Studio/Designer/dashboard default to the private lab data repo; ?repo= tab override; Rig id (LAB-227 Phase 4)

CLAUDE.md

@@ -495,6 +495,15 @@ fix flows to every page automatically; two hand-written HTML pages never will.
   `Studio._urlSuppress`. URL writing is NOT a protocol mutation — never route
   it through `pushUndo`. Any NEW shareable state must flow through
   `encodeApp()` + `Studio.updateUrl` (never hand-build `location.search`).
+  **`?repo=` alone is a tab-scoped repo override** (LAB-227 Phase 4): `Studio.sessionRepo`
+  is parsed in the classic shell and `courseSettings()` returns it ahead of the stored
+  `studio_gh_repo` and the default (`Studio.DEFAULT_COURSE_REPO` = the private
+  `reiserlab/arena-experiments`; the Pattern Designer's `DEFAULT_DATA_REPO` and the
+  dashboard's `DEFAULT_REPO` carry the same string, pinned by `tests/test-studio-shell.js`).
+  Every repo consumer reads `courseSettings().repo` — never `localStorage` directly — so the
+  override wins for previews, Open from Repo, vocab, replay AND saves; it is never written to
+  storage, `encodeApp({sessionRepo})` keeps it across the canonical rewrite, and typing a
+  repo in ⚙ Settings ends it.
 - **Top bar: Protocol ▾ vs ⚙ Settings.** `Protocol ▾` (`#fileMenu`, renamed from File)
   holds protocol ACTIONS only (new/open/replay/save/promote/copy/reset/soak). `⚙ Settings`
   (`#settingsMenu`) holds the Studio/bench settings kept in the browser, not the YAML: the

dashboard/data-browser/README.md

@@ -128,9 +128,11 @@ relative-heading pages instead of failing import.
 
 ## Public page, private data
 
-The dashboard itself is public. Runlogs live in `reiserlab/cshl-2026-course`,
-which was private during the course and has been public since 2026-08 (reads work
-signed-out; writes still need a token).
+The dashboard itself is public. Runlogs live in the lab's private data repo
+`reiserlab/arena-experiments` (the default in the repo field since LAB-227 Phase 4;
+every read needs a token). The 2026 course's logs stay in `reiserlab/cshl-2026-course`,
+public since 2026-08 (reads work signed-out) — type that repo into the field to browse
+them.
 
 The sign-in flow uses:
 

dashboard/data-browser/app.js

@@ -289,7 +289,7 @@ function updateGithubUi(user) {
         const repo = G.parseRepo(els.githubRepoInput.value);
         els.courseRepoLink.href = `https://github.com/${repo.full}`;
     } catch (_) {
-        els.courseRepoLink.href = 'https://github.com/reiserlab/cshl-2026-course';
+        els.courseRepoLink.href = `https://github.com/${G.DEFAULT_REPO}`;
     }
 }
 
@@ -951,7 +951,7 @@ async function browseGithub() {
 
 function normalizeDirectoryUrl(value) {
     const url = new URL(
-        A.safeText(value).trim() || '/cshl-2026-course/runlogs/',
+        A.safeText(value).trim() || '/arena-experiments/runlogs/',
         window.location.href
     );
     if (!url.pathname.endsWith('/')) url.pathname += '/';

dashboard/data-browser/github-repo.js

@@ -7,7 +7,10 @@
     const REPO_KEY = 'studio_gh_repo';
     const BENCH_KEY = 'studio_bench_id';
     const FOLDERS_KEY_PREFIX = 'dashboard_runlog_folders:';
-    const DEFAULT_REPO = 'reiserlab/cshl-2026-course';
+    // The lab's private data repo (LAB-227) — same default as Arena Studio and the
+    // Pattern Designer; the 2026 course's logs stay in reiserlab/cshl-2026-course
+    // (type it into the repo field). tests/test-studio-shell.js pins the three equal.
+    const DEFAULT_REPO = 'reiserlab/arena-experiments';
     // Run logs are committed as `.jsonl.gz` since Studio v0.72; fetchRaw reads
     // BYTES and lets the shared format module inflate (magic-detected, so a raw
     // `.jsonl` still works). Vendored byte-identical copy of js/runlog-format.js.

