@manuscripts/transform 2.1.1-LEAN-3352-1 → 2.1.1-LEAN-3092-10

package/dist/cjs/index.js

@@ -18,7 +18,6 @@ exports.isSectionLabelNode = void 0;
 __exportStar(require("./lib/section-group-type"), exports);
 __exportStar(require("./lib/table-cell-styles"), exports);
 __exportStar(require("./lib/utils"), exports);
-__exportStar(require("./mathjax"), exports);
 __exportStar(require("./schema"), exports);
 __exportStar(require("./transformer"), exports);
 __exportStar(require("./jats"), exports);

package/dist/cjs/jats/importer/jats-body-dom-parser.js

@@ -21,8 +21,6 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.jatsBodyDOMParser = void 0;
 const mime_1 = __importDefault(require("mime"));
 const prosemirror_model_1 = require("prosemirror-model");
-const mathml_to_svg_1 = require("../../mathjax/mathml-to-svg");
-const tex_to_svg_1 = require("../../mathjax/tex-to-svg");
 const schema_1 = require("../../schema");
 const transformer_1 = require("../../transformer");
 const XLINK_NAMESPACE = 'http://www.w3.org/1999/xlink';
@@ -39,6 +37,28 @@ const chooseContentType = (graphicNode) => {
         }
     }
 };
+const getEquationContent = (p) => {
+    var _a;
+    const element = p;
+    const id = element.getAttribute('id');
+    const container = (_a = element.querySelector('alternatives')) !== null && _a !== void 0 ? _a : element;
+    let contents = '';
+    let format = '';
+    for (const child of container.childNodes) {
+        const nodeName = child.nodeName.replace(/^[a-z]:/, '');
+        switch (nodeName) {
+            case 'tex-math':
+                contents = child.innerHTML;
+                format = 'tex';
+                break;
+            case 'mml:math':
+                contents = child.outerHTML;
+                format = 'mathml';
+                break;
+        }
+    }
+    return { id, format, contents };
+};
 const marks = [
     {
         tag: 'bold',
@@ -147,91 +167,26 @@ const nodes = [
         tag: 'inline-formula',
         node: 'inline_equation',
         getAttrs: (node) => {
-            var _a, _b, _c, _d, _e;
             const element = node;
-            const attrs = {
-                id: element.getAttribute('id'),
-                MathMLRepresentation: '',
-                SVGRepresentation: '',
-                TeXRepresentation: '',
-            };
-            const container = (_a = element.querySelector('alternatives')) !== null && _a !== void 0 ? _a : element;
-            for (const child of container.childNodes) {
-                const nodeName = child.nodeName.replace(/^[a-z]:/, '');
-                switch (nodeName) {
-                    case 'tex-math':
-                        attrs.TeXRepresentation = (_c = (_b = child.textContent) === null || _b === void 0 ? void 0 : _b.trim()) !== null && _c !== void 0 ? _c : '';
-                        if (attrs.TeXRepresentation) {
-                            attrs.SVGRepresentation =
-                                (_d = (0, tex_to_svg_1.convertTeXToSVG)(attrs.TeXRepresentation, true)) !== null && _d !== void 0 ? _d : '';
-                        }
-                        break;
-                    case 'mml:math':
-                        ;
-                        child.removeAttribute('id');
-                        attrs.MathMLRepresentation = transformer_1.xmlSerializer.serializeToString(child);
-                        if (attrs.MathMLRepresentation) {
-                            attrs.SVGRepresentation =
-                                (_e = (0, mathml_to_svg_1.convertMathMLToSVG)(attrs.MathMLRepresentation, true)) !== null && _e !== void 0 ? _e : '';
-                        }
-                        break;
-                }
-            }
-            return attrs;
+            return getEquationContent(element);
         },
     },
     {
         tag: 'disp-formula',
         node: 'equation_element',
         getAttrs: (node) => {
+            var _a, _b;
             const element = node;
-            const caption = element.querySelector('figcaption');
             return {
                 id: element.getAttribute('id'),
-                suppressCaption: !caption,
+                label: (_b = (_a = element.querySelector('label')) === null || _a === void 0 ? void 0 : _a.textContent) !== null && _b !== void 0 ? _b : '',
             };
         },
         getContent: (node, schema) => {
-            var _a, _b, _c, _d, _e;
             const element = node;
-            const attrs = {
-                MathMLStringRepresentation: '',
-                SVGStringRepresentation: '',
-                TeXRepresentation: '',
-            };
-            const container = (_a = element.querySelector('alternatives')) !== null && _a !== void 0 ? _a : element;
-            for (const child of container.childNodes) {
-                const nodeName = child.nodeName.replace(/^[a-z]:/, '');
-                switch (nodeName) {
-                    case 'tex-math':
-                        attrs.TeXRepresentation = (_c = (_b = child.textContent) === null || _b === void 0 ? void 0 : _b.trim()) !== null && _c !== void 0 ? _c : '';
-                        if (attrs.TeXRepresentation) {
-                            attrs.SVGStringRepresentation =
-                                (_d = (0, tex_to_svg_1.convertTeXToSVG)(attrs.TeXRepresentation, true)) !== null && _d !== void 0 ? _d : '';
-                        }
-                        break;
-                    case 'mml:math':
-                        ;
-                        child.removeAttribute('id');
-                        attrs.MathMLStringRepresentation =
-                            transformer_1.xmlSerializer.serializeToString(child);
-                        if (attrs.MathMLStringRepresentation) {
-                            attrs.SVGStringRepresentation =
-                                (_e = (0, mathml_to_svg_1.convertMathMLToSVG)(attrs.MathMLStringRepresentation, true)) !== null && _e !== void 0 ? _e : '';
-                        }
-                        break;
-                }
-            }
-            const caption = element.querySelector('figcaption');
-            const figcaption = schema.nodes.figcaption.create();
+            const attrs = getEquationContent(element);
             return prosemirror_model_1.Fragment.from([
-                schema.nodes.equation.createChecked(attrs),
-                caption
-                    ?
-                        exports.jatsBodyDOMParser.parse(caption, {
-                            topNode: figcaption,
-                        })
-                    : figcaption,
+                schema.nodes.equation.createChecked(Object.assign({}, attrs)),
             ]);
         },
     },

