@manuscripts/transform 4.5.2 → 4.5.4

package/src/jats/exporter/jats-versions.ts

@@ -14,35 +14,35 @@
  * limitations under the License.
  */
 
-interface VersionIds {
-  publicId: string
-  systemId: string
+interface VersionIDs {
+  publicID: string
+  systemID: string
 }
 
 export type Version = '1.1' | '1.2d1' | '1.2'
 
-const versions: { [key in Version]: VersionIds } = {
+const versions: { [key in Version]: VersionIDs } = {
   '1.1': {
-    publicId:
+    publicID:
       '-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD with OASIS Tables with MathML3 v1.1 20151215//EN',
-    systemId:
+    systemID:
       'http://jats.nlm.nih.gov/archiving/1.1/JATS-archive-oasis-article1-mathml3.dtd',
   },
   '1.2d1': {
-    publicId:
+    publicID:
       '-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD with OASIS Tables with MathML3 v1.2d1 20170631//EN',
-    systemId:
+    systemID:
       'http://jats.nlm.nih.gov/archiving/1.2d1/JATS-archive-oasis-article1-mathml3.dtd',
   },
   '1.2': {
-    publicId:
+    publicID:
       '-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD with OASIS Tables with MathML3 v1.2 20190208//EN',
-    systemId:
+    systemID:
       'http://jats.nlm.nih.gov/archiving/1.2/JATS-archive-oasis-article1-mathml3.dtd',
   },
 }
 
-export const selectVersionIds = (version: Version): VersionIds => {
+export const selectVersionIDs = (version: Version): VersionIDs => {
   if (!(version in versions)) {
     throw new Error(`Unknown version ${version}`)
   }

package/src/jats/importer/jats-dom-parser.ts

@@ -15,6 +15,10 @@
  */
 import { DOMParser, Fragment, ParseOptions, Schema } from 'prosemirror-model'
 
+import {
+  abstractTypeToCategory,
+  findMatchingCategory,
+} from '../../lib/section-categories'
 import {
   dateToTimestamp,
   getCreditRole,
@@ -46,38 +50,19 @@ export class JATSDOMParser {
     return this.parser.parse(doc, options)
   }
 
-  private isMatchingCategory(
-    secType: string | null,
-    titleNode: Element | null,
-    category: SectionCategory
-  ) {
-    if (
-      (secType && category.synonyms.includes(secType)) ||
-      category.id === secType
-    ) {
-      return true
-    }
-    if (titleNode && titleNode.nodeName === 'title' && titleNode.textContent) {
-      const textContent = titleNode.textContent.trim().toLowerCase()
-      if (category.synonyms.includes(textContent)) {
-        return true
-      }
-    }
-    return false
-  }
-
   private chooseSectionCategory(section: HTMLElement) {
     const secType = section.getAttribute('sec-type')
     const abstractType = section.getAttribute('abstract-type')
-    const effectiveSecType =
-      secType || (abstractType ? `abstract-${abstractType}` : null)
+    const effectiveSecType = secType ?? abstractType
     const titleNode = section.firstElementChild
+    const titleText =
+      titleNode?.nodeName === 'title' ? titleNode.textContent : null
 
-    for (const category of this.sectionCategories) {
-      if (this.isMatchingCategory(effectiveSecType, titleNode, category)) {
-        return category.id
-      }
-    }
+    return findMatchingCategory(
+      this.sectionCategories,
+      effectiveSecType,
+      titleText
+    )?.id
   }
 
