@manuscripts/transform 1.4.6 → 1.5.0-LEAN-2852-9

package/dist/cjs/transformer/decode.js

@@ -67,29 +67,16 @@ exports.isManuscriptNode = isManuscriptNode;
 const isParagraphElement = (0, object_types_1.hasObjectType)(json_schema_1.ObjectTypes.ParagraphElement);
 const isFootnote = (0, object_types_1.hasObjectType)(json_schema_1.ObjectTypes.Footnote);
 const isKeyword = (0, object_types_1.hasObjectType)(json_schema_1.ObjectTypes.Keyword);
+const isKeywordsSection = (model) => model.category === 'MPSectionCategory:keywords';
+const isAffiliationsSection = (model) => model.category === 'MPSectionCategory:affiliations';
+const isContributorsSection = (model) => model.category === 'MPSectionCategory:contributors';
 const hasParentSection = (id) => (section) => section.path &&
     section.path.length > 1 &&
     section.path[section.path.length - 2] === id;
 class Decoder {
-    createAffiliationListNode() {
-        const affiliationNodes = getAffiliations(this.modelMap)
-            .map((affiliation) => this.decode(affiliation))
-            .filter(Boolean);
-        return schema_1.schema.nodes.affiliation_list.createAndFill({}, affiliationNodes);
-    }
-    createContributorListNode() {
-        const contributorNodes = getContributors(this.modelMap)
-            .map((contributor) => this.decode(contributor))
-            .filter(Boolean);
-        return schema_1.schema.nodes.contributor_list.createAndFill({}, contributorNodes);
-    }
     createMetaSectionNode() {
-        const affiliationListNode = this.createAffiliationListNode();
-        const contributorListNode = this.createContributorListNode();
         const commentListNode = this.createCommentListNode();
         return schema_1.schema.nodes.meta_section.createAndFill({}, [
-            affiliationListNode,
-            contributorListNode,
             commentListNode,
         ]);
     }
@@ -98,12 +85,53 @@ class Decoder {
             ...this.comments.values(),
         ]);
     }
+    handleMissingRootSectionNodes(rootSectionNodes) {
+        if (!rootSectionNodes.find((node) => node.type.name === 'affiliations_section')) {
+            this.createAffiliationSectionNode(rootSectionNodes);
+        }
+        if (!rootSectionNodes.find((node) => node.type.name === 'contributors_section')) {
+            this.createContributorSectionNode(rootSectionNodes);
+        }
+    }
+    createAffiliationSectionNode(rootSectionNodes) {
+        const affiliationNodes = getAffiliations(this.modelMap)
+            .map((affiliation) => this.decode(affiliation))
+            .filter(Boolean);
+        if (affiliationNodes.length) {
+            const node = schema_1.schema.nodes.affiliations_section.createAndFill({
+                id: (0, id_1.generateNodeID)(schema_1.schema.nodes.section),
+            }, affiliationNodes);
+            rootSectionNodes.unshift(node);
+        }
+    }
+    createContributorSectionNode(rootSectionNodes) {
+        const contributorNodes = getContributors(this.modelMap)
+            .map((contributor) => this.decode(contributor))
+            .filter(Boolean);
+        if (contributorNodes.length) {
+            const node = schema_1.schema.nodes.contributors_section.createAndFill({
+                id: (0, id_1.generateNodeID)(schema_1.schema.nodes.section),
+            }, contributorNodes);
+            rootSectionNodes.unshift(node);
+        }
+    }
+    createTitlesNode() {
+        const titlesModel = (0, exports.getModelsByType)(this.modelMap, json_schema_1.ObjectTypes.Titles)[0];
+        if (titlesModel) {
+            const titlesNode = this.decode(titlesModel);
+            return titlesNode;
+        }
+        else {
+            return null;
+        }
+    }
     createRootSectionNodes() {
         let rootSections = getSections(this.modelMap).filter((section) => !section.path || section.path.length <= 1);
         rootSections = this.addGeneratedLabels(rootSections);
         const rootSectionNodes = rootSections
             .map(this.decode)
             .filter(exports.isManuscriptNode);
+        this.handleMissingRootSectionNodes(rootSectionNodes);
         if (!rootSectionNodes.length) {
