@manuscripts/transform 4.5.7 → 4.6.0

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

@@ -14,8 +14,12 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
 Object.defineProperty(exports, "__esModule", { value: true });
 const libxmljs2_1 = require("libxmljs2");
+const w3c_xmlserializer_1 = __importDefault(require("w3c-xmlserializer"));
 const jats_exporter_1 = require("../exporter/jats-exporter");
 const parse_jats_article_1 = require("../importer/parse-jats-article");
 const citations_1 = require("./citations");
@@ -32,10 +36,10 @@ describe('JATS exporter', () => {
         const transformer = new jats_exporter_1.JATSExporter();
         const input = await (0, files_1.readAndParseFixture)('jats-example-full.xml');
         const node = (0, parse_jats_article_1.parseJATSArticle)(input, section_categories_1.sectionCategories);
-        const result = await transformer.serializeToJATS(node, {
+        const document = await transformer.export(node, {
             csl: citations_1.DEFAULT_CSL_OPTIONS,
         });
-        expect(result).toMatchSnapshot('jats-export');
+        expect((0, w3c_xmlserializer_1.default)(document)).toMatchSnapshot('jats-export');
     });
     test('export with & and < in bibliography metadata', async () => {
         const transformer = new jats_exporter_1.JATSExporter();
@@ -48,27 +52,27 @@ describe('JATS exporter', () => {
             }
         });
         biblio.attrs.title += ' & Sons 55 < 135';
-        const result = await transformer.serializeToJATS(node, {
+        const document = await transformer.export(node, {
             csl: citations_1.DEFAULT_CSL_OPTIONS,
         });
-        expect(result).toMatchSnapshot('jats-export-with-xml-unsafe-in-biblios');
+        expect((0, w3c_xmlserializer_1.default)(document)).toMatchSnapshot('jats-export-with-xml-unsafe-in-biblios');
     });
     test('export v1.1', async () => {
         const transformer = new jats_exporter_1.JATSExporter();
         const input = await (0, files_1.readAndParseFixture)('jats-example-full.xml');
         const node = (0, parse_jats_article_1.parseJATSArticle)(input, section_categories_1.sectionCategories);
-        const result = await transformer.serializeToJATS(node, {
+        const document = await transformer.export(node, {
             csl: citations_1.DEFAULT_CSL_OPTIONS,
             version: '1.1',
         });
-        expect(result).toMatchSnapshot('jats-export-1.1');
+        expect((0, w3c_xmlserializer_1.default)(document)).toMatchSnapshot('jats-export-1.1');
     });
     test('export unknown version', async () => {
         const transformer = new jats_exporter_1.JATSExporter();
         const input = await (0, files_1.readAndParseFixture)('jats-example-full.xml');
         const node = (0, parse_jats_article_1.parseJATSArticle)(input, section_categories_1.sectionCategories);
         await expect(async () => {
-            await transformer.serializeToJATS(node, {
+            await transformer.export(node, {
                 csl: citations_1.DEFAULT_CSL_OPTIONS,
                 version: '1.0',
             });
@@ -78,9 +82,10 @@ describe('JATS exporter', () => {
         const transformer = new jats_exporter_1.JATSExporter();
         const input = await (0, files_1.readAndParseFixture)('jats-tables-example.xml');
         const node = (0, parse_jats_article_1.parseJATSArticle)(input, section_categories_1.sectionCategories);
-        const xml = await transformer.serializeToJATS(node, {
+        const document = await transformer.export(node, {
             csl: citations_1.DEFAULT_CSL_OPTIONS,
         });
+        const xml = (0, w3c_xmlserializer_1.default)(document);
         const resultDoc = parseXMLWithDTD(xml);
         const tableWrapFoot = resultDoc.get('//table-wrap/table-wrap-foot');
         const paragraph = resultDoc.get('//table-wrap/table-wrap-foot/p');
@@ -91,30 +96,30 @@ describe('JATS exporter', () => {
         const transformer = new jats_exporter_1.JATSExporter();
         const input = await (0, files_1.readAndParseFixture)('jats-import.xml');
         const node = (0, parse_jats_article_1.parseJATSArticle)(input, section_categories_1.sectionCategories);
-        const xml = await transformer.serializeToJATS(node, {
+        const document = await transformer.export(node, {
             csl: citations_1.DEFAULT_CSL_OPTIONS,
         });
-        const { errors } = parseXMLWithDTD(xml);
+        const { errors } = parseXMLWithDTD((0, w3c_xmlserializer_1.default)(document));
         expect(errors).toHaveLength(0);
     });
     test('DTD validation: article with title markup and citations', async () => {
         const transformer = new jats_exporter_1.JATSExporter();
         const input = await (0, files_1.readAndParseFixture)('jats-document.xml');
