@manuscripts/transform 2.3.33 → 2.3.34-LEAN-3911.2

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

@@ -23,44 +23,19 @@ const json_schema_1 = require("@manuscripts/json-schema");
 const library_1 = require("@manuscripts/library");
 const debug_1 = __importDefault(require("debug"));
 const prosemirror_model_1 = require("prosemirror-model");
+const prosemirror_utils_1 = require("prosemirror-utils");
 const w3c_xmlserializer_1 = __importDefault(require("w3c-xmlserializer"));
 const html_1 = require("../lib/html");
-const styled_content_1 = require("../lib/styled-content");
-const utils_1 = require("../lib/utils");
 const schema_1 = require("../schema");
-const filename_1 = require("../transformer/filename");
-const labels_1 = require("../transformer/labels");
 const node_types_1 = require("../transformer/node-types");
-const object_types_1 = require("../transformer/object-types");
-const project_bundle_1 = require("../transformer/project-bundle");
 const section_category_1 = require("../transformer/section-category");
+const filename_1 = require("./filename");
 const jats_versions_1 = require("./jats-versions");
+const labels_1 = require("./labels");
 const warn = (0, debug_1.default)('manuscripts-transform');
 const XLINK_NAMESPACE = 'http://www.w3.org/1999/xlink';
 const normalizeID = (id) => id.replace(/:/g, '_');
 const parser = prosemirror_model_1.DOMParser.fromSchema(schema_1.schema);
-const findChildNodeOfType = (node, nodeType) => {
-    for (const child of (0, utils_1.iterateChildren)(node)) {
-        if (child.type === nodeType) {
-            return child;
-        }
-    }
-};
-const isContributor = (0, object_types_1.hasObjectType)(json_schema_1.ObjectTypes.Contributor);
-const CREDIT_VOCAB_IDENTIFIER = 'https://dictionary.casrai.org/Contributor_Roles';
-const chooseRoleVocabAttributes = (role) => {
-    if (role.uri && role.uri.startsWith(CREDIT_VOCAB_IDENTIFIER)) {
-        return {
-            vocab: 'credit',
-            'vocab-identifier': CREDIT_VOCAB_IDENTIFIER,
-            'vocab-term': role.name,
-            'vocab-term-identifier': role.uri,
-        };
-    }
-    return {
-        vocab: 'uncontrolled',
-    };
-};
 const insertAbstractNode = (articleMeta, abstractNode) => {
     const siblings = [
         'kwd-group',
@@ -98,24 +73,24 @@ const createDefaultIdGenerator = () => {
         return `${element.localName}-${value}`;
     };
 };
-const chooseRefType = (objectType) => {
-    switch (objectType) {
-        case json_schema_1.ObjectTypes.Figure:
-        case json_schema_1.ObjectTypes.FigureElement:
+const chooseRefType = (type) => {
+    switch (type) {
+        case schema_1.schema.nodes.figure:
+        case schema_1.schema.nodes.figure_element:
             return 'fig';
-        case json_schema_1.ObjectTypes.Footnote:
+        case schema_1.schema.nodes.footnote:
             return 'fn';
-        case json_schema_1.ObjectTypes.Table:
-        case json_schema_1.ObjectTypes.TableElement:
+        case schema_1.schema.nodes.table:
+        case schema_1.schema.nodes.table_element:
             return 'table';
-        case json_schema_1.ObjectTypes.Section:
+        case schema_1.schema.nodes.section:
             return 'sec';
-        case json_schema_1.ObjectTypes.Equation:
-        case json_schema_1.ObjectTypes.EquationElement:
+        case schema_1.schema.nodes.equation:
+        case schema_1.schema.nodes.equation_element:
             return 'disp-formula';
     }
 };
-const sortContributors = (a, b) => Number(a.priority) - Number(b.priority);
+const sortContributors = (a, b) => Number(a.attrs.priority) - Number(b.attrs.priority);
 const buildCitations = (citations) => citations.map((citation) => ({
     citationID: citation.attrs.id,
     citationItems: citation.attrs.rids.map((rid) => ({
@@ -128,39 +103,57 @@ const buildCitations = (citations) => citations.map((citation) => ({
 exports.buildCitations = buildCitations;
 class JATSExporter {
     constructor() {
-        this.serializeToJATS = async (fragment, modelMap, manuscriptID, options) => {
-            const { version = '1.2', doi, id, frontMatterOnly = false, links, idGenerator, mediaPathGenerator, csl, } = options;
-            this.modelMap = modelMap;
-            this.models = Array.from(this.modelMap.values());
-            this.generateCitationTexts(fragment, csl);
+        this.getLibraryItem = (manuscriptID) => {
+            return (id) => {
+                var _a;
+                const node = (_a = (0, prosemirror_utils_1.findChildrenByAttr)(this.manuscriptNode, (attrs) => attrs.id === id)[0]) === null || _a === void 0 ? void 0 : _a.node;
+                if (!node) {
+                    return undefined;
+                }
+                return {
+                    _id: node.attrs.id,
+                    issued: node.attrs.issued,
+                    DOI: node.attrs.doi,
+                    manuscriptID,
+                    objectType: json_schema_1.ObjectTypes.BibliographyItem,
+                    author: node.attrs.author,
+                    'container-title': node.attrs.containerTitle,
+                    volume: node.attrs.volume,
+                    issue: node.attrs.issue,
+                    supplement: node.attrs.supplement,
+                    page: node.attrs.page,
+                    title: node.attrs.title,
+                    literal: node.attrs.literal,
+                    type: node.attrs.type,
+                };
+            };
+        };
+        this.serializeToJATS = async (manuscriptNode, csl, manuscript, jorunal) => {
+            const version = '1.2';
+            this.manuscriptNode = manuscriptNode;
+            this.generateCitationTexts(csl, manuscriptNode.attrs.id);
             this.createSerializer();
             const versionIds = (0, jats_versions_1.selectVersionIds)(version);
             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', XLINK_NAMESPACE);
-            const front = this.buildFront(doi, id, links);
+            const front = this.buildFront(manuscript, jorunal);
             article.appendChild(front);
-            const manuscript = (0, project_bundle_1.findManuscriptById)(this.modelMap, manuscriptID);
             article.setAttribute('article-type', manuscript.articleType || 'other');
-            if (!frontMatterOnly) {
-                this.labelTargets = (0, labels_1.buildTargets)(fragment);
-                const body = this.buildBody(fragment);
-                article.appendChild(body);
-                const back = this.buildBack(body);
-                this.moveCoiStatementToAuthorNotes(back, front);
-                article.appendChild(back);
-                this.unwrapBody(body);
-                this.moveAbstracts(front, body);
-                this.moveFloatsGroup(body, article);
-                this.removeBackContainer(body);
-                this.updateFootnoteTypes(front, back);
-                this.fillEmptyTableFooters(article);
-                this.fillEmptyFootnotes(article);
-            }
-            await this.rewriteIDs(idGenerator);
-            if (mediaPathGenerator) {
-                await this.rewriteMediaPaths(mediaPathGenerator);
-            }
+            this.labelTargets = (0, labels_1.buildTargets)(manuscriptNode);
+            const body = this.buildBody();
