v4: Browse, Explore refactor, AI reports, and DNA Chat improvements

.gitignore

@@ -39,3 +39,4 @@ yarn-error.log*
 /embeddings_backup.npz
 /AGENTS.md
 /CLAUDE.md
+/scripts/ga-performance.env

app/api/pubmed-abstract/route.ts

@@ -0,0 +1,43 @@
+import { NextRequest, NextResponse } from "next/server";
+
+const cache = new Map<string, { abstract: string; title: string; fetchedAt: number }>();
+const CACHE_TTL_MS = 24 * 60 * 60 * 1000; // 24 hours
+
+export async function GET(request: NextRequest) {
+  const pmid = request.nextUrl.searchParams.get("pmid");
+  if (!pmid || !/^\d+$/.test(pmid)) {
+    return NextResponse.json({ error: "Invalid PMID" }, { status: 400 });
+  }
+
+  const cached = cache.get(pmid);
+  if (cached && Date.now() - cached.fetchedAt < CACHE_TTL_MS) {
+    return NextResponse.json({ abstract: cached.abstract, title: cached.title });
+  }
+
+  try {
+    const url = `https://www.ebi.ac.uk/europepmc/webservices/rest/article/MED/${pmid}?resultType=core&format=json`;
+    const res = await fetch(url, {
+      headers: { Accept: "application/json" },
+      signal: AbortSignal.timeout(8000),
+    });
+
+    if (!res.ok) {
+      return NextResponse.json({ error: `Europe PMC returned ${res.status}` }, { status: 502 });
+    }
+
+    const data = await res.json();
+    const article = data?.result;
+    if (!article) {
+      return NextResponse.json({ error: "Article not found" }, { status: 404 });
+    }
+
+    const abstract: string = article.abstractText ?? "";
+    const title: string = article.title ?? "";
+
+    cache.set(pmid, { abstract, title, fetchedAt: Date.now() });
+    return NextResponse.json({ abstract, title });
+  } catch (err) {
+    const message = err instanceof Error ? err.message : "Fetch failed";
+    return NextResponse.json({ error: message }, { status: 502 });
+  }
+}

app/api/studies/route.ts

@@ -330,6 +330,49 @@ export async function GET(request: NextRequest) {
   if (originError) return originError;
 
   const searchParams = request.nextUrl.searchParams;
+
+  // Fast single-study lookup by primary key — used by the study detail page
+  const idParam = searchParams.get("id");
+  if (idParam !== null) {
+    const studyPk = parseInt(idParam);
+    if (isNaN(studyPk) || studyPk <= 0) {
+      return NextResponse.json({ error: "Invalid id" }, { status: 400 });
+    }
+    try {
+      const rows = await executeQuery<RawStudy>(
+        `SELECT id, study_accession, study, disease_trait, mapped_trait,
+                mapped_trait_uri, mapped_gene, first_author, date, journal,
+                pubmedid, link, initial_sample_size, replication_sample_size,
+                p_value, pvalue_mlog, or_or_beta, ci_text, risk_allele_frequency,
+                strongest_snp_risk_allele, snps
+         FROM gwas_catalog WHERE id = $1 LIMIT 1`,
+        [studyPk]
+      );
+      if (rows.length === 0) {
+        return NextResponse.json({ data: [], total: 0, limit: 1 });
+      }
+      const row = rows[0];
+      const sampleSize = parseSampleSize(row.initial_sample_size) ?? parseSampleSize(row.replication_sample_size);
+      const pValueNumeric = parsePValue(row.p_value);
+      const logPValue = parseLogPValue(row.pvalue_mlog) ?? (pValueNumeric ? -Math.log10(pValueNumeric) : null);
+      const qualityFlags = computeQualityFlags(sampleSize, pValueNumeric, logPValue);
+      const isLowQuality = qualityFlags.some(f => f.severity === 'major');
+      const confidenceBand = determineConfidenceBand(sampleSize, pValueNumeric, logPValue, qualityFlags);
+      const publicationDate = parseStudyDate(row.date);
+      const isAnalyzable = !!(row.snps && row.or_or_beta && row.strongest_snp_risk_allele);
+      const nonAnalyzableReason = !isAnalyzable
+        ? (!row.snps ? 'Missing SNP data' : !row.or_or_beta ? 'Missing effect size (OR/beta)' : 'Missing risk allele')
+        : undefined;
+      const study = { ...row, sampleSize, sampleSizeLabel: formatNumber(sampleSize), pValueNumeric,
+        pValueLabel: formatPValue(pValueNumeric), logPValue, qualityFlags, isLowQuality, confidenceBand,
+        publicationDate, isAnalyzable, nonAnalyzableReason };
+      return NextResponse.json({ data: [study], total: 1, limit: 1 });
+    } catch (error) {
+      const message = error instanceof Error ? error.message : "Failed to fetch study";
+      return NextResponse.json({ error: message }, { status: 500 });
+    }
+  }
+
   const search = searchParams.get("search")?.trim();
   const searchTerms = search ? getSearchTerms(search) : [];
   const trait = searchParams.get("trait")?.trim();

app/browse/layout.tsx

@@ -0,0 +1,20 @@
+import type { Metadata } from "next";
+
+export const metadata: Metadata = {
+  title: "Browse GWAS Studies - Monadic DNA Explorer",
+  description: "Search and filter millions of genetic associations from the GWAS Catalog. Upload your DNA data to see personalized results.",
+  keywords: ["GWAS", "genetic studies", "DNA research", "genome-wide association", "genetic variants", "SNP analysis"],
+  openGraph: {
+    title: "Browse GWAS Studies - Monadic DNA Explorer",
+    description: "Search millions of genetic associations and analyze your DNA data",
+    type: "website",
+  },
+};
+
+export default function ExploreLayout({
+  children,
+}: {
+  children: React.ReactNode;
+}) {
+  return <>{children}</>;
+}