refactor(collapse-edges): Refactor how edges are collapsed to remove clutter

[tonywu1999]

User description

Checklist Before Requesting a Review

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

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PR Type

enhancement

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Description

• Refactored the function .addAdditionalMetadataToIndraEdge to simplify the URL construction by removing the stmt_type parameter.
• Updated the .collapseDuplicateEdgesIntoEdgeToMetadataMapping function to modify key generation by excluding stmt_type, allowing for more efficient edge collapsing.
• Enhanced the handling of stmt_type by storing it as a list, ensuring uniqueness, and concatenating the values into a single string for better metadata representation.

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Changes walkthrough 📝

	Relevant files
Enhancement	utils_getSubnetworkFromIndra.R Refactor edge metadata handling and key generation              R/utils_getSubnetworkFromIndra.R Removed stmt_type from the evidence list URL construction. Modified key generation by excluding stmt_type. Updated logic to handle stmt_type as a list and ensure uniqueness. Concatenated stmt_type values into a single string. +12/-5

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[github-actions[bot]]

PR Reviewer Guide 🔍

Here are some key observations to aid the review process:

⏱️ Estimated effort to review: 2 🔵🔵⚪⚪⚪

🧪 No relevant tests

🔒 No security concerns identified

⚡ Recommended focus areas for review Code Redundancy The new implementation in `.collapseDuplicateEdgesIntoEdgeToMetadataMapping` function seems to handle `stmt_type` multiple times which could be optimized.

[github-actions[bot]]

PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Score
Possible bug	Correct the URL construction to include '@HGNC' for the target ID ___ **Ensure that the URL construction in .addAdditionalMetadataToIndraEdge function does not lead to malformed URLs due to missing '@HGNC' for the target ID.** [R/utils_getSubnetworkFromIndra.R [51]](https://github.com/Vitek-Lab/MSstatsBioNet/pull/19/files#diff-fa2a69c05887ee5c610e5d06f284de1d083ad342e76535fa9b0001e136653572R51-R51) ```diff edge$evidence_list <- paste( "https://db.indra.bio/statements/from_agents?subject=", edge$source_id, "@HGNC&object=", - edge$target_id, "&format=html", + edge$target_id, "@HGNC&format=html", sep = "" ) ``` Suggestion importance[1-10]: 9 Why: This suggestion addresses a potential bug by ensuring that the URL is correctly formed with the '@HGNC' suffix for the target ID, which is crucial for the functionality of the URL construction.	9
Performance	Streamline the conversion of statement types to a unique, comma-separated string ___ **Consolidate the operations for making statement types unique and converting them to a string to reduce redundancy and improve performance.** [R/utils_getSubnetworkFromIndra.R [85-89]](https://github.com/Vitek-Lab/MSstatsBioNet/pull/19/files#diff-fa2a69c05887ee5c610e5d06f284de1d083ad342e76535fa9b0001e136653572R85-R89) ```diff for (key in keys(edgeToMetadataMapping)) { edgeToMetadataMapping[[key]]$data$stmt_type <- - unique(edgeToMetadataMapping[[key]]$data$stmt_type) - edgeToMetadataMapping[[key]]$data$stmt_type <- - paste(edgeToMetadataMapping[[key]]$data$stmt_type, collapse = ", ") + paste(unique(edgeToMetadataMapping[[key]]$data$stmt_type), collapse = ", ") } ``` Suggestion importance[1-10]: 8 Why: This suggestion improves performance and reduces redundancy by consolidating operations into a single step, which is a beneficial optimization.	8
Enhancement	Use unique to prevent duplication when merging statement types ___ **Avoid potential duplication of statement types in the hashmap by directly using unique when adding new types.** [R/utils_getSubnetworkFromIndra.R [77-78]](https://github.com/Vitek-Lab/MSstatsBioNet/pull/19/files#diff-fa2a69c05887ee5c610e5d06f284de1d083ad342e76535fa9b0001e136653572R77-R78) ```diff -edgeToMetadataMapping[[key]]$data$stmt_type <- c( +edgeToMetadataMapping[[key]]$data$stmt_type <- unique(c( edgeToMetadataMapping[[key]]$data$stmt_type, - edge$data$stmt_type) + edge$data$stmt_type)) ``` Suggestion importance[1-10]: 7 Why: The suggestion enhances the code by preventing duplication of statement types, which improves the integrity of the data stored in the hashmap.	7

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 88.28%. Comparing base (a2e77b9) to head (2150348).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## devel #19 +/- ## ========================================== + Coverage 87.85% 88.28% +0.43% ========================================== Files 3 3 Lines 107 111 +4 ========================================== + Hits 94 98 +4 Misses 13 13 ```

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