@manuscripts/transform 1.3.7-LEAN-2707-V2 → 1.3.8

package/dist/cjs/index.js

@@ -15,6 +15,7 @@ var __exportStar = (this && this.__exportStar) || function(m, exports) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.isSectionLabelNode = void 0;
+__exportStar(require("./lib/core-section-categories"), exports);
 __exportStar(require("./lib/table-cell-styles"), exports);
 __exportStar(require("./lib/utils"), exports);
 __exportStar(require("./mathjax"), exports);

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

@@ -25,7 +25,7 @@ const createSectionContainer = (type, createElement) => {
     sectionContainer.setAttribute('sec-type', sectionCategory ? (0, transformer_1.chooseSecType)(sectionCategory) : '');
     const title = createElement('title');
     title.textContent = sectionCategory
-        ? (0, transformer_1.getSectionTitles)(sectionCategory)[0]
+        ? (0, transformer_1.getCoreSectionTitles)(sectionCategory)[0]
         : ' ';
     sectionContainer.appendChild(title);
     return sectionContainer;

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

@@ -598,11 +598,6 @@ class JATSExporter {
         this.createSerializer = () => {
             const getModel = (id) => id ? this.modelMap.get(id) : undefined;
             const nodes = {
-                contributor_list: () => '',
-                contributor: () => '',
-                affiliation_list: () => '',
-                affiliation: () => '',
-                meta_section: () => '',
                 attribution: () => ['attrib', 0],
                 bibliography_element: () => '',
                 bibliography_item: () => '',

package/dist/cjs/lib/core-section-categories.js

@@ -0,0 +1,29 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.coreSectionCategories = void 0;
+exports.coreSectionCategories = [
+    {
+        _id: 'MPSectionCategory:abstracts',
+        name: 'Abstracts',
+        desc: 'Abstracts section for grouping',
+        objectType: 'MPSectionCategory',
+        titles: [],
+        priority: 120,
+    },
+    {
+        _id: 'MPSectionCategory:backmatter',
+        name: 'Backmatter',
+        desc: 'Backmatter section for grouping',
+        objectType: 'MPSectionCategory',
+        titles: [],
+        priority: 170,
+    },
+    {
+        _id: 'MPSectionCategory:body',
+        name: 'Body',
+        desc: 'Body section for grouping',
+        objectType: 'MPSectionCategory',
+        titles: [],
+        priority: 190,
+    },
+];

package/dist/cjs/schema/index.js

@@ -32,8 +32,6 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.schema = void 0;
 const prosemirror_model_1 = require("prosemirror-model");
 const marks_1 = require("./marks");
-const affiliation_1 = require("./nodes/affiliation");
-const affiliation_list_1 = require("./nodes/affiliation_list");
 const attribution_1 = require("./nodes/attribution");
 const bibliography_element_1 = require("./nodes/bibliography_element");
 const bibliography_item_1 = require("./nodes/bibliography_item");
@@ -44,8 +42,6 @@ const caption_title_1 = require("./nodes/caption_title");
 const citation_1 = require("./nodes/citation");
 const comment_1 = require("./nodes/comment");
 const comment_list_1 = require("./nodes/comment_list");
-const contributor_1 = require("./nodes/contributor");
-const contributor_list_1 = require("./nodes/contributor_list");
 const cross_reference_1 = require("./nodes/cross_reference");
 const doc_1 = require("./nodes/doc");
 const equation_1 = require("./nodes/equation");
@@ -70,7 +66,6 @@ const list_1 = require("./nodes/list");
 const listing_1 = require("./nodes/listing");
 const listing_element_1 = require("./nodes/listing_element");
 const manuscript_1 = require("./nodes/manuscript");
-const meta_section_1 = require("./nodes/meta_section");
 const missing_figure_1 = require("./nodes/missing_figure");
 const paragraph_1 = require("./nodes/paragraph");
 const placeholder_1 = require("./nodes/placeholder");
@@ -135,11 +130,6 @@ __exportStar(require("./nodes/table_row"), exports);
 __exportStar(require("./nodes/text"), exports);
 __exportStar(require("./nodes/toc_element"), exports);
 __exportStar(require("./nodes/toc_section"), exports);
-__exportStar(require("./nodes/affiliation"), exports);
-__exportStar(require("./nodes/affiliation_list"), exports);
-__exportStar(require("./nodes/meta_section"), exports);
-__exportStar(require("./nodes/contributor_list"), exports);
-__exportStar(require("./nodes/contributor"), exports);
 exports.schema = new prosemirror_model_1.Schema({
     marks: {
         bold: marks_1.bold,
@@ -210,10 +200,5 @@ exports.schema = new prosemirror_model_1.Schema({
         text: text_1.text,
         toc_element: toc_element_1.tocElement,
         toc_section: toc_section_1.tocSection,
-        affiliation: affiliation_1.affiliation,
-        meta_section: meta_section_1.metaSection,
-        affiliation_list: affiliation_list_1.affiliationList,
-        contributor_list: contributor_list_1.contributorList,
-        contributor: contributor_1.contributor,
     },
 });

package/dist/cjs/schema/nodes/comment_list.js

@@ -21,4 +21,5 @@ exports.commentList = {
     attrs: {
         id: { default: 'COMMENT_LIST' },
     },
+    toDOM: () => ['section', 0],
 };

