R/create-advanced-batch-body.R

In cmmr: CEU Mass Mediator RESTful API

#' Create POST request Body for batch search
#'
#' \code{create_advanced_batch_body} returns a string of advanced search POST request body.
#'
#' @param chemical_alphabet "CHNOPS", "CHNOPSCL", "ALL"
#' @param modifiers_type "none", "NH3", "HCOO", "CH3COO", "HCOONH3", "CH3COONH3"
#' @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"] for negative mode ["M-H", "M+Cl", "M+FA-H", "M-H-H2O"], for neutral ["M"]
#' @param deuterium boolean 'true' 'false'
#' @param tolerance double (Range: [0..100])
#' @param tolerance_mode "ppm", "mDa"
#' @param masses double
#' @param all_masses array of doubles
#' @param retention_times double
#' @param all_retention_times array of doubles
#' @param composite_spectra array of arrays of spectra_object
#'
#' @return If all inputs are all correctly formatted, a dataframe will be returned for the result.
#'
#' @export
#'
create_advanced_batch_body <- function(
    chemical_alphabet = "all",
    modifiers_type = "none",
    metabolites_type = "all-except-peptides",
    databases = '["hmdb"]',
    masses_mode = "mz",
    ion_mode = "positive",
    adducts = '["all"]',
    deuterium = "false",
    tolerance = "7.5",
    tolerance_mode = "ppm",
    masses = "[400.3432, 288.2174]",
    all_masses = "[]",
    retention_times = "[18.842525, 4.021555]",
    all_retention_times = "[]",
    composite_spectra = paste0(
      '[[{ "mz": 400.3432, "intensity": 307034.88 }, ',
      '{ "mz": 311.20145, "intensity": 400.03336 }]]'
    )) {
  post_body <- paste0(
    '{"chemical_alphabet": "', chemical_alphabet,
    '","modifiers_type": "', modifiers_type,
    '","metabolites_type": "', metabolites_type,
    '","databases": ', databases,
    ',"masses_mode": "', masses_mode,
    '","ion_mode": "', ion_mode,
    '","adducts": ', adducts,
    ',"deuterium": ', deuterium,
    ',"tolerance": ', as.character(tolerance),
    ',"tolerance_mode":"', tolerance_mode,
    '","masses": ', masses,
    ',"all_masses": ', all_masses,
    ',"retention_times": ', retention_times,
    ',"all_retention_times": ', all_retention_times,
    ',"composite_spectra": ', composite_spectra,
    "}"
  )
}