@manuscripts/transform 4.5.7 → 4.6.0

package/dist/es/jats/exporter/lib.js

@@ -0,0 +1,55 @@
+/*!
+ * © 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 { schema } from '../../schema';
+export const normalizeID = (id) => id.replace(/:/g, '_');
+export const createCounter = () => {
+    const counts = new Map();
+    return {
+        increment: (field) => {
+            const value = counts.get(field);
+            const newValue = value === undefined ? 1 : value + 1;
+            counts.set(field, newValue);
+            return newValue;
+        },
+    };
+};
+export const createDefaultIDGenerator = () => {
+    const counter = createCounter();
+    return async (element) => {
+        const value = String(counter.increment(element.nodeName));
+        return `${element.localName}-${value}`;
+    };
+};
+export const chooseRefType = (type) => {
+    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/dist/es/jats/importer/jats-dom-parser.js

@@ -375,7 +375,7 @@ export class JATSDOMParser {
                     const footnoteIDs = [];
                     const affiliationIDs = [];
                     const correspIDs = [];
-                    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');
@@ -413,10 +413,18 @@ export class JATSDOMParser {
                         email: getTrimmedTextContent(element, 'email') || '',
                     };
                 },
-                getContent: () => {
-                    return Fragment.from(this.schema.text('_'));
+                getContent: (node) => {
+                    const bio = node.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',

package/dist/es/schema/index.js

@@ -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.
@@ -33,6 +33,7 @@ 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';
@@ -112,6 +113,7 @@ 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';
@@ -197,6 +199,7 @@ export const schema = new Schema({
         bibliography_element: bibliographyElement,
         bibliography_section: bibliographySection,
         blockquote_element: blockquoteElement,
+        bio: bio,
         list: list,
         caption,
         caption_title: captionTitle,

package/dist/es/schema/migration/migration-scripts/4.5.9.js

@@ -0,0 +1,28 @@
+const LEGACY_CONTENTS_NODES = new Set([
+    'contributor',
+    'bibliography_element',
+    'keywords_element',
+]);
+class Migration459 {
+    constructor() {
+        this.fromVersion = '4.5.8';
+        this.toVersion = '4.5.9';
+    }
+    migrateNode(node) {
+        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/dist/es/schema/migration/migration-scripts/index.js

@@ -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.
@@ -30,6 +30,7 @@ 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(),
     new Migration2322(),
@@ -48,5 +49,6 @@ const migrations = [
     new Migration442(),
     new Migration447(),
     new Migration453(),
+    new Migration459(),
 ];
 export default migrations;

package/dist/es/schema/nodes/bibliography_element.js

@@ -17,7 +17,6 @@ export const bibliographyElement = {
     content: 'bibliography_item*',
     attrs: {
         id: { default: '' },
-        contents: { default: '' },
         dataTracked: { default: null },
     },
     selectable: false,

package/dist/es/schema/nodes/bio.js

@@ -0,0 +1,20 @@
+export const bio = {
+    content: 'image_element? paragraph',
+    attrs: {
+        id: { default: '' },
+        dataTracked: { default: null },
+    },
+    group: 'block',
+    toDOM: (node) => {
+        const bioNode = node;
+        return [
+            'div',
+            {
+                class: 'bio',
+                id: bioNode.attrs.id,
+            },
+            0,
+        ];
+    },
+};
+export const isBioNode = (node) => node.type === node.type.schema.nodes.bio;

package/dist/es/schema/nodes/contributor.js

@@ -1,5 +1,5 @@
 export const contributor = {
-    content: 'inline*',
+    content: 'bio?',
     atom: true,
     attrs: {
         id: { default: '' },
@@ -20,7 +20,6 @@ export const contributor = {
         priority: { default: undefined },
         creditRoles: { default: [] },
         dataTracked: { default: null },
-        contents: { default: '' },
     },
     group: 'block',
     toDOM: (node) => {

package/dist/es/schema/nodes/keywords_element.js

@@ -18,7 +18,6 @@ export const keywordsElement = {
     content: 'keyword_group*',
     attrs: {
         id: { default: '' },
-        contents: { default: '' },
         dataTracked: { default: null },
     },
     group: 'block element',

