R/S4_connection.R

In mwhalen18/krspfecals: KRSP Auxilary Fecal Database

#' S4 Connection Class
#' @import DBI
#' @import RMySQL
#' @export
setClass("FecalConnection", contains = c("DBIConnection", "MySQLConnection"))

#' Connect to the KRSP Fecals Database
#' @description These methods are extensions of the RMySQL and DBI drivers and are therefore compatible with \code{tbl} functions.
#'
#' For additional information on underlying arguments that can be passed to this call, see documentation for \link[DBI]{dbConnect} or \link[RMySQL]{dbConnect}
#'
#' @param username,password Username and password. If username omittedd,
#'     defaults to the current user. If password is omitted, only users
#'     without a password can login. By defualt this will throw and error if no parameters are entered.
#'     This will be changed in future version to default to local instance without a password.
#' @param dbname krsp fecal database name. Defualts to "krspfecals"
#' @param host host endpoint for database instance. Defulats to remote AWS instance but can be changed to localhost.
#' @examples
#' \dontrun{
#' #connect5 to the MySQL database running remotely
#' con = fecalConnect(user = "user", password = "password")
#'
#' #connect to local instance of the database
#' con = fecalConnect(user = "user", password = "password", host = "127.0.0.1")
#'
#' #Always clean up by disconnecting from the database
#' dbDisconnect(con)
#'
#' #Alternatively, there is a handy function built in here
#' fecalDisconnect(con)
#' }
#'
#' @export
setGeneric("fecalConnect",
           def = function(...)
                          standardGeneric("fecalConnect"),
           valueClass = "MySQLConnection")


#' @export
setMethod("fecalConnect", NULL, function(drv=RMySQL::MySQL(),username=NULL, group=NULL, password=NULL, dbname=NULL, host=NULL,
                                                  unix.socket=NULL, port = 0L, client.flag = 0,
                                                  groups = 'rs-dbi', default.file = NULL, ...){
  if(is.null(group)){
    con = dbConnect(drv,
              username = username,
              password = password,
              dbname = "krspfecals",
              host = "hormonedb.cfvasuoihvfm.ca-central-1.rds.amazonaws.com",
              port = 3306,...)
  } else {
    con = dbConnect(drv,
                    group = group,...)
  }
  return(con)
})

#' Show Available tables in the database
#' @examples
#' \dontrun{
#' con = fecalConnect(user = "user", password = "pw")
#' fecalTables(con)
#'
#' #always cleanup by disconnecting
#'
#' fecalDisconnect(con)
#' }
#' @description ListTables() returns a character vector that enumerate all tables and views in the database. Tables added with \link[DBI]{dbWriteTable} are part of this list.
#'     As soon as a table is removed from the database, it is alsio removed from the list of database tables.
#'     \cr
#' @export

setGeneric("fecalTables",
           def = function(con,...) standardGeneric("fecalTables"),
           valueClass = "character")

setMethod("fecalTables", "MySQLConnection",
          function(con,...){
            dbGetQuery(con, "SHOW TABLES")[[1]]
          })


#' Disconnect from the fecal database
#' @examples
#' \dontrun{
#' #connect to the MySQL database running remotely
#' con = fecalConnect(user = "user", password = "password")
#'
#' #connect to local instance of the database
#' con = fecalConnect(user = "user", password = "password", host = "127.0.0.1")
#'
#' #Always clean up by disconnecting from the database
#' dbDisconnect(con)
#'
#' #Alternatively, there is a handy function built in here
#' fecalDisconnect(con)
#' }
#'
#' @export
setGeneric("fecalDisconnect",
           def = function(con,...) standardGeneric("fecalDisconnect"),
           valueClass = "logical")

setMethod("fecalDisconnect", "MySQLConnection",
          function(con,...){
            dbDisconnect(con)
          })

#TODO: Currently returns class MySQL connection. Would be nice to convert to formal class fecals