@manuscripts/transform 4.5.6 → 4.5.8

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Files changed (25) hide show
  1. package/dist/cjs/jats/__tests__/jats-exporter.test.js +27 -20
  2. package/dist/cjs/jats/__tests__/jats-roundtrip.test.js +6 -1
  3. package/dist/cjs/jats/exporter/jats-exporter.js +20 -8
  4. package/dist/cjs/jats/importer/jats-dom-parser.js +15 -0
  5. package/dist/cjs/schema/nodes/embed.js +1 -0
  6. package/dist/cjs/version.js +1 -1
  7. package/dist/es/jats/__tests__/jats-exporter.test.js +24 -20
  8. package/dist/es/jats/__tests__/jats-roundtrip.test.js +3 -1
  9. package/dist/es/jats/exporter/jats-exporter.js +20 -5
  10. package/dist/es/jats/importer/jats-dom-parser.js +15 -0
  11. package/dist/es/schema/nodes/embed.js +1 -0
  12. package/dist/es/version.js +1 -1
  13. package/dist/types/jats/exporter/jats-exporter.d.ts +1 -1
  14. package/dist/types/schema/nodes/embed.d.ts +7 -0
  15. package/dist/types/version.d.ts +1 -1
  16. package/package.json +4 -4
  17. package/src/jats/__tests__/__fixtures__/jats-import.xml +2 -0
  18. package/src/jats/__tests__/__snapshots__/jats-importer.test.ts.snap +14 -0
  19. package/src/jats/__tests__/__snapshots__/jats-roundtrip.test.ts.snap +1 -1
  20. package/src/jats/__tests__/jats-exporter.test.ts +26 -20
  21. package/src/jats/__tests__/jats-roundtrip.test.ts +3 -1
  22. package/src/jats/exporter/jats-exporter.ts +23 -7
  23. package/src/jats/importer/jats-dom-parser.ts +16 -0
  24. package/src/schema/nodes/embed.ts +9 -0
  25. package/src/version.ts +1 -1
package/dist/cjs/jats/__tests__/jats-exporter.test.js CHANGED
@@ -14,8 +14,12 @@
14
14
  * See the License for the specific language governing permissions and
15
15
  * limitations under the License.
16
16
  */
17
+ var __importDefault = (this && this.__importDefault) || function (mod) {
18
+ return (mod && mod.__esModule) ? mod : { "default": mod };
19
+ };
17
20
  Object.defineProperty(exports, "__esModule", { value: true });
18
21
  const libxmljs2_1 = require("libxmljs2");
22
+ const w3c_xmlserializer_1 = __importDefault(require("w3c-xmlserializer"));
19
23
  const jats_exporter_1 = require("../exporter/jats-exporter");
20
24
  const parse_jats_article_1 = require("../importer/parse-jats-article");
21
25
  const citations_1 = require("./citations");
@@ -32,10 +36,10 @@ describe('JATS exporter', () => {
32
36
  const transformer = new jats_exporter_1.JATSExporter();
33
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  const input = await (0, files_1.readAndParseFixture)('jats-example-full.xml');
34
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  const node = (0, parse_jats_article_1.parseJATSArticle)(input, section_categories_1.sectionCategories);
35
- const result = await transformer.serializeToJATS(node, {
39
+ const document = await transformer.export(node, {
36
40
  csl: citations_1.DEFAULT_CSL_OPTIONS,
37
41
  });
38
- expect(result).toMatchSnapshot('jats-export');
42
+ expect((0, w3c_xmlserializer_1.default)(document)).toMatchSnapshot('jats-export');
39
43
  });
40
44
  test('export with & and < in bibliography metadata', async () => {
41
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  const transformer = new jats_exporter_1.JATSExporter();
@@ -48,27 +52,27 @@ describe('JATS exporter', () => {
48
52
  }
49
53
  });
50
54
  biblio.attrs.title += ' & Sons 55 < 135';
51
- const result = await transformer.serializeToJATS(node, {
55
+ const document = await transformer.export(node, {
52
56
  csl: citations_1.DEFAULT_CSL_OPTIONS,
53
57
  });
54
- expect(result).toMatchSnapshot('jats-export-with-xml-unsafe-in-biblios');
58
+ expect((0, w3c_xmlserializer_1.default)(document)).toMatchSnapshot('jats-export-with-xml-unsafe-in-biblios');
55
59
  });
56
60
  test('export v1.1', async () => {
57
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  const transformer = new jats_exporter_1.JATSExporter();
58
62
  const input = await (0, files_1.readAndParseFixture)('jats-example-full.xml');
59
63
  const node = (0, parse_jats_article_1.parseJATSArticle)(input, section_categories_1.sectionCategories);
60
- const result = await transformer.serializeToJATS(node, {
64
+ const document = await transformer.export(node, {
61
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  csl: citations_1.DEFAULT_CSL_OPTIONS,
62
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  version: '1.1',
63
67
  });
64
- expect(result).toMatchSnapshot('jats-export-1.1');