package/dist/es/types.js

@@ -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/dist/es/version.js

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

package/dist/types/jats/exporter/JATSExporterBase.d.ts

@@ -0,0 +1,35 @@
+/*!
+ * © 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 { DOMSerializer, type NodeType } from 'prosemirror-model';
+import { ManuscriptNode, ManuscriptNodeType } from '../../schema';
+export declare class JATSExporterBase {
+    private nodesMap;
+    protected manuscriptNode: ManuscriptNode;
+    protected document: Document;
+    protected serializer: DOMSerializer;
+    isChildOfNodeType(targetID: string, type: NodeType, descend?: boolean): boolean;
+    protected populateNodesMap: () => void;
+    getChildrenOfType<T extends ManuscriptNode>(type: NodeType, node?: ManuscriptNode): T[];
+    getFirstChildOfType<T extends ManuscriptNode>(type: NodeType, node?: ManuscriptNode): T | undefined;
+    protected fillEmptyElements($article: Element, selector: string, tagName?: string): void;
+    protected createElement: (tag: string, content?: string, attrs?: Record<string, string | undefined>) => HTMLElement;
+    protected appendElement: ($parent: Element, tag: string, content?: string, attrs?: Record<string, string | undefined>) => HTMLElement;
+    protected changeTag: ($node: Element, tag: string) => HTMLElement;
+    protected createElementWithID(node: ManuscriptNode, nodeName: string): HTMLElement;
+    protected serializeNode(node: ManuscriptNode): Node;
+    protected appendChildIfPresent($parent: Element, tagName: string, textContent: string): void;
+    protected processChildNodes: ($element: Element, node: ManuscriptNode, contentNodeType: ManuscriptNodeType) => void;
+}

package/dist/types/jats/exporter/jats-exporter.d.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.
@@ -13,14 +13,12 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import { DOMSerializer, type NodeType } from 'prosemirror-model';
-import { ActualManuscriptNode, ManuscriptNode } from '../../schema';
+import { DOMOutputSpec } from 'prosemirror-model';
+import { ActualManuscriptNode, ManuscriptNode, ManuscriptNodeType } from '../../schema';
 import { IDGenerator } from '../types';
 import { Version } from './jats-versions';
 import { Target } from './labels';
-export declare const createCounter: () => {
-    increment: (field: string) => number;
-};
+import { JATSExporterBase } from './JATSExporterBase';
 export type CSLOptions = {
     style: string;
     locale: string;
@@ -29,20 +27,14 @@ export type ExportOptions = {
     version?: Version;
     csl: CSLOptions;
 };
-export declare class JATSExporter {
-    protected document: Document;
-    protected serializer: DOMSerializer;
+export declare class JATSExporter extends JATSExporterBase {
     protected labelTargets: Map<string, Target>;
     protected footnoteLabels: Map<string, string>;
     protected manuscriptNode: ActualManuscriptNode;
     private engine;
     private renderedCitations;
-    private nodesMap;
     private contributorLabels;
-    private populateNodesMap;
-    protected getFirstChildOfType<T extends ManuscriptNode>(type: NodeType, node?: ManuscriptNode): T | undefined;
-    protected getChildrenOfType<T extends ManuscriptNode>(type: NodeType, node?: ManuscriptNode): T[];
-    serializeToJATS: (manuscriptNode: ActualManuscriptNode, options: ExportOptions) => Promise<string>;
+    export: (manuscriptNode: ActualManuscriptNode, options: ExportOptions) => Promise<Document>;
     private appendChildNodeOfType;
     private appendChildrenNodeOfType;
     protected appendCaption: ($element: Element, node: ManuscriptNode) => void;
@@ -66,11 +58,25 @@ export declare class JATSExporter {
     private routeBackmatterSections;
     private extractCoiStatement;
     private buildRefList;
-    private createElement;
-    private appendElement;
     protected createSerializer: () => void;
+    appendLabels($element: Element, node: ManuscriptNode): void;
+    appendAttributions($element: Element, node: ManuscriptNode): void;
+    appendTable($element: Element, node: ManuscriptNode): void;
+    createBoxElement(node: ManuscriptNode): HTMLElement;
+    abstractTypeAttrs(category: string): {
+        'abstract-type': string;
+    } | {
+        'abstract-type'?: undefined;
+    };
+    createAbstract(node: ManuscriptNode): DOMOutputSpec;
+    createTransAbstract(node: ManuscriptNode): DOMOutputSpec;
+    private createGraphic;
+    createImage(node: ManuscriptNode): HTMLElement | "";
+    createFigureElement(node: ManuscriptNode, contentNodeType: ManuscriptNodeType): HTMLElement;
+    moveAltTextAndLongDescToGraphics($element: Element): void;
+    createTableElement(node: ManuscriptNode): HTMLElement;
+    processExecutableNode(node: ManuscriptNode, $element: Element): void;
     private createEquation;
-    protected serializeNode: (node: ManuscriptNode) => Node;
     private buildContributorGroup;
     private buildAuthorNotes;
     private computeContributorLabels;
@@ -83,12 +89,10 @@ export declare class JATSExporter {
     private writeFootnote;
     private appendAuthorNotes;
     private buildKeywords;
-    private changeTag;
     private normalizeTable;
     private buildAbstracts;
     sectionToFootnote: ($section: Element, fnType: string) => HTMLElement;
     private buildFloatsGroup;
-    private fillEmptyElements;
     private addParagraphsToSections;
     private fillEmptyFootnotes;
     private fillEmptyTableFooters;

