R/create-msms-body.R

In cmmr: CEU Mass Mediator RESTful API

#' Create MS/MS search POST request body
#'
#' \code{create_msms_body} returns a string of a POST request body.
#'
#' @param ion_mass ion_mass
#' @param ms_ms_peaks ms_ms_peaks
#' @param precursor_ion_tolerance precursor_ion_tolerance
#' @param precursor_ion_tolerance_mode precursor_ion_tolerance_mode
#' @param precursor_mz_tolerance precursor_mz_tolerance
#' @param precursor_mz_tolerance_mode precursor_mz_tolerance_mode
#' @param ion_mode ion_mode
#' @param ionization_voltage ionization_voltage
#' @param spectra_types spectra_types
#'
#' @return If all inputs are all correctly formatted, a string of a POST request will be returned for the result.
#' @export
#'
create_msms_body <- function(ion_mass,
                             ms_ms_peaks,
                             precursor_ion_tolerance = 500.0,
                             precursor_ion_tolerance_mode = "mDa",
                             precursor_mz_tolerance = 1000.0,
                             precursor_mz_tolerance_mode = "mDa",
                             ion_mode = "positive",
                             ionization_voltage = "all",
                             spectra_types = "experimental") {
  ms_ms_peaks_vector <- c()
  for (i in 1:nrow(ms_ms_peaks)) {
    v <- paste0('{"mz":', ms_ms_peaks[i, 1], ',"intensity":', ms_ms_peaks[i, 2], "}")
    ms_ms_peaks_vector <- c(ms_ms_peaks_vector, v)
  }
  ms_ms_peaks_vector <- paste(ms_ms_peaks_vector, collapse = ",")
  post_body <- paste0(
    "{",
    '"ion_mass":', as.character(ion_mass), ",",
    '"ms_ms_peaks":[', ms_ms_peaks_vector, "],",
    '"precursor_ion_tolerance":', as.character(precursor_ion_tolerance), ",",
    '"precursor_ion_tolerance_mode":"', precursor_ion_tolerance_mode, '",',
    '"precursor_mz_tolerance":', as.character(precursor_mz_tolerance), ",",
    '"precursor_mz_tolerance_mode":"', precursor_mz_tolerance_mode, '",',
    '"ion_mode":"', ion_mode, '",',
    '"ionization_voltage":"', ionization_voltage, '",',
    '"spectra_types":["experimental","predicted"]',
    "}"
  )
}