Example usage for java.util.concurrent BlockingQueue poll

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

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Introduction

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

Prototype

E poll();

Source Link

Document

Retrieves and removes the head of this queue, or returns null if this queue is empty.

Usage

From source file:com.brienwheeler.svc.monitor.telemetry.impl.AsynchronousTelemetryInfoProcessor.java

@Override
@GracefulShutdown/*  w w w  .ja  v  a  2 s . c  om*/
public void process(TelemetryInfo telemetryInfo) {
    telemetryInfo.checkPublished();

    BlockingQueue<TelemetryInfo> queue = this.queue.get();

    switch (queueFullPolicy.get()) {
    case DISCARD_OFFERED:
        queue.offer(telemetryInfo);
        // return regardless of success
        return;

    case DISCARD_OLDEST:
        while (!queue.offer(telemetryInfo)) {
            // if offer failed, remove and discard one element from queue and try
            // again
            queue.poll();
        }
        return;
    }
}

From source file:ubic.gemma.core.loader.association.NCBIGene2GOAssociationLoader.java

private void load(BlockingQueue<Gene2GOAssociation> queue) {

    NCBIGene2GOAssociationLoader.log.debug("Entering 'load' ");

    long millis = System.currentTimeMillis();
    int cpt = 0;//w  w w .  j  a va 2s  . com
    double secspt = 0.0;

    Collection<Gene2GOAssociation> itemsToPersist = new ArrayList<>();
    try {
        while (!(producerDone.get() && queue.isEmpty())) {
            Gene2GOAssociation associations = queue.poll();

            if (associations == null) {
                continue;
            }

            itemsToPersist.add(associations);
            if (++count % NCBIGene2GOAssociationLoader.BATCH_SIZE == 0) {
                persisterHelper.persist(itemsToPersist);
                itemsToPersist.clear();
            }

            // just some timing information.
            if (count % 10000 == 0) {
                cpt++;
                double secsperthousand = (System.currentTimeMillis() - millis) / 1000.0;
                secspt += secsperthousand;
                double meanspt = secspt / cpt;

                String progString = "Processed and loaded " + count + " (" + secsperthousand
                        + " seconds elapsed, average per thousand=" + String.format("%.2f", meanspt) + ")";
                NCBIGene2GOAssociationLoader.log.info(progString);
                millis = System.currentTimeMillis();
            }

        }
    } catch (Exception e) {
        consumerDone.set(true);
        NCBIGene2GOAssociationLoader.log.fatal(e, e);
        throw new RuntimeException(e);
    }

    // finish up.
    persisterHelper.persist(itemsToPersist);

    NCBIGene2GOAssociationLoader.log.info("Finished, loaded total of " + count + " GO associations");
    consumerDone.set(true);

}

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

/**
 * @param geneQueue//from  w  w  w.  j a  v a 2s.  c  om
 */
void doLoad(final BlockingQueue<Gene> geneQueue) {
    StopWatch timer = new StopWatch();
    timer.start();
    int skipped = 0;
    while (!(converterDone.get() && geneQueue.isEmpty())) {
        Gene gene = null;
        try {
            // the converted genes.
            gene = geneQueue.poll();
            if (gene == null) {
                continue;
            }

            if (gene.getProducts().isEmpty()) {
                // // log.warn( gene + " has no products, skipping" ); // common!!!
                // skipped++;
            }

            persisterHelper.persistOrUpdate(gene);

            if (++loadedGeneCount % 1000 == 0 || timer.getTime() > 30 * 1000) {
                log.info("Processed " + loadedGeneCount + " genes. Queue has " + geneQueue.size()
                        + " items; last gene: " + gene);
                if (skipped > 0) {
                    log.info(skipped + " skipped because they had no gene products.");
                }
                timer.reset();
                timer.start();
            }

        } catch (Exception e) {
            log.error("Error while loading gene: " + gene + ": " + e.getMessage(), e);
            loaderDone.set(true);
            throw new RuntimeException(e);
        }
    }
    log.info("Loaded " + loadedGeneCount + " genes. ");
    loaderDone.set(true);
}

From source file:ubic.gemma.loader.association.NCBIGene2GOAssociationLoader.java

/**
 * @param queue/*from  w ww  .  j ava  2  s .c o m*/
 */
protected void load(BlockingQueue<Gene2GOAssociation> queue) {

    log.debug("Entering 'load' ");

    long millis = System.currentTimeMillis();
    int cpt = 0;
    double secspt = 0.0;

