feat(website): improve SeqSet citation metadata

backend/docs/db/schema.sql

@@ -434,6 +434,7 @@ CREATE TABLE public.seqset_citation_source (
     title text NOT NULL,
     year integer NOT NULL,
     contributors jsonb NOT NULL,
+    journal text,
     CONSTRAINT seqset_citation_source_origin_check CHECK ((origin = ANY (ARRAY['CROSSREF'::text, 'CURATED'::text])))
 );
 

backend/src/main/kotlin/org/loculus/backend/api/SeqSetCitations.kt

@@ -90,6 +90,11 @@ data class CitationSource(
         description = "List of contributors to the citation source.",
     )
     val contributors: List<CitationContributor>,
+    @Schema(
+        description = "The journal in which the citation source was published, when applicable.",
+        example = "Journal of Examples",
+    )
+    val journal: String? = null,
 )
 
 data class SeqSetCitationSource(val source: CitationSource, val seqSetDOIs: Set<String> = emptySet())

backend/src/main/kotlin/org/loculus/backend/service/crossref/CrossRefService.kt

@@ -166,13 +166,15 @@ class CrossRefService(
                     CitationContributor(givenName, surname)
                 }
             }
+            val journal = citationElement.selectFirst("journal_title")?.text()?.takeIf { it.isNotBlank() }
 
             SeqSetCitationSource(
                 source = CitationSource(
                     sourceDOI = sourceDOI,
                     title = title,
                     year = year,
                     contributors = contributors,
+                    journal = journal,
                 ),
                 seqSetDOIs = setOf(seqSetDOI),
             )

backend/src/main/kotlin/org/loculus/backend/service/seqsetcitations/SeqSetCitationsDatabaseService.kt

@@ -407,6 +407,7 @@ class SeqSetCitationsDatabaseService(
                 this[SeqSetCitationSourceTable.title] = it.source.title
                 this[SeqSetCitationSourceTable.year] = it.source.year
                 this[SeqSetCitationSourceTable.contributors] = it.source.contributors
+                this[SeqSetCitationSourceTable.journal] = it.source.journal
             }
             .flatMap { result ->
                 val citationSourceId = result[SeqSetCitationSourceTable.citationSourceId]
@@ -456,6 +457,7 @@ class SeqSetCitationsDatabaseService(
                         it[SeqSetCitationSourceTable.title],
                         it[SeqSetCitationSourceTable.year],
                         it[SeqSetCitationSourceTable.contributors],
+                        it[SeqSetCitationSourceTable.journal],
                     ),
                 )
             }
@@ -494,6 +496,7 @@ class SeqSetCitationsDatabaseService(
                         title = first[SeqSetCitationSourceTable.title],
                         year = first[SeqSetCitationSourceTable.year],
                         contributors = first[SeqSetCitationSourceTable.contributors],
+                        journal = first[SeqSetCitationSourceTable.journal],
                     ),
                     seqSets = rows.map {
                         SeqSetCitingSequence(
@@ -529,6 +532,7 @@ class SeqSetCitationsDatabaseService(
                         title = first[SeqSetCitationSourceTable.title],
                         year = first[SeqSetCitationSourceTable.year],
                         contributors = first[SeqSetCitationSourceTable.contributors],
+                        journal = first[SeqSetCitationSourceTable.journal],
                     ),
                     seqSets = rows.map { it.toSeqSet() },
                     origin = first[SeqSetCitationSourceTable.origin],
@@ -584,6 +588,7 @@ class SeqSetCitationsDatabaseService(
                 this[SeqSetCitationSourceTable.title] = it.title
                 this[SeqSetCitationSourceTable.year] = it.year
                 this[SeqSetCitationSourceTable.contributors] = it.contributors
+                this[SeqSetCitationSourceTable.journal] = it.journal
             }
             .single()[SeqSetCitationSourceTable.citationSourceId]
 

backend/src/main/kotlin/org/loculus/backend/service/seqsetcitations/SeqSetsTables.kt

@@ -44,6 +44,7 @@ object SeqSetCitationSourceTable : Table("seqset_citation_source") {
     val title = text("title")
     val year = integer("year")
     val contributors = jacksonSerializableJsonb<List<CitationContributor>>("contributors")
+    val journal = text("journal").nullable()
     override val primaryKey = PrimaryKey(citationSourceId)
 }
 

backend/src/main/resources/db/migration/V1.34__add_journal_to_seqset_citation_source.sql

@@ -0,0 +1 @@
+alter table seqset_citation_source add column journal text;

backend/src/test/kotlin/org/loculus/backend/service/crossref/CrossRefServiceTest.kt

