Example usage for java.io RandomAccessFile seek

List of usage examples for java.io RandomAccessFile seek

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Introduction

In this page you can find the example usage for java.io RandomAccessFile seek.

Prototype

public void seek(long pos) throws IOException

Source Link

Document

Sets the file-pointer offset, measured from the beginning of this file, at which the next read or write occurs.

Usage

From source file:org.commoncrawl.service.listcrawler.CrawlList.java

public CrawlListMetadata getSubDomainMetadataByRootDomain(String rootDomainName) throws IOException {
    long domainHash = URLFingerprint.generate64BitURLFPrint(rootDomainName);

    CrawlListMetadata metadata = new CrawlListMetadata();
    synchronized (_subDomainMetadataFile) {
        RandomAccessFile file = new RandomAccessFile(_subDomainMetadataFile, "rw");
        try {//w w  w .ja va 2  s.c om
            int dataOffset = getOffsetForSubDomainData(domainHash);
            if (dataOffset == 0) {
                throw new IOException("Data Offset Zero for host:" + rootDomainName);
            }
            file.seek(dataOffset);
            metadata.readFields(file);
            // set the data offset on the way out so that updates write to the proper location 
            metadata.setSubDomainDataOffset(dataOffset);
        } finally {
            file.close();
        }
    }
    return metadata;
}

From source file:org.commoncrawl.service.listcrawler.CrawlList.java

void updateSubDomainQueueStatus(String rootDomainName, int deltaQueuedCount) throws IOException {
    long domainHash = URLFingerprint.generate64BitURLFPrint(rootDomainName);
    synchronized (_subDomainMetadataFile) {
        CrawlListMetadata metadata = new CrawlListMetadata();

        RandomAccessFile file = new RandomAccessFile(_subDomainMetadataFile, "rw");
        try {//  w  ww. j  a v a2s  .c o  m
            int dataOffset = getOffsetForSubDomainData(domainHash);
            if (dataOffset == 0) {
                throw new IOException("Data Offset Zero for host:" + rootDomainName);
            }
            file.seek(dataOffset);
            metadata.readFields(file);
            // set the data offset on the way out so that updates write to the proper location 
            metadata.setQueuedItemCount(metadata.getQueuedItemCount() + deltaQueuedCount);
            // ok reseek to data offset 
            file.seek(dataOffset);
            // rewrite the data structure
            metadata.write(file);
        } finally {
            file.close();
        }
    }
}

From source file:org.opencb.cellbase.mongodb.db.VariantAnnotationMongoDBAdaptorTest.java

private int getVepAnnotationBatch(RandomAccessFile raf, int nVariantsToRead,
        Set<AnnotationComparisonObject> vepAnnotationSet) throws IOException {
    /**//from   w ww. jav a 2 s. c o m
     * Loads VEP annotation
     */
    String newLine;
    int nNonRegulatoryAnnotations = 0;
    int nReadVariants = 0;
    String previousChr = "";
    String previousPosition = "";
    String previousAlt = "";
    String alt;
    long filePointer = 0;

    if (nVariantsToRead > 0) {
        while (((newLine = raf.readLine()) != null) && nReadVariants <= nVariantsToRead) {
            String[] lineFields = newLine.split("\t");
            String[] coordinatesParts = lineFields[1].split(":");
            if (lineFields[2].equals("deletion")) {
                alt = "-";
            } else {
                alt = lineFields[2];
            }
            if (!previousChr.equals(coordinatesParts[0]) || !previousPosition.equals(coordinatesParts[1])
                    || !previousAlt.equals(alt)) {
                nReadVariants++;
            }
            if (nReadVariants <= nVariantsToRead) {
                for (String SOname : lineFields[6].split(",")) {
                    if (SOname.equals("nc_transcript_variant")) {
                        SOname = "non_coding_transcript_variant";
                    }
                    if (!SOname.equals("regulatory_region_variant")) {
                        nNonRegulatoryAnnotations++;
                    }
                    vepAnnotationSet.add(new AnnotationComparisonObject(coordinatesParts[0],
                            coordinatesParts[1], alt, lineFields[3], lineFields[4], SOname));
                }
                previousChr = coordinatesParts[0];
                previousPosition = coordinatesParts[1];
                previousAlt = alt;
                filePointer = raf.getFilePointer();
            }
        }

        raf.seek(filePointer);
    }

    return nNonRegulatoryAnnotations;
}

From source file:com.aliyun.android.oss.task.GetObjectTask.java

/**
 * ???/*w  w  w .  j a v  a 2s.c o m*/
 * @param {@link OSSObject}???
 * @return {@link OSSClientUtil}
 * @throws OSSException
 */
public int getResult(OSSObject object) throws OSSException {
    int result = CloudUtil.CLOUDCLIENT_RESULT_OK;

