@manuscripts/transform 1.5.6 → 1.5.7-LEAN-3030-1

package/dist/cjs/transformer/builders.js

@@ -18,14 +18,12 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.buildTitles = exports.buildElementsOrder = exports.auxiliaryObjectTypes = exports.buildStatusLabel = exports.buildJournal = exports.buildAttribution = exports.buildInlineStyle = exports.buildContributorRole = exports.buildContribution = exports.buildHighlightMarker = exports.buildHighlight = exports.buildColor = exports.buildParagraph = exports.buildSection = exports.buildCorresp = exports.buildFootnotesOrder = exports.buildFootnote = exports.buildInlineMathFragment = exports.buildValidation = exports.buildNote = exports.buildComment = exports.buildUserProfileAffiliation = exports.buildSupplementaryMaterial = exports.buildAffiliation = exports.buildFigure = exports.buildLibraryCollection = exports.buildManuscriptKeyword = exports.buildKeywordGroup = exports.buildKeyword = exports.buildCitation = exports.buildEmbeddedCitationItem = exports.buildAuxiliaryObjectReference = exports.buildBibliographicDate = exports.buildBibliographicName = exports.buildBibliographyItem = exports.buildContributor = exports.buildManuscript = exports.buildProject = exports.DEFAULT_PAGE_LAYOUT = exports.DEFAULT_BUNDLE = void 0;
+exports.buildTitles = exports.buildElementsOrder = exports.auxiliaryObjectTypes = exports.buildJournal = exports.buildAttribution = exports.buildContributorRole = exports.buildContribution = exports.buildColor = exports.buildParagraph = exports.buildSection = exports.buildCorresp = exports.buildFootnotesOrder = exports.buildFootnote = exports.buildInlineMathFragment = exports.buildNote = exports.buildComment = exports.buildSupplementaryMaterial = exports.buildAffiliation = exports.buildFigure = exports.buildKeywordGroup = exports.buildKeyword = exports.buildBibliographyElement = exports.buildBibliographicDate = exports.buildBibliographicName = exports.buildBibliographyItem = exports.buildContributor = exports.buildManuscript = exports.buildProject = void 0;
 const json_schema_1 = require("@manuscripts/json-schema");
 const w3c_xmlserializer_1 = __importDefault(require("w3c-xmlserializer"));
 const schema_1 = require("../schema");
 const id_1 = require("./id");
 const timestamp_1 = require("./timestamp");
-exports.DEFAULT_BUNDLE = 'MPBundle:www-zotero-org-styles-nature';
-exports.DEFAULT_PAGE_LAYOUT = 'MPPageLayout:defaultA4';
 const buildProject = (owner) => ({
     _id: (0, id_1.generateID)(json_schema_1.ObjectTypes.Project),
     objectType: json_schema_1.ObjectTypes.Project,
@@ -57,34 +55,14 @@ const buildBibliographicName = (data) => (Object.assign(Object.assign({}, data),
 exports.buildBibliographicName = buildBibliographicName;
 const buildBibliographicDate = (data) => (Object.assign(Object.assign({}, data), { _id: (0, id_1.generateID)(json_schema_1.ObjectTypes.BibliographicDate), objectType: json_schema_1.ObjectTypes.BibliographicDate }));
 exports.buildBibliographicDate = buildBibliographicDate;
-const buildAuxiliaryObjectReference = (containingObject, rids) => {
-    const auxiliaryObjectReference = {
-        _id: (0, id_1.generateID)(json_schema_1.ObjectTypes.AuxiliaryObjectReference),
-        objectType: json_schema_1.ObjectTypes.AuxiliaryObjectReference,
-        containingObject: containingObject || undefined,
-    };
-    if (rids.length < 2) {
-        Object.assign(auxiliaryObjectReference, { referencedObject: rids[0] });
-    }
-    else {
-        Object.assign(auxiliaryObjectReference, { referencedObjects: rids });
-    }
-    return auxiliaryObjectReference;
-};
-exports.buildAuxiliaryObjectReference = buildAuxiliaryObjectReference;
-const buildEmbeddedCitationItem = (bibliographyItem) => ({
-    _id: (0, id_1.generateID)(json_schema_1.ObjectTypes.CitationItem),
-    objectType: json_schema_1.ObjectTypes.CitationItem,
-    bibliographyItem,
-});
-exports.buildEmbeddedCitationItem = buildEmbeddedCitationItem;
-const buildCitation = (containingObject, embeddedCitationItems) => ({
-    _id: (0, id_1.generateID)(json_schema_1.ObjectTypes.Citation),
-    objectType: json_schema_1.ObjectTypes.Citation,
-    containingObject: containingObject || undefined,
-    embeddedCitationItems: embeddedCitationItems.map(exports.buildEmbeddedCitationItem),
-});
-exports.buildCitation = buildCitation;
+const buildBibliographyElement = (bibliographyItems) => ({
+    _id: (0, id_1.generateID)(json_schema_1.ObjectTypes.BibliographyElement),
+    objectType: json_schema_1.ObjectTypes.BibliographyElement,
+    contents: '',
+    elementType: 'div',
+    containedObjectIDs: bibliographyItems.map((b) => b._id),
