R/get_xronos.R

In ropensci/c14bazAAR: Download and Prepare C14 Dates from Different Source Databases

#' @rdname db_getter_backend
#' @export
get_xronos <- function(db_url = get_db_url("xronos")) {

  check_connection_to_url(db_url)

  resp <- httr::GET(db_url)

  xronos_data <- httr::content(
    resp, as = "parsed",
    show_col_types = FALSE
  ) %>% unique()

  periods_parsed <- parse_json_lists(xronos_data[["periods"]])
  reference_parsed <- parse_json_lists(xronos_data[["reference"]])

  xronos <- xronos_data %>%
    dplyr::transmute(
      labnr = .data[["labnr"]],
      c14age = .data[["bp"]],
      c14std = .data[["std"]],
      c13val = .data[["delta_c13"]],
      material = .data[["material"]],
      species = .data[["species"]],
      country = .data[["country"]],
      site = .data[["site"]],
      sitetype = .data[["site_type"]],
      feature = .data[["feature"]],
      period = periods_parsed,
      shortref = reference_parsed,
      lat = .data[["lat"]],
      lon = .data[["lng"]]) %>%
    dplyr::mutate(
      sourcedb = "xronos",
      sourcedb_version = get_db_version("xronos")
    ) %>%
    c14bazAAR::as.c14_date_list()

  return(xronos)
}

# helper function to parse JSON to a ;-separated string list
parse_json_lists <- function(y) {
  parsed <- y %>%
    paste(collapse = ",") %>%
    paste("[", ., "]") %>%
    yyjsonr::read_json_str(opts = yyjsonr::opts_read_json(arr_of_objs_to_df = FALSE))
  rendered <- Map( \(x) { paste(unlist(x), collapse = ";") }, parsed )
  return(rendered)
}