app/routes/publications.tsx

Functions

Imports

It imports app/components/enhance.tsx, app/components/evidence-row.tsx, app/components/shell-footer.tsx, app/components/site-header.tsx, app/db/publications.ts, app/lib/citations.server.ts, app/lib/context.ts, app/lib/json-ld.mjs, app/lib/publications/coins.mjs, app/lib/publications/entities.mjs, app/lib/publications/listing.mjs, app/lib/publications/paths.mjs, app/lib/publications/types.ts, app/lib/scientific-names.tsx, app/lib/seo.ts. No module of this repo imports it.

Source

1import { Catalog } from "capsomer/react/catalog";
2import { Link, redirect } from "react-router";
3
4import { Enhance } from "~/components/enhance";
5import { EvidenceRow } from "~/components/evidence-row";
6import { ShellFooter } from "~/components/shell-footer";
7import { SiteHeader } from "~/components/site-header";
8import { listPublishedPublications } from "~/db/publications";
9import { getCitationCounts, type CitationEntry } from "~/lib/citations.server";
10import { getEnv } from "~/lib/context";
11import { jsonLd } from "~/lib/json-ld.mjs";
12import { coinsTitle } from "~/lib/publications/coins.mjs";
13import { decodeEntities } from "~/lib/publications/entities.mjs";
14import { PUBLICATIONS, legacyAddress, publicationListing, venue } from "~/lib/publications/listing.mjs";
15import { PUBLICATIONS_CACHE_TAG, PUBLICATIONS_PATH, paperPath } from "~/lib/publications/paths.mjs";
16import type { Publication, TopicId } from "~/lib/publications/types";
17import { italicizeOrganisms } from "~/lib/scientific-names";
18import {
19  isSiteOwner,
20  pageMeta,
21  publicationsJsonLd,
22  publicHtmlHeaders,
23  PUBLICATIONS_DESCRIPTION,
24  PUBLICATIONS_URL,
25  SITE,
26  SITE_ORIGIN,
27} from "~/lib/seo";
28import type { Route } from "./+types/publications";
29
30// Route-scoped: the catalog's tokens and components are Capsomer's, mapped onto the site's palette in site-catalog.css.
31import "capsomer/tokens.css";
32import "capsomer/field.css";
33import "capsomer/button.css";
34import "capsomer/table.css";
35import "capsomer/chips.css";
36import "capsomer/empty.css";
37import "capsomer/pagination.css";
38import "capsomer/catalog.css";
39import "~/styles/evidence-row.css";
40import "~/styles/listing.css";
41import "~/styles/site-catalog.css";
42import "~/styles/publications.css";
43
44const TOPIC_META: Record<TopicId, { title: string; description: string }> = {
45  "human-simian-retroviruses": {
46    title: "Human and simian retroviruses",
47    description:
48      "How the HTLV-1 accessory proteins p12, p8 and p30 support infection and persistence, plus the auxiliary proteins of simian T-lymphotropic virus type 3.",
49  },
50  "avian-retroviruses": {
51    title: "Avian retroviruses",
52    description:
53      "Molecular surveillance and genome sequencing of reticuloendotheliosis virus in wild turkeys, ducks, and an endangered Attwater's prairie chicken.",
54  },
55  bacteriophages: {
56    title: "Bacteriophages",
57    description:
58      "Complete genomes of Microbacterium, Mycobacterium and Arthrobacter bacteriophages, plus a study of how healthcare providers view phage therapy.",
59  },
60  "science-education": {
61    title: "Science education",
62    description:
63      "Course-based undergraduate research as a way to teach science: classroom assessment, faculty identity, the iREC model, and scientific writing rubrics.",
64  },
65};
66
67export function meta({ loaderData }: Route.MetaArgs) {
68  const title = loaderData?.pageTitle ?? `Publications, ${SITE.name}`;
69  const description = loaderData?.pageDescription ?? PUBLICATIONS_DESCRIPTION;
70
71  return [
72    ...pageMeta({
73      title,
74      description,
75      path: loaderData?.canonicalPath ?? PUBLICATIONS_URL,
76    }),
77    ...(loaderData?.noindex ? [{ name: "robots", content: "noindex, follow" }] : []),
78  ];
79}
80
81/** Without headers the gateway stamps `private, no-store`, making the most static page uncacheable. */
82export function headers() {
83  return publicHtmlHeaders(PUBLICATIONS_CACHE_TAG);
84}
85
86export async function loader({ request, context }: Route.LoaderArgs) {