    HttpResponse response = null;
    RandomAccessFile randomAccessFile = null;
    InputStream inputStream = null;
    object = new OSSObject(this.bucketName, this.objectKey);
    try {
        mLogMission.i("getResult", "before network request", missionObject);
        response = this.execute();
        mLogMission.i("getResult", "network response", missionObject);
        Header rangeHeader = response.getFirstHeader("Content-Range");
        if (rangeHeader != null) {
            String range = rangeHeader.getValue();
            mLogMission.i("getResult", "range:" + range.toString(), missionObject);
        }
        object.setObjectMetaData(OSSHttpTool.getObjectMetadataFromResponse(response));
        if (response.getEntity() != null) {
            mLogMission.i("getResult",
                    "the content length get from server:" + response.getEntity().getContentLength(),
                    missionObject);
            if (missionObject.getFileLength() <= 0L) {
                missionObject.setFileLength(response.getEntity().getContentLength());
                mLogMission.i("getResult",
                        "get content length and set file length. fileLength:" + missionObject.getFileLength(),
                        missionObject);
            }
            missionObject.setPaused(false);
            inputStream = response.getEntity().getContent();
            if (listener != null) {
                listener.setTotalSize(missionObject.getFileLength());
            }
        }
        result = mDatabaseAccessManager.updateDownloadFile(missionObject);
        if (result != CloudUtil.CLOUDCLIENT_RESULT_OK) {
            return result;
        }

        randomAccessFile = new RandomAccessFile(filePath, "rwd");
        long offset = 0;
        if (range != null) {
            offset = range.getStart();
            mLogMission.i("getResult", "set offset before write file, offset:" + offset, missionObject);
        }
        randomAccessFile.seek(offset);
        mLogMission.i("getResult", "before write to local, file offset:" + offset, missionObject);
        byte[] buffer = new byte[1024 * 4];
        long readTotal = offset;
        int readLength = 0;
        while (true) {
            if (readTotal == missionObject.getFileLength()) {
                missionObject.setFinished(true);
                result = CloudUtil.CLOUDCLIENT_RESULT_OK;
                mLogMission.i("getResult", "readTotal == missionObject's fileLength, readTotal:" + readTotal,
                        missionObject);
                break;
            }
            if (listener != null && listener.isCancel()) {
                missionObject.setPaused(true);
                result = CloudUtil.CLOUD_FILE_MISSION_CANCEL;
                mLogMission.i("getResult", "cancel download missionObject", missionObject);
                break;
            }
            readLength = inputStream.read(buffer);
            mLogMission.i("getResult", "read buffer length:" + readLength, missionObject);
            if (readLength == -1) {
                missionObject.setFinished(true);
                result = CloudUtil.CLOUDCLIENT_RESULT_OK;
                mLogMission.i("getResult", "buffer read finish, readLength:" + readLength, missionObject);
                break;
            }

            mLogMission.i("getResult", "write to local, length:" + readLength, missionObject);
            randomAccessFile.write(buffer, 0, readLength);
            readTotal += readLength;
            mLogMission.i("getResult", "readTotal:" + readTotal, missionObject);
            missionObject.setTransferredLength(readTotal);
            missionObject.setLastTime(System.currentTimeMillis());
            //                result = mDatabaseAccessManager.updateDownloadFile(missionObject);
            //                if (result != CloudUtil.CLOUDCLIENT_RESULT_OK) {
            //                    break;
            //                }
            if (listener != null) {
                listener.transferred(readTotal);
            }
        }
    } catch (OSSException osse) {
        throw osse;
    } catch (ParseException pe) {
        OSSException ossException = new OSSException(pe);
        ossException.setErrorCode(OSSErrorCode.PARSE_METADATA_ERROR);
        throw ossException;
    } catch (IOException ioe) {
        OSSException ossException = new OSSException(ioe);
        ossException.setErrorCode(OSSErrorCode.GET_ENTITY_CONTENT_ERROR);
        throw ossException;
    } finally {
        mDatabaseAccessManager.updateDownloadFile(missionObject);
        mLogMission.i("getResult", "finally, update db", missionObject);
        this.releaseHttpClient();
        if (randomAccessFile != null) {
            try {
                inputStream.close();
                randomAccessFile.close();
            } catch (IOException e) {
                e.printStackTrace();
            }
        }
    }
    return result;
}

