNode = this.getFirstChildOfType(schema.nodes.title)
+
+    if (titleNode) {
+      const element = this.createElement('article-title')
+      this.setTitleContent(element, titleNode.textContent)
+      titleGroup.appendChild(element)
+    }
+
+    const subtitlesNodes = this.getChildrenOfType(schema.nodes.subtitle)
+    subtitlesNodes.forEach((subtitleNode) => {
+      const element = this.createElement('subtitle')
+      this.setTitleContent(element, subtitleNode.textContent)
+      titleGroup.appendChild(element)
+    })
+
+    const altTitlesNodes = this.getChildrenOfType(schema.nodes.alt_title)
+
+    altTitlesNodes.forEach((titleNode) => {
+      const element = this.createElement('alt-title')
+      element.setAttribute('alt-title-type', titleNode.attrs.type)
+      this.setTitleContent(element, titleNode.textContent)
+      titleGroup.appendChild(element)
+    })
+
+    articleMeta.appendChild(titleGroup)
+    this.buildContributors(articleMeta)
+
+    const supplementsNodes = this.getChildrenOfType(schema.nodes.supplement)
+    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.setAttribute('mimetype', node.attrs.mimeType ?? '')
+      supplementaryMaterial.setAttribute(
+        'mime-subtype',
+        node.attrs.mimeSubType ?? ''
+      )
+      this.appendCaption(supplementaryMaterial, node)
+
+      articleMeta.append(supplementaryMaterial)
+    })
+
+    const history =
+      articleMeta.querySelector('history') || this.createElement('history')
+
+    if (this.manuscriptNode.attrs.acceptanceDate) {
+      const date = this.buildDateElement(
+        this.manuscriptNode.attrs.acceptanceDate,
+        'accepted'
+      )
+      history.appendChild(date)
+    }
+    if (this.manuscriptNode.attrs.correctionDate) {
+      const date = this.buildDateElement(
+        this.manuscriptNode.attrs.correctionDate,
+        'corrected'
+      )
+      history.appendChild(date)
+    }
+    if (this.manuscriptNode.attrs.retractionDate) {
+      const date = this.buildDateElement(
+        this.manuscriptNode.attrs.retractionDate,
+        'retracted'
+      )
+      history.appendChild(date)
+    }
+    if (this.manuscriptNode.attrs.receiveDate) {
+      const date = this.buildDateElement(
+        this.manuscriptNode.attrs.receiveDate,
+        'received'
+      )
+      history.appendChild(date)
+    }
+    if (this.manuscriptNode.attrs.revisionReceiveDate) {
+      const date = this.buildDateElement(
+        this.manuscriptNode.attrs.revisionReceiveDate,
+        'rev-recd'
+      )
+      history.appendChild(date)
+    }
+    if (this.manuscriptNode.attrs.revisionRequestDate) {
+      const date = this.buildDateElement(
+        this.manuscriptNode.attrs.revisionRequestDate,
+        'rev-request'
+      )
+      history.appendChild(date)
+    }
+
+    if (history.childElementCount) {
+      articleMeta.appendChild(history)
+    }
+
+    this.buildKeywords(articleMeta)
+
+    let countingElements = []
+    const figureCount = this.getChildrenOfType(schema.nodes.figure).length
+    countingElements.push(this.buildCountingElement('fig-count', figureCount))
+
+    const tableCount = this.getChildrenOfType(schema.nodes.table).length
+    countingElements.push(this.buildCountingElement('table-count', tableCount))
+
+    const equationCount = this.getChildrenOfType(
+      schema.nodes.equation_element
+    ).length
+    countingElements.push(
+      this.buildCountingElement('equation-count', equationCount)
+    )
+
+    const referencesCount = this.getChildrenOfType(
+      schema.nodes.bibliography_item
+    ).length
+    countingElements.push(
+      this.buildCountingElement('ref-count', referencesCount)
+    )
+
+    //todo: is this correct?
+    const wordCount = this.manuscriptNode.textContent.split(/\s+/).length
+    countingElements.push(this.buildCountingElement('word-count', wordCount))
+
+    countingElements = countingElements.filter((el) => el) as Array<HTMLElement>
+    if (countingElements.length > 0) {
+      const counts = this.createElement('counts')
+      counts.append(...countingElements)
+      articleMeta.append(counts)
+    }
+
+    const attachments = this.getChildrenOfType(schema.nodes.attachment)
+
+    attachments.forEach((attachment) => {
+      const $selfUri = this.createElement('self-uri')
+      $selfUri.setAttribute('content-type', attachment.attrs.type)
+      $selfUri.setAttributeNS(XLINK_NAMESPACE, 'href', attachment.attrs.href)
+      const insertBeforeElements = articleMeta.querySelector(
+        'related-article, related-object, abstract, trans-abstract, kwd-group, funding-group, support-group, conference, counts, custom-meta-group'
+      )
+      insertBeforeElements
+        ? articleMeta.insertBefore($selfUri, insertBeforeElements)
+        : articleMeta.appendChild($selfUri)
+    })
+
+    return front
+  }
+
+  protected buildDateElement = (timestamp: number, type: string) => {
+    const dateElement = this.createElement('date')
+
+    dateElement.setAttribute('date-type', type)
+
+    const date = new Date(timestamp * 1000) // s => ms
+    const lookup = {
+      year: date.getUTCFullYear().toString(),
+      month: (date.getUTCMonth() + 1).toString().padStart(2, '0'),
+      day: date.getUTCDate().toString().padStart(2, '0'),
+    }
+
+    for (const [key, value] of Object.entries(lookup).reverse()) {
+      const el = this.createElement(key)
+      el.textContent = value
+      dateElement.appendChild(el)
+    }
+
+    return dateElement
+  }
+  protected buildCountingElement = (
+    tagName: string,
+    count: number | undefined
+  ) => {
+    if (count) {
+      const wordCount = this.createElement(tagName)
+      wordCount.setAttribute('count', String(count))
+      return wordCount
+    }
+  }
+  protected buildBody = () => {
+    const body = this.createElement('body')
+    this.manuscriptNode.forEach((cFragment) => {
+      const serializedNode = this.serializeNode(cFragment)
+      body.append(...serializedNode.childNodes)
+    })
+    this.fixBody(body)
+
+    return body
+  }
+
+  protected buildBack = (body: HTMLElement) => {
+    const back = this.createElement('back')
+    this.moveSectionsToBack(back, body)
+
+    // footnotes elements in footnotes section (i.e. not in table footer)
+    const footnotesElements = this.document.querySelectorAll('sec > fn-group')
+
+    for (const footnotesElement of footnotesElements) {
+      // move fn-group from body to back
+      const previousParent = footnotesElement.parentElement
+      back.appendChild(footnotesElement)
+
+      if (previousParent) {
+        const title = previousParent.querySelector('title')
+        if (title) {
+          footnotesElement.insertBefore(
+            title,
+            footnotesElement.firstElementChild
+          )
+        }
+        if (!previousParent.childElementCount) {
+          previousParent.remove()
+        }
+      }
+    }
+    // bibliography element
+    let refList = this.document.querySelector('ref-list')
+    if (!refList) {
+      refList = this.createElement('ref-list')
+    }
+
+    // move ref-list from body to back
+    back.appendChild(refList)
+    const parser = new DOMParser()
+    //eslint-disable-next-line @typescript-eslint/no-unused-vars
+    const [_, bibliography] = this.engine.makeBibliography()
+
+    for (let i = 0; i < bibliography.length; i++) {
+      const item = `<template xmlns:xlink="${XLINK_NAMESPACE}">${sanitizeXmlString(bibliography[i])}</template>`
+      const ref = parser.parseFromString(item, 'text/xml').querySelector('ref')
+      if (ref) {
+        refList.appendChild(ref)
+      }
+    }
+
+    return back
+  }
+
+  //@TODO: part of the export cleanup: check if we can use this elsewhere, maybe we can use strategy pattern for each element to have its own creator.
