@manuscripts/transform 4.5.7 → 4.6.0

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

@@ -1,6 +1,6 @@
 "use strict";
 /*!
- * © 2019 Atypon Systems LLC
+ * © 2026 Atypon Systems LLC
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -47,15 +47,11 @@ var __importStar = (this && this.__importStar) || (function () {
         return result;
     };
 })();
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.JATSExporter = exports.createCounter = void 0;
+exports.JATSExporter = void 0;
 const Citeproc = __importStar(require("citeproc"));
 const prosemirror_model_1 = require("prosemirror-model");
 const prosemirror_utils_1 = require("prosemirror-utils");
-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");
@@ -66,59 +62,13 @@ const transformer_1 = require("../../transformer");
 const citeproc_2 = require("./citeproc");
 const jats_versions_1 = require("./jats-versions");
 const labels_1 = require("./labels");
-const normalizeID = (id) => id.replace(/:/g, '_');
-const createCounter = () => {
-    const counts = new Map();
-    return {
-        increment: (field) => {
-            const value = counts.get(field);
-            const newValue = value === undefined ? 1 : value + 1;
-            counts.set(field, newValue);
-            return newValue;
-        },
-    };
-};
-exports.createCounter = createCounter;
-const createDefaultIDGenerator = () => {
-    const counter = (0, exports.createCounter)();
-    return async (element) => {
-        const value = String(counter.increment(element.nodeName));
-        return `${element.localName}-${value}`;
-    };
-};
-const chooseRefType = (type) => {
-    switch (type) {
-        case schema_1.schema.nodes.figure:
-        case schema_1.schema.nodes.figure_element:
-            return 'fig';
-        case schema_1.schema.nodes.footnote:
-            return 'fn';
-        case schema_1.schema.nodes.table:
-        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:
-            return 'disp-formula';
-        case schema_1.schema.nodes.supplement:
-            return 'supplementary-material';
-    }
-};
-class JATSExporter {
+const JATSExporterBase_1 = require("./JATSExporterBase");
+const lib_1 = require("./lib");
+class JATSExporter extends JATSExporterBase_1.JATSExporterBase {
     constructor() {
-        this.nodesMap = new Map();
+        super(...arguments);
         this.contributorLabels = new Map();
-        this.populateNodesMap = () => {
-            this.manuscriptNode.descendants((node) => {
-                const type = node.type;
-                const nodes = this.nodesMap.get(type) ?? [];
-                nodes.push(node);
-                this.nodesMap.set(type, nodes);
-            });
-        };
-        this.serializeToJATS = async (manuscriptNode, options) => {
+        this.export = async (manuscriptNode, options) => {
             this.manuscriptNode = manuscriptNode;
             this.populateNodesMap();
             this.initCiteprocEngine(options);
@@ -149,7 +99,7 @@ class JATSExporter {
                 $article.appendChild($floatsGroup);
             }
             await this.rewriteIDs();
-            return (0, w3c_xmlserializer_1.default)(this.document);
+            return this.document;
         };
         this.appendChildNodeOfType = ($element, node, type) => {
             const childNode = this.getFirstChildOfType(type, node);
@@ -213,7 +163,7 @@ class JATSExporter {
             $template.innerHTML = fragment;
             return $template.firstChild;
         };
-        this.rewriteIDs = async (generator = createDefaultIDGenerator()) => {
+        this.rewriteIDs = async (generator = (0, lib_1.createDefaultIDGenerator)()) => {
             const ids = new Map();
             for (const $element of this.document.querySelectorAll('[id]')) {
                 const oldID = $element.getAttribute('id');
@@ -440,7 +390,7 @@ class JATSExporter {
             const [, bibliography] = this.engine.makeBibliography();
             const parser = new DOMParser();
             bibliography.forEach((item) => {
-                const fragment = `<template xmlns:xlink="${xml_1.XLINK_NAMESPACE}">${(0, xml_1.sanitizeXmlString)(item)}</template>`;
+                const fragment = `<wrapper xmlns:xlink="${xml_1.XLINK_NAMESPACE}">${(0, xml_1.sanitizeXmlString)(item)}</wrapper>`;
                 const $ref = parser
