Add Compound proteinIdType and entity-agnostic grounding for metabolite networks

[swaraj-neu]

Add Compound proteinIdType and entity-agnostic grounding columns:
Generalize the protein-only HgncId/HgncName contract into EntityNamespace/EntityId/EntityName grounded through Gilda, keeping multi-grounding as semicolon-joined aligned lists that fan out into the INDRA query. Gene-only annotations are skipped for compounds, and the new contract flows through annotateProteinInfoFromIndra, getSubnetworkFromIndra, and cytoscapeNetwork.

Motivation and Context

Please include relevant motivation and context of the problem along with a short summary of the solution.

Changes

Please provide a detailed bullet point list of your changes.

Testing

Please describe any unit tests you added or modified to verify your changes.

Checklist Before Requesting a Review

• I have read the MSstats contributing guidelines
• My changes generate no new warnings
• Any dependent changes have been merged and published in downstream modules
• Ran styler::style_pkg(transformers = styler::tidyverse_style(indent_by = 4))
• Ran devtools::document()

[coderabbitai]

Warning

Review limit reached

@swaraj-neu, we couldn't start this review because you've reached your PR review rate limit.

More reviews will be available in 39 minutes and 58 seconds. Learn how PR review limits work.

Your organization has run out of usage credits. Purchase more in the billing tab.

⌛ How to resolve this issue?

After more reviews become available, a review can be triggered using the @coderabbitai review command as a PR comment. Alternatively, push new commits to this PR.

We recommend that you space out your commits to avoid hitting the rate limit.

🚦 How do rate limits work?

CodeRabbit enforces hourly rate limits for each developer per organization.

Our paid plans include higher PR review limits than trial, open-source, and free plans. In all cases, reviews become available again over time. During sustained high-volume PR review activity, CodeRabbit may temporarily slow when the next review becomes available.

Please see our Fair Usage Limits Policy for further information.

ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: fbdf590d-d363-4556-8c30-1a03c1ac0a8c

📥 Commits

Reviewing files that changed from the base of the PR and between d1e6219 and 24fff4a.

⛔ Files ignored due to path filters (2)

• inst/extdata/groupComparisonModel.csv is excluded by !**/*.csv
• inst/extdata/groupComparisonModel_compound.csv is excluded by !**/*.csv

📒 Files selected for processing (30)

• R/annotateProteinInfoFromIndra.R
• R/cytoscapeNetwork.R
• R/getSubnetworkFromIndra.R
• R/utils_annotateProteinInfoFromIndra.R
• R/utils_cytoscapeNetwork.R
• R/utils_getSubnetworkFromIndra.R
• man/annotateProteinInfoFromIndra.Rd
• man/cytoscapeNetwork.Rd
• man/dot-populateEntityIdsInDataFrame.Rd
• man/dot-populateEntityNamesInDataFrame.Rd
• man/dot-populateHgncIdsInDataFrame.Rd
• man/dot-populateHgncNamesInDataFrame.Rd
• man/dot-populateKinaseInfoInDataFrame.Rd
• man/dot-populatePhophataseInfoInDataFrame.Rd
• man/dot-populateTranscriptionFactorInfoInDataFrame.Rd
• man/dot-populateUniprotIdsInDataFrame.Rd
• man/dot-validateAnnotateProteinInfoFromIndraInput.Rd
• man/exportNetworkToHTML.Rd
• man/getSubnetworkFromIndra.Rd
• man/previewNetworkInBrowser.Rd
• tests/testthat/test-annotateProteinInfoFromIndra.R
• tests/testthat/test-exportNetworkToHTML.R
• tests/testthat/test-getSubnetworkFromIndra.R
• tests/testthat/test-multi-grounding.R
• tests/testthat/test-utils_annotateProteinInfoFromIndra.R.R
• tests/testthat/test-utils_cytoscapeNetwork.R
• tests/testthat/test-utils_getSubnetworkFromIndra.R
• vignettes/Cytoscape-Visualization.Rmd
• vignettes/MSstatsBioNet.Rmd
• vignettes/PTM-Analysis.Rmd

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch MSstatsBioNet/work/20260528_compound-id-type

---

Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out.

❤️ Share

• X
• Mastodon
• Reddit
• LinkedIn

_{Comment @coderabbitai help to get the list of available commands and usage tips.}

[codecov-commenter]

Codecov Report

❌ Patch coverage is 92.40506% with 12 lines in your changes missing coverage. Please review.
✅ Project coverage is 77.13%. Comparing base (d1e6219) to head (24fff4a).

Files with missing lines	Patch %	Lines
R/utils_getSubnetworkFromIndra.R	85.71%	9 Missing ⚠️
R/utils_annotateProteinInfoFromIndra.R	90.00%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##            devel     #105      +/-   ##
==========================================
+ Coverage   75.35%   77.13%   +1.77%     
==========================================
  Files           9        9              
  Lines        1047     1124      +77     
==========================================
+ Hits          789      867      +78     
+ Misses        258      257       -1     

☔ View full report in Codecov by Harness.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[swaraj-neu]

@coderabbitai review

[coderabbitai]

✅ Action performed

Review finished.

Note: CodeRabbit is an incremental review system and does not re-review already reviewed commits. This command is applicable only when automatic reviews are paused.