         const node = (0, parse_jats_article_1.parseJATSArticle)(input, section_categories_1.sectionCategories);
-        const xml = await transformer.serializeToJATS(node, {
+        const document = await transformer.export(node, {
             csl: citations_1.DEFAULT_CSL_OPTIONS,
         });
-        const { errors } = parseXMLWithDTD(xml);
+        const { errors } = parseXMLWithDTD((0, w3c_xmlserializer_1.default)(document));
         expect(errors).toHaveLength(0);
     });
     test('Export link', async () => {
         const transformer = new jats_exporter_1.JATSExporter();
         const input = await (0, files_1.readAndParseFixture)('jats-import.xml');
         const node = (0, parse_jats_article_1.parseJATSArticle)(input, section_categories_1.sectionCategories);
-        const xml = await transformer.serializeToJATS(node, {
+        const document = await transformer.export(node, {
             csl: citations_1.DEFAULT_CSL_OPTIONS,
         });
-        const output = parseXMLWithDTD(xml);
+        const output = parseXMLWithDTD((0, w3c_xmlserializer_1.default)(document));
         const link = output.get('//ext-link[@ext-link-type="uri"]');
         expect(link).not.toBeNull();
         expect(link.text()).toBe('https//orcid.org/0000-0003-2217-5904');
@@ -129,20 +134,20 @@ describe('JATS exporter', () => {
         const transformer = new jats_exporter_1.JATSExporter();
         const input = await (0, files_1.readAndParseFixture)('jats-example-doc.xml');
         const node = (0, parse_jats_article_1.parseJATSArticle)(input, section_categories_1.sectionCategories);
-        const xml = await transformer.serializeToJATS(node, {
+        const document = await transformer.export(node, {
             csl: citations_1.DEFAULT_CSL_OPTIONS,
         });
-        const { errors } = parseXMLWithDTD(xml);
+        const { errors } = parseXMLWithDTD((0, w3c_xmlserializer_1.default)(document));
         expect(errors).toHaveLength(0);
     });
     test('export with supplement', async () => {
         const transformer = new jats_exporter_1.JATSExporter();
         const input = await (0, files_1.readAndParseFixture)('jats-import.xml');
         const node = (0, parse_jats_article_1.parseJATSArticle)(input, section_categories_1.sectionCategories);
-        const xml = await transformer.serializeToJATS(node, {
+        const document = await transformer.export(node, {
             csl: citations_1.DEFAULT_CSL_OPTIONS,
         });
-        const resultDoc = parseXMLWithDTD(xml);
+        const resultDoc = parseXMLWithDTD((0, w3c_xmlserializer_1.default)(document));
         const supplementaryMaterial = resultDoc.get('//supplementary-material');
         if (!supplementaryMaterial) {
             throw new Error('No supplementary material found');
@@ -169,9 +174,10 @@ describe('JATS exporter', () => {
                 n.attrs.rids.forEach((rid) => citedIDs.add(rid));
             }
         });
-        const xml = await new jats_exporter_1.JATSExporter().serializeToJATS(node, {
+        const document = await new jats_exporter_1.JATSExporter().export(node, {
             csl: citations_1.DEFAULT_CSL_OPTIONS,
         });
+        const xml = (0, w3c_xmlserializer_1.default)(document);
         const refCount = parseXMLWithDTD(xml).find('//ref-list/ref').length;
         expect(refCount).toBe(bibliographyItemIDs.size);
         const { errors } = parseXMLWithDTD(xml);
@@ -181,9 +187,10 @@ describe('JATS exporter', () => {
         const transformer = new jats_exporter_1.JATSExporter();
         const input = await (0, files_1.readAndParseFixture)('jats-fn-group.xml');
         const node = (0, parse_jats_article_1.parseJATSArticle)(input, section_categories_1.sectionCategories);
-        const xml = await transformer.serializeToJATS(node, {
+        const document = await transformer.export(node, {
             csl: citations_1.DEFAULT_CSL_OPTIONS,
         });
+        const xml = (0, w3c_xmlserializer_1.default)(document);
         const footnoteCategories = [
             'con',
             'deceased',
@@ -196,4 +203,27 @@ describe('JATS exporter', () => {
             expect(fn).not.toBeUndefined();
         }
     });
+    test('export contributor bio', async () => {
+        const transformer = new jats_exporter_1.JATSExporter();
+        const input = await (0, files_1.readAndParseFixture)('jats-import.xml');
+        const node = (0, parse_jats_article_1.parseJATSArticle)(input, section_categories_1.sectionCategories);
+        const xml = await transformer.export(node, {
+            csl: citations_1.DEFAULT_CSL_OPTIONS,
+        });
+        const serialized = (0, w3c_xmlserializer_1.default)(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/cjs/jats/__tests__/jats-importer.test.js