+            article.appendChild(body);
+            const back = this.buildBack(body);
+            this.moveCoiStatementToAuthorNotes(back, front);
+            article.appendChild(back);
+            this.unwrapBody(body);
+            this.moveAbstracts(front, body);
+            this.moveFloatsGroup(body, article);
+            this.removeBackContainer(body);
+            this.updateFootnoteTypes(front, back);
+            this.fillEmptyTableFooters(article);
+            this.fillEmptyFootnotes(article);
+            await this.rewriteIDs();
             return (0, w3c_xmlserializer_1.default)(this.document);
         };
         this.nodeFromJATS = (JATSFragment) => {
@@ -227,16 +220,14 @@ class JATSExporter {
                 }
             }
         };
-        this.buildFront = (doi, id, links) => {
-            var _a, _b, _c, _d, _e;
-            const manuscript = (0, project_bundle_1.findManuscript)(this.modelMap);
-            const titles = (0, project_bundle_1.findTitles)(this.modelMap);
+        this.buildFront = (manuscript, journal) => {
+            var _a;
+            const titleNode = (_a = (0, prosemirror_utils_1.findChildrenByType)(this.manuscriptNode, schema_1.schema.nodes.title)[0]) === null || _a === void 0 ? void 0 : _a.node;
             const front = this.document.createElement('front');
             const journalMeta = this.document.createElement('journal-meta');
             front.appendChild(journalMeta);
             const articleMeta = this.document.createElement('article-meta');
             front.appendChild(articleMeta);
-            const journal = [...this.modelMap.values()].find((model) => model.objectType === json_schema_1.ObjectTypes.Journal);
             if (journal) {
                 if (journal.journalIdentifiers) {
                     for (const item of journal.journalIdentifiers) {
@@ -285,92 +276,35 @@ class JATSExporter {
                     journalMeta.appendChild(publisher);
                 }
             }
-            if (id) {
-                const articleID = this.document.createElement('article-id');
-                articleID.setAttribute('pub-id-type', 'publisher-id');
-                articleID.textContent = id;
-                articleMeta.appendChild(articleID);
-            }
-            if (doi || manuscript.DOI) {
+            if (manuscript.DOI) {
                 const articleID = this.document.createElement('article-id');
                 articleID.setAttribute('pub-id-type', 'doi');
-                articleID.textContent = (_a = manuscript.DOI) !== null && _a !== void 0 ? _a : doi;
+                articleID.textContent = manuscript.DOI;
                 articleMeta.appendChild(articleID);
             }
             const titleGroup = this.document.createElement('title-group');
             articleMeta.appendChild(titleGroup);
             this.buildContributors(articleMeta);
-            if (links && links.self) {
-                for (const [key, value] of Object.entries(links.self)) {
-                    const link = this.document.createElement('self-uri');
-                    link.setAttribute('content-type', key);
-                    link.setAttributeNS(XLINK_NAMESPACE, 'href', value);
-                    articleMeta.appendChild(link);
-                }
-            }
-            if (titles.title) {
+            if (titleNode) {
                 const element = this.document.createElement('article-title');
-                this.setTitleContent(element, titles.title);
+                this.setTitleContent(element, titleNode.textContent);
                 titleGroup.appendChild(element);
             }
-            if (titles.subtitle) {
-                const element = this.document.createElement('subtitle');
-                this.setTitleContent(element, titles.subtitle);
-                titleGroup.appendChild(element);
-            }
-            if (titles.runningTitle) {
-                const element = this.document.createElement('alt-title');
-                element.setAttribute('alt-title-type', 'right-running');
-                this.setTitleContent(element, titles.runningTitle);
-                titleGroup.appendChild(element);
-            }
-            const supplements = [...this.modelMap.values()].filter((model) => model.objectType === json_schema_1.ObjectTypes.Supplement);
-            if (supplements && supplements.length > 0) {
-                for (const supplement of supplements) {
-                    const supplementaryMaterial = this.document.createElement('supplementary-material');
-                    supplementaryMaterial.setAttribute('id', normalizeID(supplement._id));
-                    supplementaryMaterial.setAttributeNS(XLINK_NAMESPACE, 'href', (_b = supplement.href) !== null && _b !== void 0 ? _b : '');
-                    const mimeType = (_c = supplement.MIME) === null || _c === void 0 ? void 0 : _c.split('/')[0];
-                    const mimeSubType = (_d = supplement.MIME) === null || _d === void 0 ? void 0 : _d.split('/')[1];
-                    supplementaryMaterial.setAttribute('mimetype', mimeType !== null && mimeType !== void 0 ? mimeType : '');
-                    supplementaryMaterial.setAttribute('mime-subtype', mimeSubType !== null && mimeSubType !== void 0 ? mimeSubType : '');
-                    const caption = this.document.createElement('caption');
-                    const title = this.document.createElement('title');
-                    title.textContent = (_e = supplement.title) !== null && _e !== void 0 ? _e : '';
-                    caption.append(title);
-                    supplementaryMaterial.append(caption);
-                    articleMeta.append(supplementaryMaterial);
-                }
-            }
-            const history = articleMeta.querySelector('history') ||
-                this.document.createElement('history');
-            if (manuscript.acceptanceDate) {
-                const date = this.buildDateElement(manuscript.acceptanceDate, 'accepted');
-                history.appendChild(date);
-            }
-            if (manuscript.correctionDate) {
-                const date = this.buildDateElement(manuscript.correctionDate, 'corrected');
-                history.appendChild(date);
-            }
-            if (manuscript.retractionDate) {
-                const date = this.buildDateElement(manuscript.retractionDate, 'retracted');
-                history.appendChild(date);
-            }
-            if (manuscript.receiveDate) {
-                const date = this.buildDateElement(manuscript.receiveDate, 'received');
-                history.appendChild(date);
-            }
-            if (manuscript.revisionReceiveDate) {
-                const date = this.buildDateElement(manuscript.revisionReceiveDate, 'rev-recd');
-                history.appendChild(date);
-            }
-            if (manuscript.revisionRequestDate) {
-                const date = this.buildDateElement(manuscript.revisionRequestDate, 'rev-request');
-                history.appendChild(date);
-            }
-            if (history.childElementCount) {
-                articleMeta.appendChild(history);
-            }
+            const supplementsNodes = (0, prosemirror_utils_1.findChildrenByType)(this.manuscriptNode, schema_1.schema.nodes.supplement);
