@manuscripts/transform 4.5.2 → 4.5.4

package/dist/cjs/jats/exporter/jats-versions.js

@@ -15,25 +15,25 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.selectVersionIds = void 0;
+exports.selectVersionIDs = void 0;
 const versions = {
     '1.1': {
-        publicId: '-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD with OASIS Tables with MathML3 v1.1 20151215//EN',
-        systemId: 'http://jats.nlm.nih.gov/archiving/1.1/JATS-archive-oasis-article1-mathml3.dtd',
+        publicID: '-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD with OASIS Tables with MathML3 v1.1 20151215//EN',
+        systemID: 'http://jats.nlm.nih.gov/archiving/1.1/JATS-archive-oasis-article1-mathml3.dtd',
     },
     '1.2d1': {
-        publicId: '-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD with OASIS Tables with MathML3 v1.2d1 20170631//EN',
-        systemId: 'http://jats.nlm.nih.gov/archiving/1.2d1/JATS-archive-oasis-article1-mathml3.dtd',
+        publicID: '-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD with OASIS Tables with MathML3 v1.2d1 20170631//EN',
+        systemID: 'http://jats.nlm.nih.gov/archiving/1.2d1/JATS-archive-oasis-article1-mathml3.dtd',
     },
     '1.2': {
-        publicId: '-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD with OASIS Tables with MathML3 v1.2 20190208//EN',
-        systemId: 'http://jats.nlm.nih.gov/archiving/1.2/JATS-archive-oasis-article1-mathml3.dtd',
+        publicID: '-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD with OASIS Tables with MathML3 v1.2 20190208//EN',
+        systemID: 'http://jats.nlm.nih.gov/archiving/1.2/JATS-archive-oasis-article1-mathml3.dtd',
     },
 };
-const selectVersionIds = (version) => {
+const selectVersionIDs = (version) => {
     if (!(version in versions)) {
         throw new Error(`Unknown version ${version}`);
     }
     return versions[version];
 };
-exports.selectVersionIds = selectVersionIds;
+exports.selectVersionIDs = selectVersionIDs;

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

@@ -2,6 +2,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.JATSDOMParser = void 0;
 const prosemirror_model_1 = require("prosemirror-model");
+const section_categories_1 = require("../../lib/section-categories");
 const utils_1 = require("../../lib/utils");
 const xml_1 = require("../../lib/xml");
 const jats_comments_1 = require("./jats-comments");
@@ -461,6 +462,10 @@ class JATSDOMParser {
                 tag: 'history',
                 ignore: true,
             },
+            {
+                tag: 'statement',
+                ignore: true,
+            },
             {
                 tag: 'break',
                 node: 'hard_break',
@@ -822,7 +827,7 @@ class JATSDOMParser {
                 },
             },
             {
-                tag: 'trans-abstract[sec-type="abstract-graphical"]',
+                tag: 'trans-abstract[abstract-type="graphical"]',
                 node: 'trans_graphical_abstract',
                 getAttrs: (node) => {
                     const element = node;
@@ -833,7 +838,7 @@ 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;
@@ -893,7 +898,7 @@ class JATSDOMParser {
                 getAttrs: (node) => this.parseRef(node),
             },
             {
-                tag: 'sec[sec-type="abstract-graphical"]',
+                tag: 'abstract[abstract-type="graphical"]',
                 node: 'graphical_abstract_section',
                 getAttrs: (node) => {
                     const element = node;
@@ -903,7 +908,7 @@ class JATSDOMParser {
                 },
             },
             {
-                tag: 'sec[sec-type="abstract-key-image"]',
+                tag: 'abstract[abstract-type="key-image"]',
                 node: 'graphical_abstract_section',
                 getAttrs: (node) => {
                     const element = node;
@@ -912,6 +917,18 @@ class JATSDOMParser {
                     };
                 },
             },
+            {
+                tag: 'abstract',
+                node: 'abstract',
+                getAttrs: (node) => {
+                    const element = node;
+                    return {
+                        id: element.getAttribute('id'),
+                        category: this.chooseSectionCategory(element) ||
+                            (0, section_categories_1.abstractTypeToCategory)(element.getAttribute('abstract-type')),
+                    };
+                },
+            },
             {
                 tag: 'sec',
                 node: 'section',
@@ -974,7 +991,7 @@ 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/',
+                context: 'section/|footnotes_section/|bibliography_section/|keywords/|supplements/|author_notes/|abstract/|graphical_abstract_section/|trans_abstract/|trans_graphical_abstract/',
             },
             {
                 tag: 'tr',
@@ -1110,29 +1127,13 @@ class JATSDOMParser {
     parse(doc, options) {
         return this.parser.parse(doc, options);
     }
-    isMatchingCategory(secType, titleNode, category) {
-        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;
-    }
     chooseSectionCategory(section) {
         const secType = section.getAttribute('sec-type');
         const abstractType = section.getAttribute('abstract-type');
-        const effectiveSecType = secType || (abstractType ? `abstract-${abstractType}` : null);
+        const effectiveSecType = secType ?? abstractType;
         const titleNode = section.firstElementChild;
-        for (const category of this.sectionCategories) {
-            if (this.isMatchingCategory(effectiveSecType, titleNode, category)) {
-                return category.id;
-            }
-        }
+        const titleText = titleNode?.nodeName === 'title' ? titleNode.textContent : null;
+        return (0, section_categories_1.findMatchingCategory)(this.sectionCategories, effectiveSecType, titleText)?.id;
     }
     getNameContent(element, type) {
         const query = `person-group[person-group-type="${type}"] > *`;

