misc/Imports/CreateTarGz_Loren.R

In cesco-lab/Vigie-Chiro_scripts: Predict Distribution Of Chiropter

library(data.table)
#library(tools)
library(foreach)

ParDir="H:/Test_VigieChiro"
OutputDir="H:/upload"
#irodsDir="C:\\wamp64\\www\\.icommands"
#SiteLoc=fread("C:/wamp64/www/sites_localites.txt")
irodsDest="/ccin2p3/home/ybas/transferts"
SevenzDir="C:/Program Files/7-Zip"

ListSites=dir(ParDir,full.names=T)

ListPar=vector()
for (h in 1:length(ListSites))
{
  ListParh=dir(ListSites[h],full.names=T)
  ListPar=c(ListPar,ListParh)
}
dir.create(OutputDir)

#check participations codes
llp=(nchar(basename(ListPar)))
if(mean(llp)!=24){
  stop("ERREUR : nom des sous-repertoires non conformes")
}

for (i in 1:length(ListPar))
{
  ListWav=list.files(ListPar[i],full.names=T,pattern=".wav$")
  ListWav2=list.files(ListPar[i],full.names=T,pattern=".WAV$")
  ListWtot=c(ListWav,ListWav2)
  ListWtot=ListWtot[order(basename(ListWtot))]
  ListBloc=dir(ListPar[i],full.names=T,pattern="bloc")
  
  if(length(ListWtot)>0)
  {
    SiteInfo=tstrsplit(basename(ListWtot),split="-")[[1]]
    if(length(unique(SiteInfo))>1)
    {
      stop(paste("ERREUR : plusieurs sites dans le repertoire"
                 ,basename(ListPar[i])))
    }
    #Sitei=gsub("Car","Vigiechiro - Point Fixe-",SiteInfo[1])
    #testSite=match(Sitei,SiteLoc$site)
    #DirSite=SiteLoc$id_site[testSite]
    DirSite=basename(dirname(ListPar[i]))
    dir.create(paste0(OutputDir,"/",DirSite))
    
    
    
    dir.create(paste0(OutputDir,"/",DirSite,"/",basename(ListPar[i])))
    dir.create(paste0(OutputDir,"/",DirSite,"/",basename(ListPar[i])
                      ,"/wav"))
    
    TarGZtot=list.files(paste0(OutputDir,"/",DirSite,"/",basename(ListPar[i])
                               ,"/wav"),pattern=".tar.gz$")
    #case 0 : dealing with failed last block
    if(length(ListBloc)>0)
    {
      stop("participation partiellement traitee")
    }else{
      Bnum=0
    }
    
    testp=foreach (j = 1:ceiling(length(ListWtot)/100)) %do% {
      
      NumBloc=j+max(Bnum)
      Numj=c(((j-1)*100+1):min(j*100,length(ListWtot)))
      Listj=ListWtot[Numj]
      BlocDir=paste0(ListPar[i],"/bloc",NumBloc)
      if(dir.exists((BlocDir))){stop(paste("ERREUR : repertoire"
                                           ,ListPar[i],"deja traite"))}
      dir.create(BlocDir)
      Newj=paste0(BlocDir,"/",basename(Listj))
      Sys.time()
      test=file.rename(from=Listj,to=Newj) #0.6 sec
      if(mean(test)!=1){stop(paste("ERREUR : copie fichier wave non permise"))}
      Sys.time()
      #ecriture liste.txt
      TarName=paste0(OutputDir,"/",DirSite,"/",basename(ListPar[i])
                     ,"/wav/"
                     ,gsub(".wav","",(basename(Listj[1])))
                     ,".tar")
      TarGZName=paste0(OutputDir,"/",DirSite,"/",basename(ListPar[i])
                       ,"/wav/"
                       ,gsub(".wav","",(basename(Listj[1])))
                       ,".tar.gz")
      TarGZtot=c(TarGZtot,basename(TarGZName))
      dir.create(dirname(TarName))
      #tar(TarName,files=Listj)
      #tar(TarGZName,files=Listj,compression="gzip")
      Sys.time()
      system(paste0("7za a -ttar ",TarName," ",BlocDir,"/*.*")
             ,intern=T) #6.5 secondes
      Sys.time()
      system(paste0("7za a -tgzip ",TarGZName," ",TarName)
             ,intern=T) #12.4 secondes
      Sys.time()
      
    }
    Listei=data.frame(liste=TarGZtot)
    Listei=as.data.table(Listei)[order(Listei$liste),]
    fwrite(Listei,paste0(OutputDir,"/",DirSite,"/",basename(ListPar[i])
                         ,"/wav/liste.txt"),col.names=F)
    
  }#else{
  #stop(paste("ERREUR : repertoire",basename(ListPar[i]),"vide"))
  #}
  
}

#suppression des *.tar
ListTar=list.files(OutputDir,pattern=".tar$",recursive=T,full.names=T)
file.remove(ListTar)

#copie irods du contenu de OutputDir
ListFilesToCopy=list.files(OutputDir,recursive=T,full.names=T)
test1=grepl(".tar.gz",ListFilesToCopy)
test2=grepl("liste.txt",ListFilesToCopy)
if(mean(test1|test2)!=1){
  stop("ERREUR : fichiers indesirables dans OutputDir")
}
ListWindows=gsub("/","\\\\",ListFilesToCopy)

TGZDest=gsub(OutputDir,irodsDest,ListFilesToCopy)


#iinit=paste0(irodsDir,"\\iinit")
#system(iinit)
Batch=vector()
DirToMake=unique(dirname(TGZDest))
DirToMake2=unique(dirname(DirToMake))
DirToMake3=unique(dirname(DirToMake2))
DirToMakeTot=c(DirToMake3,DirToMake2,DirToMake)
for (k in 1:length(DirToMakeTot))
{
  icom=paste0("imkdir ",DirToMakeTot[k])
  #icom=paste0("iput ",ListTGZ[k]," ",TGZDest[k])
  #system(paste0("icd ",irodsDir))
  #system(icom)
  Batch=c(Batch,icom)
  
}



for (k in 1:length(ListFilesToCopy))
{
  icom=paste0("iput ",ListWindows[k]," ",TGZDest[k])
  #icom=paste0("iput ",ListTGZ[k]," ",TGZDest[k])
  #system(paste0("icd ",irodsDir))
  #system(icom)
  Batch=c(Batch,icom)
  
}

ListDir=unique(dirname(TGZDest))

for (l in 1:length(ListDir))
{
  ichmod1=paste0("ichmod -r read mnhn ",ListDir[l])
  ichmod2=paste0("ichmod -r write mnhn ",ListDir[l])
  Batch=c(Batch,ichmod1)
  Batch=c(Batch,ichmod2)
}
BatchDF=data.frame(instruc=Batch)
fwrite(BatchDF,paste0(OutputDir,"/batch.txt"),col.names=F)