From 82301f0b30f2319daae35b2e425c3abd7a675ed8 Mon Sep 17 00:00:00 2001
From: Nabil-Fareed Alikhan <nabil@happykhan.com>
Date: Fri, 4 Sep 2026 08:33:55 +0100
Subject: [PATCH] Preserve hidden GC data in saved sessions

---
 hooks/useBRIGController.ts |  9 +--------
 tests/e2e/brigx.spec.ts    | 21 +++++++++++++++++++++
 2 files changed, 22 insertions(+), 8 deletions(-)

diff --git a/hooks/useBRIGController.ts b/hooks/useBRIGController.ts
index 54dcc9a..0a9dace 100644
--- a/hooks/useBRIGController.ts
+++ b/hooks/useBRIGController.ts
@@ -310,14 +310,7 @@ export function useBRIGController() {
       params,
       imageProperties,
       referenceAnnotations,
-      plotData ? {
-        ...plotData,
-        reference: {
-          ...plotData.reference,
-          gcContent: params.showGCContent !== false ? plotData.reference.gcContent : undefined,
-          gcSkew: params.showGCSkew !== false ? plotData.reference.gcSkew : undefined,
-        },
-      } : null,
+      plotData,
     );
     const blob = new Blob([json], { type: 'application/json' });
     const url = URL.createObjectURL(blob);
diff --git a/tests/e2e/brigx.spec.ts b/tests/e2e/brigx.spec.ts
index 3e0d456..2c38819 100644
--- a/tests/e2e/brigx.spec.ts
+++ b/tests/e2e/brigx.spec.ts
@@ -589,6 +589,27 @@ test.describe('BRIGX e2e — circular genome plot', () => {
     const svg = await fs.readFile(downloadedPath!, 'utf8')
     expect(svg).not.toContain('id="gc-content-ring"')
     expect(svg).toContain('id="gc-skew-ring"')
+
+    const sessionDownloadPromise = page.waitForEvent('download')
+    await page.getByRole('button', { name: 'Save session' }).click()
+    const sessionDownload = await sessionDownloadPromise
+    const sessionPath = await sessionDownload.path()
+    expect(sessionPath).not.toBeNull()
+    const session = JSON.parse(await fs.readFile(sessionPath!, 'utf8'))
+    expect(session.params.showGCContent).toBe(false)
+    expect(session.result.plot.reference.gcContent.length).toBeGreaterThan(0)
+
+    await page.getByLabel('Load session').setInputFiles(sessionPath!)
+    await expect(page.getByText('Session and saved result loaded.')).toBeVisible()
+    await expect(page.getByLabel('GC Content')).not.toBeChecked()
+    await page.getByLabel('GC Content').check()
+
+    const restoredDownloadPromise = page.waitForEvent('download')
+    await page.getByRole('button', { name: 'SVG', exact: true }).click()
+    const restoredDownload = await restoredDownloadPromise
+    const restoredPath = await restoredDownload.path()
+    expect(restoredPath).not.toBeNull()
+    expect(await fs.readFile(restoredPath!, 'utf8')).toContain('id="gc-content-ring"')
   })
 
   test('PNG export matches the live canvas after moving a legend', async ({ page }) => {