package/dist/types/jats/exporter/lib.d.ts

@@ -0,0 +1,23 @@
+/*!
+ * © 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 } from '../../schema';
+import { IDGenerator } from '../types';
+export declare const normalizeID: (id: string) => string;
+export declare const createCounter: () => {
+    increment: (field: string) => number;
+};
+export declare const createDefaultIDGenerator: () => IDGenerator;
+export declare const chooseRefType: (type: ManuscriptNodeType) => string | undefined;

package/dist/types/schema/index.d.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.
@@ -32,6 +32,7 @@ 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';

package/dist/types/schema/migration/migration-scripts/4.5.9.d.ts

@@ -0,0 +1,8 @@
+import { JSONProsemirrorNode } from '../../../types';
+import { MigrationScript } from '../migration-script';
+declare class Migration459 implements MigrationScript {
+    fromVersion: string;
+    toVersion: string;
+    migrateNode(node: JSONProsemirrorNode): JSONProsemirrorNode;
+}
+export default Migration459;

package/dist/types/schema/migration/migration-scripts/index.d.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.
@@ -30,5 +30,6 @@ import Migration4335 from './4.3.35';
 import Migration442 from './4.4.2';
 import Migration447 from './4.4.7';
 import Migration453 from './4.5.3';
-declare const migrations: (Migration125 | Migration2322 | Migration3012 | Migration3021 | Migration3030 | Migration3031 | Migration3041 | Migration3055 | Migration3056 | Migration4213 | Migration4215 | Migration4323 | Migration4334 | Migration4335 | Migration442 | Migration447 | Migration453)[];
+import Migration459 from './4.5.9';
+declare const migrations: (Migration125 | Migration2322 | Migration3012 | Migration3021 | Migration3030 | Migration3031 | Migration3041 | Migration3055 | Migration3056 | Migration4213 | Migration4215 | Migration4323 | Migration4334 | Migration4335 | Migration442 | Migration447 | Migration453 | Migration459)[];
 export default migrations;

package/dist/types/schema/nodes/bio.d.ts

@@ -0,0 +1,10 @@
+import { NodeSpec } from 'prosemirror-model';
+import { ManuscriptNode } from '../types';
+export interface BioAttrs {
+    id: string;
+}
+export interface BioNode extends ManuscriptNode {
+    attrs: BioAttrs;
+}
+export declare const bio: NodeSpec;
+export declare const isBioNode: (node: ManuscriptNode) => node is BioNode;

