@manuscripts/transform 2.1.1-LEAN-3092-9 → 2.1.1-LEAN-3336-21

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

@@ -13,8 +13,6 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import { v4 as uuidv4 } from 'uuid';
-import { schema } from '../../schema';
 import { generateID, nodeTypesMap } from '../../transformer';
 export const updateDocumentIDs = (node, replacements) => {
     const warnings = [];
@@ -28,10 +26,6 @@ function recurseDoc(node, fn) {
     node.descendants((n) => fn(n));
 }
 const updateNodeID = (node, replacements, warnings) => {
-    if (node.type === schema.nodes.inline_equation) {
-        node.attrs = Object.assign(Object.assign({}, node.attrs), { id: `InlineMathFragment:${uuidv4()}` });
-        return;
-    }
     if (!('id' in node.attrs)) {
         return;
     }

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

@@ -156,7 +156,6 @@ export class JATSExporter {
         };
         this.nodeFromJATS = (JATSFragment) => {
             JATSFragment = JATSFragment.trim();
-            JATSFragment = JATSFragment.replace(' ', ' ');
             if (!JATSFragment.length) {
                 return null;
             }
@@ -607,6 +606,11 @@ export 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: () => '',
@@ -679,20 +683,22 @@ export class JATSExporter {
                 },
                 doc: () => '',
                 equation: (node) => {
-                    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;
+                    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;
                 },
+                equation_element: (node) => createFigureElement(node, 'fig', node.type.schema.nodes.equation, 'equation'),
                 figcaption: (node) => {
                     if (!node.textContent) {
                         return '';
@@ -742,6 +748,28 @@ 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');
@@ -842,9 +870,8 @@ export class JATSExporter {
                     element.setAttribute('position', 'anchor');
                     return element;
                 },
-                table_body: () => ['tbody', 0],
                 table_cell: (node) => [
-                    node.attrs.celltype,
+                    'td',
                     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,
                 ],
@@ -925,6 +952,26 @@ export 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) {
@@ -945,7 +992,7 @@ export class JATSExporter {
                 const element = createElement(node, nodeName);
                 appendLabels(element, node);
                 appendChildNodeOfType(element, node, node.type.schema.nodes.figcaption);
-                appendChildNodeOfType(element, node, node.type.schema.nodes.table);
+                appendTable(element, node);
                 appendChildNodeOfType(element, node, node.type.schema.nodes.table_element_footer);
                 if (isExecutableNodeType(node.type)) {
                     processExecutableNode(node, element);
@@ -1558,21 +1605,6 @@ 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;
-        }
-    }
     buildKeywords(articleMeta) {
         const keywords = [...this.modelMap.values()].filter((model) => model.objectType === ObjectTypes.Keyword);
         const keywordGroups = new Map();

package/dist/es/mathjax/index.js

@@ -0,0 +1,12 @@
+export const convertMathMLToSVG = async (mathml, display) => {
+    const { convertMathMLToSVG } = await import('./mathml-to-svg');
+    return convertMathMLToSVG(mathml, display);
+};
+export const convertTeXToMathML = async (tex, display) => {
+    const { convertTeXToMathML } = await import('./tex-to-mathml');
+    return convertTeXToMathML(tex, display);
+};
+export const convertTeXToSVG = async (tex, display) => {
+    const { convertTeXToSVG } = await import('./tex-to-svg');
+    return convertTeXToSVG(tex, display);
+};

package/dist/es/mathjax/mathjax-packages.js

@@ -0,0 +1,17 @@
+/*!
+ * © 2019 Atypon Systems LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+import { AllPackages } from 'mathjax-full/js/input/tex/AllPackages';
+export const packages = AllPackages.filter((name) => name !== 'html' && name !== 'bussproofs');

