R/search.R

In michaelwitting/SwissLipidsR: R access to the SwissLipids API

#' @title SwissLipids API basic search function
#'
#' @description
#'
#' `swissLipidsSearch` Performs a basic search using the SwissLipids API
#'
#' @param term `character` Search term which shall be searched in SwissLipids
#' @param type `character` Type of search term, either metabolite or protein
#'
#' @return `data.frame` A data.frame with the search results
#'
#' @author Michael Witting#'
#'
#' @importFrom jsonlite fromJSON
#' @importFrom utils URLencode
#' @importFrom curl curl_fetch_memory
#'
#' @export
#'
#' @examples
#'
#' swissLipidsSearch("Phosphatidate (36:2)")
swissLipidsSearch <- function(term, type = c("metabolite", "protein")) {

  # check input
  match.arg(type)

  # create query url
  query_url <- paste0(BASE_URL, "search?term=", term, "&type=", type)

  # perform request
  r <- curl::curl_fetch_memory(URLencode(query_url))

  # dependent on status code return results
  if(r$status_code == as.integer(200)) {

    return(jsonlite::fromJSON(rawToChar(r$content), flatten = TRUE))

  } else {

    return(data.frame())

  }
}

#' @title SwissLipids API advanced search function
#'
#' @description
#'
#' `swissLipidsAdvancedSearch` Performs an advanced search using the SwissLipids API
#'
#' @param name `character`
#' @param smiles `character`
#' @param inchikey `character`
#' @param formula `character`
#' @param mz `numeric`
#' @param adduct `character`
#' @param massErrorRate `numeric`
#'
#' @return `data.frame` A named list with the search results
#'
#' @author Michael Witting#'
#'
#' @importFrom jsonlite fromJSON
#' @importFrom utils URLencode
#' @importFrom curl curl_fetch_memory
#'
#' @export
#'
#' @examples
#'
#'swissLipidsAdvancedSearch(name = "PC(34:2)")
#'swissLipidsAdvancedSearch(formula = "C39H76NO8P")
#'
#'swissLipidsAdvancedSearch(mz = 410.243, adduct = "MassExact", massErrorRate = 0.001)
swissLipidsAdvancedSearch <- function(name = NA_character_,
                                      smiles = NA_character_,
                                      inchikey = NA_character_,
                                      formula = NA_character_,
                                      mz = NA_real_,
                                      adduct = NA_character_,
                                      massErrorRate = NA_real_) {
  # create query
  query <- "advancedSearch?"

  if (!is.na(name)) {
    query <- paste0(query, "Name=", name, "&")
  }

  if (!is.na(smiles)) {
    query <- paste0(query, "SMILES=", smiles, "&")
  }

  if (!is.na(inchikey)) {
    query <- paste0(query, "InChIkey=", inchikey, "&")
  }

  if (!is.na(formula)) {
    query <- paste0(query, "Formula=", formula, "&")
  }

  if (!is.na(mz)) {
    query <- paste0(query, "mz=", mz, "&")
  }

  if (!is.na(adduct)) {
    if (!any(adduct %in% c("MassExact", "MassM", "MassMH", "MassMK", "MassMNa",
                       "MassMLi", "MassMNH4", "MassMmH", "MassMCl", "MassMOAc")))
      {
      stop(adduct, " is not correct, please select from MassExact, MassM, MassMH,
           MassMK, MassMNa, MassMLi, MassMNH4, MassMmH, MassMCl, MassMOAc")
    }

    query <- paste0(query, "adduct=", adduct, "&")
  }

  if (!is.na(massErrorRate)) {
    query <- paste0(query, "massErrorRate=", massErrorRate, "&")
  }

  # remove last "&"
  query <- gsub("&$", "", query)

  # create query url
  query_url <- paste0(BASE_URL, query)

  # perform request
  r <- curl::curl_fetch_memory(URLencode(query_url))

  # dependent on status code return results
  if(r$status_code == as.integer(200)) {

    return(jsonlite::fromJSON(rawToChar(r$content), flatten = TRUE))

  } else {

    return(data.frame())

  }

}

#' @title SwissLipids API basic search function
#'
#' @description
#'
#' `swissLipidsGetChildren` Performs a search for potential children
#'
#' @param entity_id `character` Search term for which children entries shall  be
#'     searched in SwissLipids
#'
#' @author Michael Witting#'
#'
#' @importFrom jsonlite fromJSON flatten
#' @importFrom utils URLencode
#' @importFrom dplyr bind_rows
#' @importFrom curl curl_fetch_memory
#'
#' @export
#'
#' @examples
#'
#' swissLipidsGetChildren("SLM:000000352")
swissLipidsGetChildren <- function(entity_id) {

  # create query url
  query_url <- paste0(BASE_URL, "/children?entity_id=", entity_id)

  # perform request
  r <- curl::curl_fetch_memory(URLencode(query_url))

  # dependent on status code return results
  if(r$status_code == as.integer(200)) {

    results <- jsonlite::fromJSON(rawToChar(r$content))

    results_df <- data.frame()

    if(length(results) > 1) {

      for(i in 1:length(results)) {

        results_df <- bind_rows(results_df, flatten(results[[i]]))

      }

    } else {

      results_df <- as.data.frame(results)

    }

    return(results_df)

  } else {

    return(data.frame())

  }
}



# ==============================================================================
# DEVELOPMENT
# ==============================================================================
swissLipidsGetEntity <- function(entity_id) {

  # create query url
  query_url <- paste0(BASE_URL, "entity/entity_id=", entity_id)

  fromJSON(URLencode(query_url))

}