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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 "";
        }
    } |