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

@@ -17,7 +17,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.manuscript = void 0;
 exports.manuscript = {
-    content: '(section | sections)+ meta_section',
+    content: '(section | sections)+ comment_list',
     attrs: {
         id: { default: '' },
     },

package/dist/cjs/transformer/decode.js

@@ -60,8 +60,6 @@ exports.getModelsByType = getModelsByType;
 const sortSectionsByPriority = (a, b) => a.priority === b.priority ? 0 : Number(a.priority) - Number(b.priority);
 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 isManuscriptNode = (model) => model !== null;
 exports.isManuscriptNode = isManuscriptNode;
 const isParagraphElement = (0, object_types_1.hasObjectType)(json_schema_1.ObjectTypes.ParagraphElement);
@@ -71,46 +69,6 @@ const hasParentSection = (id) => (section) => section.path &&
     section.path.length > 1 &&
     section.path[section.path.length - 2] === id;
 class Decoder {
-    createAffiliationListNode() {
-        const affiliationNodes = getAffiliations(this.modelMap)
-            .map((affiliation) => this.decode(affiliation))
-            .filter(Boolean);
-        return schema_1.schema.nodes.affiliation_list.createAndFill({}, affiliationNodes);
-    }
-    createContributorListNode() {
-        const contributorNodes = getContributors(this.modelMap)
-            .map((contributor) => this.decode(contributor))
-            .filter(Boolean);
-        return schema_1.schema.nodes.contributor_list.createAndFill({}, contributorNodes);
-    }
-    createMetaSectionNode() {
-        const affiliationListNode = this.createAffiliationListNode();
-        const contributorListNode = this.createContributorListNode();
-        const commentListNode = this.createCommentListNode();
-        return schema_1.schema.nodes.meta_section.createAndFill({}, [
-            affiliationListNode,
-            contributorListNode,
-            commentListNode,
-        ]);
-    }
-    createCommentListNode() {
-        return schema_1.schema.nodes.comment_list.createAndFill({}, [
-            ...this.comments.values(),
-        ]);
-    }
-    createRootSectionNodes() {
-        let rootSections = getSections(this.modelMap).filter((section) => !section.path || section.path.length <= 1);
-        rootSections = this.addGeneratedLabels(rootSections);
-        const rootSectionNodes = rootSections
-            .map(this.decode)
-            .filter(exports.isManuscriptNode);
-        if (!rootSectionNodes.length) {
-            rootSectionNodes.push(schema_1.schema.nodes.section.createAndFill({
-                id: (0, id_1.generateNodeID)(schema_1.schema.nodes.section),
-            }));
-        }
-        return rootSectionNodes;
-    }
     createCommentsNode(model) {
         const comments = [];
         for (const comment of this.getComments(model)) {
@@ -592,32 +550,6 @@ class Decoder {
                     originalText: model.originalText,
                 });
             },
-            [json_schema_1.ObjectTypes.Affiliation]: (data) => {
-                const model = data;
-                return schema_1.schema.nodes.affiliation.create({
-                    id: model._id,
-                    institution: model.institution,
-                    addressLine1: model.addressLine1,
-                    addressLine2: model.addressLine2,
-                    addressLine3: model.addressLine3,
-                    postCode: model.postCode,
-                    country: model.country,
-                    email: model.email,
-                });
-            },
-            [json_schema_1.ObjectTypes.Contributor]: (data) => {
-                const model = data;
-                return schema_1.schema.nodes.contributor.create({
-                    id: model._id,
-                    role: model.role,
-                    affiliations: model.affiliations,
-                    bibliographicName: model.bibliographicName,
-                    userID: model.userID,
-                    invitationID: model.invitationID,
-                    isCorresponding: model.isCorresponding,
-                    ORCIDIdentifier: model.ORCIDIdentifier,
-                });
-            },
         };
         this.decode = (model) => {
             if (!this.creators[model.objectType]) {
@@ -628,9 +560,21 @@ class Decoder {
         };
         this.getModel = (id) => this.modelMap.get(id);
         this.createArticleNode = (manuscriptID) => {
-            const rootSectionNodes = this.createRootSectionNodes();
-            const metaSectionNode = this.createMetaSectionNode();
-            const contents = [...rootSectionNodes, metaSectionNode];
+            let rootSections = getSections(this.modelMap).filter((section) => !section.path || section.path.length <= 1);
+            rootSections = this.addGeneratedLabels(rootSections);
+            const rootSectionNodes = rootSections
+                .map(this.decode)
+                .filter(exports.isManuscriptNode);
+            if (!rootSectionNodes.length) {
+                rootSectionNodes.push(schema_1.schema.nodes.section.createAndFill({
+                    id: (0, id_1.generateNodeID)(schema_1.schema.nodes.section),
+                }));
+            }
+            const contents = rootSectionNodes;
+            const comments = schema_1.schema.nodes.comment_list.createAndFill({}, [
+                ...this.comments.values(),
+            ]);
+            contents.push(comments);
             return schema_1.schema.nodes.manuscript.create({
                 id: manuscriptID || this.getManuscriptID(),
             }, contents);

