@manuscripts/transform 4.5.1 → 4.5.3

package/dist/cjs/jats/exporter/jats-exporter.js

@@ -59,7 +59,7 @@ const w3c_xmlserializer_1 = __importDefault(require("w3c-xmlserializer"));
 const citeproc_1 = require("../../lib/citeproc");
 const credit_roles_1 = require("../../lib/credit-roles");
 const footnotes_1 = require("../../lib/footnotes");
-const html_1 = require("../../lib/html");
+const section_categories_1 = require("../../lib/section-categories");
 const xml_1 = require("../../lib/xml");
 const schema_1 = require("../../schema");
 const transformer_1 = require("../../transformer");
@@ -67,20 +67,6 @@ const citeproc_2 = require("./citeproc");
 const jats_versions_1 = require("./jats-versions");
 const labels_1 = require("./labels");
 const normalizeID = (id) => id.replace(/:/g, '_');
-const parser = prosemirror_model_1.DOMParser.fromSchema(schema_1.schema);
-const insertAbstractNode = (front, abstractNode) => {
-    const articleMeta = front.querySelector(':scope > article-meta');
-    if (!articleMeta) {
-        return;
-    }
-    const insertBeforeElement = articleMeta.querySelector('kwd-group, funding-group, support-group, conference, counts, custom-meta-group');
-    if (insertBeforeElement) {
-        articleMeta.insertBefore(abstractNode, insertBeforeElement);
-    }
-    else {
-        articleMeta.appendChild(abstractNode);
-    }
-};
 const createCounter = () => {
     const counts = new Map();
     return {
@@ -93,7 +79,7 @@ const createCounter = () => {
     };
 };
 exports.createCounter = createCounter;
-const createDefaultIdGenerator = () => {
+const createDefaultIDGenerator = () => {
     const counter = (0, exports.createCounter)();
     return async (element) => {
         const value = String(counter.increment(element.nodeName));
@@ -111,6 +97,7 @@ const chooseRefType = (type) => {
         case schema_1.schema.nodes.table_element:
             return 'table';
         case schema_1.schema.nodes.section:
+        case schema_1.schema.nodes.abstract:
             return 'sec';
         case schema_1.schema.nodes.equation:
         case schema_1.schema.nodes.equation_element:
@@ -119,10 +106,10 @@ const chooseRefType = (type) => {
             return 'supplementary-material';
     }
 };
-const sortContributors = (a, b) => Number(a.attrs.priority) - Number(b.attrs.priority);
 class JATSExporter {
     constructor() {
         this.nodesMap = new Map();
+        this.contributorLabels = new Map();
         this.populateNodesMap = () => {
             this.manuscriptNode.descendants((node) => {
                 const type = node.type;
@@ -136,53 +123,53 @@ class JATSExporter {
             this.populateNodesMap();
             this.initCiteprocEngine(options);
             this.createSerializer();
-            const versionIds = (0, jats_versions_1.selectVersionIds)(options.version ?? '1.2');
-            this.document = document.implementation.createDocument(null, 'article', document.implementation.createDocumentType('article', versionIds.publicId, versionIds.systemId));
-            const article = this.document.documentElement;
-            article.setAttributeNS('http://www.w3.org/2000/xmlns/', 'xmlns:xlink', xml_1.XLINK_NAMESPACE);
-            const front = this.buildFront();
-            article.appendChild(front);
-            article.setAttribute('article-type', manuscriptNode.attrs.articleType || 'other');
-            article.setAttributeNS(xml_1.XML_NAMESPACE, 'lang', manuscriptNode.attrs.primaryLanguageCode || 'en');
+            const versionIDs = (0, jats_versions_1.selectVersionIDs)(options.version ?? '1.2');
+            this.document = document.implementation.createDocument(null, 'article', document.implementation.createDocumentType('article', versionIDs.publicID, versionIDs.systemID));
+            const $article = this.document.documentElement;
+            $article.setAttributeNS('http://www.w3.org/2000/xmlns/', 'xmlns:xlink', xml_1.XLINK_NAMESPACE);
             this.labelTargets = (0, labels_1.buildTargets)(manuscriptNode.descendants.bind(manuscriptNode));
             this.footnoteLabels = (0, footnotes_1.generateFootnoteLabels)(manuscriptNode);
-            const body = this.buildBody();
-            article.appendChild(body);
-            this.addParagraphsToSections(article);
-            const back = this.buildBack(body);
-            this.moveCoiStatementToAuthorNotes(back, front);
-            article.appendChild(back);
-            this.unwrapBody(body);
-            this.moveAbstracts(front, body);
-            this.removeBackContainer(body);
-            this.updateFootnoteTypes(front, back);
-            this.fillEmptyTableFooters(article);
-            this.fillEmptyFootnotes(article);
-            this.fillEmptyListItem(article);
-            this.moveAwards(front, body);
-            this.moveFloatsGroup(article);
+            const $body = this.buildBody();
+            const $back = this.buildBack();
+            this.routeBackmatterSections($body, $back);
+            const $coiStatement = this.extractCoiStatement($back);
+            $back.appendChild(this.buildRefList());
+            const $front = this.buildFront($coiStatement);
+            $article.appendChild($front);
+            $article.setAttribute('article-type', manuscriptNode.attrs.articleType || 'other');
+            $article.setAttributeNS(xml_1.XML_NAMESPACE, 'lang', manuscriptNode.attrs.primaryLanguageCode || 'en');
+            $article.appendChild($body);
+            $article.appendChild($back);
+            this.addParagraphsToSections($article);
+            this.fillEmptyTableFooters($article);
+            this.fillEmptyFootnotes($article);
+            this.fillEmptyListItem($article);
+            const $floatsGroup = this.buildFloatsGroup();
+            if ($floatsGroup) {
+                $article.appendChild($floatsGroup);
+            }
             await this.rewriteIDs();
             return (0, w3c_xmlserializer_1.default)(this.document);
         };
-        this.appendChildNodeOfType = (element, node, type) => {
+        this.appendChildNodeOfType = ($element, node, type) => {
             const childNode = this.getFirstChildOfType(type, node);
             if (childNode) {
-                element.appendChild(this.serializeNode(childNode));
+                $element.appendChild(this.serializeNode(childNode));
             }
         };
-        this.appendChildrenNodeOfType = (element, node, type) => {
+        this.appendChildrenNodeOfType = ($element, node, type) => {
             const children = this.getChildrenOfType(type, node);
-            children.map((childNode) => element.appendChild(this.serializeNode(childNode)));
+            children.map((childNode) => $element.appendChild(this.serializeNode(childNode)));
         };
-        this.appendCaption = (element, node) => {
-            const caption = this.createElement('caption');
-            this.appendChildNodeOfType(caption, node, schema_1.schema.nodes.caption_title);
+        this.appendCaption = ($element, node) => {
+            const $caption = this.createElement('caption');
+            this.appendChildNodeOfType($caption, node, schema_1.schema.nodes.caption_title);
             const captionNode = this.getChildrenOfType(schema_1.schema.nodes.caption, node)[0];
             if (captionNode && captionNode.content.size > 2) {
-                this.appendChildrenNodeOfType(caption, captionNode, schema_1.schema.nodes.text_block);
+                this.appendChildrenNodeOfType($caption, captionNode, schema_1.schema.nodes.text_block);
             }
-            if (caption.children.length > 0) {
-                element.appendChild(caption);
+            if ($caption.children.length > 0) {
+                $element.appendChild($caption);
             }
         };
         this.initCiteprocEngine = (options) => {
@@ -217,33 +204,32 @@ class JATSExporter {
             this.engine = engine;
             this.renderedCitations = new Map(output.map((i) => [i[0], i[2]]));
         };
-        this.nodeFromJATS = (JATSFragment) => {
-            JATSFragment = JATSFragment.trim();
-            JATSFragment = JATSFragment.replace(' ', ' ');
-            if (!JATSFragment.length) {
+        this.nodeFromJATS = (fragment) => {
+            fragment = fragment.trim().replace(' ', ' ');
+            if (!fragment.length) {
                 return null;
             }
-            const template = this.createElement('template');
-            template.innerHTML = JATSFragment;
-            return template.firstChild;
+            const $template = this.createElement('template');
+            $template.innerHTML = fragment;
+            return $template.firstChild;
         };
-        this.rewriteIDs = async (generator = createDefaultIdGenerator()) => {
+        this.rewriteIDs = async (generator = createDefaultIDGenerator()) => {
             const ids = new Map();
-            for (const element of this.document.querySelectorAll('[id]')) {
-                const oldID = element.getAttribute('id');
-                const newID = await generator(element);
+            for (const $element of this.document.querySelectorAll('[id]')) {
+                const oldID = $element.getAttribute('id');
+                const newID = await generator($element);
                 if (newID) {
-                    element.setAttribute('id', newID);
+                    $element.setAttribute('id', newID);
                 }
                 else {
-                    element.removeAttribute('id');
+                    $element.removeAttribute('id');
                 }
                 if (oldID) {
                     ids.set(oldID, newID);
                 }
             }
-            for (const node of this.document.querySelectorAll('[rid]')) {
-                const rids = node.getAttribute('rid');
+            for (const $node of this.document.querySelectorAll('[rid]')) {
+                const rids = $node.getAttribute('rid');
                 if (rids) {
                     const newRids = rids
                         .split(/\s+/)
@@ -251,126 +237,113 @@ class JATSExporter {
                         .map((rid) => ids.get(rid))
                         .filter(Boolean);
                     if (newRids.length) {
-                        node.setAttribute('rid', newRids.join(' '));
+                        $node.setAttribute('rid', newRids.join(' '));
                     }
                 }
             }
         };
-        this.setTitleContent = (element, title) => {
-            const htmlTitleNode = (0, html_1.nodeFromHTML)(`<h1>${title}</h1>`);
-            if (htmlTitleNode) {
-                const titleNode = parser.parse(htmlTitleNode, {
-                    topNode: schema_1.schema.nodes.section_title.create(),
-                });
-                const jatsTitleNode = this.serializeNode(titleNode);
-                while (jatsTitleNode.firstChild) {
-                    element.appendChild(jatsTitleNode.firstChild);
-                }
+        this.buildFront = ($coiStatement) => {
+            const $front = this.createElement('front');
+            const $articleMeta = this.createElement('article-meta');
+            $front.appendChild($articleMeta);
+            const contributors = this.getChildrenOfType(schema_1.schema.nodes.contributor).sort((a, b) => Number(a.attrs.priority) - Number(b.attrs.priority));
+            this.contributorLabels = this.computeContributorLabels(contributors);
+            const $frontNodes = [
+                this.buildArticleID(),
+                this.buildTitleGroup(),
+                this.buildContributorGroup(contributors),
+                this.buildAuthorNotes($coiStatement),
+                this.buildSupplements(),
+                this.buildHistory(),
+                this.buildSelfUris(),
+                this.buildAbstracts(),
+                this.buildKeywords(),
+                this.buildAwards(),
+                this.buildCounts(),
+            ];
+            $frontNodes.forEach(($nodes) => this.appendChildren($articleMeta, $nodes));
+            return $front;
+        };
+        this.appendChildren = ($parent, $elements) => {
+            if (!$elements) {
+                return;
             }
+            const list = Array.isArray($elements) ? $elements : [$elements];
+            list.forEach(($element) => $parent.appendChild($element));
         };
-        this.buildFront = () => {
-            const front = this.createElement('front');
-            const articleMeta = this.createElement('article-meta');
-            front.appendChild(articleMeta);
+        this.buildArticleID = () => {
             if (this.manuscriptNode.attrs.doi) {
-                const articleID = this.createElement('article-id');
-                articleID.setAttribute('pub-id-type', 'doi');
-                articleID.textContent = this.manuscriptNode.attrs.doi;
-                articleMeta.appendChild(articleID);
+                const $articleID = this.createElement('article-id');
+                $articleID.setAttribute('pub-id-type', 'doi');
+                $articleID.textContent = this.manuscriptNode.attrs.doi;
+                return $articleID;
             }
-            const titleGroup = this.createElement('title-group');
+        };
+        this.buildTitleGroup = () => {