+});
+exports.buildBibliographyElement = buildBibliographyElement;
 const buildKeyword = (name) => ({
     _id: (0, id_1.generateID)(json_schema_1.ObjectTypes.Keyword),
     objectType: json_schema_1.ObjectTypes.Keyword,
@@ -93,21 +71,6 @@ const buildKeyword = (name) => ({
 exports.buildKeyword = buildKeyword;
 const buildKeywordGroup = (attributes) => (Object.assign(Object.assign(Object.assign({ _id: (0, id_1.generateID)(json_schema_1.ObjectTypes.KeywordGroup), objectType: json_schema_1.ObjectTypes.KeywordGroup }, (attributes.type && { type: attributes.type })), (attributes.title && { title: attributes.title })), (attributes.label && { label: attributes.label })));
 exports.buildKeywordGroup = buildKeywordGroup;
-const buildManuscriptKeyword = (name) => ({
-    _id: (0, id_1.generateID)(json_schema_1.ObjectTypes.ManuscriptKeyword),
-    objectType: json_schema_1.ObjectTypes.ManuscriptKeyword,
-    name,
-});
-exports.buildManuscriptKeyword = buildManuscriptKeyword;
-const buildLibraryCollection = (owner, name) => ({
-    _id: (0, id_1.generateID)(json_schema_1.ObjectTypes.LibraryCollection),
-    objectType: json_schema_1.ObjectTypes.LibraryCollection,
-    owners: [owner],
-    writers: [],
-    viewers: [],
-    name,
-});
-exports.buildLibraryCollection = buildLibraryCollection;
 const buildFigure = (blob) => ({
     _id: (0, id_1.generateID)(json_schema_1.ObjectTypes.Figure),
     objectType: json_schema_1.ObjectTypes.Figure,
@@ -134,13 +97,6 @@ const buildSupplementaryMaterial = (title, href) => ({
     href,
 });
 exports.buildSupplementaryMaterial = buildSupplementaryMaterial;
-const buildUserProfileAffiliation = (institution, priority = 0) => ({
-    _id: (0, id_1.generateID)(json_schema_1.ObjectTypes.UserProfileAffiliation),
-    objectType: json_schema_1.ObjectTypes.UserProfileAffiliation,
-    institution,
-    priority,
-});
-exports.buildUserProfileAffiliation = buildUserProfileAffiliation;
 const buildComment = (target, contents = '', selector, contributions, annotationColor) => ({
     _id: (0, id_1.generateID)(json_schema_1.ObjectTypes.CommentAnnotation),
     objectType: json_schema_1.ObjectTypes.CommentAnnotation,
@@ -159,12 +115,6 @@ const buildNote = (target, source, contents = '') => ({
     contents,
 });
 exports.buildNote = buildNote;
-const buildValidation = (results) => ({
-    _id: (0, id_1.generateID)(json_schema_1.ObjectTypes.RequirementsValidation),
-    objectType: json_schema_1.ObjectTypes.RequirementsValidation,
-    results,
-});
-exports.buildValidation = buildValidation;
 const buildInlineMathFragment = (containingObject, TeXRepresentation) => ({
     _id: (0, id_1.generateID)(json_schema_1.ObjectTypes.InlineMathFragment),
     objectType: json_schema_1.ObjectTypes.InlineMathFragment,
@@ -227,20 +177,6 @@ const buildColor = (value, priority) => ({
     value,
 });
 exports.buildColor = buildColor;
-const buildHighlight = () => ({
-    _id: (0, id_1.generateID)(json_schema_1.ObjectTypes.Highlight),
-    objectType: json_schema_1.ObjectTypes.Highlight,
-});
-exports.buildHighlight = buildHighlight;
-const buildHighlightMarker = (highlightID, start, offset, field) => ({
-    highlightID,
-    objectType: json_schema_1.ObjectTypes.HighlightMarker,
-    _id: (0, id_1.generateID)(json_schema_1.ObjectTypes.HighlightMarker),
-    start,
-    offset,
-    field,
-});
-exports.buildHighlightMarker = buildHighlightMarker;
 const buildContribution = (profileID) => ({
     _id: (0, id_1.generateID)(json_schema_1.ObjectTypes.Contribution),
     objectType: json_schema_1.ObjectTypes.Contribution,
@@ -254,13 +190,6 @@ const buildContributorRole = (name) => ({
     name,
 });
 exports.buildContributorRole = buildContributorRole;
-const buildInlineStyle = (priority, title) => ({
-    _id: (0, id_1.generateID)(json_schema_1.ObjectTypes.InlineStyle),
-    objectType: json_schema_1.ObjectTypes.InlineStyle,
-    priority,
-    title,
-});
-exports.buildInlineStyle = buildInlineStyle;
 const buildAttribution = () => ({
     _id: (0, id_1.generateID)(json_schema_1.ObjectTypes.Attribution),
     objectType: json_schema_1.ObjectTypes.Attribution,
@@ -271,12 +200,6 @@ const buildJournal = () => ({
     objectType: json_schema_1.ObjectTypes.Journal,
 });
 exports.buildJournal = buildJournal;
-const buildStatusLabel = (name) => ({
-    _id: (0, id_1.generateID)(json_schema_1.ObjectTypes.StatusLabel),
-    objectType: json_schema_1.ObjectTypes.StatusLabel,
-    name,
-});
-exports.buildStatusLabel = buildStatusLabel;
 exports.auxiliaryObjectTypes = new Set([
     schema_1.schema.nodes.figure_element,
     schema_1.schema.nodes.table_element,

