From 1caaf2f45931f6494b998fe5ee5eee3cfe029e05 Mon Sep 17 00:00:00 2001
From: Aaron Lisman <lisman.aaron@gmail.com>
Date: Tue, 27 Oct 2026 00:18:34 +0000
Subject: [PATCH] Results page: a pencil by the genes edits them, and Modify
 query opens in a dialog without Explore

The summary's gene chips end in a pencil (PortalSummary's onEditGenes) that opens the gene
query dialog, titled "Edit genes", on the page's own query; Submit opens the Results page for
the same studies and filters with the new genes. "Modify query" opens the study chooser in a
dialog instead of under the summary, and there the flow offers only "Query by gene" (QueryFlow's
explore={false}), whose gene dialog starts from the page's genes; the homepage keeps both.

Verified on the dev server (coadread_tcga_pub, "KRAS: MUT / BRAF") and by the e2e lane of
scripts/gate.sh (185 pass), whose homepage check now also asserts the dialog has no Explore
button and the pencil opens "Edit genes" on the page's genes.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TyVfAhLnjshk2kWewGnLum
---
 app/_home/query-flow.tsx     | 13 ++++++++-----
 app/portal/portal-chrome.tsx | 11 ++++++++---
 app/portal/results/page.tsx  | 19 +++++++++++++++----
 e2e.cjs                      | 18 ++++++++++++++----
 4 files changed, 45 insertions(+), 16 deletions(-)

diff --git a/app/_home/query-flow.tsx b/app/_home/query-flow.tsx
index df0e925c..f04229c4 100644
--- a/app/_home/query-flow.tsx
+++ b/app/_home/query-flow.tsx
@@ -2,7 +2,8 @@
 // cBioPortal's homepage flow: choose studies, then explore them (the lab's Explore, scoped to them)
 // or query them by gene (the gene query dialog, whose "Submit query" opens the Results page). The
 // homepage holds it full width and keeps the selection in its URL; the Results page's "Modify
-// query" opens it with what the page queried, the dialog starting from the page's genes.
+// query" opens it in a dialog with what the page queried, the gene dialog starting from the page's
+// genes, and without the way into Explore.
 import { useState } from "react";
 import { Dna, LayoutDashboard } from "lucide-react";
 import { Button } from "../_ui/button";
@@ -25,8 +26,10 @@ const analyzeHref = (id: string): string => "/lab?" + new URLSearchParams({ tab:
 /** Explore on one study with Custom data → Add data open (the lab reads `custom=add`) */
 const addDataHref = (id: string): string => "/lab?" + new URLSearchParams({ tab: "explore", study: id, custom: "add" }).toString();
 
-export function QueryFlow({ initial, onStudies, queryTitle, className }: {
+export function QueryFlow({ initial, onStudies, queryTitle, explore = true, className }: {
   initial: ResultsTarget;
+  /** offer "Explore selected studies" beside "Query by gene" */
+  explore?: boolean;
   /** the gene dialog's title when "Query by gene" opens it (the homepage's own wording) */
   queryTitle?: string;
   /** the selection as it changes, for a page that keeps it in its URL */
@@ -47,7 +50,7 @@ export function QueryFlow({ initial, onStudies, queryTitle, className }: {
     <section data-tw className={cn("rounded-lg border bg-card px-4.5 py-4", className)} aria-label="choose studies">
       <QueryGenesDialog target={asking} names={names} onClose={() => setAsking(null)} />
       <div className="mb-2.5 flex flex-wrap items-baseline justify-between gap-2.5">
-        <h2 className="m-0 text-lg font-semibold">Select studies to explore or query</h2>
+        <h2 className="m-0 text-lg font-semibold">{explore ? "Select studies to explore or query" : "Select studies to query"}</h2>
         <SelectionStats studies={studies} selected={chosen} loading={loading} onClear={() => choose([])} />
       </div>
       {filters.length > 0 && (
@@ -69,10 +72,10 @@ export function QueryFlow({ initial, onStudies, queryTitle, className }: {
         <div className="flex flex-wrap justify-center gap-2.5">
           <Button className="querybygene" disabled={!!queryWhy} title={queryWhy || "enter genes to query in the selected studies"}
             onClick={() => setAsking({ studies: chosen, filters, query: initial.query, title: queryTitle })}><Dna />Query by gene</Button>
-          <Button variant="outline" className="exploreselected" disabled={!chosen.length} asChild={!!chosen.length}
+          {explore && <Button variant="outline" className="exploreselected" disabled={!chosen.length} asChild={!!chosen.length}
             title={chosen.length ? "open the selected studies' summary in Explore" + (filters.length ? " (the filters do not carry over)" : "") : "select at least one study"}>
             {chosen.length ? <a href={exploreHref(chosen)}><LayoutDashboard />Explore selected studies</a> : <><LayoutDashboard />Explore selected studies</>}
-          </Button>
+          </Button>}
         </div>
         <span aria-hidden="true" />
       </div>
diff --git a/app/portal/portal-chrome.tsx b/app/portal/portal-chrome.tsx
index 00296c5a..6a0f311d 100644
--- a/app/portal/portal-chrome.tsx
+++ b/app/portal/portal-chrome.tsx
@@ -3,6 +3,8 @@
 // tabs (the study, the query, the groups and their sizes).
 import { SeriesSwatch } from "../lab/view-chrome.tsx";
 import { Badge } from "../_ui/badge";
+import { Button } from "../_ui/button";
+import { Pencil } from "lucide-react";
 import { fmtInt, fmtPct } from "../../lib/chart/format.ts";
 