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

@@ -265,6 +265,16 @@ exports.jatsBodyTransformations = {
             }
         });
     },
+    orderTableFootnote(doc, body) {
+        const tableInlineFootnotesIds = new Set(Array.from(body.querySelectorAll('tbody > tr > td > xref[ref-type="fn"]').values()).map((inlineFootnote) => inlineFootnote.getAttribute('rid')));
+        const fnGroups = doc.querySelectorAll('table-wrap-foot > fn-group');
+        fnGroups.forEach((fnGroup) => {
+            const orderedFootnotes = Array.from(fnGroup.querySelectorAll('fn')).sort((fn) => tableInlineFootnotesIds.has(fn.getAttribute('id'))
+                ? -1
+                : 0);
+            fnGroup.replaceChildren(...orderedFootnotes);
+        });
+    },
     moveFloatsGroupToBody(doc, body, createElement) {
         const group = doc.querySelector('floats-group');
         if (group) {

package/dist/cjs/jats/importer/jats-front-parser.js

@@ -45,11 +45,6 @@ exports.jatsFrontParser = {
         }
         return titles;
     },
-    parseDOI(front) {
-        var _a;
-        const doi = front === null || front === void 0 ? void 0 : front.querySelector('article-meta > article-id[pub-id-type="doi"]');
-        return (_a = doi === null || doi === void 0 ? void 0 : doi.textContent) !== null && _a !== void 0 ? _a : undefined;
-    },
     parseCounts(counts) {
         var _a, _b, _c, _d, _e;
         if (counts) {