+            const $titleGroup = this.createElement('title-group');
             const titleNode = this.getFirstChildOfType(schema_1.schema.nodes.title);
             if (titleNode) {
-                const element = this.createElement('article-title');
-                this.setTitleContent(element, titleNode.textContent);
-                titleGroup.appendChild(element);
+                $titleGroup.appendChild(this.serializeNode(titleNode));
             }
-            const subtitlesNodes = this.getChildrenOfType(schema_1.schema.nodes.subtitle);
-            subtitlesNodes.forEach((subtitleNode) => {
-                const element = this.createElement('subtitle');
-                this.setTitleContent(element, subtitleNode.textContent);
-                titleGroup.appendChild(element);
-            });
-            const altTitlesNodes = this.getChildrenOfType(schema_1.schema.nodes.alt_title);
-            altTitlesNodes.forEach((titleNode) => {
-                const element = this.createElement('alt-title');
-                element.setAttribute('alt-title-type', titleNode.attrs.type);
-                this.setTitleContent(element, titleNode.textContent);
-                titleGroup.appendChild(element);
-            });
-            articleMeta.appendChild(titleGroup);
-            this.buildContributors(articleMeta);
-            const supplementsNodes = this.getChildrenOfType(schema_1.schema.nodes.supplement);
-            supplementsNodes.forEach((node) => {
-                const supplementaryMaterial = this.createElement('supplementary-material');
-                supplementaryMaterial.setAttribute('id', normalizeID(node.attrs.id));
-                supplementaryMaterial.setAttributeNS(xml_1.XLINK_NAMESPACE, 'href', node.attrs.href ?? '');
-                supplementaryMaterial.setAttribute('mimetype', node.attrs.mimeType ?? '');
-                supplementaryMaterial.setAttribute('mime-subtype', node.attrs.mimeSubType ?? '');
-                this.appendCaption(supplementaryMaterial, node);
-                articleMeta.append(supplementaryMaterial);
+            this.getChildrenOfType(schema_1.schema.nodes.subtitle).forEach((node) => $titleGroup.appendChild(this.serializeNode(node)));
+            this.getChildrenOfType(schema_1.schema.nodes.alt_title).forEach((node) => $titleGroup.appendChild(this.serializeNode(node)));
+            return $titleGroup;
+        };
+        this.buildSupplements = () => this.getChildrenOfType(schema_1.schema.nodes.supplement).map((node) => this.serializeNode(node));
+        this.buildHistory = () => {
+            const $history = this.createElement('history');
+            const dates = new Map([
+                ['accepted', this.manuscriptNode.attrs.acceptanceDate],
+                ['corrected', this.manuscriptNode.attrs.correctionDate],
+                ['retracted', this.manuscriptNode.attrs.retractionDate],
+                ['received', this.manuscriptNode.attrs.receiveDate],
+                ['rev-recd', this.manuscriptNode.attrs.revisionReceiveDate],
+                ['rev-request', this.manuscriptNode.attrs.revisionRequestDate],
+            ]);
+            dates.forEach((val, key) => {
+                if (val) {
+                    $history.appendChild(this.buildDateElement(val, key));
+                }
             });
-            const history = articleMeta.querySelector('history') || this.createElement('history');
-            if (this.manuscriptNode.attrs.acceptanceDate) {
-                const date = this.buildDateElement(this.manuscriptNode.attrs.acceptanceDate, 'accepted');
-                history.appendChild(date);
-            }
-            if (this.manuscriptNode.attrs.correctionDate) {
-                const date = this.buildDateElement(this.manuscriptNode.attrs.correctionDate, 'corrected');
-                history.appendChild(date);
+            if ($history.childElementCount) {
+                return $history;
             }
-            if (this.manuscriptNode.attrs.retractionDate) {
-                const date = this.buildDateElement(this.manuscriptNode.attrs.retractionDate, 'retracted');
-                history.appendChild(date);
-            }
-            if (this.manuscriptNode.attrs.receiveDate) {
-                const date = this.buildDateElement(this.manuscriptNode.attrs.receiveDate, 'received');
-                history.appendChild(date);
-            }
-            if (this.manuscriptNode.attrs.revisionReceiveDate) {
-                const date = this.buildDateElement(this.manuscriptNode.attrs.revisionReceiveDate, 'rev-recd');
-                history.appendChild(date);
-            }
-            if (this.manuscriptNode.attrs.revisionRequestDate) {
-                const date = this.buildDateElement(this.manuscriptNode.attrs.revisionRequestDate, 'rev-request');
-                history.appendChild(date);
-            }
-            if (history.childElementCount) {
-                articleMeta.appendChild(history);
+        };
+        this.buildCounts = () => {
+            const $counts = this.createElement('counts');
+            const counts = new Map([
+                ['fig-count', this.getChildrenOfType(schema_1.schema.nodes.figure).length],
+                ['table-count', this.getChildrenOfType(schema_1.schema.nodes.table).length],
+                [
+                    'equation-count',
+                    this.getChildrenOfType(schema_1.schema.nodes.equation_element).length,
+                ],
+                [
+                    'ref-count',
+                    this.getChildrenOfType(schema_1.schema.nodes.bibliography_item).length,
+                ],
+                ['word-count', this.manuscriptNode.textContent.split(/\s+/).length],
+            ]);
+            counts.forEach((val, key) => {
+                if (val) {
+                    $counts.appendChild(this.createElement(key, undefined, { count: String(val) }));
+                }
+            });
+            if ($counts.childElementCount) {
+                return $counts;
             }
-            this.buildKeywords(articleMeta);
-            let countingElements = [];
-            const figureCount = this.getChildrenOfType(schema_1.schema.nodes.figure).length;
-            countingElements.push(this.buildCountingElement('fig-count', figureCount));
-            const tableCount = this.getChildrenOfType(schema_1.schema.nodes.table).length;
-            countingElements.push(this.buildCountingElement('table-count', tableCount));
-            const equationCount = this.getChildrenOfType(schema_1.schema.nodes.equation_element).length;
-            countingElements.push(this.buildCountingElement('equation-count', equationCount));
-            const referencesCount = this.getChildrenOfType(schema_1.schema.nodes.bibliography_item).length;
-            countingElements.push(this.buildCountingElement('ref-count', referencesCount));
-            const wordCount = this.manuscriptNode.textContent.split(/\s+/).length;
-            countingElements.push(this.buildCountingElement('word-count', wordCount));
-            countingElements = countingElements.filter((el) => el);
-            if (countingElements.length > 0) {
-                const counts = this.createElement('counts');
-                counts.append(...countingElements);
-                articleMeta.append(counts);
+        };
+        this.buildAwards = () => {
+            const awards = this.getFirstChildOfType(schema_1.schema.nodes.awards);
+            if (!awards || !awards.childCount) {
+                return;
             }
-            const attachments = this.getChildrenOfType(schema_1.schema.nodes.attachment);
-            attachments.forEach((attachment) => {
-                const $selfUri = this.createElement('self-uri');
-                $selfUri.setAttribute('content-type', attachment.attrs.type);
-                $selfUri.setAttributeNS(xml_1.XLINK_NAMESPACE, 'href', attachment.attrs.href);
-                const insertBeforeElements = articleMeta.querySelector('related-article, related-object, abstract, trans-abstract, kwd-group, funding-group, support-group, conference, counts, custom-meta-group');
-                insertBeforeElements
-                    ? articleMeta.insertBefore($selfUri, insertBeforeElements)
-                    : articleMeta.appendChild($selfUri);
-            });
-            return front;
+            return this.serializeNode(awards);
         };
+        this.buildSelfUris = () => this.getChildrenOfType(schema_1.schema.nodes.attachment).map((attachment) => this.serializeNode(attachment));
         this.buildDateElement = (timestamp, type) => {
-            const dateElement = this.createElement('date');
-            dateElement.setAttribute('date-type', type);
+            const $date = this.createElement('date');
+            $date.setAttribute('date-type', type);
             const date = new Date(timestamp * 1000);
             const lookup = {
                 year: date.getUTCFullYear().toString(),
@@ -378,127 +351,154 @@ class JATSExporter {
                 day: date.getUTCDate().toString().padStart(2, '0'),
             };
             for (const [key, value] of Object.entries(lookup).reverse()) {
-                const el = this.createElement(key);
-                el.textContent = value;
-                dateElement.appendChild(el);
-            }
-            return dateElement;
-        };
-        this.buildCountingElement = (tagName, count) => {
-            if (count) {
-                const wordCount = this.createElement(tagName);
-                wordCount.setAttribute('count', String(count));
-                return wordCount;
+                const $datePart = this.createElement(key, value);
+                $date.appendChild($datePart);
             }
+            return $date;
         };
         this.buildBody = () => {
-            const body = this.createElement('body');
-            this.manuscriptNode.forEach((cFragment) => {
-                const serializedNode = this.serializeNode(cFragment);
-                body.append(...serializedNode.childNodes);
+            const body = this.getFirstChildOfType(schema_1.schema.nodes.body);
+            const $body = this.createElement('body');
+            body?.forEach((node) => {
+                $body.appendChild(this.serializeNode(node));
             });
-            this.fixBody(body);
-            return body;
+            return $body;
         };
-        this.buildBack = (body) => {
-            const back = this.createElement('back');
-            this.moveSectionsToBack(back, body);
-            const footnotesElements = this.document.querySelectorAll('sec > fn-group');
-            for (const footnotesElement of footnotesElements) {
-                const previousParent = footnotesElement.parentElement;
-                back.appendChild(footnotesElement);
-                if (previousParent) {
-                    const title = previousParent.querySelector('title');
-                    if (title) {
-                        footnotesElement.insertBefore(title, footnotesElement.firstElementChild);
-                    }
-                    if (!previousParent.childElementCount) {
-                        previousParent.remove();
-                    }
+        this.buildBack = () => {
+            const backmatter = this.getFirstChildOfType(schema_1.schema.nodes.backmatter);
+            const $back = this.createElement('back');
+            backmatter?.forEach((node) => {
+                $back.appendChild(this.serializeNode(node));
+            });
+            return $back;
+        };
+        this.findSection = (category, ...$roots) => {
+            for (const $root of $roots) {
+                const $match = $root.querySelector(`sec[sec-type="${category}"]`);
+                if ($match) {
+                    return $match;
                 }
             }
-            let refList = this.document.querySelector('ref-list');
-            if (!refList) {
-                refList = this.createElement('ref-list');
+        };
+        this.findSections = (category, ...$roots) => $roots.flatMap(($root) => Array.from($root.querySelectorAll(`sec[sec-type="${category}"]`)));
+        this.routeBackmatterSections = ($body, $back) => {
+            const $footnoteSections = section_categories_1.FOOTNOTE_SECTION_CATEGORY_IDS.flatMap((category) => this.findSections(category, $body, $back).map(($section) => ({
+                $section,
+                category,
+            })));
+            let $fnGroup;
+            if ($footnoteSections.length) {
+                $fnGroup = this.createElement('fn-group');
+                for (const { $section, category } of $footnoteSections) {
+                    $fnGroup.appendChild(this.sectionToFootnote($section, category));
+                }
             }
-            back.appendChild(refList);
-            const parser = new DOMParser();
-            const [_, bibliography] = this.engine.makeBibliography();
-            for (let i = 0; i < bibliography.length; i++) {
-                const item = `<template xmlns:xlink="${xml_1.XLINK_NAMESPACE}">${(0, xml_1.sanitizeXmlString)(bibliography[i])}</template>`;
-                const ref = parser.parseFromString(item, 'text/xml').querySelector('ref');
-                if (ref) {
-                    refList.appendChild(ref);
