@manuscripts/transform 4.3.53 → 4.4.0

package/src/jats/__tests__/citeproc.test.ts

@@ -0,0 +1,195 @@
+/*!
+ * © 2025 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 Citeproc from 'citeproc'
+
+import { buildCiteprocCitation } from '../../lib/citeproc'
+import { BibliographyItemAttrs } from '../../schema'
+import { initJats, jatsVariableWrapper } from '../exporter/citeproc'
+import { ama, chicago, DEFAULT_CSL_OPTIONS } from './citations'
+
+const bib1: BibliographyItemAttrs = {
+  id: 'bib1',
+  type: 'article-journal',
+  author: [
+    { given: 'John', family: 'Doe' },
+    { given: 'Jane', family: 'Smith' },
+  ],
+  DOI: '10.1000/xyz123',
+  issued: { 'date-parts': [[2021]] },
+  'container-title': 'AI Research Journal',
+  volume: '18',
+  issue: '2',
+  supplement: 'Suppl. 1',
+  page: '45-60',
+  title: 'Advancements in Artificial Intelligence',
+  locator: 'e012345',
+  URL: 'https://doi.org/10.1000/xyz123',
+}
+
+const bib2: BibliographyItemAttrs = {
+  id: 'bib2',
+  type: 'book',
+  author: [
+    { given: 'Michael', family: 'Brown' },
+    { given: 'Anna', family: 'Green' },
+  ],
+  issued: { 'date-parts': [[2020]] },
+  'container-title': 'Introduction to Data Science',
+  volume: '1',
+  'collection-title': 'Data Science Series',
+  edition: '2nd',
+  publisher: 'Springer',
+  'publisher-place': 'New York, USA',
+  editor: [
+    { given: 'David', family: 'Williams' },
+    { given: 'Sophia', family: 'Taylor' },
+  ],
+  'number-of-pages': '350',
+  URL: 'https://doi.org/10.1000/xyz123',
+}
+
+const bib3: BibliographyItemAttrs = {
+  id: 'bib3',
+  type: 'chapter',
+  author: [{ given: 'Susan', family: 'Miller' }],
+  issued: { 'date-parts': [[2022]] },
+  'container-title': 'Handbook of AI',
+  page: '105-120',
+  title: 'Machine Learning Applications',
+  publisher: 'Oxford University Press',
+}
+
+const bib4: BibliographyItemAttrs = {
+  id: 'bib4',
+  type: 'confproc',
+  author: [{ given: 'Emily', family: 'Johnson' }],
+  issued: { 'date-parts': [[2019]] },
+  'container-title':
+    'Proceedings of the International Conference on Machine Learning',
+  page: '223-230',
+  title: 'Deep Learning in Image Processing',
+  publisher: 'IEEE',
+  'publisher-place': 'New York, USA',
+  event: 'ICML 2019',
+  'event-place': 'San Francisco, USA',
+  'event-date': { 'date-parts': [[2019, 6, 20]] },
+  URL: 'https://icml2019.org/papers/223',
+}
+
+const bib5: BibliographyItemAttrs = {
+  id: 'bib5',
+  type: 'thesis',
+  author: [{ given: 'Daniel', family: 'Garcia' }],
+  DOI: '10.1234/thesis2021',
+  issued: { 'date-parts': [[2021]] },
+  title: 'Neural Networks for Natural Language Processing',
+  institution: 'University of California, Berkeley',
+  'number-of-pages': '350',
+  URL: 'https://escholarship.org/uc/item/xyz123',