@@ -60,6 +60,32 @@ 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 (0, files_1.readAndParseFixture)('jats-import.xml');
+            const node = (0, parse_jats_article_1.parseJATSArticle)(jats, section_categories_1.sectionCategories);
+            (0, utils_1.changeIDs)(node);
+            const [contributor] = (0, utils_1.findNodesByType)(node, schema_1.schema.nodes.contributor);
+            expect(contributor.childCount).toBe(1);
+            const bio = contributor.firstChild;
+            expect(bio.type).toBe(schema_1.schema.nodes.bio);
+            expect(bio.childCount).toBe(2);
+            const image = (0, utils_1.findNodeByType)(bio, schema_1.schema.nodes.image_element);
+            expect((0, utils_1.findNodeByType)(image, schema_1.schema.nodes.figure).attrs.src).toBe('agnete-hornnes.png');
+            expect((0, utils_1.findNodeByType)(image, schema_1.schema.nodes.alt_text).textContent).toBe('Headshot of Agnete Hviid Hornnes');
+            const paragraph = bio.lastChild;
+            expect(paragraph.type).toBe(schema_1.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 (0, files_1.readAndParseFixture)('jats-import.xml');
+            const node = (0, parse_jats_article_1.parseJATSArticle)(jats, section_categories_1.sectionCategories);
+            const [, contributor] = (0, utils_1.findNodesByType)(node, schema_1.schema.nodes.contributor);
+            expect(contributor.childCount).toBe(0);
+            expect((0, utils_1.findNodesByType)(node, schema_1.schema.nodes.bio)).toHaveLength(1);
+        });
+    });
     describe('affiliations', () => {
         it('should correctly parse affiliation nodes', async () => {
             const jats = await (0, files_1.readAndParseFixture)('jats-import.xml');

package/dist/cjs/jats/__tests__/jats-roundtrip.test.js

@@ -14,8 +14,12 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
 Object.defineProperty(exports, "__esModule", { value: true });
 const libxmljs2_1 = require("libxmljs2");
+const w3c_xmlserializer_1 = __importDefault(require("w3c-xmlserializer"));
 const jats_exporter_1 = require("../exporter/jats-exporter");
 const parse_jats_article_1 = require("../importer/parse-jats-article");
 const citations_1 = require("./citations");
@@ -31,9 +35,10 @@ const roundtrip = async (filename) => {
     const doc = new DOMParser().parseFromString(input, 'application/xml');
     const node = (0, parse_jats_article_1.parseJATSArticle)(doc, section_categories_1.sectionCategories);
     const exporter = new jats_exporter_1.JATSExporter();
-    return await exporter.serializeToJATS(node, {
+    const document = await exporter.export(node, {
         csl: citations_1.DEFAULT_CSL_OPTIONS,
     });
+    return (0, w3c_xmlserializer_1.default)(document);
 };
 describe('JATS roundtrip', () => {
     test('jats-import.xml roundtrip', async () => {

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

@@ -0,0 +1,118 @@
+"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.JATSExporterBase = void 0;
+const prosemirror_utils_1 = require("prosemirror-utils");
+const schema_1 = require("../../schema");
+const lib_1 = require("./lib");
+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) {
+                    $element.appendChild(this.serializeNode(childNode));
+                }
+            });
+        };
+    }
+    isChildOfNodeType(targetID, type, descend = false) {
+        const nodes = this.getChildrenOfType(type);
+        return nodes.some((node) => {
+            const result = (0, prosemirror_utils_1.findChildrenByAttr)(node, (attrs) => attrs.id === targetID, descend)[0];
+            return !!result;
+        });
+    }
+    getChildrenOfType(type, node) {
+        const nodes = node
+            ? (0, prosemirror_utils_1.findChildrenByType)(node, type).map(({ node }) => node)
+            : this.nodesMap.get(type);
+        return (nodes ?? []).filter((n) => (0, schema_1.isNodeOfType)(n, type));
+    }
+    getFirstChildOfType(type, node) {
+        return this.getChildrenOfType(type, node)[0];
+    }
+    fillEmptyElements($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', (0, lib_1.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);
+    }
+}
+exports.JATSExporterBase = JATSExporterBase;