@fiduswriter/document 0.1.0-alpha.3 → 0.1.0-alpha.5

package/dist/exporter/jats/convert.js

@@ -0,0 +1,816 @@
+import { convertLatexToMathMl } from "mathlive";
+import { escapeText } from "fwtoolkit";
+import { getCat } from "../../schema/i18n.js";
+import { removeHidden } from "../tools/doc_content.js";
+import { JATSExporterCitations } from "./citations.js";
+import { convertText } from "./text.js";
+export class JATSExporterConverter {
+    type;
+    doc;
+    csl;
+    imageDB;
+    bibDB;
+    imageIds;
+    categoryCounter;
+    affiliations;
+    affCounter;
+    parCounter;
+    headingCounter;
+    currentSectionLevel;
+    listCounter;
+    orderedListLengths;
+    footnotes;
+    fnCounter;
+    frontMatter;
+    citInfos;
+    citationCount;
+    citations;
+    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-${++this.parCounter}">`;
+                    end = "</p>" + end;
+                    break;
+                }
+                start += "<code>";
+                end = "</code>" + end;
+                break;
+            case "blockquote":
+                start += "<disp-quote>";
+                end = "</disp-quote>" + end;
+                break;
+            case "ordered_list": {
+                if (options.inFootnote) {
+                    // only allows <p> block level elements https://jats.nlm.nih.gov/archiving/tag-library/1.2/element/fn.html
+                    break;
+                }
+                const continuedListEndNumber = node.attrs.order - 1;
+                let lastListIndex;
+                // TODO: deal with lists that have an order number other than 1 that do not continue previous lists. Currently not possible in JATS
+                if (continuedListEndNumber) {
+                    lastListIndex = this.orderedListLengths.lastIndexOf(continuedListEndNumber);
+                }
+                if (lastListIndex !== undefined && lastListIndex > -1) {
+                    start += `<list list-type="order" id="list-${++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}">${citationText}</p></fn>`);
+                }
+                break;
+            }
+            case "figure": {
+                // Note: width and alignment are not stored due to lack of corresponding attributes in JATS.
+                if (options.inFootnote) {
+                    // only allows <p> block level elements https://jats.nlm.nih.gov/archiving/tag-library/1.2/element/fn.html
+                    break;
+                }
+                let imageFilename, copyright;
+                const image = node.content.find((node) => node.type === "image")?.attrs
+                    .image || false;
+                if (image !== false) {
+                    this.imageIds.push(image);
+                    const imageDBEntry = this.imageDB.db[image], filePathName = imageDBEntry.image;
+                    copyright = imageDBEntry.copyright;
+                    imageFilename = filePathName.toString().split("/").pop();
+                }
+                const caption = node.attrs.caption
+                    ? node.content.find((node) => node.type === "figure_caption")
+                        ?.content || []
+                    : [];
+                if (node.attrs.category === "none" &&
+                    imageFilename &&
+                    !caption.length &&
+                    (!copyright || !copyright.holder)) {
+                    content += `<graphic id="${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="${node.attrs.id}">`;
+                    end = "</fig>" + end;
+                    const category = node.attrs.category;
+                    if (category !== "none") {
+                        if (!this.categoryCounter[category]) {
+                            this.categoryCounter[category] = 0;
+                        }
+                        const catCount = ++this.categoryCounter[category];
+                        const catLabel = `${getCat(category, this.doc.settings.language || "en-US")} ${catCount}`;
+                        start += `<label>${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="${node.attrs.id}">`;
+                end = "</table-wrap>" + end;
+                const category = node.attrs.category;
+                if (category !== "none") {
+                    if (!this.categoryCounter[category]) {
+                        this.categoryCounter[category] = 0;
+                    }
+                    const catCount = ++this.categoryCounter[category];
+                    const catLabel = `${getCat(category, this.doc.settings.language || "en-US")} ${catCount}`;
+                    start += `<label>${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;
+    }
+}
+//# sourceMappingURL=convert.js.map