package/dist/cjs/transformer/encode.js

@@ -500,24 +500,6 @@ const encoders = {
             .map((childNode) => childNode.attrs.id)
             .filter((id) => id),
     }),
-    affiliation: (node) => ({
-        institution: node.attrs.institution,
-        addressLine1: node.attrs.addressLine1,
-        addressLine2: node.attrs.addressLine2,
-        addressLine3: node.attrs.addressLine3,
-        postCode: node.attrs.postCode,
-        country: node.attrs.country,
-        email: node.attrs.email,
-    }),
-    contributor: (node) => ({
-        role: node.attrs.role,
-        affiliations: node.attrs.affiliations,
-        bibliographicName: node.attrs.bibliographicName,
-        userID: node.attrs.userID,
-        invitationID: node.attrs.invitationID,
-        isCorresponding: node.attrs.isCorresponding,
-        ORCIDIdentifier: node.attrs.ORCIDIdentifier,
-    }),
 };
 const modelData = (node, parent, path, priority) => {
     const encoder = encoders[node.type.name];
@@ -557,7 +539,7 @@ const encode = (node) => {
         if ((0, schema_1.isHighlightMarkerNode)(child)) {
             return;
         }
-        if (child.type === schema_1.schema.nodes.meta_section) {
+        if (child.type === schema_1.schema.nodes.comment_list) {
             return;
         }
         if (placeholders.includes(child.type.name)) {
@@ -571,26 +553,14 @@ const encode = (node) => {
         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);
+        if (cNode.type === schema_1.schema.nodes.comment_list) {
+            cNode.forEach((child) => {
+                const { model } = (0, exports.modelFromNode)(child, cNode, [], priority);
+                models.set(model._id, model);
+            });
         }
     });
     node.forEach(addModel([], node));
     return models;
 };
 exports.encode = encode;
-const processMetaSectionNode = (node, models, priority) => {
-    processNodeRecursively(node, models, priority);
-};
-const processNodeRecursively = (node, models, priority) => {
-    if ((!node.content || node.content.size === 0) &&
-        node_types_1.nodeTypesMap.get(node.type)) {
-        const { model } = (0, exports.modelFromNode)(node, node, [], priority);
-        models.set(model._id, model);
-    }
-    else {
-        node.forEach((child) => {
-            processNodeRecursively(child, models, priority);
-        });
-    }
-};

package/dist/cjs/transformer/html.js

@@ -260,7 +260,7 @@ class HTMLTransformer {
                 };
                 return ['span', attrs];
             };
-            nodes.meta_section = () => '';
+            nodes.comment_list = () => '';
             const serializer = new prosemirror_model_1.DOMSerializer(nodes, marks);
             return serializer.serializeFragment(fragment, { document });
         };

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

@@ -53,8 +53,7 @@ exports.nodeTypesMap = new Map([
     [schema_1.schema.nodes.table_element, json_schema_1.ObjectTypes.TableElement],
     [schema_1.schema.nodes.toc_element, json_schema_1.ObjectTypes.TOCElement],
     [schema_1.schema.nodes.toc_section, json_schema_1.ObjectTypes.Section],
-    [schema_1.schema.nodes.affiliation, json_schema_1.ObjectTypes.Affiliation],
-    [schema_1.schema.nodes.meta_section, json_schema_1.ObjectTypes.MetaSection],
+    [schema_1.schema.nodes.comment_list, json_schema_1.ObjectTypes.MetaSection],
 ]);
 const isExecutableNodeType = (type) => (0, schema_1.hasGroup)(type, schema_1.GROUP_EXECUTABLE);
 exports.isExecutableNodeType = isExecutableNodeType;

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

@@ -14,13 +14,10 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.chooseSectionCategoryFromTitle = exports.chooseSectionCategory = exports.chooseSectionCategoryByType = exports.chooseSecType = exports.chooseJatsFnType = exports.buildSectionCategory = exports.guessSectionCategory = exports.chooseSectionLableName = exports.chooseSectionNodeType = exports.isAnySectionNode = exports.getSectionTitles = void 0;
-const section_categories_json_1 = __importDefault(require("@manuscripts/data/dist/shared/section-categories.json"));
+exports.chooseSectionCategoryFromTitle = exports.chooseSectionCategory = exports.chooseSectionCategoryByType = exports.chooseSecType = exports.chooseJatsFnType = exports.buildSectionCategory = exports.guessSectionCategory = exports.chooseSectionLableName = exports.chooseSectionNodeType = exports.isAnySectionNode = exports.getCoreSectionTitles = void 0;
 const json_schema_1 = require("@manuscripts/json-schema");
+const core_section_categories_1 = require("../lib/core-section-categories");
 const schema_1 = require("../schema");
 const sectionNodeTypes = [
     schema_1.schema.nodes.bibliography_section,
@@ -29,15 +26,14 @@ const sectionNodeTypes = [
     schema_1.schema.nodes.section,
     schema_1.schema.nodes.toc_section,
 ];
-const sectionCategoriesMap = new Map(section_categories_json_1.default.map((section) => [section._id, section]));
-const getSectionTitles = (sectionCategory) => {
-    const category = sectionCategoriesMap.get(sectionCategory);
+const getCoreSectionTitles = (sectionCategory) => {
+    const category = core_section_categories_1.coreSectionCategories.find((section) => section._id === sectionCategory);
     if (category) {
         return category.titles.length ? category.titles : [' '];
     }
-    throw new Error(`${sectionCategory} not found in section categories`);
+    throw new Error(`${sectionCategory} not found in core sections`);
 };
-exports.getSectionTitles = getSectionTitles;
+exports.getCoreSectionTitles = getCoreSectionTitles;
 const isAnySectionNode = (node) => sectionNodeTypes.includes(node.type);
 exports.isAnySectionNode = isAnySectionNode;
 const chooseSectionNodeType = (category) => {

package/dist/es/index.js

@@ -1,3 +1,4 @@
+export * from './lib/core-section-categories';
 export * from './lib/table-cell-styles';
 export * from './lib/utils';
 export * from './mathjax';