+  comment:
+    'Located at: Modern Manuscripts Collection,\n' +
+    '                        History of Medicine Division, National Library of\n' +
+    '                        Medicine, Bethesda, MD; MS F 179',
+}
+
+const bib6: BibliographyItemAttrs = {
+  id: 'bib6',
+  type: 'webpage',
+  author: [{ given: 'Sarah', family: 'Jones' }],
+  issued: { 'date-parts': [[2023]] },
+  'container-title': 'Data Science Blog',
+  title: 'Big Data Trends in 2023',
+  accessed: { 'date-parts': [[2024, 2, 15]] },
+  URL: 'https://www.datascienceblog.com/big-data-2023',
+}
+
+const bib7: BibliographyItemAttrs = {
+  id: 'bib7',
+  type: 'other',
+  author: [{ given: 'Lisa', family: 'Adams' }],
+  DOI: undefined,
+  issued: { 'date-parts': [[2022]] },
+  'container-title': 'Internal Research Report',
+  title: 'Private Research Report on AI Ethics',
+  publisher: 'AI Ethics Initiative',
+}
+
+const buildCitation = (id: string) =>
+  buildCiteprocCitation({
+    id: `${id}-citation`,
+    rids: [id],
+  })
+
+describe('Export formatted references', () => {
+  initJats()
+
+  const data = [
+    ['AMA', ama],
+    ['Chicago Author Date', chicago],
+  ]
+
+  test.each(data)('Export references in %s style', async (name, style) => {
+    const bibitems: Map<string, BibliographyItemAttrs> = new Map()
+    bibitems.set(bib1.id, bib1)
+    bibitems.set(bib2.id, bib2)
+    bibitems.set(bib3.id, bib3)
+    bibitems.set(bib4.id, bib4)
+    bibitems.set(bib5.id, bib5)
+    bibitems.set(bib6.id, bib6)
+    bibitems.set(bib7.id, bib7)
+
+    const citations: Citeproc.Citation[] = [
+      buildCitation(bib1.id),
+      buildCitation(bib2.id),
+      buildCitation(bib3.id),
+      buildCitation(bib4.id),
+      buildCitation(bib5.id),
+      buildCitation(bib6.id),
+      buildCitation(bib7.id),
+    ]
+
+    initJats()
+    const engine = new Citeproc.Engine(
+      {
+        retrieveLocale: () => DEFAULT_CSL_OPTIONS.locale,
+        retrieveItem: (id: string) => {
+          const item = bibitems.get(id)
+          if (!item) {
+            throw Error(`Missing bibliography item with id ${id}`)
+          }
+          return item as CSL.Data
+        },
+        variableWrapper: jatsVariableWrapper,
+      },
+      style
+    )
+    engine.setOutputFormat('jats')
+
+    const citationTexts = engine.rebuildProcessorState(citations)
+    const [meta, bibliography] = engine.makeBibliography()
+
+    //eslint-disable-next-line @typescript-eslint/no-unused-vars
+    for (const [id, _, text] of citationTexts) {
+      expect(text).toMatchSnapshot(id)
+    }
+
+    for (let i = 0; i < bibliography.length; i++) {
+      const id = meta.entry_ids[i][0]
+      const fragment = bibliography[i]
+      expect(fragment).toMatchSnapshot(id)
+    }
+  })
+})

