Julenmendieta/MILAB 6793 cleanUI

[julenmendieta]

Greptile Summary

This PR streamlines the feature-integration UI terminology and removes the duplicate sample-status column from the wide QC table while retaining the canonical rollup in each sample report.

• Renames navigation, page headings, settings labels, and explanatory copy around sample QC, tag QC, cell counts, and clonotype binding.
• Removes the QC summary's duplicated status column, column specification, and custom renderer.
• Filters zero-valued read-recovery chart segments and updates tests for the revised QC table contract.
• Important touched terms:
  • Sample QC — per-sample read and processing measurements; renamed from “Per-sample QC,” with the wide table now containing measurements but no duplicated rollup column.
  • Quality rollup — the worst judged status among a sample's measurements; retained in sampleQcReport for the Main grid and sample detail, but removed from the wide QC table.
  • Tag QC — reagent/tag-level quality measurements and distributions; replaces the “Run quality” navigation terminology, with “Per-tag QC” used as the page heading.
  • Cell counts — per-cell feature-barcode measurements; replaces “Per-cell results” in navigation and “Per-cell tag counts” in the page heading.
  • Clonotype binding — the clonotype-by-antigen verdict surface previously called “Explore readout”; the page heading now reads “Clonotype tag binding.”
  • Baseline source — the comparator used to determine binding; its declared-control and per-tag-distribution descriptions are simplified.
  • Agreement threshold — the minimum cell-vote agreement needed for a settled clonotype verdict; the UI label and minimum were changed to 51%, although execution still supports fractional values immediately above 50%.
  • Read recovery — the split between usable, off-panel, and pattern-unmatched reads; zero-valued chart segments are now omitted.

Confidence Score: 4/5

The PR appears safe to merge after addressing two non-blocking UI contract inconsistencies in the QC copy and agreement-threshold range.

The status-column removal is internally coordinated across generation, import, and rendering, but one message still promises the removed field, and the agreement control no longer exposes the model's complete valid range.

Files Needing Attention: ui/src/pages/QcSummaryPage.vue, ui/src/pages/MainPage.vue

Important Files Changed

Filename	Overview
software/per-cell-metrics/src/qc_rows.py	Removes the duplicated sample rollup from the wide QC CSV while preserving all sample measurement columns.
workflow/src/column-specs.lib.tengo	Removes the corresponding sampleStatus import specification so the workflow contract matches the generated CSV.
ui/src/pages/QcSummaryPage.vue	Removes the status renderer, but leaves empty-state copy incorrectly promising a rolled-up status column.
ui/src/pages/MainPage.vue	Simplifies labels and tooltips, but narrows the agreement control beyond the range accepted by the model and workflow.
ui/src/results.ts	Omits zero-valued read-recovery segments; no concrete rendering failure was established.
model/src/index.ts	Updates baseline guidance and top-level navigation labels without changing the underlying output routes.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart LR
  Reads[Feature-barcode reads] --> SampleQC[Sample QC measurements]
  SampleQC --> WideTable[Sample QC table]
  SampleQC --> Report[Canonical sample report]
  Report --> Main[Main Quality tag]
  Report --> Detail[Sample Quality Checks]
  Counts[Per-cell tag counts] --> Cells[Cell counts]
  Counts --> Verdicts[Clonotype binding]
  Verdicts --> TagQC[Tag QC]

Loading

Prompt To Fix All With AI

### Issue 1
ui/src/pages/QcSummaryPage.vue:27-28
**QC copy promises removed status**

The empty state says this table will carry each sample's rolled-up status, but this change removes that field from both the generated summary and its import specification. Users are therefore promised a status column that never appears.

### Issue 2
ui/src/pages/MainPage.vue:1028-1033
**Agreement range excludes valid values**

The new 51% minimum excludes fractional thresholds between 50% and 51%, even though model validation accepts every value strictly above 50% and the workflow compares the exact fraction. This prevents the settings control from representing the full execution-supported range, including stored values such as 50.5%.

```suggestion
            :min-value="50.001"
            :max-value="100"
            :step="1"
            clearable
            placeholder="50"
            label="Min agreement (>50%)"
```

---

For each issue above, determine whether it is valid and should be fixed. If so, fix it directly.

_{Reviews (1): Last reviewed commit: "Label renaming and code cleaning" | Re-trigger Greptile}

Greptile also left 1 inline comment on this PR.

Context used (5)

• Context used - Terms is a types in codebase. Provide the list of ... (source)
• Knowledge Base — Feature integration workflow
• Knowledge Base — Integration domain model
• Knowledge Base — Feature integration user interface
• Knowledge Base — UI progress and results

[greptile-apps]

Agreement range excludes valid values

The new 51% minimum excludes fractional thresholds between 50% and 51%, even though model validation accepts every value strictly above 50% and the workflow compares the exact fraction. This prevents the settings control from representing the full execution-supported range, including stored values such as 50.5%.

Suggested change

	:min-value="51"
	:max-value="100"
	:step="1"
	clearable
	label="Min agreement (>50%)"
	placeholder="50"
	label="Min agreement (≥51%)"
	:min-value="50.001"
	:max-value="100"
	:step="1"
	clearable
	placeholder="50"
	label="Min agreement (>50%)"

Prompt To Fix With AI

This is a comment left during a code review.
Path: ui/src/pages/MainPage.vue
Line: 1028-1033

Comment:
**Agreement range excludes valid values**

The new 51% minimum excludes fractional thresholds between 50% and 51%, even though model validation accepts every value strictly above 50% and the workflow compares the exact fraction. This prevents the settings control from representing the full execution-supported range, including stored values such as 50.5%.

```suggestion
            :min-value="50.001"
            :max-value="100"
            :step="1"
            clearable
            placeholder="50"
            label="Min agreement (>50%)"
```

---

For each issue above, determine whether it is valid and should be fixed. If so, fix it directly.