Example usage for java.io IOException fillInStackTrace

Introduction

In this page you can find the example usage for java.io IOException fillInStackTrace.

Prototype

public synchronized Throwable fillInStackTrace() 

Source Link

Document

Fills in the execution stack trace.

Usage

From source file:uni.bielefeld.cmg.sparkhit.main.Main.java

public static void main(String[] args) {
    InfoDumper info = new InfoDumper();
    info.readParagraphedMessages("SparkHit main initiating ... \ninterpreting parameters.");
    info.screenDump();/*from   w w w  .jav  a2  s.c  o m*/

    Parameter parameter = null;
    try {
        parameter = new Parameter(args);
    } catch (IOException e) {
        e.fillInStackTrace();
    } catch (ParseException e) {
        e.fillInStackTrace();
    }
    DefaultParam param = parameter.importCommandLine();

    Pipelines pipes = new Pipelines();
    pipes.setParameter(param);
    pipes.spark();

}

---

From source file:uni.bielefeld.cmg.sparkhit.main.MainOfParallelizer.java

public static void main(String[] args) {
    InfoDumper info = new InfoDumper();
    info.readParagraphedMessages(//from w  w w  .ja va  2 s .  c  om
            "SparkHit Parallelizer (parallel operation on different nodes) initiating ... \ninterpreting parameters.");
    info.screenDump();

    ParameterForParallelizer parameterV = null;
    try {
        parameterV = new ParameterForParallelizer(args);
    } catch (IOException e) {
        e.fillInStackTrace();
    } catch (ParseException e) {
        e.fillInStackTrace();
    }
    DefaultParam param = parameterV.importCommandLine();

    Pipelines pipes = new Pipelines();
    pipes.setParameter(param);
    pipes.sparkParallelizer();

}

---

From source file:uni.bielefeld.cmg.sparkhit.main.MainOfStatisticer.java

public static void main(String[] args) {
    InfoDumper info = new InfoDumper();
    info.readParagraphedMessages(/*from ww  w.ja  va  2  s.c o m*/
            "SparkHit Statisticer (HWE, fisher EX, ChiSq) initiating ... \ninterpreting parameters.");
    info.screenDump();

    ParameterForStatisticer parameterS = null;
    try {
        parameterS = new ParameterForStatisticer(args);
    } catch (IOException e) {
        e.fillInStackTrace();
    } catch (ParseException e) {
        e.fillInStackTrace();
    }
    DefaultParam param = parameterS.importCommandLine();

    Pipelines pipes = new Pipelines();
    pipes.setParameter(param);
    pipes.sparkStatisticer();

}

---

From source file:uni.bielefeld.cmg.sparkhit.main.MainOfVariantCaller.java

public static void main(String[] args) {
    InfoDumper info = new InfoDumper();
    info.readParagraphedMessages(//from  ww  w. j  a  v a  2s  . com
            "SparkHit VariantCaller (HDFS bam reader) initiating ... \ninterpreting parameters.");
    info.screenDump();

    ParameterForVariantCaller parameterV = null;
    try {
        parameterV = new ParameterForVariantCaller(args);
    } catch (IOException e) {
        e.fillInStackTrace();
    } catch (ParseException e) {
        e.fillInStackTrace();
    }
    DefaultParam param = parameterV.importCommandLine();

    Pipelines pipes = new Pipelines();
    pipes.setParameter(param);
    pipes.sparkVariantCaller();

}

---

From source file:org.rhq.plugins.apache.ModJKComponent.java

/**
 * Delegate method to install a simple mod_jk in an apache httpd
 * @param serverComponent The parents server component with the configuration
 * @param params Params we got passed from the GUI
 * @return The outcome of the operation//from  w  w  w.j ava  2 s. c om
 * @throws Exception see thrown exception for details; thrown exception summarizes error
 */
public static OperationResult installModJk(ApacheServerComponent serverComponent, Configuration params)
        throws Exception {

    StringBuilder builder = new StringBuilder();
    boolean needWorkersProps = false;
    boolean needUriWorkers = false;

    // First see (what) if stuff is present
    File httpdConf = serverComponent.getHttpdConfFile();
    String confPath = httpdConf.getAbsolutePath();

    // If we can't update the file, then there is nothing left to do.
    if (!httpdConf.canWrite()) {
        throw new Exception("Httpd.conf is not writable at " + confPath);
    }

    HttpdConfParser cparser = new HttpdConfParser();
    cparser.parse(confPath);
    // TODO back up original file
    try {
        BufferedWriter writer = null;
        try {
            writer = new BufferedWriter(new FileWriter(httpdConf, true));
            if (cparser.isModJkInstalled()) {
                builder.append("Mod_jk is already installed\n");
                if (cparser.getWorkerPropertiesFile() != null) {
                    builder.append("Found a worker.properties file at ")
                            .append(cparser.getWorkerPropertiesFile());
                    builder.append("\n");
                } else
                    needWorkersProps = true;

                if (cparser.getUriWorkerLocation() != null) {
                    builder.append("Found a urimap file at ").append(cparser.getUriWorkerLocation());
                } else
                    needUriWorkers = true;
            } else {
                builder.append("No mod_jk installed yet at ").append(confPath).append("\n");

                writer.append("LoadModule jk_module modules/mod_jk.so"); // TODO obtain modules location
                writer.newLine();

                builder.append(".. written a LoadModule line \n");
                needWorkersProps = true;
                needUriWorkers = true;
            }

            if (needWorkersProps) {
                writer.append("JkWorkersFile ").append("conf/workers.properties");
                writer.newLine();
                builder.append(".. installed worker.properties");
            }
            if (needUriWorkers) {
                writer.append("JkMountFile ").append("conf/uriworkermap");
                writer.newLine();
                builder.append(".. installed uriworkermap");
            }
        } finally {
            if (writer != null) {
                // close automatically flushes!
                writer.close();
            }
        }
    } catch (IOException e) {
        builder.append("Error when installing mod_jk: \n");
        builder.append(e.fillInStackTrace());
        throw new Exception(builder.toString());

