Example usage for java.util.concurrent BlockingQueue put

List of usage examples for java.util.concurrent BlockingQueue put

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Introduction

In this page you can find the example usage for java.util.concurrent BlockingQueue put.

Prototype

void put(E e) throws InterruptedException;

Source Link

Document

Inserts the specified element into this queue, waiting if necessary for space to become available.

Usage

From source file:ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneConverter.java

public void convert(final BlockingQueue<NcbiGeneData> geneInfoQueue, final BlockingQueue<Gene> geneQueue) {
    // start up thread to convert a member of geneInfoQueue to a gene/geneproduct/databaseentry
    // then push the gene onto the geneQueue for loading

    Thread convertThread = new Thread(new Runnable() {
        @Override/*from  w  w  w  .  j av a2s  . c o m*/
        @SuppressWarnings("synthetic-access")
        public void run() {
            while (!(sourceDone.get() && geneInfoQueue.isEmpty())) {
                try {
                    NcbiGeneData data = geneInfoQueue.poll();
                    if (data == null) {
                        continue;
                    }
                    Gene converted = NcbiGeneConverter.this.convert(data);

                    if (converted.getProducts().isEmpty()) {
                        log.info("Gene with no products skipped: " + converted);
                        continue;
                    }

                    geneQueue.put(converted);

                } catch (InterruptedException e) {
                    NcbiGeneConverter.log.warn("Interrupted");
                    break;
                } catch (Exception e) {
                    NcbiGeneConverter.log.error(e, e);
                    break;
                }
            }
            producerDone.set(true);
        }
    }, "Converter");

    convertThread.start();
}

From source file:ubic.gemma.loader.genome.gene.ncbi.NcbiGeneConverter.java

public void convert(final BlockingQueue<NcbiGeneData> geneInfoQueue, final BlockingQueue<Gene> geneQueue) {
    // start up thread to convert a member of geneInfoQueue to a gene/geneproduct/databaseentry
    // then push the gene onto the geneQueue for loading

    if (!retainProteinInformation) {
        log.info("Note that protein information will be ignored; set " + RETAIN_PROTEIN_INFO_PARAM
                + " to true to change");
    }/*from   www. ja  v a2  s.  c o m*/

    Thread convertThread = new Thread(new Runnable() {
        @Override
        @SuppressWarnings("synthetic-access")
        public void run() {
            while (!(sourceDone.get() && geneInfoQueue.isEmpty())) {
                try {
                    NcbiGeneData data = geneInfoQueue.poll();
                    if (data == null) {
                        continue;
                    }
                    Gene converted = convert(data);

                    geneQueue.put(converted);

                } catch (InterruptedException e) {
                    log.warn("Interrupted");
                    break;
                } catch (Exception e) {
                    log.error(e, e);
                    break;
                }
            }
            producerDone.set(true);
        }
    }, "Converter");

    convertThread.start();
}

From source file:gdsc.core.clustering.optics.ProjectedMoleculeSpace.java

/**
 * Put.//from   w ww.  j av  a 2 s.  co  m
 *
 * @param <T>
 *            the generic type
 * @param jobs
 *            the jobs
 * @param job
 *            the job
 */
private <T> void put(BlockingQueue<T> jobs, T job) {
    try {
        jobs.put(job);
    } catch (InterruptedException e) {
        throw new RuntimeException("Unexpected interruption", e);
    }
}

