@manuscripts/transform 2.1.4 → 2.1.5-LEAN-3376-1

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

@@ -13,10 +13,10 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import { ObjectTypes, } from '@manuscripts/json-schema';
+import { getModelsByType, ObjectTypes, } from '@manuscripts/json-schema';
 import { CitationProvider } from '@manuscripts/library';
 import debug from 'debug';
-import { DOMParser, DOMSerializer } from 'prosemirror-model';
+import { DOMParser as ProseMirrorDOMParser, DOMSerializer, } from 'prosemirror-model';
 import serializeToXML from 'w3c-xmlserializer';
 import { nodeFromHTML, textFromHTML } from '../lib/html';
 import { normalizeStyleName } from '../lib/styled-content';
@@ -32,7 +32,7 @@ import { selectVersionIds } from './jats-versions';
 const warn = debug('manuscripts-transform');
 const XLINK_NAMESPACE = 'http://www.w3.org/1999/xlink';
 const normalizeID = (id) => id.replace(/:/g, '_');
-const parser = DOMParser.fromSchema(schema);
+const parser = ProseMirrorDOMParser.fromSchema(schema);
 const findChildNodeOfType = (node, nodeType) => {
     for (const child of iterateChildren(node)) {
         if (child.type === nodeType) {
@@ -88,7 +88,7 @@ const createDefaultIdGenerator = () => {
     const counter = createCounter();
     return async (element) => {
         const value = String(counter.increment(element.nodeName));
-        return `${element.nodeName}-${value}`;
+        return `${element.localName}-${value}`;
     };
 };
 const chooseRefType = (objectType) => {
@@ -156,6 +156,7 @@ export class JATSExporter {
         };
         this.nodeFromJATS = (JATSFragment) => {
             JATSFragment = JATSFragment.trim();
+            JATSFragment = JATSFragment.replace(' ', ' ');
             if (!JATSFragment.length) {
                 return null;
             }
@@ -606,6 +607,7 @@ export class JATSExporter {
         this.createSerializer = () => {
             const getModel = (id) => id ? this.modelMap.get(id) : undefined;
             const nodes = {
+                author_notes: () => ['author-notes', 0],
                 title: () => '',
                 affiliations: () => '',
                 contributors: () => '',
@@ -678,22 +680,20 @@ export class JATSExporter {
                 },
                 doc: () => '',
                 equation: (node) => {
-                    const formula = this.document.createElement('disp-formula');
-                    formula.setAttribute('id', normalizeID(node.attrs.id));
-                    if (node.attrs.TeXRepresentation) {
-                        const math = this.document.createElement('tex-math');
-                        math.textContent = node.attrs.TeXRepresentation;
-                        formula.appendChild(math);
-                    }
-                    else if (node.attrs.MathMLStringRepresentation) {
-                        const math = this.nodeFromJATS(node.attrs.MathMLStringRepresentation);
-                        if (math) {
-                            formula.appendChild(math);
-                        }
-                    }
-                    return formula;
+                    return this.createEquation(node);
+                },
+                inline_equation: (node) => {
+                    const eqElement = this.document.createElement('inline-formula');
+                    const equation = this.createEquation(node, true);
+                    eqElement.append(equation);
+                    return eqElement;
+                },
+                equation_element: (node) => {
+                    const eqElement = this.document.createElement('disp-formula');
+                    eqElement.setAttribute('id', normalizeID(node.attrs.id));
+                    processChildNodes(eqElement, node, schema.nodes.equation);
+                    return eqElement;
                 },
-                equation_element: (node) => createFigureElement(node, 'fig', node.type.schema.nodes.equation, 'equation'),
                 figcaption: (node) => {
                     if (!node.textContent) {
                         return '';
@@ -743,28 +743,6 @@ export class JATSExporter {
                 },
                 hard_break: () => '',
                 highlight_marker: () => '',
-                inline_equation: (node) => {
-                    const formula = this.document.createElement('inline-formula');
-                    formula.setAttribute('id', normalizeID(node.attrs.id));
-                    if (node.attrs.TeXRepresentation) {
-                        const math = this.document.createElement('tex-math');
-                        math.textContent = node.attrs.TeXRepresentation;
-                        formula.appendChild(math);
-                    }
-                    else if (node.attrs.MathMLRepresentation) {
-                        const math = this.nodeFromJATS(node.attrs.MathMLRepresentation);
-                        if (math) {
-                            formula.appendChild(math);
-                        }
-                    }
-                    else if (node.attrs.SVGRepresentation) {
-                        const math = this.nodeFromJATS(node.attrs.SVGRepresentation);
-                        if (math) {
-                            formula.appendChild(math);
-                        }
-                    }
-                    return formula;
-                },
                 inline_footnote: (node) => {
                     const xref = this.document.createElement('xref');
                     xref.setAttribute('ref-type', 'fn');
@@ -1050,6 +1028,7 @@ export class JATSExporter {
             }
         };
         this.buildContributors = (articleMeta) => {
+            var _a;
             const contributors = this.models.filter(isContributor);
             const authorContributors = contributors
                 .filter((contributor) => contributor.role === 'author')
@@ -1268,56 +1247,64 @@ export class JATSExporter {
                         }
                     });
                 }
-                const noteIDs = [];
-                for (const contributor of [...authorContributors, ...otherContributors]) {
-                    if (contributor.footnote) {
-                        const ids = contributor.footnote.map((note) => {
-                            return note.noteID;
-                        });
-                        noteIDs.push(...ids);
-                    }
-                    if (contributor.corresp) {
-                        const ids = contributor.corresp.map((corresp) => {
-                            return corresp.correspID;
-                        });
