@fiduswriter/document 0.1.0-alpha.1

package/src/exporter/jats/convert.js

@@ -0,0 +1,871 @@
+import {convertLatexToMathMl} from "mathlive"
+
+import {escapeText} from "../../common/index.js"
+import {CATS} from "../../schema/i18n.js"
+
+import {removeHidden} from "../tools/doc_content.js"
+
+import {JATSExporterCitations} from "./citations.js"
+import {convertText} from "./text.js"
+
+export class JATSExporterConverter {
+    constructor(type, doc, csl, imageDB, bibDB) {
+        this.type = type
+        this.doc = doc
+        this.csl = csl
+        this.imageDB = imageDB
+        this.bibDB = bibDB
+        this.imageIds = []
+        this.categoryCounter = {} // counters for each type of figure (figure/table/photo)
+        this.affiliations = {} // affiliations of authors and editors
+        this.affCounter = 0
+        this.parCounter = 0
+        this.headingCounter = 0
+        this.currentSectionLevel = 0
+        this.listCounter = 0
+        this.orderedListLengths = []
+        this.footnotes = []
+        this.fnCounter = 0
+        this.frontMatter = {
+            title: {},
+            subtitle: {},
+            contributors: [],
+            abstract: {},
+            keywords: [],
+            tags: [],
+            copyright: {
+                licenses: []
+            }
+        }
+        this.citInfos = []
+        this.citationCount = 0
+        this.citations = new JATSExporterCitations(
+            this.doc,
+            this.bibDB,
+            this.csl
+        )
+    }
+
+    init() {
+        const docContent = removeHidden(this.doc.content)
+        this.preWalkJson(docContent)
+        this.findAllCitations(docContent)
+        return this.citations.init(this.citInfos).then(() => {
+            const front =
+                this.type === "article"
+                    ? this.assembleArticleFront()
+                    : this.assembleBookPartFront()
+            const body = this.assembleBody(docContent)
+            const back = this.assembleBack()
+            return {
+                front,
+                body,
+                back,
+                imageIds: this.imageIds
+            }
+        })
+    }
+
+    // Remove items from the body that should be in the front.
+    preWalkJson(node, parentNode = false) {
+        switch (node.type) {
+            case "doc":
+                this.frontMatter.copyright = node.attrs.copyright
+                break
+            case "title":
+                this.frontMatter.title["default"] = node
+                parentNode.content = parentNode.content.filter(
+                    child => child !== node
+                )
+                break
+            case "heading_part":
+                if (
+                    ["title", "subtitle"].includes(node.attrs.metadata) &&
+                    !this.frontMatter[node.attrs.metadata][
+                        node.attrs.language || "default"
+                    ] &&
+                    node.content &&
+                    node.content.length
+                ) {
+                    // We only take the first instance of title/subtitle per language
+                    this.frontMatter[node.attrs.metadata][
+                        node.attrs.language || "default"
+                    ] = {
+                        type: node.attrs.language
+                            ? `trans_${node.attrs.metadata}`
+                            : node.attrs.metadata,
+                        attrs: {
+                            id: node.content[0].attrs.id,
+                            language: node.attrs.language
+                        },
+                        content: node.content[0].content
+                    }
+                    parentNode.content = parentNode.content.filter(
+                        child => child !== node
+                    )
+                }
+                break
+            case "richtext_part":
+                if (
+                    node.attrs.metadata === "abstract" &&
+                    !this.frontMatter.abstract[node.attrs.language || "default"]
+                ) {
+                    // We only take the first instance of abstract per language
+                    this.frontMatter.abstract[
+                        node.attrs.language || "default"
+                    ] = {
+                        type: node.attrs.language
+                            ? "trans_abstract"
+                            : "abstract",
+                        attrs: {
+                            id: node.attrs.id,
+                            language: node.attrs.language
+                        },
+                        content: node.content
+                    }
+                    parentNode.content = parentNode.content.filter(
+                        child => child !== node
+                    )
+                }
+                break
+            case "tags_part":
+                if (node.attrs.metadata === "keywords" && node.content) {
+                    this.frontMatter.keywords.push({
+                        type: "keywords",
+                        attrs: {
+                            language: node.attrs.language
+                        },
+                        content: node.content
+                    })
+                } else {
+                    this.frontMatter.tags.push(node)
+                }
+                parentNode.content = parentNode.content.filter(
+                    child => child !== node
+                )
+                break
+            case "contributors_part":
+                this.frontMatter.contributors.push(node)
+                parentNode.content = parentNode.content.filter(
+                    child => child !== node
+                )
+                break
+            default:
+                break
+        }
+        if (node.content) {
+            node.content.forEach(child => this.preWalkJson(child, node))
+        }
+    }
+
+    findAllCitations(docContent) {
+        // We need to look for citations in the same order they will be found in front + body
+        // to get the formatting right.