package/dist/cjs/jats/importer/jats-transformations.js

@@ -17,7 +17,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.fixTables = exports.createAttachments = exports.orderTableFootnote = exports.moveReferencesToBackmatter = exports.createAccessibilityItems = exports.createSupplementaryMaterialsSection = exports.createKeywordsSection = exports.moveCaptionsToEnd = exports.createBackmatter = exports.createAbstracts = exports.createBody = exports.moveHeroImage = exports.moveAbstracts = exports.moveAffiliations = exports.moveContributors = exports.moveAwards = exports.moveAuthorNotes = exports.createTitles = exports.createBoxedElementSection = exports.addMissingCaptions = void 0;
 const deafults_1 = require("../../lib/deafults");
-const xml_1 = require("../../lib/xml");
+const section_categories_1 = require("../../lib/section-categories");
 const jats_parser_utils_1 = require("./jats-parser-utils");
 const removeNodeFromParent = (node) => node.parentNode && node.parentNode.removeChild(node);
 const capitalizeFirstLetter = (str) => str.charAt(0).toUpperCase() + str.slice(1);
@@ -118,8 +118,7 @@ exports.moveAffiliations = moveAffiliations;
 const moveAbstracts = (front, group, createElement, sectionCategories) => {
     const abstracts = front.querySelectorAll('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);
     });
 };
@@ -186,7 +185,7 @@ const moveSpecialFootnotes = (doc, group, sectionCategories, createElement) => {
     const fns = [...doc.querySelectorAll('fn[fn-type]')];
     for (const fn of fns) {
         const type = fn.getAttribute('fn-type') || '';
-        const category = sectionCategories.find((category) => category.synonyms.includes(type));
+        const category = (0, section_categories_1.findMatchingCategory)(sectionCategories, type);
         if (category) {
             const section = createElement('sec');
             const fnTitle = fn.querySelector('label') ||
@@ -221,35 +220,20 @@ const moveCaptionsToEnd = (body) => {
     }
 };
 exports.moveCaptionsToEnd = moveCaptionsToEnd;
-const createAbstractSection = (abstract, createElement, sectionCategories) => {
-    const abstractType = abstract.getAttribute('abstract-type');
-    const sectionType = abstractType ? `abstract-${abstractType}` : 'abstract';
-    let section = createElement('sec');
-    if (abstract.nodeName === 'trans-abstract') {
-        section = createElement('trans-abstract');
-        const lang = abstract.getAttributeNS(xml_1.XML_NAMESPACE, 'lang');
-        if (lang) {
-            section.setAttributeNS(xml_1.XML_NAMESPACE, 'lang', lang);
-        }
-    }
-    section.setAttribute('sec-type', sectionType);
+const prepareAbstract = (abstract, createElement, sectionCategories) => {
+    const rawType = abstract.getAttribute('abstract-type');
+    const category = (0, section_categories_1.abstractTypeToCategory)(rawType);
     if (!abstract.querySelector(':scope > title')) {
+        const matched = sectionCategories && (0, section_categories_1.findMatchingCategory)(sectionCategories, category);
         const title = createElement('title');
-        const category = sectionCategories?.find((c) => c.id === sectionType || c.synonyms.includes(sectionType));
-        if (category?.titles[0]) {
-            title.textContent = category.titles[0];
-        }
-        else {
-            title.textContent = abstractType
-                ? `${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 = (ack, createElement) => {
     const section = createElement('sec');

