@manuscripts/transform 4.3.53 → 4.4.0

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

@@ -0,0 +1,1260 @@
+/*!
+ * © 2020 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 { DOMParser, Fragment, ParseOptions, Schema } from 'prosemirror-model'
+
+import {
+  dateToTimestamp,
+  getCreditRole,
+  getHTMLContent,
+  getTrimmedTextContent,
+} from '../../lib/utils'
+import { XLINK_NAMESPACE, XML_NAMESPACE } from '../../lib/xml'
+import {
+  BibliographyItemAttrs,
+  BibliographyItemType,
+  ManuscriptNode,
+  MarkRule,
+  NodeRule,
+  SectionCategory,
+} from '../../schema'
+import { DEFAULT_PROFILE_ID } from './jats-comments'
+
+export class JATSDOMParser {
+  private parser: DOMParser
+
+  constructor(
+    private sectionCategories: SectionCategory[],
+    private schema: Schema
+  ) {
+    this.parser = new DOMParser(this.schema, [...this.marks, ...this.nodes])
+  }
+
+  public parse(doc: Node, options?: ParseOptions) {
+    return this.parser.parse(doc, options)
+  }
+
+  private isMatchingCategory(
+    secType: string | null,
+    titleNode: Element | null,
+    category: SectionCategory
+  ) {
+    if (
+      (secType && category.synonyms.includes(secType)) ||
+      category.id === secType
+    ) {
+      return true
+    }
+    if (titleNode && titleNode.nodeName === 'title' && titleNode.textContent) {
+      const textContent = titleNode.textContent.trim().toLowerCase()
+      if (category.synonyms.includes(textContent)) {
+        return true
+      }
+    }
+    return false
+  }
+
+  private chooseSectionCategory(section: HTMLElement) {
+    const secType = section.getAttribute('sec-type')
+    const abstractType = section.getAttribute('abstract-type')
+    const effectiveSecType =
+      secType || (abstractType ? `abstract-${abstractType}` : null)
+    const titleNode = section.firstElementChild
+
+    for (const category of this.sectionCategories) {
+      if (this.isMatchingCategory(effectiveSecType, titleNode, category)) {
+        return category.id
+      }
+    }
+  }
+
+  private parsePriority = (priority: string | null) => {
+    if (!priority) {
+      return undefined
+    }
+    return parseInt(priority)
+  }
+
+  private getEquationContent = (p: string | HTMLElement) => {
+    const element = p as HTMLElement
+    const id = element.getAttribute('id')
+    const container = element.querySelector('alternatives') ?? element
+    let contents: string | null = ''
+    let format: string | null = ''
+    for (const child of container.childNodes) {
+      const nodeName = child.nodeName.replace(/^[a-z]:/, '')
+
+      switch (nodeName) {
+        case 'tex-math':
+          contents = child.textContent
+          format = 'tex'
+          break
+        case 'mml:math':
+          contents = (child as Element).outerHTML
+          format = 'mathml'
+          break
+      }
+    }
+    return { id, format, contents }
+  }
+
+  private parseHistoryDates = (historyNode: Element | null) => {
+    if (!historyNode) {
+      return undefined
+    }
+    const history: {
+      acceptanceDate?: number
+      correctionDate?: number
+      retractionDate?: number
+      revisionRequestDate?: number
+      revisionReceiveDate?: number
+      receiveDate?: number
+    } = {}
+
+    for (const date of historyNode.children) {
+      const dateType = date.getAttribute('date-type')
+      switch (dateType) {
+        case 'received': {
+          history.receiveDate = dateToTimestamp(date)
+          break
+        }
+        case 'rev-recd': {
+          history.revisionReceiveDate = dateToTimestamp(date)
+          break
+        }
+        case 'accepted': {
+          history.acceptanceDate = dateToTimestamp(date)
+          break
+        }
+        case 'rev-request': {
+          history.revisionRequestDate = dateToTimestamp(date)
+          break
+        }
+        case 'retracted': {
+          history.retractionDate = dateToTimestamp(date)
+          break
+        }
+        case 'corrected': {
+          history.correctionDate = dateToTimestamp(date)
+          break
+        }
+      }
+    }
+    return history
+  }
+
+  private getEmail = (element: HTMLElement) => {
+    const email = element.querySelector('email')
+    if (email) {
+      return {
+        href: email.getAttributeNS(XLINK_NAMESPACE, 'href') ?? '',
+        text: getTrimmedTextContent(email) ?? '',
+      }
+    }
+  }
+
+  private getFigAttrs = (node: HTMLElement | string | Node) => {
+    const element = node as HTMLElement
+    const extLink = element.querySelector('ext-link')
+    const parentElement = element.parentElement
+    return {
+      id: element.getAttribute('id'),
+      type:
+        parentElement?.getAttribute('fig-type') ??