+  private createElement = (
+    tag: string,
+    content?: string,
+    attrs?: Record<string, string | undefined>
+  ) => {
+    const el = this.document.createElement(tag)
+    if (content) {
+      el.textContent = content
+    }
+    if (attrs) {
+      Object.entries(attrs).forEach(([k, v]) => {
+        if (v) {
+          el.setAttribute(k, v)
+        }
+      })
+    }
+    return el
+  }
+
+  private appendElement = (
+    parent: HTMLElement,
+    tag: string,
+    content?: string,
+    attrs?: Record<string, string | undefined>
+  ) => {
+    const el = this.createElement(tag, content, attrs)
+    parent.appendChild(el)
+    return el
+  }
+
+  protected createSerializer = () => {
+    const nodes: NodeSpecs = {
+      trans_abstract: (node) => {
+        const attrs: { [key: string]: string } = {
+          id: normalizeID(node.attrs.id),
+        }
+        if (node.attrs.lang) {
+          attrs[`${XML_NAMESPACE} lang`] = node.attrs.lang
+        }
+        if (node.attrs.category) {
+          attrs['sec-type'] = node.attrs.category
+        }
+        return ['trans-abstract', attrs, 0]
+      },
+      trans_graphical_abstract: (node) => {
+        const attrs: { [key: string]: string } = {
+          id: normalizeID(node.attrs.id),
+        }
+        if (node.attrs.lang) {
+          attrs[`${XML_NAMESPACE} lang`] = node.attrs.lang
+        }
+        if (node.attrs.category) {
+          attrs['sec-type'] = node.attrs.category
+        }
+        return ['trans-abstract', attrs, 0]
+      },
+      hero_image: () => '',
+      alt_text: (node) => {
+        if (node.textContent) {
+          const altText = this.createElement('alt-text')
+          altText.textContent = node.textContent
+          return altText
+        }
+        return ''
+      },
+      long_desc: (node) => {
+        if (node.textContent) {
+          const longDesc = this.createElement('long-desc')
+          longDesc.textContent = node.textContent
+          return longDesc
+        }
+        return ''
+      },
+      attachment: () => '',
+      attachments: () => '',
+      image_element: (node) => createImage(node),
+      embed: (node) => {
+        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')
+        mediaElement.setAttributeNS(XLINK_NAMESPACE, 'href', href)
+        if (mimetype) {
+          mediaElement.setAttribute('mimetype', node.attrs.mimetype)
+        }
+        if (mimeSubtype) {
+          mediaElement.setAttribute('mime-subtype', node.attrs.mimeSubtype)
+        }
+        appendLabels(mediaElement, node)
+        this.appendChildNodeOfType(mediaElement, node, schema.nodes.alt_text)
+        this.appendChildNodeOfType(mediaElement, node, schema.nodes.long_desc)
+        this.appendCaption(mediaElement, node)
+        return mediaElement
+      },
+      awards: () => ['funding-group', 0],
+      award: (node) => {
+        const awardGroup = node as AwardNode
+        const awardGroupElement = this.createElement('award-group')
+        awardGroupElement.setAttribute('id', normalizeID(awardGroup.attrs.id))
+        appendChildIfPresent(
+          awardGroupElement,
+          'funding-source',
+          awardGroup.attrs.source
+        )
+        awardGroup.attrs.code
+          ?.split(';')
+          .forEach((code) =>
+            appendChildIfPresent(awardGroupElement, 'award-id', code)
+          )
+        appendChildIfPresent(
+          awardGroupElement,
+          'principal-award-recipient',
+          awardGroup.attrs.recipient
+        )
+
+        return awardGroupElement
+      },
+      box_element: (node) => createBoxElement(node),
+      author_notes: () => '',
+      corresp: () => '',
+      title: () => '',
+      alt_title: () => '',
+      alt_titles: () => '',
+      subtitle: () => '',
+      subtitles: () => '',
+      text_block: (node) => nodes.paragraph(node),
+      affiliations: () => '',
+      contributors: () => '',
+      table_element_footer: (node) =>
+        node.childCount == 0
+          ? ['table-wrap-foot', ['fn-group', ['fn', ['p']]]]
+          : ['table-wrap-foot', 0],
+      contributor: () => '',
+      affiliation: () => '',
+      attribution: () => ['attrib', 0],
+      bibliography_element: () => '',
+      bibliography_item: () => '',
+      comments: () => '',
+      keyword_group: () => '',
+      body: () => ['body', 0],
+      abstracts: () => ['abstract', 0],
+      backmatter: () => ['backmatter', 0],
+      supplement: () => '',
+      supplements: () => '',
+      bibliography_section: () => '',
+      blockquote_element: () => ['disp-quote', { 'content-type': 'quote' }, 0],
+      list: (node) => [
+        'list',
+        {
+          'list-type': node.attrs.listStyleType ?? 'bullet',
+        },
+        0,
+      ],
+      caption: () => ['p', 0],
+      caption_title: (node) => {
+        if (!node.textContent) {
+          return ''
+        }
+        return ['title', 0]
+      },
+      citation: (node) => {
+        const citation = node as CitationNode
+        const rids = citation.attrs.rids
+        if (!rids.length) {
+          return ''
+        }
+
+        const xref = this.createElement('xref')
+        xref.setAttribute('ref-type', 'bibr')
+        xref.setAttribute('rid', normalizeID(rids.join(' ')))
+        const fragment = this.renderedCitations.get(node.attrs.id)
+        if (fragment) {
+          xref.innerHTML = fragment
+        }
+        return xref
+      },
+      cross_reference: (node) => {
+        const cross = node as CrossReferenceNode
+        const rids = cross.attrs.rids
+        if (!rids.length) {
+          return cross.attrs.label ?? ''
+        }
+
+        const rid = rids[0]
+        const text = cross.attrs.label || this.labelTargets.get(rid)?.label
+
+        const target = findChildrenByAttr(
+          this.manuscriptNode,
+          (attrs) => attrs.id === rid
+        )[0]?.node
+        if (!target) {
+          return text ?? ''
+        }
+
+        const xref = this.createElement('xref')
+
+        const type = chooseRefType(target.type)
+        if (type) {
+          xref.setAttribute('ref-type', type)
+        }
+
+        xref.setAttribute('rid', normalizeID(rids.join(' ')))
+        xref.textContent = text ?? ''
+
+        return xref
+      },
+      doc: () => '',
+      equation: (node) => {
+        return node.attrs.contents ? this.createEquation(node) : ''
+      },
+      general_table_footnote: (node) => {
+        const el = this.createElement('general-table-footnote')
+        el.setAttribute('id', normalizeID(node.attrs.id))
