@manuscripts/transform 4.3.22 → 4.3.24

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

@@ -98,7 +98,7 @@ export class JATSExporter {
             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(options.journal);
+            const front = this.buildFront();
             article.appendChild(front);
             article.setAttribute('article-type', manuscriptNode.attrs.articleType || 'other');
             article.setAttributeNS(XML_NAMESPACE, 'lang', manuscriptNode.attrs.primaryLanguageCode || 'en');
@@ -207,60 +207,10 @@ export class JATSExporter {
                 }
             }
         };
-        this.buildFront = (journal) => {
+        this.buildFront = () => {
             const front = this.createElement('front');
-            const journalMeta = this.createElement('journal-meta');
-            front.appendChild(journalMeta);
             const articleMeta = this.createElement('article-meta');
             front.appendChild(articleMeta);
-            if (journal) {
-                if (journal.journalIdentifiers) {
-                    for (const item of journal.journalIdentifiers) {
-                        const element = this.createElement('journal-id');
-                        if (item.journalIDType) {
-                            element.setAttribute('journal-id-type', item.journalIDType);
-                        }
-                        element.textContent = item.journalID;
-                        journalMeta.appendChild(element);
-                    }
-                }
-                if (journal.title || journal.abbreviatedTitles) {
-                    const parentElement = this.createElement('journal-title-group');
-                    journalMeta.appendChild(parentElement);
-                    if (journal.title) {
-                        const element = this.createElement('journal-title');
-                        element.textContent = journal.title;
-                        parentElement.appendChild(element);
-                    }
-                    if (journal.abbreviatedTitles) {
-                        for (const item of journal.abbreviatedTitles) {
-                            const element = this.createElement('abbrev-journal-title');
-                            if (item.abbrevType) {
-                                element.setAttribute('abbrev-type', item.abbrevType);
-                            }
-                            element.textContent = item.abbreviatedTitle;
-                            parentElement.appendChild(element);
-                        }
-                    }
-                }
-                if (journal.ISSNs) {
-                    for (const item of journal.ISSNs) {
-                        const element = this.createElement('issn');
-                        if (item.publicationType) {
-                            element.setAttribute('pub-type', item.publicationType);
-                        }
-                        element.textContent = item.ISSN;
-                        journalMeta.appendChild(element);
-                    }
-                }
-                if (journal.publisherName) {
-                    const publisher = this.createElement('publisher');
-                    const publisherName = this.createElement('publisher-name');
-                    publisherName.textContent = journal.publisherName;
-                    publisher.appendChild(publisherName);
-                    journalMeta.appendChild(publisher);
-                }
-            }
             if (this.manuscriptNode.attrs.doi) {
                 const articleID = this.createElement('article-id');
                 articleID.setAttribute('pub-id-type', 'doi');
@@ -345,18 +295,15 @@ export class JATSExporter {
                 counts.append(...countingElements);
                 articleMeta.append(counts);
             }
-            if (!journalMeta.hasChildNodes()) {
-                journalMeta.remove();
-            }
-            const selfUriAttachments = this.getChildrenOfType(schema.nodes.attachment);
-            selfUriAttachments.forEach((attachment) => {
-                const selfUriElement = this.createElement('self-uri');
-                selfUriElement.setAttribute('content-type', attachment.attrs.type);
-                selfUriElement.setAttributeNS(XLINK_NAMESPACE, 'href', attachment.attrs.href);
+            const attachments = this.getChildrenOfType(schema.nodes.attachment);
+            attachments.forEach((attachment) => {
+                const $selfUri = this.createElement('self-uri');
+                $selfUri.setAttribute('content-type', attachment.attrs.type);
+                $selfUri.setAttributeNS(XLINK_NAMESPACE, 'href', attachment.attrs.href);
                 const insertBeforeElements = articleMeta.querySelector('related-article, related-object, abstract, trans-abstract, kwd-group, funding-group, support-group, conference, counts, custom-meta-group');
