@manuscripts/transform 4.5.7 → 4.6.0

package/src/jats/exporter/lib.ts

@@ -0,0 +1,69 @@
+/*!
+ * © 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 { ManuscriptNodeType, schema } from '../../schema'
+import { IDGenerator } from '../types'
+
+export const normalizeID = (id: string) => id.replace(/:/g, '_')
+
+export const createCounter = () => {
+  const counts = new Map<string, number>()
+
+  return {
+    increment: (field: string) => {
+      const value = counts.get(field)
+      const newValue = value === undefined ? 1 : value + 1
+      counts.set(field, newValue)
+      return newValue
+    },
+  }
+}
+
+export const createDefaultIDGenerator = (): IDGenerator => {
+  const counter = createCounter()
+
+  return async (element: Element) => {
+    const value = String(counter.increment(element.nodeName))
+
+    return `${element.localName}-${value}`
+  }
+}
+
+export const chooseRefType = (type: ManuscriptNodeType): string | undefined => {
+  switch (type) {
+    case schema.nodes.figure:
+    case schema.nodes.figure_element:
+      return 'fig'
+
+    case schema.nodes.footnote:
+      return 'fn'
+
+    case schema.nodes.table:
+    case schema.nodes.table_element:
+      return 'table'
+
+    case schema.nodes.section:
+    case schema.nodes.abstract:
+      return 'sec'
+
+    case schema.nodes.equation:
+    case schema.nodes.equation_element:
+      return 'disp-formula'
+
+    case schema.nodes.supplement:
+      return 'supplementary-material'
+  }
+}

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

@@ -1,5 +1,5 @@
 /*!
- * © 2020 Atypon Systems LLC
+ * © 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.
@@ -525,7 +525,7 @@ export class JATSDOMParser {
         const affiliationIDs: string[] = []
         const correspIDs: string[] = []
 
-        const xrefs = element.querySelectorAll('xref')
+        const xrefs = element.querySelectorAll(':scope > xref')
         for (const xref of xrefs) {
           const rid = xref.getAttribute('rid')
           const type = xref.getAttribute('ref-type')
@@ -572,10 +572,20 @@ export class JATSDOMParser {
           email: getTrimmedTextContent(element, 'email') || '',
         }
       },
-      getContent: () => {
-        return Fragment.from(this.schema.text('_'))
+      getContent: (node) => {
+        const bio = (node as HTMLElement).querySelector('bio')
+        if (!bio) {
+          return Fragment.empty
+        }
+        return Fragment.from(
+          this.parse(bio, { topNode: this.schema.nodes.bio.create() })
+        )
       },
     },
+    {
+      tag: 'bio',
+      node: 'bio',
+    },
     {
       tag: 'affiliations',
       node: 'affiliations',
@@ -772,7 +782,7 @@ export class JATSDOMParser {
             label: getTrimmedTextContent(extLinkElement) || undefined,
           }))
           .filter((extLink) => extLink.href) // Filter out entries without href
-        
+
         return {
           id: element.getAttribute('id'),
           href: element.getAttributeNS(XLINK_NAMESPACE, 'href'),

package/src/schema/index.ts

@@ -1,5 +1,5 @@
 /*!
- * © 2019 Atypon Systems LLC
+ * © 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.
@@ -47,6 +47,7 @@ import { backmatter } from './nodes/backmatter'
 import { bibliographyElement } from './nodes/bibliography_element'
 import { bibliographyItem } from './nodes/bibliography_item'
 import { bibliographySection } from './nodes/bibliography_section'
+import { bio } from './nodes/bio'
 import { blockquoteElement } from './nodes/blockquote_element'
 import { body } from './nodes/body'
 import { box_element } from './nodes/box_element'
@@ -128,6 +129,7 @@ export * from './nodes/awards'
 export * from './nodes/bibliography_element'
 export * from './nodes/bibliography_item'
 export * from './nodes/bibliography_section'
+export * from './nodes/bio'
 export * from './nodes/blockquote_element'
 export * from './nodes/box_element'
 export * from './nodes/caption'
@@ -213,6 +215,7 @@ export const schema = new Schema<Nodes, Marks>({
     bibliography_element: bibliographyElement,
     bibliography_section: bibliographySection,
     blockquote_element: blockquoteElement,
+    bio: bio,
     list: list,
     caption,
     caption_title: captionTitle,

