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🧮 Use katex for MathML rendering in JATS (#507)
* 🧮 Use katex for MathML rendering in JATS * 🧮 Align MathML in JATS with other examples
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‎.changeset/good-apples-pump.md

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---
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'myst-to-jats': patch
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'myst-cli': patch
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'mystmd': patch
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---
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Add mathml to the exported JATS.

‎package-lock.json

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‎packages/myst-to-jats/package.json

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"dependencies": {
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"citation-js-utils": "^1.0.1",
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"jats-tags": "^1.0.1",
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"katex": "^0.15.2",
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"myst-common": "^1.1.0",
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"myst-frontmatter": "^1.1.0",
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"myst-spec": "^0.0.4",
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},
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"devDependencies": {
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"@types/js-yaml": "^4.0.5",
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"@types/katex": "^0.14.0",
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"@types/mdast": "^3.0.10",
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"jats-xml": "^1.0.3",
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"js-yaml": "^4.1.0",

‎packages/myst-to-jats/src/index.ts

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@@ -2,7 +2,8 @@ import type { Root, CrossReference, TableCell as SpecTableCell } from 'myst-spec
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import type { Cite, Code, FootnoteDefinition, FootnoteReference } from 'myst-spec-ext';
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import type { Plugin } from 'unified';
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import type { VFile } from 'vfile';
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import { js2xml } from 'xml-js';
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import { js2xml, xml2js } from 'xml-js';
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import katex from 'katex';
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import type { CitationRenderer } from 'citation-js-utils';
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import type { MessageInfo, GenericNode } from 'myst-common';
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import { copyNode, fileError } from 'myst-common';
@@ -118,6 +119,26 @@ function alternativesFromMinifiedOutput(output: MinifiedOutput, state: IJatsSeri
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state.closeNode();
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}
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function mathToMml(math?: string, inline?: boolean) {
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const katexXml = katex.renderToString(math, { output: 'mathml', throwOnError: false });
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const katexJs = xml2js(katexXml, { compact: false }) as Element;
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const spanElement = katexJs.elements?.[0];
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const mathElement = spanElement?.elements?.[0];
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if (!mathElement) return;
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if (inline) mathElement.attributes = { ...mathElement.attributes, display: 'inline' };
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delete mathElement.attributes?.xmlns;
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function addMmlAndRemoveAnnotation(el?: Element) {
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if (el?.name) el.name = `mml:${el.name}`;
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if (!el?.elements) return;
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el.elements = el.elements.filter((child: Element) => child.name !== 'annotation');
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el.elements.forEach((child: Element) => {
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addMmlAndRemoveAnnotation(child);
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});
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}
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addMmlAndRemoveAnnotation(mathElement);
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return mathElement;
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}
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const handlers: Record<string, Handler> = {
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text(node, state) {
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state.text(node.value);
@@ -181,10 +202,13 @@ const handlers: Record<string, Handler> = {
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},
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inlineMath(node, state) {
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state.openNode('inline-formula');
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state.openNode('alternatives');
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state.pushNode(mathToMml(node.value, true));
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state.openNode('tex-math');
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state.addLeaf('cdata', { cdata: node.value });
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state.closeNode();
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state.closeNode();
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state.closeNode();
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},
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math(node, state) {
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const dispFormulaAttrs: Attributes = {};
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}
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state.openNode('disp-formula', dispFormulaAttrs);
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renderLabel(node, state, (enumerator) => `(${enumerator})`);
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state.openNode('alternatives');
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state.pushNode(mathToMml(node.value));
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state.openNode('tex-math');
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state.addLeaf('cdata', { cdata: node.value });
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state.closeNode();
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state.closeNode();
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state.closeNode();
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},
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mystRole(node, state) {
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state.renderChildren(node);

‎packages/myst-to-jats/src/types.ts

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@@ -56,6 +56,7 @@ export interface IJatsSerializer<D extends Record<string, any> = StateData> {
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text: (value?: string) => void;
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renderChildren: (node: any) => void;
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renderInline: (node: GenericNode, name: string, attributes?: Attributes) => void;
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pushNode: (el?: Element) => void;
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addLeaf: (name: string, attributes?: Attributes) => void;
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openNode: (name: string, attributes?: Attributes) => void;
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closeNode: () => void;

‎packages/myst-to-jats/src/types/katex/index.d.ts

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declare module 'katex';

