@manuscripts/transform 1.5.4-LEAN-3030 → 1.5.4-LEAN-2995

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

@@ -424,11 +424,9 @@ export class JATSExporter {
             }
         };
         this.buildBody = (fragment) => {
+            const content = this.serializeFragment(fragment);
             const body = this.document.createElement('body');
-            fragment.forEach((cFragment) => {
-                const serializedNode = this.serializeNode(cFragment);
-                body.append(...serializedNode.childNodes);
-            });
+            body.appendChild(content);
             this.fixBody(body, fragment);
             return body;
         };
@@ -595,8 +593,8 @@ export class JATSExporter {
             const getModel = (id) => id ? this.modelMap.get(id) : undefined;
             const nodes = {
                 title: () => '',
-                affiliations: () => '',
-                contributors: () => '',
+                affiliations_section: () => '',
+                contributors_section: () => '',
                 table_element_footer: () => ['table-wrap-foot', 0],
                 contributor: () => '',
                 affiliation: () => '',
@@ -605,10 +603,7 @@ export class JATSExporter {
                 bibliography_element: () => '',
                 bibliography_item: () => '',
                 comment_list: () => '',
-                keyword_group: () => '',
-                body: () => ['body', 0],
-                abstracts: () => ['abstract', 0],
-                backmatter: () => ['backmatter', 0],
+                keywords_group: () => '',
                 bibliography_section: (node) => [
                     'ref-list',
                     { id: normalizeID(node.attrs.id) },
@@ -787,7 +782,7 @@ export class JATSExporter {
                 },
                 keyword: () => '',
                 keywords_element: () => '',
-                keywords: () => '',
+                keywords_section: () => '',
                 link: (node) => {
                     const text = node.textContent;
                     if (!text) {

package/dist/es/lib/utils.js

@@ -84,11 +84,3 @@ 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

@@ -16,7 +16,7 @@
 import { Schema } from 'prosemirror-model';
 import { bold, code, italic, smallcaps, strikethrough, styled, subscript, superscript, tracked_delete, tracked_insert, underline, } from './marks';
 import { affiliation } from './nodes/affiliation';
-import { affiliations } from './nodes/affiliations';
+import { affiliationsSection } from './nodes/affiliations_section';
 import { attribution } from './nodes/attribution';
 import { bibliographyElement } from './nodes/bibliography_element';
 import { bibliographyItem } from './nodes/bibliography_item';
@@ -28,8 +28,7 @@ import { citation } from './nodes/citation';
 import { comment } from './nodes/comment';
 import { commentList } from './nodes/comment_list';
 import { contributor } from './nodes/contributor';
-import { contributors } from './nodes/contributors';
-import { coreSection } from './nodes/core_section';
+import { contributorsSection } from './nodes/contributors_section';
 import { crossReference } from './nodes/cross_reference';
 import { doc } from './nodes/doc';
 import { equation } from './nodes/equation';
@@ -46,8 +45,9 @@ import { highlightMarker } from './nodes/highlight_marker';
 import { inlineEquation } from './nodes/inline_equation';
 import { inlineFootnote } from './nodes/inline_footnote';
 import { keyword } from './nodes/keyword';
-import { keywordGroup } from './nodes/keyword_group';
-import { keywords } from './nodes/keywords';
+import { keywordsElement } from './nodes/keywords_element';
+import { keywordsGroup } from './nodes/keywords_group';
+import { keywordsSection } from './nodes/keywords_section';
 import { link } from './nodes/link';
 import { bulletList, listItem, orderedList } from './nodes/list';
 import { listing } from './nodes/listing';
@@ -71,7 +71,6 @@ import { text } from './nodes/text';
 import { title } from './nodes/title';
 import { tocElement } from './nodes/toc_element';
 import { tocSection } from './nodes/toc_section';
-import { keywordsElement } from "./nodes/keywords_element";
 export * from './groups';
 export * from './types';
 export * from './nodes/comment';
@@ -101,7 +100,7 @@ export * from './nodes/inline_equation';
 export * from './nodes/inline_footnote';
 export * from './nodes/keyword';
 export * from './nodes/keywords_element';
-export * from './nodes/keywords';
+export * from './nodes/keywords_section';
 export * from './nodes/link';
 export * from './nodes/list';
 export * from './nodes/listing';
@@ -126,8 +125,8 @@ export * from './nodes/meta_section';
 export * from './nodes/contributor';
 export * from './nodes/table_element_footer';
 export * from './nodes/title';
-export * from './nodes/affiliations';
-export * from './nodes/contributors';
+export * from './nodes/affiliations_section';
+export * from './nodes/contributors_section';
 export const schema = new Schema({
     marks: {
         bold,
@@ -154,9 +153,6 @@ export const schema = new Schema({
         caption,
         caption_title: captionTitle,
         citation,
-        abstracts: coreSection,
-        body: coreSection,
-        backmatter: coreSection,
         cross_reference: crossReference,
         doc,
         equation,
@@ -174,8 +170,8 @@ export const schema = new Schema({
         inline_footnote: inlineFootnote,
         keyword,
         keywords_element: keywordsElement,
-        keywords: keywords,
-        keyword_group: keywordGroup,
+        keywords_section: keywordsSection,
+        keywords_group: keywordsGroup,
         link,
         list_item: listItem,
         listing,
@@ -206,7 +202,7 @@ export const schema = new Schema({
         contributor: contributor,
         table_element_footer: tableElementFooter,
         title: title,
-        affiliations: affiliations,
-        contributors: contributors,
+        affiliations_section: affiliationsSection,
+        contributors_section: contributorsSection,
     },
 });