+        if (this.frontMatter.subtitle.default) {
+            this.findCitations(this.frontMatter.subtitle.default)
+        }
+        Object.keys(this.frontMatter.title)
+            .filter(language => language !== "default")
+            .forEach(language => {
+                this.findCitations(this.frontMatter.title[language])
+                if (this.frontMatter.subtitle[language]) {
+                    this.findCitations(this.frontMatter.subtitle[language])
+                }
+            })
+        if (this.frontMatter.abstract.default) {
+            this.findCitations(this.frontMatter.abstract.default)
+        }
+        Object.keys(this.frontMatter.abstract)
+            .filter(language => language !== "default")
+            .forEach(language => {
+                this.findCitations(this.frontMatter.abstract[language])
+            })
+        this.findCitations(docContent)
+    }
+
+    findCitations(node) {
+        switch (node.type) {
+            case "citation":
+                this.citInfos.push(JSON.parse(JSON.stringify(node.attrs)))
+                break
+            case "footnote":
+                node.attrs.footnote.forEach(child => this.findCitations(child))
+                break
+            default:
+                break
+        }
+        if (node.content) {
+            node.content.forEach(child => this.findCitations(child))
+        }
+    }
+
+    assembleArticleFront() {
+        let front = "<front>"
+        front +=
+            "<journal-meta><journal-id></journal-id><issn></issn></journal-meta>" // Required by DTD
+        front += "<article-meta>"
+        if (this.frontMatter.tags.length) {
+            front += `<article-categories>${this.frontMatter.tags.map(node => this.walkJson(node)).join("")}</article-categories>`
+        }
+        Object.keys(this.frontMatter.subtitle)
+            .filter(language => language !== "default")
+            .forEach(language => {
+                // Making sure there is a title for each subtitle
+                if (!this.frontMatter.title[language]) {
+                    this.frontMatter.title[language] = {
+                        type: "trans_title",
+                        attrs: {language}
+                    }
+                }
+            })
+        front += "<title-group>"
+        front += this.walkJson(this.frontMatter.title.default)
+        if (this.frontMatter.subtitle.default) {
+            front += this.walkJson(this.frontMatter.subtitle.default)
+        }
+        Object.keys(this.frontMatter.title)
+            .filter(language => language !== "default")
+            .forEach(language => {
+                front += `<trans-title-group @xml:lang="${language}">`
+                front += this.walkJson(this.frontMatter.title[language])
+                if (this.frontMatter.subtitle[language]) {
+                    front += this.walkJson(this.frontMatter.subtitle[language])
+                }
+                front += "</trans-title-group>"
+            })
+        front += "</title-group>"
+        this.frontMatter.contributors.forEach(contributors => {
+            front += this.walkJson(contributors)
+        })
+        Object.entries(this.affiliations).forEach(
+            ([institution, index]) =>
+                (front += `<aff id="aff${index}"><institution>${escapeText(institution)}</institution></aff>`)
+        )
+        // https://validator.jats4r.org/ requires a <permissions> element here, but is OK with it being empty.