package/dist/cjs/jats/importer/jats-parser-utils.js

@@ -16,6 +16,8 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.htmlFromJatsNode = exports.updateDocumentIDs = void 0;
+const uuid_1 = require("uuid");
+const schema_1 = require("../../schema");
 const transformer_1 = require("../../transformer");
 const updateDocumentIDs = (node, replacements) => {
     const warnings = [];
@@ -30,6 +32,10 @@ function recurseDoc(node, fn) {
     node.descendants((n) => fn(n));
 }
 const updateNodeID = (node, replacements, warnings) => {
+    if (node.type === schema_1.schema.nodes.inline_equation) {
+        node.attrs = Object.assign(Object.assign({}, node.attrs), { id: `InlineMathFragment:${(0, uuid_1.v4)()}` });
+        return;
+    }
     if (!('id' in node.attrs)) {
         return;
     }

package/dist/cjs/jats/importer/parse-jats-article.js

@@ -31,7 +31,6 @@ const parseJATSFront = (doc, front) => {
     const createElement = createElementFn(doc);
     const journal = jats_front_parser_1.jatsFrontParser.parseJournal(front.querySelector('journal-meta'));
     const titles = jats_front_parser_1.jatsFrontParser.parseTitles(front.querySelector('article-meta > title-group'), createElement);
-    const DOI = jats_front_parser_1.jatsFrontParser.parseDOI(front);
     const { affiliations, affiliationIDs } = jats_front_parser_1.jatsFrontParser.parseAffiliations([
         ...front.querySelectorAll('article-meta > contrib-group > aff'),
     ]);
@@ -46,7 +45,7 @@ const parseJATSFront = (doc, front) => {
     ], affiliationIDs, footnoteIDs, correspondingIDs);
     const history = jats_front_parser_1.jatsFrontParser.parseDates(front.querySelector('article-meta > history'));
     const counts = jats_front_parser_1.jatsFrontParser.parseCounts(front.querySelector('article-meta counts'));
-    const manuscript = Object.assign(Object.assign(Object.assign(Object.assign({}, (0, builders_1.buildManuscript)()), counts), history), { DOI });
+    const manuscript = Object.assign(Object.assign(Object.assign({}, (0, builders_1.buildManuscript)()), counts), history);
     return generateIDs([
         manuscript,
         titles,
@@ -68,6 +67,7 @@ const parseJATSBody = (doc, body, references) => {
     jats_body_transformations_1.jatsBodyTransformations.createBackmatter(doc, body, createElement);
     jats_body_transformations_1.jatsBodyTransformations.createSuppleMaterials(doc, body, createElement);
     jats_body_transformations_1.jatsBodyTransformations.createKeywords(doc, body, createElement);
+    jats_body_transformations_1.jatsBodyTransformations.orderTableFootnote(doc, body);
     const node = jats_body_dom_parser_1.jatsBodyDOMParser.parse(body).firstChild;
     if (!node) {
         throw new Error('No content was parsed from the JATS article body');