From source file:au.org.ala.layers.intersect.Grid.java

public void mergeMissingValues(Grid sourceOfMissingValues, boolean hideMissing) {
    float[] cells = sourceOfMissingValues.getGrid();

    float[] actual = getGrid();

    int length = actual.length;

    int i;/* w w  w .j a v a  2  s .  c  o  m*/
    RandomAccessFile afile = null;
    File f2 = new File(filename + ".GRI");

    try { //read of random access file can throw an exception
        if (!f2.exists()) {
            afile = new RandomAccessFile(filename + ".gri", "rw");
        } else {
            afile = new RandomAccessFile(filename + ".GRI", "rw");
        }

        byte[] b = new byte[(int) afile.length()];

        ByteBuffer bb = ByteBuffer.wrap(b);

        if (byteorderLSB) {
            bb.order(ByteOrder.LITTLE_ENDIAN);
        }

        afile.seek(0);

        if (datatype.equalsIgnoreCase("UBYTE")) {
            for (i = 0; i < length; i++) {
                if (hideMissing == Float.isNaN(cells[i])) {
                    if (nodatavalue >= 128) {
                        bb.put((byte) (nodatavalue - 256));
                    } else {
                        bb.put((byte) nodatavalue);
                    }
                } else {
                    if (actual[i] >= 128) {
                        bb.put((byte) (actual[i] - 256));
                    } else {
                        bb.put((byte) actual[i]);
                    }
                }
            }
        } else if (datatype.equalsIgnoreCase("BYTE")) {
            for (i = 0; i < length; i++) {
                bb.put((byte) actual[i]);
            }
        } else if (datatype.equalsIgnoreCase("SHORT")) {
            for (i = 0; i < length; i++) {
                if (hideMissing == Float.isNaN(cells[i])) {
                    bb.putShort((short) nodatavalue);
                } else {
                    bb.putShort((short) actual[i]);
                }
            }
        } else if (datatype.equalsIgnoreCase("INT")) {
            for (i = 0; i < length; i++) {
                if (hideMissing == Float.isNaN(cells[i])) {
                    bb.putInt((int) nodatavalue);
                } else {
                    bb.putInt((int) actual[i]);
                }
            }
        } else if (datatype.equalsIgnoreCase("LONG")) {
            for (i = 0; i < length; i++) {
                if (hideMissing == Float.isNaN(cells[i])) {
                    bb.putLong((long) nodatavalue);
                } else {
                    bb.putLong((long) actual[i]);
                }
            }
        } else if (datatype.equalsIgnoreCase("FLOAT")) {
            for (i = 0; i < length; i++) {
                if (hideMissing == Float.isNaN(cells[i])) {
                    bb.putFloat((float) nodatavalue);
                } else {
                    bb.putFloat(actual[i]);
                }
            }
        } else if (datatype.equalsIgnoreCase("DOUBLE")) {
            for (i = 0; i < length; i++) {
                if (hideMissing == Float.isNaN(cells[i])) {
                    bb.putDouble((double) nodatavalue);
                } else {
                    bb.putDouble((double) actual[i]);
                }
            }
        } else {
            // should not happen
            logger.error("unsupported grid data type: " + datatype);
        }

        afile.write(bb.array());
    } catch (Exception e) {
        logger.error("error getting grid file values", e);
    } finally {
        if (afile != null) {
            try {
                afile.close();
            } catch (Exception e) {
                logger.error(e.getMessage(), e);
            }
        }
    }
}

From source file:org.commoncrawl.service.listcrawler.CacheManager.java

private final void flushLocalLog(final long bytesToRemove, final int itemsToRemove,
        final List<FingerprintAndOffsetTuple> flushedTupleList,
        final ArrayList<IndexDataFileTriple> tempFileTriples) {

