fix: re-use helper functions from MOSuite

Author: kelly-sovacool

CHANGELOG.md

@@ -2,6 +2,8 @@
 
 ## development version
 
+- Fix: remove `regex_moo` parameter from configuration. multiOmicDataSet input files are now required to follow the standardized naming pattern (`.*\.rds$`).
+
 ## v1.0
 
 Initial release

code/main.R

@@ -7,14 +7,8 @@ library(readr)
 library(stringr)
 library(dplyr)
 
-# set up results directory
-results_dir <- file.path('..','results')
-plots_dir <- file.path(results_dir, 'figures')
-options(moo_plots_dir = plots_dir, moo_save_plots = TRUE)
-
-# log installed packages & versions
-pkg_versions <- tibble::as_tibble(installed.packages())
-write_csv(pkg_versions, file.path(results_dir, 'r-packages.csv'))
+# set up capsule environment
+setup_capsule_environment()
 
 # parse CLI arguments
 parser <- ArgumentParser()
@@ -34,52 +28,8 @@ parser$add_argument("--plot_title", type="character", default="PCA 3D", help="Ti
 
 args <- parser$parse_args()
 
-parse_optional_vector <- function(x) {
-    if (is.null(x) || identical(x, "") || length(x) == 0) {
-        return(NULL)
-    }
-    return(trimws(unlist(strsplit(x, ","))))
-}
-
-parse_vector_with_default <- function(x, default) {
-    parsed <- parse_optional_vector(x)
-    if (is.null(parsed)) {
-        return(default)
-    }
-    return(parsed)
-}
-
-# validate inputs
-regex_moo <- ".*\\.rds$"
-data_files <- list.files(file.path('../data'), recursive = TRUE, full.names = TRUE)
-moo_files <- Filter(\(x) str_detect(x, regex(regex_moo, ignore_case = TRUE)), data_files)
-
-if (length(moo_files) == 0) {
-    stop(glue("No files matching regex: {regex_moo}"))
-}
-moo_filename <- moo_files[1]
-moo <- read_rds(moo_filename)
-message(glue('Reading multiOmicDataSet from {moo_filename}'))
-if (!inherits(moo, 'MOSuite::multiOmicDataSet')) {
-    stop(glue('The input is not a multiOmicDataSet. class: {class(moo)}'))
-}
-
-# parse samples_to_rename
-parse_samples_to_rename <- function(x) {
-    if (is.null(x) || identical(x, "") || length(x) == 0) {
-        return(NULL)
-    }
-    pairs <- trimws(unlist(strsplit(x, ",")))
-    result <- list()
-    for (pair in pairs) {
-        parts <- trimws(unlist(strsplit(pair, ":")))
-        if (length(parts) == 2) {
-            result[[parts[1]]] <- parts[2]
-        }
-    }
-    if (length(result) == 0) return(NULL)
-    return(result)
-}
+# load multiOmicDataSet from data directory
+moo <- load_moo_from_data_dir()
 
 # run MOSuite
 plot_pca(