68
+ expect((0, w3c_xmlserializer_1.default)(document)).toMatchSnapshot('jats-export-1.1');
65
69
  });
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70
  test('export unknown version', async () => {
67
71
  const transformer = new jats_exporter_1.JATSExporter();
68
72
  const input = await (0, files_1.readAndParseFixture)('jats-example-full.xml');
69
73
  const node = (0, parse_jats_article_1.parseJATSArticle)(input, section_categories_1.sectionCategories);
70
74
  await expect(async () => {
71
- await transformer.serializeToJATS(node, {
75
+ await transformer.export(node, {
72
76
  csl: citations_1.DEFAULT_CSL_OPTIONS,
73
77
  version: '1.0',
74
78
  });
@@ -78,9 +82,10 @@ describe('JATS exporter', () => {
78
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  const transformer = new jats_exporter_1.JATSExporter();
79
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  const input = await (0, files_1.readAndParseFixture)('jats-tables-example.xml');
80
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  const node = (0, parse_jats_article_1.parseJATSArticle)(input, section_categories_1.sectionCategories);
81
- const xml = await transformer.serializeToJATS(node, {
85
+ const document = await transformer.export(node, {
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  csl: citations_1.DEFAULT_CSL_OPTIONS,
83
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  });
88
+ const xml = (0, w3c_xmlserializer_1.default)(document);
84
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  const resultDoc = parseXMLWithDTD(xml);
85
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  const tableWrapFoot = resultDoc.get('//table-wrap/table-wrap-foot');
86
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  const paragraph = resultDoc.get('//table-wrap/table-wrap-foot/p');
@@ -91,30 +96,30 @@ describe('JATS exporter', () => {
91
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  const transformer = new jats_exporter_1.JATSExporter();
92
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  const input = await (0, files_1.readAndParseFixture)('jats-import.xml');
93
98
  const node = (0, parse_jats_article_1.parseJATSArticle)(input, section_categories_1.sectionCategories);
94
- const xml = await transformer.serializeToJATS(node, {
99
+ const document = await transformer.export(node, {
95
100
  csl: citations_1.DEFAULT_CSL_OPTIONS,
96
101
  });
97
- const { errors } = parseXMLWithDTD(xml);
102
+ const { errors } = parseXMLWithDTD((0, w3c_xmlserializer_1.default)(document));
98
103
  expect(errors).toHaveLength(0);
99
104
  });
100
105
  test('DTD validation: article with title markup and citations', async () => {
101
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  const transformer = new jats_exporter_1.JATSExporter();
102
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  const input = await (0, files_1.readAndParseFixture)('jats-document.xml');
103
108
  const node = (0, parse_jats_article_1.parseJATSArticle)(input, section_categories_1.sectionCategories);
104
- const xml = await transformer.serializeToJATS(node, {
109
+ const document = await transformer.export(node, {
105
110
  csl: citations_1.DEFAULT_CSL_OPTIONS,
106
111
  });
107
- const { errors } = parseXMLWithDTD(xml);
112
+ const { errors } = parseXMLWithDTD((0, w3c_xmlserializer_1.default)(document));
108
113
  expect(errors).toHaveLength(0);
109
114
  });
110
115
  test('Export link', async () => {
111
116
  const transformer = new jats_exporter_1.JATSExporter();
112
117
  const input = await (0, files_1.readAndParseFixture)('jats-import.xml');
113
118
  const node = (0, parse_jats_article_1.parseJATSArticle)(input, section_categories_1.sectionCategories);
114
- const xml = await transformer.serializeToJATS(node, {
119
+ const document = await transformer.export(node, {
115
120
  csl: citations_1.DEFAULT_CSL_OPTIONS,
116
121
  });
117
- const output = parseXMLWithDTD(xml);
122
+ const output = parseXMLWithDTD((0, w3c_xmlserializer_1.default)(document));
118
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  const link = output.get('//ext-link[@ext-link-type="uri"]');
119
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  expect(link).not.toBeNull();
120
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  expect(link.text()).toBe('https//orcid.org/0000-0003-2217-5904');
@@ -129,20 +134,20 @@ describe('JATS exporter', () => {
129
134
