app/routes/publications.$slug.tsx

Functions

Imports

It imports app/components/breadcrumb.tsx, app/components/shell-footer.tsx, app/components/site-header.tsx, app/lib/citations.server.ts, app/lib/context.ts, app/lib/json-ld.mjs, app/lib/publications/accessions.mjs, app/lib/publications/article-json-ld.mjs, app/lib/publications/by-slug.ts, app/lib/publications/citation-tags.mjs, app/lib/publications/cited-by.mjs, app/lib/publications/entities.mjs, app/lib/publications/paths.mjs, app/lib/publications/topics.mjs, app/lib/publications/update-notice.mjs, app/lib/scientific-names.tsx, app/lib/seo.ts. No module of this repo imports it.

Source

1import { Link } from "react-router";
2
3import { Breadcrumb } from "~/components/breadcrumb";
4import { ShellFooter } from "~/components/shell-footer";
5import { SiteHeader } from "~/components/site-header";
6import { getCitationCounts } from "~/lib/citations.server";
7import { getEnv } from "~/lib/context";
8import { jsonLd } from "~/lib/json-ld.mjs";
9import { paperJsonLd } from "~/lib/publications/article-json-ld.mjs";
10import { buildCitationTags } from "~/lib/publications/citation-tags.mjs";
11import { accessionLabel, accessionUrl } from "~/lib/publications/accessions.mjs";
12import { publicationBySlug } from "~/lib/publications/by-slug";
13import { TOPICS } from "~/lib/publications/topics.mjs";
14import { decodeEntities } from "~/lib/publications/entities.mjs";
15import { updateNoticeText } from "~/lib/publications/update-notice.mjs";
16import {
17  paperAskUrl,
18  paperMarkdownPath,
19  paperPath,
20  paperPdfPath,
21  PUBLICATIONS_CACHE_TAG,
22  PUBLICATIONS_PATH,
23} from "~/lib/publications/paths.mjs";
24import { citedByFetchedAt, citedByFor } from "~/lib/publications/cited-by.mjs";
25import citedByArtifact from "../../data/publications.cited-by.json";
26import { italicizeOrganisms } from "~/lib/scientific-names";
27import {
28  breadcrumbJsonLd,
29  isSiteOwner,
30  pageMeta,
31  personId,
32  personNode,
33  publicHtmlHeaders,
34  SITE,
35  SITE_ORIGIN,
36} from "~/lib/seo";
37import type { Route } from "./+types/publications.$slug";
38
39import "~/styles/paper.css";
40
41/**
42 * The URL ends in a slash: `citation_pdf_url` must sit in the HTML abstract's subdirectory. The slug
43 * is the DOI: a curated id could be re-chosen after Scholar indexed it.
44 */
45
46const TOPIC_LABEL = new Map(TOPICS.map((t) => [t.id, t.label]));
47
48export function headers() {
49  return publicHtmlHeaders(PUBLICATIONS_CACHE_TAG);
50}
51
52export async function loader({ params, context }: Route.LoaderArgs) {
53  const paper = await publicationBySlug(getEnv(context), params.slug);
54
55  const { slug } = paper;
56  const hosted = paper.access === "self-hosted" && paper.pdfPath !== null;
57
58  // The last count shows while a stale one refreshes; a paper that never had one shows none, never a zero.
59  const citations = paper.doi ? await getCitationCounts(context, [paper.doi]) : {};
60
61  return {
62    paper,
63    slug,
64    hosted,
65    pagePath: paperPath(slug),
66    pdfPath: hosted ? paperPdfPath(slug) : null,
67    cited: (paper.doi ? citations[paper.doi] : null) ?? null,
68    /* `total` and the list length are both carried: one paper exceeds the cap. */
69    citedBy: paper.doi ? citedByFor(citedByArtifact, paper.doi) : null,
70    citedByFetchedAt: citedByFetchedAt(citedByArtifact),
71    topics: paper.topics.map((id) => ({ id, label: TOPIC_LABEL.get(id) ?? id })),
72  };
73}
74
75/** Citation tags stay here, not in `pageMeta`: they are not social metadata. */
76export function meta({ loaderData }: Route.MetaArgs) {
77  if (!loaderData) return [{ title: `Publication, ${SITE.name}` }];
78
79  const { paper, slug, pagePath, pdfPath } = loaderData;
80  const title = decodeEntities(paper.title);
81  const abstractUrl = `${SITE_ORIGIN}${pagePath}`;
82  const pdfUrl = pdfPath ? `${SITE_ORIGIN}${pdfPath}` : null;
83
84  const description = paper.abstract
85    ? truncateAtWord(decodeEntities(paper.abstract), 155)
86    : `${title}. ${decodeEntities(paper.journal ?? "")} ${paper.year}`.trim();
87
88  return [
89    ...pageMeta({
90      title: `${title} | ${SITE.name}`,
91      description,
92      path: pagePath,
93      ogType: "article",
94    }),
95    // A manuscript with no DOI has no registry record to cite, so it carries no Scholar tags.
96    ...(paper.doi ? buildCitationTags(paper, { abstractUrl, pdfUrl }) : []),
