Enable cancerverse viewing. Segmentation-related functions disabled.

.gitignore

@@ -8,3 +8,7 @@ tmp/*
 downloaded.nii.gz
 PanTS/data/pdf/
 .DS_Store
+
+*.nii.gz
+CancerVerse/CancerVerse_dataset_metadata.csv
+CancerVerse/~/.cache/huggingface/.agent_harnesses.json

CancerVerse/download_partial_cancerverse.sh

@@ -0,0 +1,32 @@
+#!/bin/bash
+
+set -u
+
+REPO_ID="BodyMaps/CancerVerse"
+REPO_TYPE="dataset"
+LOCAL_DIR="."
+
+while true; do
+    echo "=========================================="
+    echo "Starting/retrying download at $(date)"
+    echo "Downloading CV_00000001 through CV_00000100"
+    echo "=========================================="
+
+    hf download "$REPO_ID" \
+        --repo-type "$REPO_TYPE" \
+        --local-dir "$LOCAL_DIR" \
+        --include "CancerVerse/CV_0000000[1-9]/*" \
+        --include "CancerVerse/CV_000000[1-9][0-9]/*" \
+        --include "CancerVerse/CV_00000100/*"
+
+    status=$?
+
+    if [ "$status" -eq 0 ]; then
+        echo "Download completed successfully at $(date)"
+        break
+    fi
+
+    echo "Download failed with exit code $status at $(date)"
+    echo "Retrying in 30 minutes..."
+    sleep 1800
+done

PanTS-Demo/src/components/Preview.tsx

@@ -1,11 +1,12 @@
 import { useState } from "react";
 import { useNavigate } from "react-router-dom";
 import { API_BASE } from "../helpers/constants";
+import { getCaseDisplay } from "../helpers/utils";
 import { prefetchViewer } from "../helpers/prefetchViewer";
 import type { PreviewType } from "../types";
 
 type Props = {
-	id: number;
+	id: string;
 	previewMetadata: PreviewType;
 	saved?: boolean;
 	onToggleSave?: () => void;
@@ -35,14 +36,16 @@ export default function Preview({
 
 	if (!previewMetadata) return null;
 
-	const caseIdStr = `PanTS_${id.toString().padStart(8, "0")}`;
+	const { dataset, label: caseIdStr } = getCaseDisplay(id);
 	// HuggingFace fallback, routed through the backend's same-origin proxy. A *direct*
 	// cross-origin image is blocked by the viewer's COEP: require-corp header (which is
 	// why thumbnails went missing); the proxy keeps it same-origin, matching home.html.
+	// CancerVerse has no HuggingFace profile-image mirror, so it skips straight to the
+	// "both sources failed" placeholder if the local endpoint 404s.
 	const hfProfileUrl = `https://huggingface.co/datasets/BodyMaps/iPanTSMini/resolve/main/profile_only/${caseIdStr}/profile.jpg`;
 	const proxyThumbUrl = `${API_BASE}/api/proxy-image?url=${encodeURIComponent(hfProfileUrl)}`;
 	const handleImgError = () => {
-		if (thumbUrl !== proxyThumbUrl) {
+		if (dataset !== "CancerVerse" && thumbUrl !== proxyThumbUrl) {
 			setThumbUrl(proxyThumbUrl); // local failed — retry via the same-origin HF proxy
 		} else {
 			setImgError(true); // both sources failed

PanTS-Demo/src/helpers/savedCases.test.ts

@@ -1,47 +1,62 @@
 import { beforeEach, describe, expect, it } from "vitest";
 import { isSavedCase, loadSavedCases, SAVED_CASES_KEY, toggleSavedCase } from "./savedCases";
 
-const meta = (id: number) => ({ id, sex: "M", age: 50, tumor: 0 });
+const meta = (id: string) => ({ id, sex: "M", age: 50, tumor: 0 });
 
 describe("savedCases", () => {
 	beforeEach(() => localStorage.clear());
 
 	it("starts empty", () => {
 		expect(loadSavedCases()).toEqual([]);
-		expect(isSavedCase(17)).toBe(false);
+		expect(isSavedCase("17")).toBe(false);
 	});
 
 	it("toggles a case on and off", () => {
-		toggleSavedCase(meta(17));
-		expect(isSavedCase(17)).toBe(true);
-		expect(loadSavedCases().map((c) => c.id)).toEqual([17]);
+		toggleSavedCase(meta("17"));
+		expect(isSavedCase("17")).toBe(true);
+		expect(loadSavedCases().map((c) => c.id)).toEqual(["17"]);
 