package/src/jats/__tests__/create-article-node.test.ts

@@ -0,0 +1,29 @@
+/*!
+ * © 2024 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 { createArticleNode } from '../importer/create-article-node'
+import { changeIDs } from './utils'
+
+describe('Create empty document', () => {
+  it('should create an empty document', () => {
+    const doc = createArticleNode({
+      id: 'manuscript:123',
+      articleType: 'research-article',
+    })
+    changeIDs(doc)
+    expect(doc).toMatchSnapshot()
+  })
+})

package/src/jats/__tests__/data/section-categories.ts

@@ -0,0 +1,212 @@
+/*!
+ * © 2024 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 { SectionCategory } from '../../../schema'
+
+export const sectionCategories: SectionCategory[] = [
+  {
+    id: 'abstract',
+    titles: ['Abstract'],
+    synonyms: [''],
+    group: 'abstracts',
+    isUnique: true,
+  },
+  {
+    id: 'abstract-graphical',
+    titles: ['Graphical Abstract'],
+    synonyms: [''],
+    group: 'abstracts-graphic',
+    isUnique: true,
+  },
+  {
+    id: 'abstract-key-image',
+    titles: ['Key Image'],
+    synonyms: [''],
+    group: 'abstracts-graphic',
+    isUnique: true,
+  },
+  {
+    id: 'abstract-short',
+    titles: ['Short'],
+    synonyms: [''],
+    group: 'abstracts',
+    isUnique: true,
+  },
+  {
+    id: 'abstract-teaser',
+    titles: ['Abstract Teaser'],
+    synonyms: [''],
+    isUnique: true,
+    group: 'abstracts',
+  },
+  {
+    id: 'abstract-toc',
+    titles: ['Table of contents'],
+    synonyms: [''],
+    group: 'abstracts',
+    isUnique: true,
+  },
+  {
+    id: 'acknowledgements',
+    synonyms: ['acknowledgements', 'acknowledgments'],
+    titles: ['Acknowledgements'],
+    group: 'backmatter',
+    isUnique: true,
+  },
+  {
+    id: 'appendices',
+    titles: ['Appendices'],
+    synonyms: ['appendices'],
+    isUnique: false,
+  },
+  {
+    id: 'availability',
+    titles: ['Availability'],
+    synonyms: ['availability', 'data-availability', 'data availability'],
+    group: 'backmatter',
+    isUnique: true,
+  },
+  {
+    id: 'coi-statement',
+    synonyms: [
+      'coi-statement',
+      'competing-interests',
+      'conflict',
+      'conflict of interest',
+      'competing interests',
+    ],
+    label: 'Conflict of Interest',
+    titles: [
+      'Conflict of Interest Statement',
+      'COI Statement',
+      'Competing Interests',
+    ],
+    group: 'backmatter',
+    isUnique: true,
+  },
+  {
+    id: 'con',
+    synonyms: ['con'],
+    titles: ['Contributed-by information'],
+    group: 'backmatter',
+    isUnique: true,
+  },
+  {
+    id: 'conclusions',
+    synonyms: ['conclusions'],
+    titles: ['Conclusions'],
+    group: 'body',
+    isUnique: false,
+  },
+  {
+    id: 'deceased',
+    titles: ['Deceased'],
+    synonyms: ['deceased'],
+    isUnique: false,
+  },
+  {
+    id: 'discussion',
+    synonyms: ['discussion'],
+    titles: ['Discussion'],
+    group: 'body',
+    isUnique: false,
+  },
+  {
+    id: 'equal',
+    titles: ['Equal'],
+    synonyms: ['equal'],
+    isUnique: false,
+  },
+  {
+    id: 'ethics-statement',
+    synonyms: ['ethics-statement'],
+    titles: ['Ethics Statement'],
+    group: 'backmatter',
+    isUnique: true,
+  },
+  {
+    id: 'financial-disclosure',
+    synonyms: ['financial-disclosure', 'funding information'],
+    titles: ['Financial Disclosure'],
+    group: 'backmatter',
+    isUnique: true,
+  },
+  {
+    id: 'intro',
+    synonyms: ['intro', 'introduction'],
+    titles: ['Introduction'],
+    group: 'body',
+    isUnique: false,
+  },
+  {
+    id: 'methods',
+    synonyms: [
+      'materials',
+      'methods',
+      'materials and methods',
+      'materials & methods',
+    ],
+    titles: ['Materials & Methods'],
+    group: 'body',
+    isUnique: false,
+  },
+  {
+    id: 'present-address',
+    titles: ['Present Address'],
+    synonyms: ['present-address'],
+    isUnique: false,
+  },
+  {
+    id: 'presented-at',
+    titles: ['Presented at'],
+    synonyms: ['presented-at'],
+    isUnique: false,
+  },
+  {
+    id: 'previously-at',
+    titles: ['Previously at'],
+    synonyms: ['previously-at'],
+    isUnique: false,
+  },
+  {
+    id: 'results',
+    synonyms: ['results'],
+    titles: ['Results'],
+    group: 'body',
+    isUnique: false,
+  },
+  {
+    id: 'review',
+    titles: ['Review'],
+    synonyms: [],
+    group: 'body',
+    isUnique: false,
+  },
+  {
+    id: 'supplementary-material',
+    synonyms: ['supplementary-material'],
+    titles: ['Supplementary Material'],
+    group: 'backmatter',
+    isUnique: true,
+  },
+  {
+    id: 'supported-by',
+    synonyms: ['supported-by'],
+    titles: ['Supported By'],
+    group: 'backmatter',
+    isUnique: true,
+  },
+]