    }

    OperationResult result = new OperationResult();

    Configuration complexResults = result.getComplexResults();
    complexResults.put(new PropertySimple(OUTPUT_RESULT_PROP, builder.toString()));

    return result;
}

---

From source file:uk.nhs.cfh.dsp.srth.distribution.TRUDLoginService.java

public TRUDLoginService(FTPClient ftpClient) {

    this.ftpClient = ftpClient;
    try {/*from  www . j av  a2s .co  m*/
        logger.addHandler(new FileHandler(System.getProperty("java.io.tmpdir")
                + System.getProperty("file.separator") + "configurator.log", true));
    } catch (IOException e) {
        logger.warning("Nested exception is : " + e.fillInStackTrace().getMessage());
    }
}

---

From source file:com.ibm.connectors.splunklog.SplunkHttpConnection.java

public Properties sendLogEvent(SplunkConnectionData connData, byte[] thePayload, Properties properties)
        throws ConnectorException {
    HttpClient myhClient = HttpClients.custom().setConnectionManager(this.cm).build();

    HttpClientContext myhContext = HttpClientContext.create();

    CredentialsProvider credsProvider = new BasicCredentialsProvider();
    credsProvider.setCredentials(new AuthScope(AuthScope.ANY_HOST, AuthScope.ANY_PORT),
            new UsernamePasswordCredentials(connData.getUser(), connData.getPass()));
    AuthCache authCache = new BasicAuthCache();
    authCache.put(new HttpHost(connData.getHost(), Integer.parseInt(connData.getPort()), connData.getScheme()),
            new BasicScheme());

    myhContext.setCredentialsProvider(credsProvider);
    myhContext.setAuthCache(authCache);/*from w w w.  j ava2 s .  c o m*/

    HttpPost myhPost = new HttpPost(connData.getSplunkURI());

    ByteArrayEntity payload = new ByteArrayEntity(thePayload);
    try {
        myhPost.setEntity(payload);
        HttpResponse response = myhClient.execute(myhPost, myhContext);
        Integer statusCode = response.getStatusLine().getStatusCode();
        if (statusCode != 200 && !connData.getIgnoreSplunkErrors()) {
            throw new ConnectorException(
                    "Error posting log event to Splunk: " + response.getStatusLine().toString());
        }
        System.out.println(response.getStatusLine().toString());
        properties.setProperty("status", String.valueOf(statusCode));
        Integer leasedConns = Integer
                .valueOf(((PoolingHttpClientConnectionManager) this.cm).getTotalStats().getLeased());
        properties.setProperty("conns_leased", leasedConns.toString());
        Integer availConns = Integer
                .valueOf(((PoolingHttpClientConnectionManager) this.cm).getTotalStats().getAvailable());
        properties.setProperty("conns_available", availConns.toString());
    } catch (IOException e) {
        e.fillInStackTrace();
        throw new ConnectorException(e.toString());
    }
    return properties;
}

---

From source file:uk.nhs.cfh.dsp.srth.distribution.TRUDLoginService.java

@Override
public boolean authenticate(String userName, char[] pwd, String server) throws Exception {
    boolean result = false;
    try {/*from  w  ww  .  j a va  2s  .  c om*/
        int reply;
        ftpClient.connect(server);
        logger.info("Connected to " + server + ".");
        ftpClient.login(userName, String.valueOf(pwd));
        logger.info(ftpClient.getReplyString());

        // After connection attempt, you should check the reply code to verify success.
        reply = ftpClient.getReplyCode();
        logger.info("reply = " + reply);
        logger.info("FTPReply.isPositiveCompletion(reply) = " + FTPReply.isPositiveCompletion(reply));

        if (!FTPReply.isPositiveCompletion(reply)) {
            ftpClient.disconnect();
            logger.warning("FTP server refused connection.");
        } else {
            result = true;
        }

    } catch (IOException e) {
        logger.warning("Nested exception is : " + e.fillInStackTrace());
    }

    return result;
}

---

From source file:uk.nhs.cfh.dsp.snomed.converters.xml.impl.SnomedConceptToXMLRenderer.java

public void exportConceptToXMLDocument(TerminologyConcept concept, File file) {

    Document doc = convertConceptToXMLDocument(concept);
    XMLOutputter outputter = new XMLOutputter(Format.getPrettyFormat());
    try {//from   w w w  .  j a  va  2  s . com
        FileWriter writer = new FileWriter(file);
        writer.flush();
        outputter.output(doc, writer);

        // close writer
        writer.close();
        logger.info("Finished exporting concept to file : " + file.getPath());

    } catch (IOException e) {
        logger.warn(e.fillInStackTrace());
    }
}

---

From source file:uk.nhs.cfh.dsp.snomed.converters.xml.impl.AbstractTerminologyConceptToXMLConverter.java

public void exportConceptToXMLDocument(TerminologyConcept concept, File file) {

    Document doc = convertConceptToXMLDocument(concept);
    XMLOutputter outputter = new XMLOutputter(Format.getPrettyFormat());
    try {//from   w  ww. j  a  va2 s .  c  o m
        FileWriter writer = new FileWriter(file);
        writer.flush();
        outputter.output(doc, writer);

        // close writer
        writer.close();

    } catch (IOException e) {
        logger.warn(e.fillInStackTrace());
    }
}

---

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