package/dist/cjs/transformer/decode.js

@@ -34,6 +34,7 @@ const json_schema_1 = require("@manuscripts/json-schema");
 const debug_1 = __importDefault(require("debug"));
 const prosemirror_model_1 = require("prosemirror-model");
 const errors_1 = require("../errors");
+const utils_1 = require("../lib/utils");
 const schema_1 = require("../schema");
 const builders_1 = require("./builders");
 const highlight_markers_1 = require("./highlight-markers");
@@ -63,18 +64,42 @@ exports.sortSectionsByPriority = sortSectionsByPriority;
 const getSections = (modelMap) => (0, exports.getModelsByType)(modelMap, json_schema_1.ObjectTypes.Section).sort(exports.sortSectionsByPriority);
 const getAffiliations = (modelMap) => (0, exports.getModelsByType)(modelMap, json_schema_1.ObjectTypes.Affiliation);
 const getContributors = (modelMap) => (0, exports.getModelsByType)(modelMap, json_schema_1.ObjectTypes.Contributor);
+const getKeywordElements = (modelMap) => (0, exports.getModelsByType)(modelMap, json_schema_1.ObjectTypes.KeywordsElement);
+const getKeywordGroups = (modelMap) => (0, exports.getModelsByType)(modelMap, json_schema_1.ObjectTypes.KeywordGroup);
+const getKeywords = (modelMap) => (0, exports.getModelsByType)(modelMap, json_schema_1.ObjectTypes.Keyword);
+const getTitles = (modelMap) => (0, exports.getModelsByType)(modelMap, json_schema_1.ObjectTypes.Titles)[0];
 const isManuscriptNode = (model) => model !== null;
 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 {
+    createTitleNode() {
+        const titles = getTitles(this.modelMap) || (0, builders_1.buildTitles)();
+        return this.decode(titles);
+    }
+    createAffiliationsNode() {
+        const affiliations = getAffiliations(this.modelMap)
+            .map((a) => this.decode(a))
+            .filter(Boolean);
+        return schema_1.schema.nodes.affiliations.createAndFill({}, affiliations);
+    }
+    createContributorsNode() {
+        const contributors = getContributors(this.modelMap)
+            .map((c) => this.decode(c))
+            .filter(Boolean);
+        return schema_1.schema.nodes.contributors.createAndFill({}, contributors);
+    }
+    createKeywordsNode() {
+        const elements = getKeywordElements(this.modelMap)
+            .map((e) => this.decode(e))
+            .filter(Boolean);
+        return schema_1.schema.nodes.keywords.createAndFill({}, [
+            schema_1.schema.nodes.section_title.create({}, schema_1.schema.text('Keywords')),
+            ...elements,
+        ]);
+    }
     createMetaSectionNode() {
         const commentListNode = this.createCommentListNode();
         return schema_1.schema.nodes.meta_section.createAndFill({}, [
@@ -86,54 +111,51 @@ 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);
-        }
-    }
-    createTitleNode() {
-        const titles = (0, exports.getModelsByType)(this.modelMap, json_schema_1.ObjectTypes.Titles)[0] ||
-            (0, builders_1.buildTitles)();
-        return this.decode(titles);
-    }
     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 = (0, utils_1.groupBy)(rootSections, (sec) => {
+            var _a;
+            return (0, section_category_1.chooseCoreSectionBySection)((_a = sec.category) !== null && _a !== void 0 ? _a : '');
+        });
+        this.ensureCoreSectionsExist(sectionGroups);
+        const absSectionNode = sectionGroups['MPSectionCategory:abstracts']
+            .map(this.decode)
+            .filter(exports.isManuscriptNode);
+        const bodySectionNodes = sectionGroups['MPSectionCategory:body']
+            .map(this.decode)
+            .filter(exports.isManuscriptNode);
+        const backmatterSectionNodes = sectionGroups['MPSectionCategory:backmatter']
             .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),
-            }));
+        const abstractCoreSectionNodes = this.createAndFill(schema_1.schema.nodes.abstracts, absSectionNode);
+        const bodyCoreSectionNodes = this.createAndFill(schema_1.schema.nodes.body, bodySectionNodes);
+        const backmatterCoreSectionNodes = this.createAndFill(schema_1.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'] = [];
         }
-        return rootSectionNodes;
+        if (!coreSections['MPSectionCategory:backmatter']) {
+            coreSections['MPSectionCategory:backmatter'] = [];
+        }
+    }
+    createAndFill(nodeType, content) {
+        return nodeType.createAndFill({
+            id: (0, id_1.generateNodeID)(nodeType),
+        }, content);
     }
     createCommentsNode(model) {
         const comments = [];
@@ -339,19 +361,34 @@ class Decoder {
             },
             [json_schema_1.ObjectTypes.KeywordsElement]: (data) => {
                 const model = data;
