@manuscripts/transform 1.5.8-LEAN-3030-2 → 1.5.8-LEAN-3030-3

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

@@ -735,7 +735,7 @@ class JATSExporter {
                     };
                     return ['sec', attrs, 0];
                 },
-                hard_break: () => ['break'],
+                hard_break: () => '',
                 highlight_marker: () => '',
                 inline_equation: (node) => {
                     const formula = this.document.createElement('inline-formula');

package/dist/cjs/lib/utils.js

@@ -15,7 +15,7 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.modelsEqual = exports.getTrimmedTextContent = exports.findParentNodeClosestToPos = exports.isInBibliographySection = exports.isInGraphicalAbstractSection = exports.findNodePositions = exports.iterateChildren = void 0;
+exports.getTrimmedTextContent = exports.findParentNodeClosestToPos = exports.isInBibliographySection = exports.isInGraphicalAbstractSection = exports.findNodePositions = exports.iterateChildren = void 0;
 const bibliography_section_1 = require("../schema/nodes/bibliography_section");
 const graphical_abstract_section_1 = require("../schema/nodes/graphical_abstract_section");
 function* iterateChildren(node, recurse = false) {
@@ -83,16 +83,3 @@ 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();
 };
 exports.getTrimmedTextContent = getTrimmedTextContent;
-function modelsEqual(model, model2) {
-    for (const v in model) {
-        for (const v2 in model2) {
-            const prepV = typeof v == 'object' ? JSON.stringify(v) : v;
-            const prepV2 = typeof v2 == 'object' ? JSON.stringify(v2) : v2;
-            if (prepV !== prepV2) {
-                return false;
-            }
-        }
-    }
-    return true;
-}
-exports.modelsEqual = modelsEqual;

package/dist/cjs/schema/index.js

@@ -32,13 +32,16 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.schema = void 0;
 const prosemirror_model_1 = require("prosemirror-model");
 const marks_1 = require("./marks");
+const abstracts_1 = require("./nodes/abstracts");
 const affiliation_1 = require("./nodes/affiliation");
 const affiliations_1 = require("./nodes/affiliations");
 const attribution_1 = require("./nodes/attribution");
+const backmatter_1 = require("./nodes/backmatter");
 const bibliography_element_1 = require("./nodes/bibliography_element");
 const bibliography_item_1 = require("./nodes/bibliography_item");
 const bibliography_section_1 = require("./nodes/bibliography_section");
 const blockquote_element_1 = require("./nodes/blockquote_element");
+const body_1 = require("./nodes/body");
 const caption_1 = require("./nodes/caption");
 const caption_title_1 = require("./nodes/caption_title");
 const citation_1 = require("./nodes/citation");
@@ -87,9 +90,6 @@ const text_1 = require("./nodes/text");
 const title_1 = require("./nodes/title");
 const toc_element_1 = require("./nodes/toc_element");
 const toc_section_1 = require("./nodes/toc_section");
-const abstracts_1 = require("./nodes/abstracts");
-const body_1 = require("./nodes/body");
-const backmatter_1 = require("./nodes/backmatter");
 __exportStar(require("./groups"), exports);
 __exportStar(require("./types"), exports);
 __exportStar(require("./nodes/comment"), exports);

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

@@ -23,5 +23,5 @@ exports.affiliations = {
     },
     group: 'block',
     selectable: false,
-    toDOM: () => ['div', { class: 'abstracts' }, 0],
+    toDOM: () => ['div', { class: 'affiliations' }, 0],
 };