+        element.getAttribute('content-type') ??
+        '',
+      src: element.getAttributeNS(XLINK_NAMESPACE, 'href'),
+      extLink: extLink?.getAttributeNS(XLINK_NAMESPACE, 'href'),
+    }
+  }
+
+  private getInstitutionDetails = (element: HTMLElement) => {
+    let department = ''
+    let institution = ''
+    for (const node of element.querySelectorAll('institution')) {
+      const content = getTrimmedTextContent(node)
+      if (!content) {
+        continue
+      }
+      const type = node.getAttribute('content-type')
+      if (type === 'dept') {
+        department = content
+      } else {
+        institution = content
+      }
+    }
+    return { department, institution }
+  }
+
+  private getAddressLine = (element: HTMLElement, index: number) => {
+    return (
+      getTrimmedTextContent(element, `addr-line:nth-of-type(${index})`) || ''
+    )
+  }
+
+  private getSurname = (element: HTMLElement) => {
+    const surname = getTrimmedTextContent(element, 'surname')
+    if (surname) {
+      return surname
+    }
+
+    const stringName = element.querySelector('string-name')
+    if (stringName && !stringName.querySelector('given-names')) {
+      return getTrimmedTextContent(element, 'string-name')
+    }
+  }
+
+  private getRefType = (element: Element): BibliographyItemType => {
+    const citation = element.querySelector('element-citation, mixed-citation')
+    const type = citation?.getAttribute('publication-type')
+    if (citation?.getAttribute('specific-use') === 'unstructured-citation') {
+      return 'literal'
+    }
+    if (!type) {
+      return 'article-journal'
+    }
+    switch (type) {
+      case 'journal':
+        return 'article-journal'
+      case 'web':
+        return 'webpage'
+      case 'data':
+        return 'dataset'
+      default:
+        return type as BibliographyItemType
+    }
+  }
+
+  private getNameContent(element: Element, type: string) {
+    const query = `person-group[person-group-type="${type}"] > *`
+    const groups = [...element.querySelectorAll(query)]
+    if (!groups.length) {
+      return
+    }
+    return groups.map((node) => ({
+      given: getTrimmedTextContent(node, 'given-names'),
+      family: getTrimmedTextContent(node, 'surname'),
+      literal:
+        node.nodeName === 'collab' ? getTrimmedTextContent(node) : undefined,
+    })) as CSL.Person[]
+  }
+
+  private getDateContent(
+    element: Element,
+    query: string
+  ): CSL.Date | undefined {
+    const date = element.querySelector(query)
+    if (date) {
+      const isoDate = date.getAttribute('iso-8601-date')
+      if (!isoDate) {
+        return
+      }
+
+      const parsedDate = new Date(Date.parse(isoDate))
+
+      const parts: [number, number, number] = [
+        parsedDate.getFullYear(),
+        parsedDate.getMonth() + 1, //month is 0 indexed.