-                const keywordGroups = this.getKeywordGroups();
+                const keywordGroups = getKeywordGroups(this.modelMap).map((k) => this.decode(k));
                 return schema_1.schema.nodes.keywords_element.create({
                     id: model._id,
                     paragraphStyle: model.paragraphStyle,
                 }, keywordGroups);
             },
+            [json_schema_1.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_1.schema.nodes.keyword_group.create({
+                    id: keywordGroup._id,
+                    type: keywordGroup.type,
+                    comments: comments.map((c) => c.attrs.id),
+                }, keywords);
+            },
             [json_schema_1.ObjectTypes.Keyword]: (data) => {
-                const model = data;
+                const keyword = data;
+                const comments = this.createCommentsNode(keyword);
+                comments.forEach((c) => this.comments.set(c.attrs.id, c));
                 return schema_1.schema.nodes.keyword.create({
-                    id: model._id,
-                    contents: model.name,
-                    comments: this.createCommentsNode(model),
-                }, schema_1.schema.text(model.name));
+                    id: keyword._id,
+                    contents: keyword.name,
+                    comments: comments.map((c) => c.attrs.id),
+                }, schema_1.schema.text(keyword.name));
             },
             [json_schema_1.ObjectTypes.ListElement]: (data) => {
                 const model = data;
@@ -473,9 +510,6 @@ 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) {
@@ -516,17 +550,11 @@ 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));
-                let content;
-                if (isAffiliationsSection(model) || isContributorsSection(model)) {
-                    content = elementNodes.concat(nestedSections);
-                }
-                else {
-                    content = (sectionLabelNode
-                        ? [sectionLabelNode, sectionTitleNode]
-                        : [sectionTitleNode])
-                        .concat(elementNodes)
-                        .concat(nestedSections);
-                }
+                const content = (sectionLabelNode
+                    ? [sectionLabelNode, sectionTitleNode]
+                    : [sectionTitleNode])
+                    .concat(elementNodes)
+                    .concat(nestedSections);
                 const sectionNode = sectionNodeType.createAndFill({
                     id: model._id,
                     category: sectionCategory,
@@ -645,13 +673,21 @@ class Decoder {
         };
         this.getModel = (id) => this.modelMap.get(id);
         this.createArticleNode = (manuscriptID) => {
-            const titlesNode = this.createTitleNode();
-            const rootSectionNodes = this.createRootSectionNodes();
-            const metaSectionNode = this.createMetaSectionNode();
+            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 contents = [
-                titlesNode,
-                ...rootSectionNodes,
-                metaSectionNode,
+                title,
+                contributors,
+                affiliations,
+                keywords,
+                abstracts,
+                body,
+                backmatter,
+                meta,
             ];
             return schema_1.schema.nodes.manuscript.create({
                 id: manuscriptID || this.getManuscriptID(),
@@ -693,23 +729,6 @@ class Decoder {
             }
             return parser.parse(template.content.firstElementChild, options);
         };
-        this.getKeywords = (id) => {
-            const keywordsOfKind = [];
-            const keywordsByGroup = [...this.modelMap.values()].filter((m) => m.objectType === json_schema_1.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_1.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 ((0, object_types_1.isManuscript)(item)) {
@@ -794,27 +813,5 @@ class Decoder {
         }
         return listing;
     }
-    getKeywordGroups() {
-        const kwdGroupNodes = [];
-        const kwdGroupsModels = [
-            ...this.modelMap.values(),
-        ].filter((model) => model.objectType === json_schema_1.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_1.schema.nodes.keywords_group.create({
-                    id: kwdGroupModel._id,
-                    type: kwdGroupModel.type,
-                    comments: commentNodes.map((c) => c.attrs.id),
-                }, contents);
-                kwdGroupNodes.push(kwdGroupNode);
-            }
-        }
-        return kwdGroupNodes;
-    }
 }
 exports.Decoder = Decoder;