package/dist/cjs/lib/section-categories.js

@@ -15,7 +15,7 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getGroupCategories = void 0;
+exports.FOOTNOTE_SECTION_CATEGORY_IDS = exports.abstractTypeToCategory = exports.findMatchingCategory = exports.getGroupCategories = void 0;
 const getGroupCategories = (sections, group) => {
     const sectionsArray = Array.isArray(sections)
         ? sections
@@ -23,3 +23,33 @@ const getGroupCategories = (sections, group) => {
     return sectionsArray.filter((section) => section.group === group);
 };
 exports.getGroupCategories = getGroupCategories;
+const findMatchingCategory = (categories, type, titleText) => {
+    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;
+    });
+};
+exports.findMatchingCategory = findMatchingCategory;
+const abstractTypeToCategory = (abstractType) => abstractType || 'abstract';
+exports.abstractTypeToCategory = abstractTypeToCategory;
+exports.FOOTNOTE_SECTION_CATEGORY_IDS = [
+    'con',
+    'conflict',
+    'deceased',
+    'equal',
+    'present-address',
+    'presented-at',
+    'previously-at',
+    'supplementary-material',
+    'supported-by',
+    'financial-disclosure',
+    'coi-statement',
+];

package/dist/cjs/schema/index.js

@@ -33,6 +33,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.schema = void 0;
 const prosemirror_model_1 = require("prosemirror-model");
 const marks_1 = require("./marks");
+const abstract_1 = require("./nodes/abstract");
 const abstracts_1 = require("./nodes/abstracts");
 const affiliation_1 = require("./nodes/affiliation");
 const affiliations_1 = require("./nodes/affiliations");
@@ -113,6 +114,7 @@ const title_1 = require("./nodes/title");
 const trans_abstract_1 = require("./nodes/trans_abstract");
 const trans_graphical_abstract_1 = require("./nodes/trans_graphical_abstract");
 __exportStar(require("./groups"), exports);
+__exportStar(require("./nodes/abstract"), exports);
 __exportStar(require("./nodes/affiliation"), exports);
 __exportStar(require("./nodes/affiliations"), exports);
 __exportStar(require("./nodes/alt_text"), exports);
@@ -216,6 +218,7 @@ exports.schema = new prosemirror_model_1.Schema({
         caption: caption_1.caption,
         caption_title: caption_title_1.captionTitle,
         citation: citation_1.citation,
+        abstract: abstract_1.abstract,
         abstracts: abstracts_1.abstracts,
         body: body_1.body,
         backmatter: backmatter_1.backmatter,

package/dist/cjs/schema/migration/migration-scripts/4.5.3.js

@@ -0,0 +1,37 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const TRANS_ABSTRACT_TYPES = ['trans_abstract', 'trans_graphical_abstract'];
+class Migration453 {
+    constructor() {
+        this.fromVersion = '4.5.2';
+        this.toVersion = '4.5.3';
+    }
+    migrateNode(node) {
+        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 = [];
+        const translated = [];
+        for (const child of children) {
+            if (TRANS_ABSTRACT_TYPES.includes(child.type)) {
+                translated.push(child);
+            }
+            else {
+                regular.push(child);
+            }
+        }
+        return {
+            ...node,
+            content: [...regular, ...translated],
+        };
+    }
+}
+exports.default = Migration453;

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

@@ -34,6 +34,7 @@ const _4_3_34_1 = __importDefault(require("./4.3.34"));
 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 migrations = [
     new _1_2_5_1.default(),
     new _2_3_22_1.default(),
@@ -51,5 +52,6 @@ const migrations = [
     new _4_3_35_1.default(),
     new _4_4_2_1.default(),
     new _4_4_7_1.default(),
+    new _4_5_3_1.default(),
 ];
 exports.default = migrations;

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

@@ -0,0 +1,51 @@
+"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.isAbstractNode = exports.abstract = void 0;
+exports.abstract = {
+    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;
+                return {
+                    id: element.getAttribute('id') || '',
+                    category: element.getAttribute('data-category') || '',
+                };
+            },
+        },
+    ],
+    toDOM: (node) => {
+        const abstractNode = node;
+        const { id, category } = abstractNode.attrs;
+        const attrs = { id, class: 'abstract' };
+        if (category) {
+            attrs['data-category'] = category;
+        }
+        return ['section', attrs, 0];
+    },
+};
+const isAbstractNode = (node) => node.type === node.type.schema.nodes.abstract;
+exports.isAbstractNode = isAbstractNode;