+            supplementsNodes.forEach(({ node }) => {
+                var _a, _b, _c, _d;
+                const supplementaryMaterial = this.document.createElement('supplementary-material');
+                supplementaryMaterial.setAttribute('id', normalizeID(node.attrs.id));
+                supplementaryMaterial.setAttributeNS(XLINK_NAMESPACE, 'href', (_a = node.attrs.href) !== null && _a !== void 0 ? _a : '');
+                supplementaryMaterial.setAttribute('mimetype', (_b = node.attrs.mimeType) !== null && _b !== void 0 ? _b : '');
+                supplementaryMaterial.setAttribute('mime-subtype', (_c = node.attrs.mimeSubType) !== null && _c !== void 0 ? _c : '');
+                const caption = this.document.createElement('caption');
+                const title = this.document.createElement('title');
+                title.textContent = (_d = node.attrs.title) !== null && _d !== void 0 ? _d : '';
+                caption.append(title);
+                supplementaryMaterial.append(caption);
+                articleMeta.append(supplementaryMaterial);
+            });
             this.buildKeywords(articleMeta);
             let countingElements = [];
             if (manuscript.genericCounts) {
@@ -383,11 +317,16 @@ class JATSExporter {
                 });
                 countingElements.push(...elements);
             }
-            countingElements.push(this.buildCountingElement('fig-count', manuscript.figureCount));
-            countingElements.push(this.buildCountingElement('table-count', manuscript.tableCount));
-            countingElements.push(this.buildCountingElement('equation-count', manuscript.equationCount));
-            countingElements.push(this.buildCountingElement('ref-count', manuscript.referencesCount));
-            countingElements.push(this.buildCountingElement('word-count', manuscript.wordCount));
+            const figureCount = (0, prosemirror_utils_1.findChildrenByType)(this.manuscriptNode, schema_1.schema.nodes.figure).length;
+            countingElements.push(this.buildCountingElement('fig-count', figureCount));
+            const equationCount = (0, prosemirror_utils_1.findChildrenByType)(this.manuscriptNode, schema_1.schema.nodes.equation_element).length;
+            const tableCount = (0, prosemirror_utils_1.findChildrenByType)(this.manuscriptNode, schema_1.schema.nodes.table).length;
+            const referencesCount = (0, prosemirror_utils_1.findChildrenByType)(this.manuscriptNode, schema_1.schema.nodes.bibliography_item).length;
+            countingElements.push(this.buildCountingElement('table-count', tableCount));
+            countingElements.push(this.buildCountingElement('equation-count', equationCount));
+            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.document.createElement('counts');
@@ -422,16 +361,17 @@ class JATSExporter {
                 return wordCount;
             }
         };
-        this.buildBody = (fragment) => {
+        this.buildBody = () => {
             const body = this.document.createElement('body');
-            fragment.forEach((cFragment) => {
+            this.manuscriptNode.forEach((cFragment) => {
                 const serializedNode = this.serializeNode(cFragment);
                 body.append(...serializedNode.childNodes);
             });
-            this.fixBody(body, fragment);
+            this.fixBody(body);
             return body;
         };
         this.buildBack = (body) => {
+            var _a;
             const back = this.document.createElement('back');
             this.moveSectionsToBack(back, body);
             const footnotesElements = this.document.querySelectorAll('sec > fn-group');
@@ -456,7 +396,7 @@ class JATSExporter {
             back.appendChild(refList);
             const [meta] = this.citationProvider.makeBibliography();
             for (const id of meta.entry_ids) {
-                const bibliographyItem = this.modelMap.get(id[0]);
+                const bibliographyNode = (_a = (0, prosemirror_utils_1.findChildrenByType)(this.manuscriptNode, schema_1.schema.nodes.bibliography_item).find(({ node }) => node.attrs.id === id[0])) === null || _a === void 0 ? void 0 : _a.node;
                 const ref = this.document.createElement('ref');
                 ref.setAttribute('id', normalizeID(id[0]));
                 const updateCitationPubType = (citationEl, pubType) => {
@@ -475,21 +415,21 @@ class JATSExporter {
                         citationEl.setAttribute('publication-type', 'journal');
                     }
                 };
-                if (bibliographyItem.literal) {
+                if (bibliographyNode === null || bibliographyNode === void 0 ? void 0 : bibliographyNode.attrs.literal) {
                     const mixedCitation = this.document.createElement('mixed-citation');
-                    updateCitationPubType(mixedCitation, bibliographyItem.type);
-                    mixedCitation.textContent = bibliographyItem.literal;
+                    updateCitationPubType(mixedCitation, bibliographyNode.attrs.type);
+                    mixedCitation.textContent = bibliographyNode.attrs.literal;
                     ref.appendChild(mixedCitation);
                     refList.appendChild(ref);
                 }
                 else {
                     const citation = this.document.createElement('element-citation');
-                    updateCitationPubType(citation, bibliographyItem.type);
-                    if (bibliographyItem.author) {
+                    updateCitationPubType(citation, bibliographyNode === null || bibliographyNode === void 0 ? void 0 : bibliographyNode.attrs.type);
+                    if (bibliographyNode === null || bibliographyNode === void 0 ? void 0 : bibliographyNode.attrs.author) {
                         const personGroupNode = this.document.createElement('person-group');
                         personGroupNode.setAttribute('person-group-type', 'author');
                         citation.appendChild(personGroupNode);
-                        bibliographyItem.author.forEach((author) => {
+                        bibliographyNode.attrs.author.forEach((author) => {
                             const name = this.document.createElement('string-name');
                             if (author.family) {
                                 const node = this.document.createElement('surname');
@@ -511,8 +451,8 @@ class JATSExporter {
                             }
                         });
                     }
-                    if (bibliographyItem.issued) {
-                        const dateParts = bibliographyItem.issued['date-parts'];
+                    if (bibliographyNode === null || bibliographyNode === void 0 ? void 0 : bibliographyNode.attrs.issued) {
+                        const dateParts = bibliographyNode === null || bibliographyNode === void 0 ? void 0 : bibliographyNode.attrs.issued['date-parts'];
                         if (dateParts && dateParts.length) {
                             const [[year, month, day]] = dateParts;
                             if (year) {
@@ -532,33 +472,33 @@ class JATSExporter {
                             }
                         }
                     }
-                    if (bibliographyItem.title) {
+                    if (bibliographyNode === null || bibliographyNode === void 0 ? void 0 : bibliographyNode.attrs.title) {