From source file:org.apache.camel.component.routebox.seda.RouteboxSedaConsumer.java

private void dispatchToInnerRoute(BlockingQueue<Exchange> queue, final Exchange exchange)
        throws InterruptedException {
    Exchange result;//from w ww . java  2s.  co m

    if (exchange != null) {
        if (isRunAllowed()) {
            try {
                if (LOG.isDebugEnabled()) {
                    LOG.debug("Dispatching to inner route: " + exchange);
                }
                RouteboxDispatcher dispatcher = new RouteboxDispatcher(producer);
                result = dispatcher.dispatchAsync(getRouteboxEndpoint(), exchange);
                AsyncProcessorHelper.process(processor, result, new AsyncCallback() {
                    public void done(boolean doneSync) {
                        // noop
                    }
                });
            } catch (Exception e) {
                getExceptionHandler().handleException("Error processing exchange", exchange, e);
            }
        } else {
            if (LOG.isWarnEnabled()) {
                LOG.warn(
                        "This consumer is stopped during polling an exchange, so putting it back on the seda queue: "
                                + exchange);
            }
            queue.put(exchange);
        }
    }
}

From source file:ubic.gemma.loader.protein.StringProteinProteinInteractionConverter.java

/**
 * Threaded conversion of domain objects to Gemma objects.
 *///  w w  w. ja  va  2  s  .c om
public void convert(final BlockingQueue<Gene2GeneProteinAssociation> gene2GeneProteinAssociationQueue,
        final Collection<StringProteinProteinInteraction> stringProteinProteinInteractions) {
    // start up thread to convert a member of geneInfoQueue to a gene/geneproduct/databaseentry
    // then push the gene onto the geneQueue for loading
    Thread convertThread = new Thread(new Runnable() {
        @Override
        @SuppressWarnings("synthetic-access")
        public void run() {

            try {
                for (StringProteinProteinInteraction stringProteinProteinInteraction : stringProteinProteinInteractions) {
                    if (stringProteinProteinInteraction == null) {
                        continue;
                    }
                    // converter
                    Collection<Gene2GeneProteinAssociation> dataColl = convert(stringProteinProteinInteraction);
                    // this returns a collection so split out and put on queue
                    for (Gene2GeneProteinAssociation gene2GeneProteinAssociation : dataColl) {
                        gene2GeneProteinAssociationQueue.put(gene2GeneProteinAssociation);
                    }
                }
            } catch (InterruptedException e) {
                log.info("Interrupted.");
            }
            producerDone.set(true);
        }

    }, "Converter");

    convertThread.start();
}

From source file:ubic.gemma.core.loader.protein.StringProteinProteinInteractionConverter.java

/**
 * Threaded conversion of domain objects to Gemma objects.
 *
 * @param gene2GeneProteinAssociationQueue queue
 * @param stringProteinProteinInteractions interactions
 *///from   w  ww. j a  va 2s .  c  om
public void convert(final BlockingQueue<Gene2GeneProteinAssociation> gene2GeneProteinAssociationQueue,
        final Collection<StringProteinProteinInteraction> stringProteinProteinInteractions) {
    // start up thread to convert a member of geneInfoQueue to a gene/geneproduct/databaseentry
    // then push the gene onto the geneQueue for loading
    Thread convertThread = new Thread(new Runnable() {
        @Override
        public void run() {

            try {
                for (StringProteinProteinInteraction stringProteinProteinInteraction : stringProteinProteinInteractions) {
                    if (stringProteinProteinInteraction == null) {
                        continue;
                    }
                    // converter
                    Collection<Gene2GeneProteinAssociation> dataColl = StringProteinProteinInteractionConverter.this
                            .convert(stringProteinProteinInteraction);
                    // this returns a collection so split out and put on queue
                    for (Gene2GeneProteinAssociation gene2GeneProteinAssociation : dataColl) {
                        gene2GeneProteinAssociationQueue.put(gene2GeneProteinAssociation);
                    }
                }
            } catch (InterruptedException e) {
                StringProteinProteinInteractionConverter.log.info("Interrupted.");
            }
            producerDone.set(true);
        }

    }, "Converter");

    convertThread.start();
}

From source file:org.apache.usergrid.tools.ImportAdmins.java

@SuppressWarnings("unchecked")
private void importMetadata(String fileName, int writeThreads) throws Exception {

    EntityManager em = emf.getEntityManager(CpNamingUtils.MANAGEMENT_APPLICATION_ID);