                     .parseFromString(fragment, 'text/xml')
                     .querySelector('ref');
@@ -450,32 +400,13 @@ class JATSExporter {
             });
             return $refList;
         };
-        this.createElement = (tag, content, attrs) => {
-            const $element = this.document.createElement(tag);
-            if (content) {
-                $element.textContent = content;
-            }
-            if (attrs) {
-                Object.entries(attrs).forEach(([k, v]) => {
-                    if (v) {
-                        $element.setAttribute(k, v);
-                    }
-                });
-            }
-            return $element;
-        };
-        this.appendElement = ($parent, tag, content, attrs) => {
-            const $element = this.createElement(tag, content, attrs);
-            $parent.appendChild($element);
-            return $element;
-        };
         this.createSerializer = () => {
             const nodes = {
-                trans_abstract: (node) => createTransAbstract(node),
-                trans_graphical_abstract: (node) => createTransAbstract(node),
+                trans_abstract: (node) => this.createTransAbstract(node),
+                trans_graphical_abstract: (node) => this.createTransAbstract(node),
                 hero_image: () => '',
                 headshot_grid: () => ['p', { 'content-type': 'headshots' }, 0],
-                headshot_element: (node) => createImage(node),
+                headshot_element: (node) => this.createImage(node),
                 headshot_image: () => '',
                 alt_text: (node) => {
                     if (node.textContent) {
@@ -500,14 +431,14 @@ class JATSExporter {
                     return $selfUri;
                 },
                 attachments: () => '',
-                image_element: (node) => createImage(node),
+                image_element: (node) => this.createImage(node),
                 embed: (node) => {
                     const { id, href, mimetype, mimeSubtype, extLinks } = node.attrs;
                     if (!href) {
                         return '';
                     }
                     const $media = this.createElement('media');
-                    $media.setAttribute('id', normalizeID(id));
+                    $media.setAttribute('id', (0, lib_1.normalizeID)(id));
                     $media.setAttributeNS(xml_1.XLINK_NAMESPACE, 'show', 'embed');
                     $media.setAttributeNS(xml_1.XLINK_NAMESPACE, 'href', href);
                     if (mimetype) {
@@ -516,7 +447,7 @@ class JATSExporter {
                     if (mimeSubtype) {
                         $media.setAttribute('mime-subtype', node.attrs.mimeSubtype);
                     }
-                    appendLabels($media, node);
+                    this.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);
@@ -542,15 +473,15 @@ class JATSExporter {
                 award: (node) => {
                     const awardGroup = node;
                     const $awardGroup = this.createElement('award-group');
-                    $awardGroup.setAttribute('id', normalizeID(awardGroup.attrs.id));
-                    appendChildIfPresent($awardGroup, 'funding-source', awardGroup.attrs.source);
+                    $awardGroup.setAttribute('id', (0, lib_1.normalizeID)(awardGroup.attrs.id));
+                    this.appendChildIfPresent($awardGroup, 'funding-source', awardGroup.attrs.source);
                     awardGroup.attrs.code
                         ?.split(';')
-                        .forEach((code) => appendChildIfPresent($awardGroup, 'award-id', code));
-                    appendChildIfPresent($awardGroup, 'principal-award-recipient', awardGroup.attrs.recipient);
+                        .forEach((code) => this.appendChildIfPresent($awardGroup, 'award-id', code));
+                    this.appendChildIfPresent($awardGroup, 'principal-award-recipient', awardGroup.attrs.recipient);
                     return $awardGroup;
                 },
-                box_element: (node) => createBoxElement(node),
+                box_element: (node) => this.createBoxElement(node),
                 author_notes: () => '',
                 corresp: () => '',
                 title: () => ['article-title', 0],
@@ -569,6 +500,7 @@ class JATSExporter {