+            const $appendices = this.findSections('appendices', $body, $back);
+            let $appGroup;
+            if ($appendices.length) {
+                $appGroup = this.createElement('app-group');
+                for (const $section of $appendices) {
+                    const $app = this.createElement('app');
+                    $app.appendChild($section);
+                    $appGroup.appendChild($app);
                 }
             }
-            return back;
+            const $ackSection = this.findSection('acknowledgements', $body, $back);
+            let $ack;
+            if ($ackSection) {
+                $ack = this.createElement('ack');
+                $ack.append(...$ackSection.childNodes);
+                $ackSection.remove();
+            }
+            const $availabilitySection = this.findSection('availability', $body, $back);
+            const $ethicsSection = this.findSection('ethics-statement', $body, $back);
+            const $prepend = [
+                $appGroup,
+                $ack,
+                $availabilitySection,
+                $ethicsSection,
+                $fnGroup,
+            ].filter((el) => el != null);
+            if ($prepend.length) {
+                $back.prepend(...$prepend);
+            }
+        };
+        this.extractCoiStatement = ($back) => {
+            const $coiStatement = $back.querySelector('fn[fn-type="coi-statement"]');
+            if (!$coiStatement) {
+                return undefined;
+            }
+            const $fnGroup = $coiStatement.parentElement;
+            $coiStatement.remove();
+            if ($fnGroup && !$fnGroup.hasChildNodes()) {
+                $fnGroup.remove();
+            }
+            return $coiStatement;
+        };
+        this.buildRefList = () => {
+            const $refList = this.createElement('ref-list');
+            const [, bibliography] = this.engine.makeBibliography();
+            const parser = new DOMParser();
+            bibliography.forEach((item) => {
+                const fragment = `<template xmlns:xlink="${xml_1.XLINK_NAMESPACE}">${(0, xml_1.sanitizeXmlString)(item)}</template>`;
+                const $ref = parser
+                    .parseFromString(fragment, 'text/xml')
+                    .querySelector('ref');
+                if ($ref) {
+                    $refList.appendChild($ref);
+                }
+            });
+            return $refList;
         };
         this.createElement = (tag, content, attrs) => {
-            const el = this.document.createElement(tag);
+            const $element = this.document.createElement(tag);
             if (content) {
-                el.textContent = content;
+                $element.textContent = content;
             }
             if (attrs) {
                 Object.entries(attrs).forEach(([k, v]) => {
                     if (v) {
-                        el.setAttribute(k, v);
+                        $element.setAttribute(k, v);
                     }
                 });
             }
-            return el;
+            return $element;
         };
-        this.appendElement = (parent, tag, content, attrs) => {
-            const el = this.createElement(tag, content, attrs);
-            parent.appendChild(el);
-            return el;
+        this.appendElement = ($parent, tag, content, attrs) => {
+            const $element = this.createElement(tag, content, attrs);
+            $parent.appendChild($element);
+            return $element;
         };
         this.createSerializer = () => {
             const nodes = {
-                trans_abstract: (node) => {
-                    const attrs = {
-                        id: normalizeID(node.attrs.id),
-                    };
-                    if (node.attrs.lang) {
-                        attrs[`${xml_1.XML_NAMESPACE} lang`] = node.attrs.lang;
-                    }
-                    if (node.attrs.category) {
-                        attrs['sec-type'] = node.attrs.category;
-                    }
-                    return ['trans-abstract', attrs, 0];
-                },
-                trans_graphical_abstract: (node) => {
-                    const attrs = {
-                        id: normalizeID(node.attrs.id),
-                    };
-                    if (node.attrs.lang) {
-                        attrs[`${xml_1.XML_NAMESPACE} lang`] = node.attrs.lang;
-                    }
-                    if (node.attrs.category) {
-                        attrs['sec-type'] = node.attrs.category;
-                    }
-                    return ['trans-abstract', attrs, 0];
-                },
+                trans_abstract: (node) => createTransAbstract(node),
+                trans_graphical_abstract: (node) => createTransAbstract(node),
                 hero_image: () => '',
                 headshot_grid: () => ['p', { 'content-type': 'headshots' }, 0],
                 headshot_element: (node) => createImage(node),
                 headshot_image: () => '',
                 alt_text: (node) => {
                     if (node.textContent) {
-                        const altText = this.createElement('alt-text');
-                        altText.textContent = node.textContent;
-                        return altText;
+                        const $altText = this.createElement('alt-text');
+                        $altText.textContent = node.textContent;
+                        return $altText;
                     }
                     return '';
                 },
                 long_desc: (node) => {
                     if (node.textContent) {
-                        const longDesc = this.createElement('long-desc');
-                        longDesc.textContent = node.textContent;
-                        return longDesc;
+                        const $longDesc = this.createElement('long-desc');
+                        $longDesc.textContent = node.textContent;
+                        return $longDesc;
                     }
                     return '';
                 },
-                attachment: () => '',
+                attachment: (node) => {
+                    const $selfUri = this.createElement('self-uri');
+                    $selfUri.setAttribute('content-type', node.attrs.type);
+                    $selfUri.setAttributeNS(xml_1.XLINK_NAMESPACE, 'href', node.attrs.href);
+                    return $selfUri;
+                },
                 attachments: () => '',
                 image_element: (node) => createImage(node),
                 embed: (node) => {
@@ -506,41 +506,45 @@ class JATSExporter {
                     if (!href) {
                         return '';
                     }
-                    const mediaElement = this.createElement('media');
-                    mediaElement.setAttribute('id', normalizeID(id));
-                    mediaElement.setAttributeNS(xml_1.XLINK_NAMESPACE, 'show', 'embed');
-                    mediaElement.setAttributeNS(xml_1.XLINK_NAMESPACE, 'href', href);
+                    const $media = this.createElement('media');
+                    $media.setAttribute('id', normalizeID(id));
+                    $media.setAttributeNS(xml_1.XLINK_NAMESPACE, 'show', 'embed');
+                    $media.setAttributeNS(xml_1.XLINK_NAMESPACE, 'href', href);
                     if (mimetype) {
-                        mediaElement.setAttribute('mimetype', node.attrs.mimetype);
+                        $media.setAttribute('mimetype', node.attrs.mimetype);
                     }
                     if (mimeSubtype) {
-                        mediaElement.setAttribute('mime-subtype', node.attrs.mimeSubtype);
+                        $media.setAttribute('mime-subtype', node.attrs.mimeSubtype);
                     }
-                    appendLabels(mediaElement, node);
-                    this.appendChildNodeOfType(mediaElement, node, schema_1.schema.nodes.alt_text);
-                    this.appendChildNodeOfType(mediaElement, node, schema_1.schema.nodes.long_desc);
-                    this.appendCaption(mediaElement, node);
-                    return mediaElement;
+                    appendLabels($media, node);
+                    this.appendChildNodeOfType($media, node, schema_1.schema.nodes.alt_text);
+                    this.appendChildNodeOfType($media, node, schema_1.schema.nodes.long_desc);
+                    this.appendCaption($media, node);
+                    return $media;
                 },
                 awards: () => ['funding-group', 0],
                 award: (node) => {
                     const awardGroup = node;
-                    const awardGroupElement = this.createElement('award-group');
-                    awardGroupElement.setAttribute('id', normalizeID(awardGroup.attrs.id));
-                    appendChildIfPresent(awardGroupElement, 'funding-source', awardGroup.attrs.source);
+                    const $awardGroup = this.createElement('award-group');
+                    $awardGroup.setAttribute('id', normalizeID(awardGroup.attrs.id));
+                    appendChildIfPresent($awardGroup, 'funding-source', awardGroup.attrs.source);
                     awardGroup.attrs.code
                         ?.split(';')
-                        .forEach((code) => appendChildIfPresent(awardGroupElement, 'award-id', code));
-                    appendChildIfPresent(awardGroupElement, 'principal-award-recipient', awardGroup.attrs.recipient);
-                    return awardGroupElement;
+                        .forEach((code) => appendChildIfPresent($awardGroup, 'award-id', code));
+                    appendChildIfPresent($awardGroup, 'principal-award-recipient', awardGroup.attrs.recipient);
+                    return $awardGroup;
                 },
                 box_element: (node) => createBoxElement(node),
                 author_notes: () => '',
                 corresp: () => '',
-                title: () => '',
-                alt_title: () => '',
+                title: () => ['article-title', 0],
+                alt_title: (node) => [
+                    'alt-title',
+                    { 'alt-title-type': node.attrs.type },
+                    0,
+                ],
                 alt_titles: () => '',
-                subtitle: () => '',
+                subtitle: () => ['subtitle', 0],
                 subtitles: () => '',
                 text_block: (node) => nodes.paragraph(node),
                 affiliations: () => '',
@@ -548,17 +552,31 @@ class JATSExporter {
                 table_element_footer: (node) => node.childCount == 0
                     ? ['table-wrap-foot', ['fn-group', ['fn', ['p']]]]
                     : ['table-wrap-foot', 0],
-                contributor: () => '',
-                affiliation: () => '',
+                contributor: (node) => this.buildContributorElement(node),
+                affiliation: (node) => this.buildAffiliationElement(node),
                 attribution: () => ['attrib', 0],
                 bibliography_element: () => '',
                 bibliography_item: () => '',
                 comments: () => '',
-                keyword_group: () => '',
+                keyword_group: (node) => {
+                    const attrs = {};
+                    if (node.attrs.type) {
+                        attrs['kwd-group-type'] = node.attrs.type;
+                    }
+                    return ['kwd-group', attrs, 0];
+                },
                 body: () => ['body', 0],
                 abstracts: () => ['abstract', 0],
                 backmatter: () => ['backmatter', 0],
-                supplement: () => '',
+                supplement: (node) => {
+                    const $supplementaryMaterial = this.createElement('supplementary-material');
+                    $supplementaryMaterial.setAttribute('id', normalizeID(node.attrs.id));
+                    $supplementaryMaterial.setAttributeNS(xml_1.XLINK_NAMESPACE, 'href', node.attrs.href ?? '');
+                    $supplementaryMaterial.setAttribute('mimetype', node.attrs.mimeType ?? '');
+                    $supplementaryMaterial.setAttribute('mime-subtype', node.attrs.mimeSubType ?? '');
+                    this.appendCaption($supplementaryMaterial, node);
+                    return $supplementaryMaterial;
+                },
                 supplements: () => '',
                 bibliography_section: () => '',
                 blockquote_element: () => ['disp-quote', { 'content-type': 'quote' }, 0],
@@ -582,14 +600,14 @@ class JATSExporter {
                     if (!rids.length) {
                         return '';
                     }
-                    const xref = this.createElement('xref');
-                    xref.setAttribute('ref-type', 'bibr');
-                    xref.setAttribute('rid', normalizeID(rids.join(' ')));
+                    const $xref = this.createElement('xref');
+                    $xref.setAttribute('ref-type', 'bibr');
+                    $xref.setAttribute('rid', normalizeID(rids.join(' ')));
                     const fragment = this.renderedCitations.get(node.attrs.id);
                     if (fragment) {
-                        xref.innerHTML = fragment;
+                        $xref.innerHTML = fragment;
                     }
-                    return xref;
