List of usage examples for java.util.zip ZipOutputStream ZipOutputStream
public ZipOutputStream(OutputStream out)
From source file:eu.europa.ejusticeportal.dss.controller.action.DownloadSignedPdf.java
/** * @param sf/*from ww w . j a v a2s. c om*/ * @param response * @throws IOException */ private void writeZip(SignedForm sf, HttpServletResponse response, String fileName) throws IOException { ZipOutputStream zos = new ZipOutputStream(response.getOutputStream()); ZipEntry ze = new ZipEntry(fileName); zos.putNextEntry(ze); zos.write(sf.getDocument()); ze = new ZipEntry(fileName + ".xml"); zos.putNextEntry(ze); zos.write(sf.getDetachedSignature()); zos.closeEntry(); zos.close(); }
From source file:com.mc.printer.model.utils.ZipHelper.java
/** * ZIP/*from www . j a v a 2 s .c om*/ * * @param sourcePath * @param zipPath ?zip?? */ public static void createZip(String sourcePath, String zipPath) { FileOutputStream fos = null; ZipOutputStream zos = null; try { fos = new FileOutputStream(zipPath); zos = new ZipOutputStream(fos); writeZip(new File(sourcePath), "", zos); } catch (FileNotFoundException e) { log.error("create zip file failed.", e); } finally { try { if (zos != null) { zos.close(); } if (fos != null) { fos.close(); } } catch (IOException e) { log.error("create zip file failed.", e); } } }
From source file:jp.co.tis.gsp.tools.dba.dialect.SolrDialect.java
@Override public void exportSchema(String user, String password, String schema, File dumpFile) throws MojoExecutionException { String solrUrl = url.substring("jdbc:solr:".length()); try {/*from w w w . ja v a2s . com*/ SolrConnection connection = ConnectionTypeDetector.getInstance().find(solrUrl); if (connection instanceof EmbeddedConnectionImpl) { System.err.println(solrUrl); EmbeddedSolrServer solrServer = (EmbeddedSolrServer) connection.getSolrServer(); SolrCore core = solrServer.getCoreContainer() .getCore(solrServer.getCoreContainer().getDefaultCoreName()); ZipOutputStream zos = new ZipOutputStream(new FileOutputStream(dumpFile.getAbsolutePath())); } } catch (Exception e) { throw new MojoExecutionException("Export error", e); } }
From source file:eu.planets_project.pp.plato.action.ProjectExportAction.java
/** * Exports all projects into separate xml files and adds them to a zip archive. * @return null Always returns null, so user stays on same screen after action performed */// ww w . j a v a 2 s . com public String exportAllProjectsToZip() { List<PlanProperties> ppList = em.createQuery("select p from PlanProperties p").getResultList(); if (!ppList.isEmpty()) { log.debug("number of plans to export: " + ppList.size()); String filename = "allprojects.zip"; String exportPath = OS.getTmpPath() + "export" + System.currentTimeMillis() + "/"; new File(exportPath).mkdirs(); String binarydataTempPath = exportPath + "binarydata/"; File binarydataTempDir = new File(binarydataTempPath); binarydataTempDir.mkdirs(); try { OutputStream out = new BufferedOutputStream(new FileOutputStream(exportPath + filename)); ZipOutputStream zipOut = new ZipOutputStream(out); for (PlanProperties pp : ppList) { log.debug("EXPORTING: " + pp.getName()); ZipEntry zipAdd = new ZipEntry(String.format("%1$03d", pp.getId()) + "-" + FileUtils.makeFilename(pp.getName()) + ".xml"); zipOut.putNextEntry(zipAdd); // export the complete project, including binary data exportComplete(pp.getId(), zipOut, binarydataTempPath); zipOut.closeEntry(); } zipOut.close(); out.close(); new File(exportPath + "finished.info").createNewFile(); FacesMessages.instance().add(FacesMessage.SEVERITY_INFO, "Export was written to: " + exportPath); log.info("Export was written to: " + exportPath); } catch (IOException e) { FacesMessages.instance().add(FacesMessage.SEVERITY_ERROR, "An error occured while generating the export file."); log.error("An error occured while generating the export file.", e); File errorInfo = new File(exportPath + "error.info"); try { Writer w = new FileWriter(errorInfo); w.write("An error occured while generating the export file:"); w.write(e.getMessage()); w.close(); } catch (IOException e1) { log.error("Could not write error file."); } } finally { // remove all binary temp files OS.deleteDirectory(binarydataTempDir); } } else { FacesMessages.instance().add("No Projects found!"); } return null; }
