Nothing
successDelete <-
function(hotFolder,sucFolder = "_RmqqcFile_Processed",destDelete = F,mqqcInfo = NULL,htmloutpath = NULL)
{
#grep("20131216_AD_ECst",folders)
folders <- listFolders(hotFolder)
folders <- folders[grep("^_RmqqcFile",basename(folders),invert = T)]
collectListPath <- paste(hotFolder,sucFolder,"list_collect.csv",sep = "/")
try(ProgressTracker(folders,htmloutpath) )
# Search only in folders which have not been processed, reduces search space
if( file.exists(collectListPath)){
collectList <- read.csv(collectListPath, check.names = F,stringsAsFactors = F)
collectListInitdim <- dim(collectList)
collectListclean <- apply(collectList,2,function(x){all(is.na(x))})
collectList <- collectList[,!collectListclean]
if(dim(collectList)[2] < collectListInitdim[2]){
write.csv(collectList, collectListPath,row.names = F,quote = F)
}
imported <- collectList[,dim(collectList)[2]]
processed <- unlist(lapply(strsplit(as.character(imported),"/combined"),function(x){return(x[1])}))
folders <- setdiff(folders,processed)
}
if(length(folders) > 0){
tempI <- list.files(folders,pattern = "evidence.txt",full.name = T,recursive = T)
tempImqqc <- list.files(folders,pattern = "mqqc",full.name = T,recursive = T, include.dirs = T)
if(length(tempImqqc) > 0 & length(tempI) > 0){
tempI <- tempI[merge.control(dirname(tempI),dirname(tempImqqc))]
if(any(!is.na(tempI))){
tempI <- tempI[!is.na(tempI)]
}
}
tempI <- unique(tempI)
tempIproc <- sapply(dirname(tempI),list.files,pattern = "mqqcProcessed")
tempIprocMoved <- sapply(dirname(tempI),list.files,pattern = "mqqcMoved")
#tempI <- tempI[!as.logical(sapply(tempIproc,length))]
tempIproc <- !as.logical(sapply(tempIproc,length))
if(length(tempI) > 0){
#preparing Path and foldername
repl <- paste(hotFolder,"/",sep = "")
repl <- gsub("//","/",repl)
folderName <- gsub(repl,"",tempI,fixed = T)
#folderName <- gsub("//","",folderName,fixed = T)
folderName <- strsplit(folderName,"/")
folderNameVec <- c()
for(i in 1:length(folderName)){
folderNameVec <- c(folderNameVec,folderName[[i]][1])
}
# Check if evidence was already processed if yes, no output of evidence path
mqqcInfo <- c()
for(i in 1:length(tempI)){
tempmqqcInfo <- list.files(dirname(tempI[i]),pattern = "mqqc",full.name = "T")
# check if mqqc is in folder
if(length(tempmqqcInfo)!=0){
write("",paste(dirname(tempI[i]),"mqqcProcessed",sep = "/"))
sucFolderPath <- paste(hotFolder,sucFolder,sep = "/")
if(!file.exists(sucFolderPath)){
dir.create(sucFolderPath, showWarnings = F)
}
qcData <- list.files(tempmqqcInfo,pattern = ".csv",full.name = T,recursive = T)
qcData <- qcData[grep("unidentified_conta",basename(qcData),invert = T)]
if(length(qcData)> 0&tempIproc[i]){
writeName <- paste(hotFolder,sucFolder,"list_collect.csv",sep = "/")
for(ba in qcData){
checkList <- list.files(paste(hotFolder,sucFolder,sep = "/"),pattern = "list_collect.csv",full.name = T)
temp <- readLines(ba)
temp <- paste(temp,c("File.Path",ba),sep = ",")
if(length(checkList) == 0){
write(temp,file = writeName)
}else{
checkListCol <- readLines(checkList,n = 1)
#checkListCol <- gsub(";",",",checkListCol)
if(checkListCol!= temp[1]){
ImprCheckListCol <- unlist(strsplit(checkListCol,","))
ImprCheckListCol <- gsub("\"","", ImprCheckListCol)
ImprTempCol <- unlist(strsplit(temp[1],","))
tempCheckList <- read.csv(checkList,quote = "")
NewData <- read.csv(ba,quote = "")
newT <- unique(c(colnames(tempCheckList),colnames(NewData)))
newOrder <- merge.control(newT,colnames(tempCheckList))
