lean-prod - Opening previously created Drafts results in "Document not found" error in Editor for some items (LEAN-5747)

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 +201,39 @@ describe('JATS exporter', () => {
     )
   })
 
+  test('export uncited references when includeUncitedReferences is set', 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 withoutUncited = await new JATSExporter().serializeToJATS(node, {
+      csl: DEFAULT_CSL_OPTIONS,
+    })
+    const withUncited = await new JATSExporter().serializeToJATS(node, {
+      csl: DEFAULT_CSL_OPTIONS,
+      includeUncitedReferences: true,
+    })
+
+    const countRefs = (xml: string) =>
+      parseXMLWithDTD(xml).find('//ref-list/ref').length
+
+    expect(countRefs(withoutUncited)).toBe(citedIDs.size)
+    expect(countRefs(withUncited)).toBe(bibliographyItemIDs.size)
+
+    const { errors } = parseXMLWithDTD(withUncited)
+    expect(errors).toHaveLength(0)
+  })
+
   test('export footnotes', async () => {
     const transformer = new JATSExporter()
     const input = await readAndParseFixture('jats-fn-group.xml')

src/jats/exporter/jats-exporter.ts

@@ -147,6 +147,7 @@ export type CSLOptions = {
 export type ExportOptions = {
   version?: Version
   csl: CSLOptions
+  includeUncitedReferences?: boolean
 }
 
 export class JATSExporter {
@@ -191,7 +192,7 @@ 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')
 
@@ -283,7 +284,8 @@ export class JATSExporter {
       element.appendChild(caption)
     }
   }
-  private initCiteprocEngine = (csl: CSLOptions) => {
+  private initCiteprocEngine = (options: ExportOptions) => {
+    const { includeUncitedReferences, csl } = options
     const bibitems: Map<string, CSL.Data> = new Map()
     const citations: Map<string, Citeproc.Citation> = new Map()
 
@@ -313,7 +315,13 @@ export class JATSExporter {
     )
     engine.setOutputFormat('jats')
 
-    const output = engine.rebuildProcessorState([...citations.values()])
+    const uncitedItemIDs = includeUncitedReferences ? [...bibitems.keys()] : []
+
+    const output = engine.rebuildProcessorState(
+      [...citations.values()],
+      undefined,
+      uncitedItemIDs
+    )
 
     this.engine = engine
     this.renderedCitations = new Map(output.map((i) => [i[0], i[2]]))

src/schema/__tests__/docs.ts

@@ -653,6 +653,46 @@ export const v2_3_20 = {
                 },
               ],
             },
+            {
+              type: 'figure_element',
+              attrs: {
+                id: 'MPFigureElement:ca6dac1a-b6ae-4227-be6e-75119186224b',
+                label: '',
+                sizeFraction: 0,
+                suppressCaption: true,
+                suppressTitle: true,
+                dataTracked: null,
+              },
+              content: [
+                {
+                  type: 'figure',
+                  attrs: {
+                    id: 'MPFigure:d377ead2-6849-4597-9caa-f3e6b73bb629',
+                    src: 'chemoji/chemoji8.png',
+                    contentType: 'image/png',
+                    dataTracked: null,
+                  },
+                },
+                {
+                  type: 'figcaption',
+                  attrs: {
+                    dataTracked: null,
+                  },
+                },
+                {
+                  type: 'listing',
+                  attrs: {
+                    id: '',
+                    contents: '',
+                    language: '',
+                    languageKey: 'null',
+                    isExpanded: false,
+                    isExecuting: false,
+                    dataTracked: null,
+                  },
+                },
+              ],
+            },
             {
               type: 'table_element',
               attrs: {

src/schema/migration/migration-scripts/4.3.34.ts

@@ -59,18 +59,26 @@ class Migration4334 implements MigrationScript {
     const foundTitle = (figCaption?.content || []).find(
       (n) => n.type === 'caption_title'
     )
-    const foundCaption = (figCaption?.content || []).filter(
-      (node) => node.type === 'caption')
-      .reduce<JSONProsemirrorNode>(
-        (caption, { content }) => ({
-          ...caption,
-          content: [
-            ...(caption.content || []),
-            { type: 'text_block', content, attrs: {} },
-          ],
-        }),
-        { type: 'caption', content: [], attrs: {} }
-      )
+    const captionNodes = (figCaption?.content || []).filter(
+      (node) => node.type === 'caption'
+    )
+    const foundCaption =
+      captionNodes.length === 0
+        ? {
+            type: 'caption',
+            content: [{ type: 'text_block', attrs: {} }],
+            attrs: {},
+          }
+        : captionNodes.reduce<JSONProsemirrorNode>(
+            (caption, { content }) => ({
+              ...caption,
+              content: [
+                ...(caption.content || []),
+                { type: 'text_block', content, attrs: {} },
+              ],
+            }),
+            { type: 'caption', content: [], attrs: {} }
+          )
 
     const cleanContent = node.content.filter((n) => n.type !== 'figcaption')