@@ -101,6 +101,7 @@ class CrossRefServiceTest(
                             CitationContributor(givenName = "Jane", surname = "Doe"),
                             CitationContributor(givenName = "John", surname = "Smith"),
                         ),
+                        journal = "Journal of Citations",
                     ),
                     seqSetDOIs = setOf("10.1234/seqset-1"),
                 ),

website/src/components/AdminDashboard/AddSeqSetCitationForm.tsx

@@ -37,6 +37,7 @@ const parseContributor = (line: string) => {
 /* eslint-disable @typescript-eslint/naming-convention */
 type CrossRefWork = {
     'title'?: string[];
+    'container-title'?: string[];
     'author'?: { given?: string; family?: string }[];
     'issued'?: { 'date-parts'?: number[][] };
     'published'?: { 'date-parts'?: number[][] };
@@ -60,6 +61,7 @@ export const AddSeqSetCitationForm: FC<Props> = ({ clientConfig, accessToken, on
     const isClient = useClientFlag();
     const [sourceDOI, setSourceDOI] = useState('');
     const [title, setTitle] = useState('');
+    const [journal, setJournal] = useState('');
     const [year, setYear] = useState('');
     const [contributorsInput, setContributorsInput] = useState('');
     const [seqSetAccessionsInput, setSeqSetAccessionsInput] = useState('');
@@ -72,6 +74,7 @@ export const AddSeqSetCitationForm: FC<Props> = ({ clientConfig, accessToken, on
     const resetForm = () => {
         setSourceDOI('');
         setTitle('');
+        setJournal('');
         setYear('');
         setContributorsInput('');
         setSeqSetAccessionsInput('');
@@ -96,6 +99,9 @@ export const AddSeqSetCitationForm: FC<Props> = ({ clientConfig, accessToken, on
             if (work.title?.[0] !== undefined) {
                 setTitle(work.title[0]);
             }
+            if (work['container-title']?.[0] !== undefined) {
+                setJournal(work['container-title'][0]);
+            }
             const year = extractYear(work);
             if (year !== undefined) {
                 setYear(String(year));
@@ -146,6 +152,7 @@ export const AddSeqSetCitationForm: FC<Props> = ({ clientConfig, accessToken, on
                 title: title.trim(),
                 year: parsedYear,
                 contributors: splitLines(contributorsInput).map(parseContributor),
+                journal: journal.trim() || undefined,
             },
             seqSetAccessionVersions,
         });
@@ -226,6 +233,19 @@ export const AddSeqSetCitationForm: FC<Props> = ({ clientConfig, accessToken, on
                     disabled={!isClient}
                 />
             </div>
+            <div className='mb-4'>
+                <label htmlFor='citation-journal' className='block mb-1 text-sm font-medium text-gray-900'>
+                    Journal
+                </label>
+                <input
+                    id='citation-journal'
+                    type='text'
+                    className={inputStyles}
+                    value={journal}
+                    onChange={(e) => setJournal(e.target.value)}
+                    disabled={!isClient}
+                />
+            </div>
             <div className='mb-4'>
                 <label htmlFor='citation-contributors' className='block mb-1 text-sm font-medium text-gray-900'>
                     Contributors (one &lsquo;Given Surname&rsquo; per line)

website/src/components/AdminDashboard/AdminSeqSetCitationsTable.tsx

@@ -3,18 +3,14 @@ import type { FC } from 'react';
 import { routes } from '../../routes/routes';
 import type { AdminSeqSetCitation } from '../../types/seqSetCitation';
 import { getAccessionVersionString } from '../../utils/extractAccessionVersion';
+import { formatCitationContributors } from '../SeqSetCitations/formatCitationContributors';
 import { Button } from '../common/Button';
 
 interface Props {
     citations: AdminSeqSetCitation[];
     onDelete?: (sourceDOI: string) => void;
 }
 
-const formatContributors = (contributors: AdminSeqSetCitation['source']['contributors']) =>
-    contributors
-        .map((contributor) => [contributor.givenName, contributor.surname].filter((name) => name).join(' '))
-        .join(', ');
-
 export const AdminSeqSetCitationsTable: FC<Props> = ({ citations, onDelete }) => {
     if (citations.length === 0) {
         return <p className='mt-4'>No publications currently cite any SeqSet.</p>;
@@ -52,8 +48,11 @@ export const AdminSeqSetCitationsTable: FC<Props> = ({ citations, onDelete }) =>
                                 {citation.source.title}
                             </a>
                             <div className='text-sm text-gray-700'>
-                                {formatContributors(citation.source.contributors)}
+                                {formatCitationContributors(citation.source.contributors)}
                             </div>
+                            {citation.source.journal !== undefined && citation.source.journal !== null && (
+                                <div className='text-sm italic text-gray-700'>{citation.source.journal}</div>
+                            )}
                             <div className='text-xs text-gray-500'>{citation.source.sourceDOI}</div>
                         </td>
                         <td className='border px-2 py-1 align-top text-right'>{citation.source.year}</td>

website/src/components/SeqSetCitations/CitationTable.tsx

@@ -1,5 +1,6 @@
 import { type FC } from 'react';
 
