@manuscripts/transform 4.4.3 → 4.4.5

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

@@ -156,6 +156,27 @@ describe('JATS exporter', () => {
         expect(mimeSubtypeAttr?.value()).toBe('vnd.openxmlformats-officedocument.wordprocessingml.document');
         expect(hrefAttr?.value()).toBe('attachment:7d9d686b-5488-44a5-a1c5-46351e7f9312');
     });
+    test('exports uncited references alongside cited ones', async () => {
+        const input = await (0, files_1.readAndParseFixture)('jats-document.xml');
+        const node = (0, parse_jats_article_1.parseJATSArticle)(input, section_categories_1.sectionCategories);
+        const bibliographyItemIDs = new Set();
+        const citedIDs = new Set();
+        node.descendants((n) => {
+            if ((0, schema_1.isBibliographyItemNode)(n)) {
+                bibliographyItemIDs.add(n.attrs.id);
+            }
+            if ((0, schema_1.isCitationNode)(n)) {
+                n.attrs.rids.forEach((rid) => citedIDs.add(rid));
+            }
+        });
+        const xml = await new jats_exporter_1.JATSExporter().serializeToJATS(node, {
+            csl: citations_1.DEFAULT_CSL_OPTIONS,
+        });
+        const refCount = parseXMLWithDTD(xml).find('//ref-list/ref').length;
+        expect(refCount).toBe(bibliographyItemIDs.size);
+        const { errors } = parseXMLWithDTD(xml);
+        expect(errors).toHaveLength(0);
+    });
     test('export footnotes', async () => {
         const transformer = new jats_exporter_1.JATSExporter();
         const input = await (0, files_1.readAndParseFixture)('jats-fn-group.xml');

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

@@ -132,7 +132,7 @@ class JATSExporter {
         this.serializeToJATS = async (manuscriptNode, options) => {
             this.manuscriptNode = manuscriptNode;
             this.populateNodesMap();
-            this.initCiteprocEngine(options.csl);
+            this.initCiteprocEngine(options);
             this.createSerializer();
             const versionIds = (0, jats_versions_1.selectVersionIds)(options.version ?? '1.2');
             this.document = document.implementation.createDocument(null, 'article', document.implementation.createDocumentType('article', versionIds.publicId, versionIds.systemId));
@@ -183,15 +183,18 @@ class JATSExporter {
                 element.appendChild(caption);
             }
         };
-        this.initCiteprocEngine = (csl) => {
+        this.initCiteprocEngine = (options) => {
+            const { csl } = options;
             const bibitems = new Map();
             const citations = new Map();
+            const citedItemIDs = new Set();
             this.manuscriptNode.descendants((n) => {
                 if ((0, schema_1.isBibliographyItemNode)(n)) {
                     bibitems.set(n.attrs.id, n.attrs);
                 }
                 if ((0, schema_1.isCitationNode)(n)) {
                     citations.set(n.attrs.id, (0, citeproc_1.buildCiteprocCitation)(n.attrs));
+                    n.attrs.rids.forEach((rid) => citedItemIDs.add(rid));
                 }
             });
             (0, citeproc_2.initJats)();
@@ -207,7 +210,8 @@ class JATSExporter {
                 variableWrapper: citeproc_2.jatsVariableWrapper,
             }, csl.style);
             engine.setOutputFormat('jats');
-            const output = engine.rebuildProcessorState([...citations.values()]);
+            const uncitedItemIDs = [...bibitems.keys()].filter((id) => !citedItemIDs.has(id));
+            const output = engine.rebuildProcessorState([...citations.values()], undefined, uncitedItemIDs);
             this.engine = engine;
             this.renderedCitations = new Map(output.map((i) => [i[0], i[2]]));
         };

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

@@ -27,7 +27,10 @@ const labelledNodeTypes = [
     schema_1.schema.nodes.embed,
     schema_1.schema.nodes.image_element,
 ];
-const excludedTypes = [schema_1.schema.nodes.graphical_abstract_section];
+const excludedTypes = [
+    schema_1.schema.nodes.graphical_abstract_section,
+    schema_1.schema.nodes.trans_graphical_abstract,
+];
 const chooseLabel = (nodeType) => {
     return node_names_1.nodeNames.get(nodeType);
 };

package/dist/cjs/version.js

@@ -1,4 +1,4 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.VERSION = void 0;
-exports.VERSION = "4.4.3";
+exports.VERSION = "4.4.5";