+        processChildNodes(el, node, schema.nodes.general_table_footnote)
+        return el
+      },
+      inline_equation: (node) => {
+        if (!node.attrs.contents) {
+          return ''
+        }
+        const eqElement = this.createElement('inline-formula')
+        const equation = this.createEquation(node, true)
+        eqElement.append(equation)
+        return eqElement
+      },
+      equation_element: (node) => {
+        const eqElement = this.createElement('disp-formula')
+        eqElement.setAttribute('id', normalizeID(node.attrs.id))
+        appendLabels(eqElement, node)
+        processChildNodes(eqElement, node, schema.nodes.equation)
+        return eqElement
+      },
+      figure: (node) => createGraphic(node),
+      figure_element: (node) =>
+        createFigureElement(node, node.type.schema.nodes.figure),
+      footnote: (node) => {
+        const attrs: Attrs = {}
+
+        if (node.attrs.id) {
+          attrs.id = normalizeID(node.attrs.id)
+        }
+        if (node.attrs.category) {
+          attrs['fn-type'] = node.attrs.category
+        }
+        return ['fn', attrs, 0]
+      },
+      footnotes_element: (node) =>
+        node.childCount == 0
+          ? ['fn-group', { id: normalizeID(node.attrs.id) }, ['fn', ['p']]]
+          : ['fn-group', { id: normalizeID(node.attrs.id) }, 0],
+      footnotes_section: (node) => {
+        const attrs: { [key: string]: string } = {
+          id: normalizeID(node.attrs.id),
+          'sec-type': 'endnotes', // chooseSecType(node.attrs.category),
+        }
+
+        return ['sec', attrs, 0]
+      },
+      hard_break: () => '',
+      highlight_marker: () => '',
+      inline_footnote: (node) => {
+        const rids: string[] = node.attrs.rids
+        const xref = this.createElement('xref')
+        xref.setAttribute('ref-type', 'fn')
+        xref.setAttribute('rid', normalizeID(rids.join(' ')))
+        xref.textContent = rids
+          .map((rid) => this.footnoteLabels.get(rid))
+          .join(', ')
+        return xref
+      },
+      keyword: () => '',
+      keywords_element: () => '',
+      keywords: () => '',
+      link: (node) => {
+        const text = node.textContent
+
+        if (!text) {
+          return ''
+        }
+
+        if (!node.attrs.href) {
+          return text
+        }
+
+        const linkNode = this.createElement('ext-link')
+        linkNode.setAttribute('ext-link-type', 'uri')
+        linkNode.setAttributeNS(XLINK_NAMESPACE, 'href', node.attrs.href)
+        linkNode.textContent = text
+
+        if (node.attrs.title) {
+          linkNode.setAttributeNS(
+            XLINK_NAMESPACE,
+            'xlink:title',
+            node.attrs.title
+          )
+        }
+
+        return linkNode
+      },
+      list_item: () => ['list-item', 0],
+      listing: (node) => {
+        const code = this.createElement('code')
+        code.setAttribute('id', normalizeID(node.attrs.id))
+        code.setAttribute('language', node.attrs.languageKey)
+        code.textContent = node.attrs.contents
+
+        return code
+      },
+      listing_element: (node) =>
+        createFigureElement(node, node.type.schema.nodes.listing),
+      manuscript: (node) => ['article', { id: normalizeID(node.attrs.id) }, 0],
+      missing_figure: () => {
+        const graphic = this.createElement('graphic')
+        graphic.setAttribute('specific-use', 'MISSING')
+        graphic.setAttributeNS(XLINK_NAMESPACE, 'xlink:href', '')
+        return graphic
+      },
+      paragraph: (node) => {
+        if (!node.childCount) {
+          return ''
+        }
+
+        const attrs: Attrs = {}
+
+        if (node.attrs.id) {
+          attrs.id = normalizeID(node.attrs.id)
+        }
+
+        if (node.attrs.contentType) {
+          attrs['content-type'] = node.attrs.contentType
+        }
+
+        return ['p', attrs, 0]
+      },
+      placeholder: () => {
+        return this.createElement('boxed-text')
+      },
+      placeholder_element: () => {
+        return this.createElement('boxed-text')
+      },
+      pullquote_element: (node) => {
+        let type = 'pullquote'
+        if (node.firstChild?.type === schema.nodes.quote_image) {
+          type = 'quote-with-image'
+        }
+        return ['disp-quote', { 'content-type': type }, 0]
+      },
+      quote_image: (node) => {
+        const img = node as QuoteImageNode
+        if (img.attrs.src) {
+          return createGraphic(node)
+        }
+        return ''
+      },
+      graphical_abstract_section: (node) => {
+        const attrs: { [key: string]: string } = {
+          id: normalizeID(node.attrs.id),
+        }
+        if (node.attrs.category) {
+          attrs['sec-type'] = node.attrs.category
+        }
+        return ['sec', attrs, 0]
+      },
+      section: (node) => {
+        const attrs: { [key: string]: string } = {
+          id: normalizeID(node.attrs.id),
+        }
+
+        if (node.attrs.category) {
+          attrs['sec-type'] = node.attrs.category
+        }
+
+        return ['sec', attrs, 0]
+      },
+      section_label: () => ['label', 0],
+      section_title: () => ['title', 0],
+      section_title_plain: () => ['title', 0],
+      table: (node) => ['table', { id: normalizeID(node.attrs.id) }, 0],
+      table_element: (node) => {
+        const element = createTableElement(node)
+        element.setAttribute('position', 'anchor')
+        return element
+      },
+      table_cell: (node) => [
+        'td',
+        {
+          valign: node.attrs.valign,
+          align: node.attrs.align,
+          scope: node.attrs.scope,
+          style: node.attrs.style,
+          ...(node.attrs.rowspan > 1 && { rowspan: node.attrs.rowspan }),
+          ...(node.attrs.colspan > 1 && { colspan: node.attrs.colspan }),
+        },
+        0,
+      ],
+      table_header: (node) => [
+        'th',
+        {
+          valign: node.attrs.valign,
+          align: node.attrs.align,
+          scope: node.attrs.scope,
+          style: node.attrs.style,
+          ...(node.attrs.rowspan > 1 && { rowspan: node.attrs.rowspan }),
+          ...(node.attrs.colspan > 1 && { colspan: node.attrs.colspan }),
+        },
+        0,
+      ],
+      table_row: () => ['tr', 0],
+      table_col: (node) => ['col', { width: node.attrs.width }],
+      table_colgroup: () => ['colgroup', 0],
+      text: (node) => node.text as string,
+      comment: () => '',
+    }
+
+    const marks: MarkSpecs = {
+      bold: () => ['bold'],