package/src/schema/migration/migration-scripts/4.5.9.ts

@@ -0,0 +1,62 @@
+/*!
+ * © 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'
+
+/**
+ * Nodes that still carried the `contents` attribute inherited from the
+ * json-schema era. The attribute was never read for these types and has been
+ * removed from their specs.
+ */
+const LEGACY_CONTENTS_NODES = new Set([
+  'contributor',
+  'bibliography_element',
+  'keywords_element',
+])
+
+/**
+ * - contributor content changed from `inline*` (holding a '_' placeholder text
+ *   node written by the JATS importer) to `bio?`. Any non-bio content is dropped.
+ * - the dead `contents` attribute is removed from the nodes listed above - this won't
+ *   invalidate the doc actually so it's added only for hygiene
+ */
+class Migration459 implements MigrationScript {
+  fromVersion = '4.5.8'
+  toVersion = '4.5.9'
+
+  migrateNode(node: JSONProsemirrorNode): JSONProsemirrorNode {
+    if (
+      LEGACY_CONTENTS_NODES.has(node.type) &&
+      node.attrs &&
+      'contents' in node.attrs
+    ) {
+      const attrs = { ...node.attrs }
+      delete attrs.contents
+      node = { ...node, attrs }
+    }
+
+    if (node.type === 'contributor') {
+      const bio = node.content?.filter((child) => child.type === 'bio')
+      const migrated = { ...node }
+      delete migrated.content
+      return bio?.length ? { ...migrated, content: bio } : migrated
+    }
+
+    return node
+  }
+}
+
+export default Migration459

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

@@ -1,5 +1,5 @@
 /*!
- * © 2024 Atypon Systems LLC
+ * © 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.
@@ -31,6 +31,7 @@ import Migration4335 from './4.3.35'
 import Migration442 from './4.4.2'
 import Migration447 from './4.4.7'
 import Migration453 from './4.5.3'
+import Migration459 from './4.5.9'
 
 const migrations = [
   new Migration125(),
@@ -50,6 +51,7 @@ const migrations = [
   new Migration442(),
   new Migration447(),
   new Migration453(),
+  new Migration459(),
 ]
 
 export default migrations

package/src/schema/nodes/bibliography_element.ts

@@ -30,7 +30,6 @@ export const bibliographyElement: NodeSpec = {
   content: 'bibliography_item*',
   attrs: {
     id: { default: '' },
-    contents: { default: '' },
     dataTracked: { default: null },
   },
   selectable: false,

package/src/schema/nodes/bio.ts

@@ -0,0 +1,48 @@
+/*!
+ * © 2023 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 BioAttrs {
+  id: string
+}
+
+export interface BioNode extends ManuscriptNode {
+  attrs: BioAttrs
+}
+
+export const bio: NodeSpec = {
+  content: 'image_element? paragraph',
+  attrs: {
+    id: { default: '' },
+    dataTracked: { default: null },
+  },
+  group: 'block',
+  toDOM: (node) => {
+    const bioNode = node as BioNode
+    return [
+      'div',
+      {
+        class: 'bio',
+        id: bioNode.attrs.id,
+      },
+      0,
+    ]
+  },
+}
+export const isBioNode = (node: ManuscriptNode): node is BioNode =>
+  node.type === node.type.schema.nodes.bio

package/src/schema/nodes/contributor.ts

@@ -47,7 +47,7 @@ export interface ContributorNode extends ManuscriptNode {
 }
 
 export const contributor: NodeSpec = {
-  content: 'inline*',
+  content: 'bio?',
   atom: true,
   attrs: {
     id: { default: '' },
@@ -68,7 +68,6 @@ export const contributor: NodeSpec = {
     priority: { default: undefined },
     creditRoles: { default: [] },
     dataTracked: { default: null },
-    contents: { default: '' },
   },
   group: 'block',
   toDOM: (node) => {

package/src/schema/nodes/keywords_element.ts

@@ -32,7 +32,6 @@ export const keywordsElement: NodeSpec = {
   content: 'keyword_group*',
   attrs: {
     id: { default: '' },
-    contents: { default: '' },
     dataTracked: { default: null },
   },
   group: 'block element',

package/src/schema/types.ts

@@ -54,6 +54,7 @@ export type Nodes =
   | 'bibliography_element'
   | 'bibliography_section'
   | 'blockquote_element'
+  | 'bio'
   | 'quote_image'
   | 'list'
   | 'caption'

package/src/types.ts

@@ -1,5 +1,5 @@
 /*!
- * © 2019 Atypon Systems LLC
+ * © 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.

package/src/version.ts

@@ -1 +1 @@
-export const VERSION = "4.5.7";
+export const VERSION = "4.6.0";