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#' 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.
#'
#' @author Yaoxiang Li \email{yl814@georgetown.edu}
#'
#' Georgetown University, USA
#'
#' License: GPL (>= 3)
#' @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,
'}')
}
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