87  const url = new URL(request.url);
88  // A link written in the page's old parameters (?sort=year-asc, ?selected=true) is sent once to the same view.
89  const moved = legacyAddress(url);
90  if (moved) throw redirect(moved, 301);
91
92  const publications = await listPublishedPublications(getEnv(context));
93  const { soleTopic, items } = publicationListing(url.searchParams, publications);
94
95  /* A path, not an absolute URL: deriving it from `url.origin` is how a preview host becomes canonical. */
96  const canonicalPath = soleTopic
97    ? `${PUBLICATIONS_URL}?topic=${soleTopic}`
98    : PUBLICATIONS_URL;
99  const pageTitle = soleTopic
100    ? `${TOPIC_META[soleTopic].title}, ${SITE.name}`
101    : `Publications, ${SITE.name}`;
102  const pageDescription = soleTopic
103    ? TOPIC_META[soleTopic].description
104    : PUBLICATIONS_DESCRIPTION;
105  const noindex = items.length === 0;
106
107  // D1 only: a stale count shows and refreshes after the response, so the page never waits on OpenAlex.
108  const citations = await getCitationCounts(context, items.flatMap((p) => (p.doi ? [p.doi] : [])));
109
110  return {
111    /* The canonical origin, never the request's: this page is shared-cached, so a preview host's JSON-LD would be served to everyone. */
112    origin: SITE_ORIGIN,
113    citations,
114    // Every paper, with the address's query: the catalog is computed from them where it is drawn, because its
115    // result holds functions and a loader's data does not.
116    publications,
117    search: url.search,
118    canonicalPath,
119    pageTitle,
120    pageDescription,
121    noindex,
122  };
123}
124
125function AuthorName({ name }: { name: string }) {
126  return isSiteOwner(name) ? <strong className="pub-author-me">{name}</strong> : <>{name}</>;
127}
128
129function Names({ names }: { names: string[] }) {
130  return (
131    <>
132      {names.map((name, i) => (
133        <span key={name + i}>
134          {i > 0 ? ", " : ""}
135          <AuthorName name={name} />
136        </span>
137      ))}
138    </>
139  );
140}
141
142/** Author order varies, so when he falls outside the first three the summary shows two, an ellipsis, then his entry. */
143function AuthorList({ authors }: { authors: string[] }) {
144  if (authors.length === 0) return null;
145  if (authors.length <= 3) {
146    return (
147      <p className="pub-authors">
148        <Names names={authors} />
149      </p>
150    );
151  }
152
153  const ownerIndex = authors.findIndex(isSiteOwner);
154  const ownerName = ownerIndex >= 3 ? authors[ownerIndex] : undefined;
155  const lead = authors.slice(0, ownerName ? 2 : 3);
156  const shown = lead.length + (ownerName ? 1 : 0);
157
158  return (
159    <details className="pub-authors pub-authors-more">
160      <summary>
161        <Names names={lead} />
162        {ownerName ? (
163          <>
164            <span className="muted">, ... </span>
165            <AuthorName name={ownerName} />
166          </>
167        ) : null}
168        <span className="muted"> and {authors.length - shown} more</span>
169      </summary>
170      <p className="pub-authors-full">
171        <Names names={authors} />
172      </p>
173    </details>
174  );
175}
176
177function PaperCell({ p, cited }: { p: Publication; cited?: CitationEntry }) {
178  const { slug } = p;
179  return (
180    <div className="paper-row">
181      <p className="paper-marks">
182        {p.type !== "article" ? <span className="paper-kind">{p.type}</span> : null}
183        {p.isOpenAccess ? <span className="paper-open">open access</span> : null}
184      </p>
185      <div className="paper-body">
186        {/* Display only. The stored title stays plain for search and JSON-LD. */}
187        <h3 className="paper-row-title">
188          <Link to={paperPath(slug)}>{italicizeOrganisms(decodeEntities(p.title))}</Link>
189        </h3>
190        <AuthorList authors={p.authors} />
191        <p className="paper-row-links">
192          {p.access === "self-hosted" && p.pdfPath ? <a href={p.pdfPath}>PDF</a> : null}
