Example usage for java.io ObjectOutputStream flush

Introduction

In this page you can find the example usage for java.io ObjectOutputStream flush.

Prototype

public void flush() throws IOException 

Source Link

Document

Flushes the stream.

Usage

From source file:ubic.gemma.analysis.report.ArrayDesignReportServiceImpl.java

@Override
public void generateAllArrayDesignReport() {
    log.info("Generating report summarizing all platforms ... ");

    // obtain time information (for timestamping)
    Date d = new Date(System.currentTimeMillis());
    String timestamp = DateFormatUtils.format(d, "yyyy.MM.dd HH:mm");

    long numCsBioSequences = arrayDesignService.numAllCompositeSequenceWithBioSequences();
    long numCsBlatResults = arrayDesignService.numAllCompositeSequenceWithBlatResults();
    long numCsGenes = arrayDesignService.numAllCompositeSequenceWithGenes();
    long numGenes = arrayDesignService.numAllGenes();

    // create a surrogate ArrayDesignValue object to represent the total of all platforms
    ArrayDesignValueObject adVo = new ArrayDesignValueObject();
    adVo.setNumProbeSequences(Long.toString(numCsBioSequences));
    adVo.setNumProbeAlignments(Long.toString(numCsBlatResults));
    adVo.setNumProbesToGenes(Long.toString(numCsGenes));
    adVo.setNumGenes(Long.toString(numGenes));
    adVo.setDateCached(timestamp);//  www  .j  a v  a2s .  c o m

    try {
        // remove file first
        File f = new File(HOME_DIR + File.separatorChar + ARRAY_DESIGN_REPORT_DIR + File.separatorChar
                + ARRAY_DESIGN_SUMMARY);
        if (f.exists()) {
            if (!f.canWrite() || !f.delete()) {
                log.warn("Cannot write to file.");
                return;
            }
        }
        FileOutputStream fos = new FileOutputStream(HOME_DIR + File.separatorChar + ARRAY_DESIGN_REPORT_DIR
                + File.separatorChar + ARRAY_DESIGN_SUMMARY);
        ObjectOutputStream oos = new ObjectOutputStream(fos);
        oos.writeObject(adVo);
        oos.flush();
        oos.close();
    } catch (Throwable e) {
        // cannot write to file. Just fail gracefully.
        log.error("Cannot write to file.");
    }
    log.info("Done making reports");
}

---

From source file:com.icantrap.collections.dawg.Dawg.java

/**
 * Writes an instance of a dawg to an OutputStream.  Once the data is written to the OutputStream, it is flushed, but
 * the stream is not closed./*from   w ww .  j  a v  a  2 s  .  com*/
 *
 * @param os the OutputStream to write the dawg to
 * @throws IOException if writing the dawg to the stream causes an IOException
 */
public void store(OutputStream os) throws IOException {
    BufferedOutputStream bos = new BufferedOutputStream(os, 8 * 1024);
    ObjectOutputStream oos = new ObjectOutputStream(bos);

    oos.writeObject(nodes);
    oos.flush();
}

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From source file:com.joliciel.lefff.LefffMemoryLoader.java

public void serializeMemoryBase(LefffMemoryBase memoryBase, File memoryBaseFile) {
    LOG.debug("serializeMemoryBase");
    boolean isZip = false;
    if (memoryBaseFile.getName().endsWith(".zip"))
        isZip = true;//from  w  ww .  j  a  v  a2s. c o  m

    FileOutputStream fos = null;
    ObjectOutputStream out = null;
    ZipOutputStream zos = null;
    try {
        fos = new FileOutputStream(memoryBaseFile);
        if (isZip) {
            zos = new ZipOutputStream(fos);
            zos.putNextEntry(new ZipEntry("lefff.obj"));
            out = new ObjectOutputStream(zos);
        } else {
            out = new ObjectOutputStream(fos);
        }

        try {
            out.writeObject(memoryBase);
        } finally {
            out.flush();
            out.close();
        }
    } catch (IOException ioe) {
        throw new RuntimeException(ioe);
    }
}

---

From source file:org.jax.haplotype.inference.CachingIdenticalByStateDataManager.java

/**
 * Find the IBS regions//from   www .  j  a v  a 2  s. c  o m
 * @param genomeName
 *          the name of the genome that we want to use
 * @param referenceStrain
 *          the reference strain
 * @param comparisonStrains
 *          the comparison strains
 * @param chromosomeNumber
 *          the chromosome number (starting with 1)
 * @param minimumExtentInSnps
 *          the minimum IBD extent in SNPs
 * @param minimumExtentInBasePairs
 *          the minimum IBD extent in base pairs
 * @return
 *          the SNP blocks
 */
public SnpIntervalListGroup findIdenticalByStateRegions(String genomeName, String referenceStrain,
        String[] comparisonStrains, int chromosomeNumber, int minimumExtentInSnps,
        long minimumExtentInBasePairs) {
    try {
        for (int i = 0; i < comparisonStrains.length; i++) {
            if (comparisonStrains[i] == null) {
                throw new NullPointerException();
            }
        }