97    /* Every paper has a twin (the markdown route reads it from D1); the head is how an agent finds it. */
98    {
99      tagName: "link",
100      rel: "alternate",
101      type: "text/markdown",
102      href: `${SITE_ORIGIN}${paperMarkdownPath(slug)}`,
103    },
104  ];
105}
106
107function truncateAtWord(text: string, limit: number) {
108  const flat = text.replace(/\s+/g, " ").trim();
109  if (flat.length <= limit) return flat;
110  const cut = flat.slice(0, limit);
111  const space = cut.lastIndexOf(" ");
112  return `${(space > limit * 0.6 ? cut.slice(0, space) : cut).trimEnd()}...`;
113}
114
115function Authors({ authors }: { authors: string[] }) {
116  /* Every author visible: `citation_author` lists them, and Scholar penalizes content that disagrees with its meta tags. */
117  return (
118    <p className="paper-authors">
119      {authors.map((name, i) => (
120        <span key={`${name}-${i}`}>
121          {i > 0 ? ", " : ""}
122          {isSiteOwner(name) ? (
123            <strong className="pub-author-me">{decodeEntities(name)}</strong>
124          ) : (
125            decodeEntities(name)
126          )}
127        </span>
128      ))}
129    </p>
130  );
131}
132
133export default function Paper({ loaderData }: Route.ComponentProps) {
134  const { paper, slug, hosted, pagePath, pdfPath, cited, citedBy, citedByFetchedAt, topics } =
135    loaderData;
136  const pageUrl = `${SITE_ORIGIN}${pagePath}`;
137  // One trail for the visible breadcrumb and its BreadcrumbList, so the two cannot disagree.
138  const trail: Array<[string, string]> = [
139    ["Research", "/research"],
140    ["Publications", PUBLICATIONS_PATH],
141    [decodeEntities(paper.title), pagePath],
142  ];
143
144  return (
145    <>
146      <SiteHeader />
147      <main id="main" className="tracks paper-tracks" tabIndex={-1}>
148        <header className="paper-head">
149          <Breadcrumb trail={trail} />
150
151          {/* The H1 is the title: Scholar reads the first heading as the paper title. */}
152          <h1 className="paper-title">{italicizeOrganisms(decodeEntities(paper.title))}</h1>
153
154          <Authors authors={paper.authors} />
155        </header>
156
157        <div className="paper-rail u-rail">
158          <p className="paper-machine">
159            <b>{paper.year}</b>
160            {paper.stage === "submitted" ? "submitted" : "published"}
161            {paper.journal ? (
162              <>
163                <b className="paper-machine-venue">{decodeEntities(paper.journal)}</b>
164                {[
165                  paper.volume ? `volume ${paper.volume}` : null,
166                  paper.issue ? `issue ${paper.issue}` : null,
167                  paper.pages ? `pages ${paper.pages}` : null,
168                ]
169                  .filter(Boolean)
170                  .join(", ")}
171              </>
172            ) : null}
173            {paper.doi ? (
174              <>
175                <b>
176                  <a href={`https://doi.org/${paper.doi}`}>{paper.doi}</a>
177                </b>
178                doi
179              </>
180            ) : null}
181            {paper.type !== "article" ? (
182              <>
183                <b>{paper.type}</b>
184                kind
185              </>
186            ) : null}
187            {paper.isOpenAccess ? (
188              <>
189                <b>open access</b>
190                license
191              </>
192            ) : null}
193          </p>
194        </div>
195
196        <div className="paper-text">
197          <p className="paper-links">
198            {hosted && pdfPath ? <a href={pdfPath}>PDF</a> : null}
199            {paper.pmcUrl ? <a href={paper.pmcUrl}>PMC</a> : null}
200            {paper.preprintDoi ? (
201              <a href={`https://doi.org/${paper.preprintDoi}`}>Preprint</a>
202            ) : null}
203            {paper.externalUrl ? <a href={paper.externalUrl}>Resource</a> : null}
204            <a href={`${PUBLICATIONS_PATH}/${slug}.bib`}>BibTeX</a>
205            <a href={`${PUBLICATIONS_PATH}/${slug}.ris`}>RIS</a>
206            {/* The quoted title alone, because the classic index ANDs its terms. */}
207            <a href={paperAskUrl(decodeEntities(paper.title))}>Ask about this paper</a>
208          </p>
209
210          {/* Only at 1 or more: a cold cache shows nothing rather than a zero that looks measured. */}
211          {cited && cited.count >= 1 ? (