package/dist/es/schema/nodes/{affiliations.js → affiliations_section.js}

@@ -1,11 +1,11 @@
-export const affiliations = {
+export const affiliationsSection = {
     content: 'section_title? affiliation*',
     attrs: {
         id: { default: '' },
         dataTracked: { default: null },
     },
-    group: 'block',
+    group: 'block sections',
     selectable: false,
     toDOM: () => ['section', 0],
 };
-export const isAffiliationsNode = (node) => node.type === node.type.schema.nodes.affiliations;
+export const isAffiliationsSectionNode = (node) => node.type === node.type.schema.nodes.affiliations_section;

package/dist/es/schema/nodes/{contributors.js → contributors_section.js}

@@ -1,11 +1,11 @@
-export const contributors = {
+export const contributorsSection = {
     content: 'section_title? contributor*',
     attrs: {
         id: { default: '' },
         dataTracked: { default: null },
     },
-    group: 'block',
+    group: 'block sections',
     selectable: false,
     toDOM: () => ['section', 0],
 };
-export const isContributorsNode = (node) => node.type === node.type.schema.nodes.contributors;
+export const isContributorsSectionNode = (node) => node.type === node.type.schema.nodes.contributors_section;

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

@@ -18,6 +18,7 @@ export const keyword = {
     content: 'inline*',
     attrs: {
         id: { default: '' },
+        contents: { default: '' },
         dataTracked: { default: null },
         comments: { default: null },
     },

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

@@ -15,7 +15,7 @@
  */
 export const keywordsElement = {
     atom: true,
-    content: 'keyword_group*',
+    content: 'keywords_group*',
     attrs: {
         id: { default: '' },
         contents: { default: '' },

package/dist/es/schema/nodes/{keyword_group.js → keywords_group.js}

@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-export const keywordGroup = {
+export const keywordsGroup = {
     content: 'keyword*',
     attrs: {
         id: { default: '' },
@@ -28,11 +28,11 @@ export const keywordGroup = {
         },
     ],
     toDOM: (node) => {
-        const keywordGroupNode = node;
+        const keywordsGroupNode = node;
         return [
             'div',
             {
-                id: keywordGroupNode.attrs.id,
+                id: keywordsGroupNode.attrs.id,
                 class: 'keywords',
                 spellcheck: 'false',
                 contenteditable: false,
@@ -41,4 +41,4 @@ export const keywordGroup = {
         ];
     },
 };
-export const isKeywordGroupNode = (node) => node.type === node.type.schema.nodes.keywords_group;
+export const isKeywordsGroupNode = (node) => node.type === node.type.schema.nodes.keywords_group;