package/dist/cjs/transformer/decode.js

@@ -71,6 +71,11 @@ const isFootnote = (0, object_types_1.hasObjectType)(json_schema_1.ObjectTypes.F
 const hasParentSection = (id) => (section) => section.path &&
     section.path.length > 1 &&
     section.path[section.path.length - 2] === id;
+const deprecatedCategories = [
+    'MPSectionCategory:contributors',
+    'MPSectionCategory:affiliations',
+    'MPSectionCategory:keywords',
+];
 class Decoder {
     createTitleNode() {
         const titles = getTitles(this.modelMap) || (0, builders_1.buildTitles)();
@@ -115,9 +120,10 @@ class Decoder {
                 continue;
             }
             const category = section.category;
-            const group = category
-                ? (0, section_category_1.getSectionGroupType)(category)
-                : section_group_type_1.bodyType;
+            if (category && deprecatedCategories.includes(category)) {
+                continue;
+            }
+            const group = category ? (0, section_category_1.getSectionGroupType)(category) : section_group_type_1.bodyType;
             groups[group._id].push(this.decode(section));
         }
         const abstracts = schema_1.schema.nodes.abstracts.createAndFill({}, groups[section_group_type_1.abstractsType._id]);
@@ -141,7 +147,7 @@ class Decoder {
     }
     extractListing(model) {
         if (model.listingID) {
-            return this.createListing(model);
+            return this.createListing(model.listingID);
         }
     }
     constructor(modelMap, allowMissingElements = false) {
@@ -561,7 +567,7 @@ class Decoder {
                     ? [table, figcaption, tableElementFooter]
                     : [table, figcaption];
                 if (model.listingID) {
-                    const listing = this.createListing(model);
+                    const listing = this.createListing(model.listingID);
                     content.push(listing);
                 }
                 else {
@@ -766,22 +772,20 @@ class Decoder {
             ? this.decode(tableElementFooterModel)
             : undefined;
     }
-    createListing(model) {
-        const listingModel = this.getModel(model.listingID);
-        let listing;
-        if (listingModel) {
-            listing = this.decode(listingModel);
+    createListing(id) {
+        const listing = this.getModel(id);
+        if (listing) {
+            return this.decode(listing);
         }
         else if (this.allowMissingElements) {
-            listing = schema_1.schema.nodes.placeholder.create({
-                id: model.listingID,
+            return schema_1.schema.nodes.placeholder.create({
+                id,
                 label: 'A listing',
             });
         }
         else {
-            throw new errors_1.MissingElement(model.listingID);
+            throw new errors_1.MissingElement(id);
         }
-        return listing;
     }
 }
 exports.Decoder = Decoder;