             rootSectionNodes.push(schema_1.schema.nodes.section.createAndFill({
                 id: (0, id_1.generateNodeID)(schema_1.schema.nodes.section),
@@ -129,6 +157,15 @@ class Decoder {
     constructor(modelMap, allowMissingElements = false) {
         this.comments = new Map();
         this.creators = {
+            [json_schema_1.ObjectTypes.Titles]: (data) => {
+                const model = data;
+                return schema_1.schema.nodes.titles.create({
+                    id: model._id,
+                    title: model.title,
+                    subtitle: model.subtitle,
+                    runningTitle: model.runningTitle,
+                });
+            },
             [json_schema_1.ObjectTypes.BibliographyElement]: (data) => {
                 var _a;
                 const model = data;
@@ -436,13 +473,12 @@ class Decoder {
             },
             [json_schema_1.ObjectTypes.Section]: (data) => {
                 const model = data;
-                const isKeywordsSection = model.category === 'MPSectionCategory:keywords';
                 const elements = [];
                 if (model.elementIDs) {
                     for (const id of model.elementIDs) {
                         const element = this.getModel(id);
                         if (element) {
-                            if (isKeywordsSection && isParagraphElement(element)) {
+                            if (isKeywordsSection(model) && isParagraphElement(element)) {
                                 continue;
                             }
                             elements.push(element);
@@ -485,11 +521,17 @@ class Decoder {
                 const sectionNodeType = (0, section_category_1.chooseSectionNodeType)(sectionCategory);
                 const commentNodes = this.createCommentsNode(model);
                 commentNodes.forEach((c) => this.comments.set(c.attrs.id, c));
-                const content = (sectionLabelNode
-                    ? [sectionLabelNode, sectionTitleNode]
-                    : [sectionTitleNode])
-                    .concat(elementNodes)
-                    .concat(nestedSections);
+                let content;
+                if (isAffiliationsSection(model) || isContributorsSection(model)) {
+                    content = elementNodes.concat(nestedSections);
+                }
+                else {
+                    content = (sectionLabelNode
+                        ? [sectionLabelNode, sectionTitleNode]
+                        : [sectionTitleNode])
+                        .concat(elementNodes)
+                        .concat(nestedSections);
+                }
                 const sectionNode = sectionNodeType.createAndFill({
                     id: model._id,
                     category: sectionCategory,
@@ -578,6 +620,8 @@ class Decoder {
                     postCode: model.postCode,
                     country: model.country,
                     email: model.email,
+                    department: model.department,
+                    priority: model.priority,
                 });
             },
             [json_schema_1.ObjectTypes.Contributor]: (data) => {
@@ -591,6 +635,9 @@ class Decoder {
                     invitationID: model.invitationID,
                     isCorresponding: model.isCorresponding,
                     ORCIDIdentifier: model.ORCIDIdentifier,
+                    footnote: model.footnote,
+                    corresp: model.corresp,
+                    priority: model.priority,
                 });
             },
         };
@@ -603,9 +650,13 @@ class Decoder {
         };
         this.getModel = (id) => this.modelMap.get(id);
         this.createArticleNode = (manuscriptID) => {
+            const titlesNode = this.createTitlesNode();
             const rootSectionNodes = this.createRootSectionNodes();
             const metaSectionNode = this.createMetaSectionNode();
             const contents = [...rootSectionNodes, metaSectionNode];
+            if (titlesNode) {
+                contents.push(titlesNode);
+            }
             return schema_1.schema.nodes.manuscript.create({
                 id: manuscriptID || this.getManuscriptID(),
             }, contents);