-                        noteIDs.push(...ids);
-                    }
-                }
-                const footnotes = [];
-                footnotes.push(...this.models.filter(hasObjectType(ObjectTypes.Footnote)));
-                const correspodings = [];
-                correspodings.push(...this.models.filter(hasObjectType(ObjectTypes.Corresponding)));
-                if (footnotes || correspodings) {
-                    const authorNotesEl = this.document.createElement('author-notes');
-                    const usedFootnotes = footnotes.filter((footnote) => {
-                        return noteIDs.includes(footnote._id);
-                    });
-                    const usedCorrespodings = correspodings.filter((corresp) => {
-                        return noteIDs.includes(corresp._id);
-                    });
-                    usedFootnotes.forEach((footnote) => {
-                        const authorFootNote = this.document.createElement('fn');
-                        authorFootNote.setAttribute('id', normalizeID(footnote._id));
-                        authorFootNote.innerHTML = footnote.contents;
-                        authorNotesEl.appendChild(authorFootNote);
-                    });
-                    usedCorrespodings.forEach((corresponding) => {
-                        const correspondingEl = this.document.createElement('corresp');
-                        correspondingEl.setAttribute('id', normalizeID(corresponding._id));
-                        if (corresponding.label) {
-                            const labelEl = this.document.createElement('label');
-                            labelEl.textContent = corresponding.label;
-                            correspondingEl.appendChild(labelEl);
+                const authorNotesEl = this.document.createElement('author-notes');
+                const usedCorrespodings = this.getUsedCorrespondings([
+                    ...authorContributors,
+                    ...otherContributors,
+                ]);
+                usedCorrespodings.forEach((corresp) => {
+                    this.appendCorrespondingToElement(corresp, authorNotesEl);
+                });
+                const authorNotes = (_a = getModelsByType(this.modelMap, ObjectTypes.AuthorNotes)) === null || _a === void 0 ? void 0 : _a[0];
+                if (authorNotes) {
+                    authorNotes.containedObjectIDs.forEach((id) => {
+                        const model = this.modelMap.get(id);
+                        if (!model) {
+                            return;
+                        }
+                        if (id.startsWith('MPParagraphElement')) {
+                            this.appendParagraphToElement(model, authorNotesEl);
+                        }
+                        else if (id.startsWith('MPFootnote')) {
+                            this.appendFootnoteToElement(model, authorNotesEl);
                         }
-                        correspondingEl.append(corresponding.contents);
-                        authorNotesEl.appendChild(correspondingEl);
                     });
-                    if (authorNotesEl.childNodes.length > 0) {
-                        articleMeta.insertBefore(authorNotesEl, contribGroup.nextSibling);
-                    }
+                }
+                if (authorNotesEl.childNodes.length > 0) {
+                    articleMeta.insertBefore(authorNotesEl, contribGroup.nextSibling);
                 }
             }
         };
+        this.appendCorrespondingToElement = (corresponding, element) => {
+            const correspondingEl = this.document.createElement('corresp');
+            correspondingEl.setAttribute('id', normalizeID(corresponding._id));
+            if (corresponding.label) {
+                const labelEl = this.document.createElement('label');
+                labelEl.textContent = corresponding.label;
+                correspondingEl.appendChild(labelEl);
+            }
+            correspondingEl.append(corresponding.contents);
+            element.appendChild(correspondingEl);
+        };
+        this.appendParagraphToElement = (paragraph, element) => {
+            const parsedDoc = new DOMParser().parseFromString(paragraph.contents, 'text/html');
+            const parsedParagraph = parsedDoc.body.querySelector('p');
+            if (parsedParagraph) {
+                const paragraphEl = this.document.createElement('p');
+                paragraphEl.innerHTML = parsedParagraph.innerHTML;
+                const value = parsedParagraph.getAttribute('id');
+                if (value) {
+                    paragraphEl.setAttribute('id', value);
+                }
+                element.appendChild(paragraphEl);
+            }
+        };
+        this.appendFootnoteToElement = (footnote, element) => {
+            const footnoteEl = this.document.createElement('fn');
+            footnoteEl.setAttribute('id', normalizeID(footnote._id));
+            footnoteEl.innerHTML = footnote.contents;
+            element.appendChild(footnoteEl);
+        };
         this.fixBody = (body, fragment) => {
             fragment.descendants((node) => {
                 if (node.attrs.id) {
@@ -1605,6 +1592,27 @@ export class JATSExporter {
             this.citationTexts.set(id, output);
         });
     }
+    createEquation(node, isInline = false) {
+        if (node.attrs.format === 'tex') {
+            const texMath = this.document.createElement('tex-math');
+            texMath.innerHTML = node.attrs.contents;
+            return texMath;
+        }
+        else {
+            const math = this.nodeFromJATS(node.attrs.contents);
+            const mathml = math;
+            if (!isInline) {
+                mathml.setAttribute('id', normalizeID(node.attrs.id));
+            }
+            return mathml;
+        }
+    }
+    getUsedCorrespondings(contributors) {
+        return contributors
+            .flatMap((c) => { var _a; return (_a = c.corresp) !== null && _a !== void 0 ? _a : []; })
+            .map((corresp) => this.modelMap.get(corresp.correspID))
+            .filter((corresp) => !!corresp);
+    }
     buildKeywords(articleMeta) {
         const keywords = [...this.modelMap.values()].filter((model) => model.objectType === ObjectTypes.Keyword);
         const keywordGroups = new Map();
@@ -1676,6 +1684,9 @@ export class JATSExporter {
                             }
                         }
                     }
+                    if (!fnGroup.hasChildNodes()) {
+                        fnGroup.remove();
+                    }
                 }
             }
         });

