@manuscripts/transform 4.5.8 → 4.6.0

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

@@ -0,0 +1,62 @@
+"use strict";
+/*!
+ * © 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.
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.chooseRefType = exports.createDefaultIDGenerator = exports.createCounter = exports.normalizeID = void 0;
+const schema_1 = require("../../schema");
+const normalizeID = (id) => id.replace(/:/g, '_');
+exports.normalizeID = normalizeID;
+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;
+        },
+    };
+};
+exports.createCounter = createCounter;
+const createDefaultIDGenerator = () => {
+    const counter = (0, exports.createCounter)();
+    return async (element) => {
+        const value = String(counter.increment(element.nodeName));
+        return `${element.localName}-${value}`;
+    };
+};
+exports.createDefaultIDGenerator = createDefaultIDGenerator;
+const chooseRefType = (type) => {
+    switch (type) {
+        case schema_1.schema.nodes.figure:
+        case schema_1.schema.nodes.figure_element:
+            return 'fig';
+        case schema_1.schema.nodes.footnote:
+            return 'fn';
+        case schema_1.schema.nodes.table:
+        case schema_1.schema.nodes.table_element:
+            return 'table';
+        case schema_1.schema.nodes.section:
+        case schema_1.schema.nodes.abstract:
+            return 'sec';
+        case schema_1.schema.nodes.equation:
+        case schema_1.schema.nodes.equation_element:
+            return 'disp-formula';
+        case schema_1.schema.nodes.supplement:
+            return 'supplementary-material';
+    }
+};
+exports.chooseRefType = chooseRefType;

package/dist/cjs/jats/importer/jats-dom-parser.js

@@ -378,7 +378,7 @@ 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');
@@ -416,10 +416,18 @@ class JATSDOMParser {
                         email: (0, utils_1.getTrimmedTextContent)(element, 'email') || '',
                     };
                 },
-                getContent: () => {
-                    return prosemirror_model_1.Fragment.from(this.schema.text('_'));
+                getContent: (node) => {
+                    const bio = node.querySelector('bio');
+                    if (!bio) {
+                        return prosemirror_model_1.Fragment.empty;
+                    }
+                    return prosemirror_model_1.Fragment.from(this.parse(bio, { topNode: this.schema.nodes.bio.create() }));
                 },
             },
+            {
+                tag: 'bio',
+                node: 'bio',
+            },
             {
                 tag: 'affiliations',
                 node: 'affiliations',

package/dist/cjs/schema/index.js

@@ -1,6 +1,6 @@
 "use strict";
 /*!
- * © 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.
@@ -50,6 +50,7 @@ const backmatter_1 = require("./nodes/backmatter");
 const bibliography_element_1 = require("./nodes/bibliography_element");
 const bibliography_item_1 = require("./nodes/bibliography_item");
 const bibliography_section_1 = require("./nodes/bibliography_section");
+const bio_1 = require("./nodes/bio");
 const blockquote_element_1 = require("./nodes/blockquote_element");
 const body_1 = require("./nodes/body");
 const box_element_1 = require("./nodes/box_element");
@@ -129,6 +130,7 @@ __exportStar(require("./nodes/awards"), exports);
 __exportStar(require("./nodes/bibliography_element"), exports);
 __exportStar(require("./nodes/bibliography_item"), exports);
 __exportStar(require("./nodes/bibliography_section"), exports);
+__exportStar(require("./nodes/bio"), exports);
 __exportStar(require("./nodes/blockquote_element"), exports);
 __exportStar(require("./nodes/box_element"), exports);
 __exportStar(require("./nodes/caption"), exports);
@@ -214,6 +216,7 @@ exports.schema = new prosemirror_model_1.Schema({
         bibliography_element: bibliography_element_1.bibliographyElement,
         bibliography_section: bibliography_section_1.bibliographySection,
         blockquote_element: blockquote_element_1.blockquoteElement,
+        bio: bio_1.bio,
         list: list_1.list,
         caption: caption_1.caption,
         caption_title: caption_title_1.captionTitle,

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

@@ -0,0 +1,30 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+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;
+    }
+}
+exports.default = Migration459;

package/dist/cjs/schema/migration/migration-scripts/index.js

@@ -1,6 +1,6 @@
 "use strict";
 /*!
- * © 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.
@@ -35,6 +35,7 @@ const _4_3_35_1 = __importDefault(require("./4.3.35"));
 const _4_4_2_1 = __importDefault(require("./4.4.2"));
 const _4_4_7_1 = __importDefault(require("./4.4.7"));
 const _4_5_3_1 = __importDefault(require("./4.5.3"));
+const _4_5_9_1 = __importDefault(require("./4.5.9"));
 const migrations = [
     new _1_2_5_1.default(),
     new _2_3_22_1.default(),
@@ -53,5 +54,6 @@ const migrations = [
     new _4_4_2_1.default(),
     new _4_4_7_1.default(),
     new _4_5_3_1.default(),
+    new _4_5_9_1.default(),
 ];
 exports.default = migrations;