package/dist/cjs/transformer/encode.js

@@ -25,7 +25,6 @@ const utils_1 = require("../lib/utils");
 const schema_1 = require("../schema");
 const builders_1 = require("./builders");
 const highlight_markers_1 = require("./highlight-markers");
-const id_1 = require("./id");
 const node_types_1 = require("./node-types");
 const section_category_1 = require("./section-category");
 const serializer = prosemirror_model_1.DOMSerializer.fromSchema(schema_1.schema);
@@ -535,7 +534,6 @@ const modelData = (node, parent, path, priority) => {
     return encoder(node, parent, path, priority);
 };
 const modelFromNode = (node, parent, path, priority) => {
-    const commentAnnotationsMap = new Map();
     const objectType = node_types_1.nodeTypesMap.get(node.type);
     if (!objectType) {
         throw new Error(`No objectType is defined for ${node.type.name}`);
@@ -546,11 +544,8 @@ const modelFromNode = (node, parent, path, priority) => {
     }
     const data = Object.assign(Object.assign({}, modelData(node, parent, path, priority)), { _id: id, objectType: objectType });
     const model = data;
-    if ((0, highlight_markers_1.isHighlightableModel)(model)) {
-        (0, highlight_markers_1.extractHighlightMarkers)(model, commentAnnotationsMap);
-    }
-    const comments = [...commentAnnotationsMap.values()];
-    return { model, comments };
+    const markers = (0, highlight_markers_1.extractCommentMarkers)(model);
+    return { model, markers };
 };
 exports.modelFromNode = modelFromNode;
 const containerTypes = [
@@ -561,14 +556,16 @@ const containerTypes = [
     schema_1.schema.nodes.abstracts,
     schema_1.schema.nodes.body,
     schema_1.schema.nodes.backmatter,
-    schema_1.schema.nodes.comments,
 ];
-const encode = (node, preserveWithRepeatedID = false) => {
+const placeholderTypes = [
+    schema_1.schema.nodes.placeholder,
+    schema_1.schema.nodes.placeholder_element,
+];
+const encode = (node) => {
     const models = new Map();
     const priority = {
         value: 1,
     };
-    const placeholders = ['placeholder', 'placeholder_element'];
     const processNode = (path, parent) => (child) => {
         if (containerTypes.includes(child.type)) {
             child.forEach(processNode([], child));
@@ -580,33 +577,33 @@ const encode = (node, preserveWithRepeatedID = false) => {
         if ((0, schema_1.isHighlightMarkerNode)(child)) {
             return;
         }
-        if (placeholders.includes(child.type.name)) {
+        if (placeholderTypes.includes(child.type)) {
             return;
         }
-        if (parent.type === schema_1.schema.nodes.paragraph) {
+        if (parent.type === schema_1.schema.nodes.paragraph &&
+            child.type !== schema_1.schema.nodes.inline_equation) {
             return;
         }
-        const { model, comments } = (0, exports.modelFromNode)(child, parent, path, priority);
-        const existingModel = models.get(model._id);
-        if (existingModel) {
-            if (preserveWithRepeatedID && !(0, utils_1.modelsEqual)(model, existingModel)) {
-                model._id = (0, id_1.generateID)(model.objectType);
-            }
-            else {
-                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);
+        const { model, markers } = (0, exports.modelFromNode)(child, parent, path, priority);
+        markers.forEach((marker) => {
+            const comment = models.get(marker._id);
+            if (comment) {
+                comment.selector = {
+                    from: marker.from,
+                    to: marker.to,
+                };
             }
         });
+        if (models.has(model._id)) {
+            throw Error(`Duplicate ids in encode: ${model._id}`);
+        }
         models.set(model._id, model);
         child.forEach(processNode(path.concat(child.attrs.id), child));
     };
+    const comments = node.lastChild;
+    if (comments && comments.type === schema_1.schema.nodes.comments) {
+        comments.forEach(processNode([], comments));
+    }
     node.forEach(processNode([], node));
     if ((0, schema_1.isManuscriptNode)(node)) {
         builders_1.auxiliaryObjectTypes.forEach((t) => {