        ScanningIdenticalByStateFinder scanningIdenticalByStateFinder = new ScanningIdenticalByStateFinder();

        LOG.fine("calling caching findIdenticalByStateRegions. " + "# comparison strains: "
                + comparisonStrains.length);

        Map<String, SnpIntervalList> snpBlockListsMap = new HashMap<String, SnpIntervalList>();
        synchronized (CachingIdenticalByStateDataManager.class) {
            Map<String, File> comparisonStrainsFileMap = new HashMap<String, File>();
            for (int i = 0; i < comparisonStrains.length; i++) {
                File uniqueFileCache = getCacheFile(genomeName, referenceStrain, comparisonStrains[i],
                        chromosomeNumber, minimumExtentInSnps, minimumExtentInBasePairs);

                // if the cache doesn't exist, create it
                if (uniqueFileCache.createNewFile()) {
                    uniqueFileCache.deleteOnExit();
                    comparisonStrainsFileMap.put(comparisonStrains[i], uniqueFileCache);
                } else {
                    LOG.fine("loading cache: " + uniqueFileCache.getAbsolutePath());
                    ObjectInputStream objectInput = new ObjectInputStream(
                            new BufferedInputStream(new FileInputStream(uniqueFileCache)));
                    snpBlockListsMap.put(comparisonStrains[i], (SnpIntervalList) objectInput.readObject());
                }
            }

            if (!comparisonStrainsFileMap.isEmpty()) {
                GenomeDataSource genomeDataSource = this.genomeDataManager.getGenomeDataMap().get(genomeName);
                ChromosomeDataSource chromosomeDataSource = genomeDataSource.getChromosomeDataSources()
                        .get(chromosomeNumber);

                String[] comparisonStrainsToCalculate = comparisonStrainsFileMap.keySet()
                        .toArray(new String[comparisonStrainsFileMap.size()]);
                for (int i = 0; i < comparisonStrainsToCalculate.length; i++) {
                    if (comparisonStrainsToCalculate[i] == null) {
                        throw new NullPointerException();
                    }
                }
                SdpInputStream sdpStream = chromosomeDataSource.getSdpInputStream(referenceStrain,
                        comparisonStrainsToCalculate);
                SnpPositionInputStream snpPositionStream = chromosomeDataSource.getSnpPositionInputStream();
                SnpIntervalListGroup newIbsRegions = scanningIdenticalByStateFinder.findIdenticalByStateRegions(
                        sdpStream, snpPositionStream, minimumExtentInSnps, minimumExtentInBasePairs);
                Map<String, List<BasePairInterval>> newIbsIntervalLists = newIbsRegions.getSnpBlocksMap();
                for (Entry<String, List<BasePairInterval>> intervalListEntry : newIbsIntervalLists.entrySet()) {
                    System.out.println("Strain Key: " + intervalListEntry.getKey());

                    SnpIntervalList snpIntervalList = new SnpIntervalList(intervalListEntry.getValue(),
                            newIbsRegions.getStartInBasePairs(), newIbsRegions.getExtentInBasePairs());

                    String strainName = intervalListEntry.getKey();
                    File uniqueFileCache = comparisonStrainsFileMap.get(strainName);
                    if (uniqueFileCache == null) {
                        throw new NullPointerException();
                    }

                    snpBlockListsMap.put(strainName, snpIntervalList);

                    ObjectOutputStream objectOutput = new ObjectOutputStream(
                            new BufferedOutputStream(new FileOutputStream(uniqueFileCache)));
                    objectOutput.writeObject(snpIntervalList);
                    objectOutput.flush();
                    objectOutput.close();
                }
            }
        }

        return new SnpIntervalListGroup(snpBlockListsMap);
    } catch (Exception ex) {
        LOG.log(Level.SEVERE, "Failed to cache IBS", ex);
        return null;
    }
}

---

From source file:org.alfresco.repo.admin.UnserializerValidatorBootstrap.java

/**
 * Check if Java unserialize remote code execution is already fixed on this
 * <b>commons collections</b> version.
 * // w  w w.  j  av  a2  s .co  m
 * @return
 */
private boolean isCommonsCollectionsDeserializerFixed() {

    try {
        Class<?> invokerTransformerClass = Class.forName(
                "org.apache.commons.collections.functors.InvokerTransformer", true,
                this.getClass().getClassLoader());

        if (invokerTransformerClass != null) {
            Constructor<?> invokerTransformerConstructor = invokerTransformerClass.getConstructor(String.class,
                    Class[].class, Object[].class);

