@manuscripts/transform 1.5.2-LEAN-3034 → 1.5.2-LEAN-3032

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

@@ -501,7 +501,7 @@ const nodes = [
     },
     {
         tag: 'sec[sec-type="affiliations"]',
-        node: 'affiliations_section',
+        node: 'affiliations',
         getAttrs: (node) => {
             const element = node;
             return {
@@ -513,7 +513,7 @@ const nodes = [
     {
         tag: 'aff',
         node: 'affiliation',
-        context: 'affiliations_section/',
+        context: 'affiliations/',
         getAttrs: (node) => {
             const element = node;
             const aff = {
@@ -560,7 +560,7 @@ const nodes = [
     },
     {
         tag: 'sec[sec-type="contributors"]',
-        node: 'contributors_section',
+        node: 'contributors',
         getAttrs: (node) => {
             const element = node;
             return {
@@ -572,7 +572,7 @@ const nodes = [
     {
         tag: 'contrib',
         node: 'contributor',
-        context: 'contributors_section/',
+        context: 'contributors/',
         getAttrs: (node) => {
             const element = node;
             const contrib = {
@@ -627,7 +627,7 @@ const nodes = [
     },
     {
         tag: 'sec[sec-type="keywords"]',
-        node: 'keywords_section',
+        node: 'keywords',
         getAttrs: (node) => {
             const element = node;
             return {
@@ -638,9 +638,21 @@ const nodes = [
     },
     {
         tag: 'kwd-group-list',
-        context: 'keywords_section/',
+        context: 'keywords/',
         node: 'keywords_element',
     },
+    {
+        tag: 'sec[sec-type="abstracts"]',
+        node: 'abstracts',
+    },
+    {
+        tag: 'sec[sec-type="body"]',
+        node: 'body',
+    },
+    {
+        tag: 'sec[sec-type="backmatter"]',
+        node: 'backmatter',
+    },
     {
         tag: 'sec',
         node: 'section',
@@ -720,7 +732,7 @@ const nodes = [
     {
         tag: 'title',
         node: 'section_title',
-        context: 'section/|footnotes_section/|bibliography_section/|keywords_section/',
+        context: 'section/|footnotes_section/|bibliography_section/|keywords/',
     },
     {
         tag: 'title',