                 insertBeforeElements
-                    ? articleMeta.insertBefore(selfUriElement, insertBeforeElements)
-                    : articleMeta.appendChild(selfUriElement);
+                    ? articleMeta.insertBefore($selfUri, insertBeforeElements)
+                    : articleMeta.appendChild($selfUri);
             });
             return front;
         };
@@ -967,219 +914,219 @@ export class JATSExporter {
         this.serializeNode = (node) => this.serializer.serializeNode(node, {
             document: this.document,
         });
-        this.validateContributor = (contributor) => {
-            if (!contributor.attrs.bibliographicName) {
-                throw new Error(`${contributor.attrs.id} has no bibliographicName`);
-            }
-            const { family, given } = contributor.attrs.bibliographicName;
-            if (!family && !given) {
-                throw new Error(`${contributor.attrs.id} has neither family nor given name`);
-            }
-        };
         this.buildContributors = (articleMeta) => {
             const contributors = this.getChildrenOfType(schema.nodes.contributor).sort(sortContributors);
-            const affiliationLabels = new Map();
-            const creatAffiliationLabel = (rid) => {
-                let label = affiliationLabels.get(rid);
+            if (!contributors.length) {
+                return;
+            }
+            const labels = new Map();
+            const createLabel = (id) => {
+                let label = labels.get(id);
                 if (!label) {
-                    label = String(affiliationLabels.size + 1);
-                    affiliationLabels.set(rid, label);
+                    label = labels.size + 1;
+                    labels.set(id, label);
                 }
                 const sup = this.createElement('sup');
                 sup.textContent = String(label);
                 return sup;
             };
-            const createFootNotesLabels = (content) => {
-                const sup = this.createElement('sup');
-                sup.textContent = String(content);
-                return sup;
-            };
-            if (contributors.length) {
-                const contribGroup = this.createElement('contrib-group');
-                contribGroup.setAttribute('content-type', 'authors');
-                articleMeta.appendChild(contribGroup);
-                contributors.forEach((contributor) => {
-                    try {
-                        this.validateContributor(contributor);
-                    }
-                    catch (error) {
-                        return;
-                    }
-                    const contrib = this.createElement('contrib');
-                    contrib.setAttribute('contrib-type', 'author');
-                    contrib.setAttribute('id', normalizeID(contributor.attrs.id));
-                    if (contributor.attrs.isCorresponding) {
-                        contrib.setAttribute('corresp', 'yes');
-                    }
-                    if (contributor.attrs.role) {
-                        this.appendElement(contrib, 'role', contributor.attrs.role);
-                    }
-                    if (contributor.attrs.ORCIDIdentifier) {
-                        this.appendElement(contrib, 'contrib-id', contributor.attrs.ORCIDIdentifier, { 'contrib-id-type': 'orcid' });
-                    }
-                    const name = this.buildContributorName(contributor);
-                    contrib.appendChild(name);
-                    if (contributor.attrs.email) {
-                        this.appendElement(contrib, 'email', contributor.attrs.email);
-                    }
-                    if (contributor.attrs.affiliations) {
-                        contributor.attrs.affiliations.forEach((rid) => {
-                            const xref = this.appendElement(contrib, 'xref', '', {
-                                'ref-type': 'aff',
-                                rid: normalizeID(rid),
-                            });
-                            xref.appendChild(creatAffiliationLabel(rid));
-                            contrib.appendChild(xref);
-                        });
-                    }
-                    if (contributor.attrs.footnote) {
-                        contributor.attrs.footnote.map((note) => {
-                            const xref = this.appendElement(contrib, 'xref', '', {
-                                'ref-type': 'fn',
-                                rid: normalizeID(note.noteID),
-                            });
-                            xref.appendChild(createFootNotesLabels(note.noteLabel));
-                            contrib.appendChild(xref);
