Example usage for java.io IOException getLocalizedMessage

List of usage examples for java.io IOException getLocalizedMessage

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Introduction

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

Prototype

public String getLocalizedMessage()

Source Link

Document

Creates a localized description of this throwable.

Usage

From source file:fr.treeptik.cloudunit.docker.DockerContainerJSON.java

/**
 * /containers/json : not same format as an inspect of container List all
 * Running or Paused containers retrieve name (with cloudunit format), image
 * and state/*  www . jav  a  2  s . com*/
 *
 * @param hostAddress
 * @return
 * @throws DockerJSONException
 */
public List<DockerContainer> listAllContainers(String hostAddress) throws DockerJSONException {

    URI uri = null;
    List<DockerContainer> listContainers = new ArrayList<>();
    try {

        uri = new URIBuilder().setScheme(dockerEndpointMode).setHost(hostAddress).setPath("/containers/json")
                .build();

        if (logger.isDebugEnabled()) {
            logger.debug("uri : " + uri);
        }

        JsonResponse jsonResponse;
        try {
            jsonResponse = client.sendGet(uri);
            switch (jsonResponse.getStatus()) {
            case 400:
                throw new ErrorDockerJSONException("docker : bad parameter");
            case 500:
                throw new ErrorDockerJSONException("docker : server error");
            }

        } catch (IOException e) {
            e.printStackTrace();
            throw new DockerJSONException("Error : listAllContainers " + e.getLocalizedMessage(), e);
        }

        if (logger.isDebugEnabled()) {
            logger.debug("response : " + jsonResponse);
        }

        JSONParser jsonParser = new JSONParser();
        Object obj = jsonParser.parse(jsonResponse.getMessage());
        JSONArray array = (JSONArray) obj;
        for (int i = 0; i < array.size(); i++) {
            String containerDescription = array.get(i).toString();
            try {
                String firstSubString = (parser(containerDescription).get("Names").toString()).substring(4);
                String Names = null;
                // for container with link where the link name is also show
                if (firstSubString.lastIndexOf(",") != -1) {
                    Names = firstSubString.substring(0, firstSubString.lastIndexOf(",") - 1);

                } else {
                    Names = firstSubString.substring(0, firstSubString.lastIndexOf("\""));
                }
                if (logger.isDebugEnabled()) {
                    logger.debug("Names=[" + Names + "]");
                }
                if (Names.trim().length() > 0) {
                    DockerContainer dockerContainer = findOne(Names, hostAddress);
                    if (dockerContainer != null) {
                        listContainers.add(dockerContainer);
                    }
                }
            } catch (ParseException e) {
                throw new DockerJSONException("Error : listAllContainers " + e.getLocalizedMessage(), e);
            }
        }
    } catch (NumberFormatException | URISyntaxException | ParseException e) {
        StringBuilder msgError = new StringBuilder(256);
        msgError.append(",hostIP=").append(hostAddress).append(",uri=").append(uri);
        logger.error("" + msgError, e);
        throw new FatalDockerJSONException("docker : error fatal");
    }
    return listContainers;
}

From source file:com.photon.phresco.framework.impl.CIManagerImpl.java

private CIJobStatus doJob(CIJob job, String jobType) throws PhrescoException {
    S_LOGGER.debug("Entering Method CIManagerImpl.createJob(CIJob job)");
    try {//  w  w  w.j  av  a2 s  . c  o m
        cli = getCLI(job);
        List<String> argList = new ArrayList<String>();
        argList.add(jobType);
        argList.add(job.getName());
        String configPath = PhrescoFrameworkFactory.getServiceManager().getCiConfigPath();
        ConfigProcessor processor = new ConfigProcessor(new URL(configPath));
        customizeNodes(processor, job);

        ByteArrayOutputStream baos = new ByteArrayOutputStream();
        S_LOGGER.debug("argList " + argList.toString());
        int result = cli.execute(argList, processor.getConfigAsStream(), System.out, baos);

        String message = "Job created successfully";
        if (result == -1) {
            byte[] byteArray = baos.toByteArray();
            message = new String(byteArray);
        }