    Collection<Gene2GOAssociation> itemsToPersist = new ArrayList<Gene2GOAssociation>();
    try {
        while (!(producerDone.get() && queue.isEmpty())) {
            Gene2GOAssociation associations = queue.poll();

            if (associations == null) {
                continue;
            }

            itemsToPersist.add(associations);
            if (++count % BATCH_SIZE == 0) {
                persisterHelper.persist(itemsToPersist);
                itemsToPersist.clear();
            }

            // just some timing information.
            if (count % 1000 == 0) {
                cpt++;
                double secsperthousand = (System.currentTimeMillis() - millis) / 1000.0;
                secspt += secsperthousand;
                double meanspt = secspt / cpt;

                String progString = "Processed and loaded " + count + " (" + secsperthousand
                        + " seconds elapsed, average per thousand=" + String.format("%.2f", meanspt) + ")";
                log.info(progString);
                millis = System.currentTimeMillis();
            }

        }
    } catch (Exception e) {
        consumerDone.set(true);
        log.fatal(e, e);
        throw new RuntimeException(e);
    }

    // finish up.
    persisterHelper.persist(itemsToPersist);

    log.info("Finished, loaded total of " + count + " GO associations");
    consumerDone.set(true);

}

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

/**
 * Poll the queue to see if any Gene2GeneProteinAssociation to load into database. If so firstly check to see if the
 * genes are in the gemma db as these identifiers came from biomart If both genes found load.
 * //from  w  ww  . j a  v  a2s  .  c o m
 * @param geneQueue queue of Gene2GeneProteinAssociation to load
 */
void doLoad(final BlockingQueue<Gene2GeneProteinAssociation> gene2GeneProteinAssociationQueue) {
    log.info("starting processing ");
    while (!(converterDone.get() && gene2GeneProteinAssociationQueue.isEmpty())) {

        try {
            Gene2GeneProteinAssociation gene2GeneProteinAssociation = gene2GeneProteinAssociationQueue.poll();
            if (gene2GeneProteinAssociation == null) {
                continue;
            }
            // check they are genes gemma knows about
            Gene geneOne = geneService.findByNCBIId(gene2GeneProteinAssociation.getFirstGene().getNcbiGeneId());
            Gene geneTwo = geneService
                    .findByNCBIId(gene2GeneProteinAssociation.getSecondGene().getNcbiGeneId());

            if (geneOne == null) {
                log.warn("Gene with NCBI id=" + gene2GeneProteinAssociation.getFirstGene().getNcbiGeneId()
                        + " not in Gemma");
                continue;
            }
            if (geneTwo == null) {
                log.warn("Gene with NCBI id=" + gene2GeneProteinAssociation.getSecondGene().getNcbiGeneId()
                        + " not in Gemma");
                continue;
            }

            gene2GeneProteinAssociation.setFirstGene(geneOne);
            gene2GeneProteinAssociation.setSecondGene(geneTwo);
            persisterHelper.persist(gene2GeneProteinAssociation);

            if (++loadedGeneCount % 1000 == 0) {
                log.info("Proceesed " + loadedGeneCount + " protein protein interactions. "
                        + "Current queue has " + gene2GeneProteinAssociationQueue.size() + " items.");
            }

        } catch (Exception e) {
            log.error(e, e);
            loaderDone.set(true);
            throw new RuntimeException(e);
        }
    }
    log.info("Loaded " + loadedGeneCount + " protein protein interactions. ");
    loaderDone.set(true);
}

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

/**
 * Poll the queue to see if any Gene2GeneProteinAssociation to load into database. If so firstly check to see if the
 * genes are in the gemma db as these identifiers came from biomart If both genes found load.
 *
 * @param gene2GeneProteinAssociationQueue queue of Gene2GeneProteinAssociation to load
 *///from  www. j  a v  a2 s  .co  m
private void doLoad(final BlockingQueue<Gene2GeneProteinAssociation> gene2GeneProteinAssociationQueue) {
    StringProteinInteractionLoader.log.info("starting processing ");
    while (!(converterDone.get() && gene2GeneProteinAssociationQueue.isEmpty())) {