   private parsePriority = (priority: string | null) => {
@@ -636,6 +621,10 @@ export class JATSDOMParser {
       tag: 'history',
       ignore: true,
     },
+    {
+      tag: 'statement',
+      ignore: true,
+    },
     {
       tag: 'break',
       node: 'hard_break',
@@ -995,10 +984,8 @@ export class JATSDOMParser {
       node: 'footnotes_section', // NOTE: higher priority than 'section'
       getAttrs: (node) => {
         const element = node as HTMLElement
-
         return {
           id: element.getAttribute('id'),
-          // category: chooseSectionCategory(element), // 'MPSectionCategory:endnotes',
         }
       },
     },
@@ -1024,7 +1011,7 @@ export class JATSDOMParser {
       },
     },
     {
-      tag: 'trans-abstract[sec-type="abstract-graphical"]',
+      tag: 'trans-abstract[abstract-type="graphical"]',
       node: 'trans_graphical_abstract',
       getAttrs: (node) => {
         const element = node as HTMLElement
@@ -1035,7 +1022,7 @@ export class JATSDOMParser {
       },
     },
     {
-      tag: 'trans-abstract[sec-type="abstract-key-image"]',
+      tag: 'trans-abstract[abstract-type="key-image"]',
       node: 'trans_graphical_abstract',
       getAttrs: (node) => {
         const element = node as HTMLElement
@@ -1095,7 +1082,7 @@ export class JATSDOMParser {
       getAttrs: (node) => this.parseRef(node as Element),
     },
     {
-      tag: 'sec[sec-type="abstract-graphical"]',
+      tag: 'abstract[abstract-type="graphical"]',
       node: 'graphical_abstract_section',
       getAttrs: (node) => {
         const element = node as HTMLElement
@@ -1105,7 +1092,7 @@ export class JATSDOMParser {
       },
     },
     {
-      tag: 'sec[sec-type="abstract-key-image"]',
+      tag: 'abstract[abstract-type="key-image"]',
       node: 'graphical_abstract_section',
       getAttrs: (node) => {
         const element = node as HTMLElement
@@ -1114,6 +1101,19 @@ export class JATSDOMParser {
         }
       },
     },
+    {
+      tag: 'abstract',
+      node: 'abstract',
+      getAttrs: (node) => {
+        const element = node as HTMLElement
+        return {
+          id: element.getAttribute('id'),
+          category:
+            this.chooseSectionCategory(element) ||
+            abstractTypeToCategory(element.getAttribute('abstract-type')),
+        }
+      },
+    },
     {
       tag: 'sec',
       node: 'section',
@@ -1179,7 +1179,7 @@ export class JATSDOMParser {
       tag: 'title',
       node: 'section_title',
       context:
-        'section/|footnotes_section/|bibliography_section/|keywords/|supplements/|author_notes/|graphical_abstract_section/|trans_abstract/|trans_graphical_abstract/',
+        'section/|footnotes_section/|bibliography_section/|keywords/|supplements/|author_notes/|abstract/|graphical_abstract_section/|trans_abstract/|trans_graphical_abstract/',
     },
     {
       tag: 'tr',

package/src/jats/importer/jats-transformations.ts

@@ -15,7 +15,10 @@
  */
 
 import { defaultTitle } from '../../lib/deafults'
-import { XML_NAMESPACE } from '../../lib/xml'
+import {
+  abstractTypeToCategory,
+  findMatchingCategory,
+} from '../../lib/section-categories'
 import { SectionCategory, SectionGroup } from '../../schema'
 import { htmlFromJatsNode } from './jats-parser-utils'
 
@@ -160,12 +163,7 @@ export const moveAbstracts = (
     'article-meta > abstract, article-meta > trans-abstract'
   )
   abstracts.forEach((abstract) => {
-    const sec = createAbstractSection(
-      abstract,
-      createElement,
-      sectionCategories
-    )
-    removeNodeFromParent(abstract)
+    const sec = prepareAbstract(abstract, createElement, sectionCategories)
     group.appendChild(sec)
   })
 }
@@ -259,9 +257,7 @@ const moveSpecialFootnotes = (
   const fns = [...doc.querySelectorAll('fn[fn-type]')]
   for (const fn of fns) {
     const type = fn.getAttribute('fn-type') || '' //Cannot be null since it is queried above
-    const category = sectionCategories.find((category) =>
-      category.synonyms.includes(type)
-    )
+    const category = findMatchingCategory(sectionCategories, type)
     if (category) {
       const section = createElement('sec')
       const fnTitle =
@@ -300,41 +296,29 @@ export const moveCaptionsToEnd = (body: Element) => {
   }
 }
 