package/src/jats/__tests__/files.ts

@@ -0,0 +1,24 @@
+/*!
+ * © 2020 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 fs from 'fs'
+import { join } from 'path'
+
+export const readFixture = (filename: string) =>
+  fs.promises.readFile(join(__dirname, '/__fixtures__/', filename), 'utf-8')
+
+export const readAndParseFixture = async (filename: string) =>
+  new DOMParser().parseFromString(await readFixture(filename), 'text/xml')

package/src/jats/__tests__/jats-exporter.test.ts

@@ -0,0 +1,223 @@
+/*!
+ * © 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 { Element as XMLElement, parseXml } from 'libxmljs2'
+
+import { JATSExporter } from '../exporter/jats-exporter'
+import { Version } from '../exporter/jats-versions'
+import { parseJATSArticle } from '../importer/parse-jats-article'
+import { DEFAULT_CSL_OPTIONS } from './citations'
+import { sectionCategories } from './data/section-categories'
+import { readAndParseFixture } from './files'
+import { BibliographyItemNode, isBibliographyItemNode } from '../../schema'
+
+const parseXMLWithDTD = (data: string) =>
+  parseXml(data, {
+    dtdload: true,
+    dtdvalid: true,
+    nonet: true,
+  })
+
+describe('JATS exporter', () => {
+  test('export latest version', async () => {
+    const transformer = new JATSExporter()
+    const input = await readAndParseFixture('jats-example-full.xml')
+    const node = parseJATSArticle(input, sectionCategories)
+    const result = await transformer.serializeToJATS(node, {
+      csl: DEFAULT_CSL_OPTIONS,
+    })
+
+    expect(result).toMatchSnapshot('jats-export')
+  })
+
+  test('export with & and < in bibliography metadata', async () => {
+    const transformer = new JATSExporter()
+    const input = await readAndParseFixture('jats-example-full.xml')
+    const node = parseJATSArticle(input, sectionCategories)
+
+    let biblio: BibliographyItemNode | null = null
+    node.descendants((n) => {
+      if (isBibliographyItemNode(n)) {
+        biblio = n
+      }
+    })
+
+    biblio!.attrs.title += ' & Sons 55 < 135'
+
+    const result = await transformer.serializeToJATS(node, {
+      csl: DEFAULT_CSL_OPTIONS,
+    })
+
+    expect(result).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, {
+      csl: DEFAULT_CSL_OPTIONS,
+      version: '1.1',
+    })
+
+    expect(result).toMatchSnapshot('jats-export-1.1')
+  })
+
+  test('export unknown version', async () => {
+    const transformer = new JATSExporter()
+    const input = await readAndParseFixture('jats-example-full.xml')
+    const node = parseJATSArticle(input, sectionCategories)
+
+    await expect(async () => {
+      await transformer.serializeToJATS(node, {
+        csl: DEFAULT_CSL_OPTIONS,
+        version: '1.0' as unknown as Version,
+      })
+    }).rejects.toThrow(Error)
+  })
+  test('export table-wrap-foot', async () => {
+    const transformer = new JATSExporter()
+    const input = await readAndParseFixture('jats-tables-example.xml')
+    const node = parseJATSArticle(input, sectionCategories)
+    const xml = await transformer.serializeToJATS(node, {
+      csl: DEFAULT_CSL_OPTIONS,
+    })
+
+    const resultDoc = parseXMLWithDTD(xml)
+    const tableWrapFoot = resultDoc.get('//table-wrap/table-wrap-foot')
+    const paragraph = resultDoc.get('//table-wrap/table-wrap-foot/p')
+    expect(paragraph).not.toBeUndefined()
+    expect(tableWrapFoot).not.toBeUndefined()
+  })
+
+  test('DTD validation', async () => {
+    const transformer = new JATSExporter()
+    const input = await readAndParseFixture('jats-import.xml')
+    const node = parseJATSArticle(input, sectionCategories)
+    const xml = await transformer.serializeToJATS(node, {