dashboard/data-browser/index.html

@@ -21,7 +21,7 @@
       <h1>Course Data Dashboard</h1>
     </div>
     <div class="header-actions">
-      <a id="courseRepoLink" class="quiet-link" href="https://github.com/reiserlab/cshl-2026-course" target="_blank" rel="noreferrer">Course repo</a>
+      <a id="courseRepoLink" class="quiet-link" href="https://github.com/reiserlab/arena-experiments" target="_blank" rel="noreferrer">Data repo</a>
       <div class="status-strip" id="statusStrip" aria-live="polite">
         <span class="status-dot" aria-hidden="true"></span>
         <span id="statusText">No data loaded</span>
@@ -50,7 +50,7 @@ <h2>Data</h2>
         </div>
 
         <div class="github-controls">
-          <input id="githubRepoInput" type="text" value="reiserlab/cshl-2026-course" aria-label="GitHub repository">
+          <input id="githubRepoInput" type="text" value="reiserlab/arena-experiments" aria-label="GitHub repository" title="GitHub data repo (owner/name) — the lab's reiserlab/arena-experiments by default; type reiserlab/cshl-2026-course for the 2026 course logs">
           <button id="githubSignInButton" type="button">Sign in</button>
           <button id="githubSignOutButton" type="button" disabled>Sign out</button>
           <button id="chooseRigsButton" type="button" title="Choose which rig folders are included in the data catalog" disabled>Select rigs</button>
@@ -60,7 +60,7 @@ <h2>Data</h2>
         <details class="local-source">
           <summary>Local server repository</summary>
           <div class="inline-control">
-            <input id="repoBaseInput" type="text" value="/cshl-2026-course/runlogs/" aria-label="Local runlog repository path">
+            <input id="repoBaseInput" type="text" value="/arena-experiments/runlogs/" aria-label="Local runlog repository path">
             <button id="scanLocalButton" type="button">Scan local</button>
           </div>
         </details>

docs/development/data-repo-token-runbook.md

@@ -1,9 +1,13 @@
 # Data-repo tokens — renewal and setup runbook
 
 Arena Studio, the Pattern Designer and the data-browser dashboard write protocols,
-patterns and run logs to a GitHub **data repo** (the CSHL course repo today; the lab's
-`reiserlab/arena-experiments` next) using a personal access token pasted once per
-browser (⚙ Settings → GitHub → **Sign in…**). The token is stored in that browser only
+patterns and run logs to a GitHub **data repo** — the lab's private
+`reiserlab/arena-experiments` by default (LAB-227 Phase 4, 2026-11); the CSHL course
+benches and `rig03-sr` type `reiserlab/cshl-2026-course` into the Repo field instead —
+using a personal access token pasted once per browser (⚙ Settings → GitHub →
+**Sign in…**). A `?repo=owner/name` link overrides the stored repo for that tab only.
+The rig's folder name is its **Rig id** (⚙ Settings; the course benches use
+`bench01`…`bench07`). The token is stored in that browser only
 (`studio_gh_pat`, sessionStorage or localStorage) and sent only as an
 `Authorization` header. This page is the operational how-to; design background is in
 `studio-github-save-proposal.md`, the course-week checklist in
@@ -38,9 +42,10 @@ the stored token; a save or run-log commit made with a dead token falls back to
    `ghp_…` value once; store it in the lab password manager.
 4. On each bench browser (served from `http://127.0.0.1:8000/`, not `file://`):
    ⚙ Settings → **Sign in…** → paste → **YES** to "Remember this token" → 🛡 advanced
-   (instructor password) → 🔓 in the GitHub block → **Repo** `reiserlab/cshl-2026-course`,
-   **Bench id** `bench01`…`bench07` (must match `roster.yaml`), tick **Commit
-   directly to default branch** → 🔒. Connect the arena; the roster pre-fills the
+   (instructor password) → 🔓 in the GitHub block → **Repo** `reiserlab/cshl-2026-course`
+   (the field is pre-filled with the lab repo — overwrite it), **Rig id**
+   `bench01`…`bench07` (must match `roster.yaml`), tick **Commit directly to default
+   branch** → 🔒. Connect the arena; the roster pre-fills the
    experimenter.
 5. Check: the run log shows `ages list from the course repo (… 5 entries)` and no
    "unreadable" lines; a test save lands in `protocols/<bench-id>/`.
@@ -63,8 +68,10 @@ the stored token; a save or run-log commit made with a dead token falls back to
 6. In the Studio: ⚙ Settings → **Sign in…** → paste. Answer **YES** to "Remember" only on a
    rig computer you control or your own laptop; answer **NO** (session-only) on a
    shared or borrowed machine. **Sign out** clears the token everywhere.
-7. Set **Repo** and your **Rig id** once (🔓 needed); saves go to `protocols/<rig-id>/`,
-   run logs to `runlogs/<rig-id>/`, and your commits carry your GitHub identity.
+7. Set your **Rig id** once (🔓 needed; **Repo** is already `reiserlab/arena-experiments`);
+   saves go to `protocols/<rig-id>/`, run logs to `runlogs/<rig-id>/`, and your commits
+   carry your GitHub identity. A rig may keep its own genotype / age / sex / fly-number
+   lists at `protocols/<rig-id>/<file>.yaml`; the Studio reads those before the root files.
 