-		toggleSavedCase(meta(17));
-		expect(isSavedCase(17)).toBe(false);
+		toggleSavedCase(meta("17"));
+		expect(isSavedCase("17")).toBe(false);
 		expect(loadSavedCases()).toEqual([]);
 	});
 
 	it("stores the card metadata and a savedAt timestamp", () => {
 		const before = Date.now();
-		toggleSavedCase({ id: 30, sex: "F", age: 66, tumor: 1 });
+		toggleSavedCase({ id: "30", sex: "F", age: 66, tumor: 1 });
 		const [saved] = loadSavedCases();
-		expect(saved).toMatchObject({ id: 30, sex: "F", age: 66, tumor: 1 });
+		expect(saved).toMatchObject({ id: "30", sex: "F", age: 66, tumor: 1 });
 		expect(saved.savedAt).toBeGreaterThanOrEqual(before);
 	});
 
 	it("keeps most-recently-saved first and de-dupes by id", () => {
-		toggleSavedCase(meta(1));
-		toggleSavedCase(meta(2));
-		expect(loadSavedCases().map((c) => c.id)).toEqual([2, 1]);
+		toggleSavedCase(meta("1"));
+		toggleSavedCase(meta("2"));
+		expect(loadSavedCases().map((c) => c.id)).toEqual(["2", "1"]);
 		// re-adding an already-saved id removes it (toggle), it does not duplicate
-		toggleSavedCase(meta(2));
-		expect(loadSavedCases().map((c) => c.id)).toEqual([1]);
+		toggleSavedCase(meta("2"));
+		expect(loadSavedCases().map((c) => c.id)).toEqual(["1"]);
+	});
+
+	it("works with a CancerVerse id, unchanged behavior", () => {
+		toggleSavedCase(meta("CV_00000012"));
+		expect(isSavedCase("CV_00000012")).toBe(true);
+		expect(loadSavedCases().map((c) => c.id)).toEqual(["CV_00000012"]);
 	});
 
 	it("ignores corrupt storage instead of throwing", () => {
 		localStorage.setItem(SAVED_CASES_KEY, "not json");
 		expect(loadSavedCases()).toEqual([]);
 		localStorage.setItem(SAVED_CASES_KEY, JSON.stringify([{ nope: true }, { id: 5, sex: "M", age: 1, tumor: 0, savedAt: 1 }]));
-		expect(loadSavedCases().map((c) => c.id)).toEqual([5]);
+		expect(loadSavedCases().map((c) => c.id)).toEqual(["5"]);
+	});
+
+	it("coerces legacy numeric ids (saved before ids became strings) to strings", () => {
+		localStorage.setItem(
+			SAVED_CASES_KEY,
+			JSON.stringify([{ id: 17, sex: "M", age: 40, tumor: 0, savedAt: 1 }])
+		);
+		expect(loadSavedCases().map((c) => c.id)).toEqual(["17"]);
+		expect(isSavedCase("17")).toBe(true);
 	});
 });

PanTS-Demo/src/helpers/savedCases.ts

@@ -5,7 +5,7 @@
 // (cross-tab) to stay in sync.
 
 export type SavedCase = {
-	id: number;
+	id: string;
 	sex: string;
 	age: number;
 	tumor: number;
@@ -18,7 +18,12 @@ export const SAVED_CASES_EVENT = "savedcaseschange";
 export const loadSavedCases = (): SavedCase[] => {
 	try {
 		const arr = JSON.parse(localStorage.getItem(SAVED_CASES_KEY) || "[]");
-		return Array.isArray(arr) ? arr.filter((c) => c && typeof c.id === "number") : [];
+		// Accept legacy entries saved before case ids became strings (`id: number`) so
+		// existing bookmarks in a user's localStorage don't silently vanish.
+		if (!Array.isArray(arr)) return [];
+		return arr
+			.filter((c) => c && (typeof c.id === "number" || typeof c.id === "string"))
+			.map((c) => ({ ...c, id: String(c.id) }));
 	} catch {
 		return [];
 	}
@@ -38,7 +43,7 @@ const persistSavedCases = (list: SavedCase[]) => {
 	}
 };
 
-export const isSavedCase = (id: number): boolean => loadSavedCases().some((c) => c.id === id);
+export const isSavedCase = (id: string): boolean => loadSavedCases().some((c) => c.id === id);
 
 // Add the case if it isn't saved, otherwise remove it. Returns the updated list (most
 // recently saved first).