-                        });
-                    }
-                    if (contributor.attrs.corresp) {
-                        contributor.attrs.corresp.map((corresp) => {
-                            const xref = this.appendElement(contrib, 'xref', '', {
-                                'ref-type': 'corresp',
-                                rid: normalizeID(corresp.correspID),
-                            });
-                            xref.appendChild(createFootNotesLabels(corresp.correspLabel));
-                            contrib.appendChild(xref);
-                        });
-                    }
-                    if (contributor.attrs.creditRoles) {
-                        contributor.attrs.creditRoles.forEach((cr) => {
-                            const role = this.createElement('role');
-                            const creditUrl = CreditRoleUrls.get(cr.vocabTerm);
-                            if (creditUrl) {
-                                role.setAttribute('vocab-identifier', 'http://credit.niso.org/');
-                                role.setAttribute('vocab', 'CRediT');
-                                role.setAttribute('vocab-term', cr.vocabTerm);
-                                role.setAttribute('vocab-term-identifier', creditUrl);
-                                role.textContent = cr.vocabTerm;
-                            }
-                            contrib.appendChild(role);
-                        });
-                    }
-                    contribGroup.appendChild(contrib);
-                });
-                const affiliationRIDs = [];
-                for (const contributor of contributors) {
-                    if (contributor.attrs.affiliations) {
-                        affiliationRIDs.push(...contributor.attrs.affiliations);
-                    }
+            const $contribGroup = this.createElement('contrib-group');
+            $contribGroup.setAttribute('content-type', 'authors');
+            articleMeta.appendChild($contribGroup);
+            contributors.forEach((contributor) => {
+                const $contrib = this.createElement('contrib');
+                $contrib.setAttribute('contrib-type', 'author');
+                $contrib.setAttribute('id', normalizeID(contributor.attrs.id));
+                if (contributor.attrs.isCorresponding) {
+                    $contrib.setAttribute('corresp', 'yes');
+                }
+                if (contributor.attrs.role) {
+                    this.appendElement($contrib, 'role', contributor.attrs.role);
                 }
-                const affiliationIDs = contributors.flatMap((n) => n.attrs.affiliations);
-                const sortAffiliations = (a, b) => affiliationIDs.indexOf(a.attrs.id) - affiliationIDs.indexOf(b.attrs.id);
-                this.getChildrenOfType(schema.nodes.affiliation)
-                    .filter((a) => affiliationIDs.includes(a.attrs.id))
-                    .sort(sortAffiliations)
-                    .forEach((affiliation) => {
-                    const $aff = this.createElement('aff', '', {
-                        id: normalizeID(affiliation.attrs.id),
+                if (contributor.attrs.ORCID) {
+                    this.appendElement($contrib, 'contrib-id', contributor.attrs.ORCID, {
+                        'contrib-id-type': 'orcid',
                     });
-                    const label = affiliationLabels.get(affiliation.attrs.id);
-                    if (label) {
-                        this.appendElement($aff, 'label', String(label));
-                    }
-                    const affiliationParts = [
-                        {
-                            value: affiliation.attrs.department,
-                            tag: 'institution',
-                            'content-type': 'dept',
-                        },
-                        { value: affiliation.attrs.institution, tag: 'institution' },
-                        { value: affiliation.attrs.addressLine1, tag: 'addr-line' },
-                        { value: affiliation.attrs.addressLine2, tag: 'addr-line' },
-                        { value: affiliation.attrs.addressLine3, tag: 'addr-line' },
-                        { value: affiliation.attrs.city, tag: 'city' },
-                        { value: affiliation.attrs.county, tag: 'state' },
-                        { value: affiliation.attrs.country, tag: 'country' },
-                        { value: affiliation.attrs.postCode, tag: 'postal-code' },
-                    ].filter((obj) => obj.value);
-                    affiliationParts.forEach((location, index) => {
-                        if (index) {
-                            const punctuation = this.document.createTextNode(', ');
-                            $aff.appendChild(punctuation);
-                        }