        S_LOGGER.debug("message " + message);
        setSvnCredential(job);

        setMailCredential(job);
        return new CIJobStatus(result, message);
    } catch (IOException e) {
        throw new PhrescoException(e);
    } catch (JDOMException e) {
        throw new PhrescoException(e);
    } finally {
        if (cli != null) {
            try {
                cli.close();
            } catch (IOException e) {
                if (debugEnabled) {
                    S_LOGGER.error(e.getLocalizedMessage());
                }
            } catch (InterruptedException e) {
                if (debugEnabled) {
                    S_LOGGER.error(e.getLocalizedMessage());
                }
            }
        }
    }
}

From source file:web.diva.server.model.SomClustering.SomClustImgGenerator.java

public SomClustTreeSelectionResult updateUpperTreeSelection(int x, int y, double w, double h) {
    upperTreeBImg = upperTree.getImage();
    Node n = this.getNodeAt(y, x, colNode);
    SomClustTreeSelectionResult result = new SomClustTreeSelectionResult();
    if (n != null) {
        upperTree.painttree(n, upperTreeBImg.getGraphics(), Color.red);

        Stack st = new Stack();
        Vector v = new Vector();
        n.fillMembers(v, st);//  www.j a  va2 s.c o m
        int[] sel = new int[v.size()];
        for (int i = 0; i < v.size(); i++) {
            sel[i] = ((Integer) v.elementAt(i));
        }
        result.setSelectedIndices(sel);
    }
    try {
        byte[] imageData = ChartUtilities.encodeAsPNG(upperTreeBImg);
        String base64 = Base64.encodeBase64String(imageData);
        base64 = "data:image/png;base64," + base64;
        result.setTreeImg1Url(base64);

        System.gc();

        //            result.setTreeImgUrl(navgStringImg);

        return result;
    } catch (IOException e) {
        System.err.println(e.getLocalizedMessage());
    }
    return null;

}

From source file:TimestreamsTests.java

/**
 * Performs HTTP post for a given URL//from   ww  w  .  j a  va2s  .  c  o  m
 * 
 * @param url
 *            is the URL to get
 * @param params
 *            is a URL encoded string in the form x=y&a=b...
 * @return a String with the contents of the get
 */
private Map<String, List<String>> doPut(URL url, String params) {
    HttpURLConnection connection;
    try {
        connection = (HttpURLConnection) url.openConnection();
        connection.setRequestMethod("PUT");
        connection.setRequestProperty("Content-Type", "application/x-www-form-urlencoded");

        connection.setRequestProperty("Content-Length", "" + Integer.toString(params.getBytes().length));

        connection.setDoInput(true);
        connection.setDoOutput(true);
        OutputStreamWriter out = new OutputStreamWriter(connection.getOutputStream());
        out.write(params);
        out.close();
        Map<String, List<String>> responseHeaderFields = connection.getHeaderFields();
        System.out.println(responseHeaderFields);
        if (responseHeaderFields.get(null).get(0).equals("HTTP/1.1 200 OK")) {
            InputStream is = connection.getInputStream();
            BufferedReader rd = new BufferedReader(new InputStreamReader(is));
            String line;
            StringBuffer response = new StringBuffer();
            while ((line = rd.readLine()) != null) {
                response.append(line);
                response.append('\r');
            }
            rd.close();
            System.out.println(response);
        }
        return responseHeaderFields;
    } catch (IOException e1) {
        fail("Post " + url + " failed: " + e1.getLocalizedMessage());
    }

    return null;
}

From source file:TimestreamsTests.java

/**
 * Performs HTTP post for a given URL//from  ww w. java2 s  .c o m
 * 
 * @param url
 *            is the URL to get
 * @param params
 *            is a URL encoded string in the form x=y&a=b...
 * @return a String with the contents of the get
 */
private Map<String, List<String>> doPost(URL url, String params) {
    HttpURLConnection connection;
    try {
        connection = (HttpURLConnection) url.openConnection();
        connection.setRequestMethod("POST");
        connection.setRequestProperty("Content-Type", "application/x-www-form-urlencoded");

        connection.setRequestProperty("Content-Length", "" + Integer.toString(params.getBytes().length));