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

@@ -20,7 +20,6 @@ exports.bibliographyElement = {
     content: 'bibliography_item*',
     attrs: {
         id: { default: '' },
-        contents: { default: '' },
         dataTracked: { default: null },
     },
     selectable: false,

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

@@ -0,0 +1,24 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.isBioNode = exports.bio = void 0;
+exports.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,
+        ];
+    },
+};
+const isBioNode = (node) => node.type === node.type.schema.nodes.bio;
+exports.isBioNode = isBioNode;

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

@@ -2,7 +2,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.isContributorNode = exports.contributor = void 0;
 exports.contributor = {
-    content: 'inline*',
+    content: 'bio?',
     atom: true,
     attrs: {
         id: { default: '' },
@@ -23,7 +23,6 @@ exports.contributor = {
         priority: { default: undefined },
         creditRoles: { default: [] },
         dataTracked: { default: null },
-        contents: { default: '' },
     },
     group: 'block',
     toDOM: (node) => {

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

@@ -21,7 +21,6 @@ exports.keywordsElement = {
     content: 'keyword_group*',
     attrs: {
         id: { default: '' },
-        contents: { default: '' },
         dataTracked: { default: null },
     },
     group: 'block element',

package/dist/cjs/types.js

@@ -1,6 +1,6 @@
 "use strict";
 /*!
- * © 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/cjs/version.js

@@ -1,4 +1,4 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.VERSION = void 0;
-exports.VERSION = "4.5.8";
+exports.VERSION = "4.6.0";

package/dist/es/jats/__tests__/jats-exporter.test.js

@@ -198,4 +198,27 @@ describe('JATS exporter', () => {
             expect(fn).not.toBeUndefined();
         }
     });
+    test('export contributor bio', async () => {
+        const transformer = new JATSExporter();
+        const input = await readAndParseFixture('jats-import.xml');
+        const node = parseJATSArticle(input, sectionCategories);
+        const xml = await transformer.export(node, {
+            csl: DEFAULT_CSL_OPTIONS,
+        });
+        const serialized = serializeToXML(xml);
+        const resultDoc = parseXMLWithDTD(serialized);
+        expect(resultDoc.errors).toHaveLength(0);
+        const contribs = resultDoc.find('//contrib-group/contrib');
+        expect(contribs).toHaveLength(2);
+        expect(contribs[0].find('bio')).toHaveLength(1);
+        expect(contribs[1].find('bio')).toHaveLength(0);
+        const graphic = resultDoc.get('//contrib/bio/graphic');
+        expect(graphic).not.toBeNull();
+        expect(graphic.attr('href')?.value()).toBe('agnete-hornnes.png');
+        expect(graphic.find('caption')).toHaveLength(0);
+        expect(resultDoc.get('//contrib/bio/graphic/alt-text').text()).toBe('Headshot of Agnete Hviid Hornnes');
+        const paragraph = resultDoc.get('//contrib/bio/p');
+        expect(paragraph.text()).toBe('Agnete is a Professor of Neurology at Herlev og Gentofte Hospital, specializing in stroke research.');
+        expect(resultDoc.get('//contrib/bio/p/italic')?.text()).toBe('Professor of Neurology');
+    });
 });