package/dist/es/schema/index.js

@@ -19,6 +19,7 @@ import { abstracts } from './nodes/abstracts';
 import { affiliation } from './nodes/affiliation';
 import { affiliations } from './nodes/affiliations';
 import { attribution } from './nodes/attribution';
+import { authorNotes } from './nodes/author_notes';
 import { backmatter } from './nodes/backmatter';
 import { bibliographyElement } from './nodes/bibliography_element';
 import { bibliographyItem } from './nodes/bibliography_item';
@@ -99,7 +100,6 @@ export * from './nodes/footnotes_section';
 export * from './nodes/graphical_abstract_section';
 export * from './nodes/hard_break';
 export * from './nodes/highlight_marker';
-export * from './nodes/inline_equation';
 export * from './nodes/inline_footnote';
 export * from './nodes/keyword';
 export * from './nodes/keywords_element';
@@ -199,6 +199,7 @@ export const schema = new Schema({
         table_row: tableRow,
         table_col: tableCol,
         table_colgroup: tableColGroup,
+        table_header: tableHeader,
         text,
         toc_element: tocElement,
         toc_section: tocSection,
@@ -210,6 +211,6 @@ export const schema = new Schema({
         contributors,
         supplements,
         supplement,
-        table_header: tableHeader,
+        author_notes: authorNotes,
     },
 });

package/dist/{types/mathjax/mathjax-packages.d.ts → es/schema/nodes/author_notes.js}

@@ -13,4 +13,12 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-export declare const packages: string[];
+export const authorNotes = {
+    attrs: {
+        id: { default: '' },
+        dataTracked: { default: null },
+    },
+    content: '(footnote | paragraph)+',
+    group: 'block element',
+    toDOM: () => ['author-notes', 0],
+};

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

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 export const contributors = {
-    content: 'contributor*',
+    content: 'contributor* author_notes?',
     attrs: {
         id: { default: '' },
     },