-                        const { tag, value, ...rest } = location;
-                        this.appendElement($aff, tag, value, rest);
+                }
+                const $name = this.buildContributorName(contributor);
+                $contrib.appendChild($name);
+                if (contributor.attrs.email) {
+                    this.appendElement($contrib, 'email', contributor.attrs.email);
+                }
+                contributor.attrs.affiliationIDs?.forEach((rid) => {
+                    const $xref = this.appendElement($contrib, 'xref', '', {
+                        'ref-type': 'aff',
+                        rid: normalizeID(rid),
+                    });
+                    $xref.appendChild(createLabel(rid));
+                });
+                contributor.attrs.footnoteIDs?.forEach((rid) => {
+                    const $xref = this.appendElement($contrib, 'xref', '', {
+                        'ref-type': 'fn',
+                        rid: normalizeID(rid),
                     });
-                    const { href, text } = affiliation.attrs.email ?? {};
-                    if (href) {
-                        const email = this.appendElement($aff, 'email', text ?? href);
-                        email.setAttributeNS(XLINK_NAMESPACE, 'href', href);
+                    $xref.appendChild(createLabel(rid));
+                });
+                contributor.attrs.correspIDs?.forEach((rid) => {
+                    const $xref = this.appendElement($contrib, 'xref', '', {
+                        'ref-type': 'corresp',
+                        rid: normalizeID(rid),
+                    });
+                    $xref.appendChild(createLabel(rid));
+                });
+                contributor.attrs.creditRoles?.forEach((credit) => {
+                    const url = CreditRoleUrls.get(credit.vocabTerm);
+                    if (!url) {
+                        return;
                     }
-                    contribGroup.appendChild($aff);
+                    this.appendElement($contrib, 'role', credit.vocabTerm, {
+                        'vocab-identifier': 'http://credit.niso.org/',
+                        'vocab': 'CRediT',
+                        'vocab-term': credit.vocabTerm,
+                        'vocab-term-identifier': url,
+                    });
                 });
-                const authorNotesEl = this.createAuthorNotesElement();
-                if (authorNotesEl.childNodes.length > 0) {
-                    articleMeta.insertBefore(authorNotesEl, contribGroup.nextSibling);
+                $contribGroup.appendChild($contrib);
+            });
+            const affiliationIDs = contributors.flatMap((n) => n.attrs.affiliationIDs);
+            const sortAffiliations = (a, b) => affiliationIDs.indexOf(a.attrs.id) - affiliationIDs.indexOf(b.attrs.id);
+            this.getChildrenOfType(schema.nodes.affiliation)
+                .filter((a) => affiliationIDs.includes(a.attrs.id))
+                .sort(sortAffiliations)
+                .forEach((affiliation) => {
+                const $content = [];
+                if (affiliation.attrs.department) {
+                    const $institution = this.createElement('institution', affiliation.attrs.department, {
+                        'content-type': 'dept',
+                    });
+                    $content.push($institution);
+                }
+                if (affiliation.attrs.institution) {
+                    const $institution = this.createElement('institution', affiliation.attrs.institution);
+                    $content.push($institution);
                 }
+                if (affiliation.attrs.addressLine1) {
+                    const $addrLine = this.createElement('addr-line', affiliation.attrs.addressLine1);
+                    $content.push($addrLine);
+                }
+                if (affiliation.attrs.addressLine2) {
+                    const $addrLine = this.createElement('addr-line', affiliation.attrs.addressLine2);
+                    $content.push($addrLine);
+                }
+                if (affiliation.attrs.addressLine3) {
+                    const $addrLine = this.createElement('addr-line', affiliation.attrs.addressLine3);
+                    $content.push($addrLine);
+                }
+                if (affiliation.attrs.city) {
+                    const $city = this.createElement('city', affiliation.attrs.city);
+                    $content.push($city);
+                }
+                if (affiliation.attrs.county) {
+                    const $state = this.createElement('state', affiliation.attrs.county);
+                    $content.push($state);
+                }
+                if (affiliation.attrs.country) {
+                    const $country = this.createElement('country', affiliation.attrs.country);