            Object invokerTransformerInstance = invokerTransformerConstructor.newInstance(null, null, null);

            ObjectOutputStream objectOut = null;
            ByteArrayOutputStream byteOut = null;
            try {
                // Write the object out to a byte array
                byteOut = new ByteArrayOutputStream();
                objectOut = new ObjectOutputStream(byteOut);
                objectOut.writeObject(invokerTransformerInstance);
                objectOut.flush();
            } catch (UnsupportedOperationException e) {
                // Expected: Serialization support is disabled for security
                // reasons.
                return true;
            } catch (IOException e) {
                throw new AlfrescoRuntimeException(ERR_UNEXPECTED_ERROR, e);
            } finally {
                if (objectOut != null) {
                    try {
                        objectOut.close();
                    } catch (Throwable e) {
                    }
                }
                if (byteOut != null) {
                    try {
                        byteOut.close();
                    } catch (Throwable e) {
                    }
                }
            }
        }
    } catch (SecurityException e) {
        // This is and expected, acceptable exception that we can ignore.
    } catch (ClassNotFoundException e) {
        // This is and expected, acceptable exception that we can ignore.
    } catch (InstantiationException e) {
        // This is and expected, acceptable exception that we can ignore.
    } catch (IllegalAccessException e) {
        // This is and expected, acceptable exception that we can ignore.
    } catch (NoSuchMethodException e) {
        throw new AlfrescoRuntimeException(ERR_UNEXPECTED_ERROR, e);
    } catch (IllegalArgumentException e) {
        throw new AlfrescoRuntimeException(ERR_UNEXPECTED_ERROR, e);
    } catch (InvocationTargetException e) {
        // This is and expected, acceptable exception that we can ignore.
    }

    return false;
}

---

From source file:dynamite.zafroshops.app.fragment.AddZopFragment.java

public ArrayList<MobileCountry> getCountries() {
    ArrayList<MobileCountry> result = new ArrayList<>();

    final SharedPreferences preferences = getActivity().getPreferences(0);
    final SharedPreferences.Editor editor = preferences.edit();
    boolean fromFile = false;

    if (preferences.contains(StorageKeys.COUNTRIES_KEY)) {
        try {// w w w.j  a  v a2 s .  c om
            ObjectInputStream ois = new ObjectInputStream(
                    getActivity().getBaseContext().openFileInput(StorageKeys.COUNTRIES_KEY));

            zopCountries = (ArrayList<MobileCountry>) ois.readObject();
            zopCountryAdapter.clear();
            zopCountryAdapter.addAll(zopCountries);
            fromFile = true;
        } catch (IOException e) {
            e.printStackTrace();
        } catch (ClassNotFoundException e) {
            e.printStackTrace();
        }
    }

    if (!fromFile) {
        if (zopCountries == null || zopCountries.size() == 0) {
            ListenableFuture<JsonElement> query = MainActivity.MobileClient.invokeApi("mobileCountry", "GET",
                    new ArrayList<Pair<String, String>>());
            Futures.addCallback(query, new FutureCallback<JsonElement>() {
                @Override
                public void onSuccess(JsonElement result) {
                    JsonArray typesAsJson = result.getAsJsonArray();
                    if (typesAsJson != null) {
                        zopCountries = new Gson().fromJson(result, new TypeToken<ArrayList<MobileCountry>>() {
                        }.getType());
                    }
                    zopCountryAdapter.clear();
                    zopCountryAdapter.addAll(zopCountries);
                    setLocation(null);

                    try {
                        ObjectOutputStream oos = new ObjectOutputStream(getActivity().getBaseContext()
                                .openFileOutput(StorageKeys.COUNTRIES_KEY, Context.MODE_PRIVATE));

                        oos.writeObject(zopCountries);
                        oos.flush();
                        oos.close();
                        editor.putString(StorageKeys.COUNTRIES_KEY, StorageKeys.COUNTRIES_KEY);
                        editor.commit();
                    } catch (IOException e) {
                        e.printStackTrace();
                    }
                }

                @Override
                public void onFailure(@NonNull Throwable t) {

                }
            });
        }
    }

    return result;
}

---

From source file:ubic.gemma.analysis.report.ArrayDesignReportServiceImpl.java

@Override
public void generateArrayDesignReport(ArrayDesignValueObject adVo) {

    ArrayDesign ad = arrayDesignService.load(adVo.getId());
    if (ad == null)
        return;/*w w  w  .j a  va2s.c o  m*/

