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LEAN-6048: Return a Document from serializeToJATS; fix bibliography ref parsing under linkedom #361

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LEAN-6048: Return a Document from serializeToJATS; fix bibliography ref parsing under linkedom #361

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2ef424e
Return a Document from serializeToJATS; use <wrapper> for bibliograph…
mnatsheh Sep 18, 2026
6e3232e
Remove ManuscriptActions enum
mnatsheh Sep 21, 2026
0c0a078
Remove Project interface, replace UserProfile with User
mnatsheh Sep 21, 2026
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6 changes: 3 additions & 3 deletions package.json
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Original file line number Diff line number Diff line change
Expand Up @@ -39,8 +39,7 @@
"prosemirror-tables": "1.7.1",
"prosemirror-utils": "1.2.2",
"semver": "7.7.4",
"uuid": "14.0.0",
"w3c-xmlserializer": "5.0.0"
"uuid": "14.0.0"
},
"devDependencies": {
"@eslint/eslintrc": "3.3.5",
Expand Down Expand Up @@ -80,7 +79,8 @@
"prosemirror-state": "1.4.3",
"prosemirror-view": "1.39.2",
"rimraf": "6.1.3",
"typescript": "6.0.3"
"typescript": "6.0.3",
"w3c-xmlserializer": "5.0.0"
},
"engines": {
"node": ">=22"
Expand Down
24 changes: 21 additions & 3 deletions pnpm-lock.yaml
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44 changes: 25 additions & 19 deletions src/jats/__tests__/jats-exporter.test.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@
*/

import { Element as XMLElement, parseXml } from 'libxmljs2'
import serializeToXML from 'w3c-xmlserializer'

import { JATSExporter } from '../exporter/jats-exporter'
import { Version } from '../exporter/jats-versions'
Expand All @@ -40,11 +41,11 @@ describe('JATS exporter', () => {
const transformer = new JATSExporter()
const input = await readAndParseFixture('jats-example-full.xml')
const node = parseJATSArticle(input, sectionCategories)
const result = await transformer.serializeToJATS(node, {
const document = await transformer.serializeToJATS(node, {
csl: DEFAULT_CSL_OPTIONS,
})

expect(result).toMatchSnapshot('jats-export')
expect(serializeToXML(document)).toMatchSnapshot('jats-export')
})

test('export with & and < in bibliography metadata', async () => {
Expand All @@ -61,23 +62,25 @@ describe('JATS exporter', () => {

biblio!.attrs.title += ' & Sons 55 < 135'

const result = await transformer.serializeToJATS(node, {
const document = await transformer.serializeToJATS(node, {
csl: DEFAULT_CSL_OPTIONS,
})

expect(result).toMatchSnapshot('jats-export-with-xml-unsafe-in-biblios')
expect(serializeToXML(document)).toMatchSnapshot(
'jats-export-with-xml-unsafe-in-biblios'
)
})

test('export v1.1', async () => {
const transformer = new JATSExporter()
const input = await readAndParseFixture('jats-example-full.xml')
const node = parseJATSArticle(input, sectionCategories)
const result = await transformer.serializeToJATS(node, {
const document = await transformer.serializeToJATS(node, {
csl: DEFAULT_CSL_OPTIONS,
version: '1.1',
})

expect(result).toMatchSnapshot('jats-export-1.1')
expect(serializeToXML(document)).toMatchSnapshot('jats-export-1.1')
})

test('export unknown version', async () => {
Expand All @@ -96,9 +99,10 @@ describe('JATS exporter', () => {
const transformer = new JATSExporter()
const input = await readAndParseFixture('jats-tables-example.xml')
const node = parseJATSArticle(input, sectionCategories)
const xml = await transformer.serializeToJATS(node, {
const document = await transformer.serializeToJATS(node, {
csl: DEFAULT_CSL_OPTIONS,
})
const xml = serializeToXML(document)

const resultDoc = parseXMLWithDTD(xml)
const tableWrapFoot = resultDoc.get('//table-wrap/table-wrap-foot')
Expand All @@ -111,11 +115,11 @@ describe('JATS exporter', () => {
const transformer = new JATSExporter()
const input = await readAndParseFixture('jats-import.xml')
const node = parseJATSArticle(input, sectionCategories)
const xml = await transformer.serializeToJATS(node, {
const document = await transformer.serializeToJATS(node, {
csl: DEFAULT_CSL_OPTIONS,
})

const { errors } = parseXMLWithDTD(xml)
const { errors } = parseXMLWithDTD(serializeToXML(document))

expect(errors).toHaveLength(0)
})
Expand All @@ -124,10 +128,10 @@ describe('JATS exporter', () => {
const transformer = new JATSExporter()
const input = await readAndParseFixture('jats-document.xml')
const node = parseJATSArticle(input, sectionCategories)
const xml = await transformer.serializeToJATS(node, {
const document = await transformer.serializeToJATS(node, {
csl: DEFAULT_CSL_OPTIONS,
})
const { errors } = parseXMLWithDTD(xml)
const { errors } = parseXMLWithDTD(serializeToXML(document))

expect(errors).toHaveLength(0)
})
Expand All @@ -136,11 +140,11 @@ describe('JATS exporter', () => {
const transformer = new JATSExporter()
const input = await readAndParseFixture('jats-import.xml')
const node = parseJATSArticle(input, sectionCategories)
const xml = await transformer.serializeToJATS(node, {
const document = await transformer.serializeToJATS(node, {
csl: DEFAULT_CSL_OPTIONS,
})

