R/connectToRaMP.R

In ncats/RaMP-DB: RaMP (Relational Database of Metabolomic Pathways)

#' Set Connection Parameters or RaMP
#'
#' @param dbname the name of the database (by default a string that is database name including all tables
#' @param username a string that is username for database (default: root)
#' @param conpass password for database (string)
#' @param host a string that stand for host
#' @param socket optional, location of mySQL.sock file (useful when running RaMP on remote clusters)
#'
#' @examples
#' \dontrun{
#' pkg.globals <- setConnectionToRaMP(dbname="ramp2",username="root",conpass="",host = "localhost")
#' }
#' @export
setConnectionToRaMP <- function(dbname="ramp",
                       username = "root",
                       conpass = "",
                       host ="localhost",
		       socket = ""){
  pkg.globals <- new.env()
  pkg.globals$dbname=dbname
  pkg.globals$username=username
  pkg.globals$conpass=conpass
  pkg.globals$host=host
  if(socket ==""){
      pkg.globals$socket=NULL
  }else{
      pkg.globals$socket = socket
  }
  return(pkg.globals)
}

#' Connect to RaMP database (requires mysql password when running locally)
#'
#' @examples
#' \dontrun{
#' pkg.globals <- setConnectionToRaMP(dbname="ramp2",username="root",conpass="",host = "localhost")
#' con <- connectToRaMP()
#' }
#' @return MySQL connection based on given dbname,username,password, and host
#' @export
connectToRaMP <- function() {
  if(!exists("pkg.globals")) {
	stop("Be sure the run the setConnectionToRaMP() and assign it to pkg.globals");
  }
  if(!is.null(get("socket",pkg.globals))) {
  	con <- RMariaDB::dbConnect(
	    drv = RMariaDB::MariaDB(),
	    dbname = get("dbname",pkg.globals),
	    username = get("username",pkg.globals),
	    password = get("conpass",pkg.globals),
	    host = get("host",pkg.globals),
	    unix.socket = get("socket",pkg.globals)
	)
  } else {
       con <- RMariaDB::dbConnect(
            drv = RMariaDB::MariaDB(),
            dbname = get("dbname",pkg.globals),
            username = get("username",pkg.globals),
            password = get("conpass",pkg.globals),
            host = get("host",pkg.globals)
	)
   }
 return(con)
}