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

@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import { chooseSectionCategoryByType, chooseSecType, getSectionTitles, } from '../../transformer';
+import { chooseSectionCategoryByType, chooseSecType, getCoreSectionTitles, } from '../../transformer';
 const removeNodeFromParent = (node) => node.parentNode && node.parentNode.removeChild(node);
 const capitalizeFirstLetter = (str) => str.charAt(0).toUpperCase() + str.slice(1);
 const createSectionContainer = (type, createElement) => {
@@ -22,7 +22,7 @@ const createSectionContainer = (type, createElement) => {
     sectionContainer.setAttribute('sec-type', sectionCategory ? chooseSecType(sectionCategory) : '');
     const title = createElement('title');
     title.textContent = sectionCategory
-        ? getSectionTitles(sectionCategory)[0]
+        ? getCoreSectionTitles(sectionCategory)[0]
         : ' ';
     sectionContainer.appendChild(title);
     return sectionContainer;

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

@@ -591,11 +591,6 @@ export class JATSExporter {
         this.createSerializer = () => {
             const getModel = (id) => id ? this.modelMap.get(id) : undefined;
             const nodes = {
-                contributor_list: () => '',
-                contributor: () => '',
-                affiliation_list: () => '',
-                affiliation: () => '',
-                meta_section: () => '',
                 attribution: () => ['attrib', 0],
                 bibliography_element: () => '',
                 bibliography_item: () => '',

package/dist/es/lib/core-section-categories.js

@@ -0,0 +1,26 @@
+export const coreSectionCategories = [
+    {
+        _id: 'MPSectionCategory:abstracts',
+        name: 'Abstracts',
+        desc: 'Abstracts section for grouping',
+        objectType: 'MPSectionCategory',
+        titles: [],
+        priority: 120,
+    },
+    {
+        _id: 'MPSectionCategory:backmatter',
+        name: 'Backmatter',
+        desc: 'Backmatter section for grouping',
+        objectType: 'MPSectionCategory',
+        titles: [],
+        priority: 170,
+    },
+    {
+        _id: 'MPSectionCategory:body',
+        name: 'Body',
+        desc: 'Body section for grouping',
+        objectType: 'MPSectionCategory',
+        titles: [],
+        priority: 190,
+    },
+];

package/dist/es/schema/index.js

@@ -15,8 +15,6 @@
  */
 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 { affiliationList } from './nodes/affiliation_list';
 import { attribution } from './nodes/attribution';
 import { bibliographyElement } from './nodes/bibliography_element';
 import { bibliographyItem } from './nodes/bibliography_item';
@@ -27,8 +25,6 @@ import { captionTitle } from './nodes/caption_title';
 import { citation } from './nodes/citation';
 import { comment } from './nodes/comment';
 import { commentList } from './nodes/comment_list';
-import { contributor } from './nodes/contributor';
-import { contributorList } from './nodes/contributor_list';
 import { crossReference } from './nodes/cross_reference';
 import { doc } from './nodes/doc';
 import { equation } from './nodes/equation';
@@ -53,7 +49,6 @@ import { bulletList, listItem, orderedList } from './nodes/list';
 import { listing } from './nodes/listing';
 import { listingElement } from './nodes/listing_element';
 import { manuscript } from './nodes/manuscript';
-import { metaSection } from './nodes/meta_section';
 import { missingFigure } from './nodes/missing_figure';
 import { paragraph } from './nodes/paragraph';
 import { placeholder } from './nodes/placeholder';
@@ -118,11 +113,6 @@ export * from './nodes/table_row';
 export * from './nodes/text';
 export * from './nodes/toc_element';
 export * from './nodes/toc_section';
-export * from './nodes/affiliation';
-export * from './nodes/affiliation_list';
-export * from './nodes/meta_section';
-export * from './nodes/contributor_list';
-export * from './nodes/contributor';
 export const schema = new Schema({
     marks: {
         bold,
@@ -193,10 +183,5 @@ export const schema = new Schema({
         text,
         toc_element: tocElement,
         toc_section: tocSection,
-        affiliation,
-        meta_section: metaSection,
-        affiliation_list: affiliationList,
-        contributor_list: contributorList,
-        contributor: contributor,
     },
 });

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

@@ -18,4 +18,5 @@ export const commentList = {
     attrs: {
         id: { default: 'COMMENT_LIST' },
     },
+    toDOM: () => ['section', 0],
 };

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

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 export const manuscript = {
-    content: '(section | sections)+ meta_section',
+    content: '(section | sections)+ comment_list',
     attrs: {
         id: { default: '' },
     },