PanTS-Demo/src/helpers/search.test.ts

@@ -10,18 +10,23 @@ import {
 
 describe("itemToId", () => {
 	it("parses the numeric id out of a PanTS case id", () => {
-		expect(itemToId({ case_id: "PanTS_00008854" })).toBe(8854);
-		expect(itemToId({ case_id: "PanTS_00000001" })).toBe(1);
+		expect(itemToId({ case_id: "PanTS_00008854" })).toBe("8854");
+		expect(itemToId({ case_id: "PanTS_00000001" })).toBe("1");
 	});
 
 	it("falls back across id fields and handles numbers", () => {
-		expect(itemToId({ "PanTS ID": "PanTS_00000900" })).toBe(900);
-		expect(itemToId({ id: 42 })).toBe(42);
+		expect(itemToId({ "PanTS ID": "PanTS_00000900" })).toBe("900");
+		expect(itemToId({ id: 42 })).toBe("42");
 	});
 
 	it("returns 0 when no usable id is present", () => {
-		expect(itemToId({})).toBe(0);
-		expect(itemToId({ case_id: "no-digits-here" })).toBe(0);
+		expect(itemToId({})).toBe("0");
+		expect(itemToId({ case_id: "no-digits-here" })).toBe("0");
+	});
+
+	it("keeps CancerVerse ids as-is, no offset/renumbering", () => {
+		expect(itemToId({ case_id: "CV_00000012" })).toBe("CV_00000012");
+		expect(itemToId({ dataset: "CancerVerse", case_id: "CV_00000012" })).toBe("CV_00000012");
 	});
 });
 
@@ -76,6 +81,7 @@ describe("parseFiltersFromParams", () => {
 			ctPhase: ["Venous"],
 			siteNat: ["US"],
 			year: ["2020"],
+			dataset: ["CancerVerse"],
 		};
 		const restored = parseFiltersFromParams(buildSearchParams(filters));
 		expect(restored).toEqual(filters);

PanTS-Demo/src/helpers/search.ts

@@ -11,6 +11,7 @@ export type SearchFilters = {
 	ctPhase: string[]; // CT phase, e.g. Arterial (from facets)
 	siteNat: string[]; // site nationality, e.g. US (from facets)
 	year: string[]; // study year (from facets)
+	dataset: string[]; // "PanTS" / "CancerVerse" (from facets)
 };
 
 export const EMPTY_FILTERS: SearchFilters = {
@@ -21,27 +22,32 @@ export const EMPTY_FILTERS: SearchFilters = {
 	ctPhase: [],
 	siteNat: [],
 	year: [],
+	dataset: [],
 };
 
 // The multi-select array keys (everything except `tumor`).
-export type MultiFilterKey = "sex" | "age" | "manufacturer" | "ctPhase" | "siteNat" | "year";
+export type MultiFilterKey = "sex" | "age" | "manufacturer" | "ctPhase" | "siteNat" | "year" | "dataset";
 
 // Minimal shape of an item returned by /api/search and /api/random.
 export type SearchItem = {
 	case_id?: string | number;
 	"PanTS ID"?: string | number;
 	id?: string | number;
+	dataset?: "PanTS" | "CancerVerse";
 	tumor?: number | null;
 	sex?: string | null;
 	age?: number | string | null;
 };
 
-// Parse the numeric case id out of any of the id-ish fields, e.g.
-// "PanTS_00008854" -> 8854. Returns 0 when nothing usable is present.
-export const itemToId = (it: SearchItem): number => {
+// Case identity as a string, e.g. "PanTS_00008854" -> "8854" (PanTS's existing bare-
+// number id, unchanged) or "CV_00000012" -> "CV_00000012" (CancerVerse's real id,
+// kept as-is — no offset/renumbering, so it stays identical to the folder name on
+// disk). Returns "0" when nothing usable is present.
+export const itemToId = (it: SearchItem): string => {
 	const raw = String(it.case_id ?? it["PanTS ID"] ?? it.id ?? "");
+	if (/^cv_?\d+$/i.test(raw.trim())) return raw.trim().toUpperCase();
 	const m = raw.match(/\d+/);
-	return m ? Number(m[0]) : 0;
+	return m ? String(Number(m[0])) : "0";
 };
 
 // Build the /api/search (and /api/facets, and URL) query string from the active
@@ -61,6 +67,7 @@ export const buildSearchParams = (
 	(filters.ctPhase ?? []).forEach((v) => params.append("ct_phase[]", v));
 	(filters.siteNat ?? []).forEach((v) => params.append("site_nat[]", v));
 	(filters.year ?? []).forEach((v) => params.append("year[]", v));
+	(filters.dataset ?? []).forEach((v) => params.append("dataset[]", v));
 	if (opts.sortBy) params.set("sort_by", opts.sortBy);
 	if (opts.perPage) params.set("per_page", String(opts.perPage));
 	return params;
@@ -79,6 +86,7 @@ export const parseFiltersFromParams = (params: URLSearchParams): SearchFilters =
 		ctPhase: params.getAll("ct_phase[]"),
 		siteNat: params.getAll("site_nat[]"),
 		year: params.getAll("year[]"),
+		dataset: params.getAll("dataset[]"),
 	};
 };
 
@@ -89,4 +97,5 @@ export const countActiveFilters = (f: SearchFilters): number =>
 	f.manufacturer.length +
 	f.ctPhase.length +
 	f.siteNat.length +
-	f.year.length;
+	f.year.length +
+	f.dataset.length;