‎packages/myst-to-jats/tests/basic.yml

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@@ -189,7 +189,7 @@ cases:
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value: Ax=b
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- type: text
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value: .
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jats: <p>This math is a role, <inline-formula><tex-math><![CDATA[e=mc^2]]></tex-math></inline-formula>, while this math is wrapped in dollar signs, <inline-formula><tex-math><![CDATA[Ax=b]]></tex-math></inline-formula>.</p>
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jats: <p>This math is a role, <inline-formula><alternatives><mml:math display="inline"><mml:semantics><mml:mrow><mml:mi>e</mml:mi><mml:mo>=</mml:mo><mml:mi>m</mml:mi><mml:msup><mml:mi>c</mml:mi><mml:mn>2</mml:mn></mml:msup></mml:mrow></mml:semantics></mml:math><tex-math><![CDATA[e=mc^2]]></tex-math></alternatives></inline-formula>, while this math is wrapped in dollar signs, <inline-formula><alternatives><mml:math display="inline"><mml:semantics><mml:mrow><mml:mi>A</mml:mi><mml:mi>x</mml:mi><mml:mo>=</mml:mo><mml:mi>b</mml:mi></mml:mrow></mml:semantics></mml:math><tex-math><![CDATA[Ax=b]]></tex-math></alternatives></inline-formula>.</p>
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- title: Display Math (label)
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tree:
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type: root
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identifier: my-equation
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enumerator: 1
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value: w_{t+1} = (1 + r_{t+1}) s(w_t) + y_{t+1}
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jats: <disp-formula id="my-equation"><label>(1)</label><tex-math><![CDATA[w_{t+1} = (1 + r_{t+1}) s(w_t) + y_{t+1}]]></tex-math></disp-formula>
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jats: <disp-formula id="my-equation"><label>(1)</label><alternatives><mml:math><mml:semantics><mml:mrow><mml:msub><mml:mi>w</mml:mi><mml:mrow><mml:mi>t</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msub><mml:mo>=</mml:mo><mml:mo stretchy="false">(</mml:mo><mml:mn>1</mml:mn><mml:mo>+</mml:mo><mml:msub><mml:mi>r</mml:mi><mml:mrow><mml:mi>t</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msub><mml:mo stretchy="false">)</mml:mo><mml:mi>s</mml:mi><mml:mo stretchy="false">(</mml:mo><mml:msub><mml:mi>w</mml:mi><mml:mi>t</mml:mi></mml:msub><mml:mo stretchy="false">)</mml:mo><mml:mo>+</mml:mo><mml:msub><mml:mi>y</mml:mi><mml:mrow><mml:mi>t</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:semantics></mml:math><tex-math><![CDATA[w_{t+1} = (1 + r_{t+1}) s(w_t) + y_{t+1}]]></tex-math></alternatives></disp-formula>
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- title: Display Math (no label)
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tree:
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type: root
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children:
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- type: math
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value: w_{t+1} = (1 + r_{t+1}) s(w_t) + y_{t+1}
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jats: <disp-formula><tex-math><![CDATA[w_{t+1} = (1 + r_{t+1}) s(w_t) + y_{t+1}]]></tex-math></disp-formula>
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jats: <disp-formula><alternatives><mml:math><mml:semantics><mml:mrow><mml:msub><mml:mi>w</mml:mi><mml:mrow><mml:mi>t</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msub><mml:mo>=</mml:mo><mml:mo stretchy="false">(</mml:mo><mml:mn>1</mml:mn><mml:mo>+</mml:mo><mml:msub><mml:mi>r</mml:mi><mml:mrow><mml:mi>t</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msub><mml:mo stretchy="false">)</mml:mo><mml:mi>s</mml:mi><mml:mo stretchy="false">(</mml:mo><mml:msub><mml:mi>w</mml:mi><mml:mi>t</mml:mi></mml:msub><mml:mo stretchy="false">)</mml:mo><mml:mo>+</mml:mo><mml:msub><mml:mi>y</mml:mi><mml:mrow><mml:mi>t</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:semantics></mml:math><tex-math><![CDATA[w_{t+1} = (1 + r_{t+1}) s(w_t) + y_{t+1}]]></tex-math></alternatives></disp-formula>
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- title: Display Math (not numbered)
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tree:
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type: root
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enumerated: false
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enumerator: 1
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value: w_{t+1} = (1 + r_{t+1}) s(w_t) + y_{t+1}
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jats: <disp-formula id="my-equation"><tex-math><![CDATA[w_{t+1} = (1 + r_{t+1}) s(w_t) + y_{t+1}]]></tex-math></disp-formula>
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jats: <disp-formula id="my-equation"><alternatives><mml:math><mml:semantics><mml:mrow><mml:msub><mml:mi>w</mml:mi><mml:mrow><mml:mi>t</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msub><mml:mo>=</mml:mo><mml:mo stretchy="false">(</mml:mo><mml:mn>1</mml:mn><mml:mo>+</mml:mo><mml:msub><mml:mi>r</mml:mi><mml:mrow><mml:mi>t</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msub><mml:mo stretchy="false">)</mml:mo><mml:mi>s</mml:mi><mml:mo stretchy="false">(</mml:mo><mml:msub><mml:mi>w</mml:mi><mml:mi>t</mml:mi></mml:msub><mml:mo stretchy="false">)</mml:mo><mml:mo>+</mml:mo><mml:msub><mml:mi>y</mml:mi><mml:mrow><mml:mi>t</mml:mi><mml:mo>+</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:semantics></mml:math><tex-math><![CDATA[w_{t+1} = (1 + r_{t+1}) s(w_t) + y_{t+1}]]></tex-math></alternatives></disp-formula>
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- title: Lists
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tree:
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type: root

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