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

@@ -95,7 +95,7 @@ const createDefaultIdGenerator = () => {
     const counter = (0, exports.createCounter)();
     return async (element) => {
         const value = String(counter.increment(element.nodeName));
-        return `${element.nodeName}-${value}`;
+        return `${element.localName}-${value}`;
     };
 };
 const chooseRefType = (objectType) => {
@@ -164,6 +164,7 @@ class JATSExporter {
         };
         this.nodeFromJATS = (JATSFragment) => {
             JATSFragment = JATSFragment.trim();
+            JATSFragment = JATSFragment.replace(' ', ' ');
             if (!JATSFragment.length) {
                 return null;
             }
@@ -248,7 +249,7 @@ class JATSExporter {
             }
         };
         this.buildFront = (doi, id, links) => {
-            var _a, _b, _c, _d, _e;
+            var _a, _b, _c, _d;
             const manuscript = (0, project_bundle_1.findManuscript)(this.modelMap);
             const titles = (0, project_bundle_1.findTitles)(this.modelMap);
             const front = this.document.createElement('front');
@@ -311,10 +312,10 @@ class JATSExporter {
                 articleID.textContent = id;
                 articleMeta.appendChild(articleID);
             }
-            if (doi || manuscript.DOI) {
+            if (doi) {
                 const articleID = this.document.createElement('article-id');
                 articleID.setAttribute('pub-id-type', 'doi');
-                articleID.textContent = (_a = manuscript.DOI) !== null && _a !== void 0 ? _a : doi;
+                articleID.textContent = doi;
                 articleMeta.appendChild(articleID);
             }
             const titleGroup = this.document.createElement('title-group');
@@ -349,14 +350,14 @@ class JATSExporter {
                 for (const supplement of supplements) {
                     const supplementaryMaterial = this.document.createElement('supplementary-material');
                     supplementaryMaterial.setAttribute('id', normalizeID(supplement._id));
-                    supplementaryMaterial.setAttributeNS(XLINK_NAMESPACE, 'href', (_b = supplement.href) !== null && _b !== void 0 ? _b : '');
-                    const mimeType = (_c = supplement.MIME) === null || _c === void 0 ? void 0 : _c.split('/')[0];
-                    const mimeSubType = (_d = supplement.MIME) === null || _d === void 0 ? void 0 : _d.split('/')[1];
+                    supplementaryMaterial.setAttributeNS(XLINK_NAMESPACE, 'href', (_a = supplement.href) !== null && _a !== void 0 ? _a : '');
+                    const mimeType = (_b = supplement.MIME) === null || _b === void 0 ? void 0 : _b.split('/')[0];
+                    const mimeSubType = (_c = supplement.MIME) === null || _c === void 0 ? void 0 : _c.split('/')[1];
                     supplementaryMaterial.setAttribute('mimetype', mimeType !== null && mimeType !== void 0 ? mimeType : '');
                     supplementaryMaterial.setAttribute('mime-subtype', mimeSubType !== null && mimeSubType !== void 0 ? mimeSubType : '');
                     const caption = this.document.createElement('caption');
                     const title = this.document.createElement('title');
-                    title.textContent = (_e = supplement.title) !== null && _e !== void 0 ? _e : '';
+                    title.textContent = (_d = supplement.title) !== null && _d !== void 0 ? _d : '';
                     caption.append(title);
                     supplementaryMaterial.append(caption);
                     articleMeta.append(supplementaryMaterial);
@@ -686,22 +687,20 @@ 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_1.schema.nodes.equation);
+                    return eqElement;
                 },
-                equation_element: (node) => createFigureElement(node, 'fig', node.type.schema.nodes.equation, 'equation'),
                 figcaption: (node) => {
                     if (!node.textContent) {
                         return '';
@@ -751,28 +750,6 @@ 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');
@@ -1589,6 +1566,21 @@ 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;
+        }
+    }
     buildKeywords(articleMeta) {
         const keywords = [...this.modelMap.values()].filter((model) => model.objectType === json_schema_1.ObjectTypes.Keyword);
         const keywordGroups = new Map();

package/dist/cjs/schema/index.js

@@ -117,7 +117,6 @@ __exportStar(require("./nodes/footnotes_section"), exports);
 __exportStar(require("./nodes/graphical_abstract_section"), exports);
 __exportStar(require("./nodes/hard_break"), exports);
 __exportStar(require("./nodes/highlight_marker"), exports);
-__exportStar(require("./nodes/inline_equation"), exports);
 __exportStar(require("./nodes/inline_footnote"), exports);
 __exportStar(require("./nodes/keyword"), exports);
 __exportStar(require("./nodes/keywords_element"), exports);

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

@@ -1,6 +1,6 @@
 "use strict";
 /*!
- * © 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.
@@ -20,9 +20,8 @@ const json_schema_1 = require("@manuscripts/json-schema");
 exports.equation = {
     attrs: {
         id: { default: '' },
-        MathMLStringRepresentation: { default: '' },
-        SVGStringRepresentation: { default: '' },
-        TeXRepresentation: { default: '' },
+        contents: { default: '' },
+        format: { default: '' },
         dataTracked: { default: null },
     },
     group: 'block',
@@ -30,26 +29,25 @@ exports.equation = {
         {
             tag: `div.${json_schema_1.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(json_schema_1.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/cjs/schema/nodes/equation_element.js