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

@@ -19,7 +19,7 @@ import { parseJATSArticle } from '../importer/parse-jats-article';
 import { DEFAULT_CSL_OPTIONS } from './citations';
 import { sectionCategories } from './data/section-categories';
 import { readAndParseFixture } from './files';
-import { isBibliographyItemNode } from '../../schema';
+import { isBibliographyItemNode, isCitationNode, } from '../../schema';
 const parseXMLWithDTD = (data) => parseXml(data, {
     dtdload: true,
     dtdvalid: true,
@@ -154,6 +154,27 @@ describe('JATS exporter', () => {
         expect(mimeSubtypeAttr?.value()).toBe('vnd.openxmlformats-officedocument.wordprocessingml.document');
         expect(hrefAttr?.value()).toBe('attachment:7d9d686b-5488-44a5-a1c5-46351e7f9312');
     });
+    test('exports uncited references alongside cited ones', async () => {
+        const input = await readAndParseFixture('jats-document.xml');
+        const node = parseJATSArticle(input, sectionCategories);
+        const bibliographyItemIDs = new Set();
+        const citedIDs = new Set();
+        node.descendants((n) => {
+            if (isBibliographyItemNode(n)) {
+                bibliographyItemIDs.add(n.attrs.id);
+            }
+            if (isCitationNode(n)) {
+                n.attrs.rids.forEach((rid) => citedIDs.add(rid));
+            }
+        });
+        const xml = await new JATSExporter().serializeToJATS(node, {
+            csl: DEFAULT_CSL_OPTIONS,
+        });
+        const refCount = parseXMLWithDTD(xml).find('//ref-list/ref').length;
+        expect(refCount).toBe(bibliographyItemIDs.size);
+        const { errors } = parseXMLWithDTD(xml);
+        expect(errors).toHaveLength(0);
+    });
     test('export footnotes', async () => {
         const transformer = new JATSExporter();
         const input = await readAndParseFixture('jats-fn-group.xml');

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

@@ -92,7 +92,7 @@ export class JATSExporter {
         this.serializeToJATS = async (manuscriptNode, options) => {
             this.manuscriptNode = manuscriptNode;
             this.populateNodesMap();
-            this.initCiteprocEngine(options.csl);
+            this.initCiteprocEngine(options);
             this.createSerializer();
             const versionIds = selectVersionIds(options.version ?? '1.2');
             this.document = document.implementation.createDocument(null, 'article', document.implementation.createDocumentType('article', versionIds.publicId, versionIds.systemId));
@@ -143,15 +143,18 @@ export class JATSExporter {
                 element.appendChild(caption);
             }
         };
-        this.initCiteprocEngine = (csl) => {
+        this.initCiteprocEngine = (options) => {
+            const { csl } = options;
             const bibitems = new Map();
             const citations = new Map();
+            const citedItemIDs = new Set();
             this.manuscriptNode.descendants((n) => {
                 if (isBibliographyItemNode(n)) {
                     bibitems.set(n.attrs.id, n.attrs);
                 }
                 if (isCitationNode(n)) {
                     citations.set(n.attrs.id, buildCiteprocCitation(n.attrs));
+                    n.attrs.rids.forEach((rid) => citedItemIDs.add(rid));
                 }
             });
             initJats();
@@ -167,7 +170,8 @@ export class JATSExporter {
                 variableWrapper: jatsVariableWrapper,
             }, csl.style);
             engine.setOutputFormat('jats');
-            const output = engine.rebuildProcessorState([...citations.values()]);
+            const uncitedItemIDs = [...bibitems.keys()].filter((id) => !citedItemIDs.has(id));
+            const output = engine.rebuildProcessorState([...citations.values()], undefined, uncitedItemIDs);
             this.engine = engine;
             this.renderedCitations = new Map(output.map((i) => [i[0], i[2]]));
         };

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

@@ -24,7 +24,10 @@ const labelledNodeTypes = [
     schema.nodes.embed,
     schema.nodes.image_element,
 ];
-const excludedTypes = [schema.nodes.graphical_abstract_section];
+const excludedTypes = [
+    schema.nodes.graphical_abstract_section,
+    schema.nodes.trans_graphical_abstract,
+];
 const chooseLabel = (nodeType) => {
     return nodeNames.get(nodeType);
 };

package/dist/es/version.js

@@ -1 +1 @@
-export const VERSION = "4.4.3";
+export const VERSION = "4.4.5";

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const VERSION = "4.4.3";
+export declare const VERSION = "4.4.5";