package/dist/es/transformer/decode.js

@@ -51,8 +51,6 @@ export const getModelsByType = (modelMap, objectType) => {
 };
 export const sortSectionsByPriority = (a, b) => a.priority === b.priority ? 0 : Number(a.priority) - Number(b.priority);
 const getSections = (modelMap) => getModelsByType(modelMap, ObjectTypes.Section).sort(sortSectionsByPriority);
-const getAffiliations = (modelMap) => getModelsByType(modelMap, ObjectTypes.Affiliation);
-const getContributors = (modelMap) => getModelsByType(modelMap, ObjectTypes.Contributor);
 export const isManuscriptNode = (model) => model !== null;
 const isParagraphElement = hasObjectType(ObjectTypes.ParagraphElement);
 const isFootnote = hasObjectType(ObjectTypes.Footnote);
@@ -61,46 +59,6 @@ const hasParentSection = (id) => (section) => section.path &&
     section.path.length > 1 &&
     section.path[section.path.length - 2] === id;
 export class Decoder {
-    createAffiliationListNode() {
-        const affiliationNodes = getAffiliations(this.modelMap)
-            .map((affiliation) => this.decode(affiliation))
-            .filter(Boolean);
-        return schema.nodes.affiliation_list.createAndFill({}, affiliationNodes);
-    }
-    createContributorListNode() {
-        const contributorNodes = getContributors(this.modelMap)
-            .map((contributor) => this.decode(contributor))
-            .filter(Boolean);
-        return schema.nodes.contributor_list.createAndFill({}, contributorNodes);
-    }
-    createMetaSectionNode() {
-        const affiliationListNode = this.createAffiliationListNode();
-        const contributorListNode = this.createContributorListNode();
-        const commentListNode = this.createCommentListNode();
-        return schema.nodes.meta_section.createAndFill({}, [
-            affiliationListNode,
-            contributorListNode,
-            commentListNode,
-        ]);
-    }
-    createCommentListNode() {
-        return schema.nodes.comment_list.createAndFill({}, [
-            ...this.comments.values(),
-        ]);
-    }
-    createRootSectionNodes() {
-        let rootSections = getSections(this.modelMap).filter((section) => !section.path || section.path.length <= 1);
-        rootSections = this.addGeneratedLabels(rootSections);
-        const rootSectionNodes = rootSections
-            .map(this.decode)
-            .filter(isManuscriptNode);
-        if (!rootSectionNodes.length) {
-            rootSectionNodes.push(schema.nodes.section.createAndFill({
-                id: generateNodeID(schema.nodes.section),
-            }));
-        }
-        return rootSectionNodes;
-    }
     createCommentsNode(model) {
         const comments = [];
         for (const comment of this.getComments(model)) {
@@ -582,32 +540,6 @@ export class Decoder {
                     originalText: model.originalText,
                 });
             },
-            [ObjectTypes.Affiliation]: (data) => {
-                const model = data;
-                return schema.nodes.affiliation.create({
-                    id: model._id,
-                    institution: model.institution,
-                    addressLine1: model.addressLine1,
-                    addressLine2: model.addressLine2,
-                    addressLine3: model.addressLine3,
-                    postCode: model.postCode,
-                    country: model.country,
-                    email: model.email,
-                });
-            },
-            [ObjectTypes.Contributor]: (data) => {
-                const model = data;
-                return schema.nodes.contributor.create({
-                    id: model._id,
-                    role: model.role,
-                    affiliations: model.affiliations,
-                    bibliographicName: model.bibliographicName,
-                    userID: model.userID,
-                    invitationID: model.invitationID,
-                    isCorresponding: model.isCorresponding,
-                    ORCIDIdentifier: model.ORCIDIdentifier,
-                });
-            },
         };
         this.decode = (model) => {
             if (!this.creators[model.objectType]) {
@@ -618,9 +550,21 @@ export class Decoder {
         };
         this.getModel = (id) => this.modelMap.get(id);
         this.createArticleNode = (manuscriptID) => {
-            const rootSectionNodes = this.createRootSectionNodes();
-            const metaSectionNode = this.createMetaSectionNode();
-            const contents = [...rootSectionNodes, metaSectionNode];
+            let rootSections = getSections(this.modelMap).filter((section) => !section.path || section.path.length <= 1);
+            rootSections = this.addGeneratedLabels(rootSections);
+            const rootSectionNodes = rootSections
+                .map(this.decode)
+                .filter(isManuscriptNode);
+            if (!rootSectionNodes.length) {
+                rootSectionNodes.push(schema.nodes.section.createAndFill({
+                    id: generateNodeID(schema.nodes.section),
+                }));
+            }
+            const contents = rootSectionNodes;
+            const comments = schema.nodes.comment_list.createAndFill({}, [
+                ...this.comments.values(),
+            ]);
+            contents.push(comments);
             return schema.nodes.manuscript.create({
                 id: manuscriptID || this.getManuscriptID(),
             }, contents);

package/dist/es/transformer/encode.js

@@ -492,24 +492,6 @@ const encoders = {
             .map((childNode) => childNode.attrs.id)
             .filter((id) => id),
     }),
-    affiliation: (node) => ({
-        institution: node.attrs.institution,
-        addressLine1: node.attrs.addressLine1,
-        addressLine2: node.attrs.addressLine2,
-        addressLine3: node.attrs.addressLine3,
-        postCode: node.attrs.postCode,
-        country: node.attrs.country,
-        email: node.attrs.email,
-    }),
-    contributor: (node) => ({
-        role: node.attrs.role,
-        affiliations: node.attrs.affiliations,
-        bibliographicName: node.attrs.bibliographicName,
-        userID: node.attrs.userID,
-        invitationID: node.attrs.invitationID,
-        isCorresponding: node.attrs.isCorresponding,
-        ORCIDIdentifier: node.attrs.ORCIDIdentifier,
-    }),
 };
 const modelData = (node, parent, path, priority) => {
     const encoder = encoders[node.type.name];
@@ -548,7 +530,7 @@ export const encode = (node) => {
         if (isHighlightMarkerNode(child)) {
             return;
         }
-        if (child.type === schema.nodes.meta_section) {
+        if (child.type === schema.nodes.comment_list) {
             return;
         }
         if (placeholders.includes(child.type.name)) {
@@ -562,25 +544,13 @@ export const encode = (node) => {
         child.forEach(addModel(path.concat(child.attrs.id), child));
     };
     node.forEach((cNode) => {
-        if (cNode.type === schema.nodes.meta_section) {
-            processMetaSectionNode(cNode, models, priority);
+        if (cNode.type === schema.nodes.comment_list) {
+            cNode.forEach((child) => {
+                const { model } = modelFromNode(child, cNode, [], priority);
+                models.set(model._id, model);
+            });
         }
     });
     node.forEach(addModel([], node));
     return models;
 };
-const processMetaSectionNode = (node, models, priority) => {
-    processNodeRecursively(node, models, priority);
-};
-const processNodeRecursively = (node, models, priority) => {
-    if ((!node.content || node.content.size === 0) &&
-        nodeTypesMap.get(node.type)) {
-        const { model } = modelFromNode(node, node, [], priority);
-        models.set(model._id, model);
-    }
-    else {
-        node.forEach((child) => {
-            processNodeRecursively(child, models, priority);
-        });
-    }
-};

package/dist/es/transformer/html.js

@@ -254,7 +254,7 @@ export class HTMLTransformer {
                 };
                 return ['span', attrs];
             };
-            nodes.meta_section = () => '';
+            nodes.comment_list = () => '';
             const serializer = new DOMSerializer(nodes, marks);
             return serializer.serializeFragment(fragment, { document });
         };