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

@@ -15,9 +15,8 @@
  */
 import { ObjectTypes, } from '@manuscripts/json-schema';
 import debug from 'debug';
-import { DOMParser, DOMSerializer, } from 'prosemirror-model';
+import { DOMParser, DOMSerializer } from 'prosemirror-model';
 import serializeToXML from 'w3c-xmlserializer';
-import { CitationProvider } from '../lib/citationProvider';
 import { nodeFromHTML, textFromHTML } from '../lib/html';
 import { normalizeStyleName } from '../lib/styled-content';
 import { iterateChildren } from '../lib/utils';
@@ -112,16 +111,9 @@ const sortContributors = (a, b) => Number(a.priority) - Number(b.priority);
 export class JATSExporter {
     constructor() {
         this.serializeToJATS = async (fragment, modelMap, manuscriptID, options = {}) => {
-            const { version = '1.2', doi, id, frontMatterOnly = false, links, idGenerator, mediaPathGenerator, citationStyle, locale, } = options;
+            const { version = '1.2', doi, id, frontMatterOnly = false, links, idGenerator, mediaPathGenerator, } = options;
             this.modelMap = modelMap;
             this.models = Array.from(this.modelMap.values());
-            if (citationStyle) {
-                this.citeProcEngine = CitationProvider.getEngine({
-                    bibliographyItemsMap: this.getBibliographyItemsMap(),
-                    citationStyle: citationStyle,
-                    locale: locale,
-                });
-            }
             this.createSerializer();
             const versionIds = selectVersionIds(version);
             this.document = document.implementation.createDocument(null, 'article', document.implementation.createDocumentType('article', versionIds.publicId, versionIds.systemId));
@@ -431,9 +423,11 @@ export class JATSExporter {
             }
         };
         this.buildBody = (fragment) => {
-            const content = this.serializeFragment(fragment);
             const body = this.document.createElement('body');
-            body.appendChild(content);
+            fragment.forEach((cFragment) => {
+                const serializedNode = this.serializeNode(cFragment);
+                body.append(...serializedNode.childNodes);
+            });
             this.fixBody(body, fragment);
             return body;
         };
@@ -599,8 +593,8 @@ export class JATSExporter {
         this.createSerializer = () => {
             const getModel = (id) => id ? this.modelMap.get(id) : undefined;
             const nodes = {
-                affiliations_section: () => '',
-                contributors_section: () => '',
+                affiliations: () => '',
+                contributors: () => '',
                 table_element_footer: () => ['table-wrap-foot', 0],
                 contributor: () => '',
                 affiliation: () => '',
@@ -610,6 +604,9 @@ export class JATSExporter {
                 bibliography_item: () => '',
                 comment_list: () => '',
                 keywords_group: () => '',
+                body: () => ['body', 0],
+                abstracts: () => ['abstract', 0],
+                backmatter: () => ['backmatter', 0],
                 bibliography_section: (node) => [
                     'ref-list',
                     { id: normalizeID(node.attrs.id) },
@@ -644,10 +641,7 @@ export class JATSExporter {
                     const xref = this.document.createElement('xref');
                     xref.setAttribute('ref-type', 'bibr');
                     xref.setAttribute('rid', rids.map((item) => normalizeID(item.bibliographyItem)).join(' '));
-                    if (this.citeProcEngine) {
-                        xref.textContent = this.generateCitationContent(node);
-                    }
-                    else if (node.attrs.contents) {
+                    if (node.attrs.contents) {
                         const text = textFromHTML(node.attrs.contents);
                         if (text !== null && text.length) {
                             xref.textContent = text;
@@ -791,7 +785,7 @@ export class JATSExporter {
                 },
                 keyword: () => '',
                 keywords_element: () => '',
-                keywords_section: () => '',
+                keywords: () => '',
                 link: (node) => {
                     const text = node.textContent;
                     if (!text) {
@@ -1577,25 +1571,6 @@ export class JATSExporter {
             return name;
         };
     }
-    getBibliographyItemsMap() {
-        const map = new Map();
-        this.modelMap.forEach((model) => {
-            if (model.objectType === ObjectTypes.BibliographyItem) {
-                map.set(model._id, model);
-            }
-        });
-        return map;
-    }
-    generateCitationContent(node) {
-        var _a;
-        const citationItems = (_a = node.attrs.embeddedCitationItems) === null || _a === void 0 ? void 0 : _a.map(({ bibliographyItem }) => ({
-            id: bibliographyItem,
-        }));
-        return this.citeProcEngine.previewCitationCluster({
-            citationID: node.attrs.rid,
-            citationItems: citationItems,
-        }, [], [], 'text');
-    }
     buildKeywords(articleMeta) {
         const keywords = [...this.modelMap.values()].filter((model) => model.objectType === ObjectTypes.Keyword);
         const keywordGroups = new Map();

package/dist/es/lib/utils.js

@@ -84,3 +84,11 @@ export const getTrimmedTextContent = (node, querySelector) => {
     }
     return (_b = (_a = node.querySelector(querySelector)) === null || _a === void 0 ? void 0 : _a.textContent) === null || _b === void 0 ? void 0 : _b.trim();
 };
+export const groupBy = (list, getKey) => list.reduce((previous, currentItem) => {
+    const group = getKey(currentItem);
+    if (!previous[group]) {
+        previous[group] = [];
+    }
+    previous[group].push(currentItem);
+    return previous;
+}, {});