 /** one group's swatch, name and size; the swatch is the colour the figures draw it in */
@@ -21,16 +23,18 @@ function GroupChip({ name, i, n }: { name: string; i: number; n?: number }) {
  * genes), the headline answer beside it, and the groups every tab compares — with what the page
  * left out for this study, so a missing tab is never silent.
  */
-export function PortalSummary({ eyebrow, title, study, studyTitle, detail, genes, groups, counts, left, stat, action, children }: {
+export function PortalSummary({ eyebrow, title, study, studyTitle, detail, genes, onEditGenes, groups, counts, left, stat, action, children }: {
   eyebrow: string; title: string;
   /** the study id, or the ids summarised; `studyTitle` lists them all */
   study: string; studyTitle?: string; detail?: React.ReactNode; genes?: string[];
+  /** opens the gene query on the page's own genes (the Results page) */
+  onEditGenes?: () => void;
   groups: string[]; counts: Record<string, number> | null; left: string[];
   /** the headline number, right of the title */
   stat?: { value: number; of: number; label: string } | null;
   /** a control over the whole page (the Results page's "Modify query"), at the end of the groups row */
   action?: React.ReactNode;
-  /** below the groups: the query form when it is open */
+  /** below the groups */
   children?: React.ReactNode;
 }) {
   return (
@@ -44,7 +48,8 @@ export function PortalSummary({ eyebrow, title, study, studyTitle, detail, genes
             {detail && <><span aria-hidden="true">·</span>{detail}</>}
             {genes && genes.length > 0 && <>
               <span aria-hidden="true">·</span>
-              <span className="inline-flex flex-wrap gap-1">{genes.map((g) => <Badge key={g} variant="outline" className="font-mono">{g}</Badge>)}</span>
+              <span className="inline-flex flex-wrap items-center gap-1">{genes.map((g) => <Badge key={g} variant="outline" className="font-mono">{g}</Badge>)}
+                {onEditGenes && <Button variant="ghost" size="icon-xs" className="editgenes" aria-label="edit genes" title="edit the query's genes" onClick={onEditGenes}><Pencil /></Button>}</span>
             </>}
           </div>
         </div>
diff --git a/app/portal/results/page.tsx b/app/portal/results/page.tsx
index 46e09283..d1f9b3cc 100644
--- a/app/portal/results/page.tsx
+++ b/app/portal/results/page.tsx
@@ -20,8 +20,9 @@ import { usePublicEnv } from "../../_env/public-env-context.tsx";
 import { fmtInt } from "../../../lib/chart/format.ts";
 import { PortalSummary, PortalLoading } from "../portal-chrome.tsx";
 import { SiteHeader } from "../../_ui/site-header.tsx";
-import { RESULTS_MAX_GENES, readResultsTarget, studiesProblem } from "../query-editor.tsx";
+import { QueryGenesDialog, RESULTS_MAX_GENES, readResultsTarget, studiesProblem } from "../query-editor.tsx";
 import { QueryFlow } from "../../_home/query-flow.tsx";
+import { Dialog, DialogContent, DialogHeader, DialogTitle } from "../../_ui/dialog";
 import { checkGeneQuery } from "../../../lib/gene-query.ts";
 import { resultsMaxStudies, crossStudyExpression, expressionAcross, isExpressionProfile, isExpressionType } from "../../../lib/results-settings.ts";
 