        try {
            Gene2GeneProteinAssociation gene2GeneProteinAssociation = gene2GeneProteinAssociationQueue.poll();
            if (gene2GeneProteinAssociation == null) {
                continue;
            }
            // check they are genes gemma knows about
            Gene geneOne = geneService.findByNCBIId(gene2GeneProteinAssociation.getFirstGene().getNcbiGeneId());
            Gene geneTwo = geneService
                    .findByNCBIId(gene2GeneProteinAssociation.getSecondGene().getNcbiGeneId());

            if (geneOne == null) {
                StringProteinInteractionLoader.log.warn("Gene with NCBI id="
                        + gene2GeneProteinAssociation.getFirstGene().getNcbiGeneId() + " not in Gemma");
                continue;
            }
            if (geneTwo == null) {
                StringProteinInteractionLoader.log.warn("Gene with NCBI id="
                        + gene2GeneProteinAssociation.getSecondGene().getNcbiGeneId() + " not in Gemma");
                continue;
            }

            FieldUtils.writeField(gene2GeneProteinAssociation, "firstGene", geneOne, true);
            FieldUtils.writeField(gene2GeneProteinAssociation, "secondGene", geneTwo, true);

            persisterHelper.persist(gene2GeneProteinAssociation);

            if (++loadedGeneCount % 1000 == 0) {
                StringProteinInteractionLoader.log
                        .info("Proceesed " + loadedGeneCount + " protein protein interactions. "
                                + "Current queue has " + gene2GeneProteinAssociationQueue.size() + " items.");
            }

        } catch (Exception e) {
            StringProteinInteractionLoader.log.error(e, e);
            loaderDone.set(true);
            throw new RuntimeException(e);
        }
    }
    StringProteinInteractionLoader.log.info("Loaded " + loadedGeneCount + " protein protein interactions. ");
    loaderDone.set(true);
}

From source file:ubic.gemma.loader.genome.goldenpath.GoldenPathBioSequenceLoader.java

/**
 * @param bioSequences//from w  w  w  .  j av a  2 s .com
 */
void load(BlockingQueue<BioSequence> queue) {
    log.debug("Entering 'load' ");

    StopWatch timer = new StopWatch();
    timer.start();

    int count = 0;
    int cpt = 0;
    double secspt = 0.0;

    Collection<BioSequence> bioSequencesToPersist = new ArrayList<BioSequence>();
    try {
        while (!(producerDone && queue.isEmpty())) {
            BioSequence sequence = queue.poll();

            if (sequence == null) {
                continue;
            }

            sequence.getSequenceDatabaseEntry().setExternalDatabase(genbank);
            sequence.setTaxon(taxon);
            bioSequencesToPersist.add(sequence);
            if (++count % BATCH_SIZE == 0) {
                bioSequenceService.create(bioSequencesToPersist);
                bioSequencesToPersist.clear();
            }

            // just some timing information.
            if (count % 1000 == 0) {
                cpt++;
                timer.stop();
                double secsperthousand = timer.getTime() / 1000.0;
                secspt += secsperthousand;
                double meanspt = secspt / cpt;

                String progString = "Processed and loaded " + count + " sequences, last one was "
                        + sequence.getName() + " (" + secsperthousand + "s for last 1000, mean per 1000 ="
                        + String.format("%.1f", meanspt) + "s)";
                log.info(progString);
                timer.reset();
                timer.start();
            }

        }
    } catch (Exception e) {
        consumerDone = true;
        throw new RuntimeException(e);
    }

    // finish up.
    bioSequenceService.create(bioSequencesToPersist);

    log.info("Loaded total of " + count + " sequences");
    consumerDone = true;

}

From source file:ubic.gemma.loader.expression.arrayDesign.ArrayDesignProbeMapperServiceImpl.java

/**
 * @param queue/*from   w w  w .j  ava 2s.c o  m*/
 * @param generatorDone
 * @param loaderDone
 */
void doLoad(final BlockingQueue<BlatAssociation> queue, AtomicBoolean generatorDone, AtomicBoolean loaderDone) {
    int loadedAssociationCount = 0;
    while (!(generatorDone.get() && queue.isEmpty())) {

        try {
            BlatAssociation ba = queue.poll();
            if (ba == null) {
                continue;
            }