package/dist/es/schema/index.js

@@ -29,6 +29,7 @@ import { comment } from './nodes/comment';
 import { commentList } from './nodes/comment_list';
 import { contributor } from './nodes/contributor';
 import { contributorsSection } from './nodes/contributors_section';
+import { coreSection } from './nodes/core_section';
 import { crossReference } from './nodes/cross_reference';
 import { doc } from './nodes/doc';
 import { equation } from './nodes/equation';
@@ -151,6 +152,9 @@ export const schema = new Schema({
         caption,
         caption_title: captionTitle,
         citation,
+        abstracts: coreSection,
+        body: coreSection,
+        backmatter: coreSection,
         cross_reference: crossReference,
         doc,
         equation,
@@ -168,7 +172,7 @@ export const schema = new Schema({
         inline_footnote: inlineFootnote,
         keyword,
         keywords_element: keywordsElement,
-        keywords_section: keywordsSection,
+        keywords: keywordsSection,
         keywords_group: keywordsGroup,
         link,
         list_item: listItem,
@@ -199,7 +203,7 @@ export const schema = new Schema({
         meta_section: metaSection,
         contributor: contributor,
         table_element_footer: tableElementFooter,
-        affiliations_section: affiliationsSection,
-        contributors_section: contributorsSection,
+        affiliations: affiliationsSection,
+        contributors: contributorsSection,
     },
 });

package/dist/es/schema/nodes/affiliations_section.js

@@ -8,4 +8,4 @@ export const affiliationsSection = {
     selectable: false,
     toDOM: () => ['section', 0],
 };
-export const isAffiliationsSectionNode = (node) => node.type === node.type.schema.nodes.affiliations_section;
+export const isAffiliationsSectionNode = (node) => node.type === node.type.schema.nodes.affiliations;

package/dist/es/schema/nodes/contributors_section.js

@@ -8,4 +8,4 @@ export const contributorsSection = {
     selectable: false,
     toDOM: () => ['section', 0],
 };
-export const isContributorsSectionNode = (node) => node.type === node.type.schema.nodes.contributors_section;
+export const isContributorsSectionNode = (node) => node.type === node.type.schema.nodes.contributors;

package/dist/es/schema/nodes/core_section.js

@@ -0,0 +1,24 @@
+/*!
+ * © 2019 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.
+ */
+export const coreSection = {
+    content: '(section | sections)*',
+    atom: true,
+    attrs: {
+        id: { default: '' },
+    },
+    group: 'block sections',
+    toDOM: () => ['section', 0],
+};

package/dist/es/schema/nodes/keywords_section.js

@@ -40,4 +40,4 @@ export const keywordsSection = {
         ];
     },
 };
-export const isKeywordsSectionNode = (node) => node.type === node.type.schema.nodes.keywords_section;
+export const isKeywordsSectionNode = (node) => node.type === node.type.schema.nodes.keywords;

package/dist/es/schema/nodes/manuscript.js

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 export const manuscript = {
-    content: '(section | sections)+ meta_section',
+    content: 'contributors? affiliations? keywords? abstracts body backmatter meta_section',
     attrs: {
         id: { default: '' },
     },