package/dist/cjs/transformer/encode.js

@@ -263,6 +263,12 @@ function figureElementEncoder(node) {
     };
 }
 const encoders = {
+    titles: (node) => ({
+        title: node.attrs.title,
+        subtitle: node.attrs.subtitle,
+        runningTitle: node.attrs.runningTitle,
+        _id: node.attrs._id,
+    }),
     bibliography_element: (node) => ({
         elementType: 'div',
         contents: '',
@@ -434,6 +440,22 @@ const encoders = {
             .map((childNode) => childNode.attrs.id)
             .filter((id) => id),
     }),
+    affiliations_section: (node, parent, path, priority) => ({
+        category: (0, section_category_1.buildSectionCategory)(node),
+        priority: priority.value++,
+        path: path.concat([node.attrs.id]),
+        elementIDs: childElements(node)
+            .map((childNode) => childNode.attrs.id)
+            .filter((id) => id),
+    }),
+    contributors_section: (node, parent, path, priority) => ({
+        category: (0, section_category_1.buildSectionCategory)(node),
+        priority: priority.value++,
+        path: path.concat([node.attrs.id]),
+        elementIDs: childElements(node)
+            .map((childNode) => childNode.attrs.id)
+            .filter((id) => id),
+    }),
     missing_figure: (node) => ({
         position: node.attrs.position || undefined,
     }),
@@ -514,6 +536,7 @@ const encoders = {
         postCode: node.attrs.postCode,
         country: node.attrs.country,
         email: node.attrs.email,
+        priority: node.attrs.priority,
     }),
     contributor: (node) => ({
         role: node.attrs.role,
@@ -523,6 +546,9 @@ const encoders = {
         invitationID: node.attrs.invitationID,
         isCorresponding: node.attrs.isCorresponding,
         ORCIDIdentifier: node.attrs.ORCIDIdentifier,
+        footnote: node.attrs.footnote,
+        corresp: node.attrs.corresp,
+        priority: node.attrs.priority,
     }),
 };
 const modelData = (node, parent, path, priority) => {

package/dist/cjs/transformer/html.js

@@ -152,6 +152,7 @@ class HTMLTransformer {
         this.buildFront = () => {
             const manuscript = (0, project_bundle_1.findManuscript)(this.modelMap);
             const journal = (0, project_bundle_1.findJournal)(this.modelMap);
+            const titles = (0, project_bundle_1.findTitles)(this.modelMap);
             if (!manuscript) {
                 throw new Error('Manuscript not found in project modelMap');
             }
@@ -170,14 +171,14 @@ class HTMLTransformer {
             }
             const articleMeta = this.document.createElement('div');
             front.appendChild(articleMeta);
-            const articleTitle = this.document.createElement('h1');
-            if (manuscript.title) {
-                articleTitle.innerHTML = manuscript.title;
+            const title = this.document.createElement('h1');
+            if (titles.title) {
+                title.innerHTML = titles.title;
             }
             if (journal === null || journal === void 0 ? void 0 : journal.title) {
-                articleTitle.setAttribute('data-journal', journal.title);
+                title.setAttribute('data-journal', journal.title);
             }
-            articleMeta.appendChild(articleTitle);
+            articleMeta.appendChild(title);
             if (manuscript.DOI) {
                 const articleID = this.document.createElement('article-id');
                 articleID.setAttribute('pub-id-type', 'doi');

package/dist/cjs/transformer/node-types.js

@@ -57,6 +57,9 @@ exports.nodeTypesMap = new Map([
     [schema_1.schema.nodes.affiliation, json_schema_1.ObjectTypes.Affiliation],
     [schema_1.schema.nodes.contributor, json_schema_1.ObjectTypes.Contributor],
     [schema_1.schema.nodes.table_element_footer, json_schema_1.ObjectTypes.TableElementFooter],
+    [schema_1.schema.nodes.titles, json_schema_1.ObjectTypes.Titles],
+    [schema_1.schema.nodes.contributors_section, json_schema_1.ObjectTypes.Section],
+    [schema_1.schema.nodes.affiliations_section, json_schema_1.ObjectTypes.Section],
 ]);
 const isExecutableNodeType = (type) => (0, schema_1.hasGroup)(type, schema_1.GROUP_EXECUTABLE);
 exports.isExecutableNodeType = isExecutableNodeType;