                         const node = this.document.createElement('article-title');
-                        this.setTitleContent(node, bibliographyItem.title);
+                        this.setTitleContent(node, bibliographyNode === null || bibliographyNode === void 0 ? void 0 : bibliographyNode.attrs.title);
                         citation.appendChild(node);
                     }
-                    if (bibliographyItem['container-title']) {
+                    if (bibliographyNode === null || bibliographyNode === void 0 ? void 0 : bibliographyNode.attrs.containerTitle) {
                         const node = this.document.createElement('source');
-                        node.textContent = bibliographyItem['container-title'];
+                        node.textContent = bibliographyNode === null || bibliographyNode === void 0 ? void 0 : bibliographyNode.attrs.containerTitle;
                         citation.appendChild(node);
                     }
-                    if (bibliographyItem.volume) {
+                    if (bibliographyNode === null || bibliographyNode === void 0 ? void 0 : bibliographyNode.attrs.volume) {
                         const node = this.document.createElement('volume');
-                        node.textContent = String(bibliographyItem.volume);
+                        node.textContent = String(bibliographyNode === null || bibliographyNode === void 0 ? void 0 : bibliographyNode.attrs.volume);
                         citation.appendChild(node);
                     }
-                    if (bibliographyItem.issue) {
+                    if (bibliographyNode === null || bibliographyNode === void 0 ? void 0 : bibliographyNode.attrs.issue) {
                         const node = this.document.createElement('issue');
-                        node.textContent = String(bibliographyItem.issue);
+                        node.textContent = String(bibliographyNode === null || bibliographyNode === void 0 ? void 0 : bibliographyNode.attrs.issue);
                         citation.appendChild(node);
                     }
-                    if (bibliographyItem.supplement) {
+                    if (bibliographyNode === null || bibliographyNode === void 0 ? void 0 : bibliographyNode.attrs.supplement) {
                         const node = this.document.createElement('supplement');
-                        node.textContent = bibliographyItem.supplement;
+                        node.textContent = bibliographyNode === null || bibliographyNode === void 0 ? void 0 : bibliographyNode.attrs.supplement;
                         citation.appendChild(node);
                     }
-                    if (bibliographyItem.page) {
-                        const pageString = String(bibliographyItem.page);
+                    if (bibliographyNode === null || bibliographyNode === void 0 ? void 0 : bibliographyNode.attrs.page) {
+                        const pageString = String(bibliographyNode === null || bibliographyNode === void 0 ? void 0 : bibliographyNode.attrs.page);
                         if (/^\d+$/.test(pageString)) {
                             const node = this.document.createElement('fpage');
                             node.textContent = pageString;
@@ -579,10 +519,10 @@ class JATSExporter {
                             citation.appendChild(node);
                         }
                     }
-                    if (bibliographyItem.DOI) {
+                    if (bibliographyNode === null || bibliographyNode === void 0 ? void 0 : bibliographyNode.attrs.doi) {
                         const node = this.document.createElement('pub-id');
                         node.setAttribute('pub-id-type', 'doi');
-                        node.textContent = String(bibliographyItem.DOI);
+                        node.textContent = String(bibliographyNode === null || bibliographyNode === void 0 ? void 0 : bibliographyNode.attrs.doi);
                         citation.appendChild(node);
                     }
                     ref.appendChild(citation);
@@ -592,7 +532,6 @@ class JATSExporter {
             return back;
         };
         this.createSerializer = () => {
-            const getModel = (id) => id ? this.modelMap.get(id) : undefined;
             const nodes = {
                 author_notes: () => '',
                 corresp: () => '',
@@ -654,24 +593,25 @@ class JATSExporter {
                     return xref;
                 },
                 cross_reference: (node) => {
+                    var _a;
                     const cross = node;
                     const rids = cross.attrs.rids;
                     if (!rids.length) {
                         return cross.attrs.label;
                     }
                     const text = cross.attrs.customLabel || cross.attrs.label;
-                    const model = getModel(rids[0]);
-                    if (!model) {
+                    const target = (_a = (0, prosemirror_utils_1.findChildrenByAttr)(this.manuscriptNode, (attrs) => attrs.id === rids[0])[0]) === null || _a === void 0 ? void 0 : _a.node;
+                    if (!target) {
                         warn('');
                         return text;
                     }
                     const xref = this.document.createElement('xref');
-                    const type = chooseRefType(model.objectType);
+                    const type = chooseRefType(target.type);
                     if (type) {
                         xref.setAttribute('ref-type', type);
                     }
                     else {
-                        warn(`Unset ref-type for objectType ${model.objectType}`);
+                        warn(`Unset ref-type for schema type ${target.type.name}`);
                     }
                     xref.setAttribute('rid', normalizeID(rids.join(' ')));
                     xref.textContent = text;
@@ -743,7 +683,10 @@ class JATSExporter {
                 hard_break: () => '',
                 highlight_marker: () => '',
                 inline_footnote: (node) => {
-                    const rids = node.attrs.rids.filter(getModel);
+                    const rids = node.attrs.rids.filter((rid) => {
+                        var _a;
+                        return (_a = (0, prosemirror_utils_1.findChildrenByAttr)(this.manuscriptNode, (attrs) => attrs.id === rid)[0]) === null || _a === void 0 ? void 0 : _a.node;
+                    });
                     if (rids.length == 0) {
                         return '';
                     }
@@ -862,14 +805,7 @@ class JATSExporter {
                 italic: () => ['italic'],
                 smallcaps: () => ['sc'],
                 strikethrough: () => ['strike'],
-                styled: (mark) => {
-                    const inlineStyle = getModel(mark.attrs.rid);
-                    const attrs = {};
-                    if (inlineStyle && inlineStyle.title) {
-                        attrs.style = (0, styled_content_1.normalizeStyleName)(inlineStyle.title);
-                    }
-                    return ['styled-content', attrs];
-                },
+                styled: () => ['styled-content'],
                 superscript: () => ['sup'],
                 subscript: () => ['sub'],
                 underline: () => ['underline'],