package/dist/es/mathjax/mathml-to-svg.js

@@ -0,0 +1,66 @@
+/*!
+ * © 2019 Atypon Systems LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+import 'mathjax-full/js/util/entities/all';
+import { HTMLAdaptor } from 'mathjax-full/js/adaptors/HTMLAdaptor';
+import { MmlFactory } from 'mathjax-full/js/core/MmlTree/MmlFactory';
+import { HTMLDocument } from 'mathjax-full/js/handlers/html/HTMLDocument';
+import { MathML } from 'mathjax-full/js/input/mathml';
+import { SVG } from 'mathjax-full/js/output/svg';
+import { xmlSerializer } from '../transformer';
+class ManuscriptsMmlFactory extends MmlFactory {
+    constructor() {
+        super();
+        this.nodeMap.set('image', this.nodeMap.get('none'));
+    }
+    create(kind, properties = {}, children = []) {
+        if (kind === 'image') {
+            return this.node['none'](properties, children);
+        }
+        return this.node[kind](properties, children);
+    }
+}
+class ManuscriptsHTMLAdaptor extends HTMLAdaptor {
+    setAttribute(node, name, value, ns) {
+        if (name !== 'xmlns') {
+            ns ? node.setAttributeNS(ns, name, value) : node.setAttribute(name, value);
+        }
+    }
+}
+const InputJax = new MathML();
+const OutputJax = new SVG({
+    fontCache: 'none',
+});
+const adaptor = new ManuscriptsHTMLAdaptor(window);
+const doc = new HTMLDocument(document, adaptor, {
+    InputJax,
+    OutputJax,
+    MmlFactory: new ManuscriptsMmlFactory(),
+});
+doc.addStyleSheet();
+export const convertMathMLToSVG = (mathml, display) => {
+    const item = doc.convert(mathml, {
+        display,
+        em: 16,
+        ex: 8,
+        containerWidth: 1000000,
+        lineWidth: 1000000,
+        scale: 1,
+    });
+    if (!item || !item.firstChild) {
+        return null;
+    }
+    return xmlSerializer.serializeToString(item.firstChild);
+};

package/dist/es/mathjax/tex-to-mathml.js

@@ -0,0 +1,45 @@
+/*!
+ * © 2019 Atypon Systems LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+import 'mathjax-full/js/util/entities/all';
+import { HTMLAdaptor } from 'mathjax-full/js/adaptors/HTMLAdaptor';
+import { STATE } from 'mathjax-full/js/core/MathItem.js';
+import { SerializedMmlVisitor } from 'mathjax-full/js/core/MmlTree/SerializedMmlVisitor';
+import { HTMLDocument } from 'mathjax-full/js/handlers/html/HTMLDocument';
+import { TeX } from 'mathjax-full/js/input/tex';
+import { packages } from './mathjax-packages';
+const InputJax = new TeX({
+    packages,
+});
+const adaptor = new HTMLAdaptor(window);
+const doc = new HTMLDocument(document, adaptor, {
+    InputJax,
+});
+const visitor = new SerializedMmlVisitor();
+export const convertTeXToMathML = (tex, display) => {
+    const item = doc.convert(tex, {
+        display,
+        em: 16,
+        ex: 8,
+        containerWidth: 1000000,
+        lineWidth: 1000000,
+        scale: 1,
+        end: STATE.CONVERT,
+    });
+    if (!item) {
+        return null;
+    }
+    return visitor.visitTree(item);
+};

package/dist/es/mathjax/tex-to-svg.js

@@ -0,0 +1,55 @@
+/*!
+ * © 2019 Atypon Systems LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+import 'mathjax-full/js/util/entities/all';
+import { HTMLAdaptor } from 'mathjax-full/js/adaptors/HTMLAdaptor';
+import { HTMLDocument } from 'mathjax-full/js/handlers/html/HTMLDocument';
+import { TeX } from 'mathjax-full/js/input/tex';
+import { SVG } from 'mathjax-full/js/output/svg';
+import { xmlSerializer } from '../transformer';
+import { packages } from './mathjax-packages';
+class ManuscriptsHTMLAdaptor extends HTMLAdaptor {
+    setAttribute(node, name, value, ns) {
+        if (name !== 'xmlns') {
+            ns ? node.setAttributeNS(ns, name, value) : node.setAttribute(name, value);
+        }
+    }
+}
+const InputJax = new TeX({
+    packages,
+});
+const OutputJax = new SVG({
+    fontCache: 'none',
+});
+const adaptor = new ManuscriptsHTMLAdaptor(window);
+const doc = new HTMLDocument(document, adaptor, {
+    InputJax,
+    OutputJax,
+});
+doc.addStyleSheet();
+export const convertTeXToSVG = (tex, display) => {
+    const item = doc.convert(tex, {
+        display,
+        em: 16,
+        ex: 8,
+        containerWidth: 1000000,
+        lineWidth: 1000000,
+        scale: 1,
+    });
+    if (!item || !item.firstChild) {
+        return null;
+    }
+    return xmlSerializer.serializeToString(item.firstChild);
+};