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@manuscripts/transform",
   "description": "ProseMirror transformer for Manuscripts applications",
-  "version": "4.4.3",
+  "version": "4.4.5",
   "repository": "github:Atypon-OpenSource/manuscripts-transform",
   "license": "Apache-2.0",
   "main": "dist/cjs",

package/src/jats/__tests__/__snapshots__/jats-roundtrip.test.ts.snap

@@ -15,4 +15,4 @@ exports[`JATS roundtrip > jats-import.xml roundtrip 1`] = `
           Registry, annual report 2011. 2011. Ref Type: Generic.</mixed-citation></ref><ref id=\\"ref-6\\"><label>6. </label><mixed-citation publication-type=\\"journal\\"><person-group person-group-type=\\"author\\"><string-name><surname>Friday</surname> <given-names>G</given-names></string-name>, <string-name><surname>Alter</surname> <given-names>M</given-names></string-name>, <string-name><surname>Lai</surname> <given-names>SM</given-names></string-name></person-group>. <article-title>Control of hypertension and risk of stroke</article-title> <source><italic>Stroke</italic></source>. <year>2002</year>;<volume>33</volume>:<fpage>2652</fpage>-<lpage>2657</lpage>. doi:<pub-id pub-id-type=\\"doi\\">https://doi.org/10.1161/01.STR.0000033929.62136.6F</pub-id></mixed-citation></ref><ref id=\\"ref-7\\"><label>7. </label><mixed-citation publication-type=\\"journal\\"><person-group person-group-type=\\"author\\"><string-name><surname>Lai</surname> <given-names>SM</given-names></string-name>, <string-name><surname>Alter</surname> <given-names>M</given-names></string-name>, <string-name><surname>Friday</surname> <given-names>G</given-names></string-name>, <string-name><surname>Sobel</surname> <given-names>E</given-names></string-name></person-group>. <article-title>A multifactorial analysis of risk</article-title> <source><italic>Stroke</italic></source>. <year>1994</year>;<volume>25</volume>:<fpage>958</fpage>-<lpage>962</lpage>. doi:<pub-id pub-id-type=\\"doi\\">https://doi.org/10.1161/01.STR.25.5.958</pub-id></mixed-citation></ref><ref id=\\"ref-8\\"><label>8. </label><mixed-citation publication-type=\\"journal\\"><person-group person-group-type=\\"author\\"><string-name><surname>Prencipe</surname> <given-names>M</given-names></string-name>, <string-name><surname>Culasso</surname> <given-names>F</given-names></string-name>, <string-name><surname>Rasura</surname> <given-names>M</given-names></string-name>, et al</person-group>. <article-title>Long-term prognosis after a minor</article-title> <source><italic>Stroke</italic></source>. <year>1998</year>;<volume>29</volume>:<fpage>126</fpage>-<lpage>132</lpage>. doi:<pub-id pub-id-type=\\"doi\\">https://doi.org/10.1161/01.STR.29.1.126</pub-id></mixed-citation></ref><ref id=\\"ref-9\\"><label>9. </label><mixed-citation publication-type=\\"journal\\"><person-group person-group-type=\\"author\\"><string-name><surname>Rashid</surname> <given-names>P</given-names></string-name>, <string-name><surname>Leonardi-Bee</surname> <given-names>J</given-names></string-name>, <string-name><surname>Bath</surname> <given-names>P</given-names></string-name></person-group>. <article-title>Blood pressure reduction and secondary</article-title> <source><italic>Stroke</italic></source>. <year>2003</year>;<volume>34</volume>:<fpage>2741</fpage>-<lpage>2748</lpage>. doi:<pub-id pub-id-type=\\"doi\\">https://doi.org/10.1161/01.STR.0000092488.40085.15</pub-id></mixed-citation></ref><ref id=\\"ref-10\\"><label>10. </label><mixed-citation publication-type=\\"journal\\"><person-group person-group-type=\\"author\\"><string-name><surname>Girot</surname> <given-names>M</given-names></string-name>, <string-name><surname>Mackowiak-Cordoliani</surname> <given-names>MA</given-names></string-name>, <string-name><surname>Deplanque</surname> <given-names>D</given-names></string-name>, <string-name><surname>Hénon</surname> <given-names>H</given-names></string-name>, <string-name><surname>Lucas</surname> <given-names>C</given-names></string-name>, <string-name><surname>Leys</surname> <given-names>D</given-names></string-name></person-group>. <article-title>Secondary prevention after ischemic</article-title> <source><italic>Journal of Neurology</italic></source>. <year>2005</year>;<volume>252</volume>:<fpage>14</fpage>-<lpage>20</lpage>. doi:<pub-id pub-id-type=\\"doi\\">https://doi.org/10.1007/s00415-005-0591-8</pub-id></mixed-citation></ref><ref id=\\"ref-11\\"><label>11. </label><mixed-citation publication-type=\\"journal\\"><person-group person-group-type=\\"author\\"><string-name><surname>Johnson</surname> <given-names>P</given-names></string-name>, <string-name><surname>Rosewell</surname> <given-names>M</given-names></string-name>, <string-name><surname>James</surname> <given-names>MA</given-names></string-name></person-group>. <article-title>How good is the management of vascular risk after stroke</article-title>, <source><italic>Cerebrovascular Diseases (Basel, Switzerland)</italic></source>. <year>2007</year>;<volume>23</volume>:<fpage>156</fpage>-<lpage>161</lpage>. doi:<pub-id pub-id-type=\\"doi\\">https://doi.org/10.1159/000097053</pub-id></mixed-citation></ref><ref id=\\"ref-12\\"><label>12. </label><mixed-citation publication-type=\\"journal\\"><person-group