+                    $content.push($country);
+                }
+                if (affiliation.attrs.postCode) {
+                    const $postalCode = this.createElement('postal-code', affiliation.attrs.postCode);
+                    $content.push($postalCode);
+                }
+                const $aff = this.createElement('aff');
+                $aff.setAttribute('id', normalizeID(affiliation.attrs.id));
+                $contribGroup.appendChild($aff);
+                const label = labels.get(affiliation.attrs.id);
+                if (label) {
+                    this.appendElement($aff, 'label', String(label));
+                }
+                $content.forEach((node, i) => {
+                    if (i > 0) {
+                        $aff.appendChild(this.document.createTextNode(', '));
+                    }
+                    $aff.appendChild(node);
+                });
+            });
+            const $authorNotes = this.createAuthorNotesElement(contributors);
+            if ($authorNotes) {
+                articleMeta.insertBefore($authorNotes, $contribGroup.nextSibling);
             }
         };
         this.buildContributorName = (contributor) => {
-            const { given, family } = contributor.attrs.bibliographicName;
+            const { given, family } = contributor.attrs;
             if (Boolean(given) !== Boolean(family)) {
                 return this.createElement('string-name', given || family);
             }
             const name = this.createElement('name');
-            if (contributor.attrs.bibliographicName.family) {
-                this.appendElement(name, 'surname', contributor.attrs.bibliographicName.family);
+            if (contributor.attrs.family) {
+                this.appendElement(name, 'surname', contributor.attrs.family);
             }
-            if (contributor.attrs.bibliographicName.given) {
-                this.appendElement(name, 'given-names', contributor.attrs.bibliographicName.given);
+            if (contributor.attrs.given) {
+                this.appendElement(name, 'given-names', contributor.attrs.given);
             }
             if (contributor.attrs.prefix) {
                 this.appendElement(name, 'prefix', contributor.attrs.prefix);
             }
             return name;
         };
-        this.createAuthorNotesElement = () => {
-            const authorNotesEl = this.createElement('author-notes');
-            const authorNotesNode = this.getFirstChildOfType(schema.nodes.author_notes);
-            if (authorNotesNode) {
-                this.appendModelsToAuthorNotes(authorNotesEl, authorNotesNode);
+        this.createAuthorNotesElement = (contributors) => {
+            const authorNotes = this.getFirstChildOfType(schema.nodes.author_notes);
+            if (!authorNotes || !authorNotes.childCount) {
+                return;
             }
-            return authorNotesEl;
+            const $authorNotes = this.createElement('author-notes');
+            const used = contributors.flatMap((c) => c.attrs.correspIDs);
+            authorNotes.descendants((node) => {
+                switch (node.type) {
+                    case schema.nodes.paragraph: {
+                        const $p = this.writeParagraph(node);
+                        $authorNotes.append($p);
+                        break;
+                    }
+                    case schema.nodes.footnote: {
+                        const $fn = this.writeFootnote(node);
+                        $authorNotes.append($fn);
+                        break;
+                    }
+                    case schema.nodes.corresp: {
+                        if (used.includes(node.attrs.id)) {
+                            const $corresp = this.writeCorresp(node);
+                            $authorNotes.append($corresp);
+                        }
+                        break;
+                    }
+                }
+                return false;
+            });
+            return $authorNotes;
         };
-        this.appendCorrespondingToElement = (corresponding, element) => {
-            const correspondingEl = this.createElement('corresp');
-            correspondingEl.setAttribute('id', normalizeID(corresponding.attrs.id));
-            if (corresponding.attrs.label) {
-                const labelEl = this.createElement('label');
-                labelEl.textContent = corresponding.attrs.label;
-                correspondingEl.appendChild(labelEl);
-            }
-            correspondingEl.append(corresponding.textContent);
-            element.appendChild(correspondingEl);
+        this.writeCorresp = (corresp) => {
+            const $corresp = this.createElement('corresp');
+            $corresp.setAttribute('id', normalizeID(corresp.attrs.id));
+            if (corresp.attrs.label) {