+      code: () => ['code', { position: 'anchor' }],
+      italic: () => ['italic'],
+      smallcaps: () => ['sc'],
+      strikethrough: () => ['strike'],
+      //I couldn't find any examples for this to test
+      styled: () => ['styled-content'],
+      superscript: () => ['sup'],
+      subscript: () => ['sub'],
+      underline: () => ['underline'],
+      tracked_insert: () => ['ins'],
+      tracked_delete: () => ['del'],
+    }
+
+    this.serializer = new DOMSerializer(nodes, marks)
+    const appendChildIfPresent = (
+      parent: Element,
+      tagName: string,
+      textContent: string
+    ) => {
+      if (!textContent) {
+        return
+      }
+      const element = this.createElement(tagName)
+      element.textContent = textContent
+      parent.appendChild(element)
+    }
+    const processChildNodes = (
+      element: HTMLElement,
+      node: ManuscriptNode,
+      contentNodeType: ManuscriptNodeType
+    ) => {
+      node.forEach((childNode) => {
+        if (childNode.type === contentNodeType) {
+          if (childNode.attrs.id) {
+            element.appendChild(this.serializeNode(childNode))
+          }
+        } else if (childNode.type === node.type.schema.nodes.paragraph) {
+          element.appendChild(this.serializeNode(childNode))
+        } else if (childNode.type === node.type.schema.nodes.missing_figure) {
+          element.appendChild(this.serializeNode(childNode))
+        }
+      })
+    }
+    const createElement = (node: ManuscriptNode, nodeName: string) => {
+      const element = this.createElement(nodeName)
+      element.setAttribute('id', normalizeID(node.attrs.id))
+      return element
+    }
+
+    const appendLabels = (element: HTMLElement, node: ManuscriptNode) => {
+      if (this.labelTargets) {
+        const target = this.labelTargets.get(node.attrs.id)
+
+        if (target) {
+          const label = this.createElement('label')
+          label.textContent = target.label
+          element.appendChild(label)
+        }
+      }
+    }
+    const appendAttributions = (element: HTMLElement, node: ManuscriptNode) => {
+      if (node.attrs.attribution) {
+        const attribution = this.createElement('attrib')
+        attribution.textContent = node.attrs.attribution.literal
+        element.appendChild(attribution)
+      }
+    }
+
+    const appendTable = (element: HTMLElement, node: ManuscriptNode) => {
+      const tableNode = this.getFirstChildOfType(schema.nodes.table, node)
+      const colGroupNode = this.getFirstChildOfType(
+        schema.nodes.table_colgroup,
+        node
+      )
+      if (!tableNode) {
+        return
+      }
+      const table = this.serializeNode(tableNode)
+      const tbodyElement = this.createElement('tbody')
+
+      while (table.firstChild) {
+        const child = table.firstChild
+        table.removeChild(child)
+        tbodyElement.appendChild(child)
+      }
+      table.appendChild(tbodyElement)
+      if (colGroupNode) {
+        const colGroup = this.serializeNode(colGroupNode)
+        table.insertBefore(colGroup, table.firstChild)
+      }
+
+      element.appendChild(table)
+    }
+    const createBoxElement = (node: ManuscriptNode) => {
+      const element = createElement(node, 'boxed-text')
+      appendLabels(element, node)
+      const child = node.firstChild
+      if (child?.type === schema.nodes.caption_title) {
+        this.appendCaption(element, node)
+      }
+
+      processChildNodes(element, node, node.type.schema.nodes.section)
+      return element
+    }
+
+    const isChildOfNodeType = (
+      targetID: string,
+      type: NodeType,
+      descend = false
+    ): boolean => {
+      const nodes = this.getChildrenOfType(type)
+      return nodes.some((node) => {
+        const result = findChildrenByAttr(
+          node,
+          (attrs) => attrs.id === targetID,
+          descend
+        )[0]
+        return !!result
+      })
+    }
+
+    const createImage = (node: ManuscriptNode) => {
+      const graphicNode = node.content.firstChild
+      if (!graphicNode) {
+        return ''
+      }
+      const graphicElement = createGraphic(graphicNode)
+      if (node.attrs.extLink) {
+        const extLink = this.appendElement(graphicElement, 'ext-link')
+        extLink.setAttributeNS(XLINK_NAMESPACE, 'href', node.attrs.extLink)
+      }
+      this.appendCaption(graphicElement, node)
+      this.appendChildNodeOfType(graphicElement, node, schema.nodes.alt_text)
+      this.appendChildNodeOfType(graphicElement, node, schema.nodes.long_desc)
+      return graphicElement
+    }
+
+    const createGraphic = (node: ManuscriptNode) => {
+      const graphic = this.createElement('graphic')
+      graphic.setAttributeNS(XLINK_NAMESPACE, 'xlink:href', node.attrs.src)
+
+      if (isChildOfNodeType(node.attrs.id, schema.nodes.hero_image)) {
+        graphic.setAttribute('content-type', 'leading')
+      } else if (
+        !isChildOfNodeType(node.attrs.id, schema.nodes.figure_element) &&
+        node.attrs.type
+      ) {
+        graphic.setAttribute('content-type', node.attrs.type)
+      }
+      return graphic
+    }
+    const createFigureElement = (
+      node: ManuscriptNode,
+      contentNodeType: ManuscriptNodeType
+    ) => {
+      const element = createElement(node, 'fig')
+      const figNode = this.getFirstChildOfType(schema.nodes.figure, node)
+      const figType = figNode?.attrs.type
+      if (figType) {
+        element.setAttribute('fig-type', figType)
+      }
+      appendLabels(element, node)
+      this.appendCaption(element, node)
+      this.appendChildNodeOfType(element, node, schema.nodes.alt_text)
+      this.appendChildNodeOfType(element, node, schema.nodes.long_desc)
+      this.appendChildNodeOfType(
+        element,
+        node,
+        node.type.schema.nodes.footnotes_element
+      )
+      processChildNodes(element, node, contentNodeType)
+      appendAttributions(element, node)
+      if (isExecutableNodeType(node.type)) {
+        processExecutableNode(node, element)
+      }
+      moveAltTextAndLongDescToGraphics(element)
+      return element
+    }
+
+    const moveAltTextAndLongDescToGraphics = (element: Element) => {
+      const altText = element.querySelector('alt-text')
+      const longDesc = element.querySelector('long-desc')
+      const graphics = element.querySelectorAll('graphic')
+
+      if (graphics.length === 0) {
+        return
+      }
+
+      graphics.forEach((graphic) => {
+        if (longDesc) {
+          graphic.prepend(longDesc.cloneNode(true))
+        }