person-group-type=\\"author\\"><string-name><surname>Paul</surname> <given-names>SL</given-names></string-name>, <string-name><surname>Thrift</surname> <given-names>AG</given-names></string-name></person-group>. <article-title>Control of hypertension 5 years after stroke in the North</article-title> <source><italic>Hypertension</italic></source>. <year>2006</year>;<volume>48</volume>:<fpage>260</fpage>-<lpage>265</lpage>. doi:<pub-id pub-id-type=\\"doi\\">https://doi.org/10.1161/01.HYP.0000230610.81947.04</pub-id></mixed-citation></ref><ref id=\\"ref-13\\"><label>13. </label><mixed-citation publication-type=\\"journal\\"><person-group person-group-type=\\"author\\"><string-name><surname>Hornnes</surname> <given-names>N</given-names></string-name>, <string-name><surname>Larsen</surname> <given-names>K</given-names></string-name>, <string-name><surname>Boysen</surname> <given-names>G</given-names></string-name></person-group>. <article-title>Little change of modifiable risk factors</article-title> <source><italic>International Journal of Stroke</italic></source>. <year>2010</year>;<volume>5</volume>:<fpage>157</fpage>-<lpage>162</lpage>. doi:<pub-id pub-id-type=\\"doi\\">https://doi.org/10.1111/j.1747-4949.2010.00424.x</pub-id></mixed-citation></ref><ref id=\\"ref-14\\"><label>14. </label><mixed-citation publication-type=\\"journal\\"><person-group person-group-type=\\"author\\"><string-name><surname>Adie</surname> <given-names>K</given-names></string-name>, <string-name><surname>James</surname> <given-names>MA</given-names></string-name></person-group>. <article-title>Does telephone follow-up improve blood pressure after minor</article-title> <source><italic>Age and Ageing</italic></source>. <year>2010</year>;<volume>39</volume>:<fpage>598</fpage>-<lpage>603</lpage>. doi:<pub-id pub-id-type=\\"doi\\">https://doi.org/10.1093/ageing/afq085</pub-id></mixed-citation></ref><ref id=\\"ref-15\\"><label>15. </label><mixed-citation publication-type=\\"journal\\"><person-group person-group-type=\\"author\\"><string-name><surname>Chiu</surname> <given-names>CC</given-names></string-name>, <string-name><surname>Wu</surname> <given-names>SS</given-names></string-name>, <string-name><surname>Lee</surname> <given-names>PY</given-names></string-name>, <string-name><surname>Huang</surname> <given-names>YC</given-names></string-name>, <string-name><surname>Tan</surname> <given-names>TY</given-names></string-name>, <string-name><surname>Chang</surname> <given-names>KC</given-names></string-name></person-group>. <article-title>Control of modifiable risk factors in ischemic stroke</article-title> <source><italic>Journal of Clinical Pharmacy and Therapeutics</italic></source>. <year>2008</year>;<volume>33</volume>:<fpage>529</fpage>-<lpage>535</lpage>. doi:<pub-id pub-id-type=\\"doi\\">https://doi.org/10.1111/j.1365-2710.2008.00940.x</pub-id></mixed-citation></ref><ref id=\\"ref-16\\"><label>16. </label><mixed-citation publication-type=\\"journal\\"><person-group person-group-type=\\"author\\"><string-name><surname>Ellis</surname> <given-names>G</given-names></string-name>, <string-name><surname>Rodger</surname> <given-names>J</given-names></string-name>, <string-name><surname>McAlpine</surname> <given-names>C</given-names></string-name>, <string-name><surname>Langhorne</surname> <given-names>P</given-names></string-name></person-group>. <article-title>The impact of stroke nurse specialist</article-title> <source><italic>Age and Ageing</italic></source>. <year>2005</year>;<volume>34</volume>:<fpage>389</fpage>-<lpage>392</lpage>. doi:<pub-id pub-id-type=\\"doi\\">https://doi.org/10.1093/ageing/afi075</pub-id></mixed-citation></ref><ref id=\\"ref-17\\"><label>17. </label><mixed-citation publication-type=\\"journal\\"><person-group person-group-type=\\"author\\"><string-name><surname>Hornnes</surname> <given-names>N</given-names></string-name>, <string-name><surname>Larsen</surname> <given-names>K</given-names></string-name>, <string-name><surname>Boysen</surname> <given-names>G</given-names></string-name></person-group>. <article-title>Blood pressure 1 year after stroke: The</article-title> <source><italic>Journal of Stroke and Cerebrovascular Diseases</italic></source>. <year>2011</year>;<volume>20</volume>:<fpage>16</fpage>-<lpage>23</lpage>. doi:<pub-id pub-id-type=\\"doi\\">https://doi.org/10.1016/j.jstrokecerebrovasdis.2009.10.002</pub-id></mixed-citation></ref><ref id=\\"ref-18\\"><label>18. </label><mixed-citation publication-type=\\"journal\\"><person-group person-group-type=\\"author\\"><string-name><surname>Johnston</surname> <given-names>SC</given-names></string-name>, <string-name><surname>Sidney</surname> <given-names>S</given-names></string-name>, <string-name><surname>Hills</surname> <given-names>NK</given-names></string-name>, et al</person-group>. <article-title>Standardized discharge orders after</article-title> <source><italic>Annals of Neurology</italic></source>. <year>2010</year>;<volume>67</volume>:<fpage>579</fpage>-<lpage>589</lpage>. doi:<pub-id pub-id-type=\\"doi\\">https://doi.org/10.1002/ana.22019</pub-id></mixed-citation></ref><ref id=\\"ref-19\\"><label>19. </label><mixed-citation publication-type=\\"journal\\"><person-group