    LOG.info("Acquiring Log Access Semaphores");
    // first boost this thread's priority ... 
    int originalThreadPriority = Thread.currentThread().getPriority();
    Thread.currentThread().setPriority(Thread.MAX_PRIORITY);
    // next acquire all permits to the local access log ... block until we get there ... 
    getLocalLogAccessSemaphore().acquireUninterruptibly(LOG_ACCESS_SEMAPHORE_COUNT);
    // now that we have all the semaphores we need, reduce the thread's priority to normal
    Thread.currentThread().setPriority(originalThreadPriority);
    LOG.info("Acquired ALL Log Access Semaphores");

    long timeStart = System.currentTimeMillis();

    // now we have exclusive access to the local transaction log ... 
    File activeLogFilePath = getActiveLogFilePath();
    File checkpointLogFilePath = getCheckpointLogFilePath();
    try {/*from  ww  w.  j a  va2 s  .co m*/
        // delete checkpoint file if it existed ... 
        checkpointLogFilePath.delete();
        // now rename activelog to checkpoint path 
        activeLogFilePath.renameTo(checkpointLogFilePath);

        long logFileConsolidationStartTime = System.currentTimeMillis();
        // now trap for exceptions in case something fails 
        try {
            // fix up the header ... 
            _header._fileSize -= bytesToRemove;
            _header._itemCount -= itemsToRemove;

            // open a old file and new file 
            RandomAccessFile newFile = new RandomAccessFile(activeLogFilePath, "rw");
            RandomAccessFile oldFile = new RandomAccessFile(checkpointLogFilePath, "r");

            LOG.info("Opened new and old files. New Header FileSize is:" + _header._fileSize + " ItemCount:"
                    + _header._itemCount);
            try {
                // write out header ...
                long bytesRemainingInLogFile = _header._fileSize;

                LOG.info("Writing Header to New File. Bytes Remaining for Data are:" + bytesRemainingInLogFile);
                // write header to new file ... 
                _header.writeHeader(newFile);
                // decrement bytes available ... 
                bytesRemainingInLogFile -= LocalLogFileHeader.SIZE;

                if (bytesRemainingInLogFile != 0) {
                    byte transferBuffer[] = new byte[(1 << 20) * 16];
                    LOG.info("Seeking old file past flushed data (pos:" + LocalLogFileHeader.SIZE
                            + bytesToRemove + ")");
                    // seek past old data ... 
                    oldFile.seek(LocalLogFileHeader.SIZE + bytesToRemove);
                    // and copy across remaining data 
                    while (bytesRemainingInLogFile != 0) {
                        int bytesToReadWriteThisIteration = Math.min((int) bytesRemainingInLogFile,
                                transferBuffer.length);
                        oldFile.read(transferBuffer, 0, bytesToReadWriteThisIteration);
                        newFile.write(transferBuffer, 0, bytesToReadWriteThisIteration);
                        LOG.info("Copied " + bytesToReadWriteThisIteration + " from Old to New");
                        bytesRemainingInLogFile -= bytesToReadWriteThisIteration;
                    }
                }
            } finally {
                if (newFile != null) {
                    newFile.close();
                }
                if (oldFile != null) {
                    oldFile.close();
                }
            }
            // if we reached here then checkpoint was successfull ... 
            LOG.info("Checkpoint - Log Consolidation Successfull! TOOK:"
                    + (System.currentTimeMillis() - logFileConsolidationStartTime));

            LOG.info("Loading Index Files");
            for (IndexDataFileTriple triple : tempFileTriples) {
                LOG.info("Loading Index File:" + triple._localIndexFilePath);
                final HDFSFileIndex fileIndex = new HDFSFileIndex(_remoteFileSystem, triple._localIndexFilePath,
                        triple._dataFilePath);
                LOG.info("Loaded Index File");
                // update hdfs index list ... 
                synchronized (CacheManager.this) {
                    LOG.info("Adding HDFS Index to list");
                    _hdfsIndexList.addElement(fileIndex);
                }
            }

            // create a semaphore to wait on 
            final Semaphore semaphore = new Semaphore(0);

            LOG.info("Scheduling Async Event");
            // now we need to schedule an async call to main thread to update data structures safely ... 
            _eventLoop.setTimer(new Timer(0, false, new Timer.Callback() {