+                this.appendElement($corresp, 'label', corresp.attrs.label);
+            }
+            $corresp.append(corresp.textContent);
+            return $corresp;
         };
-        this.appendParagraphToElement = (paragraph, element) => {
-            const parsedDoc = new DOMParser().parseFromString(paragraph.textContent, 'text/html');
-            if (parsedDoc.body.innerHTML.length) {
-                const paragraphEl = this.createElement('p');
-                paragraphEl.innerHTML = parsedDoc.body.innerHTML;
-                paragraphEl.setAttribute('id', normalizeID(paragraph.attrs.id));
-                element.appendChild(paragraphEl);
-            }
+        this.writeParagraph = (paragraph) => {
+            const dom = new DOMParser().parseFromString(paragraph.textContent, 'text/html');
+            const $p = this.createElement('p');
+            $p.setAttribute('id', normalizeID(paragraph.attrs.id));
+            if (dom.body.innerHTML.length) {
+                $p.innerHTML = dom.body.innerHTML;
+            }
+            return $p;
         };
-        this.appendFootnoteToElement = (footnote, element) => {
-            const footnoteEl = this.createElement('fn');
-            footnoteEl.setAttribute('id', normalizeID(footnote.attrs.id));
-            if (!footnote.textContent.includes('<p>')) {
-                const p = this.createElement('p');
-                p.innerHTML = footnote.textContent;
-                footnoteEl.appendChild(p);
-            }
-            else {
-                footnoteEl.innerHTML = footnote.textContent;
-            }
-            element.appendChild(footnoteEl);
+        this.writeFootnote = (footnote) => {
+            const $fn = this.createElement('fn');
+            $fn.setAttribute('id', normalizeID(footnote.attrs.id));
+            let content = footnote.textContent;
+            if (!content.includes('<p>')) {
+                content = `<p>${content}</p>`;
+            }
+            $fn.innerHTML = content;
+            return $fn;
         };
         this.fixBody = (body) => {
             this.manuscriptNode.descendants((node) => {
@@ -1237,7 +1184,6 @@ export class JATSExporter {
             }
             const tbodyRows = Array.from(tbody.childNodes);
             const thead = this.createElement('thead');
-            const tfoot = this.createElement('tfoot');
             tbodyRows.forEach((row, i) => {
                 const isRow = row instanceof Element && row.tagName.toLowerCase() === 'tr';
                 if (isRow) {
@@ -1250,18 +1196,11 @@ export class JATSExporter {
                         }
                         thead.appendChild(row);
                     }
-                    else if (i === tbodyRows.length - 1) {
-                        tbody?.removeChild(row);
-                        tfoot.appendChild(row);
-                    }
                 }
             });
             if (thead.hasChildNodes()) {
                 table.insertBefore(thead, tbody);
             }
-            if (tfoot.hasChildNodes()) {
-                table.insertBefore(tfoot, tbody);
-            }
         };
         this.unwrapBody = (body) => {
             const container = body.querySelector(':scope > sec[sec-type="body"]');
@@ -1439,34 +1378,6 @@ export class JATSExporter {
             return mathml;
         }
     }
-    appendModelsToAuthorNotes(authorNotesEl, authorNotesNode) {
-        const contributorsNodes = this.getChildrenOfType(schema.nodes.contributor);
-        const usedCorrespondings = this.getUsedCorrespondings(contributorsNodes);
-        authorNotesNode.descendants((node) => {
-            switch (node.type) {
-                case schema.nodes.paragraph:
-                    this.appendParagraphToElement(node, authorNotesEl);
-                    break;
-                case schema.nodes.footnote:
-                    this.appendFootnoteToElement(node, authorNotesEl);
-                    break;
-                case schema.nodes.corresp:
-                    if (usedCorrespondings.includes(node)) {
-                        this.appendCorrespondingToElement(node, authorNotesEl);
-                    }
-                    break;
-            }
-            return false;
-        });
-    }
-    getUsedCorrespondings(contributors) {
-        return contributors
-            .flatMap((c) => c.attrs.corresp ?? [])
-            .map((corresp) => {
-            return findChildrenByAttr(this.manuscriptNode, (attr) => attr.id === corresp.correspID)[0]?.node;
-        })
-            .filter((corresp) => !!corresp);
-    }
     buildKeywords(articleMeta) {
         const keywordGroups = this.getChildrenOfType(schema.nodes.keyword_group);
         keywordGroups.forEach((group) => {

package/dist/es/jats/importer/jats-dom-parser.js

@@ -1,19 +1,3 @@
-/*!