@@ -17,11 +17,10 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.equationElement = void 0;
 exports.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 },
     },
@@ -29,7 +28,7 @@ exports.equationElement = {
     group: 'block element',
     parseDOM: [
         {
-            tag: 'figure.equation',
+            tag: 'div.equation',
             getAttrs: (p) => {
                 const dom = p;
                 return {
@@ -41,7 +40,7 @@ exports.equationElement = {
     toDOM: (node) => {
         const equationElementNode = node;
         return [
-            'figure',
+            'div',
             {
                 class: 'equation',
                 id: equationElementNode.attrs.id,

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

@@ -16,14 +16,13 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.inlineEquation = void 0;
-const json_schema_1 = require("@manuscripts/json-schema");
 exports.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,
@@ -31,28 +30,27 @@ exports.inlineEquation = {
     group: 'inline',
     parseDOM: [
         {
-            tag: `span.${json_schema_1.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(json_schema_1.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/cjs/transformer/builders.js

@@ -18,7 +18,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.buildTitles = exports.buildElementsOrder = exports.auxiliaryObjectTypes = exports.buildJournal = exports.buildAttribution = exports.buildContributorRole = exports.buildContribution = exports.buildColor = exports.buildParagraph = exports.buildSection = exports.buildCorresp = exports.buildFootnotesOrder = exports.buildFootnote = exports.buildInlineMathFragment = exports.buildNote = exports.buildComment = exports.buildSupplementaryMaterial = exports.buildAffiliation = exports.buildFigure = exports.buildKeywordGroup = exports.buildKeyword = exports.buildBibliographyElement = exports.buildBibliographicDate = exports.buildBibliographicName = exports.buildBibliographyItem = exports.buildContributor = exports.buildManuscript = exports.buildProject = void 0;
+exports.buildTitles = exports.buildElementsOrder = exports.auxiliaryObjectTypes = exports.buildJournal = exports.buildAttribution = exports.buildContributorRole = exports.buildContribution = exports.buildColor = exports.buildParagraph = exports.buildSection = exports.buildCorresp = exports.buildFootnotesOrder = exports.buildFootnote = exports.buildNote = exports.buildComment = exports.buildSupplementaryMaterial = exports.buildAffiliation = exports.buildFigure = exports.buildKeywordGroup = exports.buildKeyword = exports.buildBibliographyElement = exports.buildBibliographicDate = exports.buildBibliographicName = exports.buildBibliographyItem = exports.buildContributor = exports.buildManuscript = exports.buildProject = void 0;
 const json_schema_1 = require("@manuscripts/json-schema");
 const w3c_xmlserializer_1 = __importDefault(require("w3c-xmlserializer"));
 const schema_1 = require("../schema");
@@ -115,13 +115,6 @@ const buildNote = (target, source, contents = '') => ({
     contents,
 });
 exports.buildNote = buildNote;
-const buildInlineMathFragment = (containingObject, TeXRepresentation) => ({
-    _id: (0, id_1.generateID)(json_schema_1.ObjectTypes.InlineMathFragment),
-    objectType: json_schema_1.ObjectTypes.InlineMathFragment,
-    containingObject: containingObject || undefined,
-    TeXRepresentation,
-});
-exports.buildInlineMathFragment = buildInlineMathFragment;
 const buildFootnote = (containingObject, contents, kind = 'footnote') => ({
     _id: (0, id_1.generateID)(json_schema_1.ObjectTypes.Footnote),
     objectType: json_schema_1.ObjectTypes.Footnote,
@@ -130,10 +123,11 @@ const buildFootnote = (containingObject, contents, kind = 'footnote') => ({
     kind,
 });
 exports.buildFootnote = buildFootnote;
-const buildFootnotesOrder = (footnotesList) => ({
+const buildFootnotesOrder = (footnotesList, containedObjectID) => ({
     _id: (0, id_1.generateID)(json_schema_1.ObjectTypes.FootnotesOrder),
     objectType: json_schema_1.ObjectTypes.FootnotesOrder,
     footnotesList,
+    containedObjectID,
 });
 exports.buildFootnotesOrder = buildFootnotesOrder;
 const buildCorresp = (contents) => ({

