Task 2

[Rudhik1904]

Motivation and Context

Protein turnover analyses require consistent tracer constants across validation, ratio calculation, generated scripts, and stored results. The previous per-condition input model could produce stale or mismatched values.

This change adds an optional tracer-constants CSV upload with validation, lifecycle tracking, provenance handling, and generated-script support.

Changes

• Added tracer-constants UI identifiers and status constants.
• Replaced per-condition tracer inputs with one optional CSV upload.
• Added validation for file readability, schema, numeric ranges, condition mapping, timepoint compatibility, and misleading units.
• Added upload states: absent, pending, rejected, and valid.
• Snapshotted validated tracer constants when the user runs an analysis.
• Cleared snapshots when the upload, template, or condition metadata became invalid.
• Passed tracer constants from qcServer to statmodelServer.
• Used the same tracer-constant snapshot for turnover calculations, displayed ratios, downloads, and generated scripts.
• Added provenance comments and validation for generated turnover scripts.
• Restored the complete MSstatsConvert import.
• Updated package ignore rules for planning files, logs, root-level CSV files, and .github.
• Updated qcServer and statmodelServer documentation.

Unit Tests

• Added tests for tracer-constants upload validation and state transitions.
• Added tests for range checks, condition matching, timepoint parsing, and misleading units.
• Added tests for default and resolved tracer constants.
• Added tests for tracer constants reaching turnover calculations.
• Added tests for provenance comments in generated scripts.
• Added lifecycle regression tests for snapshot clearing and consistency with calculated ratios.
• Updated QC UI tests for tracer-constants controls.
• Replaced legacy per-condition test inputs with snapshot-based inputs.
• Removed outdated statmodel forwarding tests.

Coding Guidelines

No coding guideline violations were identified in the provided changes.

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ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro Plus

Run ID: f272c023-4e4d-48a3-bf56-d6c5534fc85f

📥 Commits

Reviewing files that changed from the base of the PR and between c409f28 and 67e9157.

📒 Files selected for processing (1)

• R/qc-server-turnover.R

💤 Files with no reviewable changes (1)

• R/qc-server-turnover.R

Included review availability: Your plan provides up to 1 included review per hour; 0 remain after this review.

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📝 Walkthrough

Walkthrough

The PR adds optional tracer-constants CSV upload for protein turnover. It validates and snapshots constants, applies them to turnover calculations, exposes provenance to statistical-model code generation, and adds lifecycle and serialization tests.

Changes

Tracer constants workflow

Layer / File(s)	Summary
Tracer contracts and validation R/constants.R, R/qc-server-data-upload.R, tests/testthat/test-qc-data-upload.R	Defines tracer-constant states, bounds, schemas, condition matching, timepoint validation, defaults, and resolution behavior.
Upload and turnover lifecycle R/qc-server-turnover.R, R/module-qc-server.R, R/module-qc-ui.R, tests/testthat/test-module-turnover.R	Adds upload states, validation observers, panel status, run-time gating, turnover integration, snapshot lifecycle handling, and UI tests.
Analysis-code propagation and provenance R/module-statmodel-server.R, R/server.R, R/statmodel-server-download-code.R, tests/testthat/test-module-statmodel-server.R, tests/testthat/test-module-turnover.R	Passes tracer snapshots into analysis-code generation, validates serialized constants, and emits provenance comments.
Package wiring and API documentation .Rbuildignore, .gitignore, NAMESPACE, man/*.Rd, tests/testthat/test-module-qc-ui.R	Updates package ignore rules, imports, module documentation, and UI structure tests.

Estimated code review effort: 4 (Complex) | ~45 minutes

Merge Risk: ⚪ Minimal · up to 67e91

No actionable merge-blocking risk remains; the PR is merge-ready after normal checks and review.

Sequence Diagram(s)

sequenceDiagram
  participant User
  participant register_qc_turnover
  participant qc_resolve_tracer_constants
  participant calculateTurnoverRatios
  participant generate_analysis_code
  User->>register_qc_turnover: Upload tracer constants and run
  register_qc_turnover->>qc_resolve_tracer_constants: Validate and resolve values
  register_qc_turnover->>calculateTurnoverRatios: Pass resolved constants
  calculateTurnoverRatios-->>register_qc_turnover: Return ratios
  register_qc_turnover->>generate_analysis_code: Pass snapshot and provenance
  generate_analysis_code-->>User: Provide turnover analysis script

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Suggested reviewers: tonywu1999

Poem

A rabbit uploads constants with care
Validation checks each value there
Ratios run with names in line
Provenance marks the script design
Fresh snapshots keep results fair

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 inconclusive)

Check name	Status	Explanation	Resolution
Title check	❓ Inconclusive	The title "Task 2" is too generic and does not identify the tracer-constants CSV upload or related protein-turnover changes.	Replace the title with a concise, specific summary such as "Add tracer constants CSV upload for protein turnover".

✅ Passed checks (4 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check. Docstring coverage is scoped to functions touched by this diff. Analyzed 0 functions across 0…
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

Full details: Docstring Coverage

Explanation

No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check. Docstring coverage is scoped to functions touched by this diff. Analyzed 0 functions across 0 files. (1 skipped: 1 unsupported.)

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch feat/tracer-constants-file-upload

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