                     ? ['table-wrap-foot', ['fn-group', ['fn', ['p']]]]
                     : ['table-wrap-foot', 0],
                 contributor: (node) => this.buildContributorElement(node),
+                bio: () => ['bio', 0],
                 affiliation: (node) => this.buildAffiliationElement(node),
                 attribution: () => ['attrib', 0],
                 bibliography_element: () => '',
@@ -586,11 +518,11 @@ class JATSExporter {
                 backmatter: () => ['backmatter', 0],
                 supplement: (node) => {
                     const $supplementaryMaterial = this.createElement('supplementary-material');
-                    $supplementaryMaterial.setAttribute('id', normalizeID(node.attrs.id));
+                    $supplementaryMaterial.setAttribute('id', (0, lib_1.normalizeID)(node.attrs.id));
                     $supplementaryMaterial.setAttributeNS(xml_1.XLINK_NAMESPACE, 'href', node.attrs.href ?? '');
                     $supplementaryMaterial.setAttribute('mimetype', node.attrs.mimeType ?? '');
                     $supplementaryMaterial.setAttribute('mime-subtype', node.attrs.mimeSubType ?? '');
-                    appendLabels($supplementaryMaterial, node);
+                    this.appendLabels($supplementaryMaterial, node);
                     this.appendCaption($supplementaryMaterial, node);
                     return $supplementaryMaterial;
                 },
@@ -619,7 +551,7 @@ class JATSExporter {
                     }
                     const $xref = this.createElement('xref');
                     $xref.setAttribute('ref-type', 'bibr');
-                    $xref.setAttribute('rid', normalizeID(rids.join(' ')));
+                    $xref.setAttribute('rid', (0, lib_1.normalizeID)(rids.join(' ')));
                     const fragment = this.renderedCitations.get(node.attrs.id);
                     if (fragment) {
                         $xref.innerHTML = fragment;
@@ -645,11 +577,11 @@ class JATSExporter {
                         return text;
                     }
                     const $xref = this.createElement('xref');
-                    const type = chooseRefType(target.type);
+                    const type = (0, lib_1.chooseRefType)(target.type);
                     if (type) {
                         $xref.setAttribute('ref-type', type);
                     }
-                    $xref.setAttribute('rid', normalizeID(rids.join(' ')));
+                    $xref.setAttribute('rid', (0, lib_1.normalizeID)(rids.join(' ')));
                     $xref.textContent = text ?? '';
                     return $xref;
                 },
@@ -675,17 +607,17 @@ class JATSExporter {
                 },
                 equation_element: (node) => {
                     const $dispFormula = this.createElement('disp-formula');
-                    $dispFormula.setAttribute('id', normalizeID(node.attrs.id));
-                    appendLabels($dispFormula, node);
-                    processChildNodes($dispFormula, node, schema_1.schema.nodes.equation);
+                    $dispFormula.setAttribute('id', (0, lib_1.normalizeID)(node.attrs.id));
+                    this.appendLabels($dispFormula, node);
+                    this.processChildNodes($dispFormula, node, schema_1.schema.nodes.equation);
                     return $dispFormula;
                 },
-                figure: (node) => createGraphic(node),
-                figure_element: (node) => createFigureElement(node, node.type.schema.nodes.figure),
+                figure: (node) => this.createGraphic(node),
+                figure_element: (node) => this.createFigureElement(node, node.type.schema.nodes.figure),
                 footnote: (node) => {
                     const attrs = {};
                     if (node.attrs.id) {
-                        attrs.id = normalizeID(node.attrs.id);
+                        attrs.id = (0, lib_1.normalizeID)(node.attrs.id);
                     }
                     if (node.attrs.category) {
                         attrs['fn-type'] = node.attrs.category;
@@ -693,11 +625,11 @@ class JATSExporter {
                     return ['fn', attrs, 0];
                 },
                 footnotes_element: (node) => node.childCount == 0
-                    ? ['fn-group', { id: normalizeID(node.attrs.id) }, ['fn', ['p']]]
