Wrappers for bioentity endpoints and tests

[pnavada]

PR Type

Enhancement, Tests

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Description

• Introduced new API wrapper functions in R to retrieve bioentity information, such as UniProt IDs, HGNC IDs, and gene properties (kinase, phosphatase, transcription factor).
• Implemented comprehensive unit tests to ensure the correctness of the new API wrapper functions.
• Enhanced the functionality of the codebase by enabling conversion between different bioentity identifiers.

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Changes walkthrough 📝

	Relevant files
Enhancement	getBioEntityInfoFromIndra.R Add API wrappers for bioentity information retrieval          R/getBioEntityInfoFromIndra.R Added API wrapper functions for bioentity information retrieval. Implemented functions to convert between different bioentity identifiers. Functions to check gene properties like kinase, phosphatase, and transcription factor. +138/-0
Tests	test-getBioEntityInfoFromIndra.R Add unit tests for bioentity API wrapper functions              tests/testthat/test-getBioEntityInfoFromIndra.R Added unit tests for each API wrapper function. Verified correct conversion and retrieval of bioentity information. Ensured functions correctly identify gene properties. +59/-0

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[github-actions[bot]]

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 Hardcoded URL The API URLs are hardcoded to localhost, which might not be suitable for production environments. Consider using environment variables or configuration files to manage these URLs. Error Handling There is no error handling for the API requests. It's recommended to add error checking after the POST requests to handle potential failures gracefully.

[github-actions[bot]]

PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Score
Best practice	Implement error handling for API requests to manage failures gracefully ___ **Add error handling for the API request to manage cases where the request fails or the API returns an error.** [R/getBioEntityInfoFromIndra.R [15-20]](https://github.com/Vitek-Lab/MSstatsBioNet/pull/20/files#diff-2e1405d9f60b34d63f4b2b1c52b4c20b94efd715ba3349a875add7c663269037R15-R20) ```diff -res <- POST( - apiUrl, - body = requestBody, - add_headers("Content-Type" = "application/json"), - encode = "raw" -) +res <- tryCatch({ + POST( + apiUrl, + body = requestBody, + add_headers("Content-Type" = "application/json"), + encode = "raw" + ) +}, error = function(e) { + message("Error in API request: ", e$message) + NULL +}) ``` Suggestion importance[1-10]: 9 Why: Adding error handling is crucial for robustness, as it allows the program to handle API request failures gracefully, providing informative messages and preventing crashes.	9
	Ensure robustness by validating input parameters before use in API requests ___ **Validate the input parameters to ensure they meet expected formats or conditions before making API requests.** [R/getBioEntityInfoFromIndra.R [12]](https://github.com/Vitek-Lab/MSstatsBioNet/pull/20/files#diff-2e1405d9f60b34d63f4b2b1c52b4c20b94efd715ba3349a875add7c663269037R12-R12) ```diff +if (!is.list(uniprotMnemonicIds) || length(uniprotMnemonicIds) == 0) { + stop("Invalid input: 'uniprotMnemonicIds' must be a non-empty list.") +} requestBody <- list(uniprot_mnemonic_ids = uniprotMnemonicIds) ``` Suggestion importance[1-10]: 8 Why: Validating input parameters is a best practice that prevents errors and ensures that the function receives data in the expected format, enhancing the function's reliability.	8
Enhancement	Improve security and flexibility by using environment variables for API URLs ___ **Replace the hardcoded API URL with a configurable option or environment variable to enhance flexibility and security.** [R/getBioEntityInfoFromIndra.R [10]](https://github.com/Vitek-Lab/MSstatsBioNet/pull/20/files#diff-2e1405d9f60b34d63f4b2b1c52b4c20b94efd715ba3349a875add7c663269037R10-R10) ```diff -apiUrl <- "http://localhost:5000/api/get_uniprot_ids_from_uniprot_mnemonic_ids" +apiUrl <- Sys.getenv("API_URL") ``` Suggestion importance[1-10]: 8 Why: Using environment variables for API URLs enhances security and flexibility, allowing for easier configuration changes without modifying the code. This is a significant improvement over hardcoded URLs.	8
Performance	Enhance performance and reduce network load by caching API call results ___ **Consider caching results from API calls to improve performance and reduce unnecessary network traffic.** [R/getBioEntityInfoFromIndra.R [21]](https://github.com/Vitek-Lab/MSstatsBioNet/pull/20/files#diff-2e1405d9f60b34d63f4b2b1c52b4c20b94efd715ba3349a875add7c663269037R21-R21) ```diff -res <- content(res) +res <- memoise::memoise(content)(res) ``` Suggestion importance[1-10]: 6 Why: Caching API call results can improve performance by reducing redundant network requests. However, it may not be necessary for all use cases, depending on the frequency and variability of the data.	6

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 84.23645% with 32 lines in your changes missing coverage. Please review.

Project coverage is 85.66%. Comparing base (6f4bff5) to head (123cf61).

Files with missing lines	Patch %	Lines
R/utils_annotateProteinInfoFromIndra.R	77.27%	30 Missing :warning:
R/utils_onLoad.R	0.00%	2 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## devel #20 +/- ## ========================================== - Coverage 88.28% 85.66% -2.62% ========================================== Files 3 6 +3 Lines 111 314 +203 ========================================== + Hits 98 269 +171 - Misses 13 45 +32 ```

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[tonywu1999]

Great work Pruthvi - one more thing to rebase your changes to the devel branch and do a git push origin --force-with-push to this branch.