+        if (this.frontMatter.copyright.holder) {
+            front += "<permissions>"
+            const year = this.frontMatter.copyright.year
+                ? this.frontMatter.copyright.year
+                : new Date().getFullYear()
+            front += `<copyright-year>${year}</copyright-year>`
+            front += `<copyright-holder>${escapeText(this.frontMatter.copyright.holder)}</copyright-holder>`
+            if (this.frontMatter.copyright.freeToRead) {
+                front += "<ali:free_to_read/>"
+            }
+            front += this.frontMatter.copyright.licenses
+                .map(
+                    license =>
+                        `<license><ali:license_ref${license.start ? ` start_date="${license.start}"` : ""}>${escapeText(license.url)}</ali:license_ref></license>`
+                )
+                .join("")
+            front += "</permissions>"
+        } else {
+            front += "<permissions/>"
+        }
+        if (this.frontMatter.abstract.default) {
+            front += this.walkJson(this.frontMatter.abstract.default)
+            front += this.closeSections(0)
+        }
+        Object.keys(this.frontMatter.abstract)
+            .filter(language => language !== "default")
+            .forEach(language => {
+                front += this.walkJson(this.frontMatter.abstract[language])
+                front += this.closeSections(0)
+            })
+        this.frontMatter.keywords.forEach(keywords => {
+            front += this.walkJson(keywords)
+        })
+        front += "</article-meta></front>"
+        return front
+    }
+
+    assembleBookPartFront() {
+        let front = "<front-matter><book-part-meta>"
+        if (this.frontMatter.tags.length) {
+            front += `<subj-group>${this.frontMatter.tags.map(node => this.walkJson(node)).join("")}</subj-group>`
+        }
+        Object.keys(this.frontMatter.subtitle)
+            .filter(language => language !== "default")
+            .forEach(language => {
+                // Making sure there is a title for each subtitle
+                if (!this.frontMatter.title[language]) {
+                    this.frontMatter.title[language] = {
+                        type: "trans_title",
+                        attrs: {language}
+                    }
+                }
+            })
+        front += "<title-group>"
+        front += this.walkJson(this.frontMatter.title.default)
+        if (this.frontMatter.subtitle.default) {
+            front += this.walkJson(this.frontMatter.subtitle.default)
+        }
+        Object.keys(this.frontMatter.title)
+            .filter(language => language !== "default")
+            .forEach(language => {
+                front += `<trans-title-group @xml:lang="${language}">`
+                front += this.walkJson(this.frontMatter.title[language])
+                if (this.frontMatter.subtitle[language]) {
+                    front += this.walkJson(this.frontMatter.subtitle[language])
+                }
+                front += "</trans-title-group>"
+            })
+        front += "</title-group>"
+        this.frontMatter.contributors.forEach(contributors => {
+            front += this.walkJson(contributors)
+        })
+        Object.entries(this.affiliations).forEach(
+            ([institution, index]) =>
+                (front += `<aff id="aff${index}"><institution>${escapeText(institution)}</institution></aff>`)
+        )
+        // https://validator.jats4r.org/ requires a <permissions> element here, but is OK with it being empty.
+        if (this.frontMatter.copyright.holder) {
+            front += "<permissions>"
+            const year = this.frontMatter.copyright.year
+                ? this.frontMatter.copyright.year
+                : new Date().getFullYear()
+            front += `<copyright-year>${year}</copyright-year>`
+            front += `<copyright-holder>${escapeText(this.frontMatter.copyright.holder)}</copyright-holder>`
+            if (this.frontMatter.copyright.freeToRead) {
+                front += "<ali:free_to_read/>"
+            }
+            front += this.frontMatter.copyright.licenses
+                .map(
+                    license =>
+                        `<license><ali:license_ref${license.start ? ` start_date="${license.start}"` : ""}>${escapeText(license.url)}</ali:license_ref></license>`
+                )
+                .join("")
+            front += "</permissions>"
+        } else {
+            front += "<permissions/>"
+        }
+        if (this.frontMatter.abstract.default) {
+            front += this.walkJson(this.frontMatter.abstract.default)
+            front += this.closeSections(0)
+        }
+        Object.keys(this.frontMatter.abstract)
+            .filter(language => language !== "default")
+            .forEach(language => {
+                front += this.walkJson(this.frontMatter.abstract[language])
+                front += this.closeSections(0)
+            })
+        this.frontMatter.keywords.forEach(keywords => {
+            front += this.walkJson(keywords)
+        })
+        front += "</book-part-meta></front-matter>"
+        return front
+    }
+
+    walkJson(node, options = {}) {
+        let start = "",
+            content = "",
+            end = ""
+        switch (node.type) {
+            case "doc":
+                break
+            case "title":
+                if (this.type === "article") {
+                    start += "<article-title>"
+                    end = "</article-title>" + end
+                } else {
+                    start += "<title>"
+                    end = "</title>" + end
+                }
+                options = Object.assign({}, options)
+                options.breakAllowed = true
+                break
+            case "trans_title":
+                start += "<trans-title>"
+                end = "</trans-title>" + end
+                options = Object.assign({}, options)
+                options.breakAllowed = true
+                break
+            case "subtitle":
+                if (node.content) {
+                    start += "<subtitle>"
+                    end = "</subtitle>" + end
+                    options = Object.assign({}, options)
+                    options.breakAllowed = true
+                }
+                break
+            case "trans_subtitle":
+                if (node.content) {
+                    start += "<trans-subtitle>"
+                    end = "</trans-subtitle>" + end
+                    options = Object.assign({}, options)
+                    options.breakAllowed = true
+                }
+                break
+            case "heading_part":
+                // Ignore - we deal with the heading inside
+                break
+            case "contributor":
+                // Ignore - we deal with contributors_part instead.