+        if (altText) {
+          graphic.prepend(altText.cloneNode(true))
+        }
+      })
+
+      altText?.remove()
+      longDesc?.remove()
+    }
+
+    const createTableElement = (node: ManuscriptNode) => {
+      const nodeName = 'table-wrap'
+      const element = createElement(node, nodeName)
+      appendLabels(element, node)
+      this.appendCaption(element, node)
+      this.appendChildNodeOfType(element, node, schema.nodes.alt_text)
+      this.appendChildNodeOfType(element, node, schema.nodes.long_desc)
+      appendTable(element, node)
+      this.appendChildNodeOfType(
+        element,
+        node,
+        node.type.schema.nodes.table_element_footer
+      )
+      if (isExecutableNodeType(node.type)) {
+        processExecutableNode(node, element)
+      }
+      return element
+    }
+    const processExecutableNode = (node: ManuscriptNode, element: Element) => {
+      const listingNode = this.getFirstChildOfType(schema.nodes.listing, node)
+
+      if (listingNode) {
+        const { contents, languageKey } = listingNode.attrs
+
+        if (contents && languageKey) {
+          const listing = this.createElement('fig')
+          listing.setAttribute('specific-use', 'source')
+          element.appendChild(listing)
+
+          const code = this.createElement('code')
+          code.setAttribute('executable', 'true')
+          code.setAttribute('language', languageKey)
+          code.textContent = contents
+          listing.appendChild(code)
+        }
+      }
+    }
+  }
+
+  private createEquation(node: ManuscriptNode, isInline = false) {
+    if (node.attrs.format === 'tex') {
+      const texMath = this.createElement('tex-math')
+      texMath.setAttribute('notation', 'LaTeX')
+      texMath.setAttribute('version', 'MathJax')
+      if (node.attrs.contents.includes('<![CDATA[')) {
+        texMath.innerHTML = node.attrs.contents
+      } else {
+        texMath.innerHTML = `<![CDATA[ ${node.attrs.contents} ]]>`
+      }
+      return texMath
+    } else {
+      const math = this.nodeFromJATS(node.attrs.contents)
+      const mathml = math as Element
+      if (!isInline) {
+        mathml.setAttribute('id', normalizeID(node.attrs.id))
+      }
+      return mathml
+    }
+  }
+
+  protected serializeNode = (node: ManuscriptNode) =>
+    this.serializer.serializeNode(node, {
+      document: this.document,
+    })
+
+  private buildContributors = (articleMeta: Node) => {
+    const contributors = this.getChildrenOfType<ContributorNode>(
+      schema.nodes.contributor
+    ).sort(sortContributors)
+
+    if (!contributors.length) {
+      return
+    }
+
+    const labels = new Map<string, number>()
+    const createLabel = (id: string) => {
+      let label = labels.get(id)
+      if (!label) {
+        label = labels.size + 1
+        labels.set(id, label)
+      }
+      const sup = this.createElement('sup')
+      sup.textContent = String(label)
+      return sup
+    }
+
+    const $contribGroup = this.createElement('contrib-group')
+    $contribGroup.setAttribute('content-type', 'authors')
+    articleMeta.appendChild($contribGroup)
+
+    contributors.forEach((contributor) => {
+      const $contrib = this.createElement('contrib')
+      $contrib.setAttribute('contrib-type', 'author')
+      $contrib.setAttribute('id', normalizeID(contributor.attrs.id))
+
+      if (contributor.attrs.isCorresponding) {
+        $contrib.setAttribute('corresp', 'yes')
+      }
+
+      if (contributor.attrs.role) {
+        this.appendElement($contrib, 'role', contributor.attrs.role)
+      }
+
+      if (contributor.attrs.ORCID) {
+        const contribIdAttrs: Record<string, string> = {
+          'contrib-id-type': 'orcid',
+        }
+        if (contributor.attrs.isAuthenticated) {
+          contribIdAttrs['authenticated'] = 'true'
+        }
+        this.appendElement(
+          $contrib,
+          'contrib-id',
+          contributor.attrs.ORCID,
+          contribIdAttrs
+        )
+      }
+
+      const $name = this.buildContributorName(contributor)
+      $contrib.appendChild($name)
+
+      if (contributor.attrs.suffix) {
+        this.appendElement($name, 'suffix', contributor.attrs.suffix)
+      }
+
+      contributor.attrs.degrees?.forEach((degree) => {
+        this.appendElement($contrib, 'degrees', degree)
+      })
+
+      if (contributor.attrs.email) {
+        this.appendElement($contrib, 'email', contributor.attrs.email)
+      }
+
+      contributor.attrs.affiliationIDs?.forEach((rid) => {
+        const $xref = this.appendElement($contrib, 'xref', '', {
+          'ref-type': 'aff',
+          rid: normalizeID(rid),
+        })
+        $xref.appendChild(createLabel(rid))
+      })
+
+      contributor.attrs.footnoteIDs?.forEach((rid) => {
+        const $xref = this.appendElement($contrib, 'xref', '', {
+          'ref-type': 'fn',
+          rid: normalizeID(rid),
+        })
+        $xref.appendChild(createLabel(rid))
+      })
+
+      contributor.attrs.correspIDs?.forEach((rid) => {
+        const $xref = this.appendElement($contrib, 'xref', '', {
+          'ref-type': 'corresp',
+          rid: normalizeID(rid),
+        })
+        $xref.appendChild(createLabel(rid))
+      })
+
+      contributor.attrs.creditRoles?.forEach((credit) => {
+        const url = CreditRoleUrls.get(credit.vocabTerm)
+        if (!url) {
+          return
+        }
+        this.appendElement($contrib, 'role', credit.vocabTerm, {
+          'vocab-identifier': 'http://credit.niso.org/',
+          vocab: 'CRediT',
+          'vocab-term': credit.vocabTerm,
+          'vocab-term-identifier': url,
+        })
+      })
+      $contribGroup.appendChild($contrib)
+    })
+
+    const affiliationIDs = contributors.flatMap((n) => n.attrs.affiliationIDs)
+    const sortAffiliations = (a: AffiliationNode, b: AffiliationNode) =>
+      affiliationIDs.indexOf(a.attrs.id) - affiliationIDs.indexOf(b.attrs.id)
+
+    this.getChildrenOfType<AffiliationNode>(schema.nodes.affiliation)
+      .filter((a) => affiliationIDs.includes(a.attrs.id))
+      .sort(sortAffiliations)
+      .forEach((affiliation) => {
+        const $content = []
+
+        if (affiliation.attrs.department) {
+          const $institution = this.createElement(
+            'institution',
+            affiliation.attrs.department,
+            {
+              'content-type': 'dept',
+            }
+          )
+          $content.push($institution)
+        }
+
+        if (affiliation.attrs.institution) {
+          const $institution = this.createElement(