-const createAbstractSection = (
+const prepareAbstract = (
   abstract: Element,
   createElement: CreateElement,
   sectionCategories?: SectionCategory[]
 ) => {
-  const abstractType = abstract.getAttribute('abstract-type')
-  const sectionType = abstractType ? `abstract-${abstractType}` : 'abstract'
-  let section = createElement('sec')
-  if (abstract.nodeName === 'trans-abstract') {
-    section = createElement('trans-abstract')
-    const lang = abstract.getAttributeNS(XML_NAMESPACE, 'lang')
-    if (lang) {
-      section.setAttributeNS(XML_NAMESPACE, 'lang', lang)
-    }
-  }
-  section.setAttribute('sec-type', sectionType)
+  const rawType = abstract.getAttribute('abstract-type')
+  const category = abstractTypeToCategory(rawType)
+
   if (!abstract.querySelector(':scope > title')) {
+    const matched =
+      sectionCategories && findMatchingCategory(sectionCategories, category)
     const title = createElement('title')
-    const category = sectionCategories?.find(
-      (c) => c.id === sectionType || c.synonyms.includes(sectionType)
-    )
-    if (category?.titles[0]) {
-      title.textContent = category.titles[0]
-    } else {
-      title.textContent = abstractType
-        ? `${capitalizeFirstLetter(abstractType.split('-').join(' '))} Abstract`
-        : 'Abstract'
-    }
-    section.appendChild(title)
-  }
 
-  while (abstract.firstChild) {
-    section.appendChild(abstract.firstChild)
+    title.textContent =
+      matched?.titles[0] ??
+      (rawType
+        ? `${capitalizeFirstLetter(rawType.split('-').join(' '))} Abstract`
+        : 'Abstract')
+
+    abstract.insertBefore(title, abstract.firstChild)
   }
-  return section
+
+  return abstract
 }
 
 const createAcknowledgmentsSection = (

package/src/lib/section-categories.ts

@@ -25,3 +25,39 @@ export const getGroupCategories = (
     : Array.from(sections.values())
   return sectionsArray.filter((section) => section.group === group)
 }
+
+export const findMatchingCategory = (
+  categories: SectionCategory[],
+  type?: string | null,
+  titleText?: string | null
+): SectionCategory | undefined => {
+  return categories.find((category) => {
+    if (type && (category.id === type || category.synonyms.includes(type))) {
+      return true
+    }
+    if (titleText) {
+      const normalizedTitle = titleText.trim().toLowerCase()
+      if (category.synonyms.includes(normalizedTitle)) {
+        return true
+      }
+    }
+    return false
+  })
+}
+
+export const abstractTypeToCategory = (abstractType: string | null) =>
+  abstractType || 'abstract'
+
+export const FOOTNOTE_SECTION_CATEGORY_IDS = [
+  'con',
+  'conflict',
+  'deceased',
+  'equal',
+  'present-address',
+  'presented-at',
+  'previously-at',
+  'supplementary-material',
+  'supported-by',
+  'financial-disclosure',
+  'coi-statement',
+]

package/src/schema/index.ts

@@ -30,6 +30,7 @@ import {
   tracked_insert,
   underline,
 } from './marks'
+import { abstract } from './nodes/abstract'
 import { abstracts } from './nodes/abstracts'
 import { affiliation } from './nodes/affiliation'
 import { affiliations } from './nodes/affiliations'
@@ -112,6 +113,7 @@ import { transGraphicalAbstract } from './nodes/trans_graphical_abstract'
 import { Marks, Nodes } from './types'
 
 export * from './groups'
+export * from './nodes/abstract'
 export * from './nodes/affiliation'
 export * from './nodes/affiliations'
 export * from './nodes/alt_text'
@@ -215,6 +217,7 @@ export const schema = new Schema<Nodes, Marks>({
     caption,
     caption_title: captionTitle,
     citation,
+    abstract,
     abstracts,
     body,
     backmatter,

package/src/schema/migration/migration-scripts/4.5.3.ts

@@ -0,0 +1,57 @@
+/*!
+ * © 2026 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 { JSONProsemirrorNode } from '../../../types'
+import { MigrationScript } from '../migration-script'
+
+const TRANS_ABSTRACT_TYPES = ['trans_abstract', 'trans_graphical_abstract']
+
+class Migration453 implements MigrationScript {
+  fromVersion = '4.5.2'
+  toVersion = '4.5.3'
+
+  migrateNode(node: JSONProsemirrorNode): JSONProsemirrorNode {
+    if (node.type !== 'abstracts' || !node.content) {
+      return node
+    }
+
+    const children = node.content.map((child) => {
+      const type = child.type === 'section' ? 'abstract' : child.type
+      const category = child.attrs?.category
+      const attrs =
+        category && category.startsWith('abstract-')
+          ? { ...child.attrs, category: category.slice('abstract-'.length) }
+          : child.attrs
+      return { ...child, type, attrs }
+    })
+
+    const regular: JSONProsemirrorNode[] = []
+    const translated: JSONProsemirrorNode[] = []
+    for (const child of children) {
+      if (TRANS_ABSTRACT_TYPES.includes(child.type)) {
+        translated.push(child)
+      } else {
+        regular.push(child)
+      }
+    }
+
+    return {
+      ...node,
+      content: [...regular, ...translated],
+    }
+  }
+}
+
+export default Migration453