package/dist/es/schema/nodes/{keywords.js → keywords_section.js}

@@ -13,13 +13,13 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-export const keywords = {
+export const keywordsSection = {
     content: 'section_title (keywords_element | placeholder_element)',
     attrs: {
         id: { default: '' },
         dataTracked: { default: null },
     },
-    group: 'block',
+    group: 'block sections',
     selectable: false,
     parseDOM: [
         {
@@ -27,11 +27,11 @@ export const keywords = {
         },
     ],
     toDOM: (node) => {
-        const keywords = node;
+        const keywordsSectionNode = node;
         return [
             'div',
             {
-                id: keywords.attrs.id,
+                id: keywordsSectionNode.attrs.id,
                 class: 'keywords',
                 spellcheck: 'false',
                 contenteditable: false,
@@ -40,4 +40,4 @@ export const keywords = {
         ];
     },
 };
-export const isKeywordsNode = (node) => node.type === node.type.schema.nodes.keywords;
+export const isKeywordsSectionNode = (node) => node.type === node.type.schema.nodes.keywords_section;

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

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

package/dist/es/transformer/decode.js

@@ -28,13 +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 { buildTitles } from './builders';
 import { insertHighlightMarkers } from './highlight-markers';
 import { generateNodeID } from './id';
 import { ExtraObjectTypes, hasObjectType, isCommentAnnotation, isManuscript, } from './object-types';
-import { chooseCoreSectionBySection, chooseSectionLableName, chooseSectionNodeType, chooseSecType, guessSectionCategory, } from './section-category';
+import { chooseSectionLableName, chooseSectionNodeType, chooseSecType, guessSectionCategory, } from './section-category';
 import { timestamp } from './timestamp';
 const warn = debug('manuscripts-transform');
 const parser = DOMParser.fromSchema(schema);
@@ -55,41 +54,17 @@ 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);
-const getKeywordGroups = (modelMap) => getModelsByType(modelMap, ObjectTypes.KeywordGroup);
-const getKeywords = (modelMap) => getModelsByType(modelMap, ObjectTypes.Keyword);
-const getTitles = (modelMap) => getModelsByType(modelMap, ObjectTypes.Titles)[0];
 export const isManuscriptNode = (model) => model !== null;
+const isParagraphElement = hasObjectType(ObjectTypes.ParagraphElement);
 const isFootnote = hasObjectType(ObjectTypes.Footnote);
+const isKeyword = hasObjectType(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;
 export class Decoder {
-    createTitleNode() {
-        const titles = getTitles(this.modelMap) || buildTitles();
-        return this.decode(titles);
-    }
-    createAffiliationsNode() {
-        const affiliations = getAffiliations(this.modelMap)
-            .map((a) => this.decode(a))
-            .filter(Boolean);
-        return schema.nodes.affiliations.createAndFill({}, affiliations);
-    }
-    createContributorsNode() {
-        const contributors = getContributors(this.modelMap)
-            .map((c) => this.decode(c))
-            .filter(Boolean);
-        return schema.nodes.contributors.createAndFill({}, contributors);
-    }
-    createKeywordsNode() {
-        const elements = getKeywordElements(this.modelMap)
-            .map((e) => this.decode(e))
-            .filter(Boolean);
-        return schema.nodes.keywords.createAndFill({}, [
-            schema.nodes.section_title.create({}, schema.text('Keywords')),
-            ...elements,
-        ]);
-    }
     createMetaSectionNode() {
         const commentListNode = this.createCommentListNode();
         return schema.nodes.meta_section.createAndFill({}, [
@@ -101,51 +76,54 @@ export 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.nodes.affiliations_section.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({
+                id: generateNodeID(schema.nodes.section),
+            }, contributorNodes);
+            rootSectionNodes.unshift(node);
+        }
+    }
+    createTitleNode() {
+        const titles = getModelsByType(this.modelMap, ObjectTypes.Titles)[0] ||
+            buildTitles();
+        return this.decode(titles);
+    }
     createRootSectionNodes() {
-        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');
+        let rootSections = getSections(this.modelMap).filter((section) => !section.path || section.path.length <= 1);
         rootSections = this.addGeneratedLabels(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);
-        const bodySectionNodes = sectionGroups['MPSectionCategory:body']
-            .map(this.decode)
-            .filter(isManuscriptNode);
-        const backmatterSectionNodes = sectionGroups['MPSectionCategory:backmatter']
+        const rootSectionNodes = rootSections
             .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 {
-            abstracts: abstractCoreSectionNodes,
-            body: bodyCoreSectionNodes,
-            backmatter: backmatterCoreSectionNodes,
-        };
-    }
-    ensureCoreSectionsExist(coreSections) {
-        if (!coreSections['MPSectionCategory:abstracts']) {
-            coreSections['MPSectionCategory:abstracts'] = [];
-        }
-        if (!coreSections['MPSectionCategory:body']) {
-            coreSections['MPSectionCategory:body'] = [];
+        this.handleMissingRootSectionNodes(rootSectionNodes);
+        if (!rootSectionNodes.length) {
+            rootSectionNodes.push(schema.nodes.section.createAndFill({
+                id: generateNodeID(schema.nodes.section),
+            }));
         }
-        if (!coreSections['MPSectionCategory:backmatter']) {
-            coreSections['MPSectionCategory:backmatter'] = [];
-        }
-    }
-    createAndFill(nodeType, content) {
-        return nodeType.createAndFill({
-            id: generateNodeID(nodeType),
-        }, content);
+        return rootSectionNodes;
     }
     createCommentsNode(model) {