+                    return $xref;
                 },
                 cross_reference: (node) => {
                     const cross = node;
@@ -603,40 +621,41 @@ class JATSExporter {
                     if (!target) {
                         return text ?? '';
                     }
-                    const xref = this.createElement('xref');
+                    const $xref = this.createElement('xref');
                     const type = chooseRefType(target.type);
                     if (type) {
-                        xref.setAttribute('ref-type', type);
+                        $xref.setAttribute('ref-type', type);
                     }
-                    xref.setAttribute('rid', normalizeID(rids.join(' ')));
-                    xref.textContent = text ?? '';
-                    return xref;
+                    $xref.setAttribute('rid', normalizeID(rids.join(' ')));
+                    $xref.textContent = text ?? '';
+                    return $xref;
                 },
                 doc: () => '',
                 equation: (node) => {
                     return node.attrs.contents ? this.createEquation(node) : '';
                 },
                 general_table_footnote: (node) => {
-                    const el = this.createElement('general-table-footnote');
-                    el.setAttribute('id', normalizeID(node.attrs.id));
-                    processChildNodes(el, node, schema_1.schema.nodes.general_table_footnote);
-                    return el;
+                    const $fragment = this.document.createDocumentFragment();
+                    node.forEach((child) => {
+                        $fragment.appendChild(this.serializeNode(child));
+                    });
+                    return $fragment;
                 },
                 inline_equation: (node) => {
                     if (!node.attrs.contents) {
                         return '';
                     }
-                    const eqElement = this.createElement('inline-formula');
+                    const $inlineFormula = this.createElement('inline-formula');
                     const equation = this.createEquation(node, true);
-                    eqElement.append(equation);
-                    return eqElement;
+                    $inlineFormula.append(equation);
+                    return $inlineFormula;
                 },
                 equation_element: (node) => {
-                    const eqElement = this.createElement('disp-formula');
-                    eqElement.setAttribute('id', normalizeID(node.attrs.id));
-                    appendLabels(eqElement, node);
-                    processChildNodes(eqElement, node, schema_1.schema.nodes.equation);
-                    return eqElement;
+                    const $dispFormula = this.createElement('disp-formula');
+                    $dispFormula.setAttribute('id', normalizeID(node.attrs.id));
+                    appendLabels($dispFormula, node);
+                    processChildNodes($dispFormula, node, schema_1.schema.nodes.equation);
+                    return $dispFormula;
                 },
                 figure: (node) => createGraphic(node),
                 figure_element: (node) => createFigureElement(node, node.type.schema.nodes.figure),
@@ -654,25 +673,39 @@ class JATSExporter {
                     ? ['fn-group', { id: normalizeID(node.attrs.id) }, ['fn', ['p']]]
                     : ['fn-group', { id: normalizeID(node.attrs.id) }, 0],
                 footnotes_section: (node) => {
-                    const attrs = {
+                    const $fnGroup = this.createElement('fn-group', undefined, {
                         id: normalizeID(node.attrs.id),
-                        'sec-type': 'endnotes',
-                    };
-                    return ['sec', attrs, 0];
+                    });
+                    const titleNode = this.getFirstChildOfType(schema_1.schema.nodes.section_title, node);
+                    if (titleNode) {
+                        $fnGroup.appendChild(this.serializeNode(titleNode));
+                    }
+                    const footnotesNode = this.getFirstChildOfType(schema_1.schema.nodes.footnotes_element, node);
+                    if (footnotesNode?.childCount) {
+                        footnotesNode.forEach((footnote) => {
+                            $fnGroup.appendChild(this.serializeNode(footnote));
+                        });
+                    }
+                    else {
+                        const $fn = this.createElement('fn');
+                        $fn.appendChild(this.createElement('p'));
+                        $fnGroup.appendChild($fn);
+                    }
+                    return $fnGroup;
                 },
                 hard_break: () => '',
                 highlight_marker: () => '',
                 inline_footnote: (node) => {
                     const rids = node.attrs.rids;
-                    const xref = this.createElement('xref');
-                    xref.setAttribute('ref-type', 'fn');
-                    xref.setAttribute('rid', normalizeID(rids.join(' ')));
-                    xref.textContent = rids
+                    const $xref = this.createElement('xref');
+                    $xref.setAttribute('ref-type', 'fn');
+                    $xref.setAttribute('rid', normalizeID(rids.join(' ')));
+                    $xref.textContent = rids
                         .map((rid) => this.footnoteLabels.get(rid))
                         .join(', ');
-                    return xref;
+                    return $xref;
                 },
-                keyword: () => '',
+                keyword: () => ['kwd', 0],
                 keywords_element: () => '',
                 keywords: () => '',
                 link: (node) => {
@@ -683,30 +716,30 @@ class JATSExporter {
                     if (!node.attrs.href) {
                         return text;
                     }
-                    const linkNode = this.createElement('ext-link');
-                    linkNode.setAttribute('ext-link-type', 'uri');
-                    linkNode.setAttributeNS(xml_1.XLINK_NAMESPACE, 'href', node.attrs.href);
-                    linkNode.textContent = text;
+                    const $extLink = this.createElement('ext-link');
+                    $extLink.setAttribute('ext-link-type', 'uri');
+                    $extLink.setAttributeNS(xml_1.XLINK_NAMESPACE, 'href', node.attrs.href);
+                    $extLink.textContent = text;
                     if (node.attrs.title) {
-                        linkNode.setAttributeNS(xml_1.XLINK_NAMESPACE, 'xlink:title', node.attrs.title);
+                        $extLink.setAttributeNS(xml_1.XLINK_NAMESPACE, 'xlink:title', node.attrs.title);
                     }
-                    return linkNode;
+                    return $extLink;
                 },
                 list_item: () => ['list-item', 0],
                 listing: (node) => {
-                    const code = this.createElement('code');
-                    code.setAttribute('id', normalizeID(node.attrs.id));
-                    code.setAttribute('language', node.attrs.languageKey);
-                    code.textContent = node.attrs.contents;
-                    return code;
+                    const $code = this.createElement('code');
+                    $code.setAttribute('id', normalizeID(node.attrs.id));
+                    $code.setAttribute('language', node.attrs.languageKey);
+                    $code.textContent = node.attrs.contents;
+                    return $code;
                 },
                 listing_element: (node) => createFigureElement(node, node.type.schema.nodes.listing),
                 manuscript: (node) => ['article', { id: normalizeID(node.attrs.id) }, 0],
                 missing_figure: () => {
-                    const graphic = this.createElement('graphic');
-                    graphic.setAttribute('specific-use', 'MISSING');
-                    graphic.setAttributeNS(xml_1.XLINK_NAMESPACE, 'xlink:href', '');
-                    return graphic;
+                    const $graphic = this.createElement('graphic');
+                    $graphic.setAttribute('specific-use', 'MISSING');
+                    $graphic.setAttributeNS(xml_1.XLINK_NAMESPACE, 'xlink:href', '');
+                    return $graphic;
                 },
                 paragraph: (node) => {
                     if (!node.childCount) {
@@ -741,15 +774,7 @@ class JATSExporter {
                     }
                     return '';
                 },
-                graphical_abstract_section: (node) => {
-                    const attrs = {
-                        id: normalizeID(node.attrs.id),
-                    };
-                    if (node.attrs.category) {
-                        attrs['sec-type'] = node.attrs.category;
-                    }
-                    return ['sec', attrs, 0];
-                },
+                graphical_abstract_section: (node) => createAbstract(node),
                 section: (node) => {
                     const attrs = {
                         id: normalizeID(node.attrs.id),
@@ -759,17 +784,18 @@ class JATSExporter {
                     }
                     return ['sec', attrs, 0];
                 },
+                abstract: (node) => createAbstract(node),
                 section_label: () => ['label', 0],
                 section_title: () => ['title', 0],
                 section_title_plain: () => ['title', 0],
                 table: (node) => ['table', { id: normalizeID(node.attrs.id) }, 0],
                 table_element: (node) => {
-                    const element = createTableElement(node);
-                    element.setAttribute('position', 'anchor');
+                    const $tableWrap = createTableElement(node);
+                    $tableWrap.setAttribute('position', 'anchor');
                     if (node.attrs.type) {
-                        element.setAttribute('content-type', node.attrs.type);
+                        $tableWrap.setAttribute('content-type', node.attrs.type);
                     }
-                    return element;
+                    return $tableWrap;
                 },
                 table_cell: (node) => [
                     'td',
@@ -815,84 +841,99 @@ class JATSExporter {
                 tracked_delete: () => ['del'],
             };
             this.serializer = new prosemirror_model_1.DOMSerializer(nodes, marks);
-            const appendChildIfPresent = (parent, tagName, textContent) => {
+            const appendChildIfPresent = ($parent, tagName, textContent) => {
                 if (!textContent) {
                     return;
                 }
-                const element = this.createElement(tagName);
-                element.textContent = textContent;
-                parent.appendChild(element);
+                const $element = this.createElement(tagName);
+                $element.textContent = textContent;
+                $parent.appendChild($element);
             };
-            const processChildNodes = (element, node, contentNodeType) => {
+            const processChildNodes = ($element, node, contentNodeType) => {
                 node.forEach((childNode) => {
                     if (childNode.type === contentNodeType) {
                         if (childNode.attrs.id) {
-                            element.appendChild(this.serializeNode(childNode));
+                            $element.appendChild(this.serializeNode(childNode));
                         }
                     }
                     else if (childNode.type === node.type.schema.nodes.paragraph) {
-                        element.appendChild(this.serializeNode(childNode));
+                        $element.appendChild(this.serializeNode(childNode));
                     }
                     else if (childNode.type === node.type.schema.nodes.missing_figure) {
-                        element.appendChild(this.serializeNode(childNode));
+                        $element.appendChild(this.serializeNode(childNode));
                     }
                 });
             };
             const createElement = (node, nodeName) => {
-                const element = this.createElement(nodeName);
-                element.setAttribute('id', normalizeID(node.attrs.id));
-                return element;
+                const $element = this.createElement(nodeName);
+                $element.setAttribute('id', normalizeID(node.attrs.id));
+                return $element;
             };
-            const appendLabels = (element, node) => {
+            const appendLabels = ($element, node) => {
                 if (this.labelTargets) {
                     const target = this.labelTargets.get(node.attrs.id);
                     if (target) {
-                        const label = this.createElement('label');
-                        label.textContent = target.label;
-                        element.appendChild(label);
+                        const $label = this.createElement('label');
+                        $label.textContent = target.label;
+                        $element.appendChild($label);
                     }
                 }
             };
-            const appendAttributions = (element, node) => {