        connection.setDoInput(true);
        connection.setDoOutput(true);
        DataOutputStream wr = new DataOutputStream(connection.getOutputStream());
        wr.writeBytes(params);
        wr.flush();
        wr.close();
        Map<String, List<String>> responseHeaderFields = connection.getHeaderFields();
        System.out.println(responseHeaderFields);
        if (responseHeaderFields.get(null).get(0).equals("HTTP/1.1 200 OK")) {
            InputStream is = connection.getInputStream();
            BufferedReader rd = new BufferedReader(new InputStreamReader(is));
            String line;
            StringBuffer response = new StringBuffer();
            while ((line = rd.readLine()) != null) {
                response.append(line);
                response.append('\r');
            }
            rd.close();
            System.out.println(response);
        }
        return responseHeaderFields;
    } catch (IOException e1) {
        fail("Post " + url + " failed: " + e1.getLocalizedMessage());
    }

    return null;
}

From source file:ec.edu.chyc.manejopersonal.managebean.GestorArticulo.java

public void fileUploadListener(FileUploadEvent event) {
    UploadedFile file = event.getFile();
    boolean isBibtex = event.getComponent().getAttributes().get("bibtex") != null;
    //nombre del archivo que ya se encuentra almacenado en las propiedades
    String nombreArchivoGuardado;
    if (isBibtex) {
        nombreArchivoGuardado = articulo.getArchivoBibtex();
    } else {//from   w w  w  .  j  av a 2  s  .co m
        nombreArchivoGuardado = articulo.getArchivoArticulo();
    }

    if (nombreArchivoGuardado.isEmpty() && !modoModificar) {
        //si la propiedad esta llena, significa que antes ya se subi un archivo y ahora est subiendo uno nuevo para reemplazarlo
        // por lo tanto hay que eliminar el archivo anterior
        Path pathArchivoAnterior = ServerUtils.getPathTemp().resolve(nombreArchivoGuardado).normalize();
        File archivoEliminar = pathArchivoAnterior.toFile();
        //borrar el archivo anterior en caso de existir
        if (archivoEliminar.isFile()) {
            archivoEliminar.delete();
        }
    }
    if (file != null) {
        String extensionSubida = FilenameUtils.getExtension(file.getFileName());
        String nombreArchivoSubido = ServerUtils.generarNombreValidoArchivo(extensionSubida);
        Path pathArchivo = ServerUtils.getPathTemp().resolve(nombreArchivoSubido).normalize();

        File newFile = pathArchivo.toFile();

        try {
            BeansUtils.subirArchivoPrimefaces(file, newFile);

            if (isBibtex) {
                articulo.setArchivoBibtex(nombreArchivoSubido);
                tamanoArchivoBibtex = ServerUtils.humanReadableByteCount(file.getSize());
                if (!soloSubirBibtex) {
                    listaPersonaArticulo.clear();
                    leerBibtex(pathArchivo);
                }
            } else {
                articulo.setArchivoArticulo(nombreArchivoSubido);
                tamanoArchivo = ServerUtils.humanReadableByteCount(file.getSize());
            }
        } catch (IOException ex) {
            GestorMensajes.getInstance().mostrarMensajeError(ex.getLocalizedMessage());
            Logger.getLogger(GestorArticulo.class.getName()).log(Level.SEVERE, null, ex);
        }
    } else {
        System.err.println("Error al subir archivo");
    }
}

From source file:edu.ku.brc.util.FileStoreAttachmentManager.java

@Override
public boolean setStorageLocationIntoAttachment(final Attachment attachment, final boolean doDisplayErrors) {
    String attName = attachment.getOrigFilename();
    int lastPeriod = attName.lastIndexOf('.');
    String suffix = ".att";

    if (lastPeriod != -1) {
        // Make sure the file extension (if any) remains the same so the host
        // filesystem still sees the files as the proper types.  This is simply
        // to make the files browsable from a system file browser.
        suffix = ".att" + attName.substring(lastPeriod);
    }/*from  www  .  j a va 2s.c o m*/

    String errMsg = null;
    String storageFilename = "";
    try {
        if (originalsDir == null || !originalsDir.exists() || !originalsDir.canWrite()) {
            errMsg = UIRegistry.getLocalizedMessage("ATTCH_STRG_DIR_ERR",
                    (originalsDir != null ? originalsDir.getAbsolutePath() : "(missing dir name)"));
            log.error("originalsDir doesn't exist["
                    + (originalsDir != null ? originalsDir.getAbsolutePath() : "null ") + "]");
        }