+        parsedDate.getDate(),
+      ]
+
+      return {
+        'date-parts': [parts],
+      }
+    }
+  }
+
+  private getIssuedDateContent(element: Element): CSL.Date | undefined {
+    const year = getTrimmedTextContent(element, ':scope > * > year')
+    if (!year) {
+      return
+    }
+    const month = getTrimmedTextContent(element, ':scope > * > month')
+    const day = getTrimmedTextContent(element, ':scope > * > day')
+    return {
+      'date-parts': [[year, month ?? '', day ?? '']],
+    }
+  }
+
+  private getFigContent = (node: Node) => {
+    const element = node as HTMLElement
+    const content = [this.schema.nodes.figure.create(this.getFigAttrs(element))]
+    const altText = element.querySelector('alt-text')
+    if (altText) {
+      const altTextNode = this.schema.nodes.alt_text.create()
+      content.push(this.parse(altText, { topNode: altTextNode }))
+    }
+    const longDesc = element.querySelector('long-desc')
+    if (longDesc) {
+      const longDescNode = this.schema.nodes.long_desc.create()
+      content.push(this.parse(longDesc, { topNode: longDescNode }))
+    }
+    return Fragment.from(content)
+  }
+
+  private getCaptionContent = (node: Node) => {
+    const element = node as HTMLElement
+    const content = Array.from(element.querySelectorAll('p')).map((paragraph) =>
+      this.parse(paragraph, { topNode: this.schema.nodes.text_block.create() })
+    )
+    return Fragment.from(
+      content.length > 0 ? content : this.schema.nodes.text_block.create()
+    )
+  }
+
+  private parseRefPages = (element: Element) => {
+    const fpage = getTrimmedTextContent(element, 'fpage')
+    const lpage = getTrimmedTextContent(element, 'lpage')
+    if (fpage) {
+      return lpage ? `${fpage}-${lpage}` : fpage
+    }
+  }
+
+  private parseRef = (element: Element): BibliographyItemAttrs => {
+    return {
+      id: element.id,
+      type: this.getRefType(element),
+      comment: getTrimmedTextContent(element, 'comment'),
+      volume: getTrimmedTextContent(element, 'volume'),
+      issue: getTrimmedTextContent(element, 'issue'),
+      supplement: getTrimmedTextContent(element, 'supplement'),
+      DOI: getTrimmedTextContent(element, 'pub-id[pub-id-type="doi"]'),
+      URL: getTrimmedTextContent(element, 'ext-link[ext-link-type="uri"]'),
+      std: getTrimmedTextContent(
+        element,
+        'pub-id[pub-id-type="std-designation"]'
+      ),
+      'collection-title': getTrimmedTextContent(element, 'series'),
+      edition: getTrimmedTextContent(element, 'edition'),
+      publisher: getTrimmedTextContent(element, 'publisher-name'),
+      'publisher-place': getTrimmedTextContent(element, 'publisher-loc'),
+      event: getTrimmedTextContent(element, 'conf-name'),
+      'event-place': getTrimmedTextContent(element, 'conf-loc'),
+      'number-of-pages': getTrimmedTextContent(element, 'size[units="pages"]'),
+      institution: getTrimmedTextContent(element, 'institution'),
+      locator: getTrimmedTextContent(element, 'elocation-id'),
+      'container-title': getHTMLContent(element, 'source'),
+      title: getHTMLContent(element, 'article-title, data-title, part-title'),
+      author: this.getNameContent(element, 'author'),
+      editor: this.getNameContent(element, 'editor'),
+      literal: getTrimmedTextContent(element, 'mixed-citation'),
+      accessed: this.getDateContent(element, 'date-in-citation'),
+      'event-date': this.getDateContent(element, 'conf-date'),
+      issued: this.getIssuedDateContent(element),
+      page: this.parseRefPages(element),
+    }
+  }
+
+  private nodes: NodeRule[] = [
+    {
+      tag: 'long-desc',
+      node: 'long_desc',
+    },
+    {
+      tag: 'alt-text',
+      node: 'alt_text',
+    },
+    {
+      tag: 'attachments > self-uri',
+      node: 'attachment',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+        return {
+          id: element.getAttribute('id'),
+          href: element.getAttributeNS(XLINK_NAMESPACE, 'href') || '',
+          type: element.getAttribute('content-type') || '',
+        }
+      },
+    },
+    {
+      tag: 'article',
+      node: 'manuscript',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+        const doi = element.querySelector(
+          'front > article-meta > article-id[pub-id-type="doi"]'
+        )
+        const history = element.querySelector('history')
+        const dates = this.parseHistoryDates(history)
+        return {
+          doi: getTrimmedTextContent(doi),