 Sharing across the lab needs no extra permission: everyone with a token sees every
 rig's folder, **Protocol ▾ → Promote to shared…** copies a protocol and its patterns into

js/studio-replay.js

@@ -1246,7 +1246,18 @@
                 setProtoLine('Downloading ' + name + ' from ' + repo.full + '…');
                 const bytes = await readRepoBytes(repo, path);
                 if (token !== R.loadToken) return false;
-                if (!bytes) throw new Error(path + ' was not found in ' + repo.full + '.');
+                // Signed out, GitHub answers 404 for a private repo exactly as for a
+                // missing file — say so (the lab's default data repo is private).
+                if (!bytes) {
+                    throw new Error(
+                        path +
+                            ' was not found in ' +
+                            repo.full +
+                            (ghToken()
+                                ? '.'
+                                : ' (HTTP 404) — sign in if this repository is private.')
+                    );
+                }
                 const text = Fmt
                     ? await Fmt.readRunlogText(bytes)
                     : new TextDecoder().decode(bytes);
@@ -2111,7 +2122,11 @@
                     if (!hit) {
                         if (Studio.showBanner)
                             Studio.showBanner(
-                                'Replay: run ' + s.runId + ' was not found in ' + repo.full + '.'
+                                'Replay: run ' +
+                                    s.runId +
+                                    ' was not found in ' +
+                                    repo.full +
+                                    (ghToken() ? '.' : ' — sign in if this repository is private.')
                             );
                         return false;
                     }

js/studio-url-state.js

@@ -240,8 +240,9 @@
      * is bench identity, NOT doc state — emitted whenever present (the caller
      * only passes an explicit selection), regardless of doc locality. `repo`
      * is emitted ONLY alongside a valid repo-path `p` (a repo ref without a
-     * document to point at is bench localStorage config, not URL state).
-     * @param {object} state {mode, p, lib, set, rig, repo, source?: 'local'|'committed'}
+     * document to point at is bench localStorage config, not URL state) —
+     * except `sessionRepo`, the tab-scoped override a bare ?repo= link set.
+     * @param {object} state {mode, p, lib, set, rig, repo, sessionRepo, source?: 'local'|'committed'}
      */
     function encode(state) {
         const s = state || {};
@@ -261,6 +262,11 @@
         } else if (!local && isSafeKey(s.p)) {
             params.set('p', s.p);
         }
+        // sessionRepo: the tab-scoped repo override (a bare ?repo=, Studio.sessionRepo) —
+        // kept so a refresh keeps the tab on the requested repo; only when no repo-bound
+        // doc or replay already names the repo above.
+        if (!replayMode && !repoMode && isSafeRepo(s.sessionRepo))
+            params.set('repo', s.sessionRepo);
         if (!replayMode && isSafeKey(s.lib)) params.set('lib', s.lib);
         if (!replayMode && !local && isSafeKey(s.set)) params.set('set', s.set);
         if (isSafeKey(s.rig)) params.set('rig', s.rig);
@@ -293,7 +299,10 @@
      * `advanced` must be true ONLY when advanced mode is active AND was
      * URL-requested (the caller enforces this; a remembered-unlocked browser
      * passes false to keep a clean URL, mirroring the derived-rig rule).
-     * @param {object} app {mode, protocolKey, rigKey, repo, repoPath, advanced}
+     * `sessionRepo` is the tab-scoped repo override (Studio.sessionRepo, from a
+     * bare ?repo= link): emitted as `repo` only when no repo-bound doc or replay
+     * owns the link.
+     * @param {object} app {mode, protocolKey, rigKey, repo, repoPath, sessionRepo, advanced}
      * @returns {string} query string (leading '?', or '' when all defaults)
      */
     function encodeApp(app) {
@@ -323,6 +332,7 @@
         return encode({
             mode: a.mode,
             p: a.protocolKey || undefined,
+            sessionRepo: a.sessionRepo || undefined,
             rig: a.rigKey || undefined,
             advanced: a.advanced || undefined,
             soak: a.soak || undefined,