package/dist/es/transformer/decode.js

@@ -28,11 +28,12 @@ import { ObjectTypes, } from '@manuscripts/json-schema';
 import debug from 'debug';
 import { DOMParser } from 'prosemirror-model';
 import { MissingElement } from '../errors';
+import { groupBy } from '../lib/utils';
 import { schema, } from '../schema';
 import { insertHighlightMarkers } from './highlight-markers';
 import { generateNodeID } from './id';
 import { ExtraObjectTypes, hasObjectType, isCommentAnnotation, isManuscript, } from './object-types';
-import { chooseSectionLableName, chooseSectionNodeType, chooseSecType, guessSectionCategory, } from './section-category';
+import { chooseCoreSectionBySection, chooseSectionLableName, chooseSectionNodeType, chooseSecType, guessSectionCategory, } from './section-category';
 import { timestamp } from './timestamp';
 const warn = debug('manuscripts-transform');
 const parser = DOMParser.fromSchema(schema);
@@ -53,6 +54,7 @@ export const sortSectionsByPriority = (a, b) => a.priority === b.priority ? 0 :
 const getSections = (modelMap) => getModelsByType(modelMap, ObjectTypes.Section).sort(sortSectionsByPriority);
 const getAffiliations = (modelMap) => getModelsByType(modelMap, ObjectTypes.Affiliation);
 const getContributors = (modelMap) => getModelsByType(modelMap, ObjectTypes.Contributor);
+const getKeywordElements = (modelMap) => getModelsByType(modelMap, ObjectTypes.KeywordsElement);
 export const isManuscriptNode = (model) => model !== null;
 const isParagraphElement = hasObjectType(ObjectTypes.ParagraphElement);
 const isFootnote = hasObjectType(ObjectTypes.Footnote);
@@ -76,10 +78,13 @@ export class Decoder {
         ]);
     }
     handleMissingRootSectionNodes(rootSectionNodes) {
-        if (!rootSectionNodes.find((node) => node.type.name === 'affiliations_section')) {
+        if (!rootSectionNodes.find((node) => node.type.name === 'keywords')) {
+            this.createKeywordsSectionNode(rootSectionNodes);
+        }
+        if (!rootSectionNodes.find((node) => node.type.name === 'affiliations')) {
             this.createAffiliationSectionNode(rootSectionNodes);
         }
-        if (!rootSectionNodes.find((node) => node.type.name === 'contributors_section')) {
+        if (!rootSectionNodes.find((node) => node.type.name === 'contributors')) {
             this.createContributorSectionNode(rootSectionNodes);
         }
     }
@@ -87,37 +92,79 @@ export class Decoder {
         const affiliationNodes = getAffiliations(this.modelMap)
             .map((affiliation) => this.decode(affiliation))
             .filter(Boolean);
-        if (affiliationNodes.length) {
-            const node = schema.nodes.affiliations_section.createAndFill({
-                id: generateNodeID(schema.nodes.section),
-            }, affiliationNodes);
-            rootSectionNodes.unshift(node);
-        }
+        const node = schema.nodes.affiliations.createAndFill({
+            id: generateNodeID(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.nodes.contributors_section.createAndFill({
+        const node = schema.nodes.contributors.createAndFill({
+            id: generateNodeID(schema.nodes.section),
+        }, contributorNodes);
+        rootSectionNodes.unshift(node);
+    }
+    createKeywordsSectionNode(rootSectionNodes) {
+        const keywordElementNodes = getKeywordElements(this.modelMap)
+            .map((keywordEl) => this.decode(keywordEl))
+            .filter(Boolean);
+        if (keywordElementNodes) {
+            const node = schema.nodes.keywords.createAndFill({
                 id: generateNodeID(schema.nodes.section),
-            }, contributorNodes);
+            }, [
+                schema.nodes.section_title.create({}, schema.text('Keywords')),
+                ...keywordElementNodes,
+            ]);
             rootSectionNodes.unshift(node);
         }
     }
     createRootSectionNodes() {
-        let rootSections = getSections(this.modelMap).filter((section) => !section.path || section.path.length <= 1);
+        let rootSections = getSections(this.modelMap)
+            .filter((section) => !section.path || section.path.length <= 1)
+            .filter((section) => section.category !== 'MPSectionCategory:contributors' &&
+            section.category !== 'MPSectionCategory:affiliations' &&
+            section.category !== 'MPSectionCategory:keywords');
         rootSections = this.addGeneratedLabels(rootSections);
-        const rootSectionNodes = rootSections
+        const sectionGroups = groupBy(rootSections, (sec) => {
+            var _a;
+            return chooseCoreSectionBySection((_a = sec.category) !== null && _a !== void 0 ? _a : '');
+        });
+        this.ensureCoreSectionsExist(sectionGroups);
+        const absSectionNode = sectionGroups['MPSectionCategory:abstracts']
             .map(this.decode)
             .filter(isManuscriptNode);
-        this.handleMissingRootSectionNodes(rootSectionNodes);
-        if (!rootSectionNodes.length) {
-            rootSectionNodes.push(schema.nodes.section.createAndFill({
-                id: generateNodeID(schema.nodes.section),
-            }));
+        const bodySectionNodes = sectionGroups['MPSectionCategory:body']
+            .map(this.decode)
+            .filter(isManuscriptNode);
+        const backmatterSectionNodes = sectionGroups['MPSectionCategory:backmatter']
+            .map(this.decode)
+            .filter(isManuscriptNode);
+        const abstractCoreSectionNodes = this.createAndFill(schema.nodes.abstracts, absSectionNode);
+        const bodyCoreSectionNodes = this.createAndFill(schema.nodes.body, bodySectionNodes);
+        const backmatterCoreSectionNodes = this.createAndFill(schema.nodes.backmatter, backmatterSectionNodes);
+        return [
+            abstractCoreSectionNodes,
+            bodyCoreSectionNodes,
+            backmatterCoreSectionNodes,
+        ];
+    }
+    ensureCoreSectionsExist(coreSections) {
+        if (!coreSections['MPSectionCategory:abstracts']) {
+            coreSections['MPSectionCategory:abstracts'] = [];
         }
-        return rootSectionNodes;
+        if (!coreSections['MPSectionCategory:body']) {
+            coreSections['MPSectionCategory:body'] = [];
+        }
+        if (!coreSections['MPSectionCategory:backmatter']) {
+            coreSections['MPSectionCategory:backmatter'] = [];
+        }
+    }
+    createAndFill(nodeType, content) {
+        return nodeType.createAndFill({
+            id: generateNodeID(nodeType),
+        }, content);
     }
     createCommentsNode(model) {
         const comments = [];
@@ -622,6 +669,7 @@ export class Decoder {
         this.getModel = (id) => this.modelMap.get(id);
         this.createArticleNode = (manuscriptID) => {
             const rootSectionNodes = this.createRootSectionNodes();
+            this.handleMissingRootSectionNodes(rootSectionNodes);
             const metaSectionNode = this.createMetaSectionNode();
             const contents = [...rootSectionNodes, metaSectionNode];
             return schema.nodes.manuscript.create({