package/dist/cjs/transformer/project-bundle.js

@@ -15,7 +15,7 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.findManuscriptById = exports.findManuscriptModelByType = exports.findJournal = exports.findManuscript = exports.parseProjectBundle = void 0;
+exports.findTitles = exports.findManuscriptById = exports.findManuscriptModelByType = exports.findJournal = exports.findManuscript = exports.parseProjectBundle = void 0;
 const json_schema_1 = require("@manuscripts/json-schema");
 const decode_1 = require("./decode");
 const object_types_1 = require("./object-types");
@@ -71,3 +71,24 @@ const findManuscriptById = (modelMap, manuscriptID) => {
     throw new Error(`There is no manuscript found for the following _id (${manuscriptID})`);
 };
 exports.findManuscriptById = findManuscriptById;
+const isTitle = (0, object_types_1.hasObjectType)(json_schema_1.ObjectTypes.Titles);
+const findTitles = (modelMap) => {
+    for (const model of modelMap.values()) {
+        if (isTitle(model)) {
+            return model;
+        }
+    }
+    const defaultTitle = {
+        _id: 'MPTitles:8EB79C14-9F61-483A-902F-A0B8EF5973C1',
+        createdAt: 1538472121.690101,
+        updatedAt: 1538472121.690101,
+        objectType: 'MPTitles',
+        title: 'main title',
+        subtitle: 'subtitle',
+        runningTitle: 'running title',
+        manuscriptID: 'MPManuscript:E3830344-E77B-42BA-BD77-3E95489712A0',
+        containerID: 'MPProject:1',
+    };
+    return defaultTitle;
+};
+exports.findTitles = findTitles;

package/dist/cjs/transformer/section-category.js

@@ -46,6 +46,10 @@ const chooseSectionNodeType = (category) => {
             return schema_1.schema.nodes.footnotes_section;
         case 'MPSectionCategory:keywords':
             return schema_1.schema.nodes.keywords_section;
+        case 'MPSectionCategory:affiliations':
+            return schema_1.schema.nodes.affiliations_section;
+        case 'MPSectionCategory:contributors':
+            return schema_1.schema.nodes.contributors_section;
         case 'MPSectionCategory:toc':
             return schema_1.schema.nodes.toc_section;
         default:
@@ -92,6 +96,10 @@ const buildSectionCategory = (node) => {
             return 'MPSectionCategory:toc';
         case schema_1.schema.nodes.graphical_abstract_section:
             return 'MPSectionCategory:abstract-graphical';
+        case schema_1.schema.nodes.affiliations_section:
+            return 'MPSectionCategory:affiliations';
+        case schema_1.schema.nodes.contributors_section:
+            return 'MPSectionCategory:contributors';
         default:
             return node.attrs.category || undefined;
     }
@@ -185,6 +193,10 @@ const chooseSectionCategoryByType = (secType) => {
             return 'MPSectionCategory:backmatter';
         case 'abstracts':
             return 'MPSectionCategory:abstracts';
+        case 'affiliations':
+            return 'MPSectionCategory:affiliations';
+        case 'contributors':
+            return 'MPSectionCategory:contributors';
         default:
             return undefined;
     }