-                    : ['fn-group', { id: normalizeID(node.attrs.id) }, 0],
+                    ? ['fn-group', { id: (0, lib_1.normalizeID)(node.attrs.id) }, ['fn', ['p']]]
+                    : ['fn-group', { id: (0, lib_1.normalizeID)(node.attrs.id) }, 0],
                 footnotes_section: (node) => {
                     const $fnGroup = this.createElement('fn-group', undefined, {
-                        id: normalizeID(node.attrs.id),
+                        id: (0, lib_1.normalizeID)(node.attrs.id),
                     });
                     const titleNode = this.getFirstChildOfType(schema_1.schema.nodes.section_title, node);
                     if (titleNode) {
@@ -722,7 +654,7 @@ class JATSExporter {
                     const rids = node.attrs.rids;
                     const $xref = this.createElement('xref');
                     $xref.setAttribute('ref-type', 'fn');
-                    $xref.setAttribute('rid', normalizeID(rids.join(' ')));
+                    $xref.setAttribute('rid', (0, lib_1.normalizeID)(rids.join(' ')));
                     $xref.textContent = rids
                         .map((rid) => this.footnoteLabels.get(rid))
                         .join(', ');
@@ -751,13 +683,13 @@ class JATSExporter {
                 list_item: () => ['list-item', 0],
                 listing: (node) => {
                     const $code = this.createElement('code');
-                    $code.setAttribute('id', normalizeID(node.attrs.id));
+                    $code.setAttribute('id', (0, lib_1.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],
+                listing_element: (node) => this.createFigureElement(node, node.type.schema.nodes.listing),
+                manuscript: (node) => ['article', { id: (0, lib_1.normalizeID)(node.attrs.id) }, 0],
                 missing_figure: () => {
                     const $graphic = this.createElement('graphic');
                     $graphic.setAttribute('specific-use', 'MISSING');
@@ -770,7 +702,7 @@ class JATSExporter {
                     }
                     const attrs = {};
                     if (node.attrs.id) {
-                        attrs.id = normalizeID(node.attrs.id);
+                        attrs.id = (0, lib_1.normalizeID)(node.attrs.id);
                     }
                     if (node.attrs.contentType) {
                         attrs['content-type'] = node.attrs.contentType;
@@ -793,27 +725,27 @@ class JATSExporter {
                 quote_image: (node) => {
                     const img = node;
                     if (img.attrs.src) {
-                        return createGraphic(node);
+                        return this.createGraphic(node);
                     }
                     return '';
                 },
-                graphical_abstract_section: (node) => createAbstract(node),
+                graphical_abstract_section: (node) => this.createAbstract(node),
                 section: (node) => {
                     const attrs = {
-                        id: normalizeID(node.attrs.id),
+                        id: (0, lib_1.normalizeID)(node.attrs.id),
                     };
                     if (node.attrs.category) {
                         attrs['sec-type'] = node.attrs.category;
                     }
                     return ['sec', attrs, 0];
                 },
-                abstract: (node) => createAbstract(node),
+                abstract: (node) => this.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: (node) => ['table', { id: (0, lib_1.normalizeID)(node.attrs.id) }, 0],
                 table_element: (node) => {
-                    const $tableWrap = createTableElement(node);
+                    const $tableWrap = this.createTableElement(node);
                     $tableWrap.setAttribute('position', 'anchor');
                     if (node.attrs.type) {
                         $tableWrap.setAttribute('content-type', node.attrs.type);
@@ -864,210 +796,7 @@ class JATSExporter {
                 tracked_delete: () => ['del'],
             };
             this.serializer = new prosemirror_model_1.DOMSerializer(nodes, marks);
-            const appendChildIfPresent = ($parent, tagName, textContent) => {
-                if (!textContent) {
-                    return;
-                }
-                const $element = this.createElement(tagName);