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

@@ -1,5 +1,5 @@
 /*!
- * © 2019 Atypon Systems LLC
+ * © 2023 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.
@@ -17,9 +17,8 @@ import { ObjectTypes } from '@manuscripts/json-schema';
 export const equation = {
     attrs: {
         id: { default: '' },
-        MathMLStringRepresentation: { default: '' },
-        SVGStringRepresentation: { default: '' },
-        TeXRepresentation: { default: '' },
+        contents: { default: '' },
+        format: { default: '' },
         dataTracked: { default: null },
     },
     group: 'block',
@@ -27,26 +26,25 @@ export const equation = {
         {
             tag: `div.${ObjectTypes.Equation}`,
             getAttrs: (p) => {
-                const dom = p;
+                const htmlEl = p;
                 return {
-                    id: dom.getAttribute('id'),
-                    MathMLStringRepresentation: dom.getAttribute('data-mathml-string-representation'),
-                    SVGStringRepresentation: dom.innerHTML,
-                    TeXRepresentation: dom.getAttribute('data-tex-representation'),
+                    id: htmlEl.getAttribute('id'),
+                    format: htmlEl.getAttribute('data-equation-format'),
+                    contents: htmlEl.innerHTML,
                 };
             },
         },
     ],
     toDOM: (node) => {
         const equationNode = node;
+        const { id, contents, format } = equationNode.attrs;
         const dom = document.createElement('div');
-        dom.setAttribute('id', equationNode.attrs.id);
         dom.classList.add(ObjectTypes.Equation);
-        if (equationNode.attrs.MathMLStringRepresentation) {
-            dom.setAttribute('data-mathml-string-representation', equationNode.attrs.MathMLStringRepresentation);
+        dom.setAttribute('id', id);
+        if (format) {
+            dom.setAttribute('data-equation-format', format);
         }
-        dom.setAttribute('data-tex-representation', equationNode.attrs.TeXRepresentation);
-        dom.innerHTML = equationNode.attrs.SVGStringRepresentation;
+        dom.innerHTML = contents;
         return dom;
     },
 };

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

@@ -14,11 +14,10 @@
  * limitations under the License.
  */
 export const equationElement = {
-    content: '(equation | placeholder) figcaption',
+    content: '(equation | placeholder)',
     attrs: {
         id: { default: '' },
-        suppressCaption: { default: true },
-        suppressTitle: { default: undefined },
+        label: { default: '' },
         dataTracked: { default: null },
         comments: { default: null },
     },
@@ -26,7 +25,7 @@ export const equationElement = {
     group: 'block element',
     parseDOM: [
         {
-            tag: 'figure.equation',
+            tag: 'div.equation',
             getAttrs: (p) => {
                 const dom = p;
                 return {
@@ -38,7 +37,7 @@ export const equationElement = {
     toDOM: (node) => {
         const equationElementNode = node;
         return [
-            'figure',
+            'div',
             {
                 class: 'equation',
                 id: equationElementNode.attrs.id,

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

@@ -13,14 +13,13 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import { ObjectTypes } from '@manuscripts/json-schema';
 export const inlineEquation = {
     attrs: {
-        id: { default: '' },
-        MathMLRepresentation: { default: '' },
-        SVGRepresentation: { default: '' },
-        TeXRepresentation: { default: '' },
         dataTracked: { default: null },
+        comments: { default: null },
+        id: { default: '' },
+        contents: { default: '' },
+        format: { default: '' },
     },
     atom: true,
     inline: true,
@@ -28,28 +27,27 @@ export const inlineEquation = {
     group: 'inline',
     parseDOM: [
         {
-            tag: `span.${ObjectTypes.InlineMathFragment}`,
+            tag: `span.MPInlineMathFragment`,
             getAttrs: (p) => {
                 const dom = p;
                 return {
+                    format: dom.getAttribute('data-equation-format'),
                     id: dom.getAttribute('id'),
-                    MathMLRepresentation: dom.getAttribute('data-mathml-representation') || '',
-                    SVGRepresentation: dom.innerHTML || '',
-                    TeXRepresentation: dom.getAttribute('data-tex-representation') || '',
+                    contents: dom.innerHTML,
                 };
             },
         },
     ],
     toDOM: (node) => {
         const inlineEquationNode = node;
+        const { id, contents, format } = inlineEquationNode.attrs;
         const dom = document.createElement('span');
-        dom.classList.add(ObjectTypes.InlineMathFragment);
-        dom.setAttribute('id', inlineEquationNode.attrs.id);
-        dom.setAttribute('data-tex-representation', inlineEquationNode.attrs.TeXRepresentation);
-        if (inlineEquationNode.attrs.MathMLRepresentation) {
-            dom.setAttribute('data-mathml-representation', inlineEquationNode.attrs.MathMLRepresentation);
+        dom.setAttribute('id', id);
+        dom.classList.add('MPInlineMathFragment');
+        if (format) {
+            dom.setAttribute('data-equation-format', format);
         }
-        dom.innerHTML = inlineEquationNode.attrs.SVGRepresentation;
+        dom.innerHTML = contents;
         return dom;
     },
 };