                @Override
                public void timerFired(Timer timer) {
                    LOG.info("Cleaning Map");

                    synchronized (CacheManager.this) {
                        // walk tuples 
                        for (FingerprintAndOffsetTuple tuple : flushedTupleList) {
                            //TODO: HACK!
                            // remove from collection ... 
                            _fingerprintToLocalLogPos.removeAll(tuple._fingerprint);
                        }
                    }
                    LOG.info("Increment Offset Info");
                    // finally increment locallog offset by bytes removed ... 
                    _localLogStartOffset += bytesToRemove;

                    LOG.info("Releasing Wait Semaphore");
                    //release wait sempahore 
                    semaphore.release();
                }
            }));

            LOG.info("Waiting for Async Event to Complete");
            //wait for async operation to complete ...
            semaphore.acquireUninterruptibly();

            LOG.info("Async Event to Completed");
        } catch (IOException e) {
            LOG.error("Checkpoint Failed with Exception:" + CCStringUtils.stringifyException(e));
            // delete new file ... 
            activeLogFilePath.delete();
            // and rename checkpoint file to active file ... 
            checkpointLogFilePath.renameTo(activeLogFilePath);
        }
    } finally {
        LOG.info("Releasing ALL Log Access Semaphores. HELD FOR:" + (System.currentTimeMillis() - timeStart));
        getLocalLogAccessSemaphore().release(LOG_ACCESS_SEMAPHORE_COUNT);
    }
}

From source file:org.apache.hadoop.hive.service.HSSessionItem.java

public boolean uploadProto(String user, String fileName, byte[] array) throws HiveServerException {
    boolean res = true;
    String fname;/* w  w  w  .  java2  s . com*/

    String dname = getHome() + "/protobuf/upload/" + user;
    File d = new File(dname);
    if (!d.exists()) {
        if (!d.mkdirs()) {
            l4j.error(getSessionName() + " try to mkdir " + dname + " failed.");
            throw new HiveServerException("Create user proto directory failed.");
        }
    }
    if (!fileName.trim().toLowerCase().endsWith(".proto")) {
        throw new HiveServerException(
                "Upload proto command can only handle .proto file, Check your file suffix");
    }

    fname = dname + "/" + fileName;

    RandomAccessFile raf;
    File f;
    try {
        f = new File(fname);
        if (!f.exists()) {
            if (!f.createNewFile()) {
                l4j.error("Try to create file " + fname + " failed.");
                throw new HiveServerException("Create user upload file " + fname + " failed.");
            }
        }
    } catch (java.io.IOException ex) {
        l4j.error(getSessionName() + " try to create file " + fname + " failed w/ " + ex);
        return false;
    }
    if (array.length == 0) {
        if (!f.delete()) {
            l4j.error("Try to delete file " + fname + " failed.");
            throw new HiveServerException("Delete user proto file " + fname + " failed.");
        } else {
            return true;
        }
    }
    try {
        raf = new RandomAccessFile(f, "rw");
    } catch (java.io.FileNotFoundException ex) {
        l4j.error(getSessionName() + " try to open file " + fname + " failed, not found.");
        return false;
    }
    try {
        raf.setLength(0);
        raf.seek(0);
        raf.write(array);
    } catch (java.io.IOException ex) {
        l4j.error(getSessionName() + " try to truncate/write file " + fname + "failed w/ " + ex);
        return false;
    }
    return res;
}

From source file:tvbrowser.ui.mainframe.MainFrame.java

@Override
public void drop(DropTargetDropEvent dtde) {
    dtde.acceptDrop(dtde.getDropAction());
    File[] files = getDragDropPlugins(dtde.getCurrentDataFlavors(), dtde.getTransferable());

    try {/*from   w w  w  .  j  a  v  a 2 s .co  m*/
        File tmpFile = File.createTempFile("plugins", ".txt");
        StringBuilder alreadyInstalled = new StringBuilder();
        StringBuilder notCompatiblePlugins = new StringBuilder();

        for (File jarFile : files) {
            ClassLoader classLoader = null;

            try {
                URL[] urls = new URL[] { jarFile.toURI().toURL() };
                classLoader = URLClassLoader.newInstance(urls, ClassLoader.getSystemClassLoader());
            } catch (MalformedURLException exc) {