  const transformer = new jats_exporter_1.JATSExporter();
130
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  const input = await (0, files_1.readAndParseFixture)('jats-example-doc.xml');
131
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  const node = (0, parse_jats_article_1.parseJATSArticle)(input, section_categories_1.sectionCategories);
132
- const xml = await transformer.serializeToJATS(node, {
137
+ const document = await transformer.export(node, {
133
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  csl: citations_1.DEFAULT_CSL_OPTIONS,
134
139
  });
135
- const { errors } = parseXMLWithDTD(xml);
140
+ const { errors } = parseXMLWithDTD((0, w3c_xmlserializer_1.default)(document));
136
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  expect(errors).toHaveLength(0);
137
142
  });
138
143
  test('export with supplement', async () => {
139
144
  const transformer = new jats_exporter_1.JATSExporter();
140
145
  const input = await (0, files_1.readAndParseFixture)('jats-import.xml');
141
146
  const node = (0, parse_jats_article_1.parseJATSArticle)(input, section_categories_1.sectionCategories);
142
- const xml = await transformer.serializeToJATS(node, {
147
+ const document = await transformer.export(node, {
143
148
  csl: citations_1.DEFAULT_CSL_OPTIONS,
144
149
  });
145
- const resultDoc = parseXMLWithDTD(xml);
150
+ const resultDoc = parseXMLWithDTD((0, w3c_xmlserializer_1.default)(document));
146
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  const supplementaryMaterial = resultDoc.get('//supplementary-material');
147
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  if (!supplementaryMaterial) {
148
153
  throw new Error('No supplementary material found');
@@ -169,9 +174,10 @@ describe('JATS exporter', () => {
169
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  n.attrs.rids.forEach((rid) => citedIDs.add(rid));
170
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  }
171
176
  });
172
- const xml = await new jats_exporter_1.JATSExporter().serializeToJATS(node, {
177
+ const document = await new jats_exporter_1.JATSExporter().export(node, {
173
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  csl: citations_1.DEFAULT_CSL_OPTIONS,
174
179
  });
180
+ const xml = (0, w3c_xmlserializer_1.default)(document);
175
181
  const refCount = parseXMLWithDTD(xml).find('//ref-list/ref').length;
176
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  expect(refCount).toBe(bibliographyItemIDs.size);
177
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  const { errors } = parseXMLWithDTD(xml);
@@ -181,9 +187,10 @@ describe('JATS exporter', () => {
181
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  const transformer = new jats_exporter_1.JATSExporter();
182
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  const input = await (0, files_1.readAndParseFixture)('jats-fn-group.xml');
183
189
  const node = (0, parse_jats_article_1.parseJATSArticle)(input, section_categories_1.sectionCategories);
184
- const xml = await transformer.serializeToJATS(node, {
190
+ const document = await transformer.export(node, {
185
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  csl: citations_1.DEFAULT_CSL_OPTIONS,
186
192
  });
193
+ const xml = (0, w3c_xmlserializer_1.default)(document);
187
194
  const footnoteCategories = [
188
195
  'con',
189
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  'deceased',
package/dist/cjs/jats/__tests__/jats-roundtrip.test.js CHANGED
@@ -14,8 +14,12 @@
14
14
  * See the License for the specific language governing permissions and
15
15
  * limitations under the License.
16
16
  */
17
+ var __importDefault = (this && this.__importDefault) || function (mod) {
18
+ return (mod && mod.__esModule) ? mod : { "default": mod };
19
+ };
17
20
  Object.defineProperty(exports, "__esModule", { value: true });
18
21
  const libxmljs2_1 = require("libxmljs2");
22
+ const w3c_xmlserializer_1 = __importDefault(require("w3c-xmlserializer"));
19
23
  const jats_exporter_1 = require("../exporter/jats-exporter");
20
24
  const parse_jats_article_1 = require("../importer/parse-jats-article");
21
25
  const citations_1 = require("./citations");
@@ -31,9 +35,10 @@ const roundtrip = async (filename) => {
31
35
  const doc = new DOMParser().parseFromString(input, 'application/xml');
32
36
  const node = (0, parse_jats_article_1.parseJATSArticle)(doc, section_categories_1.sectionCategories);
33
37