@@ -920,14 +856,16 @@ class JATSExporter {
                 }
             };
             const appendChildNodeOfType = (element, node, type) => {
-                const childNode = findChildNodeOfType(node, type);
+                var _a;
+                const childNode = (_a = (0, prosemirror_utils_1.findChildrenByType)(node, type)[0]) === null || _a === void 0 ? void 0 : _a.node;
                 if (childNode) {
                     element.appendChild(this.serializeNode(childNode));
                 }
             };
             const appendTable = (element, node) => {
-                const tableNode = findChildNodeOfType(node, node.type.schema.nodes.table);
-                const colGroupNode = findChildNodeOfType(node, node.type.schema.nodes.table_colgroup);
+                var _a, _b;
+                const tableNode = (_a = (0, prosemirror_utils_1.findChildrenByType)(node, node.type.schema.nodes.table)[0]) === null || _a === void 0 ? void 0 : _a.node;
+                const colGroupNode = (_b = (0, prosemirror_utils_1.findChildrenByType)(node, node.type.schema.nodes.table_colgroup)[0]) === null || _b === void 0 ? void 0 : _b.node;
                 if (!tableNode) {
                     return;
                 }
@@ -973,7 +911,8 @@ class JATSExporter {
                 return element;
             };
             const processExecutableNode = (node, element) => {
-                const listingNode = findChildNodeOfType(node, node.type.schema.nodes.listing);
+                var _a;
+                const listingNode = (_a = (0, prosemirror_utils_1.findChildrenByType)(node, node.type.schema.nodes.listing)[0]) === null || _a === void 0 ? void 0 : _a.node;
                 if (listingNode) {
                     const { contents, languageKey } = listingNode.attrs;
                     if (contents && languageKey) {
@@ -1007,25 +946,25 @@ class JATSExporter {
                 }
             };
         };
-        this.serializeFragment = (fragment) => this.serializer.serializeFragment(fragment, {
-            document: this.document,
-        });
         this.serializeNode = (node) => this.serializer.serializeNode(node, {
             document: this.document,
         });
         this.validateContributor = (contributor) => {
-            if (!contributor.bibliographicName) {
-                throw new Error(`${contributor._id} has no bibliographicName`);
+            if (!contributor.attrs.bibliographicName) {
+                throw new Error(`${contributor.attrs.id} has no bibliographicName`);
             }
-            const { family, given } = contributor.bibliographicName;
+            const { family, given } = contributor.attrs.bibliographicName;
             if (!family && !given) {
-                throw new Error(`${contributor._id} has neither family nor given name`);
+                throw new Error(`${contributor.attrs.id} has neither family nor given name`);
             }
         };
         this.buildContributors = (articleMeta) => {
-            const contributors = this.models.filter(isContributor);
-            const authorContributors = contributors
-                .filter((contributor) => contributor.role === 'author')
+            const contributorNodes = (0, prosemirror_utils_1.findChildrenByType)(this.manuscriptNode, schema_1.schema.nodes.contributor).map((result) => result.node);
+            const authorContributorNodes = contributorNodes
+                .filter((n) => n.attrs.role === 'author')
+                .sort(sortContributors);
+            const otherContributorsNodes = contributorNodes
+                .filter((n) => n.attrs.role !== 'author')
                 .sort(sortContributors);
             const affiliationLabels = new Map();
             const creatAffiliationLabel = (rid) => {
@@ -1043,11 +982,11 @@ class JATSExporter {
                 sup.textContent = String(content);
                 return sup;
             };
-            if (authorContributors.length) {
+            if (authorContributorNodes.length) {
                 const contribGroup = this.document.createElement('contrib-group');
                 contribGroup.setAttribute('content-type', 'authors');
                 articleMeta.appendChild(contribGroup);
-                authorContributors.forEach((contributor) => {
+                authorContributorNodes.forEach((contributor) => {
                     try {
                         this.validateContributor(contributor);
                     }
@@ -1057,39 +996,25 @@ class JATSExporter {
                     }
                     const contrib = this.document.createElement('contrib');
                     contrib.setAttribute('contrib-type', 'author');
-                    contrib.setAttribute('id', normalizeID(contributor._id));
-                    if (contributor.isCorresponding) {
+                    contrib.setAttribute('id', normalizeID(contributor.attrs.id));
+                    if (contributor.attrs.isCorresponding) {
                         contrib.setAttribute('corresp', 'yes');
                     }
-                    if (contributor.ORCIDIdentifier) {
+                    if (contributor.attrs.ORCIDIdentifier) {
                         const identifier = this.document.createElement('contrib-id');
                         identifier.setAttribute('contrib-id-type', 'orcid');
-                        identifier.textContent = contributor.ORCIDIdentifier;
+                        identifier.textContent = contributor.attrs.ORCIDIdentifier;
                         contrib.appendChild(identifier);
                     }
                     const name = this.buildContributorName(contributor);
                     contrib.appendChild(name);
-                    if (contributor.email) {
+                    if (contributor.attrs.email) {
                         const email = this.document.createElement('email');
-                        email.textContent = contributor.email;
+                        email.textContent = contributor.attrs.email;
                         contrib.appendChild(email);
                     }
-                    if (contributor.roles) {
-                        contributor.roles.forEach((rid) => {
-                            const contributorRole = this.modelMap.get(rid);
-                            if (contributorRole) {
-                                const role = this.document.createElement('role');
-                                const attributes = chooseRoleVocabAttributes(contributorRole);
-                                for (const [key, value] of Object.entries(attributes)) {
-                                    role.setAttribute(key, value);
-                                }
-                                role.textContent = contributorRole.name;
-                                contrib.appendChild(role);
-                            }
-                        });
-                    }
-                    if (contributor.affiliations) {
-                        contributor.affiliations.forEach((rid) => {
+                    if (contributor.attrs.affiliations) {
+                        contributor.attrs.affiliations.forEach((rid) => {
                             const xref = this.document.createElement('xref');
                             xref.setAttribute('ref-type', 'aff');