pattern_editor.html

@@ -2551,7 +2551,7 @@ <h3 class="modal-title">Save to Repo</h3>
                 <input type="radio" name="repoDest" id="destProtocol" value="protocol">
                 <span class="dest-text">
                     <b>A protocol's pattern folder</b>
-                    <span>protocols/&lt;bench-id&gt;/&lt;protocol&gt;_patterns/ — travels with that protocol (needs a bench id)</span>
+                    <span>protocols/&lt;rig-id&gt;/&lt;protocol&gt;_patterns/ — travels with that protocol (needs a rig id)</span>
                     <input type="text" class="dest-proto-input" id="destProtoName" placeholder="protocol name, e.g. my_protocol" disabled>
                 </span>
             </label>
@@ -3582,9 +3582,13 @@ <h3 class="modal-title">Save to Repo</h3>
         // ============================================================
         let sessionRepo = null;       // ?repo= override for this tab
         let _urlArenaLock = false;    // ?arena= handover locks the config after initUI
+        // Same default as the Studio's DEFAULT_COURSE_REPO (LAB-227): the lab's private
+        // data repo, so a fresh browser lists it in Open from Repo… / Save to Repo…
+        // without a Studio visit; a stored repo or a ?repo= link overrides it.
+        const DEFAULT_DATA_REPO = 'reiserlab/arena-experiments';
 
         function repoSettings() {
-            const raw = (sessionRepo || localStorage.getItem('studio_gh_repo') || '').trim();
+            const raw = (sessionRepo || localStorage.getItem('studio_gh_repo') || DEFAULT_DATA_REPO).trim();
             const rm = /^([A-Za-z0-9-]{1,39})\/([A-Za-z0-9._-]{1,100})$/.exec(raw);
             const ok = rm && !raw.includes('..');
             return {
@@ -3791,13 +3795,13 @@ <h3 class="modal-title">Save to Repo</h3>
             if (!built) return;
             _pendingRepoSave = built;
             document.getElementById('repoSaveRepoLine').textContent =
-                'Repo: ' + cs.repoRaw + (cs.benchId ? ' · bench ' + cs.benchId : '');
+                'Repo: ' + cs.repoRaw + (cs.benchId ? ' · rig ' + cs.benchId : '');
             const protoRadio = document.getElementById('destProtocol');
             const protoInput = document.getElementById('destProtoName');
             protoRadio.disabled = !cs.benchId;
             protoRadio.closest('.dest-row').title = cs.benchId
                 ? 'Commits next to a protocol so they travel together'
-                : 'Needs a bench id (set in Arena Studio → ⚙ Settings) — course benches only';
+                : 'Needs a rig id (set in Arena Studio → ⚙ Settings → Rig id)';
             if (!cs.benchId) document.getElementById('destLibrary').checked = true;
             protoInput.disabled = !protoRadio.checked;
             updateRepoSavePath();

tests/test-studio-shell.js

@@ -17,6 +17,9 @@ const path = require('path');
 const root = path.join(__dirname, '..');
 const studio = fs.readFileSync(path.join(root, 'arena_studio.html'), 'utf8');
 const replay = fs.readFileSync(path.join(root, 'js/studio-replay.js'), 'utf8');
+const designer = fs.readFileSync(path.join(root, 'pattern_editor.html'), 'utf8');
+const dashRepo = fs.readFileSync(path.join(root, 'dashboard/data-browser/github-repo.js'), 'utf8');
+const dashIndex = fs.readFileSync(path.join(root, 'dashboard/data-browser/index.html'), 'utf8');
 