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

@@ -15,8 +15,7 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.insertHighlightMarkers = exports.extractHighlightMarkers = exports.isHighlightableModel = exports.highlightableFields = void 0;
-const builders_1 = require("./builders");
+exports.insertHighlightMarkers = exports.extractCommentMarkers = exports.isHighlightableModel = exports.highlightableFields = void 0;
 exports.highlightableFields = [
     'caption',
     'contents',
@@ -31,54 +30,67 @@ const isHighlightableModel = (model) => {
     return false;
 };
 exports.isHighlightableModel = isHighlightableModel;
-const extractHighlightMarkers = (model, commentAnnotationsMap) => {
+const extractCommentMarkers = (model) => {
+    if (!(0, exports.isHighlightableModel)(model)) {
+        return [];
+    }
+    const comments = new Map();
     for (const field of exports.highlightableFields) {
         let html = model[field];
-        if (html === undefined) {
+        if (!html || !html.includes('highlight-marker')) {
             continue;
         }
         const template = document.createElement('template');
         template.innerHTML = `<div>${html}</div>`;
         const element = template.content.firstChild;
-        if (!(element instanceof Element)) {
+        if (!element) {
             continue;
         }
         const markers = element.querySelectorAll('span.highlight-marker');
-        if (markers.length) {
-            for (const marker of markers) {
-                const markerHTML = marker.outerHTML;
-                const offset = html.indexOf(markerHTML);
-                if (offset === -1) {
-                    continue;
+        if (!markers.length) {
+            continue;
+        }
+        for (const marker of markers) {
+            const markerHTML = marker.outerHTML;
+            const offset = html.indexOf(markerHTML);
+            if (offset === -1) {
+                continue;
+            }
+            const id = marker.getAttribute('id');
+            const target = marker.getAttribute('data-target-id');
+            if (id && target) {
+                const position = marker.getAttribute('data-position');
+                if (position === 'start') {
+                    const comment = {
+                        _id: id,
+                        from: offset,
+                        to: -1,
+                    };
+                    comments.set(id, comment);
                 }
-                const _id = marker.getAttribute('id');
-                const target = marker.getAttribute('data-target-id');
-                if (_id && target) {
-                    const position = marker.getAttribute('data-position');
-                    const commentAnnotation = Object.assign(Object.assign({}, (0, builders_1.buildComment)(target, '')), { _id: _id });
-                    if (position === 'start') {
-                        commentAnnotationsMap.set(commentAnnotation._id, Object.assign(Object.assign({}, commentAnnotation), { selector: {
-                                from: offset,
-                                to: -1,
-                            } }));
-                    }
-                    else if (position === 'end') {
-                        const comment = commentAnnotationsMap.get(commentAnnotation._id);
-                        if (comment && comment.selector) {
-                            commentAnnotationsMap.set(comment._id, Object.assign(Object.assign({}, comment), { selector: Object.assign(Object.assign({}, comment.selector), { to: offset }) }));
-                        }
-                    }
-                    else if (position === 'point') {
-                        commentAnnotationsMap.set(commentAnnotation._id, Object.assign(Object.assign({}, commentAnnotation), { selector: { from: offset, to: offset } }));
+                else if (position === 'end') {
+                    const comment = comments.get(id);
+                    if (comment) {
+                        comment.to = offset;
                     }
                 }
-                html = html.substr(0, offset) + html.substr(offset + markerHTML.length);
+                else if (position === 'point') {
+                    const comment = {
+                        _id: id,
+                        from: offset,
+                        to: offset,
+                    };
+                    comments.set(id, comment);
+                }
             }
-            model[field] = html;
+            html =
+                html.substring(0, offset) + html.substring(offset + markerHTML.length);
         }
+        model[field] = html;
     }
+    return Array.from(comments.values());
 };
-exports.extractHighlightMarkers = extractHighlightMarkers;
+exports.extractCommentMarkers = extractCommentMarkers;
 const insertHighlightMarkers = (contents, commentAnnotations) => {
     let output = contents;
     const sortedComments = commentAnnotations.sort((a, b) => {

package/dist/cjs/transformer/html.js

@@ -210,12 +210,11 @@ class HTMLTransformer {
                 return element;
             };
             nodes.cross_reference = (node) => {
-                const crossReferenceNode = node;
+                const xref = node;
                 const element = this.document.createElement('a');
                 element.classList.add('cross-reference');
-                element.setAttribute('data-reference-ids', crossReferenceNode.attrs.rids.join(' '));
-                element.textContent =
-                    crossReferenceNode.attrs.customLabel || crossReferenceNode.attrs.label;
+                element.setAttribute('data-reference-ids', xref.attrs.rids.join(' '));
+                element.textContent = xref.attrs.customLabel || xref.attrs.label;
                 return element;
             };
             nodes.listing = (node) => {

package/dist/es/jats/index.js

@@ -13,6 +13,6 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-export { parseJATSFront, parseJATSBody, parseJATSArticle, } from './importer';
+export { parseJATSFront, parseJATSBody, parseJATSArticle } from './importer';
 export * from './jats-exporter';
 export * from './jats-versions';