const output = parseXMLWithDTD(xml)
const output = parseXMLWithDTD(serializeToXML(document))
const link = output.get<XMLElement>('//ext-link[@ext-link-type="uri"]')
expect(link).not.toBeNull()
expect(link!.text()).toBe('https//orcid.org/0000-0003-2217-5904')
Expand All @@ -159,11 +163,11 @@ describe('JATS exporter', () => {
const transformer = new JATSExporter()
const input = await readAndParseFixture('jats-example-doc.xml')
const node = parseJATSArticle(input, sectionCategories)
const xml = await transformer.serializeToJATS(node, {
const document = await transformer.serializeToJATS(node, {
csl: DEFAULT_CSL_OPTIONS,
})

const { errors } = parseXMLWithDTD(xml)
const { errors } = parseXMLWithDTD(serializeToXML(document))

expect(errors).toHaveLength(0)
})
Expand All @@ -172,10 +176,10 @@ describe('JATS exporter', () => {
const transformer = new JATSExporter()
const input = await readAndParseFixture('jats-import.xml')
const node = parseJATSArticle(input, sectionCategories)
const xml = await transformer.serializeToJATS(node, {
const document = await transformer.serializeToJATS(node, {
csl: DEFAULT_CSL_OPTIONS,
})
const resultDoc = parseXMLWithDTD(xml)
const resultDoc = parseXMLWithDTD(serializeToXML(document))
const supplementaryMaterial = resultDoc.get('//supplementary-material')
if (!supplementaryMaterial) {
throw new Error('No supplementary material found')
Expand Down Expand Up @@ -215,9 +219,10 @@ describe('JATS exporter', () => {
n.attrs.rids.forEach((rid: string) => citedIDs.add(rid))
}
})
const xml = await new JATSExporter().serializeToJATS(node, {
const document = await new JATSExporter().serializeToJATS(node, {
csl: DEFAULT_CSL_OPTIONS,
})
const xml = serializeToXML(document)
const refCount = parseXMLWithDTD(xml).find('//ref-list/ref').length
expect(refCount).toBe(bibliographyItemIDs.size)
const { errors } = parseXMLWithDTD(xml)
Expand All @@ -228,9 +233,10 @@ describe('JATS exporter', () => {
const transformer = new JATSExporter()
const input = await readAndParseFixture('jats-fn-group.xml')
const node = parseJATSArticle(input, sectionCategories)
const xml = await transformer.serializeToJATS(node, {
const document = await transformer.serializeToJATS(node, {
csl: DEFAULT_CSL_OPTIONS,
})
const xml = serializeToXML(document)
const footnoteCategories = [
'con',
'deceased',
Expand Down
4 changes: 3 additions & 1 deletion src/jats/__tests__/jats-roundtrip.test.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@
*/

import { parseXml } from 'libxmljs2'
import serializeToXML from 'w3c-xmlserializer'

import { JATSExporter } from '../exporter/jats-exporter'
import { parseJATSArticle } from '../importer/parse-jats-article'
Expand All @@ -36,9 +37,10 @@ const roundtrip = async (filename: string) => {
const node = parseJATSArticle(doc, sectionCategories)

const exporter = new JATSExporter()
return await exporter.serializeToJATS(node, {
const document = await exporter.serializeToJATS(node, {
csl: DEFAULT_CSL_OPTIONS,
})
return serializeToXML(document)
}

describe('JATS roundtrip', () => {
Expand Down
9 changes: 4 additions & 5 deletions src/jats/exporter/jats-exporter.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,6 @@
import * as Citeproc from 'citeproc'
import { DOMOutputSpec, DOMSerializer, type NodeType } from 'prosemirror-model'
import { findChildrenByAttr, findChildrenByType } from 'prosemirror-utils'
import serializeToXML from 'w3c-xmlserializer'

import { buildCiteprocCitation } from '../../lib/citeproc'
import { CreditRoleUrls } from '../../lib/credit-roles'
Expand Down Expand Up @@ -166,7 +165,7 @@ export class JATSExporter {
public serializeToJATS = async (
manuscriptNode: ActualManuscriptNode,
options: ExportOptions
): Promise<string> => {
): Promise<Document> => {
Comment on lines 165 to +168
this.manuscriptNode = manuscriptNode
this.populateNodesMap()
this.initCiteprocEngine(options)
Expand Down Expand Up @@ -223,7 +222,7 @@ export class JATSExporter {
$article.appendChild($floatsGroup)
}
await this.rewriteIDs()
return serializeToXML(this.document)
return this.document
}

private appendChildNodeOfType = (
Expand Down Expand Up @@ -616,9 +615,9 @@ export class JATSExporter {
const [, bibliography] = this.engine.makeBibliography()
const parser = new DOMParser()
bibliography.forEach((item) => {
const fragment = `<template xmlns:xlink="${XLINK_NAMESPACE}">${sanitizeXmlString(
const fragment = `<wrapper xmlns:xlink="${XLINK_NAMESPACE}">${sanitizeXmlString(
item
)}</template>`
)}</wrapper>`
const $ref = parser
.parseFromString(fragment, 'text/xml')
.querySelector('ref')
Expand Down
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