#!/usr/bin/env Rscript

# Copyright (C) 2025 Université de Reims Champagne-Ardenne.
#
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`%>%` <- magrittr::`%>%`

options (warn=1)

args <- commandArgs (trailingOnly = TRUE)

if ('-h' %in% args || '--help' %in% args) {
    cat (sprintf ("Usage: merge-annotations [-O DEST] DIR ...\n"))
    cat (sprintf ("\n"))
    cat (sprintf ("Merge annotations from all files in DIR with files in DEST. Traverse the directories recursively.\n"))
    cat (sprintf ("\n"))
    cat (sprintf ("If -O is unspecified, merge into the current working directory.\n"))
}

merge <- function (source_root) {
    source_files <- list.files (source_root, pattern = "\\.neonatal\\.annotations\\.csv$", recursive = TRUE)
    for (source in source_files) {
        existing <- tryCatch ({
            ## Operates from working directory
            readr::read_csv (source,
                             col_names = c ("onset", "duration", "figure_class", "electrode_list"),
                             col_types = list (readr::col_double (), readr::col_double (), readr::col_character (), readr::col_character ()))
        }, error = function (e) {
            print (e)
            warning (sprintf ("Cannot read existing annotation file %s/%s, assume there are no annotations.", getwd (), source))
            tibble::tibble (onset = numeric (0), duration = numeric (0), figure_class = character (0), electrode_list = character (0))
        })
        new <- tryCatch ({
            readr::read_csv (paste0 (source_root, "/", source),
                             col_names = c ("onset", "duration", "figure_class", "electrode_list"),
                             col_types = list (readr::col_double (), readr::col_double (), readr::col_character (), readr::col_character ()))
        }, error = function (e) {
            print (e)
            warning (sprintf ("Cannot read new annotation file %s/%s, ignore.", source_root, source))
            tibble::tibble (onset = numeric (0), duration = numeric (0), figure_class = character (0), electrode_list = character (0))
        })
        if (nrow (new) != 0) {
            total <- (dplyr::bind_rows (existing, new)
                %>% dplyr::arrange (onset, duration, figure_class, electrode_list)
                %>% dplyr::distinct (onset, duration, figure_class, electrode_list))
            dir.create (dirname (source), showWarnings = FALSE, recursive = TRUE)
            tryCatch ({
                readr::write_csv (total, source, col_names = FALSE)
            }, error = function (e) {
                print (e)
                warning (sprintf ("Cannot override file %s/%s, ignore.", getwd (), source))
            })
        }
    }
}

setting_output_directory <- FALSE

for (arg in args) {
    if (setting_output_directory) {
        setwd (arg)
        setting_output_directory <- FALSE
    } else if (arg == '-O') {
        setting_output_directory <- TRUE
    } else {
        merge (arg)
    }
}
