Julenmendieta/MILAB-6617_adaptToSingleCellVhh

[julenmendieta]

Greptile Summary

This PR fixes a workflow crash on VHH (heavy-chain-only) single-cell IG datasets where the chain selector previously offered "Light" even when no light-chain columns existed. A new model output availableScChains reports which chain letters actually have V-gene columns; the UI chain selector is filtered to that set and hidden when only one chain is present.

• model/src/index.ts — Adds the availableScChains output, which inspects pl7.app/vdj/geneHit / VGene columns for the primary chain index to detect which chains have real data; returns undefined (no filter) for bulk and non-IG datasets.
• ui/src/utils.ts — useScChainOptions gains a second availableChains argument and filters the receptor-derived options list, falling back to the full list while the output is still resolving (undefined).
• ui/src/pages/Settings.vue — The chain PlBtnGroup is now hidden when scChainOptions?.length ≤ 1, removing the user's ability to pick an invalid chain.

Confidence Score: 3/5

The chain selector is correctly hidden for VHH datasets, but the underlying scChain model field can remain stale when a user switches from a paired IG dataset to a VHH one, leaving the backend to fail with the same error the PR set out to fix.

The new availableScChains output and option-filtering logic are sound. The gap is in Settings.vue and app.ts: hiding the UI control does not reset model.data.scChain, so an existing block with Light chain (B) previously selected will still send B to the workflow after a VHH dataset is chosen.

ui/src/pages/Settings.vue and ui/src/app.ts — no auto-reset of model.data.scChain when the available chain list narrows to a single entry.

Important Files Changed

Filename	Overview
model/src/index.ts	Adds availableScChains output that probes the result pool for V-gene columns per chain; logic looks correct for the IG/VHH case, and the output correctly returns undefined for resolving/empty pool states which is handled upstream in the UI.
ui/src/utils.ts	Refactors useScChainOptions to accept and filter by availableChains; fall-through for undefined (resolving) is handled; TCR path is unaffected since availableScChains returns undefined for non-IG.
ui/src/pages/Settings.vue	Hides the chain selector when scChainOptions?.length ≤ 1, but does not reset model.data.scChain when a dataset switch leaves a stale chain value that will fail the backend workflow.
ui/src/app.ts	Passes availableScChains to useScChainOptions for label-generation use; no auto-reset logic added for the scChain data field.
.changeset/vhh-presence-driven-chain-menu.md	Accurate patch changeset entry describing the bug and the fix.

Sequence Diagram

%%{init: {'theme': 'neutral'}}%%
sequenceDiagram
    participant UI as Settings.vue
    participant Utils as utils.ts (useScChainOptions)
    participant Model as model/index.ts (availableScChains)
    participant Pool as ResultPool

    UI->>Model: reads availableScChains output
    Model->>Pool: getPColumnSpecByRef(datasetRef)
    alt spec is not SC-IG
        Model-->>UI: undefined (no filtering)
    else spec is SC-IG
        Model->>Pool: getAnchoredPColumns(VGene / primary index)
        alt pool still resolving
            Pool-->>Model: undefined
            Model-->>UI: undefined (no filtering)
        else columns available
            Pool-->>Model: [col_A, col_B, ...]
            Model->>Model: collect chain letters from domain
            Model-->>UI: ["A"] or ["A","B"]
        end
    end
    UI->>Utils: useScChainOptions(datasetSpec, availableScChains)
    Utils->>Utils: build full receptor options (IG to Heavy/Light)
    alt availableScChains is undefined
        Utils-->>UI: full options list (fallback)
    else availableScChains is []
        Utils-->>UI: [] (hidden, nothing to pick)
    else availableScChains is ["A"]
        Utils-->>UI: "[{Heavy, A}] (hidden, only one chain)"
    else availableScChains is ["A","B"]
        Utils-->>UI: "[{Heavy,A},{Light,B}] (shown)"
    end
    UI->>UI: "v-if length > 1, show/hide PlBtnGroup"
    Note over UI: scChain in model.data is NOT reset when selector is hidden

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sequenceDiagram
    participant UI as Settings.vue
    participant Utils as utils.ts (useScChainOptions)
    participant Model as model/index.ts (availableScChains)
    participant Pool as ResultPool

    UI->>Model: reads availableScChains output
    Model->>Pool: getPColumnSpecByRef(datasetRef)
    alt spec is not SC-IG
        Model-->>UI: undefined (no filtering)
    else spec is SC-IG
        Model->>Pool: getAnchoredPColumns(VGene / primary index)
        alt pool still resolving
            Pool-->>Model: undefined
            Model-->>UI: undefined (no filtering)
        else columns available
            Pool-->>Model: [col_A, col_B, ...]
            Model->>Model: collect chain letters from domain
            Model-->>UI: ["A"] or ["A","B"]
        end
    end
    UI->>Utils: useScChainOptions(datasetSpec, availableScChains)
    Utils->>Utils: build full receptor options (IG to Heavy/Light)
    alt availableScChains is undefined
        Utils-->>UI: full options list (fallback)
    else availableScChains is []
        Utils-->>UI: [] (hidden, nothing to pick)
    else availableScChains is ["A"]
        Utils-->>UI: "[{Heavy, A}] (hidden, only one chain)"
    else availableScChains is ["A","B"]
        Utils-->>UI: "[{Heavy,A},{Light,B}] (shown)"
    end
    UI->>UI: "v-if length > 1, show/hide PlBtnGroup"
    Note over UI: scChain in model.data is NOT reset when selector is hidden

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Prompt To Fix All With AI

Fix the following 1 code review issue. Work through them one at a time, proposing concise fixes.

---

### Issue 1 of 1
ui/src/pages/Settings.vue:36-40
**Stale `scChain` survives a dataset switch**

Hiding the selector prevents picking an invalid chain for new configurations, but `model.data.scChain` is never reset when the available-chains list narrows. If a user previously selected `"B"` (Light) on a paired IG dataset and then switches to a VHH dataset, `scChain` stays `"B"`, the `PlBtnGroup` is hidden (nothing to correct it), and the backend workflow receives a chain letter with no columns — reproducing the original "expected exactly 1 V gene column for chain, got 0" error.

The default in `initData` is `"A"`, so fresh blocks are safe; the failure only appears when a user changes the dataset reference on an existing block that had the Light chain selected. A `watchEffect` in `app.ts` that sets `model.data.scChain` to `scChainOptions.value[0].value` whenever the option list resolves to exactly one entry would close this gap.

_{Reviews (1): Last reviewed commit: "Changeset" | Re-trigger Greptile}

Greptile also left 1 inline comment on this PR.

Context used:

• Context used - Terms is a types in codebase. Provide the list of ... (source)

[gemini-code-assist]

Code Review

This pull request dynamically filters single-cell chain options based on the columns present in the selected dataset, hiding the selector when only one chain is available. Feedback points out a potential runtime TypeError in model/src/index.ts due to inconsistent null-checking of spec, and a stale state issue in ui/src/app.ts when switching datasets, suggesting a watchEffect to automatically update the selected chain.

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