R/create-batch-body.R

In cmmr: CEU Mass Mediator RESTful API

#' Create POST request Body for batch search
#'
#' \code{create_batch_body} returns a string of a POST request body.
#'
#' @param metabolites_type "all-except-peptides", "only-lipids", "all-including-peptides"
#' @param databases "all", "all-except-mine", "HMDB", "LipidMaps", "Metlin", "Kegg", "in-house", "mine"
#' @param masses_mode "neutral", "mz"
#' @param ion_mode "positive", "negative"
#' @param adducts for positive mode [M+H, M+2H, M+Na, M+K,M+NH4, M+H-H2O]
#'
#' @param tolerance double (Range: [0..100])
#' @param tolerance_mode "ppm", "mDa"
#' @param unique_mz An array of unique m/zs
#'
#' @return If all inputs are all correctly formatted, a string of a POST request will be returned for the result.
#' @examples
#'
#' batch_body <- create_batch_body(
#'   "all-except-peptides",
#'   '["all-except-mine"]',
#'   "mz",
#'   "positive",
#'   '["M+H","M+Na"]',
#'   10,
#'   "ppm",
#'   c(670.4623, 1125.2555, 602.6180)
#' )
#'
#' batch_body <- create_batch_body(
#'   "all-except-peptides",
#'   '["all-except-mine"]',
#'   "mz",
#'   "negative",
#'   '["M-H","M+Cl"]',
#'   10,
#'   "ppm",
#'   c(670.4623, 1125.2555, 602.6180)
#' )
#'
#' \dontrun{
#' create_batch_body(c(670.4623, 1125.2555, 602.6180))
#' }
#' @export
#'
create_batch_body <- function(metabolites_type = "all-except-peptides",
                              databases = '["all-except-mine"]',
                              masses_mode = "mz",
                              ion_mode = "positive",
                              adducts = '["M+H","M+Na"]',
                              tolerance = 10,
                              tolerance_mode = "ppm",
                              unique_mz) {
  masses <- paste(unique_mz, collapse = ",")
  tolerance <- as.character(tolerance)
  post_body <- paste0(
    '{"metabolites_type":"', metabolites_type,
    '","databases":', databases,
    ',"masses_mode":"', masses_mode,
    '","ion_mode":"', ion_mode,
    '","adducts":', adducts,
    ',"tolerance":', tolerance,
    ',"tolerance_mode":"', tolerance_mode,
    '","masses":[', masses,
    "]}"
  )
}