package/dist/es/transformer/encode.js

@@ -417,31 +417,6 @@ const encoders = {
     keywords_group: (node) => ({
         type: node.attrs.type,
     }),
-    keywords_section: (node, parent, path, priority) => ({
-        category: buildSectionCategory(node),
-        priority: priority.value++,
-        title: inlineContentsOfNodeType(node, node.type.schema.nodes.section_title),
-        path: path.concat([node.attrs.id]),
-        elementIDs: childElements(node)
-            .map((childNode) => childNode.attrs.id)
-            .filter((id) => id),
-    }),
-    affiliations_section: (node, parent, path, priority) => ({
-        category: 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: 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,
     }),
@@ -561,6 +536,14 @@ export const modelFromNode = (node, parent, path, priority) => {
     }
     return { model, commentAnnotationsMap };
 };
+function isCoreSection(child) {
+    return (child.type === schema.nodes.abstracts ||
+        child.type === schema.nodes.body ||
+        child.type === schema.nodes.backmatter ||
+        child.type === schema.nodes.affiliations ||
+        child.type === schema.nodes.contributors ||
+        child.type === schema.nodes.keywords);
+}
 export const encode = (node) => {
     const models = new Map();
     const priority = {
@@ -568,6 +551,10 @@ export const encode = (node) => {
     };
     const placeholders = ['placeholder', 'placeholder_element'];
     const addModel = (path, parent) => (child) => {
+        if (isCoreSection(child)) {
+            child.forEach(addModel([], child));
+            return;
+        }
         if (!child.attrs.id) {
             return;
         }

package/dist/es/transformer/node-names.js

@@ -35,6 +35,6 @@ export const nodeNames = new Map([
     [schema.nodes.table_element, 'Table'],
     [schema.nodes.blockquote_element, 'Block Quote'],
     [schema.nodes.pullquote_element, 'Pull Quote'],
-    [schema.nodes.keywords_section, 'Section'],
+    [schema.nodes.keywords, 'Section'],
     [schema.nodes.toc_section, 'Section'],
 ]);