+                break
+            case "contributors_part":
+                if (node.content) {
+                    const contributorTypes = {
+                        authors: "author",
+                        editors: "editor",
+                        translators: "translator",
+                        reviewers: "reviewer",
+                        contributors: "contributor"
+                    }
+                    const contributorType =
+                        contributorTypes[node.attrs.metadata] || "other"
+                    start += `<contrib-group content-type="${contributorType}">`
+                    end = "</contrib-group>" + end
+                    const contributorTypeId = node.attrs.id
+                    let counter = 1
+                    node.content.forEach(childNode => {
+                        const contributor = childNode.attrs
+                        if (contributor.firstname || contributor.lastname) {
+                            content += `<contrib id="${contributorTypeId}-${counter++}" contrib-type="person">`
+                            content += "<name>"
+                            if (contributor.lastname) {
+                                content += `<surname>${escapeText(contributor.lastname)}</surname>`
+                            }
+                            if (contributor.firstname) {
+                                content += `<given-names>${escapeText(contributor.firstname)}</given-names>`
+                            }
+                            content += "</name>"
+                            if (contributor.institution) {
+                                let affNumber
+                                if (
+                                    this.affiliations[contributor.institution]
+                                ) {
+                                    affNumber =
+                                        this.affiliations[
+                                            contributor.institution
+                                        ]
+                                } else {
+                                    affNumber = ++this.affCounter
+                                    this.affiliations[contributor.institution] =
+                                        affNumber
+                                }
+                                content += `<xref ref-type="aff" rid="aff${affNumber}" />`
+                            }
+                            if (contributor.id_type && contributor.id_value) {
+                                const idType = escapeText(
+                                    contributor.id_type.toLowerCase()
+                                )
+                                content += `<contrib-id contrib-id-type="${idType}">${escapeText(contributor.id_value)}</contrib-id>`
+                            }
+                            content += "</contrib>"
+                        } else if (contributor.institution) {
+                            // There is an affiliation but no first/last name. We take this
+                            // as a group collaboration.
+                            content += `<contrib id="${contributorTypeId}-${counter++}" contrib-type="group">`
+                            content += `<collab><named-content content-type="name">${escapeText(contributor.institution)}</named-content></collab>`
+                            if (contributor.id_type && contributor.id_value) {
+                                const idType = escapeText(
+                                    contributor.id_type.toLowerCase()
+                                )
+                                content += `<contrib-id contrib-id-type="${idType}">${escapeText(contributor.id_value)}</contrib-id>`
+                            }
+                            content += "</contrib>"
+                        }
+                    })
+                }
+                break
+            case "tags_part":
+                if (node.content) {
+                    start += `<subj-group subj-group-type="${node.attrs.id}"${node.attrs.language ? ` xml:lang="${node.attrs.language}"` : ""}>`
+                    end = "</subj-group>" + end
+                }
+                break
+            case "keywords":
+                if (node.content) {
+                    start += `<kwd-group${node.attrs.language ? ` xml:lang="${node.attrs.language}"` : ""}>`
+                    end = "</kwd-group>" + end
+                    options = Object.assign({}, options)
+                    options.inKeywords = true
+                }
+                break
+            case "tag":
+                if (options.inKeywords) {
+                    content += `<kwd>${node.attrs.tag}</kwd>`
+                } else {
+                    content += `<subject>${node.attrs.tag}</subject>`
+                }
+                break
+            case "abstract":
+                if (node.content) {
+                    start += "<abstract>"
+                    end = "</abstract>" + end
+                }
+                break
+            case "trans_abstract":
+                if (node.content) {
+                    start += `<trans-abstract xml:lang="${node.attrs.language}">`
+                    end = "</trans-abstract>" + end
+                }
+                break
+            case "richtext_part":
+                if (node.attrs.metadata) {
+                    options = Object.assign({}, options)
+                    options.partMetadata = node.attrs.metadata
+                }
+                break
+            case "table_of_contents":
+                // TODO: Not sure what to use here.
