Julenmendieta/milab 6505 user error

[julenmendieta]

Greptile Summary

This PR introduces a versioned block-kind contract and template parameter round-trip, adds the selected target column to generated labels and output traces, and upgrades the supporting Platforma SDK toolchain.

• BlockParams — Optional initialization parameters accepted from block templates; newly defined and runtime-validated in the kind package.
• Settings — Matching mode plus identity and coverage thresholds; moved to the kind-level contract and reused by the model.
• Modality — The antibody_tcr or peptide dataset classification; moved to the shared kind contract and retained in templates to preserve modality-aware defaults.
• BlockData — Persisted editable state for the block; extended with targetColumnLabel and initialized from template parameters.
• targetColumnLabel — Display label for the selected target sequence column; newly persisted, included in templates, and added to default block labels.
• templateParams — Portable projection of persisted block state; newly exports configuration while omitting machine-local upload handles and their dependent file fields.
• Block kind — Versioned runtime identity and initialization contract for the block; added as a new workspace package and wired into the model.
• Trace label — User-facing provenance label attached to exported results; now consistently uses the custom block label or model-derived default label.

Confidence Score: 4/5

The template settings guard should enforce supported threshold bounds before this PR is merged, because invalid template values currently reach the alignment workflow.

The new runtime initialization contract checks threshold types but not the same 0.1–1.0 bounds enforced by the UI, allowing template-created configurations to pass unsupported values into alignment processing.

Files Needing Attention: kind/src/index.ts

Important Files Changed

Filename	Overview
kind/src/index.ts	Adds the versioned initialization contract, but its settings guard permits threshold values outside the range supported by the UI and workflow.
model/src/index.ts	Wires the block kind into the model, initializes and exports template parameters, and derives labels containing the target-column label.
model/src/types.ts	Reuses kind-owned Settings and Modality types and extends persisted state with the target-column label.
ui/src/pages/MainPage.vue	Uses the shared label derivation and mirrors the selected target option's display label into persisted state.
workflow/src/build-outputs.tpl.tengo	Simplifies trace labeling to use the custom label or the model-derived default.
workflow/src/main.tpl.tengo	Removes the now-unused matching settings from output-template inputs.
pnpm-workspace.yaml	Registers the kind workspace and upgrades the SDK and builder catalog versions needed for block-kind support.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart LR
  T[Template parameters] --> K[Block kind parser]
  K --> D[Initialized BlockData]
  UI[Vue configuration UI] --> D
  D --> A[Validated workflow arguments]
  D --> L[Derived block label]
  A --> W[Assay workflow]
  L --> W
  W --> O[Tables, linker, and traced export]
  D --> P[Portable templateParams]
  P --> T

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

Greptile also left 1 inline comment on this PR.

Context used (5)

• Knowledge Base — Assay domain model
• Knowledge Base — Interactive assay interface
• Knowledge Base — Platform block integration
• Knowledge Base — Assay workflow orchestration
• Knowledge Base — Workflow output processing

[greptile-apps]

Threshold bounds are unenforced

When a hand-written or externally generated template supplies identity or coverageThreshold outside 0.1–1.0, isSettings accepts it and the model forwards it unchanged to alignment processing, causing invalid matching behavior or a failed run.

Suggested change

	const isSettings: Guard<Settings> = (v): v is Settings =>
	isPlainObject(v) &&
	isNumber(v.coverageThreshold) &&
	isNumber(v.identity) &&
	SIMILARITY_TYPES.includes(v.similarityType as Settings["similarityType"]);
	const isSettings: Guard<Settings> = (v): v is Settings =>
	isPlainObject(v) &&
	isNumber(v.coverageThreshold) &&
	v.coverageThreshold >= 0.1 &&
	v.coverageThreshold <= 1 &&
	isNumber(v.identity) &&
	v.identity >= 0.1 &&
	v.identity <= 1 &&
	SIMILARITY_TYPES.includes(v.similarityType as Settings["similarityType"]);

Knowledge Base Used: Assay domain model

[AStaroverov]

agree