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

@@ -50,8 +50,7 @@ export const nodeTypesMap = new Map([
     [schema.nodes.table_element, ObjectTypes.TableElement],
     [schema.nodes.toc_element, ObjectTypes.TOCElement],
     [schema.nodes.toc_section, ObjectTypes.Section],
-    [schema.nodes.affiliation, ObjectTypes.Affiliation],
-    [schema.nodes.meta_section, ObjectTypes.MetaSection],
+    [schema.nodes.comment_list, ObjectTypes.MetaSection],
 ]);
 export const isExecutableNodeType = (type) => hasGroup(type, GROUP_EXECUTABLE);
 export const isElementNodeType = (type) => hasGroup(type, GROUP_ELEMENT);

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

@@ -13,8 +13,8 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import sectionCategories from '@manuscripts/data/dist/shared/section-categories.json';
-import { ObjectTypes, } from '@manuscripts/json-schema';
+import { ObjectTypes } from '@manuscripts/json-schema';
+import { coreSectionCategories } from '../lib/core-section-categories';
 import { schema } from '../schema';
 const sectionNodeTypes = [
     schema.nodes.bibliography_section,
@@ -23,13 +23,12 @@ const sectionNodeTypes = [
     schema.nodes.section,
     schema.nodes.toc_section,
 ];
-const sectionCategoriesMap = new Map(sectionCategories.map((section) => [section._id, section]));
-export const getSectionTitles = (sectionCategory) => {
-    const category = sectionCategoriesMap.get(sectionCategory);
+export const getCoreSectionTitles = (sectionCategory) => {
+    const category = coreSectionCategories.find((section) => section._id === sectionCategory);
     if (category) {
         return category.titles.length ? category.titles : [' '];
     }
-    throw new Error(`${sectionCategory} not found in section categories`);
+    throw new Error(`${sectionCategory} not found in core sections`);
 };
 export const isAnySectionNode = (node) => sectionNodeTypes.includes(node.type);
 export const chooseSectionNodeType = (category) => {

package/dist/types/index.d.ts

@@ -1,3 +1,4 @@
+export * from './lib/core-section-categories';
 export * from './lib/table-cell-styles';
 export * from './lib/utils';
 export * from './mathjax';

package/dist/types/lib/core-section-categories.d.ts

@@ -0,0 +1,8 @@
+export declare const coreSectionCategories: {
+    _id: string;
+    name: string;
+    desc: string;
+    objectType: string;
+    titles: never[];
+    priority: number;
+}[];

package/dist/types/schema/index.d.ts

@@ -64,9 +64,4 @@ export * from './nodes/table_row';
 export * from './nodes/text';
 export * from './nodes/toc_element';
 export * from './nodes/toc_section';
-export * from './nodes/affiliation';
-export * from './nodes/affiliation_list';
-export * from './nodes/meta_section';
-export * from './nodes/contributor_list';
-export * from './nodes/contributor';
 export declare const schema: Schema<Nodes, Marks>;

package/dist/types/schema/types.d.ts

@@ -17,7 +17,7 @@ import { Fragment, Mark as ProsemirrorMark, MarkType, Node as ProsemirrorNode, N
 import { EditorState, NodeSelection, Plugin, TextSelection, Transaction } from 'prosemirror-state';
 import { EditorView, NodeView } from 'prosemirror-view';
 export type Marks = 'bold' | 'code' | 'italic' | 'smallcaps' | 'strikethrough' | 'styled' | 'subscript' | 'superscript' | 'underline' | 'tracked_insert' | 'tracked_delete';
-export type Nodes = 'attribution' | 'bibliography_item' | 'bibliography_element' | 'bibliography_section' | 'blockquote_element' | 'bullet_list' | 'caption' | 'caption_title' | 'comment' | 'comment_list' | 'citation' | 'cross_reference' | 'doc' | 'equation' | 'equation_element' | 'figcaption' | 'figure' | 'graphical_abstract_section' | 'figure_element' | 'footnote' | 'footnotes_element' | 'footnotes_section' | 'hard_break' | 'highlight_marker' | 'inline_equation' | 'inline_footnote' | 'keyword' | 'keywords_element' | 'keywords_group' | 'keywords_section' | 'link' | 'list_item' | 'listing' | 'listing_element' | 'manuscript' | 'missing_figure' | 'ordered_list' | 'paragraph' | 'placeholder' | 'placeholder_element' | 'pullquote_element' | 'section' | 'section_label' | 'section_title' | 'section_title_plain' | 'table' | 'table_body' | 'table_cell' | 'table_element' | 'table_row' | 'table_colgroup' | 'table_col' | 'text' | 'toc_element' | 'toc_section' | 'affiliation' | 'meta_section' | 'affiliation_list' | 'contributor_list' | 'contributor';
+export type Nodes = 'attribution' | 'bibliography_item' | 'bibliography_element' | 'bibliography_section' | 'blockquote_element' | 'bullet_list' | 'caption' | 'caption_title' | 'comment' | 'comment_list' | 'citation' | 'cross_reference' | 'doc' | 'equation' | 'equation_element' | 'figcaption' | 'figure' | 'graphical_abstract_section' | 'figure_element' | 'footnote' | 'footnotes_element' | 'footnotes_section' | 'hard_break' | 'highlight_marker' | 'inline_equation' | 'inline_footnote' | 'keyword' | 'keywords_element' | 'keywords_group' | 'keywords_section' | 'link' | 'list_item' | 'listing' | 'listing_element' | 'manuscript' | 'missing_figure' | 'ordered_list' | 'paragraph' | 'placeholder' | 'placeholder_element' | 'pullquote_element' | 'section' | 'section_label' | 'section_title' | 'section_title_plain' | 'table' | 'table_body' | 'table_cell' | 'table_element' | 'table_row' | 'table_colgroup' | 'table_col' | 'text' | 'toc_element' | 'toc_section';
 export type ManuscriptSchema = Schema<Nodes, Marks>;
 export type ManuscriptEditorState = EditorState;
 export type ManuscriptEditorView = EditorView;