package/dist/es/transformer/builders.js

@@ -95,12 +95,6 @@ export const buildNote = (target, source, contents = '') => ({
     source,
     contents,
 });
-export const buildInlineMathFragment = (containingObject, TeXRepresentation) => ({
-    _id: generateID(ObjectTypes.InlineMathFragment),
-    objectType: ObjectTypes.InlineMathFragment,
-    containingObject: containingObject || undefined,
-    TeXRepresentation,
-});
 export const buildFootnote = (containingObject, contents, kind = 'footnote') => ({
     _id: generateID(ObjectTypes.Footnote),
     objectType: ObjectTypes.Footnote,
@@ -108,6 +102,11 @@ export const buildFootnote = (containingObject, contents, kind = 'footnote') =>
     contents,
     kind,
 });
+export const buildAuthorNotes = (containedObjectIDs) => ({
+    _id: generateID(ObjectTypes.AuthorNotes),
+    objectType: ObjectTypes.AuthorNotes,
+    containedObjectIDs: containedObjectIDs,
+});
 export const buildFootnotesOrder = (footnotesList, containedObjectID) => ({
     _id: generateID(ObjectTypes.FootnotesOrder),
     objectType: ObjectTypes.FootnotesOrder,
@@ -128,13 +127,12 @@ export const buildSection = (priority = 0, path = []) => {
         path: path.concat(id),
     };
 };
-export const buildParagraph = (placeholderInnerHTML) => {
+export const buildParagraph = (innerHTML = '') => {
     const _id = generateID(ObjectTypes.ParagraphElement);
-    const element = document.createElementNS('http://www.w3.org/1999/xhtml', 'p');
+    const element = document.createElementNS(null, 'p');
     element.setAttribute('id', _id);
-    element.setAttribute('class', 'MPElement');
-    if (placeholderInnerHTML) {
-        element.setAttribute('data-placeholder-text', placeholderInnerHTML);
+    if (innerHTML) {
+        element.innerHTML = innerHTML;
     }
     const contents = serializeToXML(element);
     return {
@@ -142,7 +140,6 @@ export const buildParagraph = (placeholderInnerHTML) => {
         objectType: ObjectTypes.ParagraphElement,
         elementType: 'p',
         contents,
-        placeholderInnerHTML,
     };
 };
 export const buildColor = (value, priority) => ({