         const comments = [];
@@ -351,32 +329,19 @@ export class Decoder {
             },
             [ObjectTypes.KeywordsElement]: (data) => {
                 const model = data;
-                const keywordGroups = getKeywordGroups(this.modelMap).map(k => this.decode(k));
+                const keywordGroups = this.getKeywordGroups();
                 return schema.nodes.keywords_element.create({
                     id: model._id,
                     paragraphStyle: model.paragraphStyle,
                 }, keywordGroups);
             },
-            [ObjectTypes.KeywordGroup]: (data) => {
-                const keywordGroup = data;
-                const keywords = getKeywords(this.modelMap).filter(k => k.containedGroup === keywordGroup._id).map(k => this.decode(k));
-                const comments = this.createCommentsNode(keywordGroup);
-                comments.forEach((c) => this.comments.set(c.attrs.id, c));
-                return schema.nodes.keyword_group.create({
-                    id: keywordGroup._id,
-                    type: keywordGroup.type,
-                    comments: comments.map((c) => c.attrs.id),
-                }, keywords);
-            },
             [ObjectTypes.Keyword]: (data) => {
-                const keyword = data;
-                const comments = this.createCommentsNode(keyword);
-                comments.forEach((c) => this.comments.set(c.attrs.id, c));
+                const model = data;
                 return schema.nodes.keyword.create({
-                    id: keyword._id,
-                    contents: keyword.name,
-                    comments: comments.map((c) => c.attrs.id),
-                }, schema.text(keyword.name));
+                    id: model._id,
+                    contents: model.name,
+                    comments: this.createCommentsNode(model),
+                }, schema.text(model.name));
             },
             [ObjectTypes.ListElement]: (data) => {
                 const model = data;
@@ -498,6 +463,9 @@ export class Decoder {
                     for (const id of model.elementIDs) {
                         const element = this.getModel(id);
                         if (element) {
+                            if (isKeywordsSection(model) && isParagraphElement(element)) {
+                                continue;
+                            }
                             elements.push(element);
                         }
                         else if (this.allowMissingElements) {
@@ -538,11 +506,17 @@ export class Decoder {
                 const sectionNodeType = 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,
@@ -661,21 +635,13 @@ export class Decoder {
         };
         this.getModel = (id) => this.modelMap.get(id);
         this.createArticleNode = (manuscriptID) => {
-            const title = this.createTitleNode();
-            const contributors = this.createContributorsNode();
-            const affiliations = this.createAffiliationsNode();
-            const keywords = this.createKeywordsNode();
-            const { abstracts, body, backmatter } = this.createRootSectionNodes();
-            const meta = this.createMetaSectionNode();
+            const titlesNode = this.createTitleNode();
+            const rootSectionNodes = this.createRootSectionNodes();
+            const metaSectionNode = this.createMetaSectionNode();
             const contents = [
-                title,
-                contributors,
-                affiliations,
-                keywords,
-                abstracts,
-                body,
-                backmatter,
-                meta,
+                titlesNode,
+                ...rootSectionNodes,
+                metaSectionNode,
             ];
             return schema.nodes.manuscript.create({
                 id: manuscriptID || this.getManuscriptID(),
@@ -717,6 +683,23 @@ export class Decoder {
             }
             return parser.parse(template.content.firstElementChild, options);
         };
+        this.getKeywords = (id) => {
+            const keywordsOfKind = [];
+            const keywordsByGroup = [...this.modelMap.values()].filter((m) => m.objectType === ObjectTypes.Keyword &&
+                m.containedGroup === id);
+            for (const model of keywordsByGroup) {
+                if (isKeyword(model)) {
+                    const keyword = this.parseContents(model.name || '', 'div', this.getComments(model), {
+                        topNode: schema.nodes.keyword.create({
+                            id: model._id,
+                            contents: model.name,
+                        }),
+                    });
+                    keywordsOfKind.push(keyword);
+                }
+            }
+            return keywordsOfKind;
+        };
         this.getManuscriptID = () => {
             for (const item of this.modelMap.values()) {
                 if (isManuscript(item)) {
@@ -801,4 +784,26 @@ export class Decoder {
         }
         return listing;
     }
+    getKeywordGroups() {
+        const kwdGroupNodes = [];
+        const kwdGroupsModels = [
+            ...this.modelMap.values(),
+        ].filter((model) => model.objectType === ObjectTypes.KeywordGroup);
+        if (kwdGroupsModels.length > 0) {
+            for (const kwdGroupModel of kwdGroupsModels) {
+                const keywords = this.getKeywords(kwdGroupModel._id);
+                const commentNodes = this.createCommentsNode(kwdGroupModel);
+                commentNodes.forEach((c) => this.comments.set(c.attrs.id, c));
+                const contents = [];
+                contents.push(...keywords);
+                const kwdGroupNode = schema.nodes.keywords_group.create({
+                    id: kwdGroupModel._id,
+                    type: kwdGroupModel.type,
+                    comments: commentNodes.map((c) => c.attrs.id),
+                }, contents);
+                kwdGroupNodes.push(kwdGroupNode);
+            }
+        }
+        return kwdGroupNodes;
+    }
 }