+import { formatCitationContributors } from './formatCitationContributors';
 import { routes } from '../../routes/routes';
 import { type SeqSetCitation, type SequenceCitation } from '../../types/seqSetCitation';
 
@@ -19,7 +20,7 @@ export const CitationDetails: FC<{
     displayYear?: boolean;
 }> = ({ citation, className = '', displayYear = false }) => {
     return (
-        <div className={`flex flex-col gap-2 ${className}`}>
+        <div className={`flex flex-col gap-1 ${className}`}>
             <a
                 className='text-primary-700'
                 href={`https://doi.org/${citation.source.sourceDOI}`}
@@ -29,11 +30,10 @@ export const CitationDetails: FC<{
                 {citation.source.title}
                 {displayYear && ` (${citation.source.year})`}
             </a>
-            <div className='text-sm text-gray-700'>
-                {citation.source.contributors
-                    .map((contributor) => [contributor.givenName, contributor.surname].filter((name) => name).join(' '))
-                    .join(', ')}
-            </div>
+            <div className='text-sm text-gray-700'>{formatCitationContributors(citation.source.contributors)}</div>
+            {citation.source.journal !== undefined && citation.source.journal !== null && (
+                <div className='text-sm italic text-gray-700'>{citation.source.journal}</div>
+            )}
             {'seqSets' in citation && citation.seqSets.length > 0 && (
                 <span className='text-sm text-gray-500'>
                     From SeqSet{citation.seqSets.length > 1 ? 's' : ''}:

website/src/components/SeqSetCitations/formatCitationContributors.spec.ts

@@ -0,0 +1,35 @@
+import { describe, expect, test } from 'vitest';
+
+import { formatCitationContributors } from './formatCitationContributors';
+
+describe('formatCitationContributors', () => {
+    test('shows all contributors when there are ten or fewer', () => {
+        expect(
+            formatCitationContributors([
+                { givenName: 'Jane', surname: 'Doe' },
+                { givenName: 'John', surname: 'Smith' },
+                { givenName: 'Alex', surname: 'Jones' },
+            ]),
+        ).toBe('Jane Doe, John Smith, Alex Jones');
+    });
+
+    test('truncates contributor lists longer than ten with an ellipsis', () => {
+        expect(
+            formatCitationContributors([
+                { givenName: 'Jane', surname: 'Doe' },
+                { givenName: 'John', surname: 'Smith' },
+                { givenName: 'Alex', surname: 'Jones' },
+                { givenName: 'Sam', surname: 'Taylor' },
+                { givenName: 'Morgan', surname: 'Lee' },
+                { givenName: 'Jordan', surname: 'Patel' },
+                { givenName: 'Casey', surname: 'Brown' },
+                { givenName: 'Taylor', surname: 'Wilson' },
+                { givenName: 'Jamie', surname: 'Davis' },
+                { givenName: 'Robin', surname: 'Garcia' },
+                { givenName: 'Avery', surname: 'Martinez' },
+            ]),
+        ).toBe(
+            'Jane Doe, John Smith, Alex Jones, Sam Taylor, Morgan Lee, Jordan Patel, Casey Brown, Taylor Wilson, Jamie Davis, Robin Garcia, ...',
+        );
+    });
+});

website/src/components/SeqSetCitations/formatCitationContributors.ts

@@ -0,0 +1,16 @@
+import type { CitationContributor } from '../../types/seqSetCitation';
+
+const MAX_DISPLAYED_CONTRIBUTORS = 10;
+
+const formatContributor = ({ givenName, surname }: CitationContributor) =>
+    [givenName, surname].filter((name) => name).join(' ');
+
+export const formatCitationContributors = (contributors: CitationContributor[]) => {
+    const formattedContributors = contributors.map(formatContributor).filter((name) => name);
+
+    if (formattedContributors.length <= MAX_DISPLAYED_CONTRIBUTORS) {
+        return formattedContributors.join(', ');
+    }
+
+    return `${formattedContributors.slice(0, MAX_DISPLAYED_CONTRIBUTORS).join(', ')}, ...`;
+};

website/src/types/seqSetCitation.ts

@@ -33,16 +33,18 @@ export const authorProfile = z.object({
 });
 export type AuthorProfile = z.infer<typeof authorProfile>;
 
-const citationContributor = z.object({
+export const citationContributor = z.object({
     givenName: z.string(),
     surname: z.string(),
 });
+export type CitationContributor = z.infer<typeof citationContributor>;
 
 export const citationSource = z.object({
     sourceDOI: z.string(),
     title: z.string(),
     year: z.number(),
     contributors: z.array(citationContributor),
+    journal: z.string().nullish(),
 });
 
 export const citationOrigin = z.enum(['CROSSREF', 'CURATED']);