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

@@ -499,6 +499,132 @@ const nodes = [
             };
         },
     },
+    {
+        tag: 'sec[sec-type="affiliations"]',
+        node: 'affiliations_section',
+        getAttrs: (node) => {
+            const element = node;
+            return {
+                id: element.getAttribute('id'),
+                category: 'MPSectionCategory:affiliations',
+            };
+        },
+    },
+    {
+        tag: 'aff',
+        node: 'affiliation',
+        context: 'affiliations_section/',
+        getAttrs: (node) => {
+            const element = node;
+            const aff = {
+                id: element.getAttribute('id'),
+            };
+            const institution = element.getAttribute('institution');
+            if (institution) {
+                aff.institution = institution;
+            }
+            const email = element.getAttribute('email');
+            if (email) {
+                aff.bibliographicName = JSON.parse(email);
+            }
+            const department = element.getAttribute('department');
+            if (department) {
+                aff.department = department;
+            }
+            const addressLine1 = element.getAttribute('addressLine1');
+            if (addressLine1) {
+                aff.addressLine1 = addressLine1;
+            }
+            const addressLine2 = element.getAttribute('addressLine2');
+            if (addressLine2) {
+                aff.addressLine2 = addressLine2;
+            }
+            const addressLine3 = element.getAttribute('addressLine3');
+            if (addressLine3) {
+                aff.addressLine3 = addressLine3;
+            }
+            const postCode = element.getAttribute('postCode');
+            if (postCode) {
+                aff.postCode = postCode;
+            }
+            const country = element.getAttribute('country');
+            if (country) {
+                aff.country = country;
+            }
+            const priority = element.getAttribute('priority');
+            if (priority) {
+                aff.priority = parseInt(priority);
+            }
+            return aff;
+        },
+    },
+    {
+        tag: 'sec[sec-type="contributors"]',
+        node: 'contributors_section',
+        getAttrs: (node) => {
+            const element = node;
+            return {
+                id: element.getAttribute('id'),
+                category: 'MPSectionCategory:contributors',
+            };
+        },
+    },
+    {
+        tag: 'contrib',
+        node: 'contributor',
+        context: 'contributors_section/',
+        getAttrs: (node) => {
+            const element = node;
+            const contrib = {
+                id: element.getAttribute('id'),
+            };
+            const role = element.getAttribute('role');
+            if (role) {
+                contrib.role = role;
+            }
+            const affiliations = element.getAttribute('affiliations');
+            if (affiliations) {
+                contrib.affiliations = JSON.parse(affiliations);
+            }
+            const footnote = element.getAttribute('footnote');
+            if (footnote) {
+                contrib.footnote = JSON.parse(footnote);
+            }
+            const corresp = element.getAttribute('corresp');
+            if (corresp) {
+                contrib.corresp = JSON.parse(corresp);
+            }
+            const bibliographicName = element.getAttribute('bibliographicName');
+            if (bibliographicName) {
+                contrib.bibliographicName = JSON.parse(bibliographicName);
+            }
+            const userID = element.getAttribute('userID');
+            if (userID) {
+                contrib.userID = userID;
+            }
+            const priority = element.getAttribute('priority');
+            if (priority) {
+                contrib.priority = parseInt(priority);
+            }
+            const invitationID = element.getAttribute('invitationID');
+            if (invitationID) {
+                contrib.invitationID = invitationID;
+            }
+            const objectType = element.getAttribute('objectType');
+            if (objectType) {
+                contrib.objectType = objectType;
+            }
+            const isCorresponding = element.getAttribute('isCorresponding');
+            if (isCorresponding) {
+                contrib.isCorresponding = JSON.parse(isCorresponding);
+            }
+            const ORCIDIdentifier = element.getAttribute('ORCIDIdentifier');
+            if (ORCIDIdentifier) {
+                contrib.ORCIDIdentifier = ORCIDIdentifier;
+            }
+            return contrib;
+        },
+    },
     {
         tag: 'sec[sec-type="keywords"]',
         node: 'keywords_section',