+                break
+            case "separator_part":
+            case "table_part":
+                // part separators as in page breaks should usually already be handled
+                // by JATS renderer and table parts will simply show the table inside of them.
+                break
+            case "paragraph":
+                start += `<p id="p-${++this.parCounter}">`
+                end = "</p>" + end
+                break
+            case "heading1":
+            case "heading2":
+            case "heading3":
+            case "heading4":
+            case "heading5":
+            case "heading6": {
+                if (options.ignoreHeading) {
+                    break
+                } else if (options.inFootnote) {
+                    // only allows <p> block level elements https://jats.nlm.nih.gov/archiving/tag-library/1.2/element/fn.html
+                    start += `<p id="p-${++this.parCounter}">`
+                    end = "</p>" + end
+                    break
+                }
+                const metadata = options.partMetadata
+                if (metadata) {
+                    // the metadata should only be applied once within a part.
+                    delete options.partMetadata
+                }
+                const level = Number.parseInt(node.type.slice(-1))
+                if (this.currentSectionLevel > level - 1) {
+                    start += this.closeSections(level - 1)
+                }
+                while (this.currentSectionLevel < level) {
+                    this.currentSectionLevel++
+                    if (this.currentSectionLevel === level) {
+                        start += `<sec id="${node.attrs.id}"${metadata ? ` sec-type="${metadata}"` : ""}>`
+                    } else {
+                        start += `<sec id="h-${++this.headingCounter}">`
+                    }
+                }
+                start += "<title>"
+                end = "</title>" + end
+                options = Object.assign({}, options)
+                options.breakAllowed = true
+                break
+            }
+            case "code_block":
+                if (options.inFootnote) {
+                    // only allows <p> block level elements https://jats.nlm.nih.gov/archiving/tag-library/1.2/element/fn.html
+                    start += `<p id="p-${++this.parCounter}">`
+                    end = "</p>" + end
+                    break
+                }
+                start += "<code>"
+                end = "</code>" + end
+                break
+            case "blockquote":
+                start += "<disp-quote>"
+                end = "</disp-quote>" + end
+                break
+            case "ordered_list": {
+                if (options.inFootnote) {
+                    // only allows <p> block level elements https://jats.nlm.nih.gov/archiving/tag-library/1.2/element/fn.html
+                    break
+                }
+                const continuedListEndNumber = node.attrs.order - 1
+                let lastListIndex
+                // TODO: deal with lists that have an order number other than 1 that do not continue previous lists. Currently not possible in JATS
+                if (continuedListEndNumber) {
+                    lastListIndex = this.orderedListLengths.lastIndexOf(
+                        continuedListEndNumber
+                    )
+                    // const lastListReverseIndex = this.orderedListLengths.slice().reverse().findIndex(length => length === continuedListEndNumber)
+                    // if (lastListReverseIndex !== undefined) {
+                    //     lastListIndex = this.orderedListLengths.length-lastListReverseIndex
+                    // }
+                }
+                if (lastListIndex > -1) {
+                    start += `<list list-type="order" id="list-${++this.listCounter}" continued-from="list-${lastListIndex}">`
+                } else {
+                    start += `<list list-type="order" id="list-${++this.listCounter}">`
+                }
+                options = Object.assign({}, options)
+                options.inOrderedList = this.listCounter
+                this.orderedListLengths[options.inOrderedList] =
+                    continuedListEndNumber
+                end = "</list>" + end
+                break
+            }
+            case "bullet_list":
+                if (options.inFootnote) {
+                    // only allows <p> block level elements https://jats.nlm.nih.gov/archiving/tag-library/1.2/element/fn.html
+                    break
+                }
+                start += `<list list-type="bullet" id="list-${++this.listCounter}">`
+                end = "</list>" + end
+                options = Object.assign({}, options)
+                delete options.inOrderedList
+                break
+            case "list_item":
+                if (options.inFootnote) {
+                    // only allows <p> block level elements https://jats.nlm.nih.gov/archiving/tag-library/1.2/element/fn.html
+                    break
+                }
+                if (options.inOrderedList !== undefined) {
+                    this.orderedListLengths[options.inOrderedList] += 1
+                }
+                start += "<list-item>"
+                end = "</list-item>" + end
+                break
+            case "footnote":
+                content += `<xref ref-type="fn" rid="fn-${++this.fnCounter}">${this.fnCounter}</xref>`
+                options = Object.assign({}, options)
+                options.inFootnote = true
+                this.footnotes.push(
+                    this.walkJson(
+                        {
+                            type: "footnotecontainer",
+                            attrs: {
+                                id: `fn-${this.fnCounter}`,
+                                label: this.fnCounter // Note: it's unclear whether the footnote number is required as a label
+                            },
+                            content: node.attrs.footnote
+                        },
+                        options
+                    )
+                )