NewDatMatch <- match(newT,colnames(NewData))
NewData <-t(NewData)[NewDatMatch, ]
tempCheckListMatch <- match(newT ,colnames(tempCheckList))
if(!any(is.na(tempCheckListMatch))){
tempCheckList <- tempCheckList[,tempCheckListMatch]
}else{
tempCheckList <- t(tempCheckList)[tempCheckListMatch,]
rownames(tempCheckList) <- newT
tempCheckList <- t(tempCheckList)
}
#newOrder <- merge.control(colnames(NewData),colnames(tempCheckList))
NewOrderNew <- setdiff(1:length(newT), newOrder)
if(length(NewOrderNew) > 0){
newOrder <- c(newOrder, NewOrderNew)
}
NewData <- NewData
tempCheckList <- apply(tempCheckList,2,as.character)
tempCheckListNew <- rbind(tempCheckList,as.character(NewData))
colnames(tempCheckListNew) <- newT
try(write.csv(tempCheckListNew, writeName,row.names = F,quote = F))
#write.csv(tempCheckList, writeName,row.names = F,quote = F)
#tempCheckList<- cbind(tempCheckList,"")
#updateCheckList[is.na(updateCheckList)] <- dim(tempCheckList)[2]
#tempCheckList <- tempCheckList[, updateCheckList]
#colnames(tempCheckList) <- ImprTempCol
#file.rename(checkList,gsub("list_collect.csv$","list_collect_old.csv",checkList))
#write.csv(tempCheckList,checkList,row.names = F,quote = F)
}else{
try(write(temp[2],file = writeName,append = T))
}
}
}
## Combine Original MQ summary:
baSummary <- paste(dirname(ba),"summary.txt",sep = "/")
writeNameSum <- paste(hotFolder,sucFolder,"Summaries.txt",sep = "/")
if(!exists(writeNameSum)){
file.copy(baSummary,writeNameSum)
}else{
su <- readLines(writeNameSum,n = 2)
write(su[2],writeNameSum,append = T)
}
}
# start renaming
if(any(list.files(dirname(tempmqqcInfo)) == "mqqcProcessed")& any(basename(tempmqqcInfo) != "mqqcProcessed")){
MovTest <- tempmqqcInfo[basename(tempmqqcInfo) != "mqqcProcessed" & basename(tempmqqcInfo) != "mqqcMoved" ]
DelCont <- F
if(length(MovTest) > 0){
# DelCont <- file.rename(MovTest[1],paste(sucFolderPath,paste(Sys.Date(),folderNameVec[i],sep = "_"),sep = "/"))
DelCont <- file.copy(MovTest[1],paste(sucFolderPath,paste(Sys.Date(),folderNameVec[i],sep = "_"),sep = "/"),overwrite = T)
if(DelCont){
write("",paste(dirname(tempI[i]),"mqqcMoved",sep = "/"))
}
}
if(DelCont){
tempmqqcInfo <<- tempmqqcInfo
lengthSplitSlash <- length(unlist(strsplit(hotFolder,"/")))
tempPath <- unique(dirname(tempmqqcInfo))
write("",paste(paste(unlist(strsplit(tempPath,"/"))[1:(lengthSplitSlash +1)],collapse ="/"),"DeleteTag",sep = "/"))
}
}
}
}
# mqqcInfo <- mqqcInfo[file.info(mqqcInfo)$isdir]
}
}
files <- list.files(hotFolder,full.name = T)
files <- files[grep("^_RmqqcFile",basename(files),value = F,invert = T)]
fileDelete <- list.files(files,pattern = "^DeleteTag$",recursive = T,full.name = T)
DelFun <- function(fileDelete,time.thresh = 86400,move = T, destDelete = F,hotFolder){
time.vec <- as.numeric(Sys.time()) - as.numeric(file.info(fileDelete)$ctime)
# fileDelete <- fileDelete[time.vec > 86400]
if(time.vec >time.thresh){
if(destDelete){
unlink(dirname(fileDelete),recursive = T)
}
if(move&! destDelete){
file.rename(paste(hotFolder,basename(dirname(fileDelete)),sep = "/"),paste(hotFolder,"_RmqqcFile_Old",basename(dirname(fileDelete)),sep = "/"))
}
}
}
if(length(fileDelete) > 0){
if(destDelete){
lapply(fileDelete,DelFun,hotFolder = hotFolder, destDelete = T,move = F)
}else{
lapply(fileDelete,DelFun,hotFolder = hotFolder,move = T, destDelete = F)
}
}
# listFiles <- list.files(fileDelete,recursive = T,full.name = T)
return(mqqcInfo)
}
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