package/dist/es/transformer/decode.js

@@ -53,6 +53,7 @@ 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 getAuthorNotes = (modelMap) => getModelsByType(modelMap, ObjectTypes.AuthorNotes);
 const getContributors = (modelMap) => getModelsByType(modelMap, ObjectTypes.Contributor);
 const getKeywordElements = (modelMap) => getModelsByType(modelMap, ObjectTypes.KeywordsElement);
 const getSupplements = (modelMap) => getModelsByType(modelMap, ObjectTypes.Supplement);
@@ -82,7 +83,11 @@ export class Decoder {
         const contributors = getContributors(this.modelMap)
             .map((c) => this.decode(c))
             .filter(Boolean);
-        return schema.nodes.contributors.createAndFill({}, contributors);
+        const authorNotes = getAuthorNotes(this.modelMap)
+            .map((authorNote) => this.decode(authorNote))
+            .filter(Boolean);
+        const content = [...contributors, ...authorNotes];
+        return schema.nodes.contributors.createAndFill({}, content);
     }
     createKeywordsNode() {
         const elements = getKeywordElements(this.modelMap)
@@ -271,9 +276,8 @@ export class Decoder {
                 const model = data;
                 return schema.nodes.equation.createChecked({
                     id: model._id,
-                    MathMLStringRepresentation: model.MathMLStringRepresentation,
-                    SVGStringRepresentation: model.SVGStringRepresentation,
-                    TeXRepresentation: model.TeXRepresentation,
+                    contents: model.contents,
+                    format: model.format,
                 });
             },
             [ObjectTypes.EquationElement]: (data) => {
@@ -292,12 +296,10 @@ export class Decoder {
                 else {
                     throw new MissingElement(model.containedObjectID);
                 }
-                const figcaption = this.getFigcaption(model);
                 return schema.nodes.equation_element.createChecked({
                     id: model._id,
-                    suppressCaption: Boolean(model.suppressCaption),
-                    suppressTitle: Boolean(model.suppressTitle === undefined ? true : model.suppressTitle),
-                }, [equation, figcaption]);
+                    label: model.label,
+                }, [equation]);
             },
             [ObjectTypes.FootnotesElement]: (data) => {
                 const foonotesElementModel = data;
@@ -483,6 +485,13 @@ export class Decoder {
                     id: model._id,
                 }, content);
             },
+            [ObjectTypes.AuthorNotes]: (data) => {
+                const model = data;
+                const content = model.containedObjectIDs.map((id) => this.decode(this.modelMap.get(id)));
+                return schema.nodes.author_notes.create({
+                    id: model._id,
+                }, content);
+            },
             [ObjectTypes.Section]: (data) => {
                 const model = data;
                 const elements = [];

package/dist/es/transformer/encode.js

@@ -54,12 +54,6 @@ const listContents = (node) => {
     }
     return serializeToXML(output);
 };
-const svgDefs = (svg) => {
-    const template = document.createElement('template');
-    template.innerHTML = svg.trim();
-    const defs = template.content.querySelector('defs');
-    return defs ? serializeToXML(defs) : undefined;
-};
 const tableRowDisplayStyle = (tagName, parent) => {
     switch (tagName) {
         case 'thead':
@@ -346,20 +340,13 @@ const encoders = {
             : false,
     }),
     equation: (node) => ({
-        MathMLStringRepresentation: node.attrs.MathMLStringRepresentation || undefined,
-        TeXRepresentation: node.attrs.TeXRepresentation,
-        SVGStringRepresentation: node.attrs.SVGStringRepresentation,
+        contents: node.attrs.contents,
+        format: node.attrs.format,
     }),
     equation_element: (node) => ({
         containedObjectID: attributeOfNodeType(node, 'equation', 'id'),
-        caption: inlineContentOfChildNodeType(node, node.type.schema.nodes.figcaption, node.type.schema.nodes.caption),
-        title: inlineContentOfChildNodeType(node, node.type.schema.nodes.figcaption, node.type.schema.nodes.caption_title, false),
-        elementType: 'p',
-        suppressCaption: Boolean(node.attrs.suppressCaption) || undefined,
-        suppressTitle: node.attrs.suppressTitle === undefined ||
-            node.attrs.suppressTitle === true
-            ? undefined
-            : false,
+        elementType: 'div',
+        label: node.attrs.label,
     }),
     figure: (node) => ({
         contentType: node.attrs.contentType || undefined,
@@ -388,6 +375,9 @@ const encoders = {
     table_element_footer: (node) => ({
         containedObjectIDs: containedObjectIDs(node),
     }),
+    author_notes: (node) => ({
+        containedObjectIDs: containedObjectIDs(node),
+    }),
     footnotes_section: (node, parent, path, priority) => ({
         category: buildSectionCategory(node),
         priority: priority.value++,
@@ -406,12 +396,6 @@ const encoders = {
             .map((childNode) => childNode.attrs.id)
             .filter((id) => id),
     }),
-    inline_equation: (node, parent) => ({
-        containingObject: parent.attrs.id,
-        TeXRepresentation: node.attrs.TeXRepresentation,
-        SVGRepresentation: node.attrs.SVGRepresentation,
-        SVGGlyphs: svgDefs(node.attrs.SVGRepresentation),
-    }),
     keyword: (node, parent) => ({
         containedGroup: parent.attrs.id,
         name: keywordContents(node),
@@ -584,8 +568,7 @@ export const encode = (node) => {
         if (placeholderTypes.includes(child.type)) {
             return;
         }
-        if (parent.type === schema.nodes.paragraph &&
-            child.type !== schema.nodes.inline_equation) {
+        if (parent.type === schema.nodes.paragraph) {
             return;
         }
         if (child.type === schema.nodes.footnotes_element) {