+                break
+            case "footnotecontainer":
+                start += `<fn id="${node.attrs.id}"><label>${node.attrs.label}</label>`
+                end = "</fn>" + end
+                break
+            case "text": {
+                content += convertText(node)
+                break
+            }
+            case "cross_reference": {
+                start += `<xref rid="${node.attrs.id}">`
+                content += escapeText(node.attrs.title || "MISSING TARGET")
+                end = "</xref>" + end
+                break
+            }
+            case "citation": {
+                const citationText =
+                    this.citations.citationTexts[this.citationCount++]
+                if (
+                    options.inFootnote ||
+                    this.citations.citFm.citationType !== "note"
+                ) {
+                    content += citationText
+                } else {
+                    content += `<xref ref-type="fn" rid="fn-${++this.fnCounter}">${this.fnCounter}</xref>`
+                    this.footnotes.push(
+                        `<fn id="fn-${this.fnCounter}"><label>${this.fnCounter}</label><p id="p-${++this.parCounter}">${citationText}</p></fn>`
+                    )
+                }
+                break
+            }
+            case "figure": {
+                // Note: width and alignment are not stored due to lack of corresponding attributes in JATS.
+                if (options.inFootnote) {
+                    // only allows <p> block level elements https://jats.nlm.nih.gov/archiving/tag-library/1.2/element/fn.html
+                    break
+                }
+                let imageFilename, copyright
+                const image =
+                    node.content.find(node => node.type === "image")?.attrs
+                        .image || false
+                if (image !== false) {
+                    this.imageIds.push(image)
+                    const imageDBEntry = this.imageDB.db[image],
+                        filePathName = imageDBEntry.image
+                    copyright = imageDBEntry.copyright
+                    imageFilename = filePathName.split("/").pop()
+                }
+                const caption = node.attrs.caption
+                    ? node.content.find(node => node.type === "figure_caption")
+                          ?.content || []
+                    : []
+                if (
+                    node.attrs.category === "none" &&
+                    imageFilename &&
+                    !caption.length &&
+                    (!copyright || !copyright.holder)
+                ) {
+                    content += `<graphic id="${node.attrs.id}" position="anchor" xlink:href="${imageFilename}">`
+                    content += `<alt-text>${escapeText(caption.map(node => node.text || "").join("") || imageFilename)}</alt-text>`
+                    content += "</graphic>"
+                } else {
+                    start += `<fig id="${node.attrs.id}">`
+                    end = "</fig>" + end
+
+                    const category = node.attrs.category
+                    if (category !== "none") {
+                        if (!this.categoryCounter[category]) {
+                            this.categoryCounter[category] = 0
+                        }
+                        const catCount = ++this.categoryCounter[category]
+                        const catLabel = `${CATS[category][this.doc.settings.language]} ${catCount}`
+                        start += `<label>${escapeText(catLabel)}</label>`
+                    }
+                    if (caption.length) {
+                        start += `<caption><p>${caption.map(node => this.walkJson(node)).join("")}</p></caption>`
+                    }
+                    const equation = node.content.find(
+                        node => node.type === "figure_equation"
+                    )?.attrs.equation
+                    if (equation) {
+                        start += "<disp-formula>"
+                        end = "</disp-formula>" + end
+                        const equationML = convertLatexToMathMl(equation)
+                        content = `
+                            <alternatives>
+                                <tex-math><![CDATA[${equation}]]></tex-math>
+                                <mml:math>${equationML}</mml:math>
+                            </alternatives>
+                        `
+                    } else {
+                        if (copyright?.holder) {
+                            start += "<permissions>"
+                            const year = copyright.year
+                                ? copyright.year
+                                : new Date().getFullYear()
+                            start += `<copyright-year>${year}</copyright-year>`
+                            start += `<copyright-holder>${escapeText(copyright.holder)}</copyright-holder>`
+                            if (copyright.freeToRead) {
+                                start += "<ali:free_to_read/>"
+                            }
+                            start += copyright.licenses
+                                .map(
+                                    license =>
+                                        `<license><ali:license_ref${license.start ? ` start_date="${license.start}"` : ""}>${escapeText(license.url)}</ali:license_ref></license>`
+                                )
+                                .join("")
+                            start += "</permissions>"
+                        }
+                        if (imageFilename) {
+                            content += `<graphic position="anchor" xlink:href="${imageFilename}">`
+                            content += `<alt-text>${escapeText(caption.map(node => node.text || "").join("") || imageFilename)}</alt-text>`
+                            content += "</graphic>"
+                        }
+                    }
+                }
+                break
+            }
+            case "figure_caption":
+                // We are already dealing with this in the figure. Prevent content from being added a second time.