package/dist/es/jats/importer/jats-body-transformations.js

@@ -281,6 +281,65 @@ export const jatsBodyTransformations = {
             }
         }
     },
+    moveAffiliationsToBody(doc, affiliations, body, createElement) {
+        if (affiliations === null || affiliations === void 0 ? void 0 : affiliations.length) {
+            const section = createElement('sec');
+            section.setAttribute('sec-type', 'affiliations');
+            affiliations.forEach((affiliation) => {
+                const item = doc.createElement('aff');
+                item.setAttribute('id', affiliation._id);
+                affiliation.institution &&
+                    item.setAttribute('institution', affiliation.institution);
+                affiliation.email &&
+                    item.setAttribute('email', JSON.stringify(affiliation.email));
+                affiliation.department &&
+                    item.setAttribute('department', affiliation.department);
+                affiliation.addressLine1 &&
+                    item.setAttribute('addressLine1', affiliation.addressLine1);
+                affiliation.addressLine2 &&
+                    item.setAttribute('addressLine2', affiliation.addressLine2);
+                affiliation.addressLine3 &&
+                    item.setAttribute('addressLine3', affiliation.addressLine3);
+                affiliation.postCode &&
+                    item.setAttribute('postCode', affiliation.postCode);
+                affiliation.country && item.setAttribute('country', affiliation.country);
+                (affiliation.priority === 0 || affiliation.priority) &&
+                    item.setAttribute('priority', affiliation.priority.toString());
+                section.appendChild(item);
+            });
+            body.prepend(section);
+        }
+    },
+    moveAuthorsToBody(doc, authors, body, createElement) {
+        if (authors === null || authors === void 0 ? void 0 : authors.length) {
+            const section = createElement('sec');
+            section.setAttribute('sec-type', 'contributors');
+            authors.forEach((author) => {
+                const item = doc.createElement('contrib');
+                item.setAttribute('id', author._id);
+                author.role && item.setAttribute('role', author.role);
+                author.affiliations &&
+                    item.setAttribute('affiliations', JSON.stringify(author.affiliations));
+                author.footnote &&
+                    item.setAttribute('footnote', JSON.stringify(author.footnote));
+                author.corresp &&
+                    item.setAttribute('corresp', JSON.stringify(author.corresp));
+                author.bibliographicName &&
+                    item.setAttribute('bibliographicName', JSON.stringify(author.bibliographicName));
+                author.userID && item.setAttribute('userID', author.userID);
+                author.invitationID &&
+                    item.setAttribute('invitationID', author.invitationID);
+                author.isCorresponding &&
+                    item.setAttribute('isCorresponding', JSON.stringify(author.isCorresponding));
+                author.ORCIDIdentifier &&
+                    item.setAttribute('ORCIDIdentifier', author.ORCIDIdentifier);
+                (author.priority === 0 || author.priority) &&
+                    item.setAttribute('priority', author.priority.toString());
+                section.appendChild(item);
+            });
+            body.prepend(section);
+        }
+    },
     moveFloatsGroupToBody(doc, body, createElement) {
         const floatsGroup = doc.querySelector('floats-group');
         if (floatsGroup) {

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

@@ -15,7 +15,7 @@
  */
 import debug from 'debug';
 import { getTrimmedTextContent } from '../../lib/utils';
-import { buildAffiliation, buildBibliographicName, buildContributor, buildCorresp, buildFootnote, buildSupplementaryMaterial, } from '../../transformer/builders';
+import { buildAffiliation, buildBibliographicName, buildContributor, buildCorresp, buildFootnote, buildSupplementaryMaterial, } from '../../transformer';
 import { parseJournalMeta } from './jats-journal-meta-parser';
 const warn = debug('manuscripts-transform');
 const XLINK_NAMESPACE = 'http://www.w3.org/1999/xlink';

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

@@ -16,6 +16,7 @@
 import { ObjectTypes, } from '@manuscripts/json-schema';
 import { generateID, hasObjectType, nodeTypesMap } from '../../transformer';
 const isAuxiliaryObjectReference = hasObjectType(ObjectTypes.AuxiliaryObjectReference);
+const excludedObjectTypes = [ObjectTypes.Contributor, ObjectTypes.Affiliation];
 export function flatten(arrays) {
     return [].concat(...arrays);
 }
@@ -44,6 +45,9 @@ const addMissingID = (node, replacements, warnings) => {
         warnings.push(`Unknown object type for node type ${node.type.name}`);
         return;
     }
+    if (excludedObjectTypes.includes(objectType)) {
+        return;
+    }
     const previousID = node.attrs.id;
     const nextID = generateID(objectType);
     if (previousID) {