+          articleType: element.getAttribute('article-type') || '',
+          primaryLanguageCode: element.getAttributeNS(XML_NAMESPACE, 'lang'),
+          ...dates,
+        }
+      },
+    },
+    {
+      tag: 'subtitle',
+      node: 'subtitle',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+        return {
+          id: element.getAttribute('id'),
+        }
+      },
+    },
+    {
+      tag: 'alt-title[alt-title-type]',
+      node: 'alt_title',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+        return {
+          id: element.getAttribute('id'),
+          type: element.getAttribute('alt-title-type'),
+        }
+      },
+    },
+    {
+      tag: 'article-title',
+      node: 'title',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+        return {
+          id: element.getAttribute('id'),
+          type: element.getAttribute('type') || '',
+        }
+      },
+    },
+
+    {
+      tag: 'highlight-marker',
+      node: 'highlight_marker',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+        return {
+          id: element.id,
+          position: element.getAttribute('position'),
+        }
+      },
+    },
+    {
+      tag: 'comments',
+      node: 'comments',
+    },
+    {
+      tag: 'comment',
+      node: 'comment',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+        return {
+          id: element.getAttribute('id'),
+          target: element.getAttribute('target-id'),
+          contents: getTrimmedTextContent(element),
+          userID: DEFAULT_PROFILE_ID,
+          timestamp: Date.now(),
+        }
+      },
+    },
+    {
+      tag: 'author-notes',
+      node: 'author_notes',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+        if (!getTrimmedTextContent(element)) {
+          return false
+        }
+        return {
+          id: element.getAttribute('id'),
+        }
+      },
+    },
+    {
+      tag: 'funding-group',
+      node: 'awards',
+    },
+    {
+      tag: 'award-group',
+      node: 'award',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+        return {
+          id: element.getAttribute('id'),
+          recipient: getTrimmedTextContent(
+            element,
+            'principal-award-recipient'
+          ),
+          code: Array.from(element.querySelectorAll('award-id'))
+            .map((awardID) => getTrimmedTextContent(awardID))
+            .reduce((acc, text) => (acc ? `${acc};${text}` : text), ''),
+          source: getTrimmedTextContent(element, 'funding-source'),
+        }
+      },
+    },
+    {
+      tag: 'fn[fn-type]', // all supported fn-types should be moved out by the time we parse into prosemirror
+      context: 'author_notes/',
+      ignore: true,
+    },
+    {
+      tag: 'fn:not([fn-type])',
+      node: 'footnote',
+      context: 'author_notes/',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+        return {
+          id: element.getAttribute('id'),
+          kind: 'footnote',
+        }
+      },
+    },
+    {
+      tag: 'corresp',
+      node: 'corresp',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+        const label = element.querySelector('label')
+        if (label) {
+          label.remove()
+        }
+        return {
+          id: element.getAttribute('id'),
+          label: getTrimmedTextContent(label),
+        }
+      },
+      getContent: (node) => {
+        const element = node as HTMLElement
+        return Fragment.from(
+          this.schema.text(getTrimmedTextContent(element) || '')
+        )
+      },
+    },
+    {
+      tag: 'contrib[contrib-type="author"]',
+      node: 'contributor',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+        const footnoteIDs: string[] = []
+        const affiliationIDs: string[] = []
+        const correspIDs: string[] = []
+
+        const xrefs = element.querySelectorAll('xref')
+        for (const xref of xrefs) {
+          const rid = xref.getAttribute('rid')
+          const type = xref.getAttribute('ref-type')
+          if (!rid) {
+            continue
+          }
+          switch (type) {
+            case 'fn':
+              footnoteIDs.push(rid)
+              break
+            case 'corresp':
+              correspIDs.push(rid)
+              break
+            case 'aff':
+              affiliationIDs.push(rid)
+              break
+          }
+        }
+
+        return {
+          id: element.getAttribute('id') || undefined,
+          role: getTrimmedTextContent(element, 'role'),
+          affiliationIDs,
