Resolve legacy-import paths and perform fast-fail argument checks

Combines explicit arguments with a YAML config (if given), expands every relative path to an absolute path (relative paths are evaluated against dirname(config_yaml) (!!!) when YAML is used, otherwise against the directory that contains the first supplied data matrix (!!!)), and returns a fully populated list of file locations and options ready for downstream conversion. Only cheap, load-blocking checks are done here:

• input_file and hit_file must be supplied together or both omitted.

• At least one matrix source (exist_file, fold_change_file, or the input_file + hit_file pair) must be present.

• Deprecated output_dir triggers a soft warning.

All deeper table-content validation is deferred to phip_data class validation.

Usage

.ph_resolve_paths(
  exist_file = NULL,
  fold_change_file = NULL,
  samples_file = NULL,
  input_file = NULL,
  hit_file = NULL,
  timepoints_file = NULL,
  extra_cols = NULL,
  output_dir = NULL,
  data_long_path = NULL,
  peptide_library = TRUE,
  n_cores = NULL,
  materialise_table = NULL,
  auto_expand = NULL,
  sample_id_from_filenames = NULL,
  config_yaml = NULL
)

Arguments

exist_file, fold_change_file, input_file, hit_file, samples_file, timepoints_file

Character paths (relative or absolute) to the respective CSV/Parquet inputs. NULL means "not supplied".

extra_cols

Character vector of extra metadata columns to keep; may be NULL.

output_dir

Ignored (soft-deprecated).

config_yaml

Optional path to a YAML file whose keys mirror the function arguments; relative paths inside the YAML are resolved against the YAML’s own directory.

Value

A named list with absolute paths, extra_cols, and base_dir; suitable for downstream helper functions.