From source file:nc.noumea.mairie.appock.services.impl.ExportExcelServiceImpl.java
@Override public void genereExcelFournisseur(Commande commande) throws IOException { List<String> listeMessageErreurAdresseService = construitMessageErreurAdresseService(commande); if (org.apache.commons.collections4.CollectionUtils.isNotEmpty(listeMessageErreurAdresseService)) { Messagebox.show(StringUtils.join(listeMessageErreurAdresseService, "\n"), "Erreur d'adresse", Messagebox.OK, Messagebox.ERROR); return;/*from w ww . j a v a2 s. c o m*/ } Map<AbstractEntity, Map<Service, List<ArticleDemande>>> map = commandeService .construitMapFournisseurServiceListeArticleDemande(commande); List<AbstractEntity> listeAbstractEntity = new ArrayList(map.keySet()); Comparator abstractEntityComparator = Comparator .comparing((AbstractEntity abstractEntity) -> abstractEntity.getLibelleCourt()); Collections.sort(listeAbstractEntity, abstractEntityComparator); File result = File.createTempFile(UUID.randomUUID().toString(), ".zip"); FileOutputStream fos = new FileOutputStream(result); ZipOutputStream zos = new ZipOutputStream(fos); for (AbstractEntity abstractEntity : listeAbstractEntity) { String nomFichierSansExtension = construitNomFichier(abstractEntity); File tempFile = createExcelTempFile(map, abstractEntity, nomFichierSansExtension); addToZipFile(tempFile, nomFichierSansExtension + ".xlsx", zos); tempFile.delete(); } zos.close(); fos.close(); downloadService.downloadToUser(result, "Fichiers fournisseurs.zip"); result.delete(); }
From source file:fr.cirad.mgdb.exporting.markeroriented.GFFExportHandler.java
@Override public void exportData(OutputStream outputStream, String sModule, List<SampleId> sampleIDs, ProgressIndicator progress, DBCursor markerCursor, Map<Comparable, Comparable> markerSynonyms, int nMinimumGenotypeQuality, int nMinimumReadDepth, Map<String, InputStream> readyToExportFiles) throws Exception { MongoTemplate mongoTemplate = MongoTemplateManager.get(sModule); ZipOutputStream zos = new ZipOutputStream(outputStream); if (readyToExportFiles != null) for (String readyToExportFile : readyToExportFiles.keySet()) { zos.putNextEntry(new ZipEntry(readyToExportFile)); InputStream inputStream = readyToExportFiles.get(readyToExportFile); byte[] dataBlock = new byte[1024]; int count = inputStream.read(dataBlock, 0, 1024); while (count != -1) { zos.write(dataBlock, 0, count); count = inputStream.read(dataBlock, 0, 1024); }//from www . j av a 2 s. com } File warningFile = File.createTempFile("export_warnings_", ""); FileWriter warningFileWriter = new FileWriter(warningFile); int markerCount = markerCursor.count(); List<Individual> individuals = getIndividualsFromSamples(sModule, sampleIDs); ArrayList<String> individualList = new ArrayList<String>(); for (int i = 0; i < sampleIDs.size(); i++) { Individual individual = individuals.get(i); if (!individualList.contains(individual.getId())) { individualList.add(individual.getId()); } } String exportName = sModule + "_" + markerCount + "variants_" + individualList.size() + "individuals"; zos.putNextEntry(new ZipEntry(exportName + ".gff3")); String header = "##gff-version 3" + LINE_SEPARATOR; zos.write(header.getBytes()); TreeMap<String, String> typeToOntology = new TreeMap<String, String>(); typeToOntology.put(Type.SNP.toString(), "SO:0000694"); typeToOntology.put(Type.INDEL.toString(), "SO:1000032"); typeToOntology.put(Type.MIXED.toString(), "SO:0001059"); typeToOntology.put(Type.SYMBOLIC.toString(), "SO:0000109"); typeToOntology.put(Type.MNP.toString(), "SO:0001059"); int avgObjSize = (Integer) mongoTemplate .getCollection(mongoTemplate.getCollectionName(VariantRunData.class)).getStats().get("avgObjSize"); int nChunkSize = nMaxChunkSizeInMb * 1024 * 1024 / avgObjSize; short nProgress = 0, nPreviousProgress = 0; long nLoadedMarkerCount = 0; while (markerCursor.hasNext()) { int nLoadedMarkerCountInLoop = 0; Map<Comparable, String> markerChromosomalPositions = new LinkedHashMap<Comparable, String>(); boolean fStartingNewChunk = true; markerCursor.batchSize(nChunkSize); while (markerCursor.hasNext() && (fStartingNewChunk || nLoadedMarkerCountInLoop % nChunkSize != 0)) { DBObject exportVariant = markerCursor.next(); DBObject refPos = (DBObject) exportVariant.get(VariantData.FIELDNAME_REFERENCE_POSITION); markerChromosomalPositions.put((Comparable) exportVariant.get("_id"), refPos.get(ReferencePosition.FIELDNAME_SEQUENCE) + ":" + refPos.get(ReferencePosition.FIELDNAME_START_SITE)); nLoadedMarkerCountInLoop++; fStartingNewChunk = false; } List<Comparable> currentMarkers = new ArrayList<Comparable>(markerChromosomalPositions.keySet()); LinkedHashMap<VariantData, Collection<VariantRunData>> variantsAndRuns = MgdbDao.getSampleGenotypes( mongoTemplate, sampleIDs, currentMarkers, true, null /*new Sort(VariantData.FIELDNAME_REFERENCE_POSITION + "." + ChromosomalPosition.FIELDNAME_SEQUENCE).and(new Sort(VariantData.FIELDNAME_REFERENCE_POSITION + "." + ChromosomalPosition.FIELDNAME_START_SITE))*/); // query mongo db for matching genotypes for (VariantData variant : variantsAndRuns.keySet()) // read data and write results into temporary files (one per sample) { Comparable variantId = variant.getId(); List<String> variantDataOrigin = new ArrayList<String>(); Map<String, Integer> gqValueForSampleId = new LinkedHashMap<String, Integer>(); Map<String, Integer> dpValueForSampleId = new LinkedHashMap<String, Integer>(); Map<String, List<String>> individualGenotypes = new LinkedHashMap<String, List<String>>(); List<String> chromAndPos = Helper.split(markerChromosomalPositions.get(variantId), ":"); if (chromAndPos.size() == 0) LOG.warn("Chromosomal position not found for marker " + variantId); // LOG.debug(marker + "\t" + (chromAndPos.length == 0 ? "0" : chromAndPos[0]) + "\t" + 0 + "\t" + (chromAndPos.length == 0 ? 0l : Long.parseLong(chromAndPos[1])) + LINE_SEPARATOR); if (markerSynonyms != null) { Comparable syn = markerSynonyms.get(variantId); if (syn != null) variantId = syn; } Collection<VariantRunData> runs = variantsAndRuns.get(variant); if (runs != null) for (VariantRunData run : runs) for (Integer sampleIndex : run.getSampleGenotypes().keySet()) { SampleGenotype sampleGenotype = run.getSampleGenotypes().get(sampleIndex); String individualId = individuals .get(sampleIDs.indexOf(new SampleId(run.getId().getProjectId(), sampleIndex))) .getId(); Integer gq = null; try { gq = (Integer) sampleGenotype.getAdditionalInfo().get(VariantData.GT_FIELD_GQ); } catch (Exception ignored) { } if (gq != null && gq < nMinimumGenotypeQuality) continue; Integer dp = null; try { dp = (Integer) sampleGenotype.getAdditionalInfo().get(VariantData.GT_FIELD_DP); } catch (Exception ignored) { } if (dp != null && dp < nMinimumReadDepth) continue; String gtCode = sampleGenotype.getCode(); List<String> storedIndividualGenotypes = individualGenotypes.get(individualId); if (storedIndividualGenotypes == null) { storedIndividualGenotypes = new ArrayList<String>(); individualGenotypes.put(individualId, storedIndividualGenotypes); } storedIndividualGenotypes.add(gtCode); } zos.write((chromAndPos.get(0) + "\t" + StringUtils.join(variantDataOrigin, ";") /*source*/ + "\t" + typeToOntology.get(variant.getType()) + "\t" + Long.parseLong(chromAndPos.get(1)) + "\t" + Long.parseLong(chromAndPos.get(1)) + "\t" + "." + "\t" + "+" + "\t" + "." + "\t") .getBytes()); Comparable syn = markerSynonyms == null ? null : markerSynonyms.get(variant.getId()); zos.write(("ID=" + variant.getId() + ";" + (syn != null ? "Name=" + syn + ";" : "") + "alleles=" + StringUtils.join(variant.getKnownAlleleList(), "/") + ";" + "refallele=" + variant.getKnownAlleleList().get(0) + ";").getBytes()); for (int j = 0; j < individualList .size(); j++ /* we use this list because it has the proper ordering*/) { NumberFormat nf = NumberFormat.getInstance(Locale.US); nf.setMaximumFractionDigits(4); HashMap<String, Integer> compt1 = new HashMap<String, Integer>(); int highestGenotypeCount = 0; int sum = 0; String individualId = individualList.get(j); List<String> genotypes = individualGenotypes.get(individualId); HashMap<Object, Integer> genotypeCounts = new HashMap<Object, Integer>(); // will help us to keep track of missing genotypes String mostFrequentGenotype = null; if (genotypes != null) for (String genotype : genotypes) { if (genotype.length() == 0) continue; /* skip missing genotypes */ int count = 0; for (String t : variant.getAllelesFromGenotypeCode(genotype)) { for (String t1 : variant.getKnownAlleleList()) { if (t.equals(t1) && !(compt1.containsKey(t1))) { count++; compt1.put(t1, count); } else if (t.equals(t1) && compt1.containsKey(t1)) { if (compt1.get(t1) != 0) { count++; compt1.put(t1, count); } else compt1.put(t1, count); } else if (!(compt1.containsKey(t1))) { compt1.put(t1, 0); } } } for (int countValue : compt1.values()) { sum += countValue; } int gtCount = 1 + MgdbDao.getCountForKey(genotypeCounts, genotype); if (gtCount > highestGenotypeCount) { highestGenotypeCount = gtCount; mostFrequentGenotype = genotype; } genotypeCounts.put(genotype, gtCount); } List<String> alleles = mostFrequentGenotype == null ? new ArrayList<String>() : variant.getAllelesFromGenotypeCode(mostFrequentGenotype); if (alleles.size() != 0) { zos.write(("acounts=" + individualId + ":").getBytes()); for (String knowAllelesCompt : compt1.keySet()) { zos.write( (knowAllelesCompt + " " + nf.format(compt1.get(knowAllelesCompt) / (float) sum) + " " + compt1.get(knowAllelesCompt) + " ").getBytes()); } zos.write((alleles.size() + ";").getBytes()); } if (genotypeCounts.size() > 1) { Comparable sVariantId = markerSynonyms != null ? markerSynonyms.get(variant.getId()) : variant.getId(); warningFileWriter.write("- Dissimilar genotypes found for variant " + (sVariantId == null ? variant.getId() : sVariantId) + ", individual " + individualId + ". Exporting most frequent: " + StringUtils.join(alleles, ",") + "\n"); } } zos.write((LINE_SEPARATOR).getBytes()); } if (progress.hasAborted()) return; nLoadedMarkerCount += nLoadedMarkerCountInLoop; nProgress = (short) (nLoadedMarkerCount * 100 / markerCount); if (nProgress > nPreviousProgress) { // if (nProgress%5 == 0) // LOG.info("========================= exportData: " + nProgress + "% =========================" + (System.currentTimeMillis() - before)/1000 + "s"); progress.setCurrentStepProgress(nProgress); nPreviousProgress = nProgress; } } warningFileWriter.close(); if (warningFile.length() > 0) { zos.putNextEntry(new ZipEntry(exportName + "-REMARKS.txt")); int nWarningCount = 0; BufferedReader in = new BufferedReader(new FileReader(warningFile)); String sLine; while ((sLine = in.readLine()) != null) { zos.write((sLine + "\n").getBytes()); in.readLine(); nWarningCount++; } LOG.info("Number of Warnings for export (" + exportName + "): " + nWarningCount); in.close(); } warningFile.delete(); zos.close(); progress.setCurrentStepProgress((short) 100); }
From source file:com.meltmedia.cadmium.core.util.WarUtils.java
/** * <p>This method updates a template war with the following settings.