-                $element.textContent = textContent;
-                $parent.appendChild($element);
-            };
-            const processChildNodes = ($element, node, contentNodeType) => {
-                node.forEach((childNode) => {
-                    if (childNode.type === contentNodeType) {
-                        if (childNode.attrs.id) {
-                            $element.appendChild(this.serializeNode(childNode));
-                        }
-                    }
-                    else if (childNode.type === node.type.schema.nodes.paragraph) {
-                        $element.appendChild(this.serializeNode(childNode));
-                    }
-                    else if (childNode.type === node.type.schema.nodes.missing_figure) {
-                        $element.appendChild(this.serializeNode(childNode));
-                    }
-                });
-            };
-            const createElement = (node, nodeName) => {
-                const $element = this.createElement(nodeName);
-                $element.setAttribute('id', normalizeID(node.attrs.id));
-                return $element;
-            };
-            const appendLabels = ($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 appendAttributions = ($element, node) => {
-                if (node.attrs.attribution) {
-                    const $attrib = this.createElement('attrib');
-                    $attrib.textContent = node.attrs.attribution.literal;
-                    $element.appendChild($attrib);
-                }
-            };
-            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 $tbody = this.createElement('tbody');
-                while ($table.firstChild) {
-                    const $child = $table.firstChild;
-                    $table.removeChild($child);
-                    $tbody.appendChild($child);
-                }
-                $table.appendChild($tbody);
-                this.normalizeTable($table);
-                if (colGroupNode) {
-                    const $colGroup = this.serializeNode(colGroupNode);
-                    $table.insertBefore($colGroup, $table.firstChild);
-                }
-                $element.appendChild($table);
-            };
-            const createBoxElement = (node) => {
-                const $boxedText = createElement(node, 'boxed-text');
-                if (node.attrs.type) {
-                    $boxedText.setAttribute('content-type', node.attrs.type);
-                }
-                appendLabels($boxedText, node);
-                const child = node.firstChild;
-                if (child?.type === schema_1.schema.nodes.caption_title) {
-                    this.appendCaption($boxedText, node);
-                }
-                processChildNodes($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) => {
-                    const result = (0, prosemirror_utils_1.findChildrenByAttr)(node, (attrs) => attrs.id === targetID, descend)[0];
-                    return !!result;
-                });
-            };
-            const findParentHeroImage = (targetID) => {
-                const heroes = this.getChildrenOfType(schema_1.schema.nodes.hero_image);
-                return heroes.find((hero) => !!(0, prosemirror_utils_1.findChildrenByAttr)(hero, (attrs) => attrs.id === targetID)[0]);
-            };
-            const createImage = (node) => {
-                const graphicNode = node.content.firstChild;
-                if (!graphicNode) {
-                    return '';
-                }
-                const $graphic = createGraphic(graphicNode);
-                if (node.attrs.extLink) {
-                    const $extLink = this.appendElement($graphic, 'ext-link');
-                    $extLink.setAttributeNS(xml_1.XLINK_NAMESPACE, 'href', node.attrs.extLink);
-                }
-                this.appendCaption($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 hero = findParentHeroImage(node.attrs.id);
-                if (hero) {
-                    $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);
-                }
-                return $graphic;
-            };
-            const createFigureElement = (node, contentNodeType) => {
-                const $fig = createElement(node, 'fig');
-                const figNode = this.getFirstChildOfType(schema_1.schema.nodes.figure, node);