package/dist/es/schema/index.js

@@ -66,11 +66,10 @@ import { sectionLabel } from './nodes/section_label';
 import { sectionTitle } from './nodes/section_title';
 import { supplement } from './nodes/supplement';
 import { supplements } from './nodes/supplements';
-import { table, tableBody } from './nodes/table';
+import { table, tableCell, tableHeader, tableRow } from './nodes/table';
 import { tableCol, tableColGroup } from './nodes/table_col';
 import { tableElement } from './nodes/table_element';
 import { tableElementFooter } from './nodes/table_element_footer';
-import { tableCell, tableRow } from './nodes/table_row';
 import { text } from './nodes/text';
 import { title } from './nodes/title';
 import { tocElement } from './nodes/toc_element';
@@ -100,6 +99,7 @@ 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';
@@ -119,7 +119,6 @@ export * from './nodes/section_title';
 export * from './nodes/table';
 export * from './nodes/table_col';
 export * from './nodes/table_element';
-export * from './nodes/table_row';
 export * from './nodes/text';
 export * from './nodes/toc_element';
 export * from './nodes/toc_section';
@@ -195,7 +194,6 @@ export const schema = new Schema({
         section_title: sectionTitle,
         section_title_plain: sectionTitle,
         table,
-        table_body: tableBody,
         table_cell: tableCell,
         table_element: tableElement,
         table_row: tableRow,
@@ -212,5 +210,6 @@ export const schema = new Schema({
         contributors,
         supplements,
         supplement,
+        table_header: tableHeader,
     },
 });

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

@@ -1,5 +1,5 @@
 /*!
- * © 2023 Atypon Systems LLC
+ * © 2019 Atypon Systems LLC
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -17,8 +17,9 @@ import { ObjectTypes } from '@manuscripts/json-schema';
 export const equation = {
     attrs: {
         id: { default: '' },
-        contents: { default: '' },
-        format: { default: '' },
+        MathMLStringRepresentation: { default: '' },
+        SVGStringRepresentation: { default: '' },
+        TeXRepresentation: { default: '' },
         dataTracked: { default: null },
     },
     group: 'block',
@@ -26,25 +27,26 @@ export const equation = {
         {
             tag: `div.${ObjectTypes.Equation}`,
             getAttrs: (p) => {
-                const htmlEl = p;
+                const dom = p;
                 return {
-                    id: htmlEl.getAttribute('id'),
-                    format: htmlEl.getAttribute('data-equation-format'),
-                    contents: htmlEl.innerHTML,
+                    id: dom.getAttribute('id'),
+                    MathMLStringRepresentation: dom.getAttribute('data-mathml-string-representation'),
+                    SVGStringRepresentation: dom.innerHTML,
+                    TeXRepresentation: dom.getAttribute('data-tex-representation'),
                 };
             },
         },
     ],
     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);
-        dom.setAttribute('id', id);
-        if (format) {
-            dom.setAttribute('data-equation-format', format);
+        if (equationNode.attrs.MathMLStringRepresentation) {
+            dom.setAttribute('data-mathml-string-representation', equationNode.attrs.MathMLStringRepresentation);
         }
-        dom.innerHTML = contents;
+        dom.setAttribute('data-tex-representation', equationNode.attrs.TeXRepresentation);
+        dom.innerHTML = equationNode.attrs.SVGStringRepresentation;
         return dom;
     },
 };

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

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

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

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