package/dist/cjs/transformer/encode.js

@@ -428,34 +428,9 @@ const encoders = {
         elementType: 'div',
         paragraphStyle: node.attrs.paragraphStyle || undefined,
     }),
-    keywords_group: (node) => ({
+    keyword_group: (node) => ({
         type: node.attrs.type,
     }),
-    keywords_section: (node, parent, path, priority) => ({
-        category: (0, section_category_1.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: (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,
     }),
@@ -577,6 +552,14 @@ const modelFromNode = (node, parent, path, priority) => {
     return { model, comments };
 };
 exports.modelFromNode = modelFromNode;
+function isCoreSection(child) {
+    return (child.type === schema_1.schema.nodes.abstracts ||
+        child.type === schema_1.schema.nodes.body ||
+        child.type === schema_1.schema.nodes.backmatter ||
+        child.type === schema_1.schema.nodes.affiliations ||
+        child.type === schema_1.schema.nodes.contributors ||
+        child.type === schema_1.schema.nodes.keywords);
+}
 const encode = (node) => {
     const models = new Map();
     const priority = {
@@ -584,6 +567,10 @@ 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;
         }
@@ -596,6 +583,9 @@ const encode = (node) => {
         if (placeholders.includes(child.type.name)) {
             return;
         }
+        if (parent.type === schema_1.schema.nodes.paragraph) {
+            return;
+        }
         const { model, comments } = (0, exports.modelFromNode)(child, parent, path, priority);
         if (models.has(model._id)) {
             throw Error(`Encountered duplicate ids in models map while encoding: ${model._id}`);
@@ -611,12 +601,20 @@ const encode = (node) => {
         models.set(model._id, model);
         child.forEach(addModel(path.concat(child.attrs.id), child));
     };
-    node.forEach((cNode) => {
-        if (cNode.type === schema_1.schema.nodes.meta_section) {
-            processMetaSectionNode(cNode, models, priority);
+    node.forEach((child) => {
+        if (child.type === schema_1.schema.nodes.meta_section) {
+            processMetaSectionNode(child, models, priority);
         }
     });
     node.forEach(addModel([], node));
+    if (node.type === schema_1.schema.nodes.manuscript) {
+        builders_1.auxiliaryObjectTypes.forEach((t) => {
+            const order = generateElementOrder(node, t);
+            if (order) {
+                models.set(order._id, order);
+            }
+        });
+    }
     return models;
 };
 exports.encode = encode;
@@ -629,3 +627,22 @@ const processMetaSectionNode = (node, models, priority) => {
         }
     });
 };
+const generateElementOrder = (node, nodeType) => {
+    const ids = [];
+    node.descendants((n) => {
+        if (n.type === nodeType) {
+            ids.push(n.attrs.id);
+        }
+        return true;
+    });
+    if (!ids.length) {
+        return undefined;
+    }
+    const type = node_types_1.nodeTypesMap.get(nodeType);
+    if (!type) {
+        return undefined;
+    }
+    const order = (0, builders_1.buildElementsOrder)(type);
+    order.elements = ids;
+    return order;
+};