-                const figType = figNode?.attrs.type;
-                if (figType) {
-                    $fig.setAttribute('fig-type', figType);
-                }
-                appendLabels($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, $fig);
-                }
-                moveAltTextAndLongDescToGraphics($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) {
-                    return;
-                }
-                $graphics.forEach(($graphic) => {
-                    if ($longDesc) {
-                        $graphic.prepend($longDesc.cloneNode(true));
-                    }
-                    if ($altText) {
-                        $graphic.prepend($altText.cloneNode(true));
-                    }
-                });
-                $altText?.remove();
-                $longDesc?.remove();
-            };
-            const createTableElement = (node) => {
-                const nodeName = 'table-wrap';
-                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, $tableWrap);
-                }
-                return $tableWrap;
-            };
-            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 $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);
-                    }
-                }
-            };
         };
-        this.serializeNode = (node) => this.serializer.serializeNode(node, {
-            document: this.document,
-        });
         this.buildContributorGroup = (contributors) => {
             if (!contributors.length) {
                 return;
@@ -1126,7 +855,7 @@ class JATSExporter {
         this.buildContributorElement = (contributor) => {
             const $contrib = this.createElement('contrib');
             $contrib.setAttribute('contrib-type', 'author');
-            $contrib.setAttribute('id', normalizeID(contributor.attrs.id));
+            $contrib.setAttribute('id', (0, lib_1.normalizeID)(contributor.attrs.id));
             if (contributor.attrs.isCorresponding) {
                 $contrib.setAttribute('corresp', 'yes');
             }
@@ -1156,21 +885,21 @@ class JATSExporter {
             contributor.attrs.affiliationIDs?.forEach((rid) => {
                 const $xref = this.appendElement($contrib, 'xref', '', {
                     'ref-type': 'aff',
-                    rid: normalizeID(rid),
+                    rid: (0, lib_1.normalizeID)(rid),
                 });
                 $xref.appendChild(this.createLabelSup(rid));
             });
             contributor.attrs.footnoteIDs?.forEach((rid) => {
                 const $xref = this.appendElement($contrib, 'xref', '', {
                     'ref-type': 'fn',
-                    rid: normalizeID(rid),
+                    rid: (0, lib_1.normalizeID)(rid),
                 });
                 $xref.appendChild(this.createLabelSup(rid));
             });
             contributor.attrs.correspIDs?.forEach((rid) => {
                 const $xref = this.appendElement($contrib, 'xref', '', {
                     'ref-type': 'corresp',
-                    rid: normalizeID(rid),
+                    rid: (0, lib_1.normalizeID)(rid),
                 });
                 $xref.appendChild(this.createLabelSup(rid));
             });
@@ -1186,6 +915,10 @@ class JATSExporter {
                     'vocab-term-identifier': url,
                 });
             });
+            const bio = this.getFirstChildOfType(schema_1.schema.nodes.bio, contributor);
+            if (bio?.childCount) {
+                $contrib.appendChild(this.serializeNode(bio));
+            }
             return $contrib;
         };
         this.buildAffiliationElement = (affiliation) => {
@@ -1220,7 +953,7 @@ class JATSExporter {
                 $content.push(this.createElement('postal-code', affiliation.attrs.postCode));
             }
             const $aff = this.createElement('aff');
-            $aff.setAttribute('id', normalizeID(affiliation.attrs.id));
+            $aff.setAttribute('id', (0, lib_1.normalizeID)(affiliation.attrs.id));
             const label = this.contributorLabels.get(affiliation.attrs.id);
             if (label) {
                 this.appendElement($aff, 'label', String(label));
@@ -1252,7 +985,7 @@ class JATSExporter {
         };
         this.writeCorresp = (corresp) => {