package/dist/es/transformer/node-title.js

@@ -45,7 +45,7 @@ export const nodeTitle = (node) => {
         case nodes.section:
         case nodes.bibliography_section:
         case nodes.footnotes_section:
-        case nodes.keywords_section:
+        case nodes.keywords:
         case nodes.toc_section:
         case nodes.graphical_abstract_section:
             return snippetOfNodeType(node, nodes.section_title);

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

@@ -16,6 +16,9 @@
 import { ObjectTypes } from '@manuscripts/json-schema';
 import { GROUP_ELEMENT, GROUP_EXECUTABLE, GROUP_SECTION, hasGroup, schema, } from '../schema';
 export const nodeTypesMap = new Map([
+    [schema.nodes.abstracts, ObjectTypes.Section],
+    [schema.nodes.body, ObjectTypes.Section],
+    [schema.nodes.backmatter, ObjectTypes.Section],
     [schema.nodes.comment, ObjectTypes.CommentAnnotation],
     [schema.nodes.bibliography_item, ObjectTypes.BibliographyItem],
     [schema.nodes.bibliography_element, ObjectTypes.BibliographyElement],
@@ -37,7 +40,7 @@ export const nodeTypesMap = new Map([
     [schema.nodes.inline_equation, ObjectTypes.InlineMathFragment],
     [schema.nodes.keyword, ObjectTypes.Keyword],
     [schema.nodes.keywords_element, ObjectTypes.KeywordsElement],
-    [schema.nodes.keywords_section, ObjectTypes.Section],
+    [schema.nodes.keywords, ObjectTypes.Section],
     [schema.nodes.keywords_group, ObjectTypes.KeywordGroup],
     [schema.nodes.listing, ObjectTypes.Listing],
     [schema.nodes.listing_element, ObjectTypes.ListingElement],
@@ -54,8 +57,8 @@ export const nodeTypesMap = new Map([
     [schema.nodes.affiliation, ObjectTypes.Affiliation],
     [schema.nodes.contributor, ObjectTypes.Contributor],
     [schema.nodes.table_element_footer, ObjectTypes.TableElementFooter],
-    [schema.nodes.contributors_section, ObjectTypes.Section],
-    [schema.nodes.affiliations_section, ObjectTypes.Section],
+    [schema.nodes.contributors, ObjectTypes.Section],
+    [schema.nodes.affiliations, ObjectTypes.Section],
 ]);
 export const isExecutableNodeType = (type) => hasGroup(type, GROUP_EXECUTABLE);
 export const isElementNodeType = (type) => hasGroup(type, GROUP_ELEMENT);