  const exporter = new jats_exporter_1.JATSExporter();
34
- return await exporter.serializeToJATS(node, {
38
+ const document = await exporter.export(node, {
35
39
  csl: citations_1.DEFAULT_CSL_OPTIONS,
36
40
  });
41
+ return (0, w3c_xmlserializer_1.default)(document);
37
42
  };
38
43
  describe('JATS roundtrip', () => {
39
44
  test('jats-import.xml roundtrip', async () => {
package/dist/cjs/jats/exporter/jats-exporter.js CHANGED
@@ -47,15 +47,11 @@ var __importStar = (this && this.__importStar) || (function () {
47
47
  return result;
48
48
  };
49
49
  })();
50
- var __importDefault = (this && this.__importDefault) || function (mod) {
51
- return (mod && mod.__esModule) ? mod : { "default": mod };
52
- };
53
50
  Object.defineProperty(exports, "__esModule", { value: true });
54
51
  exports.JATSExporter = exports.createCounter = void 0;
55
52
  const Citeproc = __importStar(require("citeproc"));
56
53
  const prosemirror_model_1 = require("prosemirror-model");
57
54
  const prosemirror_utils_1 = require("prosemirror-utils");
58
- const w3c_xmlserializer_1 = __importDefault(require("w3c-xmlserializer"));
59
55
  const citeproc_1 = require("../../lib/citeproc");
60
56
  const credit_roles_1 = require("../../lib/credit-roles");
61
57
  const footnotes_1 = require("../../lib/footnotes");
@@ -118,7 +114,7 @@ class JATSExporter {
118
114
  this.nodesMap.set(type, nodes);
119
115
  });
120
116
  };
121
- this.serializeToJATS = async (manuscriptNode, options) => {
117
+ this.export = async (manuscriptNode, options) => {
122
118
  this.manuscriptNode = manuscriptNode;
123
119
  this.populateNodesMap();
124
120
  this.initCiteprocEngine(options);
@@ -149,7 +145,7 @@ class JATSExporter {
149
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  $article.appendChild($floatsGroup);
150
146
  }
151
147
  await this.rewriteIDs();
152
- return (0, w3c_xmlserializer_1.default)(this.document);
148
+ return this.document;
153
149
  };
154
150
  this.appendChildNodeOfType = ($element, node, type) => {
155
151
  const childNode = this.getFirstChildOfType(type, node);
@@ -440,7 +436,7 @@ class JATSExporter {
440
436
  const [, bibliography] = this.engine.makeBibliography();
441
437
  const parser = new DOMParser();
442
438
  bibliography.forEach((item) => {
443
- const fragment = `<template xmlns:xlink="${xml_1.XLINK_NAMESPACE}">${(0, xml_1.sanitizeXmlString)(item)}</template>`;
439
+ const fragment = `<wrapper xmlns:xlink="${xml_1.XLINK_NAMESPACE}">${(0, xml_1.sanitizeXmlString)(item)}</wrapper>`;
444
440
  const $ref = parser
445
441
  .parseFromString(fragment, 'text/xml')
446
442
  .querySelector('ref');
@@ -502,7 +498,7 @@ class JATSExporter {
502
498
  attachments: () => '',
503
499
  image_element: (node) => createImage(node),
504
500
  embed: (node) => {
505
- const { id, href, mimetype, mimeSubtype } = node.attrs;
501
+ const { id, href, mimetype, mimeSubtype, extLinks } = node.attrs;
506
502
  if (!href) {
507
503
  return '';
508
504
  }
@@ -520,6 +516,22 @@ class JATSExporter {
520
516
  this.appendChildNodeOfType($media, node, schema_1.schema.nodes.alt_text);
521
517
  this.appendChildNodeOfType($media, node, schema_1.schema.nodes.long_desc);
522
518
  this.appendCaption($media, node);
519
+ if (extLinks && extLinks.length > 0) {
520
+ extLinks.forEach((extLink) => {
521
+ if (extLink.href) {
522
+ const extLinkElement = this.createElement('ext-link');
523
+ extLinkElement.setAttribute('ext-link-type', extLink.type);
524
+ extLinkElement.setAttributeNS(xml_1.XLINK_NAMESPACE, 'href', extLink.href);
525
+ if (extLink.lang) {
526
+ extLinkElement.setAttributeNS(xml_1.XML_NAMESPACE, 'lang', extLink.lang);
527
+ }
528
+ if (extLink.label) {
529
+ extLinkElement.textContent = extLink.label;
530
+ }
531
+ $media.appendChild(extLinkElement);
532
+ }
533
+ });
534
+ }
523
535
  return $media;
524
536
  },
525
537
  awards: () => ['funding-group', 0],
package/dist/cjs/jats/importer/jats-dom-parser.js CHANGED
@@ -566,6 +566,11 @@ class JATSDOMParser {
566
566
  context: 'pullquote_element/',
567
567
  getAttrs: this.getFigAttrs,
568
568
  },
569
+ {
570
+ tag: 'ext-link',
571
+ context: 'embed/',
572
+ ignore: true,
573
+ },
569
574
  {
570
575
  tag: 'ext-link',
571
576
  node: 'link',
@@ -592,11 +597,21 @@ class JATSDOMParser {
592
597
  node: 'embed',
593
598
  getAttrs: (node) => {
594
599
  const element = node;
600
+ const extLinkElements = element.querySelectorAll('ext-link');
