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public String doImport() {
long begin = System.currentTimeMillis();
if (verifImport == true) {
// ouvre le fichier d'import
File fileTraitement = new File(File.separator + repository + "outImportSample" + sessionId + ".csv");
List<AllResSample> listeAllResSample = new ArrayList<AllResSample>();
if (fileTraitement.isFile()) {
StringTokenizer st;
try {
FileReader fr = new FileReader(fileTraitement);
BufferedReader br = new BufferedReader(fr);
String ligne;
try {
AllResSample all1;
AllResSample all2;
AllResSamplePk pk1;
AllResSamplePk pk2;
StringBuilder sampleT = new StringBuilder();
StringBuilder locusT = new StringBuilder();
StringBuilder runT = new StringBuilder();
StringBuilder dyeT = new StringBuilder();
StringBuilder alleleT1 = new StringBuilder();
StringBuilder peakT1 = new StringBuilder();
StringBuilder qualT1 = new StringBuilder();
StringBuilder volumeT1 = new StringBuilder();
StringBuilder alleleT2 = new StringBuilder();
StringBuilder peakT2 = new StringBuilder();
StringBuilder qualT2 = new StringBuilder();
StringBuilder volumeT2 = new StringBuilder();
StringBuilder commentT = new StringBuilder();
int t = 0;
while ((ligne = br.readLine()) != null) {
alleleAmount = 1;
// System.out.println(ligne);
/*set les attributs temporaire*/
st = new StringTokenizer(ligne);
sampleT.insert(0, st.nextToken(";"));
locusT.insert(0, st.nextToken(";"));
runT.insert(0, st.nextToken(";"));
dyeT.insert(0, st.nextToken(";"));
alleleT1.insert(0, st.nextToken(";"));
peakT1.insert(0, st.nextToken(";"));
qualT1.insert(0, st.nextToken(";"));
volumeT1.insert(0, st.nextToken(";"));
alleleT2.insert(0, st.nextToken(";"));
peakT2.insert(0, st.nextToken(";"));
qualT2.insert(0, st.nextToken(";"));
volumeT2.insert(0, st.nextToken(";"));
commentT.insert(0, st.nextToken(";"));
all1 = new AllResSample();
all2 = new AllResSample();
pk1 = new AllResSamplePk();
pk2 = new AllResSamplePk();
pk1.setLocusId(locusT.substring(0));
pk1.setProjetId(projetId);
pk1.setSampleId(sampleT.substring(0));
/*pour une ligne qui possède la meme allele*/
if (alleleT1.equals(alleleT2)) {
pk1.setAlleleId(alleleT1.substring(0));
all1.setClePrimaire(pk1);
all1.setAlleleAmount(alleleAmount);
all1.setComment(commentT.substring(0));
all1.setDiscard(false);
all1.setDye(dyeT.substring(0));
all1.setPeak(Double.valueOf(peakT1.substring(0)));
all1.setQuality(Integer.parseInt(qualT1.substring(0)));
all1.setRun(runT.substring(0));
all1.setVolume(Integer.parseInt(volumeT1.substring(0)));
listeAllResSample.add(all1);
} else {
pk2.setLocusId(locusT.substring(0));
pk2.setProjetId(projetId);
pk2.setSampleId(sampleT.substring(0));
alleleAmount = (float) 0.5;
pk1.setAlleleId(alleleT1.substring(0));
pk2.setAlleleId(alleleT2.substring(0));
all1.setClePrimaire(pk1);
all2.setClePrimaire(pk2);
all1.setAlleleAmount(alleleAmount);
all1.setComment(commentT.substring(0));
all1.setDiscard(false);
all1.setDye(dyeT.substring(0));
all1.setPeak(Double.valueOf(peakT1.substring(0)));
all1.setQuality(Integer.parseInt(qualT1.substring(0)));
all1.setRun(runT.substring(0));
all1.setVolume(Integer.parseInt(volumeT1.substring(0)));
all2.setAlleleAmount(alleleAmount);
all2.setComment(commentT.substring(0));
all2.setDiscard(false);
all2.setDye(dyeT.substring(0));
all2.setPeak(Double.valueOf(peakT2.substring(0)));
all2.setQuality(Integer.parseInt(qualT2.substring(0)));
all2.setRun(runT.substring(0));
all2.setVolume(Integer.parseInt(volumeT2.substring(0)));
listeAllResSample.add(all1);
listeAllResSample.add(all2);
sampleT.delete(0, sampleT.length());
locusT.delete(0, locusT.length());
runT.delete(0, runT.length());
dyeT.delete(0, dyeT.length());
alleleT1.delete(0, alleleT1.length());
peakT1.delete(0, peakT1.length());
qualT1.delete(0, qualT1.length());
volumeT1.delete(0, volumeT1.length());
alleleT2.delete(0, alleleT2.length());
peakT2.delete(0, peakT2.length());
qualT2.delete(0, qualT2.length());
volumeT2.delete(0, volumeT2.length());
commentT.delete(0, commentT.length());
}
t++;
} // fin while
Projet p = psbl.findProjet(projetId);
p.getListeAllResSample().addAll(listeAllResSample);
psbl.updateProjet(p);
doDeleteFile();
} catch (IOException ex) {
Logger.getLogger(importAccGermSamp.class.getName()).log(Level.SEVERE, null, ex);
}
} catch (FileNotFoundException ex) {
Logger.getLogger(importAccGermSamp.class.getName()).log(Level.SEVERE, null, ex);
}
}
FacesContext facesContext = FacesContext.getCurrentInstance();
FacesMessage message2 = new FacesMessage();
message2.setSeverity(message2.SEVERITY_INFO);
message2.setSummary("l'import des données est terminé");
facesContext.addMessage(null, message2);
long end = System.currentTimeMillis();
float time = (end - begin) / 1000;
System.out.println("time doImport() : " + time);
doDeleteFile();
return "";
} else {
FacesContext facesContext = FacesContext.getCurrentInstance();
FacesMessage message2 = new FacesMessage();
message2.setSeverity(message2.SEVERITY_ERROR);
message2.setSummary("Aucun Import n'a été effectué");
facesContext.addMessage(null, message2);
doDeleteFile();
return "";
}
} |