R/ThreadControl.R

In mqqc: Quality control of LCMS derived proteomic data

ThreadControl <- 
function(folder,maxHours = 2,tableTC =  "_RmqqcFile_ThreadControl"){
  TL1 <- NA
  try(TL1 <- system("tasklist", intern = T),silent = T)
  if(!is.na(TL1)){
    wd <- getwd()

    try(TL <- tasklistCheck())
    
    
   if(length(TL) > 0){
  TLobserve <- TL1[TL]
  #TLobserve2 <- TLobserve
  #TLobserve2 <- gsub("6984","2948",TLobserve2)
  #TLobserve <- c(TLobserve2, TLobserve) 
  
  temp <- lapply(TLobserve,function(x){
  	tempX <- strsplit(x," ")
  	tempX <- unlist(tempX)
  	tempX  <-(tempX[tempX != ""])
  
  	return(tempX) 
  })
  
  TC <- list.files(folder,pattern = tableTC )
  
  Table.Dat <- sapply(temp,function(x){
  	return((c(x[1],x[2],as.numeric(Sys.time()))))
  	
  	
  })
  Table.Dat <- t(Table.Dat)
  
  if(length(TC) == 0){
  	if(is.vector(Table.Dat)){Table.Dat <- t(as.matrix(Table.Dat))}
  	rownames(Table.Dat) <- NULL
  	write.csv(Table.Dat, tableTC, row.names = F)
  }else{
  	
  	
  }
  
  ControlTC <- 	read.csv(tableTC)	
  if(all(dim(ControlTC) == c(3,1))){ControlTC <- t(ControlTC)}
  Delete 	<- setdiff(ControlTC[,2], Table.Dat[,2])
  Add 		<- setdiff(Table.Dat[,2],ControlTC[,2] )
  if(length(Add) > 0){
  	
  	if(is.vector(Table.Dat)){Table.Dat <- t(as.matrix(Table.Dat))}
  	write.csv(Table.Dat[Table.Dat[,2] == Add], tableTC, row.names = F,append = T)
  
  }
  ControlTC <- 	read.csv(tableTC)	
  if(all(dim(ControlTC) == c(3,1))){ControlTC <- t(ControlTC)}
  
  if(length(Delete) > 0){
  	for(i in Delete){
  		ControlTC <- ControlTC[ControlTC[,2] !=i ,]
  	}
  	write.csv(ControlTC,tableTC,row.names = F)
  	
  }
  ControlTC <- 	read.csv(tableTC)	
  if(all(dim(ControlTC) == c(3,1))){ControlTC <- t(ControlTC)}
  
  ######
  # Force Quit if Program runs longer than 3 hours
  ######
  DiffTime<- as.numeric(Sys.time())-ControlTC[,3] 
  DiffTime <- ControlTC[DiffTime > 60*60* maxHours,2]
  if(length(DiffTime)){
  sapply(DiffTime,function(x){
  	system(paste("taskkill /pid",x,"/f"))
  })
  }
  }
  setwd(wd)
}
}