+            const appendAttributions = ($element, node) => {
                 if (node.attrs.attribution) {
-                    const attribution = this.createElement('attrib');
-                    attribution.textContent = node.attrs.attribution.literal;
-                    element.appendChild(attribution);
+                    const $attrib = this.createElement('attrib');
+                    $attrib.textContent = node.attrs.attribution.literal;
+                    $element.appendChild($attrib);
                 }
             };
-            const appendTable = (element, node) => {
+            const appendTable = ($element, node) => {
                 const tableNode = this.getFirstChildOfType(schema_1.schema.nodes.table, node);
                 const colGroupNode = this.getFirstChildOfType(schema_1.schema.nodes.table_colgroup, node);
                 if (!tableNode) {
                     return;
                 }
-                const table = this.serializeNode(tableNode);
-                const tbodyElement = this.createElement('tbody');
-                while (table.firstChild) {
-                    const child = table.firstChild;
-                    table.removeChild(child);
-                    tbodyElement.appendChild(child);
+                const $table = this.serializeNode(tableNode);
+                const $tbody = this.createElement('tbody');
+                while ($table.firstChild) {
+                    const $child = $table.firstChild;
+                    $table.removeChild($child);
+                    $tbody.appendChild($child);
                 }
-                table.appendChild(tbodyElement);
+                $table.appendChild($tbody);
+                this.normalizeTable($table);
                 if (colGroupNode) {
-                    const colGroup = this.serializeNode(colGroupNode);
-                    table.insertBefore(colGroup, table.firstChild);
+                    const $colGroup = this.serializeNode(colGroupNode);
+                    $table.insertBefore($colGroup, $table.firstChild);
                 }
-                element.appendChild(table);
+                $element.appendChild($table);
             };
             const createBoxElement = (node) => {
-                const element = createElement(node, 'boxed-text');
+                const $boxedText = createElement(node, 'boxed-text');
                 if (node.attrs.type) {
-                    element.setAttribute('content-type', node.attrs.type);
+                    $boxedText.setAttribute('content-type', node.attrs.type);
                 }
-                appendLabels(element, node);
+                appendLabels($boxedText, node);
                 const child = node.firstChild;
                 if (child?.type === schema_1.schema.nodes.caption_title) {
-                    this.appendCaption(element, node);
+                    this.appendCaption($boxedText, node);
                 }
-                processChildNodes(element, node, node.type.schema.nodes.section);
-                return element;
+                processChildNodes($boxedText, node, node.type.schema.nodes.section);
+                return $boxedText;
             };
+            const abstractTypeAttrs = (category) => category && category !== 'abstract' ? { 'abstract-type': category } : {};
+            const createAbstract = (node) => [
+                'abstract',
+                abstractTypeAttrs(node.attrs.category),
+                0,
+            ];
+            const createTransAbstract = (node) => [
+                'trans-abstract',
+                {
+                    [`${xml_1.XML_NAMESPACE} lang`]: node.attrs.lang ?? '',
+                    ...abstractTypeAttrs(node.attrs.category),
+                },
+                0,
+            ];
             const isChildOfNodeType = (targetID, type, descend = false) => {
                 const nodes = this.getChildrenOfType(type);
                 return nodes.some((node) => {
@@ -909,94 +950,94 @@ class JATSExporter {
                 if (!graphicNode) {
                     return '';
                 }
-                const graphicElement = createGraphic(graphicNode);
+                const $graphic = createGraphic(graphicNode);
                 if (node.attrs.extLink) {
-                    const extLink = this.appendElement(graphicElement, 'ext-link');
-                    extLink.setAttributeNS(xml_1.XLINK_NAMESPACE, 'href', node.attrs.extLink);
+                    const $extLink = this.appendElement($graphic, 'ext-link');
+                    $extLink.setAttributeNS(xml_1.XLINK_NAMESPACE, 'href', node.attrs.extLink);
                 }
-                this.appendCaption(graphicElement, node);
-                this.appendChildNodeOfType(graphicElement, node, schema_1.schema.nodes.alt_text);
-                this.appendChildNodeOfType(graphicElement, node, schema_1.schema.nodes.long_desc);
-                return graphicElement;
+                this.appendCaption($graphic, node);
+                this.appendChildNodeOfType($graphic, node, schema_1.schema.nodes.alt_text);
+                this.appendChildNodeOfType($graphic, node, schema_1.schema.nodes.long_desc);
+                return $graphic;
             };
             const createGraphic = (node) => {
-                const graphic = this.createElement('graphic');
-                graphic.setAttributeNS(xml_1.XLINK_NAMESPACE, 'xlink:href', node.attrs.src);
+                const $graphic = this.createElement('graphic');
+                $graphic.setAttributeNS(xml_1.XLINK_NAMESPACE, 'xlink:href', node.attrs.src);
                 const hero = findParentHeroImage(node.attrs.id);
                 if (hero) {
-                    graphic.setAttribute('content-type', hero.attrs.type || 'leading');
+                    $graphic.setAttribute('content-type', hero.attrs.type || 'leading');
                 }
                 else if (!isChildOfNodeType(node.attrs.id, schema_1.schema.nodes.figure_element) &&
                     node.attrs.type) {
-                    graphic.setAttribute('content-type', node.attrs.type);
+                    $graphic.setAttribute('content-type', node.attrs.type);
                 }
-                return graphic;
+                return $graphic;
             };
             const createFigureElement = (node, contentNodeType) => {
-                const element = createElement(node, 'fig');
+                const $fig = createElement(node, 'fig');
                 const figNode = this.getFirstChildOfType(schema_1.schema.nodes.figure, node);
                 const figType = figNode?.attrs.type;
                 if (figType) {
-                    element.setAttribute('fig-type', figType);
+                    $fig.setAttribute('fig-type', figType);
                 }
-                appendLabels(element, node);
-                this.appendCaption(element, node);
-                this.appendChildNodeOfType(element, node, schema_1.schema.nodes.alt_text);
-                this.appendChildNodeOfType(element, node, schema_1.schema.nodes.long_desc);
-                this.appendChildNodeOfType(element, node, node.type.schema.nodes.footnotes_element);
-                processChildNodes(element, node, contentNodeType);
-                appendAttributions(element, node);
+                appendLabels($fig, node);
+                this.appendCaption($fig, node);
+                this.appendChildNodeOfType($fig, node, schema_1.schema.nodes.alt_text);
+                this.appendChildNodeOfType($fig, node, schema_1.schema.nodes.long_desc);
+                this.appendChildNodeOfType($fig, node, node.type.schema.nodes.footnotes_element);
+                processChildNodes($fig, node, contentNodeType);
+                appendAttributions($fig, node);
                 if ((0, transformer_1.isExecutableNodeType)(node.type)) {
-                    processExecutableNode(node, element);
+                    processExecutableNode(node, $fig);
                 }
-                moveAltTextAndLongDescToGraphics(element);
-                return element;
+                moveAltTextAndLongDescToGraphics($fig);
+                return $fig;
             };
-            const moveAltTextAndLongDescToGraphics = (element) => {
-                const altText = element.querySelector('alt-text');
-                const longDesc = element.querySelector('long-desc');
-                const graphics = element.querySelectorAll('graphic');
-                if (graphics.length === 0) {
+            const moveAltTextAndLongDescToGraphics = ($element) => {
+                const $altText = $element.querySelector('alt-text');
+                const $longDesc = $element.querySelector('long-desc');
+                const $graphics = $element.querySelectorAll('graphic');
+                if ($graphics.length === 0) {
                     return;
                 }
-                graphics.forEach((graphic) => {
-                    if (longDesc) {
-                        graphic.prepend(longDesc.cloneNode(true));
+                $graphics.forEach(($graphic) => {
+                    if ($longDesc) {
+                        $graphic.prepend($longDesc.cloneNode(true));
                     }
-                    if (altText) {
-                        graphic.prepend(altText.cloneNode(true));
+                    if ($altText) {
+                        $graphic.prepend($altText.cloneNode(true));
                     }
                 });
-                altText?.remove();
-                longDesc?.remove();
+                $altText?.remove();
+                $longDesc?.remove();
             };
             const createTableElement = (node) => {
                 const nodeName = 'table-wrap';
-                const element = createElement(node, nodeName);
-                appendLabels(element, node);
-                this.appendCaption(element, node);
-                this.appendChildNodeOfType(element, node, schema_1.schema.nodes.alt_text);
-                this.appendChildNodeOfType(element, node, schema_1.schema.nodes.long_desc);
-                appendTable(element, node);
-                this.appendChildNodeOfType(element, node, node.type.schema.nodes.table_element_footer);
+                const $tableWrap = createElement(node, nodeName);
+                appendLabels($tableWrap, node);
+                this.appendCaption($tableWrap, node);
+                this.appendChildNodeOfType($tableWrap, node, schema_1.schema.nodes.alt_text);
+                this.appendChildNodeOfType($tableWrap, node, schema_1.schema.nodes.long_desc);
+                appendTable($tableWrap, node);
+                this.appendChildNodeOfType($tableWrap, node, node.type.schema.nodes.table_element_footer);
                 if ((0, transformer_1.isExecutableNodeType)(node.type)) {
-                    processExecutableNode(node, element);
+                    processExecutableNode(node, $tableWrap);
                 }
-                return element;
+                return $tableWrap;
             };
-            const processExecutableNode = (node, element) => {
+            const processExecutableNode = (node, $element) => {
                 const listingNode = this.getFirstChildOfType(schema_1.schema.nodes.listing, node);
                 if (listingNode) {
                     const { contents, languageKey } = listingNode.attrs;
                     if (contents && languageKey) {
-                        const listing = this.createElement('fig');
-                        listing.setAttribute('specific-use', 'source');
-                        element.appendChild(listing);
-                        const code = this.createElement('code');
-                        code.setAttribute('executable', 'true');
-                        code.setAttribute('language', languageKey);
-                        code.textContent = contents;
-                        listing.appendChild(code);
+                        const $fig = this.createElement('fig');
+                        $fig.setAttribute('specific-use', 'source');
+                        $element.appendChild($fig);
+                        const $code = this.createElement('code');
+                        $code.setAttribute('executable', 'true');
+                        $code.setAttribute('language', languageKey);
+                        $code.textContent = contents;
+                        $fig.appendChild($code);
                     }
                 }
             };
@@ -1004,201 +1045,187 @@ class JATSExporter {
         this.serializeNode = (node) => this.serializer.serializeNode(node, {
             document: this.document,
         });
-        this.buildContributors = (articleMeta) => {
-            const contributors = this.getChildrenOfType(schema_1.schema.nodes.contributor).sort(sortContributors);
+        this.buildContributorGroup = (contributors) => {
             if (!contributors.length) {
                 return;
             }
-            const labels = new Map();
-            const createLabel = (id) => {
-                let label = labels.get(id);
-                if (!label) {
-                    label = labels.size + 1;
-                    labels.set(id, label);
+            const affiliationIDs = contributors.flatMap((n) => n.attrs.affiliationIDs);
+            const affiliationOrder = new Map();