PanTS-Demo/src/helpers/utils.test.ts

@@ -7,7 +7,9 @@ import {
 	closestColorIndex,
 	deepIsEqual,
 	filenameToName,
+	getCaseDisplay,
 	getPanTSId,
+	isCancerVerseId,
 	prettify_segmentation_category,
 	roundDigits,
 } from "./utils";
@@ -27,6 +29,19 @@ describe("case-ID formatting", () => {
 		expect(cleanName("PanTS_00008854")).toBe("8854");
 		expect(cleanName("PanTS_00000001")).toBe("1");
 	});
+
+	it("isCancerVerseId recognizes CV-prefixed ids, not plain PanTS numbers", () => {
+		expect(isCancerVerseId("CV_00000012")).toBe(true);
+		expect(isCancerVerseId("cv12")).toBe(true);
+		expect(isCancerVerseId("17")).toBe(false);
+		expect(isCancerVerseId("PanTS_00000017")).toBe(false);
+	});
+
+	it("getCaseDisplay keeps PanTS's existing label and gives CancerVerse its real id, no offset", () => {
+		expect(getCaseDisplay("17")).toEqual({ dataset: "PanTS", label: "PanTS_00000017" });
+		expect(getCaseDisplay("CV_00000012")).toEqual({ dataset: "CancerVerse", label: "CV_00000012" });
+		expect(getCaseDisplay("cv12")).toEqual({ dataset: "CancerVerse", label: "CV_00000012" });
+	});
 });
 
 describe("equality helpers", () => {

PanTS-Demo/src/helpers/utils.ts

@@ -99,6 +99,23 @@ export const getPanTSId = (case_id: string) => {
     return `PanTS_${new_id}`;
 }
 
+// Whether a case id string identifies a CancerVerse case ("CV_00000012", or a bare
+// "cv12" as typed by a user) rather than a PanTS case (a plain number, "17").
+// CancerVerse has no offset/renumbering — the id here is exactly the on-disk folder
+// name, "CV_########".
+export const isCancerVerseId = (case_id: string): boolean => /^cv_?\d+$/i.test(case_id.trim());
+
+// Dataset-aware display label for a case id: PanTS keeps its existing
+// `PanTS_<8-digit>` form (unchanged), CancerVerse cases show their real
+// `CV_<8-digit>` folder name (no arithmetic — id "12" is CV_00000012's actual number).
+export const getCaseDisplay = (case_id: string): { dataset: "PanTS" | "CancerVerse"; label: string } => {
+    const m = case_id.trim().match(/^cv_?(\d+)$/i);
+    if (m) {
+        return { dataset: "CancerVerse", label: `CV_${m[1].padStart(8, "0")}` };
+    }
+    return { dataset: "PanTS", label: getPanTSId(case_id) };
+}
+
 export function capitalize(word: string) {
 	if (!word) return "";
 	return word.charAt(0).toUpperCase() + word.slice(1);

PanTS-Demo/src/routes/ComparePage.tsx

@@ -10,6 +10,7 @@ import { alignStatRows } from "../helpers/compareStats";
 import { API_BASE } from "../helpers/constants";
 import { loadOrganNorms, type OrganNorms } from "../helpers/organNorms";
 import { computeStatRows, type OrganMetric } from "../helpers/organStatsExport";
+import { getCaseDisplay } from "../helpers/utils";
 import "./ComparePage.css";
 
 type Demographics = { sex: string | null; age: number | null; tumor: number | null };
@@ -78,13 +79,15 @@ function useCaseData(id: string): CaseData {
 // (mirrors the dashboard Preview's chain). In dev/demo both endpoints 404 → placeholder.
 function Thumbnail({ id }: { id: string }) {
 	const local = `${API_BASE}/api/get_image_preview/${id}`;
-	const caseIdStr = `PanTS_${id.toString().padStart(8, "0")}`;
+	const { dataset, label: caseIdStr } = getCaseDisplay(id);
 	const hf = `${API_BASE}/api/proxy-image?url=${encodeURIComponent(
 		`https://huggingface.co/datasets/BodyMaps/iPanTSMini/resolve/main/profile_only/${caseIdStr}/profile.jpg`
 	)}`;
+	// CancerVerse has no HuggingFace profile-image mirror to fall back to.
 	const [stage, setStage] = useState<0 | 1 | 2>(0);
 	useEffect(() => setStage(0), [id]);
-	if (stage === 2) return <div className="cmp-thumb cmp-thumb--empty">No preview</div>;
+	if (stage === 2 || (stage === 1 && dataset === "CancerVerse"))
+		return <div className="cmp-thumb cmp-thumb--empty">No preview</div>;
 	return (
 		<img
 			className="cmp-thumb"