            }

            if (classLoader != null) {
                // Get the plugin name
                String pluginName = jarFile.getName();
                pluginName = pluginName.substring(0, pluginName.length() - 4);

                try {
                    String pluginId = "java." + pluginName.toLowerCase() + "." + pluginName;

                    PluginProxy installedPlugin = PluginProxyManager.getInstance().getPluginForId(pluginId);
                    TvDataServiceProxy service = TvDataServiceProxyManager.getInstance()
                            .findDataServiceById(pluginName.toLowerCase() + '.' + pluginName);

                    Class<?> pluginClass = classLoader.loadClass(pluginName.toLowerCase() + '.' + pluginName);

                    Method getVersion = pluginClass.getMethod("getVersion", new Class[0]);

                    Version version1 = null;
                    try {
                        version1 = (Version) getVersion.invoke(pluginClass, new Object[0]);
                    } catch (Throwable t1) {
                        t1.printStackTrace();
                    }

                    if (installedPlugin != null
                            && (installedPlugin.getInfo().getVersion().compareTo(version1) > 0
                                    || (installedPlugin.getInfo().getVersion().compareTo(version1) == 0
                                            && version1.isStable()))) {
                        alreadyInstalled.append(installedPlugin.getInfo().getName()).append('\n');
                    } else if (service != null && (service.getInfo().getVersion().compareTo(version1) > 0
                            || (service.getInfo().getVersion().compareTo(version1) == 0
                                    && version1.isStable()))) {
                        alreadyInstalled.append(service.getInfo().getName()).append('\n');
                    } else {
                        RandomAccessFile write = new RandomAccessFile(tmpFile, "rw");

                        String versionString = Integer.toString(version1.getMajor()) + '.'
                                + (version1.getMinor() / 10) + (version1.getMinor() % 10) + '.'
                                + version1.getSubMinor();

                        write.seek(write.length());

                        write.writeBytes("[plugin:" + pluginName + "]\n");
                        write.writeBytes("name_en=" + pluginName + "\n");
                        write.writeBytes("filename=" + jarFile.getName() + "\n");
                        write.writeBytes("version=" + versionString + "\n");
                        write.writeBytes("stable=" + version1.isStable() + "\n");
                        write.writeBytes("download=" + jarFile.toURI().toURL() + "\n");
                        write.writeBytes("category=unknown\n");

                        write.close();

                    }
                } catch (Exception e) {
                    notCompatiblePlugins.append(jarFile.getName()).append("\n");
                }
            }
        }

        if (alreadyInstalled.length() > 0) {
            showInfoTextMessage(
                    mLocalizer.msg("update.alreadyInstalled",
                            "The following Plugin in current version are already installed:"),
                    alreadyInstalled.toString(), 400);
        }

        if (notCompatiblePlugins.length() > 0) {
            showInfoTextMessage(
                    mLocalizer.msg("update.noTVBPlugin", "This following files are not TV-Browser Plugins:"),
                    notCompatiblePlugins.toString(), 400);
        }

        if (tmpFile.length() > 0) {
            java.net.URL url = tmpFile.toURI().toURL();
            SoftwareUpdater softwareUpdater = new SoftwareUpdater(url, false, true);
            mSoftwareUpdateItems = softwareUpdater.getAvailableSoftwareUpdateItems();
            dtde.dropComplete(true);

            SoftwareUpdateDlg updateDlg = new SoftwareUpdateDlg(this, false, mSoftwareUpdateItems);
            updateDlg.setVisible(true);
        } else {
            dtde.rejectDrop();
            dtde.dropComplete(false);
        }

        if (!tmpFile.delete()) {
            tmpFile.deleteOnExit();
        }
    } catch (MalformedURLException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
}

From source file:au.org.ala.layers.intersect.Grid.java

/**
 * @param points input array for longitude and latitude
 *               double[number_of_points][2]
 * @return array of .gri file values corresponding to the
 * points provided//from w w w . j  av a 2 s  .  c o m
 */
public float[] getValues(double[][] points) {

    //confirm inputs since they come from somewhere else
    if (points == null || points.length == 0) {
        return null;
    }