    File metadataFile = new File(importDir, fileName);

    logger.info("----- Loading metadata file: " + metadataFile.getAbsolutePath());

    JsonParser jp = getJsonParserForFile(metadataFile);

    JsonToken jsonToken = null; // jp.nextToken();// START_OBJECT this is the outer hashmap

    int depth = 1;

    BlockingQueue<ImportMetadataTask> workQueue = new LinkedBlockingQueue<ImportMetadataTask>();
    startMetadataWorkers(workQueue, writeThreads);

    while (depth > 0) {

        jsonToken = jp.nextToken();// www  .  j av a2 s  .  c  o m

        if (jsonToken == null) {
            logger.info("token is null, breaking");
            break;
        }

        if (jsonToken.equals(JsonToken.START_OBJECT)) {
            depth++;
        } else if (jsonToken.equals(JsonToken.END_OBJECT)) {
            depth--;
        }

        if (jsonToken.equals(JsonToken.FIELD_NAME) && depth == 2) {

            jp.nextToken();
            String entityOwnerId = jp.getCurrentName();

            try {
                EntityRef entityRef = new SimpleEntityRef("user", UUID.fromString(entityOwnerId));
                Map<String, Object> metadata = (Map<String, Object>) jp.readValueAs(Map.class);

                workQueue.put(new ImportMetadataTask(entityRef, metadata));
                logger.debug("Put user {} in metadata queue", entityRef.getUuid());

            } catch (Exception e) {
                logger.debug("Error with user {}, not putting in metadata queue", entityOwnerId);
            }
        }
    }

    waitForQueueAndMeasure(workQueue, metadataEmptyCount, metadataWorkerThreadMap, "Metadata Load");

    logger.info("----- End of metadata -----");
    jp.close();
}

From source file:com.nridge.connector.fs.con_fs.core.RunTransformFS.java

/**
 * When an object implementing interface <code>Runnable</code> is used
 * to create a thread, starting the thread causes the object's
 * <code>run</code> method to be called in that separately executing
 * thread.//from  w w w .  j  av  a2 s. c om
 * 
 * The general contract of the method <code>run</code> is that it may
 * take any action whatsoever.
 *
 * @see Thread#run()
 */
@Override
public void run() {
    DocumentXML documentXML;
    Document srcDoc, dstDoc;
    String docId, queueItem, srcPathFileName;
    Logger appLogger = mAppMgr.getLogger(this, "run");

    appLogger.trace(mAppMgr.LOGMSG_TRACE_ENTER);

    Pipeline pipeline = new Pipeline(mAppMgr, Constants.CFG_PROPERTY_PREFIX);

    BlockingQueue extractQueue = (BlockingQueue) mAppMgr.getProperty(Connector.QUEUE_EXTRACT_NAME);
    BlockingQueue transformQueue = (BlockingQueue) mAppMgr.getProperty(Connector.QUEUE_TRANSFORM_NAME);

    long queueWaitTimeout = mAppMgr.getLong(Constants.CFG_PROPERTY_PREFIX + ".queue.wait_timeout",
            Constants.QUEUE_POLL_TIMEOUT_DEFAULT);
    do {
        try {
            queueItem = (String) extractQueue.poll(queueWaitTimeout, TimeUnit.SECONDS);
            if (mCrawlQueue.isQueueItemDocument(queueItem)) {
                StopWatch stopWatch = new StopWatch();
                stopWatch.start();

                docId = Connector.docIdFromQueueItem(queueItem);

                appLogger.debug(String.format("Extract Queue Item: %s", docId));
                srcPathFileName = mCrawlQueue.docPathFileName(Connector.QUEUE_EXTRACT_NAME, docId);
                try {
                    documentXML = new DocumentXML();
                    documentXML.load(srcPathFileName);
                    srcDoc = documentXML.getDocument();