package/dist/es/transformer/encode.js

@@ -420,9 +420,34 @@ const encoders = {
         elementType: 'div',
         paragraphStyle: node.attrs.paragraphStyle || undefined,
     }),
-    keyword_group: (node) => ({
+    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,
     }),
@@ -540,16 +565,9 @@ export const modelFromNode = (node, parent, path, priority) => {
     if (isHighlightableModel(model)) {
         extractHighlightMarkers(model, commentAnnotationsMap);
     }
-    return { model, commentAnnotationsMap };
+    const comments = [...commentAnnotationsMap.values()];
+    return { model, comments };
 };
-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 = {
@@ -557,10 +575,6 @@ 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;
         }
@@ -573,10 +587,18 @@ export const encode = (node) => {
         if (placeholders.includes(child.type.name)) {
             return;
         }
-        const { model } = modelFromNode(child, parent, path, priority);
+        const { model, comments } = modelFromNode(child, parent, path, priority);
         if (models.has(model._id)) {
             throw Error(`Encountered duplicate ids in models map while encoding: ${model._id}`);
         }
+        comments.forEach((comment) => {
+            const proseMirrorComment = models.get(comment._id);
+            if (proseMirrorComment) {
+                ;
+                proseMirrorComment.selector = comment.selector;
+                models.set(comment._id, proseMirrorComment);
+            }
+        });
         models.set(model._id, model);
         child.forEach(addModel(path.concat(child.attrs.id), child));
     };