+            affiliationIDs.forEach((id, index) => {
+                if (!affiliationOrder.has(id)) {
+                    affiliationOrder.set(id, index);
                 }
-                const sup = this.createElement('sup');
-                sup.textContent = String(label);
-                return sup;
-            };
+            });
+            const affiliations = this.getChildrenOfType(schema_1.schema.nodes.affiliation)
+                .filter((a) => affiliationIDs.includes(a.attrs.id))
+                .sort((a, b) => (affiliationOrder.get(a.attrs.id) ?? Infinity) -
+                (affiliationOrder.get(b.attrs.id) ?? Infinity));
             const $contribGroup = this.createElement('contrib-group');
             $contribGroup.setAttribute('content-type', 'authors');
-            articleMeta.appendChild($contribGroup);
             contributors.forEach((contributor) => {
-                const $contrib = this.createElement('contrib');
-                $contrib.setAttribute('contrib-type', 'author');
-                $contrib.setAttribute('id', normalizeID(contributor.attrs.id));
-                if (contributor.attrs.isCorresponding) {
-                    $contrib.setAttribute('corresp', 'yes');
-                }
-                if (contributor.attrs.role) {
-                    this.appendElement($contrib, 'role', contributor.attrs.role);
-                }
-                if (contributor.attrs.ORCID) {
-                    const contribIdAttrs = {
-                        'contrib-id-type': 'orcid',
-                    };
-                    if (contributor.attrs.isAuthenticated) {
-                        contribIdAttrs['authenticated'] = 'true';
-                    }
-                    this.appendElement($contrib, 'contrib-id', contributor.attrs.ORCID, contribIdAttrs);
-                }
-                const $name = this.buildContributorName(contributor);
-                $contrib.appendChild($name);
-                if (contributor.attrs.suffix) {
-                    this.appendElement($name, 'suffix', contributor.attrs.suffix);
+                $contribGroup.appendChild(this.serializeNode(contributor));
+            });
+            affiliations.forEach((affiliation) => {
+                $contribGroup.appendChild(this.serializeNode(affiliation));
+            });
+            return $contribGroup;
+        };
+        this.buildAuthorNotes = ($coiStatement) => {
+            const authorNotes = this.getFirstChildOfType(schema_1.schema.nodes.author_notes);
+            const $authorNotes = this.createElement('author-notes');
+            if (authorNotes) {
+                this.appendAuthorNotes($authorNotes, authorNotes);
+            }
+            if ($coiStatement) {
+                $authorNotes.appendChild($coiStatement);
+            }
+            return $authorNotes.hasChildNodes() ? $authorNotes : undefined;
+        };
+        this.computeContributorLabels = (contributors) => {
+            const labels = new Map();
+            const assign = (id) => {
+                if (!labels.has(id)) {
+                    labels.set(id, labels.size + 1);
                 }
-                contributor.attrs.degrees?.forEach((degree) => {
-                    this.appendElement($contrib, 'degrees', degree);
-                });
-                if (contributor.attrs.email) {
-                    this.appendElement($contrib, 'email', contributor.attrs.email);
+            };
+            contributors.forEach((contributor) => {
+                contributor.attrs.affiliationIDs?.forEach(assign);
+                contributor.attrs.footnoteIDs?.forEach(assign);
+                contributor.attrs.correspIDs?.forEach(assign);
+            });
+            return labels;
+        };
+        this.createLabelSup = (id) => {
+            const $sup = this.createElement('sup');
+            $sup.textContent = String(this.contributorLabels.get(id));
+            return $sup;
+        };
+        this.buildContributorElement = (contributor) => {
+            const $contrib = this.createElement('contrib');
+            $contrib.setAttribute('contrib-type', 'author');
+            $contrib.setAttribute('id', normalizeID(contributor.attrs.id));
+            if (contributor.attrs.isCorresponding) {
+                $contrib.setAttribute('corresp', 'yes');
+            }
+            if (contributor.attrs.role) {
+                this.appendElement($contrib, 'role', contributor.attrs.role);
+            }
+            if (contributor.attrs.ORCID) {
+                const contribIDAttrs = {
+                    'contrib-id-type': 'orcid',
+                };
+                if (contributor.attrs.isAuthenticated) {
+                    contribIDAttrs['authenticated'] = 'true';
                 }
-                contributor.attrs.affiliationIDs?.forEach((rid) => {
-                    const $xref = this.appendElement($contrib, 'xref', '', {
-                        'ref-type': 'aff',
-                        rid: normalizeID(rid),
-                    });
-                    $xref.appendChild(createLabel(rid));
-                });
-                contributor.attrs.footnoteIDs?.forEach((rid) => {
-                    const $xref = this.appendElement($contrib, 'xref', '', {
-                        'ref-type': 'fn',
-                        rid: normalizeID(rid),
-                    });
-                    $xref.appendChild(createLabel(rid));
+                this.appendElement($contrib, 'contrib-id', contributor.attrs.ORCID, contribIDAttrs);
+            }
+            const $name = this.buildContributorName(contributor);
+            $contrib.appendChild($name);
+            if (contributor.attrs.suffix) {
+                this.appendElement($name, 'suffix', contributor.attrs.suffix);
+            }
+            contributor.attrs.degrees?.forEach((degree) => {
+                this.appendElement($contrib, 'degrees', degree);
+            });
+            if (contributor.attrs.email) {
+                this.appendElement($contrib, 'email', contributor.attrs.email);
+            }
+            contributor.attrs.affiliationIDs?.forEach((rid) => {
+                const $xref = this.appendElement($contrib, 'xref', '', {
+                    'ref-type': 'aff',
+                    rid: normalizeID(rid),
                 });
-                contributor.attrs.correspIDs?.forEach((rid) => {
-                    const $xref = this.appendElement($contrib, 'xref', '', {
-                        'ref-type': 'corresp',
-                        rid: normalizeID(rid),
-                    });
-                    $xref.appendChild(createLabel(rid));
+                $xref.appendChild(this.createLabelSup(rid));
+            });
+            contributor.attrs.footnoteIDs?.forEach((rid) => {
+                const $xref = this.appendElement($contrib, 'xref', '', {
+                    'ref-type': 'fn',
+                    rid: normalizeID(rid),
                 });
-                contributor.attrs.creditRoles?.forEach((credit) => {
-                    const url = credit_roles_1.CreditRoleUrls.get(credit.vocabTerm);
-                    if (!url) {
-                        return;
-                    }
-                    this.appendElement($contrib, 'role', credit.vocabTerm, {
-                        'vocab-identifier': 'http://credit.niso.org/',
-                        vocab: 'CRediT',
-                        'vocab-term': credit.vocabTerm,
-                        'vocab-term-identifier': url,
-                    });
+                $xref.appendChild(this.createLabelSup(rid));
+            });
+            contributor.attrs.correspIDs?.forEach((rid) => {
+                const $xref = this.appendElement($contrib, 'xref', '', {
+                    'ref-type': 'corresp',
+                    rid: normalizeID(rid),
                 });
-                $contribGroup.appendChild($contrib);
+                $xref.appendChild(this.createLabelSup(rid));
             });
-            const affiliationIDs = contributors.flatMap((n) => n.attrs.affiliationIDs);
-            const sortAffiliations = (a, b) => affiliationIDs.indexOf(a.attrs.id) - affiliationIDs.indexOf(b.attrs.id);
-            this.getChildrenOfType(schema_1.schema.nodes.affiliation)
-                .filter((a) => affiliationIDs.includes(a.attrs.id))
-                .sort(sortAffiliations)
-                .forEach((affiliation) => {
-                const $content = [];
-                if (affiliation.attrs.department) {
-                    const $institution = this.createElement('institution', affiliation.attrs.department, {
-                        'content-type': 'dept',
-                    });
-                    $content.push($institution);
-                }
-                if (affiliation.attrs.institution) {
-                    const $institution = this.createElement('institution', affiliation.attrs.institution);
-                    $content.push($institution);
-                }
-                if (affiliation.attrs.addressLine1) {
-                    const $addrLine = this.createElement('addr-line', affiliation.attrs.addressLine1);
-                    $content.push($addrLine);
-                }
-                if (affiliation.attrs.addressLine2) {
-                    const $addrLine = this.createElement('addr-line', affiliation.attrs.addressLine2);
-                    $content.push($addrLine);
-                }
-                if (affiliation.attrs.addressLine3) {
-                    const $addrLine = this.createElement('addr-line', affiliation.attrs.addressLine3);
-                    $content.push($addrLine);
-                }
-                if (affiliation.attrs.city) {
-                    const $city = this.createElement('city', affiliation.attrs.city);
-                    $content.push($city);
-                }
-                if (affiliation.attrs.county) {
-                    const $state = this.createElement('state', affiliation.attrs.county);
-                    $content.push($state);
-                }
-                if (affiliation.attrs.country) {
-                    const $country = this.createElement('country', affiliation.attrs.country);
-                    $content.push($country);
-                }
-                if (affiliation.attrs.postCode) {
-                    const $postalCode = this.createElement('postal-code', affiliation.attrs.postCode);
-                    $content.push($postalCode);
-                }
-                const $aff = this.createElement('aff');
-                $aff.setAttribute('id', normalizeID(affiliation.attrs.id));
-                $contribGroup.appendChild($aff);
-                const label = labels.get(affiliation.attrs.id);
-                if (label) {
-                    this.appendElement($aff, 'label', String(label));
+            contributor.attrs.creditRoles?.forEach((credit) => {
+                const url = credit_roles_1.CreditRoleUrls.get(credit.vocabTerm);
+                if (!url) {
+                    return;
                 }
-                $content.forEach((node, i) => {
-                    if (i > 0) {
-                        $aff.appendChild(this.document.createTextNode(', '));
-                    }
-                    $aff.appendChild(node);
+                this.appendElement($contrib, 'role', credit.vocabTerm, {
+                    'vocab-identifier': 'http://credit.niso.org/',
+                    vocab: 'CRediT',
+                    'vocab-term': credit.vocabTerm,
+                    'vocab-term-identifier': url,
                 });
             });
-            const $authorNotes = this.createAuthorNotesElement(contributors);
-            if ($authorNotes) {
-                articleMeta.insertBefore($authorNotes, $contribGroup.nextSibling);
+            return $contrib;
+        };
+        this.buildAffiliationElement = (affiliation) => {
+            const $content = [];
+            if (affiliation.attrs.department) {
+                $content.push(this.createElement('institution', affiliation.attrs.department, {
+                    'content-type': 'dept',
+                }));
+            }
+            if (affiliation.attrs.institution) {
+                $content.push(this.createElement('institution', affiliation.attrs.institution));
+            }
+            if (affiliation.attrs.addressLine1) {
+                $content.push(this.createElement('addr-line', affiliation.attrs.addressLine1));
+            }
+            if (affiliation.attrs.addressLine2) {
+                $content.push(this.createElement('addr-line', affiliation.attrs.addressLine2));
+            }
+            if (affiliation.attrs.addressLine3) {
+                $content.push(this.createElement('addr-line', affiliation.attrs.addressLine3));
+            }
+            if (affiliation.attrs.city) {
+                $content.push(this.createElement('city', affiliation.attrs.city));
+            }
+            if (affiliation.attrs.county) {
+                $content.push(this.createElement('state', affiliation.attrs.county));
+            }
+            if (affiliation.attrs.country) {
+                $content.push(this.createElement('country', affiliation.attrs.country));
+            }
+            if (affiliation.attrs.postCode) {