        // find an unused filename in the originals dir
        File storageFile = File.createTempFile("sp6-", suffix, originalsDir);
        System.err.println("[" + storageFile.getAbsolutePath() + "] " + storageFile.canWrite());
        FileOutputStream fos = new FileOutputStream(storageFile);
        fos.write(1);
        fos.flush();
        fos.close();
        if (storageFile.exists()) {
            attachment.setAttachmentLocation(storageFile.getName());
            unfilledFiles.add(attachment.getAttachmentLocation());
            return true;
        }
        errMsg = UIRegistry.getLocalizedMessage("ATTCH_NOT_SAVED_REPOS",
                (storageFile != null ? storageFile.getAbsolutePath() : "(missing file name)"),
                "File may not exist.");
        log.error("storageFile doesn't exist[" + (storageFile != null ? storageFile.getAbsolutePath() : "null")
                + "]");
    } catch (IOException e) {
        e.printStackTrace();

        if (doDisplayErrors) {
            errMsg = UIRegistry.getLocalizedMessage("ATTCH_NOT_SAVED_REPOS", storageFilename,
                    e.getLocalizedMessage());
        } else {
            // This happens when errors are not displayed.
            e.printStackTrace();
            edu.ku.brc.af.core.UsageTracker.incrHandledUsageCount();
            edu.ku.brc.exceptions.ExceptionTracker.getInstance().capture(FileStoreAttachmentManager.class, e);
        }
    }

    if (doDisplayErrors && errMsg != null) {
        UIRegistry.showError(errMsg);
    }
    return false;
}

From source file:it.geosolutions.geobatch.flow.event.consumer.file.FileBasedEventConsumer.java

/**
 * remove all Cumulating progress listener from the Consumer and containing
 * action(s) remove all the actions from the action list remove
 * contextRunningDir/*from  w  w w.  ja  va2s  .c  om*/
 */
private void clear() {
    // Progress Logging...
    // remove all Cumulating progress listener from the Consumer and
    // containing action(s)
    final ProgressListenerForwarder lf = this.getListenerForwarder();
    final Collection<? extends IProgressListener> listeners = lf.getListeners();
    if (listeners != null) {
        for (IProgressListener listener : listeners) {

            if (listener instanceof CumulatingProgressListener) {
                ((CumulatingProgressListener) listener).clearMessages();
            }
        }
    }

    // Current Action Status...
    // remove all the actions from the action list
    if (actions != null) {
        for (Action action : this.actions) {

            if (action instanceof BaseAction<?>) {
                final BaseAction<?> baseAction = (BaseAction) action;
                // try the most interesting information holder
                Collection<IProgressListener> coll = baseAction.getListeners(CumulatingProgressListener.class);
                for (IProgressListener cpl : coll) {
                    if (cpl != null && cpl instanceof CumulatingProgressListener) {
                        ((CumulatingProgressListener) cpl).clearMessages();
                    }
                }

            }
        }
        this.actions.clear();
    }

    // remove contextRunningDir
    if (!keepTempDir) {
        // removing running context directory
        try {
            FileUtils.deleteDirectory(getFlowInstanceTempDir());
        } catch (IOException e) {
            if (LOGGER.isWarnEnabled()) {
                LOGGER.warn("Problem trying to remove the running context directory: "
                        + getFlowInstanceTempDir() + ".\n " + e.getLocalizedMessage());
            }
        }
    }
}

From source file:com.apelon.akcds.loinc.LoincToEConcepts.java

public void execute() throws MojoExecutionException {
    ConsoleUtil.println("LOINC Processing Begins " + new Date().toString());

