R/rc.cmpd.get.classyfire.R

In RAMClustR: Mass Spectrometry Metabolomics Feature Clustering and Interpretation

#' getClassyFire
#'
#' use classyfire web API to look up full ClassyFire hirarchy for each inchikey
#' @details The $inchikey slot is used to look up the 
#' 
#' @param ramclustObj ramclustR object to ClassyFy.  Must supply one of either ramclustObj or inchikey (see below)
#' @param inchikey vector of text inchikeys to ClassyFy.  Must supply one of either ramclustObj or inchikey.
#' @param get.all logical; if TRUE, when inchikey classyfire lookup fails, submits for classyfication.  Can be slow. max.wait (below) sets max time to spend on each compound before moving on. default = FALSE.
#' @param max.wait  numeric; maximum time (seconds) to wait per compound when 'get.all' = TRUE.   
#' @param posts.per.minute  integer; a limit set when 'get.all' is true.  ClassyFire server accepts no more than 5 posts per minute when calculating new ClassyFire results.  Slows down submission process to keep server from denying access.  
#' @return returns a ramclustR object.  new dataframe in $classyfire slot with rows equal to number of compounds.  
#' @importFrom jsonlite fromJSON
#' @importFrom httr http_error
#' @concept ramclustR
#' @concept RAMClustR
#' @concept metabolomics
#' @concept mass spectrometry
#' @concept clustering
#' @concept feature
#' @concept MSFinder
#' @concept xcms
#' @concept classyFire
#' @author Corey Broeckling
#' @references Djoumbou Feunang Y, Eisner R, Knox C, Chepelev L, Hastings J, Owen G, Fahy E, Steinbeck C, Subramanian S, Bolton E, Greiner R, and Wishart DS. ClassyFire: Automated Chemical Classification With A Comprehensive, Computable Taxonomy. Journal of Cheminformatics, 2016, 8:61. DOI: 10.1186/s13321-016-0174-y

#' @export 

rc.cmpd.get.classyfire <- function (ramclustObj = NULL, inchikey = NULL, get.all = TRUE, 
                                    max.wait = 10, posts.per.minute = 5) 
{
  
  if(is.null(ramclustObj) & is.null(inchikey)) {
    stop("must supply ramclustObj or vector of inchikeys as input.  i.e. ramclustObj = RC; inchikey = c('MCPFEAJYKIXPQF-DXZAWUHFSA-N','GLZPCOQZEFWAFX-JXMROGBWSA-N')", '\n')
  }
  
  if(is.null(ramclustObj)) {
    ramclustObj <- list()
    ramclustObj$cmpd <- paste0("C", 1:length(inchikey))
    ramclustObj[['inchikey']] <- inchikey

  }

  if (!requireNamespace("httr", quietly = TRUE)) {
    stop("The use of this function requires package 'httr'.")
  }
  
  params <- c(
    "ramclustObj" = ramclustObj, 
    "inchikey" = inchikey, 
    "get.all" = get.all, 
    "max.wait" = max.wait, 
    "posts.per.minute" = posts.per.minute
  )
  if (is.null(ramclustObj$inchikey)) {
    stop("no inchikey slot found, please 'annotate' first", 
         "\n")
  }
  if (get.all & is.null(ramclustObj$smiles)) {
    warning(" - getting smiles from inchikey", '\n')
    ramclustObj <- getSmilesInchi(ramclustObj = ramclustObj)
    # stop("obtaining new classyfication (get.all option) requires a smiles notation", 
    #      "\n", "and no smiles slot found in ramclustObj.  Please first run 'getSmilesInchi()'", 
    #      "\n")
  }
  if (any(names(ramclustObj) == "classyfire")) {
    redo <- TRUE} else {redo <- FALSE}
  if (!redo) {
    ramclustObj$classyfire <- data.frame(inchikey = rep(NA, 
                                                        length(ramclustObj$inchikey)), kingdom = rep(NA, 
                                                                                                     length(ramclustObj$inchikey)), superclass = rep(NA, 
                                                                                                                                                     length(ramclustObj$inchikey)), class = rep(NA, length(ramclustObj$inchikey)), 
                                         subclass = rep(NA, length(ramclustObj$inchikey)), 
                                         parent = rep(NA, length(ramclustObj$inchikey)), 
                                         description = rep(NA, length(ramclustObj$inchikey)))
  }
  
  
  url = "http://classyfire.wishartlab.com"
  
  ## check server
  out <- tryCatch(jsonlite::fromJSON(paste0(url, "/entities/", "RYYVLZVUVIJVGH-UHFFFAOYSA-N", 
                                            ".json")), error = function(y) {
                                              return(NA)
                                            })
  if(length(out) == 1) {
    if(is.na(out)) {
      stop("  classyfire server appears to be down", '\n')
    }
  }
                                              