person-group-type=\\"author\\"><string-name><surname>Joubert</surname> <given-names>J</given-names></string-name>, <string-name><surname>Reid</surname> <given-names>C</given-names></string-name>, <string-name><surname>Barton</surname> <given-names>D</given-names></string-name>, et al</person-group>. <article-title>Integrated care improves risk-factor</article-title> <source><italic>Journal of Neurology, Neurosurgery, and Psychiatry</italic></source>. <year>2009</year>;<volume>80</volume>:<fpage>279</fpage>-<lpage>284</lpage>. doi:<pub-id pub-id-type=\\"doi\\">https://doi.org/10.1136/jnnp.2008.148122</pub-id></mixed-citation></ref><ref id=\\"ref-20\\"><label>20. </label><mixed-citation publication-type=\\"journal\\"><person-group person-group-type=\\"author\\"><string-name><surname>Fahey</surname> <given-names>T</given-names></string-name>, <string-name><surname>Schroeder</surname> <given-names>K</given-names></string-name>, <string-name><surname>Ebrahim</surname> <given-names>S</given-names></string-name></person-group>. <article-title>Interventions used to improve control of</article-title> <source><italic>Cochrane Database of Systematic Reviews</italic></source>. <year>2006</year>.</mixed-citation></ref><ref id=\\"ref-21\\"><label>21. </label><mixed-citation publication-type=\\"journal\\"><person-group person-group-type=\\"author\\"><string-name><surname>Furie</surname> <given-names>KL</given-names></string-name>, <string-name><surname>Kasner</surname> <given-names>SE</given-names></string-name>, <string-name><surname>Adams</surname> <given-names>RJ</given-names></string-name>, et al</person-group>. <article-title>Guidelines for the prevention of stroke</article-title> <source><italic>Stroke</italic></source>. <year>2011</year>;<volume>42</volume>:<fpage>227</fpage>-<lpage>276</lpage>. doi:<pub-id pub-id-type=\\"doi\\">https://doi.org/10.1161/STR.0b013e3181f7d043</pub-id></mixed-citation></ref><ref id=\\"ref-22\\"><label>22. </label><mixed-citation publication-type=\\"journal\\"><person-group person-group-type=\\"author\\"><string-name><surname>Bridgwood</surname> <given-names>B</given-names></string-name>, <string-name><surname>Lager</surname> <given-names>KE</given-names></string-name>, <string-name><surname>Mistri</surname> <given-names>AK</given-names></string-name>, <string-name><surname>Khunti</surname> <given-names>K</given-names></string-name>, <string-name><surname>Wilson</surname> <given-names>AD</given-names></string-name>, <string-name><surname>Modi</surname> <given-names>P</given-names></string-name></person-group>. <article-title>Interventions for improving modifiable</article-title> <source><italic>Cochrane Database of Systematic Reviews</italic></source>. <year>2018</year>;<volume>5</volume>.</mixed-citation></ref><ref id=\\"ref-23\\"><label>23. </label><mixed-citation publication-type=\\"journal\\"><person-group person-group-type=\\"author\\"><string-name><surname>Mancia</surname> <given-names>G</given-names></string-name>, <string-name><surname>Fagard</surname> <given-names>R</given-names></string-name>, <string-name><surname>Narkiewicz</surname> <given-names>K</given-names></string-name>, et al</person-group>. <article-title>2013 Practice guidelines for the management of arterial</article-title> <source><italic>Journal of Hypertension</italic></source>. <year>2013</year>;<volume>31</volume>:<fpage>1925</fpage>-<lpage>1938</lpage>. doi:<pub-id pub-id-type=\\"doi\\">https://doi.org/10.1097/HJH.0b013e328364ca4c</pub-id></mixed-citation></ref><ref id=\\"ref-24\\"><label>24. </label><mixed-citation publication-type=\\"journal\\"><person-group person-group-type=\\"author\\"><string-name><surname>Boan</surname> <given-names>AD</given-names></string-name>, <string-name><surname>Lackland</surname> <given-names>DT</given-names></string-name>, <string-name><surname>Ovbiagele</surname> <given-names>B</given-names></string-name></person-group>. <article-title>Lowering of blood pressure for recurrent</article-title> <source><italic>Stroke</italic></source>. <year>2014</year>;<volume>45</volume>:<fpage>2506</fpage>-<lpage>2513</lpage>. doi:<pub-id pub-id-type=\\"doi\\">https://doi.org/10.1161/STROKEAHA.114.003666</pub-id></mixed-citation></ref><ref id=\\"ref-25\\"><label>25. </label><mixed-citation publication-type=\\"journal\\"><person-group person-group-type=\\"author\\"><string-name><surname>McAlister</surname> <given-names>FA</given-names></string-name>, <string-name><surname>Majumdar</surname> <given-names>SR</given-names></string-name>, <string-name><surname>Padwal</surname> <given-names>RS</given-names></string-name>, et al</person-group>. <article-title>Case management for blood pressure and</article-title> <source><italic>Canadian Medical Association Journal</italic></source>. <year>2014</year>;<volume>186</volume>:<fpage>577</fpage>-<lpage>584</lpage>. doi:<pub-id pub-id-type=\\"doi\\">https://doi.org/10.1503/cmaj.140053</pub-id></mixed-citation></ref></ref-list></back><floats-group><graphic xlink:href=\\"fig1.png\\" content-type=\\"leading\\"><alt-text>example of alt text for hero-image</alt-text><long-desc>example of long desc for hero image</long-desc></graphic></floats-group></article>"
 `;
 