+            'institution',
+            affiliation.attrs.institution
+          )
+          $content.push($institution)
+        }
+
+        if (affiliation.attrs.addressLine1) {
+          const $addrLine = this.createElement(
+            'addr-line',
+            affiliation.attrs.addressLine1
+          )
+          $content.push($addrLine)
+        }
+
+        if (affiliation.attrs.addressLine2) {
+          const $addrLine = this.createElement(
+            'addr-line',
+            affiliation.attrs.addressLine2
+          )
+          $content.push($addrLine)
+        }
+
+        if (affiliation.attrs.addressLine3) {
+          const $addrLine = this.createElement(
+            'addr-line',
+            affiliation.attrs.addressLine3
+          )
+          $content.push($addrLine)
+        }
+
+        if (affiliation.attrs.city) {
+          const $city = this.createElement('city', affiliation.attrs.city)
+          $content.push($city)
+        }
+
+        if (affiliation.attrs.county) {
+          const $state = this.createElement('state', affiliation.attrs.county)
+          $content.push($state)
+        }
+
+        if (affiliation.attrs.country) {
+          const $country = this.createElement(
+            'country',
+            affiliation.attrs.country
+          )
+          $content.push($country)
+        }
+
+        if (affiliation.attrs.postCode) {
+          const $postalCode = this.createElement(
+            'postal-code',
+            affiliation.attrs.postCode
+          )
+          $content.push($postalCode)
+        }
+
+        const $aff = this.createElement('aff')
+        $aff.setAttribute('id', normalizeID(affiliation.attrs.id))
+        $contribGroup.appendChild($aff)
+
+        const label = labels.get(affiliation.attrs.id)
+        if (label) {
+          this.appendElement($aff, 'label', String(label))
+        }
+
+        $content.forEach((node, i) => {
+          if (i > 0) {
+            $aff.appendChild(this.document.createTextNode(', '))
+          }
+          $aff.appendChild(node)
+        })
+      })
+
+    const $authorNotes = this.createAuthorNotesElement(contributors)
+    if ($authorNotes) {
+      articleMeta.insertBefore($authorNotes, $contribGroup.nextSibling)
+    }
+  }
+
+  private buildContributorName = (contributor: ContributorNode) => {
+    const { given, family } = contributor.attrs
+    if (Boolean(given) !== Boolean(family)) {
+      return this.createElement('string-name', given || family)
+    }
+
+    const name = this.createElement('name')
+
+    if (contributor.attrs.family) {
+      this.appendElement(name, 'surname', contributor.attrs.family)
+    }
+
+    if (contributor.attrs.given) {
+      this.appendElement(name, 'given-names', contributor.attrs.given)
+    }
+
+    if (contributor.attrs.prefix) {
+      this.appendElement(name, 'prefix', contributor.attrs.prefix)
+    }
+
+    return name
+  }
+
+  private createAuthorNotesElement = (contributors: ContributorNode[]) => {
+    const authorNotes = this.getFirstChildOfType<AuthorNotesNode>(
+      schema.nodes.author_notes
+    )
+    if (!authorNotes || !authorNotes.childCount) {
+      return
+    }
+
+    const $authorNotes = this.createElement('author-notes')
+
+    const used = contributors.flatMap((c) => c.attrs.correspIDs)
+
+    authorNotes.descendants((node) => {
+      switch (node.type) {
+        case schema.nodes.paragraph: {
+          const $p = this.writeParagraph(node as ParagraphNode)
+          $authorNotes.append($p)
+          break
+        }
+        case schema.nodes.footnote: {
+          const $fn = this.writeFootnote(node as FootnoteNode)
+          $authorNotes.append($fn)
+          break
+        }
+        case schema.nodes.corresp: {
+          if (used.includes(node.attrs.id)) {
+            const $corresp = this.writeCorresp(node as CorrespNode)
+            $authorNotes.append($corresp)
+          }
+          break
+        }
+      }
+      return false
+    })
+    return $authorNotes.hasChildNodes() ? $authorNotes : undefined
+  }
+
+  private writeCorresp = (corresp: CorrespNode) => {
+    const $corresp = this.createElement('corresp')
+    $corresp.setAttribute('id', normalizeID(corresp.attrs.id))
+    if (corresp.attrs.label) {
+      this.appendElement($corresp, 'label', corresp.attrs.label)
+    }
+    $corresp.append(corresp.textContent)
+    return $corresp
+  }
+
+  private writeParagraph = (paragraph: ParagraphNode) => {
+    const dom = new DOMParser().parseFromString(
+      paragraph.textContent,
+      'text/html'
+    )
+    const $p = this.createElement('p')
+    $p.setAttribute('id', normalizeID(paragraph.attrs.id))
+    if (dom.body.innerHTML.length) {
+      $p.innerHTML = dom.body.innerHTML
+    }
+    return $p
+  }
+
+  private writeFootnote = (footnote: FootnoteNode) => {
+    const $fn = this.createElement('fn')
+    $fn.setAttribute('id', normalizeID(footnote.attrs.id))
+    let content = footnote.textContent
+    if (!content.includes('<p>')) {
+      content = `<p>${content}</p>`
+    }
+    $fn.innerHTML = content
+    return $fn
+  }
+
+  private buildKeywords(articleMeta: Node) {
+    const keywordGroups = this.getChildrenOfType(schema.nodes.keyword_group)
+
+    keywordGroups.forEach((group) => {
+      const kwdGroup = this.createElement('kwd-group')
+      if (group.attrs.type) {
+        kwdGroup.setAttribute('kwd-group-type', group.attrs.type)
+      }
+      articleMeta.appendChild(kwdGroup)
+      group.content.forEach((keyword) => {
+        const kwd = this.createElement('kwd')
+        kwd.textContent = keyword.textContent
+        kwdGroup.appendChild(kwd)
+      })
+      articleMeta.appendChild(kwdGroup)
+    })
+  }
+
+  private fixBody = (body: Element) => {
+    this.manuscriptNode.descendants((node) => {
+      if (node.attrs.id) {
+        if (
+          isNodeType<TableElementFooterNode>(node, 'general_table_footnote')
+        ) {
+          const generalTableFootnote = body.querySelector(
+            `#${normalizeID(node.attrs.id)}`
+          )
+          if (generalTableFootnote) {
+            Array.from(generalTableFootnote.childNodes).forEach((cn) => {
+              generalTableFootnote.before(cn)
+            })
+            generalTableFootnote.remove()
+          }
+        }
+        // move captions to the top of tables
+        if (isNodeType<TableElementNode>(node, 'table_element')) {
+          const tableElement = body.querySelector(
+            `#${normalizeID(node.attrs.id)}`
+          )
+
+          if (tableElement) {
