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| # Prompt — colour-code reference genes in Coordinated modules + fix missing symbols | |
| Two presentation fixes to the Coordinated-modules table. Verified against the code: `_compute_module_ranking` (api/app.py ~lines 1244–1457) returns each module as `{gene_ids (opaque), size, combined_holdout, coherence, per_gene:[{id,single_gene_metric,rank,total}]}` — **opaque IDs only, no symbols and no reference-set flag**. The table's "—" cells are module genes that were never revealed (e.g. `g09647` = LIG1); they resolve fine (HNSC reuses the single colorectal sealed map, its genes a subset), they're just not fetched. Read the current `_compute_module_ranking` and the modules UI component first. Airgap stays absolute; `pytest`/`tsc` after. | |
| ## 1. Flag + colour-code reference-set membership on EVERY module row (so no expanding needed) | |
| - In `_compute_module_ranking`, resolve the **active dataset's reference sets** to opaque IDs ONCE (HNSC → `p16`={CDKN2A}, `cell_cycle`=the 20-gene set; CRC → `MMR`, `immune`). Reuse the existing reference→opaque resolution already used by `/diagnostic/full-rank` (its `reference_marks`) / the highlighted-genes table — don't re-implement. This is a bounded reveal of a known small set, not the whole map. | |
| - For each module add `ref_sets: list[str]` = the reference-set names whose opaque IDs intersect that module's `gene_ids` (e.g. `["cell_cycle"]`, `["p16","cell_cycle"]`, or `[]`). | |
| - Frontend modules table: on each **collapsed** row, render a small badge per matched set and tint the row using the existing three-way colour scheme (winner accent / p16 deep-gold / cell_cycle muted-amber — the same palette the highlighted-genes table uses). A module containing a p16 or cell_cycle gene must be scannable in the ranked list without expanding it. | |
| - Airgap note: only a boolean membership (derived from the bounded reference reveal) crosses the wire here — no module gene NAMES are sent for the collapsed list. | |
| ## 2. Fix the missing symbols ("—") on expand | |
| - The per-gene `symbol` is blank because module genes outside the already-revealed subset are never translated. When a module is **expanded**, reveal that module's `gene_ids` via the existing `/reveal` endpoint (bounded — only that module's ~2–5 genes) and show the symbol on each per-gene row. `g09647` should then read **LIG1**. | |
| - Reveal **lazily, per expanded module only**. Do NOT reveal all modules' genes up front — there are ~2,900 modules and that would approach translating the whole map (airgap violation). | |
| - Keep the per-gene single-gene AUROC / rank already returned; just add the revealed symbol alongside. Where a gene has no rank (not in the diagnostic series) leave its metric blank but still show its symbol. | |
| ## CONSTRAINTS | |
| - Airgap: reference-membership flag = bounded reference-set reveal; per-module symbols = bounded on-expand reveal. Never translate the full map; the collapsed ranking stays opaque + scores + ref_sets booleans. | |
| - No change to module harvesting, scoring, or sorting — purely additive (ref_sets field + lazy symbol reveal + row colouring). | |
| ## Checkpoint | |
| - Collapsed module rows show a p16 / cell_cycle (or MMR / immune) badge and matching row tint wherever the module contains such a gene — visible without expanding. | |
| - Expanding any module shows a symbol for every gene (e.g. LIG1), no "—". | |
| - Ranking payload stays opaque + ref_sets booleans; symbols revealed only for expanded modules; airgap tests green; `tsc`/`pytest` clean. | |