R/msms_search.R

In cmmr: CEU Mass Mediator RESTful API

#' Encapsulation of CEU Mass Mediator batch search API.
#'
#' \code{batch_search} returns the dataframe of all the database search results.
#'   using the following code to install the dependencies:
#'   install.packages(c("httr", "progress", "RJSONIO"))
#'
#' @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 ionizationVoltage ionizationVoltage
#' @param spectra_types spectra_types
#' @param cmm_url "http://ceumass.eps.uspceu.es/mediator/api/msmssearch" or your local one
#'
#' @return If all inputs are all correctly formatted, a dataframe will be returned for the result.
#' @examples ms_ms_peaks = matrix(
#' c(40.948, 0.174,
#'   56.022, 0.424,
#'   84.37, 53.488,
#'   101.50, 8.285,
#'   102.401, 0.775,
#'   129.670, 100.000,
#'   146.966, 20.070),
#' ncol = 2,
#' byrow = TRUE)
#'
#' msms_search(ion_mass = 147, ms_ms_peaks = ms_ms_peaks, ion_mode = 'positive')
#'
#' @author Yaoxiang Li \email{yl814@georgetown.edu}
#'
#' Georgetown University, USA
#'
#' License: GPL (>= 3)
#' @export
#'
msms_search = function(ion_mass,
                       ms_ms_peaks,
                       precursor_ion_tolerance = 100.0,
                       precursor_ion_tolerance_mode = "mDa",
                       precursor_mz_tolerance = 500.0,
                       precursor_mz_tolerance_mode = "mDa",
                       ion_mode,
                       ionizationVoltage = "all",
                       spectra_types = "experimental",
                       cmm_url = "http://ceumass.eps.uspceu.es/mediator/api/msmssearch") {

  columns_to_save = c("spectral_display_tools",
                      "identifier",
                      "hmdb_compound",
                      "name",
                      "formula",
                      "mass",
                      "score")

  columns_to_name = c("Spectral_display_tools",
                      "Identifier",
                      "HMDB_ID",
                      "Name",
                      "Formula",
                      "Mass",
                      "Score")

  body <- create_msms_body(ion_mass, ms_ms_peaks,
                           precursor_ion_tolerance, precursor_ion_tolerance_mode,
                           precursor_mz_tolerance, precursor_mz_tolerance_mode,
                           ion_mode,ionizationVoltage, spectra_types)
  if (cmm_url == 'http://ceumass.eps.uspceu.es/mediator/api/msmssearch') {
    # print("Using the CEU Mass Mediator server API.")
  } else {
    print("Using the local/3rd party server API.")
  }

  r <- httr::POST(url = cmm_url, body = body, httr::content_type("application/json"))

  if (r$status_code == 200) {
    cat(paste0("Status: ", r$status_code, ", Success!\n"))
    cat(paste0("Date: ", r$date, "\n"))
    json_file <- RJSONIO::fromJSON(httr::content(r, "text", encoding = "UTF-8"))$results
    if (length(json_file) == 0) {
      print("No validation found in MS/MS search.")
      return("No validation found in MS/MS search")
    }

    pb <- progress::progress_bar$new(
      format = "  Parsing database search results [:bar] :percent in :elapsed",
      total  = length(json_file) - 1,
      clear  = FALSE,
      width  = 100)

    df <- json_file[[1]]
    df <- as.data.frame(df[names(df) %in% columns_to_save])
    if (length(json_file) > 1) {
      for (i in 2:length(json_file)) {
        pb$tick()
        dfi <- json_file[[i]]
        dfi <- as.data.frame(dfi[names(dfi) %in% columns_to_save])
        df <- rbind(df, dfi)
      }
    }


    df <- df[, columns_to_save]
    colnames(df) <- columns_to_name

    return(df)
  } else {
    cat(paste0("Status: ", r$status_code, ", Fail to connect the API service!\n"))
    cat(paste0("Date: ", r$date, "\n"))
  }
}