            GeneProduct geneProduct = ba.getGeneProduct();
            if (geneProduct.getId() == null) {
                GeneProduct existing = geneProductService.find(geneProduct);

                if (existing == null) {

                    existing = checkForAlias(geneProduct);
                    if (existing == null) {
                        /*
                         * We have to be careful not to cruft up the gene table now that I so carefully cleaned it.
                         * But this is a problem if we aren't adding some other association to the gene at least.
                         * But generally the mRNAs that GP has that NCBI doesn't are "alternative" or "additional".
                         */
                        if (log.isDebugEnabled())
                            log.debug("New gene product from GoldenPath is not in Gemma: " + geneProduct
                                    + " skipping association to " + ba.getBioSequence()
                                    + " [skipping policy in place]");
                        continue;
                    }
                }
                ba.setGeneProduct(existing);
            }

            persisterHelper.persist(ba);

            if (++loadedAssociationCount % 1000 == 0) {
                log.info("Persisted " + loadedAssociationCount + " blat associations. " + "Current queue has "
                        + queue.size() + " items.");
            }

        } catch (Exception e) {
            log.error(e, e);
            loaderDone.set(true);
            throw new RuntimeException(e);
        }
    }
    log.info("Load thread done: loaded " + loadedAssociationCount + " blat associations. ");
    loaderDone.set(true);
}

From source file:org.springframework.integration.ftp.outbound.FtpServerOutboundTests.java

private Session<FTPFile> spyOnSession() {
    Session<FTPFile> session = spy(this.ftpSessionFactory.getSession());
    session.close();/*from w  w  w  .ja  v  a 2  s  .  c o m*/
    @SuppressWarnings("unchecked")
    BlockingQueue<Session<FTPFile>> cache = TestUtils.getPropertyValue(ftpSessionFactory, "pool.available",
            BlockingQueue.class);
    assertNotNull(cache.poll());
    cache.offer(session);
    @SuppressWarnings("unchecked")
    Set<Session<FTPFile>> allocated = TestUtils.getPropertyValue(ftpSessionFactory, "pool.allocated",
            Set.class);
    allocated.clear();
    allocated.add(session);
    return session;
}

From source file:ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperServiceImpl.java

private void doLoad(final BlockingQueue<BACS> queue, AtomicBoolean generatorDone, AtomicBoolean loaderDone,
        boolean persist) {
    int loadedAssociationCount = 0;
    while (!(generatorDone.get() && queue.isEmpty())) {

        try {//from  w w  w  .  j  ava2 s. com
            BACS bacs = queue.poll();
            if (bacs == null) {
                continue;
            }

            GeneProduct geneProduct = bacs.ba.getGeneProduct();

            if (geneProduct.getId() == null) {
                GeneProduct existing = geneProductService.find(geneProduct);

                if (existing == null) {

                    existing = this.checkForAlias(geneProduct);
                    if (existing == null) {
                        /*
                         * We have to be careful not to cruft up the gene table now that I so carefully cleaned it.
                         * But this is a problem if we aren't adding some other association to the gene at least.
                         * But generally the mRNAs that GP has that NCBI doesn't are "alternative" or "additional".
                         */
                        if (ArrayDesignProbeMapperServiceImpl.log.isDebugEnabled())
                            ArrayDesignProbeMapperServiceImpl.log
                                    .debug("New gene product from GoldenPath is not in Gemma: " + geneProduct
                                            + " skipping association to " + bacs.ba.getBioSequence()
                                            + " [skipping policy in place]");
                        continue;
                    }
                }
                bacs.ba.setGeneProduct(existing);
            }

            if (persist) {
                persisterHelper.persist(bacs.ba);

                if (++loadedAssociationCount % 1000 == 0) {
                    ArrayDesignProbeMapperServiceImpl.log.info("Persisted " + loadedAssociationCount
                            + " blat associations. " + "Current queue has " + queue.size() + " items.");
                }
            } else {
                this.printResult(bacs.cs, bacs.ba);
            }

        } catch (Exception e) {
            ArrayDesignProbeMapperServiceImpl.log.error(e, e);
            loaderDone.set(true);
            throw new RuntimeException(e);
        }
    }
    ArrayDesignProbeMapperServiceImpl.log
            .info("Load thread done: loaded " + loadedAssociationCount + " blat associations. ");
    loaderDone.set(true);
}