package/dist/cjs/transformer/highlight-markers.js

@@ -15,15 +15,15 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.insertHighlightMarkers = exports.extractHighlightMarkers = exports.isHighlightableModel = void 0;
+exports.insertHighlightMarkers = exports.extractHighlightMarkers = exports.isHighlightableModel = exports.highlightableFields = void 0;
 const builders_1 = require("./builders");
-const highlightableFields = [
+exports.highlightableFields = [
     'caption',
     'contents',
     'title',
 ];
 const isHighlightableModel = (model) => {
-    for (const field of highlightableFields) {
+    for (const field of exports.highlightableFields) {
         if (field in model) {
             return true;
         }
@@ -32,7 +32,7 @@ const isHighlightableModel = (model) => {
 };
 exports.isHighlightableModel = isHighlightableModel;
 const extractHighlightMarkers = (model, commentAnnotationsMap) => {
-    for (const field of highlightableFields) {
+    for (const field of exports.highlightableFields) {
         let html = model[field];
         if (html === undefined) {
             continue;

package/dist/cjs/transformer/html.js

@@ -200,11 +200,9 @@ class HTMLTransformer {
                 const citationNode = node;
                 const element = this.document.createElement('span');
                 element.setAttribute('class', 'citation');
-                const citation = getModel(citationNode.attrs.rid);
-                if (citation) {
-                    element.setAttribute('data-reference-ids', citation.embeddedCitationItems
-                        .map((item) => item.bibliographyItem)
-                        .join(' '));
+                const rids = citationNode.attrs.rids;
+                if (rids.length) {
+                    element.setAttribute('data-reference-ids', rids.join(' '));
                 }
                 if (citationNode.attrs.contents) {
                     element.innerHTML = citationNode.attrs.contents;
@@ -215,20 +213,7 @@ class HTMLTransformer {
                 const crossReferenceNode = node;
                 const element = this.document.createElement('a');
                 element.classList.add('cross-reference');
-                const auxiliaryObjectReference = getModel(crossReferenceNode.attrs.rid);
-                if (auxiliaryObjectReference &&
-                    auxiliaryObjectReference.referencedObject) {
-                    if (auxiliaryObjectReference.referencedObject.startsWith('MPFigureElement')) {
-                        const model = getModel(auxiliaryObjectReference.referencedObject);
-                        if (model && model.containedObjectIDs.length > 0) {
-                            element.setAttribute('href', `#${model.containedObjectIDs[0]}`);
-                        }
-                    }
-                    else {
-                        element.setAttribute('href', `#${auxiliaryObjectReference.referencedObject}`);
-                    }
-                    element.setAttribute('data-reference-ids', crossReferenceNode.attrs.rid);
-                }
+                element.setAttribute('data-reference-ids', crossReferenceNode.attrs.rids.join(' '));
                 element.textContent =
                     crossReferenceNode.attrs.customLabel || crossReferenceNode.attrs.label;
                 return element;

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

@@ -38,6 +38,6 @@ exports.nodeNames = new Map([
     [schema_1.schema.nodes.table_element, 'Table'],
     [schema_1.schema.nodes.blockquote_element, 'Block Quote'],
     [schema_1.schema.nodes.pullquote_element, 'Pull Quote'],
-    [schema_1.schema.nodes.keywords_section, 'Section'],
+    [schema_1.schema.nodes.keywords, 'Section'],
     [schema_1.schema.nodes.toc_section, 'Section'],
 ]);

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

@@ -50,7 +50,7 @@ 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);