@@ -49,7 +50,8 @@ export default function ResultsPage() {
     : null, [known, studies, filters, check, genes, queryError, across]);
   const page = usePageDoc(fresh, linked);
   const [counts, setCounts] = useState<Record<string, number> | null>(null);
-  const [editing, setEditing] = useState(false);
+  const [modifying, setModifying] = useState(false);
+  const [editingGenes, setEditingGenes] = useState(false);
   const shell = (body: React.ReactNode) => <><SiteHeader page="query results" /><main className="analysis-main">{body}</main></>;
   // a query that is not one yet, or cannot be read, opens the homepage's flow at the step it needs
   const flow = (note?: string | null) => shell(<>
@@ -73,9 +75,10 @@ export default function ResultsPage() {
     <PortalSummary eyebrow="Query results" title={known ? known.name : studies.length === 1 ? studies[0] : studies.length + " studies"} study={ids}
       studyTitle={studies.map((s) => s + (known?.names[s] ? " — " + known.names[s] : "")).join("\n")} genes={check.entries.map((e) => e.text)}
       detail={known && <span className="tabular-nums">{filters.length ? fmtInt(known.patients) + " patients after filters" : fmtInt(known.samples) + " samples · " + fmtInt(known.patients) + " patients"}</span>}
+      onEditGenes={() => setEditingGenes(true)}
       groups={Object.keys(fresh?.doc.cohorts || {})} counts={counts} left={fresh?.left || []}
       stat={altered != null && profiled ? { value: altered, of: profiled, label: "of " + fmtInt(profiled) + " profiled patients altered in " + (check.entries.length === 1 ? check.entries[0].text : "any of the " + check.entries.length + " query lines") } : null}
-      action={<Button variant="outline" size="sm" className={TB} aria-expanded={editing} onClick={() => setEditing((e) => !e)}><Pencil />Modify query</Button>}>
+      action={<Button variant="outline" size="sm" className={TB} aria-haspopup="dialog" onClick={() => setModifying(true)}><Pencil />Modify query</Button>}>
       {filters.length > 0 && (
         <div className="mt-2.5 flex flex-wrap items-center gap-2 text-sm">
           <span className="font-semibold tracking-[0.12em] text-muted-foreground uppercase">Filters</span>
@@ -89,7 +92,15 @@ export default function ResultsPage() {
         </p>
       ) : null}
     </PortalSummary>
-    {editing && <QueryFlow initial={target} className="mb-4" />}
+    <QueryGenesDialog target={editingGenes ? { studies, filters, query: target.query, title: "Edit genes" } : null}
+      names={new Map(Object.entries(known?.names || {}))} onClose={() => setEditingGenes(false)} />
+    <Dialog open={modifying} onOpenChange={setModifying}>
+      <DialogContent aria-describedby={undefined}
+        className="modifyquerydialog flex h-[90vh] w-[94vw] max-w-[94vw] flex-col gap-3 overflow-auto p-6 sm:max-w-[94vw]">
+        <DialogHeader><DialogTitle className="text-base">Modify query</DialogTitle></DialogHeader>
+        {modifying && <QueryFlow initial={target} explore={false} />}
+      </DialogContent>
+    </Dialog>
     {page.note && <p className="note">{page.note}</p>}
     {!ready
       ? <PortalLoading />
diff --git a/e2e.cjs b/e2e.cjs
index ff4bc34e..03cf6815 100644
--- a/e2e.cjs
+++ b/e2e.cjs
@@ -1625,7 +1625,8 @@ async function main() {
 
   // The homepage, as cBioPortal's: choose studies (cancer types, filters, select all), then explore
   // them or query them by gene in a modal whose Submit opens the Results page; a row's icons act on
-  // that study alone, and the Results page's "Modify query" reopens the modal on its own genes.
+  // that study alone. On the Results page, "Modify query" opens the flow in a dialog, without Explore,
+  // whose gene query starts from the page's genes, and the pencil by the genes opens that query directly.
   {
     const ctx = await browser.newContext({ viewport: { width: 1400, height: 1000 } });
     const page = await ctx.newPage();
@@ -1672,13 +1673,22 @@ async function main() {
       const q = new URL(page.url()).searchParams;
       await page.waitForFunction(() => /profiled patients altered/.test(document.body.innerText), null, { timeout: 240000 });
       await page.getByRole("button", { name: "Modify query" }).click();
-      await page.locator("button.querybygene").click();
+      const modify = page.locator("[role=dialog].modifyquerydialog");
+      await modify.locator("button.querybygene").click();
       const again = await dlg.locator("textarea").inputValue();
+      const modifyExplore = await modify.locator(".exploreselected").count();
+      await page.keyboard.press("Escape");
+      await dlg.waitFor({ state: "detached" });
+      await page.keyboard.press("Escape");
+      await modify.waitFor({ state: "detached" });
+      await page.locator("button.editgenes").click();
+      const pencilGenes = await dlg.locator("textarea").inputValue(), pencilTitle = await dlg.getByRole("heading").first().innerText();
       ok(name, res.status() === 200 && landed === "/" &&
         empty.disabled && /select at least one study/.test(empty.why || "") && byType < all && byData < all && picked >= 1 &&
         /^\/lab\?tab=explore&study=/.test(explore || "") && /^Query genes in /.test(rowTitle) && rowTicked === 0 &&
-        title === "Select genes to query:" && q.get("study") === "coadread_tcga_pub" && q.get("genes") === "KRAS: MUT\nBRAF" && again === "KRAS: MUT\nBRAF",
-        JSON.stringify({ status: res.status(), landed, empty, rows: [all, byType, byData], picked, explore, rowTitle, rowTicked, title, results: [q.get("study"), q.get("genes")], again }));
+        title === "Select genes to query:" && q.get("study") === "coadread_tcga_pub" && q.get("genes") === "KRAS: MUT\nBRAF" && again === "KRAS: MUT\nBRAF" &&
+        modifyExplore === 0 && pencilGenes === "KRAS: MUT\nBRAF" && pencilTitle === "Edit genes",
+        JSON.stringify({ status: res.status(), landed, empty, rows: [all, byType, byData], picked, explore, rowTitle, rowTicked, title, results: [q.get("study"), q.get("genes")], again, modifyExplore, pencilGenes, pencilTitle }));
     } catch (e) {
       ok(name, false, String(e.message).split("\n")[0].slice(0, 200));
     }