+          correspIDs,
+          footnoteIDs,
+          isCorresponding: element.getAttribute('corresp') === 'yes',
+          given: getTrimmedTextContent(element, 'given-names'),
+          family: this.getSurname(element),
+          prefix: getTrimmedTextContent(element, 'prefix'),
+          suffix: getTrimmedTextContent(element, 'suffix'),
+          degrees:
+            Array.from(element.querySelectorAll('degrees')).map((degree) =>
+              getTrimmedTextContent(degree)
+            ) || [],
+          ORCID: getTrimmedTextContent(
+            element,
+            'contrib-id[contrib-id-type="orcid"]'
+          ),
+          isAuthenticated: !!element.querySelector(
+            'contrib-id[contrib-id-type="orcid"][authenticated="true"]'
+          ),
+          creditRoles: getCreditRole(element),
+          priority: this.parsePriority(element.getAttribute('priority')),
+          email: getTrimmedTextContent(element, 'email') || '',
+        }
+      },
+      getContent: () => {
+        return Fragment.from(this.schema.text('_'))
+      },
+    },
+    {
+      tag: 'affiliations',
+      node: 'affiliations',
+    },
+    {
+      tag: 'aff',
+      node: 'affiliation',
+      context: 'affiliations/',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+
+        const { department, institution } = this.getInstitutionDetails(element)
+
+        return {
+          id: element.getAttribute('id'),
+          institution: institution ?? '',
+          department: department ?? '',
+          addressLine1: this.getAddressLine(element, 1),
+          addressLine2: this.getAddressLine(element, 2),
+          addressLine3: this.getAddressLine(element, 3),
+          postCode: getTrimmedTextContent(element, 'postal-code') ?? '',
+          country: getTrimmedTextContent(element, 'country') ?? '',
+          county: getTrimmedTextContent(element, 'state') ?? '',
+          city: getTrimmedTextContent(element, 'city') ?? '',
+          email: this.getEmail(element),
+          priority: this.parsePriority(element.getAttribute('priority')),
+        }
+      },
+      getContent: () => {
+        return Fragment.from(this.schema.text('_'))
+      },
+    },
+
+    {
+      tag: 'attrib',
+      node: 'attribution',
+    },
+    {
+      tag: 'back',
+      ignore: true,
+    },
+    {
+      tag: 'history',
+      ignore: true,
+    },
+    {
+      tag: 'break',
+      node: 'hard_break',
+    },
+    {
+      tag: 'caption > p',
+      context: 'table_element/',
+      ignore: true,
+    },
+    {
+      tag: 'caption > title',
+      node: 'caption_title',
+    },
+    {
+      tag: 'caption',
+      node: 'caption',
+      context: 'image_element/|figure_element/',
+      getContent: this.getCaptionContent,
+    },
+    {
+      tag: 'caption',
+      node: 'caption',
+      context: 'listing_element/|embed/|supplement/',
+      getContent: (node) => {
+        const element = node as HTMLElement
+        const title = element.querySelector('title')
+        const caption_title = title
+          ? this.parse(title, {
+              topNode: this.schema.nodes.caption_title.create(),
+            })
+          : this.schema.nodes.caption_title.create()
+        const caption = this.schema.nodes.caption.create(
+          undefined,
+          this.getCaptionContent(node)
+        )
+        return Fragment.from([caption_title, caption])
+      },
+    },
+    {
+      tag: 'code',
+      node: 'listing',
+      context: 'listing_element/',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+
+        return {
+          id: element.getAttribute('id'),
+          language: element.getAttribute('language') ?? '',
+          contents: getTrimmedTextContent(element),
+        }
+      },
+    },
+    {
+      tag: 'inline-formula',
+      node: 'inline_equation',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+        return this.getEquationContent(element)
+      },
+    },
+    {
+      tag: 'disp-formula',
+      node: 'equation_element',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+        return {
+          id: element.getAttribute('id'),
+        }
+      },
+      getContent: (node, schema) => {
+        const element = node as HTMLElement
+        const attrs = this.getEquationContent(element)
+        return Fragment.from([
+          schema.nodes.equation.createChecked({ ...attrs }),
+        ]) as Fragment
+      },
+    },
+    {
+      tag: 'disp-quote[content-type=quote]',