601
+ const extLinks = Array.from(extLinkElements)
602
+ .map((extLinkElement) => ({
603
+ type: extLinkElement.getAttribute('ext-link-type') || '',
604
+ href: extLinkElement.getAttributeNS(xml_1.XLINK_NAMESPACE, 'href') || '',
605
+ lang: extLinkElement.getAttributeNS(xml_1.XML_NAMESPACE, 'lang') || '',
606
+ label: (0, utils_1.getTrimmedTextContent)(extLinkElement) || undefined,
607
+ }))
608
+ .filter((extLink) => extLink.href);
595
609
  return {
596
610
  id: element.getAttribute('id'),
597
611
  href: element.getAttributeNS(xml_1.XLINK_NAMESPACE, 'href'),
598
612
  mimetype: element.getAttribute('mimetype'),
599
613
  mimeSubtype: element.getAttribute('mime-subtype'),
614
+ extLinks: extLinks.length > 0 ? extLinks : undefined,
600
615
  };
601
616
  },
602
617
  },
package/dist/cjs/schema/nodes/embed.js CHANGED
@@ -25,6 +25,7 @@ exports.embed = {
25
25
  mimetype: { default: undefined },
26
26
  mimeSubtype: { default: undefined },
27
27
  longDesc: { default: '' },
28
+ extLinks: { default: [] },
28
29
  },
29
30
  group: 'block element',
30
31
  toDOM: (node) => {
package/dist/cjs/version.js CHANGED
@@ -1,4 +1,4 @@
1
1
  "use strict";
2
2
  Object.defineProperty(exports, "__esModule", { value: true });
3
3
  exports.VERSION = void 0;
4
- exports.VERSION = "4.5.6";
4
+ exports.VERSION = "4.5.8";
package/dist/es/jats/__tests__/jats-exporter.test.js CHANGED
@@ -14,6 +14,7 @@
14
14
  * limitations under the License.
15
15
  */
16
16
  import { parseXml } from 'libxmljs2';
17
+ import serializeToXML from 'w3c-xmlserializer';
17
18
  import { JATSExporter } from '../exporter/jats-exporter';
18
19
  import { parseJATSArticle } from '../importer/parse-jats-article';
19
20
  import { DEFAULT_CSL_OPTIONS } from './citations';
@@ -30,10 +31,10 @@ describe('JATS exporter', () => {
30
31
  const transformer = new JATSExporter();
31
32
  const input = await readAndParseFixture('jats-example-full.xml');
32
33
  const node = parseJATSArticle(input, sectionCategories);
33
- const result = await transformer.serializeToJATS(node, {
34
+ const document = await transformer.export(node, {
34
35
  csl: DEFAULT_CSL_OPTIONS,
35
36
  });
36
- expect(result).toMatchSnapshot('jats-export');
37
+ expect(serializeToXML(document)).toMatchSnapshot('jats-export');
37
38
  });
38
39
  test('export with & and < in bibliography metadata', async () => {
39
40
  const transformer = new JATSExporter();
@@ -46,27 +47,27 @@ describe('JATS exporter', () => {
46
47
  }
47
48
  });
48
49
  biblio.attrs.title += ' & Sons 55 < 135';
49
- const result = await transformer.serializeToJATS(node, {
50
+ const document = await transformer.export(node, {
50
51
  csl: DEFAULT_CSL_OPTIONS,
51
52
  });
52
- expect(result).toMatchSnapshot('jats-export-with-xml-unsafe-in-biblios');
53
+ expect(serializeToXML(document)).toMatchSnapshot('jats-export-with-xml-unsafe-in-biblios');
53
54
  });
54
55
  test('export v1.1', async () => {
55
56
  const transformer = new JATSExporter();
56
57
  const input = await readAndParseFixture('jats-example-full.xml');
57
58
  const node = parseJATSArticle(input, sectionCategories);
58
- const result = await transformer.serializeToJATS(node, {
59
+ const document = await transformer.export(node, {
59
60
  csl: DEFAULT_CSL_OPTIONS,
60
61
  version: '1.1',
61
62
  });
62
- expect(result).toMatchSnapshot('jats-export-1.1');
63
+ expect(serializeToXML(document)).toMatchSnapshot('jats-export-1.1');
63
64
  });
64
65
  test('export unknown version', async () => {
65
66
  const transformer = new JATSExporter();
66
67
  const input = await readAndParseFixture('jats-example-full.xml');
67
68
  const node = parseJATSArticle(input, sectionCategories);
68
69
  await expect(async () => {
69
- await transformer.serializeToJATS(node, {
70
+ await transformer.export(node, {
70
71
  csl: DEFAULT_CSL_OPTIONS,
71
72
  version: '1.0',
72
73
  });
@@ -76,9 +77,10 @@ describe('JATS exporter', () => {
76
77
  const transformer = new JATSExporter();
77
78
  const input = await readAndParseFixture('jats-tables-example.xml');
78
79
  const node = parseJATSArticle(input, sectionCategories);
79
- const xml = await transformer.serializeToJATS(node, {
80
+ const document = await transformer.export(node, {
80
81
  csl: DEFAULT_CSL_OPTIONS,
81
82
  });
83
+ const xml = serializeToXML(document);
82
84
  const resultDoc = parseXMLWithDTD(xml);
83
85
  const tableWrapFoot = resultDoc.get('//table-wrap/table-wrap-foot');