package/src/schema/migration/migration-scripts/index.ts

@@ -30,6 +30,7 @@ import Migration4334 from './4.3.34'
 import Migration4335 from './4.3.35'
 import Migration442 from './4.4.2'
 import Migration447 from './4.4.7'
+import Migration453 from './4.5.3'
 
 const migrations = [
   new Migration125(),
@@ -48,6 +49,7 @@ const migrations = [
   new Migration4335(),
   new Migration442(),
   new Migration447(),
+  new Migration453(),
 ]
 
 export default migrations

package/src/schema/nodes/abstract.ts

@@ -0,0 +1,66 @@
+/*!
+ * © 2026 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 { NodeSpec } from 'prosemirror-model'
+
+import { ManuscriptNode } from '../types'
+
+export interface AbstractAttrs {
+  id: string
+  category: string
+}
+
+export interface AbstractNode extends ManuscriptNode {
+  attrs: AbstractAttrs
+}
+
+export const abstract: NodeSpec = {
+  content: 'section_label? section_title (paragraph | element)* sections*',
+  attrs: {
+    id: { default: '' },
+    category: { default: '' },
+    dataTracked: { default: null },
+  },
+  group: 'block sections',
+  selectable: false,
+  parseDOM: [
+    {
+      tag: 'section.abstract',
+      getAttrs: (dom) => {
+        const element = dom as HTMLElement
+        return {
+          id: element.getAttribute('id') || '',
+          category: element.getAttribute('data-category') || '',
+        }
+      },
+    },
+  ],
+  toDOM: (node) => {
+    const abstractNode = node as AbstractNode
+    const { id, category } = abstractNode.attrs
+
+    const attrs: { [key: string]: string } = { id, class: 'abstract' }
+
+    if (category) {
+      attrs['data-category'] = category
+    }
+
+    return ['section', attrs, 0]
+  },
+}
+
+export const isAbstractNode = (node: ManuscriptNode): node is AbstractNode =>
+  node.type === node.type.schema.nodes.abstract

package/src/schema/nodes/abstracts.ts

@@ -20,7 +20,8 @@ import { NodeSpec } from 'prosemirror-model'
 // It exists for the purpose of styling in the UI
 
 export const abstracts: NodeSpec = {
-  content: 'sections* (trans_abstract | trans_graphical_abstract)*',
+  content:
+    '(abstract | graphical_abstract_section)* (trans_abstract | trans_graphical_abstract)*',
   attrs: {
     id: { default: '' },
   },

package/src/schema/types.ts

@@ -84,6 +84,7 @@ export type Nodes =
   | 'listing'
   | 'listing_element'
   | 'manuscript'
+  | 'abstract'
   | 'abstracts'
   | 'body'
   | 'backmatter'

package/src/transformer/node-names.ts

@@ -54,6 +54,7 @@ export const nodeNames: Map<ManuscriptNodeType, string> = new Map([
   [schema.nodes.paragraph, 'Paragraph'],
   [schema.nodes.text_block, 'Paragraph'],
   [schema.nodes.section, 'Section'],
+  [schema.nodes.abstract, 'Abstract'],
   [schema.nodes.graphical_abstract_section, 'Graphical Abstract'],
   [schema.nodes.trans_abstract, 'Trans Abstract'],
   [schema.nodes.trans_graphical_abstract, 'Trans Graphical Abstract'],

package/src/transformer/node-title.ts

@@ -62,6 +62,7 @@ export const nodeTitle = (node: ManuscriptNode) => {
       return snippetOfNodeType(node, nodes.title)
 
     case nodes.section:
+    case nodes.abstract:
     case nodes.bibliography_section:
     case nodes.footnotes_section:
     case nodes.keywords:
@@ -105,6 +106,7 @@ export const nodeTitlePlaceholder = (nodeType: NodeType) => {
       return 'Untitled Manuscript'
 
     case nodes.section:
+    case nodes.abstract:
       return 'Untitled Section'
 
     case nodes.bibliography_section:

package/src/version.ts

@@ -1 +1 @@
-export const VERSION = "4.5.2";
+export const VERSION = "4.5.4";