-exports[`JATS roundtrip > jats-roundtrip.xml roundtrip 1`] = `"<!DOCTYPE article PUBLIC \\"-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD with OASIS Tables with MathML3 v1.2 20190208//EN\\" \\"http://jats.nlm.nih.gov/archiving/1.2/JATS-archive-oasis-article1-mathml3.dtd\\"><article xmlns:xlink=\\"http://www.w3.org/1999/xlink\\" article-type=\\"research-article\\" xml:lang=\\"en\\"><front><article-meta><title-group><article-title>A complete manuscript</article-title></title-group><contrib-group content-type=\\"authors\\"><contrib contrib-type=\\"author\\" id=\\"contrib-1\\"><name><surname>Macintosh</surname><given-names>Alfred</given-names></name><email>flinserl@hotmail.com</email></contrib><contrib contrib-type=\\"author\\" id=\\"contrib-2\\" corresp=\\"yes\\"><name><surname>Adam</surname><given-names>Rein</given-names></name><email>rein.brys@inbo.be</email></contrib></contrib-group><author-notes><p id=\\"p-1\\">rana nofal testing</p></author-notes><counts><fig-count count=\\"2\\"/><ref-count count=\\"2\\"/><word-count count=\\"107\\"/></counts></article-meta></front><body><sec id=\\"sec-1\\"><title>Figures</title><fig id=\\"fig-1\\" fig-type=\\"half-left\\"><label>Figure 1</label><caption><p>Test1</p><p>Test2</p></caption><p id=\\"p-2\\">A paragraph</p><graphic xlink:href=\\"graphic/111111.jpeg\\"/><graphic specific-use=\\"MISSING\\" xlink:href=\\"\\"/><graphic xlink:href=\\"graphic/333333.jpeg\\"/><attrib>Source: Wikipedia.</attrib></fig></sec></body><back><app-group/><fn-group><fn fn-type=\\"con\\"><label>Author contributions</label><p id=\\"p-3\\">JM and AB wrote the manuscript. All co-authors provided comments and helped revising the manuscript.</p></fn><fn fn-type=\\"financial-disclosure\\"><label>FUNDING INFORMATION</label><p id=\\"p-4\\">This work was supported by the National Natural Science Foundation of China (81771439), Jiangsu Provincial Key <xref ref-type=\\"bibr\\" rid=\\"ref-1\\"><sup>1</sup></xref>Research and Development Program (BE2020661 and BE2018662), Jiangsu Provincial Health Commission Science Research Program (QNRC2016228, H2019056 and LGY2018010), Jiangsu Provincial Six Talent Peaks Project (WSN-165), Suzhou Municipal Health Commission Science Research Program (SZYJTD201715, LCZX201820, Kjxw2018048 and Gwzx201801), Suzhou Municipal Sci-Tech Bureau Program (SZS201722, SS201706, SYS2019113 and SS2019009), and CAS Key Laboratory of Mental Health, Institute of Psychology (KLMH2019K03).</p></fn></fn-group><ref-list><ref id=\\"ref-1\\"><label>1. </label><mixed-citation publication-type=\\"journal\\"><person-group person-group-type=\\"author\\"><string-name><surname>Caldwell</surname> <given-names>CB</given-names></string-name>, <string-name><surname>Gottesman</surname> <given-names>II</given-names></string-name></person-group>. <article-title>Schizophrenia-a high-risk factor for suicide: clues to risk reduction</article-title>. <source><italic>Suicide Life Threat Behav</italic></source>. <year>1992</year>;<volume>22</volume><issue>(4)</issue>:<fpage>479</fpage>-<lpage>493</lpage>.</mixed-citation></ref></ref-list></back></article>"`;