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

@@ -728,7 +728,7 @@ export class JATSExporter {
                     };
                     return ['sec', attrs, 0];
                 },
-                hard_break: () => ['break'],
+                hard_break: () => '',
                 highlight_marker: () => '',
                 inline_equation: (node) => {
                     const formula = this.document.createElement('inline-formula');

package/dist/es/lib/utils.js

@@ -74,15 +74,3 @@ 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 function modelsEqual(model, model2) {
-    for (const v in model) {
-        for (const v2 in model2) {
-            const prepV = typeof v == 'object' ? JSON.stringify(v) : v;
-            const prepV2 = typeof v2 == 'object' ? JSON.stringify(v2) : v2;
-            if (prepV !== prepV2) {
-                return false;
-            }
-        }
-    }
-    return true;
-}

package/dist/es/schema/index.js

@@ -15,13 +15,16 @@
  */
 import { Schema } from 'prosemirror-model';
 import { bold, code, italic, smallcaps, strikethrough, styled, subscript, superscript, tracked_delete, tracked_insert, underline, } from './marks';
+import { abstracts } from './nodes/abstracts';
 import { affiliation } from './nodes/affiliation';
 import { affiliations } from './nodes/affiliations';
 import { attribution } from './nodes/attribution';
+import { backmatter } from './nodes/backmatter';
 import { bibliographyElement } from './nodes/bibliography_element';
 import { bibliographyItem } from './nodes/bibliography_item';
 import { bibliographySection } from './nodes/bibliography_section';
 import { blockquoteElement } from './nodes/blockquote_element';
+import { body } from './nodes/body';
 import { caption } from './nodes/caption';
 import { captionTitle } from './nodes/caption_title';
 import { citation } from './nodes/citation';
@@ -70,9 +73,6 @@ import { text } from './nodes/text';
 import { title } from './nodes/title';
 import { tocElement } from './nodes/toc_element';
 import { tocSection } from './nodes/toc_section';
-import { abstracts } from "./nodes/abstracts";
-import { body } from "./nodes/body";
-import { backmatter } from "./nodes/backmatter";
 export * from './groups';
 export * from './types';
 export * from './nodes/comment';

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

@@ -20,5 +20,5 @@ export const affiliations = {
     },
     group: 'block',
     selectable: false,
-    toDOM: () => ['div', { class: 'abstracts' }, 0],
+    toDOM: () => ['div', { class: 'affiliations' }, 0],
 };

package/dist/es/transformer/decode.js

@@ -62,6 +62,11 @@ const isFootnote = hasObjectType(ObjectTypes.Footnote);
 const hasParentSection = (id) => (section) => section.path &&
     section.path.length > 1 &&
     section.path[section.path.length - 2] === id;
+const deprecatedCategories = [
+    'MPSectionCategory:contributors',
+    'MPSectionCategory:affiliations',
+    'MPSectionCategory:keywords',
+];
 export class Decoder {
     createTitleNode() {
         const titles = getTitles(this.modelMap) || buildTitles();
@@ -106,9 +111,10 @@ export class Decoder {
                 continue;
             }
             const category = section.category;
-            const group = category
-                ? getSectionGroupType(category)
-                : bodyType;
+            if (category && deprecatedCategories.includes(category)) {
+                continue;
+            }
+            const group = category ? getSectionGroupType(category) : bodyType;
             groups[group._id].push(this.decode(section));
         }
         const abstracts = schema.nodes.abstracts.createAndFill({}, groups[abstractsType._id]);
@@ -132,7 +138,7 @@ export class Decoder {
     }
     extractListing(model) {
         if (model.listingID) {
-            return this.createListing(model);
+            return this.createListing(model.listingID);
         }
     }
     constructor(modelMap, allowMissingElements = false) {
@@ -552,7 +558,7 @@ export class Decoder {
                     ? [table, figcaption, tableElementFooter]
                     : [table, figcaption];
                 if (model.listingID) {
-                    const listing = this.createListing(model);
+                    const listing = this.createListing(model.listingID);
                     content.push(listing);
                 }
                 else {
@@ -757,21 +763,19 @@ export class Decoder {
             ? this.decode(tableElementFooterModel)
             : undefined;
     }
-    createListing(model) {
-        const listingModel = this.getModel(model.listingID);
-        let listing;
-        if (listingModel) {
-            listing = this.decode(listingModel);
+    createListing(id) {
+        const listing = this.getModel(id);
+        if (listing) {
+            return this.decode(listing);
         }
         else if (this.allowMissingElements) {
-            listing = schema.nodes.placeholder.create({
-                id: model.listingID,
+            return schema.nodes.placeholder.create({
+                id,
                 label: 'A listing',
             });
         }
         else {
-            throw new MissingElement(model.listingID);
+            throw new MissingElement(id);
         }
-        return listing;
     }
 }