212            <p className="paper-cited">
213              {cited.url ? (
214                <a href={cited.url}>Cited by {cited.count}</a>
215              ) : (
216                <>Cited by {cited.count}</>
217              )}{" "}
218              <span className="paper-provenance">OpenAlex, read {cited.fetchedAt}</span>
219            </p>
220          ) : null}
221
222          {/* `role="status"`, not `alert`, which interrupts a screen reader mid-sentence. */}
223          {paper.updateNotice ? (
224            <aside className="paper-update-notice" role="status">
225              <strong>{updateNoticeText(paper.updateNotice).label}.</strong>{" "}
226              {updateNoticeText(paper.updateNotice).sentence}{" "}
227              <a href={updateNoticeText(paper.updateNotice).url}>Read the notice</a>
228            </aside>
229          ) : null}
230
231          {paper.summary ? (
232            <p className="paper-summary">{italicizeOrganisms(paper.summary)}</p>
233          ) : null}
234
235          {/* Visible, never in a `details`: a crawler that must open a disclosure does not find the abstract. */}
236          {paper.abstract ? (
237            <section className="paper-abstract" aria-labelledby="abstract-heading">
238              <h2 id="abstract-heading">Abstract</h2>
239              <p>{italicizeOrganisms(decodeEntities(paper.abstract))}</p>
240            </section>
241          ) : null}
242
243          {/* `accessionUrl` refuses a kind with no registry: a wrong registry is a 404 that looks like a working link. */}
244          {paper.accessions.length > 0 ? (
245            <section className="paper-data" aria-labelledby="data-heading">
246              <h2 id="data-heading">Data</h2>
247              <p className="paper-links">
248                {paper.accessions.map((accession) => (
249                  <a key={accession.id} href={accessionUrl(accession)}>
250                    {accessionLabel(accession.kind)} {accession.id}
251                  </a>
252                ))}
253              </p>
254            </section>
255          ) : null}
256
257          {citedBy && citedBy.citing.length > 0 ? (
258            <section className="paper-citedby" aria-labelledby="citedby-heading">
259              <h2 id="citedby-heading">
260                Cited by{" "}
261                {citedBy.total > citedBy.citing.length
262                  ? `${citedBy.citing.length} of ${citedBy.total}`
263                  : citedBy.total}
264              </h2>
265              <p className="paper-provenance paper-citedby-source">
266                OpenAlex, read {citedByFetchedAt ?? "an unrecorded date"}. Newest first.
267              </p>
268              <ol className="paper-citedby-list">
269                {citedBy.citing.map((w, i) => (
270                  <li key={`${w.doi ?? w.title}-${i}`}>
271                    {w.doi ? (
272                      <a href={`https://doi.org/${w.doi}`}>{w.title ?? w.doi}</a>
273                    ) : (
274                      (w.title ?? "Untitled")
275                    )}
276                    {w.venue ? <span className="paper-provenance">, {w.venue}</span> : null}
277                    {w.year ? <span className="paper-provenance">, {w.year}</span> : null}
278                  </li>
279                ))}
280              </ol>
281            </section>
282          ) : null}
283
284          {topics.length > 0 ? (
285            <p className="paper-topics">
286              {topics.map((t) => (
287                <Link key={t.id} to={`${PUBLICATIONS_PATH}?topic=${t.id}`}>
288                  {t.label}
289                </Link>
290              ))}
291            </p>
292          ) : null}
293        </div>
294
295        <script
296          type="application/ld+json"
297          dangerouslySetInnerHTML={{
298            __html: jsonLd([
299              ...paperJsonLd(paper, {
300                origin: SITE_ORIGIN,
301                pageUrl,
302                pdfUrl: pdfPath ? `${SITE_ORIGIN}${pdfPath}` : null,
303                isOwner: isSiteOwner,
304                personId: personId(SITE_ORIGIN),
305                personNode: personNode(SITE_ORIGIN),
306                topics,
307              }),
308              breadcrumbJsonLd(SITE_ORIGIN, trail),
309            ]),
310          }}
311        />
312      </main>
313      <ShellFooter />
314    </>
315  );
316}