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🧹 Serialize JATS in a standardized way #666

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merged 1 commit into from
Oct 13, 2023
Merged

🧹 Serialize JATS in a standardized way #666

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77 changes: 47 additions & 30 deletions package-lock.json
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4 changes: 2 additions & 2 deletions packages/jats-to-myst/package.json
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Expand Up @@ -36,8 +36,8 @@
},
"dependencies": {
"doi-utils": "^2.0.0",
"jats-tags": "^1.0.0",
"jats-xml": "^1.0.6",
"jats-tags": "^1.0.8",
"jats-xml": "^1.0.8",
"myst-common": "^1.1.7",
"myst-frontmatter": "^1.1.7",
"myst-spec": "^0.0.4",
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2 changes: 1 addition & 1 deletion packages/myst-cli/package.json
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Expand Up @@ -64,7 +64,7 @@
"jtex": "^1.0.8",
"latest-version": "^7.0.0",
"mdast": "^3.0.0",
"meca": "^1.0.6",
"meca": "^1.0.8",
"mime-types": "^2.1.35",
"myst-cli-utils": "^2.0.4",
"myst-common": "^1.1.8",
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2 changes: 1 addition & 1 deletion packages/myst-cli/src/build/jats/single.ts
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Expand Up @@ -53,7 +53,7 @@ export async function runJatsExport(
const jats = writeJats(vfile, processedArticle as any, {
subArticles: processedSubArticles as any,
writeFullArticle: true,
spaces: 0,
format: 'pretty',
abstractParts: [
{ part: 'abstract' },
{
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5 changes: 3 additions & 2 deletions packages/myst-to-jats/package.json
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Expand Up @@ -38,7 +38,8 @@
"citation-js-utils": "^1.0.2",
"credit-roles": "^2.1.0",
"doi-utils": "^2.0.1",
"jats-tags": "^1.0.1",
"jats-tags": "^1.0.8",
"jats-utils": "^1.0.8",
"katex": "^0.15.2",
"myst-common": "^1.1.7",
"myst-frontmatter": "^1.1.7",
Expand All @@ -55,7 +56,7 @@
"@types/js-yaml": "^4.0.5",
"@types/katex": "^0.14.0",
"@types/mdast": "^3.0.10",
"jats-xml": "^1.0.6",
"jats-xml": "^1.0.7",
"js-yaml": "^4.1.0",
"myst-cli-utils": "^2.0.4"
}
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18 changes: 4 additions & 14 deletions packages/myst-to-jats/src/index.ts
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Expand Up @@ -2,7 +2,7 @@ import type { Root, CrossReference, TableCell as SpecTableCell } from 'myst-spec
import type { Cite, Code, FootnoteDefinition, FootnoteReference } from 'myst-spec-ext';
import type { Plugin } from 'unified';
import type { VFile } from 'vfile';
import { js2xml, xml2js } from 'xml-js';
import { xml2js } from 'xml-js';
import katex from 'katex';
import type { CitationRenderer } from 'citation-js-utils';
import type { MessageInfo, GenericNode, GenericParent } from 'myst-common';
Expand All @@ -11,6 +11,7 @@ import type { PageFrontmatter, Contributor } from 'myst-frontmatter';
import { SourceFileKind } from 'myst-spec-ext';
import type { Affiliation } from 'jats-tags';
import { Tags, RefType } from 'jats-tags';
import { serializeJatsXml } from 'jats-utils';
import type { MinifiedOutput } from 'nbtx';
import { getBack } from './backmatter.js';
import { getArticleMeta, getFront } from './frontmatter.js';
Expand Down Expand Up @@ -870,19 +871,8 @@ export function writeJats(file: VFile, content: ArticleContent, opts?: DocumentO
declaration: { attributes: { version: '1.0', encoding: 'UTF-8' } },
}
: doc.body();
const jats = js2xml(element, {
compact: false,
// No way to write XML with new lines, but no indentation with js2xml.
// If you use 0 or '', you get a single line.
spaces: opts?.spaces === 'flat' ? 0 : opts?.spaces || 1,
attributeValueFn: escapeForXML,
});
if (!opts?.spaces) {
// either `0` or `''`
file.result = jats.replace(/\n(\s*)</g, '\n<');
} else {
file.result = jats;
}
const xml = serializeJatsXml(element, opts);
file.result = xml;
return file;
}

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16 changes: 6 additions & 10 deletions packages/myst-to-jats/src/types.ts
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Expand Up @@ -3,6 +3,7 @@ import type { PageFrontmatter } from 'myst-frontmatter';
import type { Root } from 'myst-spec';
import type { SourceFileKind } from 'myst-spec-ext';
import type { CitationRenderer } from 'citation-js-utils';
import type { SerializationOptions } from 'jats-utils';

export type Attributes = Record<string, string | undefined>;

Expand Down Expand Up @@ -31,16 +32,11 @@ export type Options = {
backSections?: JatsPart[];
};

export type DocumentOptions = Options & {
subArticles?: ArticleContent[];
/**
* When 'flat', the xml will be on a single line (with exception of CDATA),
* When `0`, the XML will be on different lines with 0 spaces.
* When any other value (e.g. `2` or `\t`) the XML will be indented at the start of the line by that amount.
*/
spaces?: number | 'flat' | '\t';
writeFullArticle?: boolean;
};
export type DocumentOptions = Options &
SerializationOptions & {
subArticles?: ArticleContent[];
writeFullArticle?: boolean;
};

export type StateData = {
isInContainer?: boolean;
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14 changes: 7 additions & 7 deletions packages/myst-to-jats/tests/basic.spec.ts
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Expand Up @@ -81,7 +81,7 @@ describe('Basic JATS body', () => {
undefined,
undefined,
undefined,
{ spaces: 'flat' },
{ format: 'flat' },
);
pipe.runSync(tree as any);
const vfile = pipe.stringify(tree as any);
Expand Down Expand Up @@ -110,7 +110,7 @@ describe('JATS full article', () => {
undefined,
{
writeFullArticle: true,
spaces: 2,
format: 2,
abstractParts: [
{ part: 'abstract' },
{
Expand All @@ -126,7 +126,7 @@ describe('JATS full article', () => {
);
pipe.runSync(tree as any);
const vfile = pipe.stringify(tree as any);
expect(vfile.result).toEqual(jats);
expect((vfile.result as string).trim()).toEqual(jats);
if (TEST_DTD) expect(await writeValidateDelete(vfile.result as string)).toBeTruthy();
},
);
Expand All @@ -151,10 +151,10 @@ describe('JATS multi-article', () => {
{
subArticles: subArticles as any,
writeFullArticle: true,
spaces: 2,
format: 2,
},
);
expect(vfile.result).toEqual(jats);
expect((vfile.result as string)?.trim()).toEqual(jats);
if (TEST_DTD) expect(await writeValidateDelete(vfile.result as string)).toBeTruthy();
},
);
Expand All @@ -173,12 +173,12 @@ describe('JATS full notebook', () => {
undefined,
{
writeFullArticle: true,
spaces: 2,
format: 2,
},
);
pipe.runSync(tree as any);
const vfile = pipe.stringify(tree as any);
expect(vfile.result).toEqual(jats);
expect((vfile.result as string).trim()).toEqual(jats);
if (TEST_DTD) expect(await writeValidateDelete(vfile.result as string)).toBeTruthy();
},
);
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2 changes: 1 addition & 1 deletion packages/mystmd/tests/outputs/basic-md-and-config.xml
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Expand Up @@ -11,4 +11,4 @@
<body>
<p>Hello world</p>
</body>
</article>
</article>
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