package/dist/es/transformer/encode.js

@@ -15,11 +15,10 @@
  */
 import { DOMSerializer } from 'prosemirror-model';
 import serializeToXML from 'w3c-xmlserializer';
-import { iterateChildren, modelsEqual } from '../lib/utils';
+import { iterateChildren } from '../lib/utils';
 import { hasGroup, isHighlightMarkerNode, isManuscriptNode, isSectionNode, schema, } from '../schema';
 import { auxiliaryObjectTypes, buildAttribution, buildElementsOrder, } from './builders';
-import { extractHighlightMarkers, isHighlightableModel, } from './highlight-markers';
-import { generateID } from './id';
+import { extractCommentMarkers } from './highlight-markers';
 import { nodeTypesMap } from './node-types';
 import { buildSectionCategory } from './section-category';
 const serializer = DOMSerializer.fromSchema(schema);
@@ -527,7 +526,6 @@ const modelData = (node, parent, path, priority) => {
     return encoder(node, parent, path, priority);
 };
 export const modelFromNode = (node, parent, path, priority) => {
-    const commentAnnotationsMap = new Map();
     const objectType = nodeTypesMap.get(node.type);
     if (!objectType) {
         throw new Error(`No objectType is defined for ${node.type.name}`);
@@ -538,11 +536,8 @@ export const modelFromNode = (node, parent, path, priority) => {
     }
     const data = Object.assign(Object.assign({}, modelData(node, parent, path, priority)), { _id: id, objectType: objectType });
     const model = data;
-    if (isHighlightableModel(model)) {
-        extractHighlightMarkers(model, commentAnnotationsMap);
-    }
-    const comments = [...commentAnnotationsMap.values()];
-    return { model, comments };
+    const markers = extractCommentMarkers(model);
+    return { model, markers };
 };
 const containerTypes = [
     schema.nodes.affiliations,
@@ -552,14 +547,16 @@ const containerTypes = [
     schema.nodes.abstracts,
     schema.nodes.body,
     schema.nodes.backmatter,
-    schema.nodes.comments,
 ];
-export const encode = (node, preserveWithRepeatedID = false) => {
+const placeholderTypes = [
+    schema.nodes.placeholder,
+    schema.nodes.placeholder_element,
+];
+export const encode = (node) => {
     const models = new Map();
     const priority = {
         value: 1,
     };
-    const placeholders = ['placeholder', 'placeholder_element'];
     const processNode = (path, parent) => (child) => {
         if (containerTypes.includes(child.type)) {
             child.forEach(processNode([], child));
@@ -571,33 +568,33 @@ export const encode = (node, preserveWithRepeatedID = false) => {
         if (isHighlightMarkerNode(child)) {
             return;
         }
-        if (placeholders.includes(child.type.name)) {
+        if (placeholderTypes.includes(child.type)) {
             return;
         }
-        if (parent.type === schema.nodes.paragraph) {
+        if (parent.type === schema.nodes.paragraph &&
+            child.type !== schema.nodes.inline_equation) {
             return;
         }
-        const { model, comments } = modelFromNode(child, parent, path, priority);
-        const existingModel = models.get(model._id);
-        if (existingModel) {
-            if (preserveWithRepeatedID && !modelsEqual(model, existingModel)) {
-                model._id = generateID(model.objectType);
-            }
-            else {
-                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);
+        const { model, markers } = modelFromNode(child, parent, path, priority);
+        markers.forEach((marker) => {
+            const comment = models.get(marker._id);
+            if (comment) {
+                comment.selector = {
+                    from: marker.from,
+                    to: marker.to,
+                };
             }
         });
+        if (models.has(model._id)) {
+            throw Error(`Duplicate ids in encode: ${model._id}`);
+        }
         models.set(model._id, model);
         child.forEach(processNode(path.concat(child.attrs.id), child));
     };
+    const comments = node.lastChild;
+    if (comments && comments.type === schema.nodes.comments) {
+        comments.forEach(processNode([], comments));
+    }
     node.forEach(processNode([], node));
     if (isManuscriptNode(node)) {
         auxiliaryObjectTypes.forEach((t) => {