  
  
  cat("performing inchikey based lookup:", '\n')
  for (i in 1:length(ramclustObj$inchikey)) {
    
    if (is.na(ramclustObj$inchikey[i])) {
      next
    }
    if (!is.na(ramclustObj$classyfire[i, "kingdom"])) {
      next
    }
    Sys.sleep(1/posts.per.minute)
    cat(i, " ")
    out <- tryCatch(jsonlite::fromJSON(paste0(url, "/entities/", ramclustObj$inchikey[i], 
                                              ".json")), error = function(y) {
                                                return(NA)
                                              })
    
    tryn <- 1 
    if(length(out) < 2 & tryn <= 3) {
      # cat("retry", i, '\n')
      tryn <- tryn + 1
      Sys.sleep(1)
      out <- tryCatch(jsonlite::fromJSON(paste0(url, "/entities/", ramclustObj$inchikey[i], 
                                                ".json")), error = function(y) {
                                                  return(NA)
                                                })
    }
    
    if (length(out) > 1) {
      a <- ramclustObj$inchikey[i]
      b <- out$kingdom$name
      if (is.null(b)) 
        b <- NA
      c <- out$superclass$name
      if (is.null(c)) 
        c <- NA
      d <- out$class$name
      if (is.null(d)) 
        d <- NA
      e <- out$subclass$name
      if (is.null(e)) 
        e <- NA
      f <- out$direct_parent$name
      if (is.null(f)) 
        f <- NA
      g <- out$description
      if (is.null(g)) 
        g <- NA
      ramclustObj$classyfire[i, ] <- c(a, b, c, d, e, 
                                       f, g)
      
      rm(out); rm(a); rm(b); rm(c); rm(d); rm(e); rm(f); rm(g); rm(tryn)
    }
  }
  if (get.all) {
    get.full <- which(
      !is.na(ramclustObj$inchikey) & is.na(ramclustObj$classyfire[,2])
    )
    cat("this will take some time - maximum of", posts.per.minute, "posts per minute", '\n')
    for (i in get.full) {
      
      cat(i, " ")
      if (!is.na(ramclustObj$smiles[i])) {
        params <- list(label = "ramclustR", query_input = ramclustObj$smiles[i], 
                       query_type = "STRUCTURE")
        submit <- httr::POST("http://classyfire.wishartlab.com/queries", 
                             body = params, encode = "json", httr::accept_json(), 
                             httr::add_headers(`Content-Type` = "application/json"))
        Sys.sleep(1)
        query_id <- jsonlite::fromJSON(httr::content(submit, 
                                                     "text"))
        
        if(any(names(query_id) == "error")) {
          if(query_id$error == "Limit exceeded") {
            Sys.sleep(60)
            params <- list(label = "ramclustR", query_input = ramclustObj$smiles[i], 
                           query_type = "STRUCTURE")
            submit <- httr::POST("http://classyfire.wishartlab.com/queries", 
                                 body = params, encode = "json", httr::accept_json(), 
                                 httr::add_headers(`Content-Type` = "application/json"))
            query_id <- jsonlite::fromJSON(httr::content(submit, 
                                                         "text"))
          }
        }
        
        
        if(any(names(query_id) == "status")) {
          if(query_id$status == "500") {
            cat(" failed", '\n')
            next
          }
        }
        
        out <- list()
        out$classification_status <- "not done"
        out$number_of_elements <- 0
        Sys.sleep(1)
        skiptonext <- FALSE
        time.a <- Sys.time()
        while (out$number_of_elements == 0) {
          Sys.sleep(1)
          
          if(httr::http_error(paste0("http://classyfire.wishartlab.com/queries/",  query = query_id$id, ".json"))) {
            cat(" not done", '\n')
            break
          }
          out <- tryCatch( 
            {
              out <- jsonlite::fromJSON(paste0("http://classyfire.wishartlab.com/queries/", query = query_id$id, ".json"))
            }, 
            error = function(y) {
              out <- list()
              out$classification_status <- "not done"
              out$number_of_elements <- 0
              out
            }
          )
          
          if (round(as.numeric(difftime(Sys.time(), 
                                        time.a, units = "secs")), 3) >= max.wait) {
            cat("timed out", "\n")
            skiptonext <- TRUE
            break
          }
        }
        if (out$number_of_elements == 0) {
          ramclustObj$classyfire[i, ] <- c(ramclustObj$inchikey[i], 
                                           rep(NA, 6))
          rm(out)
        } else {
          a <- out$entities$inchikey
          if(is.null(a)) {
            a <- ramclustObj$inchikey[i]
          } else {
            a <- gsub("InChIKey=", "", a)
          }
          b <- out$entities$kingdom$name
          if (is.null(b)) {
            b <- NA
            c <- NA
            d <- NA 
            e <- NA
            f <- NA
            g <- NA
          } else {
            c <- if(length(out$entities$superclass)>1) {out$entities$superclass$name} else {c <- NA}
            if (is.null(c)) {c <- NA}
            d <- if(length(out$entities$class)>1) {out$entities$class$name} else {d <- NA}
            if (is.null(d)) {d <- NA}
            e <- if(length(out$entities$subclass)>1) {out$entities$subclass$name} else {e <- NA}
            if (is.null(e)) {e <- NA}
            f <- if(length(out$entities$direct_parent)>1) {out$entities$direct_parent$name} else {f <- NA}
            if (is.null(f)) {f <- NA}
            g <- if(nchar(out$entities$description)>1) {out$entities$description} else {g <- NA}
            if (is.null(g)) {g <- NA}
          }
          cat(" done", '\n')
          ramclustObj$classyfire[i, ] <- c(a, b, c, 
                                           d, e, f, g)
          rm(out)
        }
      }
      Sys.sleep(ceiling(60/posts.per.minute))
    }
  }
  
  ramclustObj$history$classyfire <- paste(
    "Compounds were assigned to chemical ontogenies using the ClassyFire API (Djoumbou 2016)."
  )
  
  if(is.null(ramclustObj$params)) {ramclustObj$params <- list()}
  ramclustObj$params$rc.cmpd.get.classyfire <- params
  
  
  return(ramclustObj)
}