package/dist/es/jats/__tests__/jats-importer.test.js

@@ -58,6 +58,32 @@ describe('JATS importer', () => {
             expect(contributorsNode).toHaveLength(0);
         });
     });
+    describe('bio', () => {
+        it('should parse bio with graphic and paragraph into the contributor node', async () => {
+            const jats = await readAndParseFixture('jats-import.xml');
+            const node = parseJATSArticle(jats, sectionCategories);
+            changeIDs(node);
+            const [contributor] = findNodesByType(node, schema.nodes.contributor);
+            expect(contributor.childCount).toBe(1);
+            const bio = contributor.firstChild;
+            expect(bio.type).toBe(schema.nodes.bio);
+            expect(bio.childCount).toBe(2);
+            const image = findNodeByType(bio, schema.nodes.image_element);
+            expect(findNodeByType(image, schema.nodes.figure).attrs.src).toBe('agnete-hornnes.png');
+            expect(findNodeByType(image, schema.nodes.alt_text).textContent).toBe('Headshot of Agnete Hviid Hornnes');
+            const paragraph = bio.lastChild;
+            expect(paragraph.type).toBe(schema.nodes.paragraph);
+            expect(paragraph.textContent).toBe('Agnete is a Professor of Neurology at Herlev og Gentofte Hospital, specializing in stroke research.');
+            expect(bio).toMatchSnapshot();
+        });
+        it('should not add bio content to contributors without a bio element', async () => {
+            const jats = await readAndParseFixture('jats-import.xml');
+            const node = parseJATSArticle(jats, sectionCategories);
+            const [, contributor] = findNodesByType(node, schema.nodes.contributor);
+            expect(contributor.childCount).toBe(0);
+            expect(findNodesByType(node, schema.nodes.bio)).toHaveLength(1);
+        });
+    });
     describe('affiliations', () => {
         it('should correctly parse affiliation nodes', async () => {
             const jats = await readAndParseFixture('jats-import.xml');

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

@@ -0,0 +1,114 @@
+/*!
+ * © 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 { findChildrenByAttr, findChildrenByType } from 'prosemirror-utils';
+import { isNodeOfType } from '../../schema';
+import { normalizeID } from './lib';
+export class JATSExporterBase {
+    constructor() {
+        this.nodesMap = new Map();
+        this.populateNodesMap = () => {
+            this.manuscriptNode.descendants((node) => {
+                const type = node.type;
+                const nodes = this.nodesMap.get(type) ?? [];
+                nodes.push(node);
+                this.nodesMap.set(type, nodes);
+            });
+        };
+        this.createElement = (tag, content, attrs) => {
+            const $element = this.document.createElement(tag);
+            if (content) {
+                $element.textContent = content;
+            }
+            if (attrs) {
+                Object.entries(attrs).forEach(([k, v]) => {
+                    if (v) {
+                        $element.setAttribute(k, v);
+                    }
+                });
+            }
+            return $element;
+        };
+        this.appendElement = ($parent, tag, content, attrs) => {
+            const $element = this.createElement(tag, content, attrs);
+            $parent.appendChild($element);
+            return $element;
+        };
+        this.changeTag = ($node, tag) => {
+            const $clone = this.createElement(tag);
+            for (const attr of $node.attributes) {
+                $clone.setAttributeNS(null, attr.name, attr.value);
+            }
+            while ($node.firstChild) {
+                $clone.appendChild($node.firstChild);
+            }
+            $node.replaceWith($clone);
+            return $clone;
+        };
+        this.processChildNodes = ($element, node, contentNodeType) => {
+            node.forEach((childNode) => {
+                if (childNode.type === contentNodeType) {
+                    if (childNode.attrs.id) {
+                        $element.appendChild(this.serializeNode(childNode));
+                    }
+                }
+                else if (childNode.type === node.type.schema.nodes.paragraph) {
+                    $element.appendChild(this.serializeNode(childNode));
+                }
+                else if (childNode.type === node.type.schema.nodes.missing_figure) {
+                    $element.appendChild(this.serializeNode(childNode));
+                }
+            });
+        };
+    }
+    isChildOfNodeType(targetID, type, descend = false) {
+        const nodes = this.getChildrenOfType(type);
+        return nodes.some((node) => {
+            const result = findChildrenByAttr(node, (attrs) => attrs.id === targetID, descend)[0];
+            return !!result;
+        });
+    }
+    getChildrenOfType(type, node) {
+        const nodes = node
+            ? findChildrenByType(node, type).map(({ node }) => node)
+            : this.nodesMap.get(type);
+        return (nodes ?? []).filter((n) => isNodeOfType(n, type));
+    }
+    getFirstChildOfType(type, node) {
+        return this.getChildrenOfType(type, node)[0];
+    }
+    fillEmptyElements($article, selector, tagName = 'p') {
+        const $empty = Array.from($article.querySelectorAll(selector)).filter(($el) => !$el.innerHTML);
+        $empty.forEach(($element) => $element.appendChild(this.createElement(tagName)));
+    }
+    createElementWithID(node, nodeName) {
+        const $element = this.createElement(nodeName);
+        $element.setAttribute('id', normalizeID(node.attrs.id));
+        return $element;
+    }
+    serializeNode(node) {
+        return this.serializer.serializeNode(node, {
+            document: this.document,
+        });
+    }
+    appendChildIfPresent($parent, tagName, textContent) {
+        if (!textContent) {
+            return;
+        }
+        const $element = this.createElement(tagName);
+        $element.textContent = textContent;
+        $parent.appendChild($element);
+    }
+}