    LOINCReader loincData = null;//from  w w w . j  ava  2  s  .co m
    LOINCReader mapTo = null;
    LOINCReader sourceOrg = null;
    LOINCReader loincMultiData = null;

    try {
        super.execute();

        if (!inputFileLocation.isDirectory()) {
            throw new MojoExecutionException(
                    "LoincDataFiles must point to a directory containing the 3 required loinc data files");
        }

        for (File f : inputFileLocation.listFiles()) {
            if (f.getName().toLowerCase().equals("loincdb.txt")) {
                loincData = new TxtFileReader(f);
            } else if (f.getName().toLowerCase().equals("loinc.csv")) {
                loincData = new CSVFileReader(f);
            } else if (f.getName().toLowerCase().equals("map_to.csv")) {
                mapTo = new CSVFileReader(f);
            } else if (f.getName().toLowerCase().equals("source_organization.csv")) {
                sourceOrg = new CSVFileReader(f);
            } else if (f.getName().toLowerCase().endsWith("multi-axial_hierarchy.csv")) {
                loincMultiData = new CSVFileReader(f);
            }
        }

        if (loincData == null) {
            throw new MojoExecutionException(
                    "Could not find the loinc data file in " + inputFileLocation.getAbsolutePath());
        }
        if (loincMultiData == null) {
            throw new MojoExecutionException(
                    "Could not find the multi-axial file in " + inputFileLocation.getAbsolutePath());
        }

        SimpleDateFormat dateReader = new SimpleDateFormat("MMMMMMMMMMMMM yyyy"); //Parse things like "June 2014"
        Date releaseDate = dateReader.parse(loincData.getReleaseDate());

        File binaryOutputFile = new File(outputDirectory, "loincEConcepts.jbin");
        dos_ = new DataOutputStream(new BufferedOutputStream(new FileOutputStream(binaryOutputFile)));
        conceptUtility_ = new EConceptUtility(loincNamespaceBaseSeed_, "LOINC Path", dos_,
                releaseDate.getTime());

        contentVersion_ = new PT_ContentVersion();
        pt_SkipAxis_ = new PT_SkipAxis();
        pt_SkipClass_ = new PT_SkipClass();

        String version = loincData.getVersion();
        //String releaseDate = ;
        fieldMap_ = loincData.getFieldMap();
        fieldMapInverse_ = loincData.getFieldMapInverse();

        String mapFileName = null;

        if (version.contains("2.36")) {
            PropertyType.setSourceVersion(1);
            mapFileName = "classMappings-2.36.txt";
        } else if (version.contains("2.38")) {
            PropertyType.setSourceVersion(2);
            mapFileName = "classMappings-2.36.txt"; // Yes, wrong one, never made the file for 2.38
        } else if (version.contains("2.40")) {
            PropertyType.setSourceVersion(3);
            mapFileName = "classMappings-2.40.txt";
        } else if (version.contains("2.44")) {
            PropertyType.setSourceVersion(4);
            mapFileName = "classMappings-2.44.txt";
        } else if (version.contains("2.46")) {
            PropertyType.setSourceVersion(4);
            mapFileName = "classMappings-2.46.txt";
        } else if (version.contains("2.48")) {
            PropertyType.setSourceVersion(4);
            mapFileName = "classMappings-2.48.txt";
        } else if (version.contains("2.50")) {
            PropertyType.setSourceVersion(5);
            mapFileName = "classMappings-2.52.txt"; //never did a 2.50, skipped to 2.52
        } else if (version.contains("2.52")) {
            PropertyType.setSourceVersion(6);
            mapFileName = "classMappings-2.52.txt";
        } else {
            ConsoleUtil.printErrorln("ERROR: UNTESTED VERSION - NO TESTED PROPERTY MAPPING EXISTS!");
            PropertyType.setSourceVersion(6);
            mapFileName = "classMappings-2.52.txt";
        }

        classMapping_ = new NameMap(mapFileName);

        if (mapTo != null) {
            String[] line = mapTo.readLine();
            while (line != null) {
                if (line.length > 0) {
                    HashMap<String, String> nestedData = mapToData.get(line[0]);
                    if (nestedData == null) {
                        nestedData = new HashMap<>();
                        mapToData.put(line[0], nestedData);
                    }
                    if (nestedData.put(line[1], line[2]) != null) {
                        throw new Exception("Oops - " + line[0] + " " + line[1] + " " + line[2]);
                    }
                }
                line = mapTo.readLine();
            }
        }

        initProperties();

        ConsoleUtil.println("Loading Metadata");