- * © 2020 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.
- * You may obtain a copy of the License at
- *
- *    http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-import { buildContribution, ObjectTypes } from '@manuscripts/json-schema';
 import { DOMParser, Fragment } from 'prosemirror-model';
 import { dateToTimestamp, getCreditRole, getHTMLContent, getTrimmedTextContent, } from '../../lib/utils';
 import { XLINK_NAMESPACE, XML_NAMESPACE } from '../../lib/xml';
@@ -304,7 +288,8 @@ export class JATSDOMParser {
                         id: element.getAttribute('id'),
                         target: element.getAttribute('target-id'),
                         contents: getTrimmedTextContent(element),
-                        contributions: [buildContribution(DEFAULT_PROFILE_ID)],
+                        userID: DEFAULT_PROFILE_ID,
+                        timestamp: Date.now(),
                     };
                 },
             },
@@ -378,9 +363,9 @@ export class JATSDOMParser {
                 node: 'contributor',
                 getAttrs: (node) => {
                     const element = node;
-                    const footnote = [];
-                    const affiliations = [];
-                    const corresp = [];
+                    const footnoteIDs = [];
+                    const affiliationIDs = [];
+                    const correspIDs = [];
                     const xrefs = element.querySelectorAll('xref');
                     for (const xref of xrefs) {
                         const rid = xref.getAttribute('rid');
@@ -390,41 +375,30 @@ export class JATSDOMParser {
                         }
                         switch (type) {
                             case 'fn':
-                                footnote.push({
-                                    noteID: rid,
-                                    noteLabel: getTrimmedTextContent(xref) || '',
-                                });
+                                footnoteIDs.push(rid);
                                 break;
                             case 'corresp':
-                                corresp.push({
-                                    correspID: rid,
-                                    correspLabel: getTrimmedTextContent(xref) || '',
-                                });
+                                correspIDs.push(rid);
                                 break;
                             case 'aff':
-                                affiliations.push(rid);
+                                affiliationIDs.push(rid);
                                 break;
                         }
                     }
                     return {
                         id: element.getAttribute('id') || undefined,
                         role: getTrimmedTextContent(element, 'role'),
-                        affiliations,
-                        corresp,
-                        footnote,
-                        isCorresponding: element.getAttribute('corresp')
-                            ? element.getAttribute('corresp') === 'yes'
-                            : undefined,
-                        bibliographicName: {
-                            given: getTrimmedTextContent(element, 'given-names'),
-                            family: this.getSurname(element),
-                            ObjectType: ObjectTypes.BibliographicName,
-                        },
-                        ORCIDIdentifier: getTrimmedTextContent(element, 'contrib-id[contrib-id-type="orcid"]'),
+                        affiliationIDs,
+                        correspIDs,
+                        footnoteIDs,
+                        isCorresponding: element.getAttribute('corresp') === 'yes',
+                        given: getTrimmedTextContent(element, 'given-names'),
+                        family: this.getSurname(element),
+                        prefix: getTrimmedTextContent(element, 'prefix'),
+                        ORCID: getTrimmedTextContent(element, 'contrib-id[contrib-id-type="orcid"]'),
                         creditRoles: getCreditRole(element),
                         priority: this.parsePriority(element.getAttribute('priority')),
                         email: getTrimmedTextContent(element, 'email') || '',
-                        prefix: getTrimmedTextContent(element, 'prefix'),
                     };
                 },
                 getContent: () => {