+            for (const childNode of tableElement.childNodes) {
+              switch (childNode.nodeName) {
+                case 'caption': {
+                  const label = tableElement.querySelector('label')
+
+                  tableElement.insertBefore(
+                    childNode,
+                    label ? label.nextSibling : tableElement.firstChild
+                  )
+                  break
+                }
+
+                case 'table': {
+                  this.fixTable(childNode)
+                  break
+                }
+              }
+            }
+          }
+        }
+      }
+    })
+  }
+
+  private changeTag = (node: Element, tag: string) => {
+    const clone = this.createElement(tag)
+    for (const attr of node.attributes) {
+      clone.setAttributeNS(null, attr.name, attr.value)
+    }
+    while (node.firstChild) {
+      clone.appendChild(node.firstChild)
+    }
+    node.replaceWith(clone)
+    return clone
+  }
+
+  private fixTable = (table: ChildNode) => {
+    let tbody: Element | undefined
+
+    Array.from(table.childNodes).forEach((child) => {
+      if (child instanceof Element && child.tagName.toLowerCase() === 'tbody') {
+        tbody = child
+      }
+    })
+
+    if (!tbody) {
+      return
+    }
+
+    const tbodyRows = Array.from(tbody.childNodes)
+    const thead = this.createElement('thead')
+
+    tbodyRows.forEach((row, i) => {
+      const isRow = row instanceof Element && row.tagName.toLowerCase() === 'tr'
+      if (isRow) {
+        // we assume that <th scope="col | colgroup"> always belongs to <thead>
+        const headerCell = (row as Element).querySelector(
+          'th[scope="col"], th[scope="colgroup"]'
+        )
+        if (i === 0 || headerCell) {
+          tbody?.removeChild(row)
+          const tableCells = (row as Element).querySelectorAll('td')
+          for (const td of tableCells) {
+            // for backwards compatibility since older docs use tds for header cells
+            this.changeTag(td, 'th')
+          }
+          thead.appendChild(row)
+        }
+      }
+    })
+
+    if (thead.hasChildNodes()) {
+      table.insertBefore(thead, tbody as Element)
+    }
+  }
+
+  private unwrapBody = (body: HTMLElement) => {
+    const container = body.querySelector(':scope > sec[sec-type="body"]')
+    if (!container) {
+      return
+    }
+    const sections = container.querySelectorAll(':scope > sec')
+    sections.forEach((section) => {
+      body.appendChild(section.cloneNode(true))
+    })
+    body.removeChild(container)
+  }
+
+  private removeBackContainer = (body: HTMLElement) => {
+    const container = body.querySelector(':scope > sec[sec-type="backmatter"]')
+    if (!container) {
+      return
+    }
+    body.removeChild(container)
+  }
+  private moveAwards = (front: HTMLElement, body: HTMLElement) => {
+    const awardGroups = body.querySelectorAll(':scope > award-group')
+    if (!awardGroups.length) {
+      return
+    }
+    const fundingGroup = this.createElement('funding-group')
+    awardGroups.forEach((award) => {
+      fundingGroup.appendChild(award)
+    })
+    const articleMeta = front.querySelector(':scope > article-meta')
+
+    if (articleMeta) {
+      const insertBeforeElement = articleMeta.querySelector(
+        ':scope > support-group, :scope > conference, :scope > counts, :scope > custom-meta-group'
+      )
+      insertBeforeElement
+        ? articleMeta.insertBefore(fundingGroup, insertBeforeElement)
+        : articleMeta.appendChild(fundingGroup)
+    }
+  }
+
+  private moveAbstracts = (front: HTMLElement, body: HTMLElement) => {
+    const abstractSections = this.getAbstractSections(body)
+
+    for (const abstractSection of abstractSections) {
+      const node =
+        abstractSection.nodeName === 'trans-abstract'
+          ? this.createTransAbstractNode(abstractSection)
+          : this.createAbstractNode(abstractSection)
+      abstractSection.remove()
+      insertAbstractNode(front, node)
+    }
+  }
+
+  private getAbstractCategories(
+    abstractsNode: ManuscriptNode | undefined
+  ): string[] {
+    const categories: string[] = []
+    abstractsNode?.content.descendants((node) => {
+      categories.push(node.attrs.category)
+      return false
+    })
+    return categories
+  }
+
+  private getAbstractSections(body: HTMLElement) {
+    {
+      const abstractsNode = this.getFirstChildOfType(schema.nodes.abstracts)
+      const abstractCategories = this.getAbstractCategories(abstractsNode)
+      const sections = Array.from(
+        body.querySelectorAll(':scope > sec, :scope > trans-abstract')
+      )
+      return sections.filter((section) =>
+        this.isAbstractSection(section, abstractCategories)
+      )
+    }
+  }
+
+  private isAbstractSection(
+    section: Element,
+    abstractCategories: string[]
+  ): boolean {
+    const sectionType = section.getAttribute('sec-type')
+    return sectionType ? abstractCategories.includes(sectionType) : false
+  }
+
+  private createTransAbstractNode(transAbstract: Element): Element {
+    const transAbstractNode = this.createElement('trans-abstract')
+    transAbstractNode.setAttributeNS(
+      XML_NAMESPACE,
+      'lang',
+      transAbstract.getAttributeNS(XML_NAMESPACE, 'lang') ?? ''
+    )
+    this.setAbstractType(transAbstractNode, transAbstract)
+    transAbstractNode.append(...transAbstract.childNodes)
+    return transAbstractNode
+  }
+
+  private createAbstractNode(abstractSection: Element): Element {
+    const abstractNode = this.createElement('abstract')
+    for (const node of abstractSection.childNodes) {
+      if (node.nodeName !== 'title') {
+        abstractNode.appendChild(node.cloneNode(true))
+      }
+    }
+    this.setAbstractType(abstractNode, abstractSection)
+    return abstractNode
+  }
+
+  private setAbstractType(abstractNode: Element, abstractSection: Element) {
+    const sectionType = abstractSection.getAttribute('sec-type')
+    if (sectionType && sectionType !== 'abstract') {
+      const abstractType = sectionType.replace('abstract-', '')
+      abstractNode.setAttribute('abstract-type', abstractType)
+    }
+  }
+
+  private moveSectionsToBack = (back: HTMLElement, body: HTMLElement) => {
+    const availabilitySection = body.querySelector(
+      'sec[sec-type="availability"]'
+    )
+
+    if (availabilitySection) {
+      back.insertBefore(availabilitySection, back.firstChild)
+    }
+
+    const ethicsSection = body.querySelector('sec[sec-type="ethics-statement"]')
+    if (ethicsSection) {
+      back.appendChild(ethicsSection)