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

@@ -19,7 +19,7 @@ import { schema } from '../schema';
 const sectionNodeTypes = [
     schema.nodes.bibliography_section,
     schema.nodes.footnotes_section,
-    schema.nodes.keywords_section,
+    schema.nodes.keywords,
     schema.nodes.section,
     schema.nodes.toc_section,
 ];
@@ -40,11 +40,11 @@ export const chooseSectionNodeType = (category) => {
         case 'MPSectionCategory:endnotes':
             return schema.nodes.footnotes_section;
         case 'MPSectionCategory:keywords':
-            return schema.nodes.keywords_section;
+            return schema.nodes.keywords;
         case 'MPSectionCategory:affiliations':
-            return schema.nodes.affiliations_section;
+            return schema.nodes.affiliations;
         case 'MPSectionCategory:contributors':
-            return schema.nodes.contributors_section;
+            return schema.nodes.contributors;
         case 'MPSectionCategory:toc':
             return schema.nodes.toc_section;
         default:
@@ -82,15 +82,15 @@ export const buildSectionCategory = (node) => {
             return 'MPSectionCategory:bibliography';
         case schema.nodes.footnotes_section:
             return 'MPSectionCategory:endnotes';
-        case schema.nodes.keywords_section:
+        case schema.nodes.keywords:
             return 'MPSectionCategory:keywords';
         case schema.nodes.toc_section:
             return 'MPSectionCategory:toc';
         case schema.nodes.graphical_abstract_section:
             return 'MPSectionCategory:abstract-graphical';
-        case schema.nodes.affiliations_section:
+        case schema.nodes.affiliations:
             return 'MPSectionCategory:affiliations';
-        case schema.nodes.contributors_section:
+        case schema.nodes.contributors:
             return 'MPSectionCategory:contributors';
         default:
             return node.attrs.category || undefined;
@@ -117,6 +117,32 @@ export const chooseSecType = (sectionCategory) => {
             return suffix;
     }
 };
+export const chooseCoreSectionBySection = (section) => {
+    switch (section) {
+        case 'MPSectionCategory:abstract':
+        case 'MPSectionCategory:abstract-teaser':
+        case 'MPSectionCategory:abstract-graphical':
+            return 'MPSectionCategory:abstracts';
+        case 'MPSectionCategory:acknowledgement':
+        case 'MPSectionCategory:availability':
+        case 'MPSectionCategory:conclusions':
+        case 'MPSectionCategory:bibliography':
+        case 'MPSectionCategory:discussion':
+        case 'MPSectionCategory:endnotes':
+        case 'MPSectionCategory:appendices':
+        case 'MPSectionCategory:competing-interests':
+        case 'MPSectionCategory:con':
+        case 'MPSectionCategory:deceased':
+        case 'MPSectionCategory:ethics-statement':
+        case 'MPSectionCategory:financial-disclosure':
+        case 'MPSectionCategory:supplementary-material':
+        case 'MPSectionCategory:supported-by':
+        case 'MPSectionCategory:abbreviations':
+        case 'MPSectionCategory:results':
+            return 'MPSectionCategory:backmatter';
+    }
+    return 'MPSectionCategory:body';
+};
 export const chooseSectionCategoryByType = (secType) => {
     switch (secType) {
         case 'abstract':

package/dist/types/jats/jats-exporter.d.ts

@@ -13,8 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import { BibliographyItem, Model } from '@manuscripts/json-schema';
-import CiteProc from 'citeproc';
+import { Model } from '@manuscripts/json-schema';
 import { DOMSerializer } from 'prosemirror-model';
 import { ManuscriptFragment, ManuscriptNode } from '../schema';
 import { Target } from '../transformer/labels';
@@ -37,19 +36,13 @@ export interface JATSExporterOptions {
     citationType?: 'element' | 'mixed';
     idGenerator?: IDGenerator;
     mediaPathGenerator?: MediaPathGenerator;
-    citationStyle?: string;
-    locale?: string;
 }
 export declare class JATSExporter {
     protected document: Document;
-    protected citeProcEngine: CiteProc.Engine;
     protected modelMap: Map<string, Model>;
-    protected bibliographyItemsMap: Map<string, BibliographyItem>;
     protected models: Model[];
     protected serializer: DOMSerializer;
     protected labelTargets?: Map<string, Target>;
-    private getBibliographyItemsMap;
-    private generateCitationContent;
     serializeToJATS: (fragment: ManuscriptFragment, modelMap: Map<string, Model>, manuscriptID: string, options?: JATSExporterOptions) => Promise<string>;
     private nodeFromJATS;
     protected rewriteCrossReferenceTypes: () => void;

package/dist/types/lib/utils.d.ts

@@ -27,3 +27,4 @@ export declare const findParentNodeClosestToPos: ($pos: ResolvedPos, predicate:
     node: ProsemirrorNode;
 } | undefined;
 export declare const getTrimmedTextContent: (node: Element | Document, querySelector: string) => string | null | undefined;
+export declare const groupBy: <T, K extends string | number | symbol>(list: T[], getKey: (item: T) => K) => Record<K, T[]>;