@manuscripts/transform 3.0.21-LEAN-4076.1 → 3.0.21

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

@@ -17,17 +17,12 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.fixTables = exports.orderTableFootnote = exports.moveReferencesToBackmatter = exports.createSupplementaryMaterialsSection = exports.createKeywordsSection = exports.moveCaptionsToEnd = exports.createBackmatter = exports.createAbstracts = exports.createBody = exports.createBoxedElementSection = exports.moveAbstracts = exports.moveAffiliations = exports.moveContributors = exports.moveAwards = exports.moveAuthorNotes = exports.moveTitle = void 0;
 const deafults_1 = require("../../lib/deafults");
-const section_group_type_1 = require("../../lib/section-group-type");
-const transformer_1 = require("../../transformer");
 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);
 const createSectionGroup = (type, createElement) => {
     const sec = createElement('sec');
-    sec.setAttribute('sec-type', type._id);
-    const title = createElement('title');
-    title.textContent = type.title;
-    sec.appendChild(title);
+    sec.setAttribute('sec-type', type);
     return sec;
 };
 const moveTitle = (front, createElement) => {
@@ -115,7 +110,7 @@ const createBoxedElementSection = (body, createElement) => {
 };
 exports.createBoxedElementSection = createBoxedElementSection;
 const createBody = (doc, body, createElement) => {
-    const group = createSectionGroup(section_group_type_1.bodyType, createElement);
+    const group = createSectionGroup('body', createElement);
     const paragraphs = doc.querySelectorAll('body > p');
     group.append(...paragraphs);
     const sections = doc.querySelectorAll('body > sec:not([sec-type="backmatter"]), body > sec:not([sec-type])');
@@ -128,16 +123,16 @@ const createBody = (doc, body, createElement) => {
 };
 exports.createBody = createBody;
 const createAbstracts = (doc, body, createElement) => {
-    const group = createSectionGroup(section_group_type_1.abstractsType, createElement);
+    const group = createSectionGroup('abstracts', createElement);
     (0, exports.moveAbstracts)(doc, group, createElement);
     body.insertBefore(group, body.lastElementChild);
 };
 exports.createAbstracts = createAbstracts;
-const createBackmatter = (doc, body, createElement) => {
-    const group = createSectionGroup(section_group_type_1.backmatterType, createElement);
+const createBackmatter = (doc, body, sectionCategories, createElement) => {
+    const group = createSectionGroup('backmatter', createElement);
     moveBackSections(doc, group);
     moveAppendices(doc, group, createElement);
-    moveSpecialFootnotes(doc, group, createElement);
+    moveSpecialFootnotes(doc, group, sectionCategories, createElement);
     moveFootnotes(doc, group, createElement);
     moveAcknowledgments(doc, group, createElement);
     body.append(group);
@@ -162,12 +157,12 @@ const moveFootnotes = (doc, group, createElement) => {
         group.insertBefore(section, ((_a = group.firstChild) === null || _a === void 0 ? void 0 : _a.nextSibling) || group.firstChild);
     }
 };
-const moveSpecialFootnotes = (doc, group, createElement) => {
+const moveSpecialFootnotes = (doc, group, sectionCategories, createElement) => {
     var _a;
     const fns = [...doc.querySelectorAll('fn[fn-type]')];
     for (const fn of fns) {
         const type = fn.getAttribute('fn-type') || '';
-        const category = (0, transformer_1.chooseSectionCategoryByType)(type);
+        const category = sectionCategories.find((category) => category.synonyms.includes(type));
         if (category) {
             const section = createElement('sec');
             const fnTitle = fn.querySelector('p[content-type="fn-title"]');
@@ -182,7 +177,7 @@ const moveSpecialFootnotes = (doc, group, createElement) => {
             }
             section.append(...fn.children);
             removeNodeFromParent(fn);
-            section.setAttribute('sec-type', (0, transformer_1.chooseSecType)(category));
+            section.setAttribute('sec-type', category.id);
             group.append(section);
         }
     }