package/dist/types/transformer/decode.d.ts

@@ -25,11 +25,6 @@ export declare class Decoder {
     private readonly allowMissingElements;
     private comments;
     private creators;
-    private createAffiliationListNode;
-    private createContributorListNode;
-    private createMetaSectionNode;
-    private createCommentListNode;
-    private createRootSectionNodes;
     private createCommentsNode;
     private getComments;
     private extractListing;

package/dist/types/transformer/section-category.d.ts

@@ -15,7 +15,7 @@
  */
 import { Element } from '@manuscripts/json-schema';
 import { ManuscriptNode, ManuscriptNodeType } from '../schema';
-export declare const getSectionTitles: (sectionCategory: SectionCategory) => string[];
+export declare const getCoreSectionTitles: (sectionCategory: SectionCategory) => string[];
 export declare const isAnySectionNode: (node: ManuscriptNode) => boolean;
 export type SectionCategory = 'MPSectionCategory:abstract' | 'MPSectionCategory:abstract-teaser' | 'MPSectionCategory:abstract-graphical' | 'MPSectionCategory:acknowledgement' | 'MPSectionCategory:availability' | 'MPSectionCategory:bibliography' | 'MPSectionCategory:conclusions' | 'MPSectionCategory:discussion' | 'MPSectionCategory:endnotes' | 'MPSectionCategory:introduction' | 'MPSectionCategory:keywords' | 'MPSectionCategory:materials-method' | 'MPSectionCategory:results' | 'MPSectionCategory:toc' | 'MPSectionCategory:floating-element' | 'MPSectionCategory:appendices' | 'MPSectionCategory:competing-interests' | 'MPSectionCategory:financial-disclosure' | 'MPSectionCategory:con' | 'MPSectionCategory:deceased' | 'MPSectionCategory:equal' | 'MPSectionCategory:present-address' | 'MPSectionCategory:presented-at' | 'MPSectionCategory:previously-at' | 'MPSectionCategory:supplementary-material' | 'MPSectionCategory:supported-by' | 'MPSectionCategory:ethics-statement' | 'MPSectionCategory:body' | 'MPSectionCategory:abstracts' | 'MPSectionCategory:backmatter';
 export type SecType = 'abstract' | 'abstract-teaser' | 'abstract-graphical' | 'acknowledgments' | 'availability' | 'bibliography' | 'conclusions' | 'data-availability' | 'discussion' | 'endnotes' | 'intro' | 'keywords' | 'materials' | 'methods' | 'results' | 'toc' | 'floating-element' | 'appendices' | 'competing-interests' | 'financial-disclosure' | 'con' | 'deceased' | 'equal' | 'present-address' | 'presented-at' | 'previously-at' | 'supplementary-material' | 'supported-by' | 'ethics-statement' | 'abstracts' | 'body' | 'backmatter';

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@manuscripts/transform",
   "description": "ProseMirror transformer for Manuscripts applications",
-  "version": "1.3.7-LEAN-2707-V2",
+  "version": "1.3.8",
   "repository": "github:Atypon-OpenSource/manuscripts-transform",
   "license": "Apache-2.0",
   "main": "dist/cjs",
@@ -43,7 +43,6 @@
     "@babel/preset-env": "^7.20.2",
     "@babel/preset-typescript": "^7.18.6",
     "@jats4r/dtds": "^0.0.8",
-    "@manuscripts/data": "^1.0.2",
     "@manuscripts/eslint-config": "^0.5.1",
     "@types/debug": "^4.1.7",
     "@types/jest": "^29.2.4",

package/dist/cjs/schema/nodes/affiliation.js

@@ -1,23 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.isAffiliationNode = exports.affiliation = void 0;
-exports.affiliation = {
-    attrs: {
-        id: { default: '' },
-        institution: { default: '' },
-        department: { default: '' },
-        addressLine1: { default: '' },
-        addressLine2: { default: '' },
-        addressLine3: { default: '' },
-        postCode: { default: '' },
-        country: { default: '' },
-        email: {
-            default: {
-                href: undefined,
-                text: undefined,
-            },
-        },
-    },
-};
-const isAffiliationNode = (node) => node.type === node.type.schema.nodes.affiliation;
-exports.isAffiliationNode = isAffiliationNode;

package/dist/cjs/schema/nodes/affiliation_list.js

@@ -1,10 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.affiliationList = void 0;
-exports.affiliationList = {
-    content: 'affiliation*',
-    attrs: {
-        id: { default: 'AFFILIATION_LIST' },
-    },
-    toDOM: () => ['section', 0],
-};