+exports[`JATS roundtrip > jats-roundtrip.xml roundtrip 1`] = `"<!DOCTYPE article PUBLIC \\"-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD with OASIS Tables with MathML3 v1.2 20190208//EN\\" \\"http://jats.nlm.nih.gov/archiving/1.2/JATS-archive-oasis-article1-mathml3.dtd\\"><article xmlns:xlink=\\"http://www.w3.org/1999/xlink\\" article-type=\\"research-article\\" xml:lang=\\"en\\"><front><article-meta><title-group><article-title>A complete manuscript</article-title></title-group><contrib-group content-type=\\"authors\\"><contrib contrib-type=\\"author\\" id=\\"contrib-1\\"><name><surname>Macintosh</surname><given-names>Alfred</given-names></name><email>flinserl@hotmail.com</email></contrib><contrib contrib-type=\\"author\\" id=\\"contrib-2\\" corresp=\\"yes\\"><name><surname>Adam</surname><given-names>Rein</given-names></name><email>rein.brys@inbo.be</email></contrib></contrib-group><author-notes><p id=\\"p-1\\">rana nofal testing</p></author-notes><counts><fig-count count=\\"2\\"/><ref-count count=\\"2\\"/><word-count count=\\"107\\"/></counts></article-meta></front><body><sec id=\\"sec-1\\"><title>Figures</title><fig id=\\"fig-1\\" fig-type=\\"half-left\\"><label>Figure 1</label><caption><p>Test1</p><p>Test2</p></caption><p id=\\"p-2\\">A paragraph</p><graphic xlink:href=\\"graphic/111111.jpeg\\"/><graphic specific-use=\\"MISSING\\" xlink:href=\\"\\"/><graphic xlink:href=\\"graphic/333333.jpeg\\"/><attrib>Source: Wikipedia.</attrib></fig></sec></body><back><app-group/><fn-group><fn fn-type=\\"con\\"><label>Author contributions</label><p id=\\"p-3\\">JM and AB wrote the manuscript. All co-authors provided comments and helped revising the manuscript.</p></fn><fn fn-type=\\"financial-disclosure\\"><label>FUNDING INFORMATION</label><p id=\\"p-4\\">This work was supported by the National Natural Science Foundation of China (81771439), Jiangsu Provincial Key <xref ref-type=\\"bibr\\" rid=\\"ref-1\\"><sup>1</sup></xref>Research and Development Program (BE2020661 and BE2018662), Jiangsu Provincial Health Commission Science Research Program (QNRC2016228, H2019056 and LGY2018010), Jiangsu Provincial Six Talent Peaks Project (WSN-165), Suzhou Municipal Health Commission Science Research Program (SZYJTD201715, LCZX201820, Kjxw2018048 and Gwzx201801), Suzhou Municipal Sci-Tech Bureau Program (SZS201722, SS201706, SYS2019113 and SS2019009), and CAS Key Laboratory of Mental Health, Institute of Psychology (KLMH2019K03).</p></fn></fn-group><ref-list><ref id=\\"ref-1\\"><label>1. </label><mixed-citation publication-type=\\"journal\\"><person-group person-group-type=\\"author\\"><string-name><surname>Caldwell</surname> <given-names>CB</given-names></string-name>, <string-name><surname>Gottesman</surname> <given-names>II</given-names></string-name></person-group>. <article-title>Schizophrenia-a high-risk factor for suicide: clues to risk reduction</article-title>. <source><italic>Suicide Life Threat Behav</italic></source>. <year>1992</year>;<volume>22</volume><issue>(4)</issue>:<fpage>479</fpage>-<lpage>493</lpage>.</mixed-citation></ref><ref id=\\"ref-2\\"><label>2. </label><mixed-citation publication-type=\\"journal\\"><person-group person-group-type=\\"author\\"><string-name><surname>Hor</surname> <given-names>K</given-names></string-name>, <string-name><surname>Taylor</surname> <given-names>M</given-names></string-name></person-group>. <article-title>Suicide and schizophrenia: a systematic review of rates and risk factors</article-title>. <source><italic>J Psychopharmacol</italic></source>. <year>2010</year>;<volume>24</volume><issue>(4)</issue>:<fpage>81</fpage>-<lpage>90</lpage>. doi:<pub-id pub-id-type=\\"doi\\">https://doi.org/10.1177/1359786810385490</pub-id></mixed-citation></ref></ref-list></back></article>"`;

