@manuscripts/transform 2.1.1-LEAN-3336-16 → 2.1.1-LEAN-3092-3

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 +37,27 @@ const chooseContentType = (graphicNode) => {
         }
     }
 };
+const getEquationContent = (p) => {
+    var _a;
+    const element = p;
+    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 { format, contents };
+};
 const marks = [
     {
         tag: 'bold',
@@ -147,91 +166,27 @@ 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);
+            const id = element.getAttribute('id');
             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({ id }, attrs)),
             ]);
         },
     },
@@ -530,6 +485,10 @@ const nodes = [
             };
         },
     },
+    {
+        tag: 'tbody',
+        skip: true,
+    },
     {
         tag: 'tfoot',
         skip: true,
@@ -564,12 +523,12 @@ const nodes = [
     },
     {
         tag: 'th',
-        node: 'table_header',
+        node: 'table_cell',
         getAttrs: (node) => {
             const element = node;
             const colspan = element.getAttribute('colspan');
             const rowspan = element.getAttribute('rowspan');
-            return Object.assign(Object.assign(Object.assign({}, (colspan && { colspan })), (rowspan && { rowspan })), { valign: element.getAttribute('valign'), align: element.getAttribute('align'), scope: element.getAttribute('scope'), style: element.getAttribute('style') });
+            return Object.assign(Object.assign(Object.assign({ celltype: 'th' }, (colspan && { colspan })), (rowspan && { rowspan })), { valign: element.getAttribute('valign'), align: element.getAttribute('align'), scope: element.getAttribute('scope'), style: element.getAttribute('style') });
         },
     },
     {

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

@@ -164,6 +164,7 @@ class JATSExporter {
         };
         this.nodeFromJATS = (JATSFragment) => {
             JATSFragment = JATSFragment.trim();
+            JATSFragment = JATSFragment.replace(' ', ' ');
             if (!JATSFragment.length) {
                 return null;
             }
@@ -614,11 +615,6 @@ class JATSExporter {
         this.createSerializer = () => {
             const getModel = (id) => id ? this.modelMap.get(id) : undefined;
             const nodes = {
-                table_header: (node) => [
-                    'th',
-                    Object.assign(Object.assign({ valign: node.attrs.valign, align: node.attrs.align, scope: node.attrs.scope, style: node.attrs.style }, (node.attrs.rowspan > 1 && { rowspan: node.attrs.rowspan })), (node.attrs.colspan > 1 && { colspan: node.attrs.colspan })),
-                    0,
-                ],
                 title: () => '',
                 affiliations: () => '',
                 contributors: () => '',
@@ -691,22 +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 '';
@@ -756,28 +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');
@@ -878,8 +850,9 @@ class JATSExporter {
                     element.setAttribute('position', 'anchor');
                     return element;
                 },
+                table_body: () => ['tbody', 0],
                 table_cell: (node) => [
-                    'td',
+                    node.attrs.celltype,
                     Object.assign(Object.assign({ valign: node.attrs.valign, align: node.attrs.align, scope: node.attrs.scope, style: node.attrs.style }, (node.attrs.rowspan > 1 && { rowspan: node.attrs.rowspan })), (node.attrs.colspan > 1 && { colspan: node.attrs.colspan })),
                     0,
                 ],
@@ -960,26 +933,6 @@ class JATSExporter {
                     element.appendChild(this.serializeNode(childNode));
                 }
             };
-            const appendTable = (element, node) => {
-                const tableNode = findChildNodeOfType(node, node.type.schema.nodes.table);
-                const colGroupNode = findChildNodeOfType(node, node.type.schema.nodes.table_colgroup);
-                if (!tableNode) {
-                    return;
-                }
-                const table = this.serializeNode(tableNode);
-                const tbodyElement = this.document.createElement('tbody');
-                while (table.firstChild) {
-                    const child = table.firstChild;
-                    table.removeChild(child);
-                    tbodyElement.appendChild(child);
-                }
-                table.appendChild(tbodyElement);
-                if (colGroupNode) {
-                    const colGroup = this.serializeNode(colGroupNode);
-                    table.insertBefore(colGroup, table.firstChild);
-                }
-                element.appendChild(table);
-            };
             const createFigureElement = (node, nodeName, contentNodeType, figType) => {
                 const element = createElement(node, nodeName);
                 if (figType) {
@@ -1000,7 +953,7 @@ class JATSExporter {
                 const element = createElement(node, nodeName);
                 appendLabels(element, node);
                 appendChildNodeOfType(element, node, node.type.schema.nodes.figcaption);
-                appendTable(element, node);
+                appendChildNodeOfType(element, node, node.type.schema.nodes.table);
                 appendChildNodeOfType(element, node, node.type.schema.nodes.table_element_footer);
                 if ((0, node_types_1.isExecutableNodeType)(node.type)) {
                     processExecutableNode(node, element);
@@ -1613,6 +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