package/dist/cjs/transformer/decode.js

@@ -68,7 +68,6 @@ const getSupplements = (modelMap) => (0, exports.getModelsByType)(modelMap, json
 const getKeywordGroups = (modelMap) => (0, exports.getModelsByType)(modelMap, json_schema_1.ObjectTypes.KeywordGroup);
 const getKeywords = (modelMap) => (0, exports.getModelsByType)(modelMap, json_schema_1.ObjectTypes.Keyword);
 const getTitles = (modelMap) => (0, exports.getModelsByType)(modelMap, json_schema_1.ObjectTypes.Titles)[0];
-const isFootnote = (0, object_types_1.hasObjectType)(json_schema_1.ObjectTypes.Footnote);
 const hasParentSection = (id) => (section) => section.path &&
     section.path.length > 1 &&
     section.path[section.path.length - 2] === id;
@@ -281,9 +280,8 @@ class Decoder {
                 const model = data;
                 return schema_1.schema.nodes.equation.createChecked({
                     id: model._id,
-                    MathMLStringRepresentation: model.MathMLStringRepresentation,
-                    SVGStringRepresentation: model.SVGStringRepresentation,
-                    TeXRepresentation: model.TeXRepresentation,
+                    contents: model.contents,
+                    format: model.format,
                 });
             },
             [json_schema_1.ObjectTypes.EquationElement]: (data) => {
@@ -302,32 +300,32 @@ class Decoder {
                 else {
                     throw new errors_1.MissingElement(model.containedObjectID);
                 }
-                const figcaption = this.getFigcaption(model);
                 return schema_1.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]);
             },
             [json_schema_1.ObjectTypes.FootnotesElement]: (data) => {
                 const foonotesElementModel = data;
-                const collateByKind = foonotesElementModel.collateByKind || 'footnote';
                 const footnotesOfKind = [];
-                for (const model of this.modelMap.values()) {
-                    if (isFootnote(model) &&
-                        model.kind === collateByKind &&
-                        model.containingObject === foonotesElementModel._id) {
-                        const comments = this.createCommentNodes(model);
-                        comments.forEach((c) => this.comments.set(c.attrs.id, c));
-                        const footnote = this.parseContents(model.contents || '<div></div>', undefined, this.getComments(model), {
-                            topNode: schema_1.schema.nodes.footnote.create({
-                                id: model._id,
-                                kind: model.kind,
-                                comments: comments.map((c) => c.attrs.id),
-                            }),
-                        });
-                        footnotesOfKind.push(footnote);
-                    }
+                const footnoteOrder = (0, exports.getModelsByType)(this.modelMap, json_schema_1.ObjectTypes.FootnotesOrder).find((model) => model.containedObjectID === data._id);
+                if (footnoteOrder) {
+                    footnoteOrder.footnotesList.map(({ id }) => {
+                        const model = this.modelMap.get(id);
+                        const collateByKind = foonotesElementModel.collateByKind || 'footnote';
+                        if (model.kind === collateByKind) {
+                            const comments = this.createCommentNodes(model);
+                            comments.forEach((c) => this.comments.set(c.attrs.id, c));
+                            const footnote = this.parseContents(model.contents || '<div></div>', undefined, this.getComments(model), {
+                                topNode: schema_1.schema.nodes.footnote.create({
+                                    id: model._id,
+                                    kind: model.kind,
+                                    comments: comments.map((c) => c.attrs.id),
+                                }),
+                            });
+                            footnotesOfKind.push(footnote);
+                        }
+                    });
                 }
                 return schema_1.schema.nodes.footnotes_element.create({
                     id: foonotesElementModel._id,