                             xref.setAttribute('rid', normalizeID(rid));
@@ -1097,8 +1022,8 @@ class JATSExporter {
                             contrib.appendChild(xref);
                         });
                     }
-                    if (contributor.footnote) {
-                        contributor.footnote.map((note) => {
+                    if (contributor.attrs.footnote) {
+                        contributor.attrs.footnote.map((note) => {
                             const xref = this.document.createElement('xref');
                             xref.setAttribute('ref-type', 'fn');
                             xref.setAttribute('rid', normalizeID(note.noteID));
@@ -1106,8 +1031,8 @@ class JATSExporter {
                             contrib.appendChild(xref);
                         });
                     }
-                    if (contributor.corresp) {
-                        contributor.corresp.map((corresp) => {
+                    if (contributor.attrs.corresp) {
+                        contributor.attrs.corresp.map((corresp) => {
                             const xref = this.document.createElement('xref');
                             xref.setAttribute('ref-type', 'corresp');
                             xref.setAttribute('rid', normalizeID(corresp.correspID));
@@ -1117,13 +1042,10 @@ class JATSExporter {
                     }
                     contribGroup.appendChild(contrib);
                 });
-                const otherContributors = contributors
-                    .filter((contributor) => contributor.role !== 'author')
-                    .sort(sortContributors);
-                if (otherContributors.length) {
+                if (otherContributorsNodes.length) {
                     const contribGroup = this.document.createElement('contrib-group');
                     articleMeta.appendChild(contribGroup);
-                    otherContributors.forEach((contributor) => {
+                    otherContributorsNodes.forEach((contributor) => {
                         try {
                             this.validateContributor(contributor);
                         }
@@ -1132,30 +1054,16 @@ class JATSExporter {
                             return;
                         }
                         const contrib = this.document.createElement('contrib');
-                        contrib.setAttribute('id', normalizeID(contributor._id));
+                        contrib.setAttribute('id', normalizeID(contributor.attrs.id));
                         const name = this.buildContributorName(contributor);
                         contrib.appendChild(name);
-                        if (contributor.email) {
+                        if (contributor.attrs.email) {
                             const email = this.document.createElement('email');
-                            email.textContent = contributor.email;
+                            email.textContent = contributor.attrs.email;
                             contrib.appendChild(email);
                         }
-                        if (contributor.roles) {
-                            contributor.roles.forEach((rid) => {
-                                const contributorRole = this.modelMap.get(rid);
-                                if (contributorRole) {
-                                    const role = this.document.createElement('role');
-                                    const attributes = chooseRoleVocabAttributes(contributorRole);
-                                    for (const [key, value] of Object.entries(attributes)) {
-                                        role.setAttribute(key, value);
-                                    }
-                                    role.textContent = contributorRole.name;
-                                    contrib.appendChild(role);
-                                }
-                            });
-                        }
-                        if (contributor.affiliations) {
-                            contributor.affiliations.forEach((rid) => {
+                        if (contributor.attrs.affiliations) {
+                            contributor.attrs.affiliations.forEach((rid) => {
                                 const xref = this.document.createElement('xref');
                                 xref.setAttribute('ref-type', 'aff');
                                 xref.setAttribute('rid', normalizeID(rid));
@@ -1163,8 +1071,8 @@ class JATSExporter {
                                 contrib.appendChild(xref);
                             });
                         }
-                        if (contributor.footnote) {
-                            contributor.footnote.map((note) => {
+                        if (contributor.attrs.footnote) {
+                            contributor.attrs.footnote.map((note) => {
                                 const xref = this.document.createElement('xref');
                                 xref.setAttribute('ref-type', 'fn');
                                 xref.setAttribute('rid', normalizeID(note.noteID));
@@ -1176,64 +1084,68 @@ class JATSExporter {
                     });
                 }
                 const affiliationRIDs = [];
-                const sortedContributors = [...authorContributors, ...otherContributors];
+                const sortedContributors = [
+                    ...authorContributorNodes,
+                    ...otherContributorsNodes,
+                ];
                 for (const contributor of sortedContributors) {
-                    if (contributor.affiliations) {
-                        affiliationRIDs.push(...contributor.affiliations);
+                    if (contributor.attrs.affiliations) {
+                        affiliationRIDs.push(...contributor.attrs.affiliations);
                     }
                 }
-                const affiliations = this.models.filter((0, object_types_1.hasObjectType)(json_schema_1.ObjectTypes.Affiliation));
+                const affiliations = (0, prosemirror_utils_1.findChildrenByType)(this.manuscriptNode, schema_1.schema.nodes.affiliation).map((result) => result.node);
                 if (affiliations) {
-                    const usedAffiliations = affiliations.filter((affiliation) => affiliationRIDs.includes(affiliation._id));
-                    usedAffiliations.sort((a, b) => affiliationRIDs.indexOf(a._id) - affiliationRIDs.indexOf(b._id));
+                    const usedAffiliations = affiliations.filter((affiliation) => affiliationRIDs.includes(affiliation.attrs.id));
+                    usedAffiliations.sort((a, b) => affiliationRIDs.indexOf(a.attrs.id) -
+                        affiliationRIDs.indexOf(b.attrs.id));
                     usedAffiliations.forEach((affiliation) => {
                         var _a, _b;
                         const aff = this.document.createElement('aff');
-                        aff.setAttribute('id', normalizeID(affiliation._id));
+                        aff.setAttribute('id', normalizeID(affiliation.attrs.id));
                         contribGroup.appendChild(aff);
-                        if (affiliation.department) {
+                        if (affiliation.attrs.department) {
                             const department = this.document.createElement('institution');
