R/runDocker.R

In kendomaniac/docker4seq: Running NGS computing demanding applications, e.g reads mapping and counting, wrapped in docker containers

#' @title Run docker container
#' @description This is an internal function executing a docker container. Not to be used by users.
#' @param group, a character string. Two options: \code{"sudo"} or \code{"docker"}, depending to which group the user belongs
#' @param params, a character string containing all parameters needed to tun the docker container
#' @param DockerSwarm, a bolean value used to enable docker execution in swarm mode.
#' @return 0 if success, 1 if parameters are missing, 2 if the group is neither sudo or docker, 3 if docker execution fails.
#' @author Raffaele Calogero
#'
#' @examples
#'\dontrun{
##'     #running runDocker
#'      runDocker(group="docker", params=NULL)
#'
#' }
#' @export
runDocker <- function(group="docker", params=NULL, DockerSwarm=FALSE){

  if(is.null(params)){
    cat("\nNo parameters where provided!\n")
    system("echo 1 > ExitStatusFile 2>&1")
    return(1)
  }
  
  if (DockerSwarm==FALSE){#Normal Docker execution
    
    # to obtain the Docker ID by file
    if (file.exists("dockerID")){
      cat("\n\nDocker does not start, there is already a docker container running che dockerID file!!!\n\n")
      system("echo 2 > ExitStatusFile 2>&1")
      return(2)
    }
    
    if(group=="sudo"){
      #      system(paste("sudo docker pull ",container, sep=""))
      system(paste("sudo docker run --privileged=true --platform linux/amd64 ",params, sep=""))
    }else if(group=="docker"){
      #      system(paste("docker pull ",container, sep=""))
      system(paste("docker run --privileged=true --platform linux/amd64 ",params, sep=""))
    }else{
      cat("\nThe group provides is neither sudo or docker\n")
      system("echo 2 > ExitStatusFile 2>&1")
      return(2)
    }
    
    dockerid=readLines("dockerID", warn = FALSE)
    cat("\nDocker ID is:\n",substr(dockerid,1, 12),"\n")
    ## to obtain the Docker ID by file
    
    ## to check the Docker container status
    dockerStatus=system(paste("docker inspect -f {{.State.Running}}",dockerid),intern= T)
    while(dockerStatus=="true"){
      Sys.sleep(10);
      dockerStatus=system(paste("docker inspect -f {{.State.Running}}",dockerid),intern= T)
      cat(".")
    }
    cat(".\n\n")
    ## to check the Docker container status
    dockerExit <- system(paste("docker inspect -f {{.State.ExitCode}}",dockerid),intern= T)
    cat("\nDocker exit status:",dockerExit,"\n")
    if(as.numeric(dockerExit)!=0){
        system(paste("docker logs ", substr(dockerid,1,12), " &> ", substr(dockerid,1,12),"_error.log", sep=""))
        cat(paste("\nDocker container ", substr(dockerid,1,12), " had exit different from 0\n", sep=""))
        cat("\nExecution is interrupted\n")
        cat(paste("Please send to raffaele.calogero@unito.it this error: Docker failed exit 0,\n
                  the description of the function you were using and the following error log file,\n
                  which is saved in your working folder:\n", substr(dockerid,1,12),"_error.log\n", sep=""))
        
        system("echo 3 > ExitStatusFile 2>&1")
        return(3)
    }
    
    }#Normal Docker execution
  else
  {#Swarm Docker execution
    stringExcution=""
    if (group=="sudo")
      stringExcution="sudo"
    #all this part must be replaced in locus
    nameService=paste("Service",gsub(":","-",gsub(" ","-",date())),sep="")
    params= strsplit(params , split = "dockerID")[[1]][2]#remove dockerID file
    params=gsub("-v ","--mount src=",params)#remove -v
    params=gsub(":",",dst=",params)#remove ":"
    params=gsub("-d "," ",params)#remove "-d"
    #all this part must replaced in locus
    stringExcution=paste(stringExcution,"docker service create --replicas 1 --name",nameService,"--restart-condition=\"none\" ",params," ")
    system(stringExcution)
    
    dockerStatus=strsplit(system(paste("docker service ps ",nameService),intern= T)[2],split=" ")[6]
    cat("\n\nBefore while, docker status: ",dockerStatus,"\n")
    while(dockerStatus=="running"){
      Sys.sleep(10);
      dockerStatus=strsplit(system(paste("docker service ps ",nameService),intern= T)[2],split=" ")[6]
      cat(".")
    }
    cat(".\n\n")
  }#Swarm Docker execution
  system("echo 0 > ExitStatusFile 2>&1")
  return(0)
  
    }