package/dist/cjs/jats/importer/parse-jats-article.js

@@ -16,12 +16,13 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.parseJATSArticle = void 0;
+const schema_1 = require("../../schema");
 const jats_comments_1 = require("./jats-comments");
 const jats_dom_parser_1 = require("./jats-dom-parser");
 const jats_journal_meta_parser_1 = require("./jats-journal-meta-parser");
 const jats_parser_utils_1 = require("./jats-parser-utils");
 const jats_transformations_1 = require("./jats-transformations");
-const processJATS = (doc) => {
+const processJATS = (doc, sectionCategories) => {
     const createElement = createElementFn(doc);
     (0, jats_comments_1.markComments)(doc);
     const front = doc.querySelector('front');
@@ -41,7 +42,7 @@ const processJATS = (doc) => {
     (0, jats_transformations_1.createBoxedElementSection)(body, createElement);
     (0, jats_transformations_1.createBody)(doc, body, createElement);
     (0, jats_transformations_1.createAbstracts)(doc, body, createElement);
-    (0, jats_transformations_1.createBackmatter)(doc, body, createElement);
+    (0, jats_transformations_1.createBackmatter)(doc, body, sectionCategories, createElement);
     (0, jats_transformations_1.createSupplementaryMaterialsSection)(doc, body, createElement);
     (0, jats_transformations_1.createKeywordsSection)(doc, body, createElement);
     (0, jats_transformations_1.fixTables)(doc, body, createElement);
@@ -53,10 +54,11 @@ const processJATS = (doc) => {
     (0, jats_transformations_1.moveReferencesToBackmatter)(body, back, createElement);
 };
 const createElementFn = (doc) => (tagName) => doc.createElement(tagName);
-const parseJATSArticle = (doc, template) => {
+const parseJATSArticle = (doc, sectionCategories, template) => {
     const journal = (0, jats_journal_meta_parser_1.parseJournal)(doc);
-    processJATS(doc);
-    const node = jats_dom_parser_1.jatsDOMParser.parse(doc).firstChild;
+    processJATS(doc, sectionCategories);
+    const node = new jats_dom_parser_1.JATSDOMParser(sectionCategories, schema_1.schema).parse(doc)
+        .firstChild;
     if (!node) {
         throw new Error('No content was parsed from the JATS article body');
     }

package/dist/cjs/lib/{section-group-type.js → section-categories.js}

@@ -1,6 +1,6 @@
 "use strict";
 /*!
- * © 2023 Atypon Systems LLC
+ * © 2024 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.
@@ -15,16 +15,6 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.backmatterType = exports.bodyType = exports.abstractsType = void 0;
-exports.abstractsType = {
-    _id: 'abstracts',
-    title: 'Abstracts',
-};
-exports.bodyType = {
-    _id: 'body',
-    title: 'Body',
-};
-exports.backmatterType = {
-    _id: 'backmatter',
-    title: 'Backmatter',
-};
+exports.getGroupCateogries = void 0;
+const getGroupCateogries = (sectionsMap, group) => Array.from(sectionsMap.values()).filter((section) => section.group === group);
+exports.getGroupCateogries = getGroupCateogries;

package/dist/cjs/schema/index.js

@@ -154,8 +154,6 @@ __exportStar(require("./nodes/supplement"), exports);
 __exportStar(require("./nodes/supplements"), exports);
 __exportStar(require("./nodes/corresp"), exports);
 __exportStar(require("./nodes/author_notes"), exports);
-__exportStar(require("./nodes/award"), exports);
-__exportStar(require("./nodes/awards"), exports);
 exports.schema = new prosemirror_model_1.Schema({
     marks: {
         bold: marks_1.bold,

package/dist/cjs/schema/migration/migration-scripts/3.0.21.js

@@ -0,0 +1,25 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+class Migration3021 {
+    constructor() {
+        this.fromVersion = '3.0.20';
+        this.toVersion = '3.0.21';
+        this.suffixMap = new Map([
+            ['competing-interests', 'coi-statement'],
+            ['acknowledgement', 'acknowledgements'],
+            ['introduction', 'intro'],
+            ['materials-method', 'methods'],
+            ['subsection', ''],
+        ]);
+    }
+    migrateNode(node) {
+        if (node.type === 'section' &&
+            node.attrs.category.startsWith('MPSectionCategory:')) {
+            const [, suffix] = node.attrs.category.split(':', 2);
+            const newCategory = this.suffixMap.get(suffix) || suffix;
+            return Object.assign(Object.assign({}, node), { attrs: Object.assign(Object.assign({}, node.attrs), { category: newCategory }) });
+        }
+        return node;
+    }
+}
+exports.default = Migration3021;

