fix(getSubnetworkFromIndra): Fix bugs related to multiple matches for an HGNC ID

[tonywu1999]

User description

Motivation and Context

Got this error [Error in vapply ... values must be length 1, but FUN(X[[1]]) result is length 0](https://stackoverflow.com/questions/42426914/error-in-vapply-values-must-be-length-1-but-funx11-result-is-length-0)

Changes

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Testing

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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()

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PR Type

Bug fix, Tests

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Description

• Fixed handling of multiple matches for HGNC IDs in getSubnetworkFromIndra.

• Improved error handling for invalid UniProt mnemonic ID inputs.

• Enhanced unit tests to validate new error messages and edge cases.

• Updated error messages for clarity and user guidance.

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Changes walkthrough 📝

	Relevant files
Bug fix	utils_annotateProteinInfoFromIndra.R Enhanced error handling for UniProt mnemonic ID inputs      R/utils_annotateProteinInfoFromIndra.R Added error handling for converting non-character inputs to character. Improved validation of UniProt mnemonic ID inputs. Introduced tryCatch to handle conversion errors gracefully. +18/-4    utils_getSubnetworkFromIndra.R Fixed HGNC ID matching and improved error messages              R/utils_getSubnetworkFromIndra.R Fixed logic for matching HGNC IDs to ensure unique matches. Added error message for multiple or zero matches in input data. Updated error message for input size exceeding 400 proteins. +19/-3
Tests	test-getSubnetworkFromIndra.R Updated and enhanced unit tests for error handling              tests/testthat/test-getSubnetworkFromIndra.R Updated test to reflect new error message for input size limit. Enhanced tests to validate error handling for missing columns. +1/-1

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[github-actions]

PR Reviewer Guide 🔍

Here are some key observations to aid the review process:

⏱️ Estimated effort to review: 3 🔵🔵🔵⚪⚪

🧪 PR contains tests

🔒 No security concerns identified

⚡ Recommended focus areas for review Error Handling The new error handling for converting uniprotMnemonicIds to character strings should be validated to ensure it properly handles edge cases and does not introduce unexpected behavior. tryCatch({ # Attempt to convert all elements to character if not already character uniprotMnemonicIds <- lapply(uniprotMnemonicIds, function(x) { if (!is.character(x)) { as.character(x) } else { x } }) # Check if conversion was successful if (any(!sapply(uniprotMnemonicIds, is.character))) { stop("All elements in the list must be character strings representing UniProt mnemonic IDs.") } }, error = function(e) { stop("An error occurred converting uniprot mnemonic IDs to character strings: ", e$message) Input Validation The new validation for matching HGNC IDs in .addAdditionalMetadataToIndraEdge should be reviewed to confirm it correctly identifies and handles cases with 0 or multiple matches. if (nrow(matched_rows_source) != 1 || nrow(matched_rows_target) != 1) { stop(paste0( "INDRA Exception: Unexpected number of matches for the following HGNC IDs in the input data: ", edge$source_id, " or ", edge$target_id, ". Each ID must match exactly one entry in the input data, but 0 or multiple matches were found. Please check the input data for duplicates or missing entries." ))

[github-actions]

PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Score
Possible issue	Validate that the Protein column in the input dataframe contains valid data before processing Add a check to ensure that the Protein column in the input dataframe is not empty or entirely NA before attempting to match rows, as this could lead to runtime errors or incorrect results. R/utils_getSubnetworkFromIndra.R [69-70] +if (all(is.na(input$Protein) | input$Protein == "")) { + stop("Input data must contain valid entries in the 'Protein' column.") +} matched_rows_source <- input[input$HgncId == edge$source_id & !is.na(input$Protein), ] matched_rows_target <- input[input$HgncId == edge$target_id & !is.na(input$Protein), ] Suggestion importance[1-10]: 9 Why: This suggestion adds a crucial validation step to ensure the Protein column contains valid data before proceeding with matching rows. This prevents runtime errors and ensures the function operates on valid input, significantly improving reliability.	9
	Improve error handling for non-convertible elements in the input list to avoid unexpected failures Ensure that the tryCatch block properly handles cases where uniprotMnemonicIds contains non-convertible elements, as the current implementation may not account for all edge cases, such as complex objects or NULL values. R/utils_annotateProteinInfoFromIndra.R [18-34] tryCatch({ # Attempt to convert all elements to character if not already character uniprotMnemonicIds <- lapply(uniprotMnemonicIds, function(x) { if (!is.character(x)) { - as.character(x) + tryCatch(as.character(x), error = function(e) NULL) } else { x } }) # Check if conversion was successful - if (any(!sapply(uniprotMnemonicIds, is.character))) { + if (any(is.null(uniprotMnemonicIds) | !sapply(uniprotMnemonicIds, is.character))) { stop("All elements in the list must be character strings representing UniProt mnemonic IDs.") } }, error = function(e) { stop("An error occurred converting uniprot mnemonic IDs to character strings: ", e$message) }) Suggestion importance[1-10]: 8 Why: The suggestion enhances the robustness of the tryCatch block by handling cases where elements in uniprotMnemonicIds cannot be converted to character strings. This improvement addresses potential edge cases and ensures the function behaves predictably, which is critical for input validation.	8
General	Add a test to ensure the function validates the Protein column in the input dataframe Add a test case to verify that the function throws an error when the Protein column in the input dataframe is entirely NA or empty, ensuring robust validation of input data. tests/testthat/test-getSubnetworkFromIndra.R [27-37] -test_that("Exception is thrown for 400+ proteins in dataframe", { - input_400 <- data.frame( - Protein = paste0("Protein", 1:400), - HgncId = paste0("HGNCID", 1:400), +test_that("Exception is thrown for empty or NA Protein column", { + input_invalid <- data.frame( + Protein = rep(NA, 10), + HgncId = paste0("HGNCID", 1:10), issue = NA, adj.pvalue = 0.05 ) expect_error( - getSubnetworkFromIndra(input_400), - "Invalid Input Error: INDRA query must contain less than 400 proteins. Consider lowering your p-value cutoff" + getSubnetworkFromIndra(input_invalid), + "Input data must contain valid entries in the 'Protein' column." ) }) Suggestion importance[1-10]: 8 Why: Adding a test case to validate the Protein column ensures that the function's input validation logic is robust and correctly handles cases where the column is empty or entirely NA. This strengthens the overall reliability of the code.	8
	Enhance error messages to provide more specific details about problematic rows in the input data Refactor the error message in .addAdditionalMetadataToIndraEdge to include more specific details about the problematic rows, such as their indices or content, to aid debugging. R/utils_getSubnetworkFromIndra.R [73-79] stop(paste0( "INDRA Exception: Unexpected number of matches for the following HGNC IDs in the input data: ", edge$source_id, " or ", edge$target_id, - ". Each ID must match exactly one entry in the input data, but 0 or multiple matches were found. Please check the input data for duplicates or missing entries." + ". Each ID must match exactly one entry in the input data, but 0 or multiple matches were found. Problematic rows: ", + paste(which(input$HgncId %in% c(edge$source_id, edge$target_id)), collapse = ", "), + ". Please check the input data for duplicates or missing entries." )) Suggestion importance[1-10]: 7 Why: The suggestion improves the error message by including specific details about problematic rows, aiding debugging and making it easier for users to identify and resolve issues in their input data.	7

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 62.96296% with 10 lines in your changes missing coverage. Please review.

Project coverage is 86.69%. Comparing base (4c5c730) to head (6504dc4).

Files with missing lines	Patch %	Lines
R/utils_getSubnetworkFromIndra.R	46.15%	7 Missing ⚠️
R/utils_annotateProteinInfoFromIndra.R	78.57%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##            devel      #28      +/-   ##
==========================================
- Coverage   88.28%   86.69%   -1.59%     
==========================================
  Files           7        7              
  Lines         384      406      +22     
==========================================
+ Hits          339      352      +13     
- Misses         45       54       +9     

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