Example usage for org.apache.commons.configuration Configuration getInt

Introduction

In this page you can find the example usage for org.apache.commons.configuration Configuration getInt.

Prototype

int getInt(String key);

Source Link

Document

Get a int associated with the given configuration key.

Usage

From source file:uk.ac.ebi.fg.jobs.PubMedDataMinerWrapperJob.java

public void doExecute(JobExecutionContext jobExecutionContext) throws SchedulerException, InterruptedException {
    JobDataMap dataMap = jobExecutionContext.getMergedJobDataMap();

    Set<String> pubMedNewIds = (Set<String>) dataMap.get("pubMedNewIds");
    ConcurrentHashMap<String, SortedSet<PubMedId>> pubMedIdRelationMap = (ConcurrentHashMap<String, SortedSet<PubMedId>>) dataMap
            .get("pubMedIdRelationMap");
    Configuration properties = (Configuration) dataMap.get("properties");
    PubMedRetriever pubMedRetriever = (PubMedRetriever) dataMap.get("pubMedRetriever");
    IJobsController jobsController = (IJobsController) dataMap.get("jobsController");
    String jobGroup = properties.getString("quartz_job_group_name");
    int maxPubMedDist = properties.getInt("max_pubmed_distance");

    AtomicInteger pubMedCounter = new AtomicInteger();
    int i = 0;/* w  ww  .j  a  v  a2  s.  co m*/

    if (!pubMedNewIds.isEmpty() && maxPubMedDist >= 0) {
        for (String entry : pubMedNewIds) {
            ++i;

            JobDetail pubMedJobDetail = newJob(PubMedDataMinerJob.class)
                    .withIdentity("pubMedDataMinerJob" + i, jobGroup).storeDurably(true).requestRecovery(false)
                    .build();

            pubMedJobDetail.getJobDataMap().put("pubMedNewIds", pubMedNewIds);
            pubMedJobDetail.getJobDataMap().put("pubMedIdRelationMap", pubMedIdRelationMap);
            pubMedJobDetail.getJobDataMap().put("properties", properties);
            pubMedJobDetail.getJobDataMap().put("pubMedCounter", pubMedCounter);
            pubMedJobDetail.getJobDataMap().put("pubMedRetriever", pubMedRetriever);
            pubMedJobDetail.getJobDataMap().put("entry", entry);

            jobsController.addJob("pubMedDataMinerJob" + i, PubMedDataMinerJob.class, pubMedJobDetail);

            Thread.currentThread().wait(1);
        }

        // start first 3 jobs
        jobsController.executeJob("pubMedDataMinerJob" + 1, jobGroup);
        if (i > 1) {
            jobsController.executeJob("pubMedDataMinerJob" + 2, jobGroup);
            if (i > 2)
                jobsController.executeJob("pubMedDataMinerJob" + 3, jobGroup);
        }
    }
}

---

From source file:uk.ac.ebi.fg.jobs.PubMedSimilarityJob.java

public void doExecute(JobExecutionContext jobExecutionContext)
        throws JobExecutionException, InterruptedException {
    JobDataMap dataMap = jobExecutionContext.getMergedJobDataMap();

    Map<String, String> expToPubMedIdMap = (ConcurrentHashMap<String, String>) dataMap.get("expToPubMedIdMap");
    Map<String, SortedSet<PubMedId>> pubMedIdRelationMap = (Map<String, SortedSet<PubMedId>>) dataMap
            .get("pubMedIdRelationMap");
    ConcurrentHashMap<String, SortedSet<ExperimentId>> pubMedResults = (ConcurrentHashMap<String, SortedSet<ExperimentId>>) dataMap
            .get("pubMedResults");
    Configuration properties = (Configuration) dataMap.get("properties");

    final int maxPubMedSimilarityCount = properties.getInt("max_displayed_PubMed_similarities");
    Map<String, SortedSet<String>> pubMedIdToExpAccessionMap = reverseMap(expToPubMedIdMap);
    expToPubMedIdMap.clear();/*from   w w  w .j a v a 2s .  c o  m*/

    logger.info("PubMedSimilarityJob started");

    for (Map.Entry<String, SortedSet<String>> pubMedIdToExpAccession : pubMedIdToExpAccessionMap.entrySet()) {
        SortedSet<ExperimentId> result = new TreeSet<ExperimentId>();

        if (pubMedIdRelationMap.containsKey(pubMedIdToExpAccession.getKey())) { // false - failed to get similar PubMed ids
            for (PubMedId publication : pubMedIdRelationMap.get(pubMedIdToExpAccession.getKey())) {
                result.addAll(getExperiments(pubMedIdToExpAccessionMap, publication));
            }

            for (String expAccession : pubMedIdToExpAccession.getValue()) {
                pubMedResults.putIfAbsent(expAccession,
                        limitPubMedExperimentCount(result, maxPubMedSimilarityCount, expAccession));
            }
        }

        Thread.currentThread().wait(1);
    }

    pubMedIdToExpAccessionMap.clear();
    pubMedIdRelationMap.clear();
    logger.info("PubMedSimilarityJob finished");
}

---

From source file:uk.ac.ebi.fg.jobs.TermToURIMappingWrapperJob.java

public void doExecute(JobExecutionContext jobExecutionContext) throws InterruptedException, SchedulerException {
    JobDataMap dataMap = jobExecutionContext.getJobDetail().getJobDataMap();