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

@@ -17,7 +17,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.abstracts = void 0;
 exports.abstracts = {
-    content: 'sections* (trans_abstract | trans_graphical_abstract)*',
+    content: '(abstract | graphical_abstract_section)* (trans_abstract | trans_graphical_abstract)*',
     attrs: {
         id: { default: '' },
     },

package/dist/cjs/transformer/node-names.js

@@ -54,6 +54,7 @@ exports.nodeNames = new Map([
     [schema_1.schema.nodes.paragraph, 'Paragraph'],
     [schema_1.schema.nodes.text_block, 'Paragraph'],
     [schema_1.schema.nodes.section, 'Section'],
+    [schema_1.schema.nodes.abstract, 'Abstract'],
     [schema_1.schema.nodes.graphical_abstract_section, 'Graphical Abstract'],
     [schema_1.schema.nodes.trans_abstract, 'Trans Abstract'],
     [schema_1.schema.nodes.trans_graphical_abstract, 'Trans Graphical Abstract'],

package/dist/cjs/transformer/node-title.js

@@ -53,6 +53,7 @@ const nodeTitle = (node) => {
         case nodes.manuscript:
             return snippetOfNodeType(node, nodes.title);
         case nodes.section:
+        case nodes.abstract:
         case nodes.bibliography_section:
         case nodes.footnotes_section:
         case nodes.keywords:
@@ -90,6 +91,7 @@ const nodeTitlePlaceholder = (nodeType) => {
         case nodes.manuscript:
             return 'Untitled Manuscript';
         case nodes.section:
+        case nodes.abstract:
             return 'Untitled Section';
         case nodes.bibliography_section:
             return 'Bibliography';

package/dist/cjs/version.js

@@ -1,4 +1,4 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.VERSION = void 0;
-exports.VERSION = "4.5.2";
+exports.VERSION = "4.5.4";

package/dist/es/jats/__tests__/data/section-categories.js

@@ -22,35 +22,35 @@ export const sectionCategories = [
         isUnique: true,
     },
     {
-        id: 'abstract-graphical',
+        id: 'graphical',
         titles: ['Graphical Abstract'],
         synonyms: [''],
         group: 'abstracts-graphic',
         isUnique: true,
     },
     {
-        id: 'abstract-key-image',
+        id: 'key-image',
         titles: ['Key Image'],
         synonyms: [''],
         group: 'abstracts-graphic',
         isUnique: true,
     },
     {
-        id: 'abstract-short',
+        id: 'short',
         titles: ['Short'],
         synonyms: [''],
         group: 'abstracts',
         isUnique: true,
     },
     {
-        id: 'abstract-teaser',
+        id: 'teaser',
         titles: ['Abstract Teaser'],
         synonyms: [''],
         isUnique: true,
         group: 'abstracts',
     },
     {
-        id: 'abstract-toc',
+        id: 'toc',
         titles: ['Table of contents'],
         synonyms: [''],
         group: 'abstracts',

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

@@ -289,8 +289,22 @@ describe('JATS importer', () => {
             }
             const node = parseJATSArticle(jats, sectionCategories);
             const abstractsNode = findNodeByType(node, schema.nodes.abstracts);
-            const sections = findNodesByType(abstractsNode, schema.nodes.section);
-            expect(sections).toHaveLength(6);
+            const abstracts = findNodesByType(abstractsNode, schema.nodes.abstract);
+            expect(abstracts).toHaveLength(2);
+        });
+        it('should order abstracts children per the schema', async () => {
+            const jats = await readAndParseFixture('jats-import.xml');
+            const node = parseJATSArticle(jats, sectionCategories);
+            const abstractsNode = findNodeByType(node, schema.nodes.abstracts);
+            const childTypes = [];
+            abstractsNode.content.forEach((child) => childTypes.push(child.type.name));
+            expect(childTypes).toEqual([
+                'abstract',
+                'graphical_abstract_section',
+                'graphical_abstract_section',
+                'abstract',
+                'trans_abstract',
+            ]);
         });
         it('should set the title to Abstract if no title is provided', async () => {
             const jats = await readAndParseFixture('jats-import.xml');
@@ -300,9 +314,9 @@ describe('JATS importer', () => {
             }
             const node = parseJATSArticle(jats, sectionCategories);
             const abstractsNode = findNodeByType(node, schema.nodes.abstracts);
-            const sections = findNodesByType(abstractsNode, schema.nodes.section);
-            const firstSection = sections[0];
-            const titleNode = findNodeByType(firstSection, schema.nodes.section_title);
+            const abstracts = findNodesByType(abstractsNode, schema.nodes.abstract);
+            const firstAbstract = abstracts[0];
+            const titleNode = findNodeByType(firstAbstract, schema.nodes.section_title);
             expect(titleNode.textContent).toBe('Abstract');
         });
     });