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

@@ -13,7 +13,6 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import { buildComment } from './builders';
 export const highlightableFields = [
     'caption',
     'contents',
@@ -27,52 +26,65 @@ export const isHighlightableModel = (model) => {
     }
     return false;
 };
-export const extractHighlightMarkers = (model, commentAnnotationsMap) => {
+export const extractCommentMarkers = (model) => {
+    if (!isHighlightableModel(model)) {
+        return [];
+    }
+    const comments = new Map();
     for (const field of highlightableFields) {
         let html = model[field];
-        if (html === undefined) {
+        if (!html || !html.includes('highlight-marker')) {
             continue;
         }
         const template = document.createElement('template');
         template.innerHTML = `<div>${html}</div>`;
         const element = template.content.firstChild;
-        if (!(element instanceof Element)) {
+        if (!element) {
             continue;
         }
         const markers = element.querySelectorAll('span.highlight-marker');
-        if (markers.length) {
-            for (const marker of markers) {
-                const markerHTML = marker.outerHTML;
-                const offset = html.indexOf(markerHTML);
-                if (offset === -1) {
-                    continue;
+        if (!markers.length) {
+            continue;
+        }
+        for (const marker of markers) {
+            const markerHTML = marker.outerHTML;
+            const offset = html.indexOf(markerHTML);
+            if (offset === -1) {
+                continue;
+            }
+            const id = marker.getAttribute('id');
+            const target = marker.getAttribute('data-target-id');
+            if (id && target) {
+                const position = marker.getAttribute('data-position');
+                if (position === 'start') {
+                    const comment = {
+                        _id: id,
+                        from: offset,
+                        to: -1,
+                    };
+                    comments.set(id, comment);
                 }
-                const _id = marker.getAttribute('id');
-                const target = marker.getAttribute('data-target-id');
-                if (_id && target) {
-                    const position = marker.getAttribute('data-position');
-                    const commentAnnotation = Object.assign(Object.assign({}, buildComment(target, '')), { _id: _id });
-                    if (position === 'start') {
-                        commentAnnotationsMap.set(commentAnnotation._id, Object.assign(Object.assign({}, commentAnnotation), { selector: {
-                                from: offset,
-                                to: -1,
-                            } }));
-                    }
-                    else if (position === 'end') {
-                        const comment = commentAnnotationsMap.get(commentAnnotation._id);
-                        if (comment && comment.selector) {
-                            commentAnnotationsMap.set(comment._id, Object.assign(Object.assign({}, comment), { selector: Object.assign(Object.assign({}, comment.selector), { to: offset }) }));
-                        }
-                    }
-                    else if (position === 'point') {
-                        commentAnnotationsMap.set(commentAnnotation._id, Object.assign(Object.assign({}, commentAnnotation), { selector: { from: offset, to: offset } }));
+                else if (position === 'end') {
+                    const comment = comments.get(id);
+                    if (comment) {
+                        comment.to = offset;
                     }
                 }
-                html = html.substr(0, offset) + html.substr(offset + markerHTML.length);
+                else if (position === 'point') {
+                    const comment = {
+                        _id: id,
+                        from: offset,
+                        to: offset,
+                    };
+                    comments.set(id, comment);
+                }
             }
-            model[field] = html;
+            html =
+                html.substring(0, offset) + html.substring(offset + markerHTML.length);
         }
+        model[field] = html;
     }
+    return Array.from(comments.values());
 };
 export const insertHighlightMarkers = (contents, commentAnnotations) => {
     let output = contents;