                    dstDoc = pipeline.execute(srcDoc);

                    mCrawlQueue.transition(Connector.QUEUE_EXTRACT_NAME, Connector.QUEUE_TRANSFORM_NAME, dstDoc,
                            docId);
                    stopWatch.stop();
                    queueItem = Connector.queueItemIdPhaseTime(queueItem, Connector.PHASE_TRANSFORM,
                            stopWatch.getTime());
                    try {
                        // If queue is full, this thread may block.
                        transformQueue.put(queueItem);
                    } catch (InterruptedException e) {
                        // Restore the interrupted status so parent can handle (if it wants to).
                        Thread.currentThread().interrupt();
                    }
                } catch (Exception e) {
                    String msgStr = String.format("%s: %s", docId, e.getMessage());
                    appLogger.error(msgStr, e);
                    MailManager mailManager = (MailManager) mAppMgr.getProperty(Connector.PROPERTY_MAIL_NAME);
                    mailManager.addMessage(Connector.PHASE_TRANSFORM, Connector.STATUS_MAIL_ERROR, msgStr,
                            Constants.MAIL_DETAIL_MESSAGE);
                }
            }
        } catch (InterruptedException e) {
            queueItem = StringUtils.EMPTY;
        }
    } while (!mCrawlQueue.isPhaseComplete(Connector.PHASE_EXTRACT, queueItem));

    // Forward the marker queue item to the next queue.

    if (mCrawlQueue.isQueueItemMarker(queueItem)) {
        try {
            // If queue is full, this thread may block.
            transformQueue.put(queueItem);
        } catch (InterruptedException e) {
            // Restore the interrupted status so parent can handle (if it wants to).
            Thread.currentThread().interrupt();
        }
    }

    appLogger.trace(mAppMgr.LOGMSG_TRACE_DEPART);
}

From source file:coral.service.ExpServable.java

private void sendRes(BlockingQueue<Message> outQueue, String... res) {
    for (String line : res) {
        try {/*from  www  .  java2 s . co  m*/
            File file = new File(basepath, line);

            long version = file.lastModified();

            logger.info("sync file " + line + " version:" + version + " path " + file.getCanonicalPath());

            try {
                /*
                 * outQueue.put(new Message("ressync:" + file.getName() +
                 * "?show=NO&version=" + version + "&synccmd=" +
                 * URLEncoder.encode("get://host/" +
                 * file.getCanonicalPath(), "utf-8"), new byte[] {}));
                 */

                // InputStream is;
                // byte[] bytes = null;

                String mime = GetServable.getMime(file);

                BufferedInputStream reader = new BufferedInputStream(new FileInputStream(file));

                byte[] buffer = new byte[8096]; // == 1024

                ByteArrayOutputStream baos = new ByteArrayOutputStream();
                int read;
                while ((read = reader.read(buffer)) >= 0) {
                    baos.write(buffer, 0, read);
                }
                byte[] readbytes = baos.toByteArray();

                outQueue.put(new Message("vset", file.getName(), mime, "NO&version=" + version, readbytes));

                reader.close();

            } catch (InterruptedException e) {
                logger.error("i error", e);
            }
        } catch (FileNotFoundException e) {
            logger.error("file not found", e);
        } catch (IOException e) {
            logger.error("I/O", e);
        }
    }
}

From source file:com.nridge.connector.fs.con_fs.core.RunPublishFS.java

/**
 * When an object implementing interface <code>Runnable</code> is used
 * to create a thread, starting the thread causes the object's
 * <code>run</code> method to be called in that separately executing
 * thread.//  w w w . j  av a  2  s.c  o  m
 * 
 * The general contract of the method <code>run</code> is that it may
 * take any action whatsoever.
 *
 * @see Thread#run()
 */
@Override
public void run() {
    Document conDoc;
    DocumentXML documentXML;
    String docId, queueItem, srcPathFileName;
    Logger appLogger = mAppMgr.getLogger(this, "run");