             const $corresp = this.createElement('corresp');
-            $corresp.setAttribute('id', normalizeID(corresp.attrs.id));
+            $corresp.setAttribute('id', (0, lib_1.normalizeID)(corresp.attrs.id));
             if (corresp.attrs.label) {
                 this.appendElement($corresp, 'label', corresp.attrs.label);
             }
@@ -1262,7 +995,7 @@ class JATSExporter {
         this.writeParagraph = (paragraph) => {
             const dom = new DOMParser().parseFromString(paragraph.textContent, 'text/html');
             const $p = this.createElement('p');
-            $p.setAttribute('id', normalizeID(paragraph.attrs.id));
+            $p.setAttribute('id', (0, lib_1.normalizeID)(paragraph.attrs.id));
             if (dom.body.innerHTML.length) {
                 $p.innerHTML = dom.body.innerHTML;
             }
@@ -1270,7 +1003,7 @@ class JATSExporter {
         };
         this.writeFootnote = (footnote) => {
             const $fn = this.createElement('fn');
-            $fn.setAttribute('id', normalizeID(footnote.attrs.id));
+            $fn.setAttribute('id', (0, lib_1.normalizeID)(footnote.attrs.id));
             let content = footnote.textContent;
             if (!content.includes('<p>')) {
                 content = `<p>${content}</p>`;
@@ -1300,17 +1033,6 @@ class JATSExporter {
             });
         };
         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);
-            }
-            $node.replaceWith($clone);
-            return $clone;
-        };
         this.normalizeTable = ($table) => {
             let $tbody;
             Array.from($table.childNodes).forEach(($child) => {
@@ -1395,14 +1117,174 @@ class JATSExporter {
             }
         };
     }
-    getFirstChildOfType(type, node) {
-        return this.getChildrenOfType(type, node)[0];
+    appendLabels($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);
+            }
+        }
+    }
+    appendAttributions($element, node) {
+        if (node.attrs.attribution) {
+            const $attrib = this.createElement('attrib');
+            $attrib.textContent = node.attrs.attribution.literal;
+            $element.appendChild($attrib);
+        }
+    }
+    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 $tbody = this.createElement('tbody');
+        while ($table.firstChild) {
+            const $child = $table.firstChild;
+            $table.removeChild($child);
+            $tbody.appendChild($child);
+        }
+        $table.appendChild($tbody);
+        this.normalizeTable($table);
+        if (colGroupNode) {
+            const $colGroup = this.serializeNode(colGroupNode);
+            $table.insertBefore($colGroup, $table.firstChild);
+        }
+        $element.appendChild($table);
+    }
+    createBoxElement(node) {
+        const $boxedText = this.createElementWithID(node, 'boxed-text');
+        if (node.attrs.type) {
+            $boxedText.setAttribute('content-type', node.attrs.type);
+        }
+        this.appendLabels($boxedText, node);
+        const child = node.firstChild;
+        if (child?.type === schema_1.schema.nodes.caption_title) {
+            this.appendCaption($boxedText, node);
+        }
+        this.processChildNodes($boxedText, node, node.type.schema.nodes.section);
+        return $boxedText;
+    }
+    abstractTypeAttrs(category) {
+        return category && category !== 'abstract'
+            ? { 'abstract-type': category }
+            : {};
+    }
+    createAbstract(node) {
+        return ['abstract', this.abstractTypeAttrs(node.attrs.category), 0];
+    }
+    createTransAbstract(node) {
+        return [
+            'trans-abstract',
+            {
+                [`${xml_1.XML_NAMESPACE} lang`]: node.attrs.lang ?? '',
+                ...this.abstractTypeAttrs(node.attrs.category),
+            },
+            0,
+        ];
+    }
+    createGraphic(node) {
+        const $graphic = this.createElement('graphic');
+        $graphic.setAttributeNS(xml_1.XLINK_NAMESPACE, 'xlink:href', node.attrs.src);
+        const findParentHeroImage = (targetID) => {
+            const heroes = this.getChildrenOfType(schema_1.schema.nodes.hero_image);
+            return heroes.find((hero) => !!(0, prosemirror_utils_1.findChildrenByAttr)(hero, (attrs) => attrs.id === targetID)[0]);
+        };
+        const hero = findParentHeroImage(node.attrs.id);
