make_study_bounds <- function(range_shapefile, expand_degrees = 5) {
  seal_range <- terra::vect(range_shapefile)
  bbox <- terra::ext(seal_range) |> terra::extend(expand_degrees)
  list(
    seal_range = seal_range,
    lon_range = c(bbox$xmin, bbox$xmax),
    lat_range = c(bbox$ymin, bbox$ymax)
  )
}

download_biooracle_slice <- function(dynamic_layers, scenario_value, decade_start, lon_range, lat_range, download_root = "./data/bio-oracle-2") {
  scenario_layers <- dynamic_layers |>
    dplyr::filter(scenario == scenario_value)

  time_point <- paste0(decade_start, "-01-01T00:00:00Z")
  slice_constraints <- list(
    time = c(time_point, time_point),
    longitude = lon_range,
    latitude = lat_range
  )

  download_dir <- file.path(download_root, scenario_value, decade_start)
  dir.create(download_dir, recursive = TRUE, showWarnings = FALSE)

  sapply(
    scenario_layers$dataset_id,
    function(id) biooracler::download_layers(
      id,
      constraints = slice_constraints,
      directory = download_dir
    ),
    simplify = TRUE
  )
}

download_biooracle_slice_subset <- function(dynamic_layers, scenario_value, decade_start, layers_to_download, lon_range, lat_range, download_root = "./data/bio-oracle-2") {
  scenario_layers <- dynamic_layers |>
    dplyr::filter(
      scenario == scenario_value &
        var %in% layers_to_download$var &
        depth %in% layers_to_download$depth
    )

  time_point <- paste0(decade_start, "-01-01T00:00:00Z")
  slice_constraints <- list(
    time = c(time_point, time_point),
    longitude = lon_range,
    latitude = lat_range
  )

  download_dir <- file.path(download_root, scenario_value, decade_start)
  dir.create(download_dir, recursive = TRUE, showWarnings = FALSE)

  sapply(
    scenario_layers$dataset_id,
    function(id) biooracler::download_layers(
      id,
      constraints = slice_constraints,
      directory = download_dir
    ),
    simplify = TRUE
  )
}

set_brick_names_with_depth <- function(r) {
  r_depths <- names(r) |> stringr::str_extract("depth[:alpha:]+")
  r_longnames <- terra::longnames(r)
  names(r) <- paste(r_longnames, r_depths)
  r
}

assert_required_files <- function(paths) {
  missing_paths <- paths[!file.exists(paths)]
  if (length(missing_paths) > 0) {
    stop(
      paste0(
        "Missing required file(s): ",
        paste(missing_paths, collapse = ", "),
        ". Run learning pipeline first."
      ),
      call. = FALSE
    )
  }
}