+                $content.push(this.createElement('postal-code', affiliation.attrs.postCode));
             }
+            const $aff = this.createElement('aff');
+            $aff.setAttribute('id', normalizeID(affiliation.attrs.id));
+            const label = this.contributorLabels.get(affiliation.attrs.id);
+            if (label) {
+                this.appendElement($aff, 'label', String(label));
+            }
+            $content.forEach((node, i) => {
+                if (i > 0) {
+                    $aff.appendChild(this.document.createTextNode(', '));
+                }
+                $aff.appendChild(node);
+            });
+            return $aff;
         };
         this.buildContributorName = (contributor) => {
             const { given, family } = contributor.attrs;
             if (Boolean(given) !== Boolean(family)) {
                 return this.createElement('string-name', given || family);
             }
-            const name = this.createElement('name');
+            const $name = this.createElement('name');
             if (contributor.attrs.family) {
-                this.appendElement(name, 'surname', contributor.attrs.family);
+                this.appendElement($name, 'surname', contributor.attrs.family);
             }
             if (contributor.attrs.given) {
-                this.appendElement(name, 'given-names', contributor.attrs.given);
+                this.appendElement($name, 'given-names', contributor.attrs.given);
             }
             if (contributor.attrs.prefix) {
-                this.appendElement(name, 'prefix', contributor.attrs.prefix);
-            }
-            return name;
-        };
-        this.createAuthorNotesElement = (contributors) => {
-            const authorNotes = this.getFirstChildOfType(schema_1.schema.nodes.author_notes);
-            if (!authorNotes || !authorNotes.childCount) {
-                return;
+                this.appendElement($name, 'prefix', contributor.attrs.prefix);
             }
-            const $authorNotes = this.createElement('author-notes');
-            const used = contributors.flatMap((c) => c.attrs.correspIDs);
-            authorNotes.descendants((node) => {
-                switch (node.type) {
-                    case schema_1.schema.nodes.paragraph: {
-                        const $p = this.writeParagraph(node);
-                        $authorNotes.append($p);
-                        break;
-                    }
-                    case schema_1.schema.nodes.footnote: {
-                        const $fn = this.writeFootnote(node);
-                        $authorNotes.append($fn);
-                        break;
-                    }
-                    case schema_1.schema.nodes.corresp: {
-                        if (used.includes(node.attrs.id)) {
-                            const $corresp = this.writeCorresp(node);
-                            $authorNotes.append($corresp);
-                        }
-                        break;
-                    }
-                }
-                return false;
-            });
-            return $authorNotes.hasChildNodes() ? $authorNotes : undefined;
+            return $name;
         };
         this.writeCorresp = (corresp) => {
             const $corresp = this.createElement('corresp');
@@ -1228,222 +1255,120 @@ class JATSExporter {
             $fn.innerHTML = content;
             return $fn;
         };
-        this.fixBody = (body) => {
-            this.manuscriptNode.descendants((node) => {
-                if (node.attrs.id) {
-                    if ((0, transformer_1.isNodeType)(node, 'general_table_footnote')) {
-                        const generalTableFootnote = body.querySelector(`#${normalizeID(node.attrs.id)}`);
-                        if (generalTableFootnote) {
-                            Array.from(generalTableFootnote.childNodes).forEach((cn) => {
-                                generalTableFootnote.before(cn);
-                            });
-                            generalTableFootnote.remove();
-                        }
+        this.appendAuthorNotes = ($authorNotes, authorNotes) => {
+            const correspIDs = new Set(this.getChildrenOfType(schema_1.schema.nodes.contributor).flatMap((contributor) => contributor.attrs.correspIDs));
+            authorNotes.forEach((node) => {
+                switch (node.type) {
+                    case schema_1.schema.nodes.paragraph: {
+                        $authorNotes.append(this.writeParagraph(node));
+                        break;
                     }
-                    if ((0, transformer_1.isNodeType)(node, 'table_element')) {
-                        const tableElement = body.querySelector(`#${normalizeID(node.attrs.id)}`);
-                        if (tableElement) {
-                            for (const childNode of tableElement.childNodes) {
-                                switch (childNode.nodeName) {
-                                    case 'caption': {
-                                        const label = tableElement.querySelector('label');
-                                        tableElement.insertBefore(childNode, label ? label.nextSibling : tableElement.firstChild);
-                                        break;
-                                    }
-                                    case 'table': {
-                                        this.fixTable(childNode);
-                                        break;
-                                    }
-                                }
-                            }
+                    case schema_1.schema.nodes.footnote: {
+                        $authorNotes.append(this.writeFootnote(node));
+                        break;
+                    }
+                    case schema_1.schema.nodes.corresp: {
+                        if (correspIDs.has(node.attrs.id)) {
+                            $authorNotes.append(this.writeCorresp(node));
                         }
+                        break;
                     }
                 }
             });
         };
-        this.changeTag = (node, tag) => {
-            const clone = this.createElement(tag);
-            for (const attr of node.attributes) {
-                clone.setAttributeNS(null, attr.name, attr.value);
+        this.buildKeywords = () => this.getChildrenOfType(schema_1.schema.nodes.keyword_group).map((group) => this.serializeNode(group));
+        this.changeTag = ($node, tag) => {
+            const $clone = this.createElement(tag);
+            for (const attr of $node.attributes) {
+                $clone.setAttributeNS(null, attr.name, attr.value);
             }
-            while (node.firstChild) {
-                clone.appendChild(node.firstChild);
+            while ($node.firstChild) {
+                $clone.appendChild($node.firstChild);
             }
-            node.replaceWith(clone);
-            return clone;
+            $node.replaceWith($clone);
+            return $clone;
         };
-        this.fixTable = (table) => {
-            let tbody;
-            Array.from(table.childNodes).forEach((child) => {
-                if (child instanceof Element && child.tagName.toLowerCase() === 'tbody') {
-                    tbody = child;
+        this.normalizeTable = ($table) => {
+            let $tbody;
+            Array.from($table.childNodes).forEach(($child) => {
+                if ($child instanceof Element &&
+                    $child.tagName.toLowerCase() === 'tbody') {
+                    $tbody = $child;
                 }
             });
-            if (!tbody) {
+            if (!$tbody) {
                 return;
             }
-            const tbodyRows = Array.from(tbody.childNodes);
-            const thead = this.createElement('thead');
-            tbodyRows.forEach((row, i) => {
-                const isRow = row instanceof Element && row.tagName.toLowerCase() === 'tr';
+            const tbodyRows = Array.from($tbody.childNodes);
+            const $thead = this.createElement('thead');
+            tbodyRows.forEach(($row, i) => {
+                const isRow = $row instanceof Element && $row.tagName.toLowerCase() === 'tr';
                 if (isRow) {
-                    const headerCell = row.querySelector('th[scope="col"], th[scope="colgroup"]');
-                    if (i === 0 || headerCell) {
-                        tbody?.removeChild(row);
-                        const tableCells = row.querySelectorAll('td');
-                        for (const td of tableCells) {
-                            this.changeTag(td, 'th');
+                    const $headerCell = $row.querySelector('th[scope="col"], th[scope="colgroup"]');
+                    if (i === 0 || $headerCell) {
+                        $tbody?.removeChild($row);
+                        const $tableCells = $row.querySelectorAll('td');
+                        for (const $td of $tableCells) {
+                            this.changeTag($td, 'th');
                         }
-                        thead.appendChild(row);
+                        $thead.appendChild($row);
                     }
                 }
             });
-            if (thead.hasChildNodes()) {
-                table.insertBefore(thead, tbody);
-            }
-        };
-        this.unwrapBody = (body) => {
-            const container = body.querySelector(':scope > sec[sec-type="body"]');
-            if (!container) {
-                return;
-            }
-            const sections = container.querySelectorAll(':scope > sec');
-            sections.forEach((section) => {
-                body.appendChild(section.cloneNode(true));
-            });
-            body.removeChild(container);
-        };
-        this.removeBackContainer = (body) => {
-            const container = body.querySelector(':scope > sec[sec-type="backmatter"]');
-            if (!container) {
-                return;
-            }
-            body.removeChild(container);
-        };
-        this.moveAwards = (front, body) => {
-            const awardGroups = body.querySelectorAll(':scope > award-group');
-            if (!awardGroups.length) {
-                return;
-            }
-            const fundingGroup = this.createElement('funding-group');
-            awardGroups.forEach((award) => {
-                fundingGroup.appendChild(award);
-            });
-            const articleMeta = front.querySelector(':scope > article-meta');
-            if (articleMeta) {
-                const insertBeforeElement = articleMeta.querySelector(':scope > support-group, :scope > conference, :scope > counts, :scope > custom-meta-group');
-                insertBeforeElement
-                    ? articleMeta.insertBefore(fundingGroup, insertBeforeElement)
-                    : articleMeta.appendChild(fundingGroup);
+            if ($thead.hasChildNodes()) {
+                $table.insertBefore($thead, $tbody);
             }
         };
-        this.moveAbstracts = (front, body) => {
-            const abstractSections = this.getAbstractSections(body);
-            for (const abstractSection of abstractSections) {
-                const node = abstractSection.nodeName === 'trans-abstract'
-                    ? this.createTransAbstractNode(abstractSection)
-                    : this.createAbstractNode(abstractSection);
-                abstractSection.remove();
-                insertAbstractNode(front, node);
-            }
-        };
-        this.moveSectionsToBack = (back, body) => {
-            const availabilitySection = body.querySelector('sec[sec-type="availability"]');
-            if (availabilitySection) {
-                back.insertBefore(availabilitySection, back.firstChild);
-            }
-            const ethicsSection = body.querySelector('sec[sec-type="ethics-statement"]');
-            if (ethicsSection) {
-                back.appendChild(ethicsSection);
-            }
-            const section = body.querySelector('sec[sec-type="acknowledgements"]');
-            if (section) {
-                const ack = this.createElement('ack');
-                while (section.firstChild) {
-                    ack.appendChild(section.firstChild);
-                }
-                if (section.parentNode) {
-                    section.parentNode.removeChild(section);
-                }
-                back.insertBefore(ack, back.firstChild);
-            }
-            const appendicesSections = body.querySelectorAll('sec[sec-type="appendices"]');
-            if (appendicesSections) {
-                const appGroup = this.createElement('app-group');
-                appendicesSections.forEach((section) => {
-                    if (section.parentNode) {
-                        section.parentNode.removeChild(section);
-                    }
-                    const app = this.createElement('app');
-                    app.appendChild(section);
-                    appGroup.appendChild(app);
-                });
-                back.insertBefore(appGroup, back.firstChild);
-            }
-            const footNotes = [];
-            const footnoteCategories = [
-                'con',
-                'conflict',
-                'deceased',
-                'equal',
-                'present-address',
-                'presented-at',