    appLogger.trace(mAppMgr.LOGMSG_TRACE_ENTER);

    boolean isPublisherInitialized = true;
    DataBag schemaBag = (DataBag) mAppMgr.getProperty(Connector.PROPERTY_SCHEMA_NAME);
    Publishers indexPublishers = new Publishers(mAppMgr, mCrawlQueue, Constants.CFG_PROPERTY_PREFIX);
    try {
        indexPublishers.initialize(schemaBag);
    } catch (NSException e) {
        isPublisherInitialized = false;
        appLogger.error("Publisher initialization: " + e.getMessage());
    }

    if (isPublisherInitialized) {
        BlockingQueue transformQueue = (BlockingQueue) mAppMgr.getProperty(Connector.QUEUE_TRANSFORM_NAME);
        BlockingQueue publishQueue = (BlockingQueue) mAppMgr.getProperty(Connector.QUEUE_PUBLISH_NAME);

        long queueWaitTimeout = mAppMgr.getLong(Constants.CFG_PROPERTY_PREFIX + ".queue.wait_timeout",
                Constants.QUEUE_POLL_TIMEOUT_DEFAULT);
        do {
            try {
                queueItem = (String) transformQueue.poll(queueWaitTimeout, TimeUnit.SECONDS);
                if (mCrawlQueue.isQueueItemDocument(queueItem)) {
                    StopWatch stopWatch = new StopWatch();
                    stopWatch.start();

                    docId = Connector.docIdFromQueueItem(queueItem);

                    appLogger.debug(String.format("Transform Queue Item: %s", docId));
                    srcPathFileName = mCrawlQueue.docPathFileName(Connector.QUEUE_TRANSFORM_NAME, docId);
                    try {
                        documentXML = new DocumentXML();
                        documentXML.load(srcPathFileName);
                        conDoc = documentXML.getDocument();

                        indexPublishers.send(conDoc);

                        File srcFile = new File(srcPathFileName);
                        if (!srcFile.delete())
                            appLogger.warn(String.format("%s: Unable to delete.", srcPathFileName));

                        stopWatch.stop();
                        queueItem = Connector.queueItemIdPhaseTime(queueItem, Connector.PHASE_PUBLISH,
                                stopWatch.getTime());
                        try {
                            // If queue is full, this thread may block.
                            publishQueue.put(queueItem);
                        } catch (InterruptedException e) {
                            // Restore the interrupted status so parent can handle (if it wants to).
                            Thread.currentThread().interrupt();
                        }
                    } catch (Exception e) {
                        String msgStr = String.format("%s: %s", docId, e.getMessage());
                        appLogger.error(msgStr, e);
                        MailManager mailManager = (MailManager) mAppMgr
                                .getProperty(Connector.PROPERTY_MAIL_NAME);
                        mailManager.addMessage(Connector.PHASE_PUBLISH, Connector.STATUS_MAIL_ERROR, msgStr,
                                Constants.MAIL_DETAIL_MESSAGE);
                    }
                }
            } catch (InterruptedException e) {
                queueItem = StringUtils.EMPTY;
            }
        } while (!mCrawlQueue.isPhaseComplete(Connector.PHASE_TRANSFORM, queueItem));

        // Forward the marker queue item to the next queue.

        if (mCrawlQueue.isQueueItemMarker(queueItem)) {
            try {
                // If queue is full, this thread may block.
                publishQueue.put(queueItem);
            } catch (InterruptedException e) {
                // Restore the interrupted status so parent can handle (if it wants to).
                Thread.currentThread().interrupt();
            }
        }

        // Now we can shutdown our search indexer publisher.

        try {
            indexPublishers.shutdown();
        } catch (NSException e) {
            appLogger.error("Publisher shutdown: " + e.getMessage());
        }
    }

    appLogger.trace(mAppMgr.LOGMSG_TRACE_DEPART);
}