package/src/jats/__tests__/jats-exporter.test.ts

@@ -22,7 +22,11 @@ import { parseJATSArticle } from '../importer/parse-jats-article'
 import { DEFAULT_CSL_OPTIONS } from './citations'
 import { sectionCategories } from './data/section-categories'
 import { readAndParseFixture } from './files'
-import { BibliographyItemNode, isBibliographyItemNode } from '../../schema'
+import {
+  BibliographyItemNode,
+  isBibliographyItemNode,
+  isCitationNode,
+} from '../../schema'
 
 const parseXMLWithDTD = (data: string) =>
   parseXml(data, {
@@ -197,6 +201,29 @@ describe('JATS exporter', () => {
     )
   })
 
+  test('exports uncited references alongside cited ones', async () => {
+    const input = await readAndParseFixture('jats-document.xml')
+    const node = parseJATSArticle(input, sectionCategories)
+
+    const bibliographyItemIDs = new Set<string>()
+    const citedIDs = new Set<string>()
+    node.descendants((n) => {
+      if (isBibliographyItemNode(n)) {
+        bibliographyItemIDs.add(n.attrs.id)
+      }
+      if (isCitationNode(n)) {
+        n.attrs.rids.forEach((rid: string) => citedIDs.add(rid))
+      }
+    })
+    const xml = await new JATSExporter().serializeToJATS(node, {
+      csl: DEFAULT_CSL_OPTIONS,
+    })
+    const refCount = parseXMLWithDTD(xml).find('//ref-list/ref').length
+    expect(refCount).toBe(bibliographyItemIDs.size)
+    const { errors } = parseXMLWithDTD(xml)
+    expect(errors).toHaveLength(0)
+  })
+
   test('export footnotes', async () => {
     const transformer = new JATSExporter()
     const input = await readAndParseFixture('jats-fn-group.xml')

package/src/jats/exporter/jats-exporter.ts

@@ -191,7 +191,7 @@ export class JATSExporter {
   ): Promise<string> => {
     this.manuscriptNode = manuscriptNode
     this.populateNodesMap()
-    this.initCiteprocEngine(options.csl)
+    this.initCiteprocEngine(options)
     this.createSerializer()
     const versionIds = selectVersionIds(options.version ?? '1.2')
 
@@ -283,9 +283,11 @@ export class JATSExporter {
       element.appendChild(caption)
     }
   }
-  private initCiteprocEngine = (csl: CSLOptions) => {
+  private initCiteprocEngine = (options: ExportOptions) => {
+    const { csl } = options
     const bibitems: Map<string, CSL.Data> = new Map()
     const citations: Map<string, Citeproc.Citation> = new Map()
+    const citedItemIDs: Set<string> = new Set()
 
     this.manuscriptNode.descendants((n) => {
       if (isBibliographyItemNode(n)) {
@@ -293,6 +295,7 @@ export class JATSExporter {
       }
       if (isCitationNode(n)) {
         citations.set(n.attrs.id, buildCiteprocCitation(n.attrs))
+        n.attrs.rids.forEach((rid: string) => citedItemIDs.add(rid))
       }
     })
 
@@ -313,7 +316,15 @@ export class JATSExporter {
     )
     engine.setOutputFormat('jats')
 
-    const output = engine.rebuildProcessorState([...citations.values()])
+    const uncitedItemIDs = [...bibitems.keys()].filter(
+      (id) => !citedItemIDs.has(id)
+    )
+
+    const output = engine.rebuildProcessorState(
+      [...citations.values()],
+      undefined,
+      uncitedItemIDs
+    )
 
     this.engine = engine
     this.renderedCitations = new Map(output.map((i) => [i[0], i[2]]))

package/src/jats/exporter/labels.ts

@@ -43,7 +43,10 @@ const labelledNodeTypes: ManuscriptNodeType[] = [
   schema.nodes.image_element,
 ]
 
-const excludedTypes = [schema.nodes.graphical_abstract_section]
+const excludedTypes = [
+  schema.nodes.graphical_abstract_section,
+  schema.nodes.trans_graphical_abstract,
+]
 
 const chooseLabel = (nodeType: ManuscriptNodeType): string => {
   return nodeNames.get(nodeType) as string

package/src/version.ts

@@ -1 +1 @@
-export const VERSION = "4.4.3";
+export const VERSION = "4.4.5";