    IJobsController jobsController = (IJobsController) dataMap.get("jobsController");
    Map<ExperimentId, SortedSet<EfoTerm>> expToURIMap = (ConcurrentHashMap<ExperimentId, SortedSet<EfoTerm>>) dataMap
            .get("expToURIMap");
    Map<String, String> expToPubMedIdMap = (ConcurrentHashMap<String, String>) dataMap.get("expToPubMedIdMap");
    List experiments = (List) dataMap.get("experiments");
    XPath xp = (XPath) dataMap.get("experimentXPath");
    Configuration properties = (Configuration) dataMap.get("properties");
    String jobGroup = properties.getString("quartz_job_group_name");
    int threadLimit = (properties.getInt("concurrent_job_limit") > 1)
            ? properties.getInt("concurrent_job_limit")
            : 1;//from   w  ww .j  a  va  2  s .c o  m

    List smallExperimentList = new LinkedList();
    int counter = 0;
    int separateAt = experiments.size() / threadLimit + experiments.size() % threadLimit;

    logger.info("Term to URI mapping jobs started");
    for (Object node : experiments) {
        smallExperimentList.add(node);
        ++counter;

        if (counter % separateAt == 0 || counter == experiments.size()) {
            JobDetail termToURIMappingJobDetail = newJob(TermToURIMappingJob.class)
                    .withIdentity("termToURIMappingJob" + counter, jobGroup).storeDurably(false)
                    .requestRecovery(false).build();

            termToURIMappingJobDetail.getJobDataMap().put("experiments", new LinkedList(smallExperimentList));
            termToURIMappingJobDetail.getJobDataMap().put("expToURIMap", expToURIMap);
            termToURIMappingJobDetail.getJobDataMap().put("expToPubMedIdMap", expToPubMedIdMap);
            termToURIMappingJobDetail.getJobDataMap().put("experimentXPath", xp);
            termToURIMappingJobDetail.getJobDataMap().put("counter", new Integer(counter));
            termToURIMappingJobDetail.getJobDataMap().put("separateAt", separateAt); // for jobListener use

            jobsController.addJob("termToURIMappingJob" + counter, TermToURIMappingJob.class,
                    termToURIMappingJobDetail);
            jobsController.executeJob("termToURIMappingJob" + counter, jobGroup);

            // clear list
            smallExperimentList.clear();
            Thread.currentThread().wait(1);
        }
    }
}

---

From source file:uk.co.gidley.jmxmonitor.RegistryManager.java

public void stop() throws InitialisationException, IOException {
    Configuration config = readConfiguration(configurationFile);
    String stopKey = config.getString(ThreadManager.JMXMONITOR_STOPKEY);
    int stopPort = config.getInt(ThreadManager.JMXMONITOR_STOPPORT);

    Socket socket = new Socket("localhost", stopPort);
    PrintWriter printWriter = new PrintWriter(socket.getOutputStream(), true);
    printWriter.write(stopKey);/*from  ww  w . j a  va2  s .  c  o  m*/
    printWriter.flush();

}

---

From source file:uk.co.gidley.jmxmonitor.services.InternalJmx.java

private void startRmiRegistry(Configuration configuration) throws InitialisationException {
    try {/*from w  w w  . ja  v a 2 s .c o  m*/
        int port = configuration.getInt(PROPERTY_PREFIX + LOCAL_RMI_PORT);
        logger.debug("Creating RMI Registry on {}", port);
        registry = LocateRegistry.createRegistry(port);
    } catch (RemoteException e) {
        logger.error("{}", e);
        throw new InitialisationException(e);
    }
}

---

From source file:uk.trainwatch.nrod.feed.NetworkRailConnection.java

@PostConstruct
public void start() {
    Configuration config = configurationService.getPrivateConfiguration("networkrail");

    activemq = new RemoteActiveMQConnection(config.getString("server"), config.getInt("port"),
            config.getString("clientid"), config.getString("username"), config.getString("password"));

    activemq.start();/*from w ww . j  a v  a  2s  .c o  m*/
}

---

From source file:util.AbstractReadSystemConfigurations.java

private static int readAnonymizationAfterMonths() {

    int months = 3; // Default, if in the configuration file a not valid value was specified

    try {//from   w  ww.j  a va2 s.c o m
        final Configuration config = new PropertiesConfiguration(PATH);
        months = config.getInt("anonymization.after.months");

    } catch (final ConfigurationException e) {
        LOG.error(e.toString());
    }

    return months;
}

---

From source file:util.AbstractReadSystemConfigurations.java

private static int maxResultsDisplay() {

    int maxResults = 0;

    try {//from w  ww  .  j  a v a 2s .c om
        final Configuration config = new PropertiesConfiguration(PATH);
        maxResults = config.getInt("maxResults.display");

    } catch (final ConfigurationException e) {
        LOG.error(e.toString());
    }

    return maxResults;
}

---

From source file:xcmailrstarter.StarterConf.java

public StarterConf(String[] args) throws Exception {
    // get the server file-location
    XCM_HOME = System.getProperty("xcmailr.xcmstarter.home");

    // get the config file-location
    String confFile = System.getProperty("ninja.external.configuration");
    PropertiesConfiguration cfg = new PropertiesConfiguration();
    cfg.setEncoding("utf-8");
    cfg.setDelimiterParsingDisabled(true);
    String confPath = XCM_HOME + "/" + confFile;

    // try to load the config
    cfg.load(confPath);/*from   w  w  w  .  j a  v a 2 s  .com*/
    final Configuration conf = (Configuration) cfg;
    XCM_DB_URL = conf.getString("ebean.datasource.databaseUrl");
    XCM_DB_USER = conf.getString("ebean.datasource.username");
    XCM_DB_PASS = conf.getString("ebean.datasource.password");
    XCM_DB_DRIVER = conf.getString("ebean.datasource.databaseDriver");
    XCM_PORT = conf.getInt("application.port");
    XCM_CONTEXT_PATH = conf.getString("application.basedir");
    XCM_HOST = conf.getString("application.host", "localhost");

}

---

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