+      node: 'blockquote_element',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+
+        return {
+          id: element.getAttribute('id'),
+        }
+      },
+    },
+    {
+      tag: 'disp-quote',
+      node: 'pullquote_element',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+
+        return {
+          id: element.getAttribute('id'),
+        }
+      },
+    },
+    {
+      tag: 'graphic',
+      node: 'quote_image',
+      context: 'pullquote_element/',
+      getAttrs: this.getFigAttrs,
+    },
+    {
+      tag: 'ext-link',
+      node: 'link',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+
+        return {
+          href: element.getAttributeNS(XLINK_NAMESPACE, 'href') || '',
+          title: element.getAttributeNS(XLINK_NAMESPACE, 'title') || '',
+        }
+      },
+    },
+    {
+      tag: 'fig[fig-type=equation]',
+      node: 'equation_element',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+
+        return {
+          id: element.getAttribute('id'),
+        }
+      },
+    },
+    {
+      tag: 'media',
+      node: 'embed',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+        return {
+          id: element.getAttribute('id'),
+          href: element.getAttributeNS(XLINK_NAMESPACE, 'href'),
+          mimetype: element.getAttribute('mimetype'),
+          mimeSubtype: element.getAttribute('mime-subtype'),
+        }
+      },
+    },
+    {
+      tag: 'fig[fig-type=listing]',
+      node: 'listing_element',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+
+        return {
+          id: element.getAttribute('id'),
+        }
+      },
+    },
+    {
+      tag: 'graphic[specific-use=MISSING]',
+      node: 'missing_figure',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+
+        return {
+          id: element.getAttribute('id'),
+        }
+      },
+    },
+    {
+      tag: 'graphic[content-type=leading]',
+      node: 'hero_image',
+      getContent: this.getFigContent,
+    },
+    {
+      tag: 'graphic',
+      node: 'figure',
+      context: 'figure_element/',
+      getAttrs: this.getFigAttrs,
+    },
+    {
+      tag: 'graphic',
+      node: 'image_element',
+      getContent: (node) => {
+        const element = node as HTMLElement
+        const caption = this.schema.nodes.caption.create(
+          undefined,
+          this.getCaptionContent(node)
+        )
+        const fig = this.getFigContent(element).content
+        return Fragment.from([...fig.slice(0, 1), caption, ...fig.slice(1)])
+      },
+      getAttrs: this.getFigAttrs,
+    },
+    {
+      tag: 'fig',
+      node: 'figure_element',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+        const attrib = element.querySelector('attrib')
+        const attribution = attrib
+          ? {
+              literal: getTrimmedTextContent(attrib) ?? '',
+            }
+          : undefined
+        return {
+          id: element.getAttribute('id'),
+          attribution,
+        }
+      },
+    },
+    {
+      tag: 'fn-group',
+      node: 'footnotes_element',
+      context: 'footnotes_section/|table_element_footer/',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+
+        return {
+          id: element.getAttribute('id'),
+          kind: 'footnote', // TODO: 'endnote' depending on position or attribute?
+        }
+      },
+    },
+    {
+      tag: 'table-wrap-foot',
+      node: 'table_element_footer',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+
+        return {
+          id: element.getAttribute('id'),
+        }
+      },
+    },
+    {
+      tag: 'general-table-footnote',
+      node: 'general_table_footnote',
+      context: 'table_element_footer/',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+        return {
+          id: element.getAttribute('id'),
+        }
+      },
+      getContent: (node) => {
+        const paragraphs: ManuscriptNode[] = []
+        node.childNodes.forEach((p) => {
+          const paragraph = this.schema.nodes.paragraph.create()
+          const content = this.parse(p, {
+            topNode: paragraph,
+          })
+          paragraphs.push(content)
+        })
+        return Fragment.from([...paragraphs]) as Fragment
+      },
+    },
+    {
+      tag: 'fn',
+      node: 'footnote',
+      context: 'footnotes_element/|table_element_footer/',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+
+        return {
+          id: element.getAttribute('id'),
+          kind: 'footnote', // TODO: 'endnote' depending on position or attribute?