package/dist/es/jats/importer/parse-jats-article.js

@@ -13,6 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
+import { ObjectTypes, } from '@manuscripts/json-schema';
 import { DOMParser } from 'prosemirror-model';
 import { InvalidInput } from '../../errors';
 import { nodeFromHTML } from '../../lib/html';
@@ -48,9 +49,16 @@ export const parseJATSFront = async (front) => {
     const title = (_a = articleMeta === null || articleMeta === void 0 ? void 0 : articleMeta.querySelector('title-group > article-title')) === null || _a === void 0 ? void 0 : _a.innerHTML;
     const subtitle = (_b = articleMeta === null || articleMeta === void 0 ? void 0 : articleMeta.querySelector('title-group > subtitle')) === null || _b === void 0 ? void 0 : _b.innerHTML;
     const runningTitle = (_c = articleMeta === null || articleMeta === void 0 ? void 0 : articleMeta.querySelector('title-group > alt-title[alt-title-type="right-running"]')) === null || _c === void 0 ? void 0 : _c.innerHTML;
-    const manuscriptMeta = Object.assign({ title: title ? inlineContentsFromJATSTitle(title) : undefined, subtitle: subtitle ? inlineContentsFromJATSTitle(subtitle) : undefined, runningTitle: runningTitle
+    const manuscriptMeta = Object.assign({}, jatsFrontParser.parseCounts(articleMeta === null || articleMeta === void 0 ? void 0 : articleMeta.querySelector('counts')));
+    const titles = {
+        objectType: ObjectTypes.Titles,
+        _id: generateID(ObjectTypes.Titles),
+        title: title ? inlineContentsFromJATSTitle(title) : undefined,
+        subtitle: subtitle ? inlineContentsFromJATSTitle(subtitle) : undefined,
+        runningTitle: runningTitle
             ? inlineContentsFromJATSTitle(runningTitle)
-            : undefined }, jatsFrontParser.parseCounts(articleMeta === null || articleMeta === void 0 ? void 0 : articleMeta.querySelector('counts')));
+            : undefined,
+    };
     const { affiliations, affiliationIDs } = jatsFrontParser.parseAffiliationNodes([
         ...front.querySelectorAll('article-meta > contrib-group > aff'),
     ]);
@@ -70,14 +78,15 @@ export const parseJATSFront = async (front) => {
     const manuscript = Object.assign(Object.assign(Object.assign({}, buildManuscript()), manuscriptMeta), history);
     return {
         models: generateModelIDs([
+            titles,
             manuscript,
-            ...affiliations,
-            ...authors,
             ...footnotes,
             ...correspondingList,
             journal,
             ...supplements,
         ]),
+        authors: [...authors],
+        affiliations: [...affiliations],
     };
 };
 export const parseJATSReferences = (back, body, createElement) => {
@@ -101,7 +110,7 @@ export const parseJATSReferences = (back, body, createElement) => {
         referenceIdsMap,
     };
 };
-export const parseJATSBody = (document, body, bibliographyItems, refModels, referenceIdsMap, footnotesOrder) => {
+export const parseJATSBody = (document, body, bibliographyItems, authors, affiliations, refModels, referenceIdsMap, footnotesOrder) => {
     const createElement = createElementFn(document);
     const orderedFootnotesIDs = createOrderedFootnotesIDs(document);
     jatsBodyTransformations.moveFloatsGroupToBody(document, body, createElement);
@@ -111,6 +120,8 @@ export const parseJATSBody = (document, body, bibliographyItems, refModels, refe
     jatsBodyTransformations.moveTableFooterToEnd(body);
     jatsBodyTransformations.moveBlockNodesFromParagraph(document, body, createElement);
     jatsBodyTransformations.moveKeywordsToBody(document, body, createElement);
+    jatsBodyTransformations.moveAffiliationsToBody(document, affiliations, body, createElement);
+    jatsBodyTransformations.moveAuthorsToBody(document, authors, body, createElement);
     const node = jatsBodyDOMParser.parse(body);
     if (!node.firstChild) {
         throw new Error('No content was parsed from the JATS article body');
@@ -162,14 +173,14 @@ export const parseJATSArticle = async (doc) => {
     }
     const authorQueriesMap = markProcessingInstructions(doc);
     const createElement = createElementFn(document);
-    const { models: frontModels } = await parseJATSFront(front);
+    const { models: frontModels, authors, affiliations, } = await parseJATSFront(front);
     const { references, crossReferences, referenceQueriesMap, referenceIdsMap } = parseJATSReferences(back, body, createElement);
     transformTables(doc.querySelectorAll('table-wrap > table'), createElement);
     const footnotesOrder = createEmptyFootnotesOrder();
     let elementsOrder = [];
     const bodyModels = [];
     if (body) {
-        const bodyDoc = parseJATSBody(doc, body, references, crossReferences, referenceIdsMap, footnotesOrder);
+        const bodyDoc = parseJATSBody(doc, body, references, authors, affiliations, crossReferences, referenceIdsMap, footnotesOrder);
         bodyModels.push(...encode(bodyDoc).values());
         elementsOrder = getElementsOrder(bodyDoc);
     }