84
86
  const paragraph = resultDoc.get('//table-wrap/table-wrap-foot/p');
@@ -89,30 +91,30 @@ describe('JATS exporter', () => {
89
91
  const transformer = new JATSExporter();
90
92
  const input = await readAndParseFixture('jats-import.xml');
91
93
  const node = parseJATSArticle(input, sectionCategories);
92
- const xml = await transformer.serializeToJATS(node, {
94
+ const document = await transformer.export(node, {
93
95
  csl: DEFAULT_CSL_OPTIONS,
94
96
  });
95
- const { errors } = parseXMLWithDTD(xml);
97
+ const { errors } = parseXMLWithDTD(serializeToXML(document));
96
98
  expect(errors).toHaveLength(0);
97
99
  });
98
100
  test('DTD validation: article with title markup and citations', async () => {
99
101
  const transformer = new JATSExporter();
100
102
  const input = await readAndParseFixture('jats-document.xml');
101
103
  const node = parseJATSArticle(input, sectionCategories);
102
- const xml = await transformer.serializeToJATS(node, {
104
+ const document = await transformer.export(node, {
103
105
  csl: DEFAULT_CSL_OPTIONS,
104
106
  });
105
- const { errors } = parseXMLWithDTD(xml);
107
+ const { errors } = parseXMLWithDTD(serializeToXML(document));
106
108
  expect(errors).toHaveLength(0);
107
109
  });
108
110
  test('Export link', async () => {
109
111
  const transformer = new JATSExporter();
110
112
  const input = await readAndParseFixture('jats-import.xml');
111
113
  const node = parseJATSArticle(input, sectionCategories);
112
- const xml = await transformer.serializeToJATS(node, {
114
+ const document = await transformer.export(node, {
113
115
  csl: DEFAULT_CSL_OPTIONS,
114
116
  });
115
- const output = parseXMLWithDTD(xml);
117
+ const output = parseXMLWithDTD(serializeToXML(document));
116
118
  const link = output.get('//ext-link[@ext-link-type="uri"]');
117
119
  expect(link).not.toBeNull();
118
120
  expect(link.text()).toBe('https//orcid.org/0000-0003-2217-5904');
@@ -127,20 +129,20 @@ describe('JATS exporter', () => {
127
129
  const transformer = new JATSExporter();
128
130
  const input = await readAndParseFixture('jats-example-doc.xml');
129
131
  const node = parseJATSArticle(input, sectionCategories);
130
- const xml = await transformer.serializeToJATS(node, {
132
+ const document = await transformer.export(node, {
131
133
  csl: DEFAULT_CSL_OPTIONS,
132
134
  });
133
- const { errors } = parseXMLWithDTD(xml);
135
+ const { errors } = parseXMLWithDTD(serializeToXML(document));
134
136
  expect(errors).toHaveLength(0);
135
137
  });
136
138
  test('export with supplement', async () => {
137
139
  const transformer = new JATSExporter();
138
140
  const input = await readAndParseFixture('jats-import.xml');
139
141
  const node = parseJATSArticle(input, sectionCategories);
140
- const xml = await transformer.serializeToJATS(node, {
142
+ const document = await transformer.export(node, {
141
143
  csl: DEFAULT_CSL_OPTIONS,
142
144
  });
143
- const resultDoc = parseXMLWithDTD(xml);
145
+ const resultDoc = parseXMLWithDTD(serializeToXML(document));
144
146
  const supplementaryMaterial = resultDoc.get('//supplementary-material');
145
147
  if (!supplementaryMaterial) {
146
148
  throw new Error('No supplementary material found');
@@ -167,9 +169,10 @@ describe('JATS exporter', () => {
167
169
  n.attrs.rids.forEach((rid) => citedIDs.add(rid));
168
170
  }
169
171
  });
170
- const xml = await new JATSExporter().serializeToJATS(node, {
172
+ const document = await new JATSExporter().export(node, {
171
173
  csl: DEFAULT_CSL_OPTIONS,
172
174
  });
175
+ const xml = serializeToXML(document);
173
176
  const refCount = parseXMLWithDTD(xml).find('//ref-list/ref').length;
174
177
  expect(refCount).toBe(bibliographyItemIDs.size);
175
178
  const { errors } = parseXMLWithDTD(xml);
@@ -179,9 +182,10 @@ describe('JATS exporter', () => {
179
182
  const transformer = new JATSExporter();
180
183
  const input = await readAndParseFixture('jats-fn-group.xml');
181
184
  const node = parseJATSArticle(input, sectionCategories);
182
- const xml = await transformer.serializeToJATS(node, {
185
+ const document = await transformer.export(node, {
183
186
  csl: DEFAULT_CSL_OPTIONS,
184
187
  });
188
+ const xml = serializeToXML(document);
185
189
  const footnoteCategories = [
186
190
  'con',
187
191
  'deceased',
package/dist/es/jats/__tests__/jats-roundtrip.test.js CHANGED
@@ -14,6 +14,7 @@
14
14
  * limitations under the License.