+      csl: DEFAULT_CSL_OPTIONS,
+    })
+
+    const { errors } = parseXMLWithDTD(xml)
+
+    expect(errors).toHaveLength(0)
+  })
+
+  test('DTD validation: article with title markup and citations', async () => {
+    const transformer = new JATSExporter()
+    const input = await readAndParseFixture('jats-document.xml')
+    const node = parseJATSArticle(input, sectionCategories)
+    const xml = await transformer.serializeToJATS(node, {
+      csl: DEFAULT_CSL_OPTIONS,
+    })
+    const { errors } = parseXMLWithDTD(xml)
+
+    expect(errors).toHaveLength(0)
+  })
+
+  test('Export link', async () => {
+    const transformer = new JATSExporter()
+    const input = await readAndParseFixture('jats-import.xml')
+    const node = parseJATSArticle(input, sectionCategories)
+    const xml = await transformer.serializeToJATS(node, {
+      csl: DEFAULT_CSL_OPTIONS,
+    })
+
+    const output = parseXMLWithDTD(xml)
+    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')
+
+    const attrs: { [key: string]: string } = {}
+
+    for (const attr of link!.attrs()) {
+      attrs[attr.name()] = attr.value()
+    }
+
+    expect(attrs.href).toBe('https://orcid.org/0000-0003-2217-5904')
+    expect(attrs['ext-link-type']).toBe('uri')
+  })
+
+  test('DTD validation for MathML representation', async () => {
+    const transformer = new JATSExporter()
+    const input = await readAndParseFixture('jats-example-doc.xml')
+    const node = parseJATSArticle(input, sectionCategories)
+    const xml = await transformer.serializeToJATS(node, {
+      csl: DEFAULT_CSL_OPTIONS,
+    })
+
+    const { errors } = parseXMLWithDTD(xml)
+
+    expect(errors).toHaveLength(0)
+  })
+
+  test('export with supplement', async () => {
+    const transformer = new JATSExporter()
+    const input = await readAndParseFixture('jats-import.xml')
+    const node = parseJATSArticle(input, sectionCategories)
+    const xml = await transformer.serializeToJATS(node, {
+      csl: DEFAULT_CSL_OPTIONS,
+    })
+    const resultDoc = parseXMLWithDTD(xml)
+    const supplementaryMaterial = resultDoc.get('//supplementary-material')
+    if (!supplementaryMaterial) {
+      throw new Error('No supplementary material found')
+    }
+    //@ts-ignore
+    const textContent = supplementaryMaterial.text().trim()
+    //@ts-ignore
+    const mimeTypeAttr = supplementaryMaterial.attr('mimetype')
+    //@ts-ignore
+    const mimeSubtypeAttr = supplementaryMaterial.attr('mime-subtype')
+    //@ts-ignore
+    const hrefAttr = supplementaryMaterial.attr('href')
+
+    expect(textContent).toBe(
+      'final manuscript-hum-huili-dbh-suicide-20200707_figures (9)'
+    )
+    expect(mimeTypeAttr?.value()).toBe('application')
+    expect(mimeSubtypeAttr?.value()).toBe(
+      'vnd.openxmlformats-officedocument.wordprocessingml.document'
+    )
+    expect(hrefAttr?.value()).toBe(
+      'attachment:7d9d686b-5488-44a5-a1c5-46351e7f9312'
+    )
+  })
+
+  test('export footnotes', async () => {
+    const transformer = new JATSExporter()
+    const input = await readAndParseFixture('jats-fn-group.xml')
+    const node = parseJATSArticle(input, sectionCategories)
+    const xml = await transformer.serializeToJATS(node, {
+      csl: DEFAULT_CSL_OPTIONS,
+    })
+    const footnoteCategories = [
+      'con',
+      'deceased',
+      'equal',
+      'financial-disclosure',
+    ]
+
+    const resultDoc = parseXMLWithDTD(xml)
+
+    for (const category of footnoteCategories) {
+      const fn = resultDoc.get(
+        `/article/back/fn-group/fn[@fn-type="${category}"]`
+      )
+      expect(fn).not.toBeUndefined()
+    }
+  })
+})