import Link from 'next/link';
import { Section, Note } from '@/components/ui/section';
import { EmptyState } from '@/components/ui/empty-state';
import { FrequencyTables } from '@/components/data/frequency-table';
import { cohortsForCancer, frequenciesForCancer } from '@/lib/queries/genomics';
import { loadProvenance } from '@/lib/queries/provenance';
import { fmtInt } from '@/lib/format';
import type { CancerBundle } from '../load';

/**
 * Cohort selector renders ONE cohort by default — the one with the largest number of cases
 * profiled — plus an explicit "All cohorts" option (`?cohort=all`). Cohorts are never pooled.
 */
export async function GenomicsTab({ b, cohort }: { b: CancerBundle; cohort: string | null }) {
  const cohorts = await cohortsForCancer(b.descendants);
  if (cohorts.length === 0) {
    return (
      <Section id="genomics" kicker="Genomics" title="Gene alteration frequencies by cohort">
        <EmptyState knows={[{ label: 'Variants & evidence', href: `/cancer/${b.cancer.slug}/evidence` }, { label: 'Genes index', href: '/genes' }]}>
          No genomic cohort is mapped to this entity or its descendants. Frequencies come from open-access cohorts (GDC projects) and always carry their denominator (cases profiled); they are never pooled across cohorts.
        </EmptyState>
      </Section>
    );
  }
  const withRows = cohorts.filter((c) => c.frequency_rows > 0);
  const defaultCohort = (withRows[0] ?? cohorts[0])!;
  const showAll = cohort === 'all';
  const selected = showAll ? null : cohorts.find((c) => c.cohort_id === cohort || c.study_id === cohort) ?? defaultCohort;
  const rows = await frequenciesForCancer(b.descendants, { cohortId: selected?.cohort_id ?? null });
  const prov = await loadProvenance(rows.map((r) => r.provenance_id));
  const base = `/cancer/${b.cancer.slug}/genomics`;
  const hrefFor = (c: (typeof cohorts)[number]) => (c.cohort_id === defaultCohort.cohort_id ? base : `${base}?cohort=${encodeURIComponent(c.study_id)}`);

  return (
    <div className="space-y-6">
      <Section
        id="genomics"
        kicker="Genomics"
        title="Gene alteration frequencies by cohort"
        description={`${fmtInt(cohorts.length)} cohort${cohorts.length === 1 ? '' : 's'} mapped to this entity or its descendants. Each frequency is affected / profiled within one cohort; cohorts are shown separately because case selection, sequencing depth and definitions differ. By default the cohort with the most cases profiled is shown.`}
      >
        <nav aria-label="Cohort" className="mb-4">
          <ul className="m-0 flex list-none flex-wrap gap-1.5 p-0 text-[12.5px]">
            {cohorts.map((c) => {
              const isCurrent = !showAll && selected?.cohort_id === c.cohort_id;
              return (
                <li key={c.cohort_id}>
                  <Link href={hrefFor(c)} aria-current={isCurrent ? 'page' : undefined} className="ci-chip" title={`${c.cohort_name} · ${fmtInt(c.cases_profiled)} cases profiled · ${fmtInt(c.frequency_rows)} gene rows`}>
                    {c.study_id}
                    <span className="ci-num ml-1 text-ink-3">{fmtInt(c.cases_profiled)}</span>
                    {c.cancer_name && c.cancer_id !== b.cancer.id ? <span className="ml-1 text-ink-3">({c.cancer_name})</span> : null}
                  </Link>
                </li>
              );
            })}
            {cohorts.length > 1 ? (
              <li>
                <Link href={`${base}?cohort=all`} aria-current={showAll ? 'page' : undefined} className="ci-chip">
                  All cohorts
                </Link>
              </li>
            ) : null}
          </ul>
          <p className="mt-1 text-[11.5px] text-ink-3">Chip number = cases profiled in that cohort.</p>
        </nav>
        {rows.length ? (
          <FrequencyTables rows={rows} prov={prov} showCancer />
        ) : (
          <EmptyState compact title="No frequency rows for this cohort">
            The cohort is mapped to this entity but no gene frequency has been ingested for it yet.
          </EmptyState>
        )}
      </Section>
      <Note>Cohorts mapped to a descendant (e.g. a subtype) are included because their cases belong to this entity by definition; the mapping and its match type are shown per cohort.</Note>
    </div>
  );
}