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| # Prompt — Lab polish: plain-English "?" copy, no all-caps, fix the clipped program graph | |
| Three presentation-only fixes to the Lab (web/). No engine, API, DSL, or airgap changes. Read the named files first; don't assume. After each part, build (`tsc`/`next build`) and confirm clean. | |
| ## 1. Audit EVERY "?" so it's clear to a layperson and correct per objective (including HPV) | |
| The reader is not a cancer expert or an ML expert. Every tooltip and every click-to-open modal must explain its concept in plain English, define any term it uses, and read correctly for whichever objective/dataset is active. | |
| Where the copy lives (read all of these): | |
| - `web/app/Lab.tsx` — the `TIPS` record (short InfoTip strings), `FITNESS_TIP_BY_TARGET`, `FITNESS_LABEL_BY_TARGET`, and every inline `tip=` / `<InfoTip>` usage (objective cards, parameters, run/live/result/evaluator labels, discovered-axes, rank panels). | |
| - `web/app/paramHelpContent.tsx` — `PARAM_TIPS` (short + detailed), the objective modals `obj_msi`, `obj_tmb`, `obj_unsupervised`, `obj_hpv`, and the shared `ObjectiveIntro` / `ObjectiveFooter` / breakdown components. | |
| Requirements: | |
| - **Plain language.** No undefined jargon. If a term is unavoidable (AUROC, permutation, held-out, silhouette, residualise), give a one-line plain gloss in the same tip — e.g. "held-out = patients the engine never saw during the search, used to check the result isn't a fluke." | |
| - **Objective- and dataset-aware.** Any tip shown during an HPV run must talk about HPV+/HPV− separation, not MSI or TMB. Sweep for tips that hardcode MSI/TMB wording and make them branch on the active objective (the per-target records already exist for the fitness curve — extend the same pattern wherever a result/verdict/axis/chart tip is objective-specific). Confirm each of the four objectives (MSI, TMB, Unsupervised, HPV) shows tips that match what that run actually produces. | |
| - **HPV specifically.** The HPV "?" should make clear, in plain words: the engine is *detecting a known viral signature* (high CDKN2A/p16 and the cell-cycle program the virus switches on), not discovering new causation — the cause is the virus itself. Keep `obj_hpv` consistent with that. | |
| - Keep tone and length consistent with the existing good tips; don't bloat. | |
| ## 2. Never write in all caps (anywhere in the Lab UI) | |
| All-caps text is currently produced two ways — fix both: | |
| - **Tailwind `uppercase` classes.** In `web/app/Lab.tsx` there are many label/eyebrow elements using `uppercase tracking-wide` (e.g. lines ~1757, 1799, 1850, 2110, 2119, 2248, 2290, 2298, 2342, 2386, 2394, 2436 — and any others). Remove the `uppercase` utility from every one so labels render in their natural case. Keep `tracking-wide`/sizing if you like, just drop the uppercasing. Then make sure the underlying strings read well in sentence case (e.g. "Held-out", "Permutation p", "Revealed genes", "Winning program", "Post-hoc alignment", "Opaque ID", "Symbol", "Discovered axes", "Paste a program", "Nodes", "Genes"). | |
| - **`textTransform: "uppercase"`** in `web/app/ProgramGraph.tsx` (~line 196, the Tier label). Remove it; the labels are already literal strings "Tier-1" / "Tier-2 program" — render them as-is (Title case), not uppercased. | |
| - Grep the whole `web/app` tree for any remaining `uppercase` class, `textTransform`, or literal ALL-CAPS string constants in UI copy and convert them to sentence/Title case. No visible UI text should be all-caps after this. | |
| ## 3. Fix the program graph being clipped | |
| Symptom (see screenshot): for a two-tier (`Combine`) program the dashed "Tier-2 program" wrapper and the lower "Tier-1" group are cut off — the graph overflows on the right and the bottom is sliced by the "Paste a program" section. | |
| In `web/app/ProgramGraph.tsx` (the `ProgramGraph` component, ~lines 725-760) and `ProgramGraph.css`: | |
| - The container height is `Math.max(220, height)` where `height` is the laid-out bounding box. Confirm that `height` for the `Combine`/Tier-2 case includes the full Tier-2 wrapper (label padding + both Tier-1 lanes + the Combine/Output column). If the wrapper's bbox isn't fully accounted for, the container is too short and clips the bottom. | |
| - `fitView` only fits on first mount; when the selected program changes (winner ↔ candidate, or a paste) it doesn't re-fit, so a larger graph overflows instead of scaling down. Make `fitView` re-run whenever the program changes — e.g. give `<ReactFlow>` a `key` derived from the program (so it remounts), or call `fitView()` from an `onInit`/effect keyed on `props`. | |
| - The `minZoom={0.4}` floor stops `fitView` from shrinking a large 2-tier graph enough to fit, so it clips. Lower the floor (e.g. `minZoom={0.2}`) so the whole graph always scales to fit the card width. | |
| - Ensure the card/section wrapping the graph has no fixed height or `overflow: hidden` that crops it, and that there's vertical separation from the "Paste a program" block below. | |
| Result: the entire program (both tiers, all Select/Reduce/Combine/Split nodes) is always fully visible inside the card, scaled to fit, for single-tier and two-tier programs alike. | |
| ## Checkpoint | |
| - Every "?" reads in plain English and is correct for each of the four objectives; an HPV run shows HPV-framed tips (no MSI/TMB leftovers). | |
| - No all-caps text anywhere in the Lab. | |
| - A two-tier program renders fully inside the Program graph card with nothing clipped; switching candidates re-fits. | |
| - `tsc` clean; colorectal/HPV runs and airgap tests unaffected. | |