    //use preloaded grid data if available
    Grid g = Grid.getLoadedGrid(filename);
    if (g != null) {
        return g.getValues2(points);
    }

    if (subgrids != null) {
        return getValues3(points, Math.min(1024 * 1024, 64 * points.length));
    }

    float[] ret = new float[points.length];

    int length = points.length;
    long size;
    int i, pos;
    byte[] b;
    RandomAccessFile afile = null;
    File f2 = new File(filename + ".GRI");

    try { //read of random access file can throw an exception
        if (!f2.exists()) {
            afile = new RandomAccessFile(filename + ".gri", "r");
        } else {
            afile = new RandomAccessFile(filename + ".GRI", "r");
        }

        if (datatype.equalsIgnoreCase("BYTE")) {
            size = 1;
            b = new byte[(int) size];
            for (i = 0; i < length; i++) {
                pos = (int) getcellnumber(points[i][0], points[i][1]);
                if (pos >= 0) {
                    afile.seek(pos * size);
                    ret[i] = afile.readByte();
                } else {
                    ret[i] = Float.NaN;
                }
            }
        } else if (datatype.equalsIgnoreCase("UBYTE")) {
            size = 1;
            b = new byte[(int) size];
            for (i = 0; i < length; i++) {
                pos = (int) getcellnumber(points[i][0], points[i][1]);
                if (pos >= 0) {
                    afile.seek(pos * size);
                    ret[i] = afile.readByte();
                    if (ret[i] < 0) {
                        ret[i] += 256;
                    }
                } else {
                    ret[i] = Float.NaN;
                }
            }
        } else if (datatype.equalsIgnoreCase("SHORT")) {
            size = 2;
            b = new byte[(int) size];
            for (i = 0; i < length; i++) {
                pos = (int) getcellnumber(points[i][0], points[i][1]);
                if (pos >= 0) {
                    afile.seek(pos * size);
                    afile.read(b);
                    if (byteorderLSB) {
                        ret[i] = (short) (((0xFF & b[1]) << 8) | (b[0] & 0xFF));
                    } else {
                        ret[i] = (short) (((0xFF & b[0]) << 8) | (b[1] & 0xFF));
                    }
                    //ret[i] = afile.readShort();
                } else {
                    ret[i] = Float.NaN;
                }
            }
        } else if (datatype.equalsIgnoreCase("INT")) {
            size = 4;
            b = new byte[(int) size];
            for (i = 0; i < length; i++) {
                pos = (int) getcellnumber(points[i][0], points[i][1]);
                if (pos >= 0) {
                    afile.seek(pos * size);
                    afile.read(b);
                    if (byteorderLSB) {
                        ret[i] = ((0xFF & b[3]) << 24)
                                | ((0xFF & b[2]) << 16) + ((0xFF & b[1]) << 8) + (b[0] & 0xFF);
                    } else {
                        ret[i] = ((0xFF & b[0]) << 24)
                                | ((0xFF & b[1]) << 16) + ((0xFF & b[2]) << 8) + ((0xFF & b[3]) & 0xFF);
                    }
                    //ret[i] = afile.readInt();
                } else {
                    ret[i] = Float.NaN;
                }
            }
        } else if (datatype.equalsIgnoreCase("LONG")) {
            size = 8;
            b = new byte[(int) size];
            for (i = 0; i < length; i++) {
                pos = (int) getcellnumber(points[i][0], points[i][1]);
                if (pos >= 0) {
                    afile.seek(pos * size);
                    afile.read(b);
                    if (byteorderLSB) {
                        ret[i] = ((long) (0xFF & b[7]) << 56) + ((long) (0xFF & b[6]) << 48)
                                + ((long) (0xFF & b[5]) << 40) + ((long) (0xFF & b[4]) << 32)
                                + ((long) (0xFF & b[3]) << 24) + ((long) (0xFF & b[2]) << 16)
                                + ((long) (0xFF & b[1]) << 8) + (0xFF & b[0]);
                    } else {
                        ret[i] = ((long) (0xFF & b[0]) << 56) + ((long) (0xFF & b[1]) << 48)
                                + ((long) (0xFF & b[2]) << 40) + ((long) (0xFF & b[3]) << 32)
                                + ((long) (0xFF & b[4]) << 24) + ((long) (0xFF & b[5]) << 16)
                                + ((long) (0xFF & b[6]) << 8) + (0xFF & b[7]);
                    }
                    //ret[i] = afile.readLong();
                } else {
                    ret[i] = Float.NaN;
                }
            }
        } else if (datatype.equalsIgnoreCase("FLOAT")) {
            size = 4;
            b = new byte[(int) size];
            for (i = 0; i < length; i++) {
                pos = (int) getcellnumber(points[i][0], points[i][1]);
                if (pos >= 0) {
                    afile.seek(pos * size);
                    afile.read(b);
                    ByteBuffer bb = ByteBuffer.wrap(b);
                    if (byteorderLSB) {
                        bb.order(ByteOrder.LITTLE_ENDIAN);
                    }
                    ret[i] = bb.getFloat();
                } else {
                    ret[i] = Float.NaN;
                }