                             department.setAttribute('content-type', 'dept');
-                            department.textContent = affiliation.department;
+                            department.textContent = affiliation.attrs.department;
                             aff.appendChild(department);
                         }
-                        if (affiliation.institution) {
+                        if (affiliation.attrs.institution) {
                             const institution = this.document.createElement('institution');
-                            institution.textContent = affiliation.institution;
+                            institution.textContent = affiliation.attrs.institution;
                             aff.appendChild(institution);
                         }
-                        if (affiliation.addressLine1) {
+                        if (affiliation.attrs.addressLine1) {
                             const addressLine = this.document.createElement('addr-line');
-                            addressLine.textContent = affiliation.addressLine1;
+                            addressLine.textContent = affiliation.attrs.addressLine1;
                             aff.appendChild(addressLine);
                         }
-                        if (affiliation.addressLine2) {
+                        if (affiliation.attrs.addressLine2) {
                             const addressLine = this.document.createElement('addr-line');
-                            addressLine.textContent = affiliation.addressLine2;
+                            addressLine.textContent = affiliation.attrs.addressLine2;
                             aff.appendChild(addressLine);
                         }
-                        if (affiliation.addressLine3) {
+                        if (affiliation.attrs.addressLine3) {
                             const addressLine = this.document.createElement('addr-line');
-                            addressLine.textContent = affiliation.addressLine3;
+                            addressLine.textContent = affiliation.attrs.addressLine3;
                             aff.appendChild(addressLine);
                         }
-                        if (affiliation.city) {
+                        if (affiliation.attrs.city) {
                             const city = this.document.createElement('city');
-                            city.textContent = affiliation.city;
+                            city.textContent = affiliation.attrs.city;
                             aff.appendChild(city);
                         }
-                        if (affiliation.country) {
+                        if (affiliation.attrs.country) {
                             const country = this.document.createElement('country');
-                            country.textContent = affiliation.country;
+                            country.textContent = affiliation.attrs.country;
                             aff.appendChild(country);
                         }
-                        if (affiliation.email) {
+                        if (affiliation.attrs.email) {
                             const email = this.document.createElement('email');
-                            email.setAttributeNS(XLINK_NAMESPACE, 'href', (_a = affiliation.email.href) !== null && _a !== void 0 ? _a : '');
-                            email.textContent = (_b = affiliation.email.text) !== null && _b !== void 0 ? _b : '';
+                            email.setAttributeNS(XLINK_NAMESPACE, 'href', (_a = affiliation.attrs.email.href) !== null && _a !== void 0 ? _a : '');
+                            email.textContent = (_b = affiliation.attrs.email.text) !== null && _b !== void 0 ? _b : '';
                             aff.appendChild(email);
                         }
-                        const labelNumber = affiliationLabels.get(affiliation._id);
+                        const labelNumber = affiliationLabels.get(affiliation.attrs.id);
                         if (labelNumber) {
                             const label = this.document.createElement('label');
                             label.textContent = String(labelNumber);
@@ -1250,41 +1162,48 @@ class JATSExporter {
         this.createAuthorNotesElement = () => {
             var _a;
             const authorNotesEl = this.document.createElement('author-notes');
-            const authorNotes = (_a = (0, json_schema_1.getModelsByType)(this.modelMap, json_schema_1.ObjectTypes.AuthorNotes)) === null || _a === void 0 ? void 0 : _a[0];
-            if (authorNotes) {
-                this.appendModelsToAuthorNotes(authorNotesEl, authorNotes.containedObjectIDs);
+            const authorNotesNode = (_a = (0, prosemirror_utils_1.findChildrenByType)(this.manuscriptNode, schema_1.schema.nodes.author_notes)[0]) === null || _a === void 0 ? void 0 : _a.node;
+            if (authorNotesNode) {
+                this.appendModelsToAuthorNotes(authorNotesEl, authorNotesNode);
             }
             return authorNotesEl;
         };
         this.appendCorrespondingToElement = (corresponding, element) => {
             const correspondingEl = this.document.createElement('corresp');
-            correspondingEl.setAttribute('id', normalizeID(corresponding._id));
-            if (corresponding.label) {
+            correspondingEl.setAttribute('id', normalizeID(corresponding.attrs.id));
+            if (corresponding.attrs.label) {
                 const labelEl = this.document.createElement('label');
-                labelEl.textContent = corresponding.label;
+                labelEl.textContent = corresponding.attrs.label;
                 correspondingEl.appendChild(labelEl);
             }
-            correspondingEl.append(corresponding.contents);
+            correspondingEl.append(corresponding.textContent);
             element.appendChild(correspondingEl);
         };
         this.appendParagraphToElement = (paragraph, element) => {
-            const parsedDoc = new DOMParser().parseFromString(paragraph.contents, 'text/html');
+            const parsedDoc = new DOMParser().parseFromString(paragraph.textContent, 'text/html');
             const parsedParagraph = parsedDoc.body.querySelector('p');
             if (parsedParagraph) {
                 const paragraphEl = this.document.createElement('p');
                 paragraphEl.innerHTML = parsedParagraph.innerHTML;
-                paragraphEl.setAttribute('id', normalizeID(paragraph._id));
+                paragraphEl.setAttribute('id', normalizeID(paragraph.attrs.id));
                 element.appendChild(paragraphEl);
             }
         };
         this.appendFootnoteToElement = (footnote, element) => {
             const footnoteEl = this.document.createElement('fn');
-            footnoteEl.setAttribute('id', normalizeID(footnote._id));
-            footnoteEl.innerHTML = footnote.contents;
+            footnoteEl.setAttribute('id', normalizeID(footnote.attrs.id));
+            if (!footnote.textContent.includes('<p>')) {
+                const p = this.document.createElement('p');
+                p.innerHTML = footnote.textContent;
+                footnoteEl.appendChild(p);
+            }
+            else {
+                footnoteEl.innerHTML = footnote.textContent;
+            }
             element.appendChild(footnoteEl);
         };