@@ -87,6 +87,7 @@ const table_1 = require("./nodes/table");
 const table_col_1 = require("./nodes/table_col");
 const table_element_1 = require("./nodes/table_element");
 const table_element_footer_1 = require("./nodes/table_element_footer");
+const table_row_1 = require("./nodes/table_row");
 const text_1 = require("./nodes/text");
 const title_1 = require("./nodes/title");
 const toc_element_1 = require("./nodes/toc_element");
@@ -116,7 +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);
@@ -136,6 +136,7 @@ __exportStar(require("./nodes/section_title"), exports);
 __exportStar(require("./nodes/table"), exports);
 __exportStar(require("./nodes/table_col"), exports);
 __exportStar(require("./nodes/table_element"), exports);
+__exportStar(require("./nodes/table_row"), exports);
 __exportStar(require("./nodes/text"), exports);
 __exportStar(require("./nodes/toc_element"), exports);
 __exportStar(require("./nodes/toc_section"), exports);
@@ -211,9 +212,10 @@ exports.schema = new prosemirror_model_1.Schema({
         section_title: section_title_1.sectionTitle,
         section_title_plain: section_title_1.sectionTitle,
         table: table_1.table,
-        table_cell: table_1.tableCell,
+        table_body: table_1.tableBody,
+        table_cell: table_row_1.tableCell,
         table_element: table_element_1.tableElement,
-        table_row: table_1.tableRow,
+        table_row: table_row_1.tableRow,
         table_col: table_col_1.tableCol,
         table_colgroup: table_col_1.tableColGroup,
         text: text_1.text,
@@ -227,6 +229,5 @@ exports.schema = new prosemirror_model_1.Schema({
         contributors: contributors_1.contributors,
         supplements: supplements_1.supplements,
         supplement: supplement_1.supplement,
-        table_header: table_1.tableHeader,
     },
 });

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

@@ -16,43 +16,39 @@
  */
 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 },
+        contents: { default: '' },
+        format: { default: '' },
     },
+    selectable: false,
     atom: true,
     inline: true,
     draggable: true,
     group: 'inline',
     parseDOM: [
         {
-            tag: `span.${json_schema_1.ObjectTypes.InlineMathFragment}`,
+            tag: `span.MPInlineMathFragment`,
             getAttrs: (p) => {
                 const dom = p;
                 return {
-                    id: dom.getAttribute('id'),
-                    MathMLRepresentation: dom.getAttribute('data-mathml-representation') || '',
-                    SVGRepresentation: dom.innerHTML || '',
-                    TeXRepresentation: dom.getAttribute('data-tex-representation') || '',
+                    format: dom.getAttribute('data-equation-format'),
+                    contents: dom.innerHTML,
                 };
             },
         },
     ],
     toDOM: (node) => {
         const inlineEquationNode = node;
+        const { 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.classList.add('MPInlineMathFragment');
+        if (format) {
+            dom.setAttribute('data-equation-format', format);
         }
-        dom.innerHTML = inlineEquationNode.attrs.SVGRepresentation;
+        dom.innerHTML = contents;
         return dom;
     },
 };