package/dist/types/schema/types.d.ts

@@ -17,7 +17,7 @@ import { Fragment, Mark as ProsemirrorMark, MarkType, Node as ProsemirrorNode, N
 import { EditorState, NodeSelection, Plugin, TextSelection, Transaction } from 'prosemirror-state';
 import { EditorView, NodeView } from 'prosemirror-view';
 export type Marks = 'bold' | 'code' | 'italic' | 'smallcaps' | 'strikethrough' | 'styled' | 'subscript' | 'superscript' | 'underline' | 'tracked_insert' | 'tracked_delete';
-export type Nodes = 'attribution' | 'bibliography_item' | 'bibliography_element' | 'bibliography_section' | 'blockquote_element' | 'quote_image' | 'list' | 'caption' | 'caption_title' | 'comment' | 'comments' | 'citation' | 'cross_reference' | 'doc' | 'equation' | 'equation_element' | 'figure' | 'graphical_abstract_section' | 'figure_element' | 'footnote' | 'footnotes_element' | 'footnotes_section' | 'hard_break' | 'highlight_marker' | 'inline_equation' | 'inline_footnote' | 'keyword' | 'keywords_element' | 'keyword_group' | 'keywords' | 'link' | 'list_item' | 'listing' | 'listing_element' | 'manuscript' | 'abstract' | 'abstracts' | 'body' | 'backmatter' | 'missing_figure' | 'paragraph' | 'placeholder' | 'placeholder_element' | 'pullquote_element' | 'section' | 'section_label' | 'section_title' | 'section_title_plain' | 'table' | 'table_cell' | 'table_element' | 'table_row' | 'table_colgroup' | 'table_col' | 'table_header' | 'text' | 'text_block' | 'affiliation' | 'contributor' | 'table_element_footer' | 'title' | 'affiliations' | 'contributors' | 'supplements' | 'supplement' | 'author_notes' | 'corresp' | 'general_table_footnote' | 'box_element' | 'awards' | 'award' | 'embed' | 'image_element' | 'attachment' | 'attachments' | 'alt_title' | 'alt_text' | 'alt_titles' | 'long_desc' | 'hero_image' | 'headshot_grid' | 'headshot_element' | 'headshot_image' | 'trans_abstract' | 'trans_graphical_abstract' | 'subtitle' | 'subtitles';
+export type Nodes = 'attribution' | 'bibliography_item' | 'bibliography_element' | 'bibliography_section' | 'blockquote_element' | 'bio' | 'quote_image' | 'list' | 'caption' | 'caption_title' | 'comment' | 'comments' | 'citation' | 'cross_reference' | 'doc' | 'equation' | 'equation_element' | 'figure' | 'graphical_abstract_section' | 'figure_element' | 'footnote' | 'footnotes_element' | 'footnotes_section' | 'hard_break' | 'highlight_marker' | 'inline_equation' | 'inline_footnote' | 'keyword' | 'keywords_element' | 'keyword_group' | 'keywords' | 'link' | 'list_item' | 'listing' | 'listing_element' | 'manuscript' | 'abstract' | 'abstracts' | 'body' | 'backmatter' | 'missing_figure' | 'paragraph' | 'placeholder' | 'placeholder_element' | 'pullquote_element' | 'section' | 'section_label' | 'section_title' | 'section_title_plain' | 'table' | 'table_cell' | 'table_element' | 'table_row' | 'table_colgroup' | 'table_col' | 'table_header' | 'text' | 'text_block' | 'affiliation' | 'contributor' | 'table_element_footer' | 'title' | 'affiliations' | 'contributors' | 'supplements' | 'supplement' | 'author_notes' | 'corresp' | 'general_table_footnote' | 'box_element' | 'awards' | 'award' | 'embed' | 'image_element' | 'attachment' | 'attachments' | 'alt_title' | 'alt_text' | 'alt_titles' | 'long_desc' | 'hero_image' | 'headshot_grid' | 'headshot_element' | 'headshot_image' | 'trans_abstract' | 'trans_graphical_abstract' | 'subtitle' | 'subtitles';
 export type ManuscriptSchema = Schema<Nodes, Marks>;
 export type ManuscriptEditorState = EditorState;
 export type ManuscriptEditorView = EditorView;

package/dist/types/types.d.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/dist/types/version.d.ts

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

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@manuscripts/transform",
   "description": "ProseMirror transformer for Manuscripts applications",
-  "version": "4.5.7",
+  "version": "4.6.0",
   "repository": "github:Atypon-OpenSource/manuscripts-transform",
   "license": "Apache-2.0",
   "main": "dist/cjs",
@@ -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",
@@ -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"

package/src/jats/__tests__/__fixtures__/jats-import.xml

@@ -49,6 +49,13 @@
             vocab-term-identifier=
             "http://credit.niso.org/contributor-roles/writing-original-draft/"
             degree-contribution="lead">writer</role>
+          <bio>
+            <graphic xlink:href="agnete-hornnes.png">
+              <alt-text>Headshot of Agnete Hviid Hornnes</alt-text>
+            </graphic>
+            <p>Agnete is a <italic>Professor of Neurology</italic> at Herlev og
+              Gentofte Hospital, specializing in stroke research.</p>
+          </bio>
         </contrib>
         <contrib contrib-type="author">
           <name>