15
15
  */
16
16
  import { parseXml } from 'libxmljs2';
17
+ import serializeToXML from 'w3c-xmlserializer';
17
18
  import { JATSExporter } from '../exporter/jats-exporter';
18
19
  import { parseJATSArticle } from '../importer/parse-jats-article';
19
20
  import { DEFAULT_CSL_OPTIONS } from './citations';
@@ -29,9 +30,10 @@ const roundtrip = async (filename) => {
29
30
  const doc = new DOMParser().parseFromString(input, 'application/xml');
30
31
  const node = parseJATSArticle(doc, sectionCategories);
31
32
  const exporter = new JATSExporter();
32
- return await exporter.serializeToJATS(node, {
33
+ const document = await exporter.export(node, {
33
34
  csl: DEFAULT_CSL_OPTIONS,
34
35
  });
36
+ return serializeToXML(document);
35
37
  };
36
38
  describe('JATS roundtrip', () => {
37
39
  test('jats-import.xml roundtrip', async () => {
package/dist/es/jats/exporter/jats-exporter.js CHANGED
@@ -16,7 +16,6 @@
16
16
  import * as Citeproc from 'citeproc';
17
17
  import { DOMSerializer } from 'prosemirror-model';
18
18
  import { findChildrenByAttr, findChildrenByType } from 'prosemirror-utils';
19
- import serializeToXML from 'w3c-xmlserializer';
20
19
  import { buildCiteprocCitation } from '../../lib/citeproc';
21
20
  import { CreditRoleUrls } from '../../lib/credit-roles';
22
21
  import { generateFootnoteLabels } from '../../lib/footnotes';
@@ -78,7 +77,7 @@ export class JATSExporter {
78
77
  this.nodesMap.set(type, nodes);
79
78
  });
80
79
  };
81
- this.serializeToJATS = async (manuscriptNode, options) => {
80
+ this.export = async (manuscriptNode, options) => {
82
81
  this.manuscriptNode = manuscriptNode;
83
82
  this.populateNodesMap();
84
83
  this.initCiteprocEngine(options);
@@ -109,7 +108,7 @@ export class JATSExporter {
109
108
  $article.appendChild($floatsGroup);
110
109
  }
111
110
  await this.rewriteIDs();
112
- return serializeToXML(this.document);
111
+ return this.document;
113
112
  };
114
113
  this.appendChildNodeOfType = ($element, node, type) => {
115
114
  const childNode = this.getFirstChildOfType(type, node);
@@ -400,7 +399,7 @@ export class JATSExporter {
400
399
  const [, bibliography] = this.engine.makeBibliography();
401
400
  const parser = new DOMParser();
402
401
  bibliography.forEach((item) => {
403
- const fragment = `<template xmlns:xlink="${XLINK_NAMESPACE}">${sanitizeXmlString(item)}</template>`;
402
+ const fragment = `<wrapper xmlns:xlink="${XLINK_NAMESPACE}">${sanitizeXmlString(item)}</wrapper>`;
404
403
  const $ref = parser
405
404
  .parseFromString(fragment, 'text/xml')
406
405
  .querySelector('ref');
@@ -462,7 +461,7 @@ export class JATSExporter {
462
461
  attachments: () => '',
463
462
  image_element: (node) => createImage(node),
464
463
  embed: (node) => {
465
- const { id, href, mimetype, mimeSubtype } = node.attrs;
464
+ const { id, href, mimetype, mimeSubtype, extLinks } = node.attrs;
466
465
  if (!href) {
467
466
  return '';
468
467
  }
@@ -480,6 +479,22 @@ export class JATSExporter {
480
479
  this.appendChildNodeOfType($media, node, schema.nodes.alt_text);
481
480
  this.appendChildNodeOfType($media, node, schema.nodes.long_desc);
482
481
  this.appendCaption($media, node);
482
+ if (extLinks && extLinks.length > 0) {
483
+ extLinks.forEach((extLink) => {
484
+ if (extLink.href) {
485
+ const extLinkElement = this.createElement('ext-link');
486
+ extLinkElement.setAttribute('ext-link-type', extLink.type);
487
+ extLinkElement.setAttributeNS(XLINK_NAMESPACE, 'href', extLink.href);
488
