R/solvers_cplex__write_cplex_command_file.R

In saezlab/CARNIVAL: A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming

writeCplexCommandFile <- function(carnivalOptions){

  message("Writing cplex command file")

  lpFilename <- carnivalOptions$filenames$lpFilename
  resultCplexFile <- carnivalOptions$filenames$resultFile
  cplexCommandFilename <- carnivalOptions$filenames$cplexCommandFile

  write(paste0("read ", lpFilename),
        cplexCommandFilename, append = FALSE)
  write(paste0("set mip tolerances mipgap ", carnivalOptions$mipGap),
        cplexCommandFilename, append = TRUE)
  write(paste0("set mip pool relgap ", carnivalOptions$poolrelGap),
        cplexCommandFilename, append = TRUE)
  write(paste0("set mip pool replace ", carnivalOptions$poolReplace),
        cplexCommandFilename, append = TRUE)
  write(paste0("set mip limits populate ", carnivalOptions$limitPop),
        cplexCommandFilename, append = TRUE)
  write(paste0("set mip pool capacity ", carnivalOptions$poolCap),
        cplexCommandFilename, append = TRUE)
  write(paste0("set mip pool intensity ", carnivalOptions$poolIntensity),
        cplexCommandFilename, append = TRUE)
  write(paste0("set timelimit ", carnivalOptions$timelimit), cplexCommandFilename, append = TRUE)
  write(paste0("set threads ", carnivalOptions$threads), cplexCommandFilename, append = TRUE)
  write(paste0("set output clonelog ", carnivalOptions$clonelog), cplexCommandFilename, append = TRUE)
  write(paste0("set workdir ", carnivalOptions$workdir), cplexCommandFilename, append = TRUE)
  write("populate", cplexCommandFilename, append = TRUE)
  write(paste0("write ", resultCplexFile, " sol all"),
        cplexCommandFilename, append = TRUE)
  write("quit", cplexCommandFilename, append = TRUE)

  message("Done: writing cplex command file")
  return(cplexCommandFilename)
}

#' writeCplexCommandFileFromJson
#' @importFrom  rjson fromJSON 
#' @param carnivalOptions list of options for the CPLEX solver
#' @param jsonFileName name to JSONfile containing the solver parameters
#' @return list of params
writeCplexCommandFileFromJson <- function(carnivalOptions,
                                          jsonFileName = "parameters/cplex_parameters_cmd_file.json") {
  message("Writing cplex command file")

  message("Loading parameters file for cplex command file:", jsonFileName)
  cplexCommands <- rjson::fromJSON(file = jsonFileName)
  cplexCommandsFilename <- carnivalOptions$cplexCommandFilename

  params <- lapply(seq(1:length(cplexCommands)), function(i) {
    parameterName <- names(cplexCommands[i])
    if (parameterName == "") {
      write(cplexCommands[[i]], cplexCommandsFilename, append=TRUE)
    } else {
      write(paste(cplexCommands[parameterName], carnivalOptions[parameterName]),
            cplexCommandsFilename, append=TRUE)
    }
  })

}