</p> * @param templateWar The name of the template war to pull from the classpath. * @param war The path of an external war to update (optional). * @param newWarNames The name to give the new war. (note: only the first element of this list is used.) * @param repoUri The uri to a github repo to pull content from. * @param branch The branch of the github repo to pull content from. * @param configRepoUri The uri to a github repo to pull config from. * @param configBranch The branch of the github repo to pull config from. * @param domain The domain to bind a vHost to. * @param context The context root that this war will deploy to. * @param secure A flag to set if this war needs to have its contents password protected. * @throws Exception/*from w w w .ja v a2s . com*/ */ public static void updateWar(String templateWar, String war, List<String> newWarNames, String repoUri, String branch, String configRepoUri, String configBranch, String domain, String context, boolean secure, Logger log) throws Exception { ZipFile inZip = null; ZipOutputStream outZip = null; InputStream in = null; OutputStream out = null; try { if (war != null) { if (war.equals(newWarNames.get(0))) { File tmpZip = File.createTempFile(war, null); tmpZip.delete(); tmpZip.deleteOnExit(); new File(war).renameTo(tmpZip); war = tmpZip.getAbsolutePath(); } inZip = new ZipFile(war); } else { File tmpZip = File.createTempFile("cadmium-war", "war"); tmpZip.delete(); tmpZip.deleteOnExit(); in = WarUtils.class.getClassLoader().getResourceAsStream(templateWar); out = new FileOutputStream(tmpZip); FileSystemManager.streamCopy(in, out); inZip = new ZipFile(tmpZip); } outZip = new ZipOutputStream(new FileOutputStream(newWarNames.get(0))); ZipEntry cadmiumPropertiesEntry = null; cadmiumPropertiesEntry = inZip.getEntry("WEB-INF/cadmium.properties"); Properties cadmiumProps = updateProperties(inZip, cadmiumPropertiesEntry, repoUri, branch, configRepoUri, configBranch); ZipEntry jbossWeb = null; jbossWeb = inZip.getEntry("WEB-INF/jboss-web.xml"); Enumeration<? extends ZipEntry> entries = inZip.entries(); while (entries.hasMoreElements()) { ZipEntry e = entries.nextElement(); if (e.getName().equals(cadmiumPropertiesEntry.getName())) { storeProperties(outZip, cadmiumPropertiesEntry, cadmiumProps, newWarNames); } else if (((domain != null && domain.length() > 0) || (context != null && context.length() > 0)) && e.getName().equals(jbossWeb.getName())) { updateDomain(inZip, outZip, jbossWeb, domain, context); } else if (secure && e.getName().equals("WEB-INF/web.xml")) { addSecurity(inZip, outZip, e); } else { outZip.putNextEntry(e); if (!e.isDirectory()) { FileSystemManager.streamCopy(inZip.getInputStream(e), outZip, true); } outZip.closeEntry(); } } } finally { if (FileSystemManager.exists("tmp_cadmium-war.war")) { new File("tmp_cadmium-war.war").delete(); } try { if (inZip != null) { inZip.close(); } } catch (Exception e) { if (log != null) { log.error("Failed to close " + war); } } try { if (outZip != null) { outZip.close(); } } catch (Exception e) { if (log != null) { log.error("Failed to close " + newWarNames.get(0)); } } try { if (out != null) { out.close(); } } catch (Exception e) { } try { if (in != null) { in.close(); } } catch (Exception e) { } } }
From source file:com.googlecode.osde.internal.ui.wizards.export.OpenSocialApplicationExportWizard.java
private void export() { final IProject project = page.getProject(); final String url = page.getUrl(); final String output = page.getOutput(); IRunnableWithProgress op = new IRunnableWithProgress() { public void run(IProgressMonitor monitor) throws InvocationTargetException, InterruptedException { ZipOutputStream out = null; try { ResourceCounter resourceCounter = new ResourceCounter(); project.accept(resourceCounter); int fileCount = resourceCounter.getFileCount(); monitor.beginTask("Exporting application", fileCount); out = new ZipOutputStream(new FileOutputStream(new File(output))); project.accept(new ApplicationExporter(out, project, url, monitor)); monitor.done();/*from w w w . j a v a 2 s . c o m*/ } catch (CoreException e) { throw new InvocationTargetException(e); } catch (IOException e) { throw new InvocationTargetException(e); } finally { IOUtils.closeQuietly(out); } } }; try { getContainer().run(true, true, op); } catch (InterruptedException e) { throw new RuntimeException(e); } catch (InvocationTargetException e) { Throwable t = e.getTargetException(); if (t.getCause() instanceof CoreException) { CoreException cause = (CoreException) t.getCause(); StatusAdapter status = new StatusAdapter(StatusUtil.newStatus(cause.getStatus().getSeverity(), "Error occurred when exporting application.", cause)); status.setProperty(IStatusAdapterConstants.TITLE_PROPERTY, "Error occurred when exporting application."); StatusManager.getManager().handle(status, StatusManager.BLOCK); } else { StatusAdapter status = new StatusAdapter( StatusUtil.newStatus(IStatus.WARNING, "Error occurred when exporting application.", t)); status.setProperty(IStatusAdapterConstants.TITLE_PROPERTY, "Error occurred when exporting application."); StatusManager.getManager().handle(status, StatusManager.BLOCK); } } }
From source file:org.openmrs.module.omodexport.util.OmodExportUtil.java
/** * Utility method for exporting a module with its dependencies * /*from w ww .ja v a2s .c o m*/ * @param module -The module to export. It will be exported with all its dependencies and * compressed in a file called "modules.zip" * @param response * @throws IOException */ public static void exportModuleWithDependecies(Module module, HttpServletResponse response) throws IOException { List<File> files = new ArrayList<File>(); List<String> dependecies = module.getRequiredModules(); for (String name : dependecies) { Module m = ModuleFactory.getModuleByPackage(name); files.add(m.getFile()); } files.add(module.getFile()); response.setContentType("application/zip"); response.setHeader("Content-Disposition", "attachment; filename=\"modules.ZIP\""); ZipOutputStream out = new ZipOutputStream(response.getOutputStream()); zipFiles(files, out); }
From source file:fr.cirad.mgdb.exporting.individualoriented.PLinkExportHandler.java
@Override public void exportData(OutputStream outputStream, String sModule, Collection<File> individualExportFiles, boolean fDeleteSampleExportFilesOnExit, ProgressIndicator progress, DBCursor markerCursor, Map<Comparable, Comparable> markerSynonyms, Map<String, InputStream> readyToExportFiles) throws Exception { File warningFile = File.createTempFile("export_warnings_", ""); FileWriter warningFileWriter = new FileWriter(warningFile); ZipOutputStream zos = new ZipOutputStream(outputStream); if (readyToExportFiles != null) for (String readyToExportFile : readyToExportFiles.keySet()) { zos.putNextEntry(new ZipEntry(readyToExportFile)); InputStream inputStream = readyToExportFiles.get(readyToExportFile); byte[] dataBlock = new byte[1024]; int count = inputStream.read(dataBlock, 0, 1024); while (count != -1) { zos.write(dataBlock, 0, count); count = inputStream.read(dataBlock, 0, 1024); }/* ww w . j a v a2 s .c o m*/ } MongoTemplate mongoTemplate = MongoTemplateManager.get(sModule); int markerCount = markerCursor.count(); String exportName = sModule + "_" + markerCount + "variants_" + individualExportFiles.size() + "individuals"; zos.putNextEntry(new ZipEntry(exportName + ".ped")); TreeMap<Integer, Comparable> problematicMarkerIndexToNameMap = new TreeMap<Integer, Comparable>(); short nProgress = 0, nPreviousProgress = 0; int i = 0; for (File f : individualExportFiles) { BufferedReader in = new BufferedReader(new FileReader(f)); try { String individualId, line = in.readLine(); // read sample id if (line != null) { individualId = line; String population = getIndividualPopulation(sModule, line); String individualInfo = (population == null ? "." : population) + " " + individualId; zos.write((individualInfo + " 0 0 0 " + getIndividualGenderCode(sModule, individualId)) .getBytes()); } else throw new Exception("Unable to read first line of temp export file " + f.getName()); int nMarkerIndex = 0; while ((line = in.readLine()) != null) { List<String> genotypes = MgdbDao.split(line, "|"); HashMap<Object, Integer> genotypeCounts = new HashMap<Object, Integer>(); // will help us to keep track of missing genotypes int highestGenotypeCount = 0; String mostFrequentGenotype = null; for (String genotype : genotypes) { if (genotype.length() == 0) continue; /* skip missing genotypes */ int gtCount = 1 + MgdbDao.getCountForKey(genotypeCounts, genotype); if (gtCount > highestGenotypeCount) { highestGenotypeCount = gtCount; mostFrequentGenotype = genotype; } genotypeCounts.put(genotype, gtCount); } if (genotypeCounts.size() > 1) { warningFileWriter.write("- Dissimilar genotypes found for variant " + nMarkerIndex + ", individual " + individualId + ". Exporting most frequent: " + mostFrequentGenotype + "\n"); problematicMarkerIndexToNameMap.put(nMarkerIndex, ""); } String[] alleles = mostFrequentGenotype == null ? new String[0] : mostFrequentGenotype.split(" "); if (alleles.length > 2) { warningFileWriter.write("- More than 2 alleles found for variant " + nMarkerIndex + ", individual " + individualId + ". Exporting only the first 2 alleles.\n"); problematicMarkerIndexToNameMap.put(nMarkerIndex, ""); } String all1 = alleles.length == 0 ? "0" : alleles[0]; String all2 = alleles.length == 0 ? "0" : alleles[alleles.length == 1 ? 0 : 1]; if (all1.length() != 1 || all2.length() != 1) { warningFileWriter .write("- SNP expected, but alleles are not coded on a single char for variant " + nMarkerIndex + ", individual " + individualId + ". Ignoring this genotype.\n"); problematicMarkerIndexToNameMap.put(nMarkerIndex, ""); } else zos.write((" " + all1 + " " + all2).getBytes()); nMarkerIndex++; } } catch (Exception e) { LOG.error("Error exporting data", e); progress.setError("Error exporting data: " + e.getClass().getSimpleName() + (e.getMessage() != null ? " - " + e.getMessage() : "")); return; } finally { in.close(); } if (progress.hasAborted()) return; nProgress = (short) (++i * 100 / individualExportFiles.size()); if (nProgress > nPreviousProgress) { progress.setCurrentStepProgress(nProgress); nPreviousProgress = nProgress; } zos.write('\n'); if (!f.delete()) { f.deleteOnExit(); LOG.info("Unable to delete tmp export file " + f.getAbsolutePath()); } } warningFileWriter.close(); zos.putNextEntry(new ZipEntry(exportName + ".map")); int avgObjSize = (Integer) mongoTemplate .getCollection(mongoTemplate.getCollectionName(VariantRunData.class)).getStats().get("avgObjSize"); int nChunkSize = nMaxChunkSizeInMb * 1024 * 1024 / avgObjSize; markerCursor.batchSize(nChunkSize); int nMarkerIndex = 0; while (markerCursor.hasNext()) { DBObject exportVariant = markerCursor.next(); DBObject refPos = (DBObject) exportVariant.get(VariantData.FIELDNAME_REFERENCE_POSITION); Comparable markerId = (Comparable) exportVariant.get("_id"); String chrom = (String) refPos.get(ReferencePosition.FIELDNAME_SEQUENCE); Long pos = ((Number) refPos.get(ReferencePosition.FIELDNAME_START_SITE)).longValue(); if (chrom == null) LOG.warn("Chromosomal position not found for marker " + markerId); Comparable exportedId = markerSynonyms == null ? markerId : markerSynonyms.get(markerId); zos.write(((chrom == null ? "0" : chrom) + " " + exportedId + " " + 0 + " " + (pos == null ? 0 : pos) + LINE_SEPARATOR).getBytes()); if (problematicMarkerIndexToNameMap.containsKey(nMarkerIndex)) { // we are going to need this marker's name for the warning file Comparable variantName = markerId; if (markerSynonyms != null) { Comparable syn = markerSynonyms.get(markerId); if (syn != null) variantName = syn; } problematicMarkerIndexToNameMap.put(nMarkerIndex, variantName); } nMarkerIndex++; } if (warningFile.length() > 0) { zos.putNextEntry(new ZipEntry(exportName + "-REMARKS.txt")); int nWarningCount = 0; BufferedReader in = new BufferedReader(new FileReader(warningFile)); String sLine; while ((sLine = in.readLine()) != null) { for (Integer aMarkerIndex : problematicMarkerIndexToNameMap.keySet()) sLine = sLine.replaceAll("__" + aMarkerIndex + "__", problematicMarkerIndexToNameMap.get(aMarkerIndex).toString()); zos.write((sLine + "\n").getBytes()); in.readLine(); nWarningCount++; } LOG.info("Number of Warnings for export (" + exportName + "): " + nWarningCount); in.close(); } warningFile.delete(); zos.close(); progress.setCurrentStepProgress((short) 100); }