-        this.fixBody = (body, fragment) => {
-            fragment.descendants((node) => {
+        this.fixBody = (body) => {
+            this.manuscriptNode.descendants((node) => {
                 if (node.attrs.id) {
                     if (node.attrs.titleSuppressed) {
                         const title = body.querySelector(`#${normalizeID(node.attrs.id)} > title`);
@@ -1545,36 +1464,36 @@ class JATSExporter {
         };
         this.buildContributorName = (contributor) => {
             const name = this.document.createElement('name');
-            if (contributor.bibliographicName.family) {
+            if (contributor.attrs.bibliographicName.family) {
                 const surname = this.document.createElement('surname');
-                surname.textContent = contributor.bibliographicName.family;
+                surname.textContent = contributor.attrs.bibliographicName.family;
                 name.appendChild(surname);
             }
-            if (contributor.bibliographicName.given) {
+            if (contributor.attrs.bibliographicName.given) {
                 const givenNames = this.document.createElement('given-names');
-                givenNames.textContent = contributor.bibliographicName.given;
+                givenNames.textContent = contributor.attrs.bibliographicName.given;
                 name.appendChild(givenNames);
             }
             return name;
         };
     }
-    generateCitations(fragment) {
+    generateCitations() {
         const nodes = [];
-        fragment.descendants((node) => {
+        this.manuscriptNode.descendants((node) => {
             if ((0, schema_1.isCitationNode)(node)) {
                 nodes.push(node);
             }
         });
         return (0, exports.buildCitations)(nodes);
     }
-    generateCitationTexts(fragment, csl) {
+    generateCitationTexts(csl, manuscriptID) {
         this.citationTexts = new Map();
         this.citationProvider = new library_1.CitationProvider({
-            getLibraryItem: (id) => this.modelMap.get(id),
+            getLibraryItem: this.getLibraryItem(manuscriptID),
             locale: csl.locale,
             citationStyle: csl.style,
         });
-        const citations = this.generateCitations(fragment);
+        const citations = this.generateCitations();
         this.citationProvider.rebuildState(citations).forEach(([id, , output]) => {
             this.citationTexts.set(id, output);
         });
@@ -1601,72 +1520,50 @@ class JATSExporter {
             return mathml;
         }
     }
-    appendModelsToAuthorNotes(authorNotesEl, containedObjectIDs) {
-        const contributors = this.models.filter(isContributor);
-        const usedCorrespondings = this.getUsedCorrespondings(contributors);
-        containedObjectIDs.forEach((id) => {
-            const model = this.modelMap.get(id);
-            if (!model) {
-                return;
-            }
-            switch (model.objectType) {
-                case json_schema_1.ObjectTypes.ParagraphElement:
-                    this.appendParagraphToElement(model, authorNotesEl);
+    appendModelsToAuthorNotes(authorNotesEl, authorNotesNode) {
+        const contributorsNodes = (0, prosemirror_utils_1.findChildrenByType)(this.manuscriptNode, schema_1.schema.nodes.contributor).map((result) => result.node);
+        const usedCorrespondings = this.getUsedCorrespondings(contributorsNodes);
+        authorNotesNode.descendants((node) => {
+            switch (node.type) {
+                case schema_1.schema.nodes.paragraph:
+                    this.appendParagraphToElement(node, authorNotesEl);
                     break;
-                case json_schema_1.ObjectTypes.Footnote:
-                    this.appendFootnoteToElement(model, authorNotesEl);
+                case schema_1.schema.nodes.footnote:
+                    this.appendFootnoteToElement(node, authorNotesEl);
                     break;
-                case json_schema_1.ObjectTypes.Corresponding:
-                    if (usedCorrespondings.includes(model)) {
-                        this.appendCorrespondingToElement(model, authorNotesEl);
+                case schema_1.schema.nodes.corresp:
+                    if (usedCorrespondings.includes(node)) {
+                        this.appendCorrespondingToElement(node, authorNotesEl);
                     }
                     break;
             }
+            return false;
         });
     }
     getUsedCorrespondings(contributors) {
         return contributors
-            .flatMap((c) => { var _a; return (_a = c.corresp) !== null && _a !== void 0 ? _a : []; })
-            .map((corresp) => this.modelMap.get(corresp.correspID))
+            .flatMap((c) => { var _a; return (_a = c.attrs.corresp) !== null && _a !== void 0 ? _a : []; })
+            .map((corresp) => {
+            var _a;
+            return (_a = (0, prosemirror_utils_1.findChildrenByAttr)(this.manuscriptNode, (attr) => attr.id === corresp.correspID)[0]) === null || _a === void 0 ? void 0 : _a.node;
+        })
             .filter((corresp) => !!corresp);
     }
     buildKeywords(articleMeta) {
-        const keywords = [...this.modelMap.values()].filter((model) => model.objectType === json_schema_1.ObjectTypes.Keyword);
-        const keywordGroups = new Map();
-        keywords.forEach((keyword) => {
-            const containedGroup = keyword.containedGroup || '';
-            const group = keywordGroups.get(containedGroup);
-            if (group) {
-                group.push(keyword);
-            }
-            else {
-                keywordGroups.set(containedGroup, [keyword]);
-            }
-        });
-        for (const [groupID, keywords] of keywordGroups) {
-            const keywordGroup = (this.modelMap.get(groupID) || {});
+        const keywordGroups = (0, prosemirror_utils_1.findChildrenByType)(this.manuscriptNode, schema_1.schema.nodes.keyword_group).map((result) => result.node);
+        keywordGroups.forEach((group) => {
             const kwdGroup = this.document.createElement('kwd-group');
-            if (keywordGroup.type) {
-                kwdGroup.setAttribute('kwd-group-type', keywordGroup.type);
-            }
-            if (keywordGroup.label) {
-                const label = this.document.createElement('label');
-                label.textContent = keywordGroup.label;
-                kwdGroup.appendChild(label);
-            }
-            if (keywordGroup.title) {
-                const title = this.document.createElement('title');
-                title.textContent = keywordGroup.title;
-                kwdGroup.appendChild(title);
+            if (group.attrs.type) {
+                kwdGroup.setAttribute('kwd-group-type', group.attrs.type);
             }
             articleMeta.appendChild(kwdGroup);
-            for (const keyword of keywords) {
+            group.content.forEach((keyword) => {
                 const kwd = this.document.createElement('kwd');
-                kwd.textContent = keyword.name;
+                kwd.textContent = keyword.textContent;
                 kwdGroup.appendChild(kwd);
-            }
+            });
             articleMeta.appendChild(kwdGroup);
-        }
+        });
     }
     moveCoiStatementToAuthorNotes(back, front) {
         const fnGroups = back.querySelectorAll('fn-group');