fix protein turnover download zipfile

[tonywu1999]

Motivation and Context

Protein turnover plot downloads lacked the turnover_ratios reactive required by response-curve templates, causing zipfile download behavior to fail. The download handler now receives this reactive explicitly.

Changes

• Added turnover_ratios to create_download_plot_handler() as an optional reactive argument.
• Passed turnover_ratios from statmodelServer into the download handler.
• Preserved a reactive(NULL) default for compatibility.
• Updated the initialization test to expect nine handler arguments.

Unit Tests

• Modified test-module-statmodel-server.R to verify the updated nine-argument handler initialization.

Coding Guidelines

• No coding guideline violations identified.

[coderabbitai]

📝 Walkthrough

Walkthrough

The plot download handler now accepts a turnover_ratios reactive, statmodelServer passes it during initialization, and the corresponding test expects the additional argument.

Changes

Plot download handler input wiring

Layer / File(s)	Summary
Handler contract and server wiring R/statmodel-server-visualization.R, R/module-statmodel-server.R, tests/testthat/test-module-statmodel-server.R	create_download_plot_handler accepts turnover_ratios, the server passes the reactive, and the initialization test expects nine arguments.

Estimated code review effort: 1 (Trivial) | ~5 minutes

Possibly related PRs

• Vitek-Lab/MSstatsShiny#155: Introduced the related plot download handler wiring.
• Vitek-Lab/MSstatsShiny#174: Updated related download-handler inputs for response-curve behavior.

Suggested reviewers: swaraj-neu, rudhik1904, deril2605

Poem

A bunny wired the ratios in,
So plots can hop when downloads begin.
The handler counts one more thread,
Tests nod their ears: “Well fed!”
Response curves bounce ahead.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title is concise and matches the main change: fixing the protein turnover download zipfile behavior.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
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.

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch fix-turnover

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[coderabbitai]

🧹 Nitpick comments (1)

tests/testthat/test-module-statmodel-server.R (1)

784-785: 📐 Maintainability & Code Quality | 🔵 Trivial | ⚡ Quick win

Assert the new reactive arguments, not only the count.

length(handler_args) == 9 still passes if turnover_ratios and condition_metadata are swapped or replaced. Pass distinct sentinel reactives and verify positions 8 and 9 (or capture named arguments) so this test covers the wiring this PR changes.

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@tests/testthat/test-module-statmodel-server.R` around lines 784 - 785,
Strengthen the test around create_download_plot_handler by supplying distinct
sentinel reactives for turnover_ratios and condition_metadata, then assert that
handler_args positions 8 and 9 contain the corresponding reactives rather than
only checking the argument count. Preserve the existing nine-argument assertion
while verifying the changed wiring.

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Nitpick comments:
In `@tests/testthat/test-module-statmodel-server.R`:
- Around line 784-785: Strengthen the test around create_download_plot_handler
by supplying distinct sentinel reactives for turnover_ratios and
condition_metadata, then assert that handler_args positions 8 and 9 contain the
corresponding reactives rather than only checking the argument count. Preserve
the existing nine-argument assertion while verifying the changed wiring.

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 6ff26d83-5726-4d58-9f1a-b42bc7c2e872

📥 Commits

Reviewing files that changed from the base of the PR and between f8f426b and f2231ee.

📒 Files selected for processing (3)

• R/module-statmodel-server.R
• R/statmodel-server-visualization.R
• tests/testthat/test-module-statmodel-server.R