+        if (hero) {
+            $graphic.setAttribute('content-type', hero.attrs.type || 'leading');
+        }
+        else if (!this.isChildOfNodeType(node.attrs.id, schema_1.schema.nodes.figure_element) &&
+            node.attrs.type) {
+            $graphic.setAttribute('content-type', node.attrs.type);
+        }
+        return $graphic;
+    }
+    createImage(node) {
+        const graphicNode = node.content.firstChild;
+        if (!graphicNode) {
+            return '';
+        }
+        const $graphic = this.createGraphic(graphicNode);
+        if (node.attrs.extLink) {
+            const $extLink = this.appendElement($graphic, 'ext-link');
+            $extLink.setAttributeNS(xml_1.XLINK_NAMESPACE, 'href', node.attrs.extLink);
+        }
+        this.appendCaption($graphic, node);
+        this.appendChildNodeOfType($graphic, node, schema_1.schema.nodes.alt_text);
+        this.appendChildNodeOfType($graphic, node, schema_1.schema.nodes.long_desc);
+        return $graphic;
     }
-    getChildrenOfType(type, node) {
-        const nodes = node
-            ? (0, prosemirror_utils_1.findChildrenByType)(node, type).map(({ node }) => node)
-            : this.nodesMap.get(type);
-        return (nodes ?? []).filter((n) => (0, schema_1.isNodeOfType)(n, type));
+    createFigureElement(node, contentNodeType) {
+        const $fig = this.createElementWithID(node, 'fig');
+        const figNode = this.getFirstChildOfType(schema_1.schema.nodes.figure, node);
+        const figType = figNode?.attrs.type;
+        if (figType) {
+            $fig.setAttribute('fig-type', figType);
+        }
+        this.appendLabels($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);
+        this.processChildNodes($fig, node, contentNodeType);
+        this.appendAttributions($fig, node);
+        if ((0, transformer_1.isExecutableNodeType)(node.type)) {
+            this.processExecutableNode(node, $fig);
+        }
+        this.moveAltTextAndLongDescToGraphics($fig);
+        return $fig;
+    }
+    moveAltTextAndLongDescToGraphics($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));
+            }
+            if ($altText) {
+                $graphic.prepend($altText.cloneNode(true));
+            }
+        });
+        $altText?.remove();
+        $longDesc?.remove();
+    }
+    createTableElement(node) {
+        const nodeName = 'table-wrap';
+        const $tableWrap = this.createElementWithID(node, nodeName);
+        this.appendLabels($tableWrap, node);
+        this.appendCaption($tableWrap, node);
+        this.appendChildNodeOfType($tableWrap, node, schema_1.schema.nodes.alt_text);
+        this.appendChildNodeOfType($tableWrap, node, schema_1.schema.nodes.long_desc);
+        this.appendTable($tableWrap, node);
+        this.appendChildNodeOfType($tableWrap, node, node.type.schema.nodes.table_element_footer);
+        if ((0, transformer_1.isExecutableNodeType)(node.type)) {
+            this.processExecutableNode(node, $tableWrap);
+        }
+        return $tableWrap;
+    }
+    processExecutableNode(node, $element) {
+        const listingNode = this.getFirstChildOfType(schema_1.schema.nodes.listing, node);
+        if (listingNode) {
+            const { contents, languageKey } = listingNode.attrs;
+            if (contents && languageKey) {
+                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);
+            }
+        }
     }
     createEquation(node, isInline = false) {
         if (node.attrs.format === 'tex') {
@@ -1421,15 +1303,11 @@ class JATSExporter {
             const math = this.nodeFromJATS(node.attrs.contents);
             const $mathml = math;
             if (!isInline) {
-                $mathml.setAttribute('id', normalizeID(node.attrs.id));
+                $mathml.setAttribute('id', (0, lib_1.normalizeID)(node.attrs.id));
             }
             return $mathml;
         }
     }
-    fillEmptyElements($article, selector, tagName = 'p') {
-        const $empty = Array.from($article.querySelectorAll(selector)).filter(($el) => !$el.innerHTML);
-        $empty.forEach(($element) => $element.appendChild(this.createElement(tagName)));
-    }
     addParagraphsToSections($article) {
         const $sections = $article.querySelectorAll('sec, abstract');
         const TITLE_TAGS = new Set(['title', 'label', 'sec-meta']);