            }
        } else if (datatype.equalsIgnoreCase("DOUBLE")) {
            size = 8;
            b = new byte[8];
            for (i = 0; i < length; i++) {
                pos = (int) getcellnumber(points[i][0], points[i][1]);
                if (pos >= 0) {
                    afile.seek(pos * size);
                    afile.read(b);
                    ByteBuffer bb = ByteBuffer.wrap(b);
                    if (byteorderLSB) {
                        bb.order(ByteOrder.LITTLE_ENDIAN);
                    }
                    ret[i] = (float) bb.getDouble();

                    //ret[i] = afile.readFloat();
                } else {
                    ret[i] = Float.NaN;
                }
            }
        } else {
            logger.error("datatype not supported in Grid.getValues: " + datatype);
            // / should not happen; catch anyway...
            for (i = 0; i < length; i++) {
                ret[i] = Float.NaN;
            }
        }
        //replace not a number
        for (i = 0; i < length; i++) {
            if ((float) ret[i] == (float) nodatavalue) {
                ret[i] = Float.NaN;
            } else {
                ret[i] *= rescale;
            }
        }
    } catch (Exception e) {
        logger.error("error getting grid file values", e);
    } finally {
        if (afile != null) {
            try {
                afile.close();
            } catch (Exception e) {
                logger.error(e.getMessage(), e);
            }
        }
    }
    return ret;
}

From source file:org.apache.hadoop.hive.service.HSSessionItem.java

public boolean upload(String rtype, String user, String fileName, String data) throws HiveServerException {
    boolean res = true;
    String fname;//w  w w .ja v a2  s. co  m
    if (rtype.equalsIgnoreCase("jar")) {
        fname = getHome() + "/auxlib/" + fileName;
    } else if (rtype.equalsIgnoreCase("proto")) {
        String dname = getHome() + "/protobuf/upload/" + user;
        File d = new File(dname);
        if (!d.exists()) {
            if (!d.mkdirs()) {
                l4j.error(getSessionName() + " try to mkdir " + dname + " failed.");
                throw new HiveServerException("Create user proto directory failed.");
            }
        }
        if (!fileName.trim().toLowerCase().endsWith(".proto")) {
            throw new HiveServerException(
                    "Upload proto command can only handle .proto file, Check your file suffix");
        }

        fname = dname + "/" + fileName;
    } else {
        String errorMsg = "Can't upload filetype: " + rtype;
        l4j.error(getSessionName() + " upload failed: " + errorMsg);
        throw new HiveServerException("errorMsg");
    }

    RandomAccessFile raf;
    File f;
    try {
        f = new File(fname);
        if (!f.exists()) {
            if (!f.createNewFile()) {
                l4j.error("Try to create file " + fname + " failed.");
                throw new HiveServerException("Create user upload file " + fname + " failed.");
            }
        }
    } catch (java.io.IOException ex) {
        l4j.error(getSessionName() + " try to create file " + fname + " failed w/ " + ex);
        return false;
    }
    if (data.equalsIgnoreCase("")) {
        if (!f.delete()) {
            l4j.error("Try to delete file " + fname + " failed.");
            throw new HiveServerException("Delete user file " + fname + " failed.");
        } else {
            return true;
        }
    }

    try {
        raf = new RandomAccessFile(f, "rw");
    } catch (java.io.FileNotFoundException ex) {
        l4j.error(getSessionName() + " try to open file " + fname + " failed, not found.");
        return false;
    }
    try {
        raf.setLength(0);
        raf.seek(0);
        raf.write(data.getBytes());
    } catch (java.io.IOException ex) {
        l4j.error(getSessionName() + " try to truncate/write file " + fname + "failed w/ " + ex);
        return false;
    }
    return res;
}