+    }
+
+    const section = body.querySelector('sec[sec-type="acknowledgements"]')
+
+    if (section) {
+      const ack = this.createElement('ack')
+
+      while (section.firstChild) {
+        ack.appendChild(section.firstChild)
+      }
+
+      if (section.parentNode) {
+        section.parentNode.removeChild(section)
+      }
+
+      back.insertBefore(ack, back.firstChild)
+    }
+    const appendicesSections = body.querySelectorAll(
+      'sec[sec-type="appendices"]'
+    )
+
+    if (appendicesSections) {
+      const appGroup = this.createElement('app-group')
+      appendicesSections.forEach((section) => {
+        if (section.parentNode) {
+          section.parentNode.removeChild(section)
+        }
+        const app = this.createElement('app')
+        app.appendChild(section)
+        appGroup.appendChild(app)
+      })
+      back.insertBefore(appGroup, back.firstChild)
+    }
+
+    const footNotes = []
+
+    const footnoteCategories = [
+      'con',
+      'conflict',
+      'deceased',
+      'equal',
+      'present-address',
+      'presented-at',
+      'previously-at',
+      'supplementary-material',
+      'supported-by',
+      'financial-disclosure',
+      'coi-statement',
+    ]
+
+    const sections = body.querySelectorAll('sec')
+    for (const currentSection of sections) {
+      const currentSectionType = currentSection.getAttribute('sec-type')
+      if (
+        currentSectionType &&
+        footnoteCategories.indexOf(currentSectionType) >= 0
+      ) {
+        footNotes.push(
+          this.sectionToFootnote(currentSection, currentSectionType)
+        )
+      }
+    }
+
+    if (footNotes.length > 0) {
+      const fnGroup = this.createElement('fn-group')
+      fnGroup.append(...footNotes)
+      back.append(fnGroup)
+    }
+  }
+
+  sectionToFootnote = (section: Element, fnType: string) => {
+    const footNote = this.createElement('fn')
+    footNote.setAttribute('fn-type', fnType)
+    const title = section.querySelector('title')
+    if (title) {
+      const footNoteTitle = this.createElement('label')
+      footNoteTitle.textContent = title.textContent
+      section.removeChild(title)
+      footNote.append(footNoteTitle)
+    }
+    footNote.append(...section.children)
+    if (section.parentNode) {
+      section.parentNode.removeChild(section)
+    }
+    return footNote
+  }
+  private moveFloatsGroup = (article: HTMLElement) => {
+    const heroImage = this.getFirstChildOfType(schema.nodes.hero_image)
+    if (!heroImage) {
+      return
+    }
+    const floatsGroup = this.createElement('floats-group')
+    let figure: HTMLElement | null = null
+    heroImage.descendants((node) => {
+      if (node.type === schema.nodes.figure) {
+        figure = this.serializeNode(node) as HTMLElement
+        floatsGroup.appendChild(figure)
+      } else {
+        const serializedNode = this.serializeNode(node)
+        figure?.appendChild(serializedNode)
+      }
+      return false
+    })
+
+    if (floatsGroup.children.length > 0) {
+      article.appendChild(floatsGroup)
+    }
+  }
+
+  private moveCoiStatementToAuthorNotes(back: HTMLElement, front: HTMLElement) {
+    const fnGroups = back.querySelectorAll('fn-group')
+    fnGroups.forEach((fnGroup) => {
+      if (fnGroup) {
+        const coiStatement = fnGroup.querySelector(
+          'fn[fn-type="coi-statement"]'
+        )
+        if (coiStatement) {
+          const authorNotes = this.createElement('author-notes')
+          authorNotes.append(coiStatement)
+          const articleMeta = front.querySelector('article-meta')
+          if (articleMeta) {
+            const authorNoteEl = articleMeta.querySelector('author-notes')
+            if (authorNoteEl) {
+              authorNoteEl.append(...authorNotes.childNodes)
+            } else {
+              const appendableSelectors = [
+                'contrib-group',
+                'title-group',
+                'article-id',
+              ]
+              const appendable = [
+                ...(articleMeta as HTMLElement).querySelectorAll(
+                  appendableSelectors.join(', ')
+                ),
+              ]
+              for (let i = 0; i < appendableSelectors.length; i++) {
+                const sel = appendableSelectors[i]
+                const match = appendable.find((el) => el.matches(sel))
+                if (match) {
+                  articleMeta.insertBefore(authorNotes, match.nextSibling)
+                  break
+                }
+              }
+            }
+          }
+          if (!fnGroup.hasChildNodes()) {
+            fnGroup.remove()
+          }
+        }
+      }
+    })
+  }
+
+  private updateFootnoteTypes(front: HTMLElement, body: HTMLElement) {
+    const footnotes: Element[] = [...front.querySelectorAll('fn').values()]
+    footnotes.push(...body.querySelectorAll('fn'))
+    footnotes.forEach((fn) => {
+      const fnType = fn.getAttribute('fn-type')
+      if (fnType) {
+        fn.setAttribute('fn-type', fnType)
+      }
+    })
+  }
+
+  private fillEmptyElements(
+    articleElement: Element,
+    selector: string,
+    tagName = 'p'
+  ) {
+    const emptyElements = Array.from(
+      articleElement.querySelectorAll(selector)
+    ).filter((element) => !element.innerHTML)
+    emptyElements.forEach((element) =>
+      element.appendChild(this.createElement(tagName))
+    )
+  }
+  private addParagraphsToSections(articleElement: Element) {
+    const sections = articleElement.querySelectorAll('sec')
+    const TITLE_TAGS = new Set(['title', 'label', 'sec-meta'])
+    for (const section of sections) {
+      const hasContent = Array.from(section.children).some(
+        (child) => !TITLE_TAGS.has(child.tagName)
+      )
+      if (hasContent) {
+        continue
+      }
+      const p = this.createElement('p')
+      const insertAfterElement =
+        section.querySelector(':scope > title') ??
+        section.querySelector(':scope > label') ??
+        section.querySelector(':scope > sec-meta')
+
+      if (insertAfterElement) {
+        insertAfterElement.insertAdjacentElement('afterend', p)
+      } else {
+        section.prepend(p)
+      }
+    }
+  }
+
+  private fillEmptyFootnotes(articleElement: Element) {
+    this.fillEmptyElements(articleElement, 'fn')
+  }
+
+  private fillEmptyTableFooters(articleElement: Element) {
+    this.fillEmptyElements(articleElement, 'table-wrap-foot')
+  }
+
+  private fillEmptyListItem(articleElement: Element) {
+    this.fillEmptyElements(articleElement, 'list-item')
+  }
+}