Issue-48: Update extract_ids_from_metadata() to accept logical values

[johanna0321]

Description of your changes

Update extract_ids_from_metadata() to accept logical values and style files

Issue ticket number and link

#48 for https://github.com/calico/mass_spec/issues/1889

Type of change

• Bug fix
• New feature
  • Backwards Incompatible?
• Refactoring / code clean-up
• Documentation add / update
• Automated Test
• Other (please specify)

(If applicable) How has this been tested?

[Copilot]

Pull request overview

This pull request updates the extract_ids_from_metadata() function to accept logical values for the filter_ids parameter, in addition to character vectors, and applies consistent code styling across multiple R files.

Changes:

• Added support for logical filter_ids in extract_ids_from_metadata() with type validation
• Applied consistent function parameter formatting (2-space indentation with closing parenthesis on separate line)
• Removed extraneous blank lines for cleaner code

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated no comments.

File	Description
R/filter_mzroll_list.R	Core functionality change: added logical support to extract_ids_from_metadata() with new validate_filter_ids() helper; removed blank lines
R/mutate_mzroll_list.R	Removed 2 blank lines for consistent formatting
R/import_mzroll.R	Reformatted process_mzroll_multi() function parameters with consistent indentation
R/differential_expression.R	Reformatted plot_volcano() function parameters with consistent indentation

Comments suppressed due to low confidence (1)

R/filter_mzroll_list.R:313

• The new helper function validate_filter_ids lacks test coverage. Given that this function is critical for validating the type compatibility between filter_ids and the column values, and the codebase has test files for filters, consider adding tests to verify the behavior when both are logical, when there's a type mismatch, and when both are non-logical types.

validate_filter_ids <- function(col_values, filter_ids) {
  col_is_logical <- is.logical(col_values)
  ids_are_logical <- is.logical(filter_ids)
  if (col_is_logical && !ids_are_logical) {
    stop("\nfilter_var column is logical but filter_ids is not logical")
  }
  if (!col_is_logical && ids_are_logical) {
    stop("\nfilter_ids is logical but filter_var column is not logical")
  }
}

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[PMSeitzer]

Not a big deal, but wondering why the nested asserts here?

[johanna0321]

Could be written in another way, but just checking that it is a character or logical

[PMSeitzer]

LGTM