+        }
+      },
+    },
+    {
+      tag: 'front',
+      ignore: true,
+    },
+    {
+      tag: 'list',
+      node: 'list',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+
+        return {
+          id: element.getAttribute('id'),
+          listStyleType: element.getAttribute('list-type'),
+        }
+      },
+    },
+    {
+      tag: 'list-item',
+      node: 'list_item',
+    },
+    {
+      tag: 'p',
+      node: 'paragraph',
+      context: 'section/',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+
+        return {
+          id: element.getAttribute('id'),
+        }
+      },
+    },
+    {
+      tag: 'p',
+      node: 'paragraph',
+    },
+    {
+      tag: 'sec[sec-type="endnotes"]',
+      node: 'footnotes_section', // NOTE: higher priority than 'section'
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+
+        return {
+          id: element.getAttribute('id'),
+          // category: chooseSectionCategory(element), // 'MPSectionCategory:endnotes',
+        }
+      },
+    },
+    {
+      tag: 'sec[sec-type="keywords"]',
+      node: 'keywords', // NOTE: higher priority than 'section'
+    },
+    {
+      tag: 'sec[sec-type="supplementary-material"]',
+      node: 'supplements', // NOTE: higher priority than 'section'
+    },
+    {
+      tag: 'supplementary-material',
+      node: 'supplement', // NOTE: higher priority than 'section'
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+        return {
+          id: element.getAttribute('id'),
+          href: element.getAttributeNS(XLINK_NAMESPACE, 'href'),
+          mimeType: element.getAttribute('mimetype'),
+          mimeSubType: element.getAttribute('mime-subtype'),
+        }
+      },
+    },
+    {
+      tag: 'trans-abstract[sec-type="abstract-graphical"]',
+      node: 'trans_graphical_abstract',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+        return {
+          lang: element.getAttributeNS(XML_NAMESPACE, 'lang') ?? '',
+          category: this.chooseSectionCategory(element),
+        }
+      },
+    },
+    {
+      tag: 'trans-abstract[sec-type="abstract-key-image"]',
+      node: 'trans_graphical_abstract',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+        return {
+          lang: element.getAttributeNS(XML_NAMESPACE, 'lang') ?? '',
+          category: this.chooseSectionCategory(element),
+        }
+      },
+    },
+    {
+      tag: 'trans-abstract',
+      node: 'trans_abstract',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+        return {
+          lang: element.getAttributeNS(XML_NAMESPACE, 'lang') ?? '',
+          category: this.chooseSectionCategory(element),
+        }
+      },
+    },
+    {
+      tag: 'sec[sec-type="abstracts"]',
+      node: 'abstracts',
+    },
+    {
+      tag: 'sec[sec-type="body"]',
+      node: 'body',
+    },
+    {
+      tag: 'sec[sec-type="backmatter"]',
+      node: 'backmatter',
+    },
+    {
+      tag: 'boxed-text',
+      node: 'box_element',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+        return {
+          id: element.getAttribute('id'),
+        }
+      },
+    },
+    {
+      tag: 'sec[sec-type="bibliography"]',
+      node: 'bibliography_section',
+    },
+    {
+      tag: 'ref-list',
+      context: 'bibliography_section/',
+      node: 'bibliography_element',
+    },
+    {
+      tag: 'ref',
+      context: 'bibliography_element/',
+      node: 'bibliography_item',
+      getAttrs: (node) => this.parseRef(node as Element),
+    },
+    {
+      tag: 'sec[sec-type="abstract-graphical"]',
+      node: 'graphical_abstract_section',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+        return {
+          category: this.chooseSectionCategory(element),
+        }
+      },
+    },
+    {
+      tag: 'sec[sec-type="abstract-key-image"]',
+      node: 'graphical_abstract_section',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+        return {
+          category: this.chooseSectionCategory(element),
+        }
+      },
+    },
+    {
+      tag: 'sec',
+      node: 'section',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+        return {
+          id: element.getAttribute('id'),
+          category: this.chooseSectionCategory(element),
+        }
+      },