-                'previously-at',
-                'supplementary-material',
-                'supported-by',
-                'financial-disclosure',
-                'coi-statement',
-            ];
-            const sections = body.querySelectorAll('sec');
-            for (const currentSection of sections) {
-                const currentSectionType = currentSection.getAttribute('sec-type');
-                if (currentSectionType &&
-                    footnoteCategories.indexOf(currentSectionType) >= 0) {
-                    footNotes.push(this.sectionToFootnote(currentSection, currentSectionType));
+        this.buildAbstracts = () => {
+            const $abstracts = [];
+            const abstractsNode = this.getFirstChildOfType(schema_1.schema.nodes.abstracts);
+            abstractsNode?.forEach((child) => {
+                const $abstract = this.serializeNode(child);
+                if ($abstract.nodeName === 'abstract') {
+                    $abstract
+                        .querySelectorAll(':scope > title')
+                        .forEach((title) => title.remove());
                 }
-            }
-            if (footNotes.length > 0) {
-                const fnGroup = this.createElement('fn-group');
-                fnGroup.append(...footNotes);
-                back.append(fnGroup);
-            }
+                $abstracts.push($abstract);
+            });
+            return $abstracts;
         };
-        this.sectionToFootnote = (section, fnType) => {
-            const footNote = this.createElement('fn');
-            footNote.setAttribute('fn-type', fnType);
-            const title = section.querySelector('title');
-            if (title) {
-                const footNoteTitle = this.createElement('label');
-                footNoteTitle.textContent = title.textContent;
-                section.removeChild(title);
-                footNote.append(footNoteTitle);
+        this.sectionToFootnote = ($section, fnType) => {
+            const $fn = this.createElement('fn');
+            $fn.setAttribute('fn-type', fnType);
+            const $title = $section.querySelector(':scope > title');
+            if ($title) {
+                const $label = this.createElement('label');
+                $label.textContent = $title.textContent;
+                $section.removeChild($title);
+                $fn.append($label);
             }
-            footNote.append(...section.children);
-            if (section.parentNode) {
-                section.parentNode.removeChild(section);
+            $fn.append(...$section.children);
+            if ($section.parentNode) {
+                $section.parentNode.removeChild($section);
             }
-            return footNote;
+            return $fn;
         };
-        this.moveFloatsGroup = (article) => {
+        this.buildFloatsGroup = () => {
             const heroImage = this.getFirstChildOfType(schema_1.schema.nodes.hero_image);
             if (!heroImage) {
                 return;
             }
-            const floatsGroup = this.createElement('floats-group');
-            let figure = null;
+            const $floatsGroup = this.createElement('floats-group');
+            let $graphic = null;
             heroImage.descendants((node) => {
                 if (node.type === schema_1.schema.nodes.figure) {
-                    figure = this.serializeNode(node);
-                    floatsGroup.appendChild(figure);
+                    $graphic = this.serializeNode(node);
+                    $floatsGroup.appendChild($graphic);
                 }
                 else {
-                    const serializedNode = this.serializeNode(node);
-                    figure?.appendChild(serializedNode);
+                    const $serializedNode = this.serializeNode(node);
+                    $graphic?.appendChild($serializedNode);
                 }
                 return false;
             });
-            if (floatsGroup.children.length > 0) {
-                article.appendChild(floatsGroup);
+            if ($floatsGroup.children.length > 0) {
+                return $floatsGroup;
             }
         };
     }
@@ -1458,168 +1383,58 @@ class JATSExporter {
     }
     createEquation(node, isInline = false) {
         if (node.attrs.format === 'tex') {
-            const texMath = this.createElement('tex-math');
-            texMath.setAttribute('notation', 'LaTeX');
-            texMath.setAttribute('version', 'MathJax');
+            const $texMath = this.createElement('tex-math');
+            $texMath.setAttribute('notation', 'LaTeX');
+            $texMath.setAttribute('version', 'MathJax');
             if (node.attrs.contents.includes('<![CDATA[')) {
-                texMath.innerHTML = node.attrs.contents;
+                $texMath.innerHTML = node.attrs.contents;
             }
             else {
-                texMath.innerHTML = `<![CDATA[ ${node.attrs.contents} ]]>`;
+                $texMath.innerHTML = `<![CDATA[ ${node.attrs.contents} ]]>`;
             }
-            return texMath;
+            return $texMath;
         }
         else {
             const math = this.nodeFromJATS(node.attrs.contents);
-            const mathml = math;
+            const $mathml = math;
             if (!isInline) {
-                mathml.setAttribute('id', normalizeID(node.attrs.id));
-            }
-            return mathml;
-        }
-    }
-    buildKeywords(articleMeta) {
-        const keywordGroups = this.getChildrenOfType(schema_1.schema.nodes.keyword_group);
-        keywordGroups.forEach((group) => {
-            const kwdGroup = this.createElement('kwd-group');
-            if (group.attrs.type) {
-                kwdGroup.setAttribute('kwd-group-type', group.attrs.type);
-            }
-            articleMeta.appendChild(kwdGroup);
-            group.content.forEach((keyword) => {
-                const kwd = this.createElement('kwd');
-                kwd.textContent = keyword.textContent;
-                kwdGroup.appendChild(kwd);
-            });
-            articleMeta.appendChild(kwdGroup);
-        });
-    }
-    getAbstractCategories(abstractsNode) {
-        const categories = [];
-        abstractsNode?.content.descendants((node) => {
-            categories.push(node.attrs.category);
-            return false;
-        });
-        return categories;
-    }
-    getAbstractSections(body) {
-        {
-            const abstractsNode = this.getFirstChildOfType(schema_1.schema.nodes.abstracts);
-            const abstractCategories = this.getAbstractCategories(abstractsNode);
-            const sections = Array.from(body.querySelectorAll(':scope > sec, :scope > trans-abstract'));
-            return sections.filter((section) => this.isAbstractSection(section, abstractCategories));
-        }
-    }
-    isAbstractSection(section, abstractCategories) {
-        const sectionType = section.getAttribute('sec-type');
-        return sectionType ? abstractCategories.includes(sectionType) : false;
-    }
-    createTransAbstractNode(transAbstract) {
-        const transAbstractNode = this.createElement('trans-abstract');
-        transAbstractNode.setAttributeNS(xml_1.XML_NAMESPACE, 'lang', transAbstract.getAttributeNS(xml_1.XML_NAMESPACE, 'lang') ?? '');
-        this.setAbstractType(transAbstractNode, transAbstract);
-        transAbstractNode.append(...transAbstract.childNodes);
-        return transAbstractNode;
-    }
-    createAbstractNode(abstractSection) {
-        const abstractNode = this.createElement('abstract');
-        for (const node of abstractSection.childNodes) {
-            if (node.nodeName !== 'title') {
-                abstractNode.appendChild(node.cloneNode(true));
+                $mathml.setAttribute('id', normalizeID(node.attrs.id));
             }
+            return $mathml;
         }
-        this.setAbstractType(abstractNode, abstractSection);
-        return abstractNode;
     }
-    setAbstractType(abstractNode, abstractSection) {
-        const sectionType = abstractSection.getAttribute('sec-type');
-        if (sectionType && sectionType !== 'abstract') {
-            const abstractType = sectionType.replace('abstract-', '');
-            abstractNode.setAttribute('abstract-type', abstractType);
-        }
+    fillEmptyElements($article, selector, tagName = 'p') {
+        const $empty = Array.from($article.querySelectorAll(selector)).filter(($el) => !$el.innerHTML);
+        $empty.forEach(($element) => $element.appendChild(this.createElement(tagName)));
     }
-    moveCoiStatementToAuthorNotes(back, front) {
-        const fnGroups = back.querySelectorAll('fn-group');
-        fnGroups.forEach((fnGroup) => {
-            if (fnGroup) {
-                const coiStatement = fnGroup.querySelector('fn[fn-type="coi-statement"]');
-                if (coiStatement) {
-                    const authorNotes = this.createElement('author-notes');
-                    authorNotes.append(coiStatement);
-                    const articleMeta = front.querySelector('article-meta');
-                    if (articleMeta) {
-                        const authorNoteEl = articleMeta.querySelector('author-notes');
-                        if (authorNoteEl) {
-                            authorNoteEl.append(...authorNotes.childNodes);
-                        }
-                        else {
-                            const appendableSelectors = [
-                                'contrib-group',
-                                'title-group',
-                                'article-id',
-                            ];
-                            const appendable = [
-                                ...articleMeta.querySelectorAll(appendableSelectors.join(', ')),
-                            ];
-                            for (let i = 0; i < appendableSelectors.length; i++) {
-                                const sel = appendableSelectors[i];
-                                const match = appendable.find((el) => el.matches(sel));
-                                if (match) {
-                                    articleMeta.insertBefore(authorNotes, match.nextSibling);
-                                    break;
-                                }
-                            }
-                        }
-                    }
-                    if (!fnGroup.hasChildNodes()) {
-                        fnGroup.remove();
-                    }
-                }
-            }
-        });
-    }
-    updateFootnoteTypes(front, body) {
-        const footnotes = [...front.querySelectorAll('fn').values()];
-        footnotes.push(...body.querySelectorAll('fn'));
-        footnotes.forEach((fn) => {
-            const fnType = fn.getAttribute('fn-type');
-            if (fnType) {
-                fn.setAttribute('fn-type', fnType);
-            }
-        });
-    }
-    fillEmptyElements(articleElement, selector, tagName = 'p') {
-        const emptyElements = Array.from(articleElement.querySelectorAll(selector)).filter((element) => !element.innerHTML);
-        emptyElements.forEach((element) => element.appendChild(this.createElement(tagName)));
-    }
-    addParagraphsToSections(articleElement) {
-        const sections = articleElement.querySelectorAll('sec');
+    addParagraphsToSections($article) {
+        const $sections = $article.querySelectorAll('sec, abstract');
         const TITLE_TAGS = new Set(['title', 'label', 'sec-meta']);
-        for (const section of sections) {
-            const hasContent = Array.from(section.children).some((child) => !TITLE_TAGS.has(child.tagName));
+        for (const $section of $sections) {
+            const hasContent = Array.from($section.children).some(($child) => !TITLE_TAGS.has($child.tagName));
             if (hasContent) {
                 continue;
             }
-            const p = this.createElement('p');
-            const insertAfterElement = section.querySelector(':scope > title') ??
-                section.querySelector(':scope > label') ??
-                section.querySelector(':scope > sec-meta');
-            if (insertAfterElement) {
-                insertAfterElement.insertAdjacentElement('afterend', p);
+            const $p = this.createElement('p');
+            const $insertAfter = $section.querySelector(':scope > title') ??
+                $section.querySelector(':scope > label') ??
+                $section.querySelector(':scope > sec-meta');
+            if ($insertAfter) {
+                $insertAfter.insertAdjacentElement('afterend', $p);
             }
             else {
-                section.prepend(p);
+                $section.prepend($p);
             }
         }
     }
-    fillEmptyFootnotes(articleElement) {
-        this.fillEmptyElements(articleElement, 'fn');
+    fillEmptyFootnotes($article) {
+        this.fillEmptyElements($article, 'fn');
     }
-    fillEmptyTableFooters(articleElement) {
-        this.fillEmptyElements(articleElement, 'table-wrap-foot');
+    fillEmptyTableFooters($article) {
+        this.fillEmptyElements($article, 'table-wrap-foot');
     }
-    fillEmptyListItem(articleElement) {
-        this.fillEmptyElements(articleElement, 'list-item');
+    fillEmptyListItem($article) {
+        this.fillEmptyElements($article, 'list-item');
     }
 }
 exports.JATSExporter = JATSExporter;