package/dist/cjs/schema/nodes/contributor.js

@@ -1,15 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.contributor = void 0;
-exports.contributor = {
-    attrs: {
-        id: { default: '' },
-        role: { default: '' },
-        affiliations: { default: [] },
-        bibliographicName: { default: {} },
-        userID: { default: '' },
-        invitationID: { default: '' },
-        isCorresponding: { default: undefined },
-        ORCIDIdentifier: { default: '' },
-    },
-};

package/dist/cjs/schema/nodes/contributor_list.js

@@ -1,10 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.contributorList = void 0;
-exports.contributorList = {
-    content: 'contributor*',
-    attrs: {
-        id: { default: 'CONTRIBUTOR_LIST' },
-    },
-    toDOM: () => ['section', 0],
-};

package/dist/cjs/schema/nodes/meta_section.js

@@ -1,26 +0,0 @@
-"use strict";
-/*!
- * © 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.
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.metaSection = void 0;
-exports.metaSection = {
-    content: 'affiliation_list contributor_list comment_list',
-    attrs: {
-        id: { default: 'META_SECTION' },
-    },
-    group: 'block sections',
-    toDOM: () => ['section', 0],
-};

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

@@ -1,19 +0,0 @@
-export const affiliation = {
-    attrs: {
-        id: { default: '' },
-        institution: { default: '' },
-        department: { default: '' },
-        addressLine1: { default: '' },
-        addressLine2: { default: '' },
-        addressLine3: { default: '' },
-        postCode: { default: '' },
-        country: { default: '' },
-        email: {
-            default: {
-                href: undefined,
-                text: undefined,
-            },
-        },
-    },
-};
-export const isAffiliationNode = (node) => node.type === node.type.schema.nodes.affiliation;

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

@@ -1,7 +0,0 @@
-export const affiliationList = {
-    content: 'affiliation*',
-    attrs: {
-        id: { default: 'AFFILIATION_LIST' },
-    },
-    toDOM: () => ['section', 0],
-};

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

@@ -1,12 +0,0 @@
-export const contributor = {
-    attrs: {
-        id: { default: '' },
-        role: { default: '' },
-        affiliations: { default: [] },
-        bibliographicName: { default: {} },
-        userID: { default: '' },
-        invitationID: { default: '' },
-        isCorresponding: { default: undefined },
-        ORCIDIdentifier: { default: '' },
-    },
-};

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

@@ -1,7 +0,0 @@
-export const contributorList = {
-    content: 'contributor*',
-    attrs: {
-        id: { default: 'CONTRIBUTOR_LIST' },
-    },
-    toDOM: () => ['section', 0],
-};

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

@@ -1,23 +0,0 @@
-/*!
- * © 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 metaSection = {
-    content: 'affiliation_list contributor_list comment_list',
-    attrs: {
-        id: { default: 'META_SECTION' },
-    },
-    group: 'block sections',
-    toDOM: () => ['section', 0],
-};

package/dist/types/schema/nodes/affiliation.d.ts

@@ -1,24 +0,0 @@
-import { NodeSpec } from 'prosemirror-model';
-import { ManuscriptNode } from '../types';
-interface Email {
-    href: string;
-    text: string;
-}
-interface Attrs {
-    id: string;
-    objectType: string;
-    institution: string;
-    department: string;
-    addressLine1: string;
-    addressLine2: string;
-    addressLine3: string;
-    postCode: string;
-    country: string;
-    email: Email;
-}
-export interface AffiliationNode extends ManuscriptNode {
-    attrs: Attrs;
-}
-export declare const affiliation: NodeSpec;
-export declare const isAffiliationNode: (node: ManuscriptNode) => node is AffiliationNode;
-export {};

package/dist/types/schema/nodes/affiliation_list.d.ts

@@ -1,10 +0,0 @@
-import { NodeSpec } from 'prosemirror-model';
-import { ManuscriptNode } from '../types';
-interface Attrs {
-    id: string;
-}
-export interface AffiliationListNode extends ManuscriptNode {
-    attrs: Attrs;
-}
-export declare const affiliationList: NodeSpec;
-export {};

package/dist/types/schema/nodes/contributor.d.ts

@@ -1,18 +0,0 @@
-import { Affiliation, BibliographicName } from '@manuscripts/json-schema';
-import { NodeSpec } from 'prosemirror-model';
-import { ManuscriptNode } from '../types';
-interface Attrs {
-    id: string;
-    role: string;
-    affiliations: Affiliation[];
-    bibliographicName: BibliographicName;
-    userID: string;
-    invitationID: string;
-    isCorresponding: boolean;
-    ORCIDIdentifier: string;
-}
-export interface ContributorNode extends ManuscriptNode {
-    attrs: Attrs;
-}
-export declare const contributor: NodeSpec;
-export {};

package/dist/types/schema/nodes/contributor_list.d.ts

@@ -1,10 +0,0 @@
-import { NodeSpec } from 'prosemirror-model';
-import { ManuscriptNode } from '../types';
-interface Attrs {
-    id: string;
-}
-export interface ContributorListNode extends ManuscriptNode {
-    attrs: Attrs;
-}
-export declare const contributorList: NodeSpec;
-export {};

package/dist/types/schema/nodes/meta_section.d.ts

@@ -1,25 +0,0 @@
-/*!
- * © 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.
- */
-import { NodeSpec } from 'prosemirror-model';
-import { ManuscriptNode } from '../types';
-interface Attrs {
-    id: string;
-}
-export interface MetaSectionNode extends ManuscriptNode {
-    attrs: Attrs;
-}
-export declare const metaSection: NodeSpec;
-export {};