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🧮 Clean up MathML tagging in JATS #665

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merged 2 commits into from
Oct 13, 2023
Merged

🧮 Clean up MathML tagging in JATS #665

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🧮 Clean up MathML tagging in JATS
rowanc1 Oct 13, 2023
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rowanc1 Oct 13, 2023
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7 changes: 7 additions & 0 deletions .changeset/wild-trains-pay.md
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Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
---
'myst-to-jats': patch
---

Improve MathML tagging, removing unnecessay mml:semantics and mml:mrow if there is only a single element.

Clean up latex in the CDATA output.
46 changes: 35 additions & 11 deletions packages/myst-to-jats/src/index.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -121,6 +121,15 @@ function alternativesFromMinifiedOutput(output: MinifiedOutput, state: IJatsSeri
state.closeNode();
}

function addMmlAndRemoveAnnotation(el?: Element) {
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Unchanged, just moved 👍

if (el?.name) el.name = `mml:${el.name}`;
if (!el?.elements) return;
el.elements = el.elements.filter((child: Element) => child.name !== 'annotation');
el.elements.forEach((child: Element) => {
addMmlAndRemoveAnnotation(child);
});
}

function mathToMml(math?: string, inline?: boolean) {
const katexXml = katex.renderToString(math, { output: 'mathml', throwOnError: false });
const katexJs = xml2js(katexXml, { compact: false }) as Element;
Expand All @@ -129,18 +138,29 @@ function mathToMml(math?: string, inline?: boolean) {
if (!mathElement) return;
if (inline) mathElement.attributes = { ...mathElement.attributes, display: 'inline' };
delete mathElement.attributes?.xmlns;
function addMmlAndRemoveAnnotation(el?: Element) {
if (el?.name) el.name = `mml:${el.name}`;
if (!el?.elements) return;
el.elements = el.elements.filter((child: Element) => child.name !== 'annotation');
el.elements.forEach((child: Element) => {
addMmlAndRemoveAnnotation(child);
});
}
addMmlAndRemoveAnnotation(mathElement);
// Remove the wrapping `<mml:semantics><mml:mrow>` if it is the only element
if (mathElement?.elements?.length === 1 && mathElement.elements[0].name === 'mml:semantics') {
mathElement.elements = mathElement.elements[0].elements;
}
if (mathElement?.elements?.length === 1 && mathElement.elements[0].name === 'mml:mrow') {
mathElement.elements = mathElement.elements[0].elements;
}
return mathElement;
}

/**
* Remove comments and consolidate to one line
*/
function cleanLatex(value?: string): string | undefined {
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if (!value) return;
return value
.split('\n')
.map((s) => s.replace(/%(.*)/, '').trim())
.join(' ')
.trim();
}

const handlers: Record<string, Handler> = {
text(node, state) {
state.text(node.value);
Expand Down Expand Up @@ -203,11 +223,15 @@ const handlers: Record<string, Handler> = {
);
},
inlineMath(node, state) {
state.openNode('inline-formula');
const inlineFormulaAttrs: Attributes = {};
if (node.identifier) {
inlineFormulaAttrs.id = node.identifier;
}
state.openNode('inline-formula', inlineFormulaAttrs);
state.openNode('alternatives');
state.pushNode(mathToMml(node.value, true));
state.openNode('tex-math');
state.addLeaf('cdata', { cdata: node.value });
state.addLeaf('cdata', { cdata: cleanLatex(node.value) });
state.closeNode();
state.closeNode();
state.closeNode();
Expand All @@ -222,7 +246,7 @@ const handlers: Record<string, Handler> = {
state.openNode('alternatives');
state.pushNode(mathToMml(node.value));
state.openNode('tex-math');
state.addLeaf('cdata', { cdata: node.value });
state.addLeaf('cdata', { cdata: cleanLatex(node.value) });
state.closeNode();
state.closeNode();
state.closeNode();
Expand Down
22 changes: 18 additions & 4 deletions packages/myst-to-jats/tests/basic.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -189,7 +189,7 @@ cases:
value: Ax=b
- type: text
value: .
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>
jats: <p>This math is a role, <inline-formula><alternatives><mml:math display="inline"><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: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:mi>A</mml:mi><mml:mi>x</mml:mi><mml:mo>=</mml:mo><mml:mi>b</mml:mi></mml:math><tex-math><![CDATA[Ax=b]]></tex-math></alternatives></inline-formula>.</p>
- title: Display Math (label)
tree:
type: root
Expand All @@ -198,14 +198,14 @@ cases:
identifier: my-equation
enumerator: 1
value: w_{t+1} = (1 + r_{t+1}) s(w_t) + y_{t+1}
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>
jats: <disp-formula id="my-equation"><label>(1)</label><alternatives><mml:math><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:math><tex-math><![CDATA[w_{t+1} = (1 + r_{t+1}) s(w_t) + y_{t+1}]]></tex-math></alternatives></disp-formula>
- title: Display Math (no label)
tree:
type: root
children:
- type: math
value: w_{t+1} = (1 + r_{t+1}) s(w_t) + y_{t+1}
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>
jats: <disp-formula><alternatives><mml:math><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:math><tex-math><![CDATA[w_{t+1} = (1 + r_{t+1}) s(w_t) + y_{t+1}]]></tex-math></alternatives></disp-formula>
- title: Display Math (not numbered)
tree:
type: root
Expand All @@ -215,7 +215,21 @@ cases:
enumerated: false
enumerator: 1
value: w_{t+1} = (1 + r_{t+1}) s(w_t) + y_{t+1}
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>
jats: <disp-formula id="my-equation"><alternatives><mml:math><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:math><tex-math><![CDATA[w_{t+1} = (1 + r_{t+1}) s(w_t) + y_{t+1}]]></tex-math></alternatives></disp-formula>
- title: Display Math strips latex comments and is on a single line
tree:
type: root
children:
- type: math
identifier: my-equation
enumerated: false
enumerator: 1
value: |
A
x
= % some saucy comment
b
jats: <disp-formula id="my-equation"><alternatives><mml:math><mml:mi>A</mml:mi><mml:mi>x</mml:mi><mml:mo>=</mml:mo><mml:mi>b</mml:mi></mml:math><tex-math><![CDATA[A x = b]]></tex-math></alternatives></disp-formula>
- title: Lists
tree:
type: root
Expand Down
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