package/dist/es/transformer/html.js

@@ -204,12 +204,11 @@ export class HTMLTransformer {
                 return element;
             };
             nodes.cross_reference = (node) => {
-                const crossReferenceNode = node;
+                const xref = node;
                 const element = this.document.createElement('a');
                 element.classList.add('cross-reference');
-                element.setAttribute('data-reference-ids', crossReferenceNode.attrs.rids.join(' '));
-                element.textContent =
-                    crossReferenceNode.attrs.customLabel || crossReferenceNode.attrs.label;
+                element.setAttribute('data-reference-ids', xref.attrs.rids.join(' '));
+                element.textContent = xref.attrs.customLabel || xref.attrs.label;
                 return element;
             };
             nodes.listing = (node) => {

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

@@ -13,6 +13,6 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-export { parseJATSFront, parseJATSBody, parseJATSArticle, } from './importer';
+export { parseJATSFront, parseJATSBody, parseJATSArticle } from './importer';
 export * from './jats-exporter';
 export * from './jats-versions';

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

@@ -13,7 +13,6 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import { Model } from '@manuscripts/json-schema';
 import { Node as ProsemirrorNode, ResolvedPos } from 'prosemirror-model';
 import { ManuscriptEditorState, ManuscriptNode } from '../schema';
 export declare function iterateChildren(node: ManuscriptNode, recurse?: boolean): Iterable<ManuscriptNode>;
@@ -27,4 +26,3 @@ export declare const findParentNodeClosestToPos: ($pos: ResolvedPos, predicate:
     node: ProsemirrorNode;
 } | undefined;
 export declare const getTrimmedTextContent: (node: Element | Document | null, querySelector: string) => string | null | undefined;
-export declare function modelsEqual(model: Model, model2: Model): boolean;

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

@@ -13,17 +13,17 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import { CommentAnnotation, Model } from '@manuscripts/json-schema';
+import { Model } from '@manuscripts/json-schema';
 import { ManuscriptNode } from '../schema';
-import { Build } from './builders';
+import { CommentMarker } from './highlight-markers';
 export declare const inlineContents: (node: ManuscriptNode) => string;
 export declare const inlineText: (node: ManuscriptNode) => string;
 export declare const modelFromNode: (node: ManuscriptNode, parent: ManuscriptNode, path: string[], priority: PrioritizedValue) => {
     model: Model;
-    comments: Build<CommentAnnotation>[];
+    markers: CommentMarker[];
 };
 interface PrioritizedValue {
     value: number;
 }
-export declare const encode: (node: ManuscriptNode, preserveWithRepeatedID?: boolean) => Map<string, Model>;
+export declare const encode: (node: ManuscriptNode) => Map<string, Model>;
 export {};

package/dist/types/transformer/highlight-markers.d.ts

@@ -14,7 +14,6 @@
  * limitations under the License.
  */
 import { CommentAnnotation, Model } from '@manuscripts/json-schema';
-import { Build } from './builders';
 export type HighlightableField = 'title' | 'caption' | 'contents';
 export declare const highlightableFields: HighlightableField[];
 export declare const isHighlightableModel: (model: Model) => model is HighlightableModel;
@@ -23,5 +22,10 @@ export interface HighlightableModel extends Model {
     title?: string;
     caption?: string;
 }
-export declare const extractHighlightMarkers: (model: HighlightableModel, commentAnnotationsMap: Map<string, Build<CommentAnnotation>>) => void;
+export type CommentMarker = {
+    _id: string;
+    from: number;
+    to: number;
+};
+export declare const extractCommentMarkers: (model: Model) => CommentMarker[];
 export declare const insertHighlightMarkers: (contents: string, commentAnnotations: CommentAnnotation[]) => string;

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@manuscripts/transform",
   "description": "ProseMirror transformer for Manuscripts applications",
-  "version": "1.5.8-LEAN-3030-2",
+  "version": "1.5.8-LEAN-3030-3",
   "repository": "github:Atypon-OpenSource/manuscripts-transform",
   "license": "Apache-2.0",
   "main": "dist/cjs",