    // obtain time information (for timestamping)
    Date d = new Date(System.currentTimeMillis());
    String timestamp = DateFormatUtils.format(d, "yyyy.MM.dd HH:mm");

    long numProbes = arrayDesignService.getCompositeSequenceCount(ad);
    long numCsBioSequences = arrayDesignService.numCompositeSequenceWithBioSequences(ad);
    long numCsBlatResults = arrayDesignService.numCompositeSequenceWithBlatResults(ad);
    long numCsGenes = arrayDesignService.numCompositeSequenceWithGenes(ad);
    long numGenes = arrayDesignService.numGenes(ad);

    adVo.setDesignElementCount(numProbes);
    adVo.setNumProbeSequences(Long.toString(numCsBioSequences));
    adVo.setNumProbeAlignments(Long.toString(numCsBlatResults));
    adVo.setNumProbesToGenes(Long.toString(numCsGenes));
    adVo.setNumGenes(Long.toString(numGenes));
    adVo.setDateCached(timestamp);

    // check the directory exists.
    String reportDir = HOME_DIR + File.separatorChar + ARRAY_DESIGN_REPORT_DIR;
    File reportDirF = new File(reportDir);
    if (!reportDirF.exists()) {
        reportDirF.mkdirs();
    }

    String reportFileName = reportDir + File.separatorChar + ARRAY_DESIGN_REPORT_FILE_NAME_PREFIX + "."
            + adVo.getId();

    try {
        // remove old file first (possible todo: don't do this until after new file is okayed - maybe this delete
        // isn't needed, just clobber.)

        File f = new File(reportFileName);

        if (f.exists()) {
            if (!f.canWrite() || !f.delete()) {
                log.error(
                        "Report exists but cannot overwrite, leaving the old one in place: " + reportFileName);
                return;
            }
        }
        FileOutputStream fos = new FileOutputStream(reportFileName);
        ObjectOutputStream oos = new ObjectOutputStream(fos);
        oos.writeObject(adVo);
        oos.flush();
        oos.close();
    } catch (Throwable e) {
        log.error("Cannot write to file: " + reportFileName);
        return;
    }
    log.info("Generated report for " + ad);
}

---

From source file:com.orange.matosweb.MatosCampaign.java

/**
 * Backup the steps.//  w w w.  j a va 2  s.c  om
 */
private void backup() {
    try {
        FileOutputStream fos = new FileOutputStream(new File(privateFolder, BACKUP));
        try {
            ObjectOutputStream oos = new ObjectOutputStream(fos);
            try {
                oos.writeObject(steps);
                oos.flush();
            } finally {
                oos.close();
            }
        } finally {
            fos.close();
        }
    } catch (IOException e) {
        e.printStackTrace();
    }
}

---

From source file:org.hyperic.hq.events.FileAlertConditionEvaluatorStateRepository.java

private void persistStates(Map<Integer, Serializable> states, File out) {
    ObjectOutputStream objectOutputStream = null;
    FileOutputStream fileOutputStream = null;
    try {//from   w  w  w .  j a v  a2  s  . c o m
        if (out.isFile()) {
            log.warn(out.getAbsolutePath() + " already exists.  It will be deleted.");
        }
        out.delete();
        fileOutputStream = new FileOutputStream(out);
        objectOutputStream = new ObjectOutputStream(new BufferedOutputStream(fileOutputStream));
        objectOutputStream.writeObject(states);
        objectOutputStream.flush();
        if (log.isInfoEnabled()) {
            log.info("Successfully saved alert condition evaluator states to " + out.getAbsolutePath());
        }
    } catch (Exception e) {
        log.warn("Unable to save alert condition evaluator states", e);
    } finally {
        closeStream(objectOutputStream);
        closeStream(fileOutputStream);
    }
}

---

From source file:org.kepler.util.AuthNamespace.java

/**
 * Serialize the authority:namespace String to the AuthorizedNamespace file.
 *//*from  w  w w.  j  av  a  2s .c o m*/
private void writeAuthorizedNamespace() throws Exception {
    if (isDebugging)
        log.debug("writeAuthorizedNamespace()");

    File ianFile = new File(_anFileName);
    if (!ianFile.exists()) {
        ianFile.delete();
    }
    String authNamespace = getAuthNamespace();
    if (authNamespace == null) {
        throw new Exception("authNamespace is null");
    }
    OutputStream os = new FileOutputStream(_anFileName);
    ObjectOutputStream oos = null;
    try {
        oos = new ObjectOutputStream(os);
        oos.writeObject(authNamespace);
        oos.flush();
    } finally {
        if (oos != null) {
            oos.close();
        }
    }

    try {
        // Every time we write a new AuthNamespace make sure there is
        // at least one row added to the LSID_GENERATOR table for the
        // new Authority and Namespace, this is how LSIDGenerator
        // can tell if the LSID_GENERATOR table has been deleted since
        // the last time it accessed it.
        LSIDGenerator.insertRow(getAuthority(), getNamespace(), 0, 1);
    } catch (Exception e) {
        e.printStackTrace();
    }
}

---

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