 let totalChecks = 0;
 let failures = 0;
@@ -407,6 +410,76 @@ check(
         !/:root\[data-ui-theme="night"\] (img|canvas)\b/.test(studio) &&
         studio.includes('filter:url(#uiNightRed)')
 );
+console.log('=== data repo defaults + rig id (LAB-227 Phase 4) ===');
+// ONE default string across the three tools: the lab's private data repo. The course
+// repo stays reachable by typing it (course benches + rig03-sr still write there).
+const DATA_REPO = 'reiserlab/arena-experiments';
+check(
+    'Studio, Pattern Designer and dashboard default to the lab data repo',
+    studio.includes("Studio.DEFAULT_COURSE_REPO = '" + DATA_REPO + "';") &&
+        designer.includes("const DEFAULT_DATA_REPO = '" + DATA_REPO + "';") &&
+        dashRepo.includes("const DEFAULT_REPO = '" + DATA_REPO + "';")
+);
+check(
+    'Studio Repo field + dashboard repo field show the data repo, not the course repo',
+    /id="ghRepoInput" placeholder="reiserlab\/arena-experiments"/.test(studio) &&
+        /id="githubRepoInput" type="text" value="reiserlab\/arena-experiments"/.test(dashIndex) &&
+        dashIndex.includes('href="https://github.com/reiserlab/arena-experiments"')
+);
+check(
+    'the Pattern Designer falls back to the same default when no repo is stored',
+    designer.includes(
+        "(sessionRepo || localStorage.getItem('studio_gh_repo') || DEFAULT_DATA_REPO).trim()"
+    )
+);
+check(
+    '?repo= is a tab-scoped override applied in courseSettings (wins signed in or out)',
+    studio.includes('Studio.sessionRepo = (function () {') &&
+        studio.includes(
+            "Studio.sessionRepo ||\n            localStorage.getItem('studio_gh_repo') ||\n            Studio.DEFAULT_COURSE_REPO"
+        ) &&
+        studio.includes('sessionRepo: Studio.sessionRepo || null,') &&
+        !studio.includes("localStorage.setItem('studio_gh_repo', Studio.sessionRepo")
+);
+check(
+    'typing a repo in ⚙ Settings ends the ?repo= override',
+    studio.includes('Studio.sessionRepo = null;')
+);
+check(
+    'the shared-pattern listing names the repo it came from',
+    studio.includes(
+        "'shared pattern library: ' + n + ' preview(s) wired from ' + repo.full + '/patterns/'"
+    ) && !studio.includes("'course repo: ' + n + ' shared pattern preview(s)")
+);
+check(
+    'Patterns ↗ passes the effective repo (default, stored, or ?repo=)',
+    studio.includes(
+        'var cs=window.Studio && Studio.courseSettings ? Studio.courseSettings() : null;'
+    ) && studio.includes("var repo=cs && cs.repo ? cs.repo.full : '';")
+);
+check(
+    'UI says "Rig id" (the storage key studio_bench_id keeps its name)',
+    /<label for="ghBenchId">Rig id<\/label>/.test(studio) &&
+        !/Settings → Bench id/.test(studio) &&
+        !/[Bb]ench id not set/.test(studio) &&
+        !/set bench id/.test(studio) &&
+        studio.includes("localStorage.getItem('studio_bench_id')") &&
+        !/needs a bench id|bench id \(set in/.test(designer)
+);
+check(
+    'per-rig vocabularies: protocols/<rig-id>/<file> is tried before the repo root',
+    studio.includes('async function readCourseVocabFile(cs, token, file) {') &&
+        studio.includes("paths.push('protocols/' + cs.benchId + '/' + file);") &&
+        studio.includes("await readCourseVocabFile(cs, token, 'genotypes.yaml')") &&
+        studio.includes('await readCourseVocabFile(cs, token, file);')
+);
+check(
+    'replay: a signed-out 404 says "sign in if this repository is private"',
+    /ghToken\(\)\s*\?\s*'\.'\s*:\s*' \(HTTP 404\) — sign in if this repository is private\.'/.test(
+        replay
+    ) && /ghToken\(\)\s*\?\s*'\.'\s*:\s*' — sign in if this repository is private\.'/.test(replay)
+);
+
 console.log('=== bridge-loss policy wiring (LAB-303 S1 review) ===');
 check(
     'bridgeRequired only for a recorded run the bridge is logging',