+                return ""
+            case "figure_equation":
+                // We are already dealing with this in the figure.
+                break
+            case "image":
+                // We are already dealing with this in the figure.
+                break
+            case "table": {
+                // Note: We ignore right/left/center aligned and table layout
+                if (options.inFootnote) {
+                    // only allows <p> block level elements https://jats.nlm.nih.gov/archiving/tag-library/1.2/element/fn.html
+                    break
+                }
+                start += `<table-wrap id="${node.attrs.id}">`
+                end = "</table-wrap>" + end
+                const category = node.attrs.category
+                if (category !== "none") {
+                    if (!this.categoryCounter[category]) {
+                        this.categoryCounter[category] = 0
+                    }
+                    const catCount = ++this.categoryCounter[category]
+                    const catLabel = `${CATS[category][this.doc.settings.language]} ${catCount}`
+                    start += `<label>${escapeText(catLabel)}</label>`
+                }
+                const caption = node.attrs.caption
+                    ? node.content[0].content || []
+                    : []
+                if (caption.length) {
+                    start += `<caption><p>${caption.map(node => this.walkJson(node)).join("")}</p></caption>`
+                }
+                start += `<table width="${node.attrs.width}%"><tbody>`
+                end = "</tbody></table>" + end
+                break
+            }
+            case "table_body":
+                // Pass through to table.
+                break
+            case "table_caption":
+                // We already deal with this in 'table'.
+                return ""
+            case "table_row":
+                start += "<tr>"
+                end = "</tr>" + end
+                break
+            case "table_cell":
+                start += `<td${node.attrs.colspan === 1 ? "" : ` colspan="${node.attrs.colspan}"`}${node.attrs.rowspan === 1 ? "" : ` rowspan="${node.attrs.rowspan}"`}>`
+                end = "</td>" + end
+                break
+            case "table_header":
+                start += `<th${node.attrs.colspan === 1 ? "" : ` colspan="${node.attrs.colspan}"`}${node.attrs.rowspan === 1 ? "" : ` rowspan="${node.attrs.rowspan}"`}>`
+                end = "</th>" + end
+                break
+            case "equation": {
+                start += "<inline-formula>"
+                end = "</inline-formula>" + end
+                const equationML = convertLatexToMathMl(node.attrs.equation)
+                content = `
+                    <alternatives>
+                        <tex-math><![CDATA[${node.attrs.equation}]]></tex-math>
+                        <mml:math>${equationML}</mml:math>
+                    </alternatives>
+                `
+                break
+            }
+            case "hard_break":
+                // Forbidden inside of most elements. We only render it if explicitly allowed.
+                // https://jats.nlm.nih.gov/publishing/tag-library/1.3/element/break.html
+                if (options.breakAllowed) {
+                    content += "<break />"
+                } else {
+                    content += " "
+                }
+                break
+            default:
+                break
+        }
+
+        if (!content.length && node.content) {
+            node.content.forEach(child => {
+                content += this.walkJson(child, options)
+            })
+        }
+
+        return start + content + end
+    }
+
+    closeSections(targetLevel) {
+        let returnValue = ""
+        while (this.currentSectionLevel > targetLevel) {
+            returnValue += "</sec>"
+            this.currentSectionLevel--
+        }
+
+        return returnValue
+    }
+
+    assembleBody(docContent) {
+        return `<body id="body">${this.walkJson(docContent) + this.closeSections(0)}</body>`
+    }
+
+    assembleBack() {
+        let back = "<back>"
+        if (this.footnotes.length) {
+            back += `<fn-group>${this.footnotes.join("")}</fn-group>`
+        }
+        if (this.citations.jatsBib.length) {
+            back += `<ref-list>${this.citations.jatsBib}</ref-list>`
+        }
+        back += "</back>"
+        return back
+    }
+}