193          {p.doi ? <a href={`https://doi.org/${p.doi}`}>DOI</a> : null}
194          {p.pmcUrl ? <a href={p.pmcUrl}>PMC</a> : null}
195          {p.externalUrl && (p.type === "teaching-resource" || p.type === "abstract") ? (
196            <a href={p.externalUrl}>Resource</a>
197          ) : null}
198          {p.preprintDoi ? (
199            <a href={`https://doi.org/${p.preprintDoi}`}>Preprint</a>
200          ) : null}
201          <a href={`${PUBLICATIONS_PATH}/${slug}.bib`}>BibTeX</a>
202          <a href={`${PUBLICATIONS_PATH}/${slug}.ris`}>RIS</a>
203          {cited && cited.count >= 1 && cited.url ? (
204            <a
205              className="paper-cited-link"
206              href={cited.url}
207              title={`OpenAlex, retrieved ${cited.fetchedAt}`}
208            >
209              Cited by {cited.count}
210            </a>
211          ) : null}
212        </p>
213        {/* COinS on the index only: Highwire `citation_*` tags describe the one document they sit in. */}
214        <span className="Z3988" title={coinsTitle(p)} />
215        {p.abstract ? (
216          <details className="paper-abstract-peek">
217            <summary>Abstract</summary>
218            <p>{italicizeOrganisms(decodeEntities(p.abstract))}</p>
219          </details>
220        ) : null}
221      </div>
222    </div>
223  );
224}
225
226function bibliographyFacts(span: {
227  papers: number;
228  firstYear: number | null;
229  lastYear: number | null;
230  venues: number;
231}) {
232  return [
233    `${span.papers} paper${span.papers === 1 ? "" : "s"}`,
234    span.firstYear && span.lastYear
235      ? span.firstYear === span.lastYear
236        ? String(span.firstYear)
237        : `${span.firstYear} to ${span.lastYear}`
238      : null,
239    span.venues > 0 ? `${span.venues} venue${span.venues === 1 ? "" : "s"}` : null,
240  ];
241}
242
243export default function Publications({ loaderData }: Route.ComponentProps) {
244  const { origin, publications, search, citations } = loaderData;
245  const { items, result, span } = publicationListing(new URLSearchParams(search), publications);
246
247  return (
248    <>
249      <SiteHeader />
250      <main id="main" className="tracks list-tracks" tabIndex={-1}>
251        <header className="list-head">
252          <h1 className="list-label" id="publications-title">
253            Publications
254          </h1>
255          <p className="list-dek">
256            Peer-reviewed work on retroviruses, bacteriophage genomics, and how
257            undergraduate research is taught. Full text is hosted here where I have the
258            publisher version, with links out to the record of version otherwise.
259          </p>
260          <EvidenceRow facts={bibliographyFacts(span)} />
261        </header>
262
263        <div className="papers site-catalog">
264          <Catalog
265            definition={PUBLICATIONS}
266            result={result}
267            labelledBy="publications-title"
268            title={(p) => <PaperCell p={p} cited={p.doi ? citations[p.doi] : undefined} />}
269            cells={{ journal: (p) => <span className="paper-venue">{venue(p)}</span> }}
270            emptyText={{ noMatch: "No publications match this filter." }}
271            actions={
272              /* Always the full list: a citation file carrying only the filtered subset is one nobody asked for. */
273              <span className="paper-feeds">
274                Export all <a href="/research/publications.bib">BibTeX</a>{" "}
275                <a href="/research/publications.ris">RIS</a> <a href="/research/publications.json">CSL JSON</a>
276              </span>
277            }
278          />
279        </div>
280
281        {/* `jsonLd`, not `JSON.stringify`: only `</script` ends a script element, and these strings come from third-party registries. */}
282        <script
283          type="application/ld+json"
284          dangerouslySetInnerHTML={{ __html: jsonLd(publicationsJsonLd(origin, items)) }}
285        />
286        <Enhance module="catalog" />
287      </main>
288      <ShellFooter />
289    </>
290  );
291}