+    },
+    {
+      tag: 'kwd-group-list',
+      context: 'keywords/',
+      node: 'keywords_element',
+    },
+    {
+      tag: 'kwd-group',
+      context: 'keywords_element/',
+      node: 'keyword_group',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+        return {
+          id: element.id,
+          type: element.getAttribute('kwd-group-type'),
+        }
+      },
+    },
+    {
+      tag: 'kwd',
+      context: 'keyword_group//',
+      node: 'keyword',
+    },
+    {
+      tag: 'label',
+      context: 'section/',
+      node: 'section_label',
+    },
+    {
+      tag: 'table',
+      node: 'table',
+      // TODO: count thead and tfoot rows
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+
+        return {
+          id: element.getAttribute('id'),
+        }
+      },
+    },
+    {
+      tag: 'table-wrap',
+      node: 'table_element',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+        return {
+          id: element.getAttribute('id'),
+        }
+      },
+    },
+    {
+      tag: 'title',
+      node: 'section_title',
+      context:
+        'section/|footnotes_section/|bibliography_section/|keywords/|supplements/|author_notes/|graphical_abstract_section/|trans_abstract/|trans_graphical_abstract/',
+    },
+    {
+      tag: 'tr',
+      node: 'table_row',
+    },
+    {
+      tag: 'td',
+      node: 'table_cell',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+        const colspan = parseInt(element.getAttribute('colspan') || '1')
+        const rowspan = parseInt(element.getAttribute('rowspan') || '1')
+        return {
+          ...(colspan && { colspan }),
+          ...(rowspan && { rowspan }),
+          valign: element.getAttribute('valign'),
+          align: element.getAttribute('align'),
+          scope: element.getAttribute('scope'),
+          style: element.getAttribute('style'),
+        }
+      },
+    },
+    {
+      tag: 'th',
+      node: 'table_header',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+        const colspan = parseInt(element.getAttribute('colspan') || '1')
+        const rowspan = parseInt(element.getAttribute('rowspan') || '1')
+        return {
+          ...(colspan && { colspan }),
+          ...(rowspan && { rowspan }),
+          valign: element.getAttribute('valign'),
+          align: element.getAttribute('align'),
+          scope: element.getAttribute('scope'),
+          style: element.getAttribute('style'),
+        }
+      },
+    },
+    {
+      tag: 'col',
+      node: 'table_col',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+
+        return {
+          width: element.getAttribute('width'),
+        }
+      },
+    },
+    {
+      tag: 'colgroup',
+      node: 'table_colgroup',
+    },
+    {
+      tag: 'xref[ref-type="bibr"]',
+      node: 'citation',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+        return {
+          rids: element.getAttribute('rid')?.split(/\s+/) || [],
+          contents: getTrimmedTextContent(element),
+        }
+      },
+    },
+    {
+      tag: 'xref[ref-type="fn"]',
+      node: 'inline_footnote',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+
+        return {
+          rids: element.getAttribute('rid')?.split(/\s+/) || [],
+        }
+      },
+    },
+    {
+      tag: 'xref',
+      node: 'cross_reference',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+        return {
+          rids: element.getAttribute('rid')?.split(/\s+/) || [],
+        }
+      },
+    },
+    {
+      tag: 'label',
+      ignore: true,
+    },
+  ]
+
+  private marks: MarkRule[] = [
+    {
+      tag: 'bold',
+      mark: 'bold',
+    },
+    {
+      tag: 'code',
+      mark: 'code',
+    },
+    {
+      tag: 'italic',
+      mark: 'italic',
+    },
+    {
+      tag: 'sc',
+      mark: 'smallcaps',
+    },
+    {
+      tag: 'strike',
+      mark: 'strikethrough',
+    },
+    {
+      tag: 'styled-content',
+      mark: 'styled',
+      getAttrs: (node) => ({
+        style: (node as Element).getAttribute('style'),
+      }),
+    },
+    {
+      tag: 'sub',
+      mark: 'subscript',
+    },
+    {
+      tag: 'sup',
+      mark: 'superscript',
+    },
+    {
+      tag: 'underline',
+      mark: 'underline',
+    },
+  ]
+}