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

@@ -21,9 +21,11 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const _1_2_5_1 = __importDefault(require("./1.2.5"));
 const _2_3_22_1 = __importDefault(require("./2.3.22"));
 const _3_0_12_1 = require("./3.0.12");
+const _3_0_21_1 = __importDefault(require("./3.0.21"));
 const migrations = [
     new _1_2_5_1.default(),
     new _2_3_22_1.default(),
     new _3_0_12_1.Migration3012(),
+    new _3_0_21_1.default(),
 ];
 exports.default = migrations;

package/dist/cjs/transformer/index.js

@@ -33,4 +33,3 @@ __exportStar(require("./id"), exports);
 __exportStar(require("./node-names"), exports);
 __exportStar(require("./node-title"), exports);
 __exportStar(require("./node-types"), exports);
-__exportStar(require("./section-category"), exports);

package/dist/cjs/version.js

@@ -1,4 +1,4 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.VERSION = void 0;
-exports.VERSION = "3.0.21-LEAN-4076.1";
+exports.VERSION = "3.0.21";

package/dist/es/index.js

@@ -2,10 +2,9 @@ export * from './errors';
 export { getVersion } from './getVersion';
 export * from './jats';
 export * from './jats/types';
-export * from './lib/section-group-type';
-export * from './lib/table-cell-styles';
 export * from './lib/footnotes';
 export * from './lib/utils';
+export * from './lib/section-categories';
 export * from './schema';
 export { migrateFor } from './schema/migration/migrate';
 export { isSectionLabelNode } from './schema/nodes/section_label';

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

@@ -22,7 +22,7 @@ import serializeToXML from 'w3c-xmlserializer';
 import { generateFootnoteLabels } from '../../lib/footnotes';
 import { nodeFromHTML, textFromHTML } from '../../lib/html';
 import { isCitationNode, schema, } from '../../schema';
-import { chooseJatsFnType, chooseSecType, isExecutableNodeType, isNodeType, } from '../../transformer';
+import { isExecutableNodeType, isNodeType } from '../../transformer';
 import { selectVersionIds } from './jats-versions';
 import { buildTargets } from './labels';
 const warn = debug('manuscripts-transform');
@@ -776,7 +776,7 @@ export class JATSExporter {
                         id: normalizeID(node.attrs.id),
                     };
                     if (node.attrs.category) {
-                        attrs['sec-type'] = chooseSecType(node.attrs.category);
+                        attrs['sec-type'] = node.attrs.category;
                     }
                     return ['sec', attrs, 0];
                 },
@@ -1229,7 +1229,7 @@ export class JATSExporter {
                                         break;
                                     }
                                     case 'table': {
-                                        this.fixTable(childNode, node);
+                                        this.fixTable(childNode);
                                         break;
                                     }
                                 }
@@ -1250,7 +1250,7 @@ export class JATSExporter {
             node.replaceWith(clone);
             return clone;
         };
-        this.fixTable = (table, node) => {
+        this.fixTable = (table) => {
             let tbody;
             Array.from(table.childNodes).forEach((child) => {
                 if (child instanceof Element && child.tagName.toLowerCase() === 'tbody') {
@@ -1377,7 +1377,7 @@ export class JATSExporter {
             if (availabilitySection) {
                 back.insertBefore(availabilitySection, back.firstChild);
             }
-            const section = body.querySelector('sec[sec-type="acknowledgments"]');
+            const section = body.querySelector('sec[sec-type="acknowledgements"]');
             if (section) {
                 const ack = this.document.createElement('ack');
                 while (section.firstChild) {
@@ -1414,7 +1414,7 @@ export class JATSExporter {
                 'supported-by',
                 'financial-disclosure',
                 'ethics-statement',
-                'competing-interests',
+                'coi-statement',
             ];
             const sections = body.querySelectorAll('sec');
             for (const currentSection of sections) {
@@ -1565,7 +1565,7 @@ export class JATSExporter {
         const fnGroups = back.querySelectorAll('fn-group');
         fnGroups.forEach((fnGroup) => {
             if (fnGroup) {
-                const coiStatement = fnGroup.querySelector('fn[fn-type="competing-interests"]');
+                const coiStatement = fnGroup.querySelector('fn[fn-type="coi-statement"]');
                 if (coiStatement) {
                     const authorNotes = this.document.createElement('author-notes');
                     authorNotes.append(coiStatement);
@@ -1607,7 +1607,7 @@ export class JATSExporter {
         footnotes.forEach((fn) => {
             const fnType = fn.getAttribute('fn-type');
             if (fnType) {
-                fn.setAttribute('fn-type', chooseJatsFnType(fnType));
+                fn.setAttribute('fn-type', fnType);
             }
         });
     }