+ if (extLink.lang) {
489
+ extLinkElement.setAttributeNS(XML_NAMESPACE, 'lang', extLink.lang);
490
+ }
491
+ if (extLink.label) {
492
+ extLinkElement.textContent = extLink.label;
493
+ }
494
+ $media.appendChild(extLinkElement);
495
+ }
496
+ });
497
+ }
483
498
  return $media;
484
499
  },
485
500
  awards: () => ['funding-group', 0],
package/dist/es/jats/importer/jats-dom-parser.js CHANGED
@@ -563,6 +563,11 @@ export class JATSDOMParser {
563
563
  context: 'pullquote_element/',
564
564
  getAttrs: this.getFigAttrs,
565
565
  },
566
+ {
567
+ tag: 'ext-link',
568
+ context: 'embed/',
569
+ ignore: true,
570
+ },
566
571
  {
567
572
  tag: 'ext-link',
568
573
  node: 'link',
@@ -589,11 +594,21 @@ export class JATSDOMParser {
589
594
  node: 'embed',
590
595
  getAttrs: (node) => {
591
596
  const element = node;
597
+ const extLinkElements = element.querySelectorAll('ext-link');
598
+ const extLinks = Array.from(extLinkElements)
599
+ .map((extLinkElement) => ({
600
+ type: extLinkElement.getAttribute('ext-link-type') || '',
601
+ href: extLinkElement.getAttributeNS(XLINK_NAMESPACE, 'href') || '',
602
+ lang: extLinkElement.getAttributeNS(XML_NAMESPACE, 'lang') || '',
603
+ label: getTrimmedTextContent(extLinkElement) || undefined,
604
+ }))
605
+ .filter((extLink) => extLink.href);
592
606
  return {
593
607
  id: element.getAttribute('id'),
594
608
  href: element.getAttributeNS(XLINK_NAMESPACE, 'href'),
595
609
  mimetype: element.getAttribute('mimetype'),
596
610
  mimeSubtype: element.getAttribute('mime-subtype'),
611
+ extLinks: extLinks.length > 0 ? extLinks : undefined,
597
612
  };
598
613
  },
599
614
  },
package/dist/es/schema/nodes/embed.js CHANGED
@@ -22,6 +22,7 @@ export const embed = {
22
22
  mimetype: { default: undefined },
23
23
  mimeSubtype: { default: undefined },
24
24
  longDesc: { default: '' },
25
+ extLinks: { default: [] },
25
26
  },
26
27
  group: 'block element',
27
28
  toDOM: (node) => {
package/dist/es/version.js CHANGED
@@ -1 +1 @@
1
- export const VERSION = "4.5.6";
1
+ export const VERSION = "4.5.8";
package/dist/types/jats/exporter/jats-exporter.d.ts CHANGED
@@ -42,7 +42,7 @@ export declare class JATSExporter {
42
42
  private populateNodesMap;
43
43
  protected getFirstChildOfType<T extends ManuscriptNode>(type: NodeType, node?: ManuscriptNode): T | undefined;
44
44
  protected getChildrenOfType<T extends ManuscriptNode>(type: NodeType, node?: ManuscriptNode): T[];
45
- serializeToJATS: (manuscriptNode: ActualManuscriptNode, options: ExportOptions) => Promise<string>;
45
+ export: (manuscriptNode: ActualManuscriptNode, options: ExportOptions) => Promise<Document>;
46
46
  private appendChildNodeOfType;
47
47
  private appendChildrenNodeOfType;
48
48
  protected appendCaption: ($element: Element, node: ManuscriptNode) => void;
package/dist/types/schema/nodes/embed.d.ts CHANGED
@@ -15,11 +15,18 @@
15
15
  */
16
16
  import { NodeSpec } from 'prosemirror-model';
17
17
  import { ManuscriptNode } from '../types';
18
+ export interface ExtLink {
19
+ type: string;
20
+ href: string;
21
+ lang: string;
22
+ label?: string;
23
+ }
18
24
  export interface EmbedAttrs {
19
25
  id: string;
20
26
  href: string;
21
27
  mimetype: string;
22
28
  mimeSubtype: string;
29
+ extLinks?: ExtLink[];
23
30
  }
24
31
  export interface EmbedNode extends ManuscriptNode {
25
32
  attrs: EmbedAttrs;
package/dist/types/version.d.ts CHANGED
@@ -1 +1 @@
1
- export declare const VERSION = "4.5.6";
1
+ export declare const VERSION = "4.5.8";