        // Set up a meta-data root concept
        UUID archRoot = ArchitectonicAuxiliary.Concept.ARCHITECTONIC_ROOT_CONCEPT.getPrimoridalUid();
        UUID metaDataRoot = ConverterUUID.createNamespaceUUIDFromString("metadata");
        conceptUtility_.createAndStoreMetaDataConcept(metaDataRoot, "LOINC Metadata", false, archRoot, dos_);

        conceptUtility_.loadMetaDataItems(propertyTypes_, metaDataRoot, dos_);

        // Load up the propertyType map for speed, perform basic sanity check
        for (PropertyType pt : propertyTypes_) {
            for (String propertyName : pt.getPropertyNames()) {
                if (propertyToPropertyType_.containsKey(propertyName)) {
                    ConsoleUtil
                            .printErrorln("ERROR: Two different property types each contain " + propertyName);
                }
                propertyToPropertyType_.put(propertyName, pt);
            }
        }

        if (sourceOrg != null) {
            EConcept sourceOrgConcept = conceptUtility_.createAndStoreMetaDataConcept("Source Organization",
                    false, metaDataRoot, dos_);
            String[] line = sourceOrg.readLine();
            while (line != null) {
                //"COPYRIGHT_ID","NAME","COPYRIGHT","TERMS_OF_USE","URL"
                if (line.length > 0) {
                    EConcept c = conceptUtility_.createConcept(line[0], sourceOrgConcept.getPrimordialUuid());
                    conceptUtility_.addDescription(c, line[1], DescriptionType.SYNONYM, true,
                            propertyToPropertyType_.get("NAME").getProperty("NAME").getUUID(), null, false);
                    conceptUtility_.addStringAnnotation(c, line[2],
                            propertyToPropertyType_.get("COPYRIGHT").getProperty("COPYRIGHT").getUUID(), false);
                    conceptUtility_.addStringAnnotation(c, line[3],
                            propertyToPropertyType_.get("TERMS_OF_USE").getProperty("TERMS_OF_USE").getUUID(),
                            false);
                    conceptUtility_.addStringAnnotation(c, line[4],
                            propertyToPropertyType_.get("URL").getProperty("URL").getUUID(), false);
                    c.writeExternal(dos_);
                }
                line = sourceOrg.readLine();
            }
        }

        // write this at the end
        EConcept loincRefset = pt_refsets_.getConcept(PT_Refsets.Refsets.ALL.getProperty());

        // The next line of the file is the header.
        String[] headerFields = loincData.getHeader();

        // validate that we are configured to map all properties properly
        checkForLeftoverPropertyTypes(headerFields);

        ConsoleUtil.println("Metadata summary:");
        for (String s : conceptUtility_.getLoadStats().getSummary()) {
            ConsoleUtil.println("  " + s);
        }
        conceptUtility_.clearLoadStats();

        // Root
        EConcept rootConcept = conceptUtility_.createConcept("LOINC");
        conceptUtility_.addDescription(rootConcept, "LOINC", DescriptionType.SYNONYM, true, null, null, false);
        conceptUtility_.addDescription(rootConcept, "Logical Observation Identifiers Names and Codes",
                DescriptionType.SYNONYM, false, null, null, false);
        ConsoleUtil.println("Root concept FSN is 'LOINC' and the UUID is " + rootConcept.getPrimordialUuid());

        conceptUtility_.addStringAnnotation(rootConcept, version,
                contentVersion_.getProperty("Source Version").getUUID(), false);
        conceptUtility_.addStringAnnotation(rootConcept, loincData.getReleaseDate(),
                contentVersion_.getProperty("Release Date").getUUID(), false);
        conceptUtility_.addStringAnnotation(rootConcept, converterResultVersion,
                contentVersion_.RELEASE.getUUID(), false);
        conceptUtility_.addStringAnnotation(rootConcept, loaderVersion,
                contentVersion_.LOADER_VERSION.getUUID(), false);

        concepts_.put(rootConcept.primordialUuid, rootConcept);

        // Build up the Class metadata

        EConcept classConcept = conceptUtility_.createConcept(pt_SkipClass_.getPropertyTypeUUID(),
                pt_SkipClass_.getPropertyTypeDescription(), rootConcept.primordialUuid);
        concepts_.put(classConcept.primordialUuid, classConcept);

        for (String property : pt_SkipClass_.getPropertyNames()) {
            EConcept temp = conceptUtility_.createConcept(pt_SkipClass_.getProperty(property).getUUID(),
                    property, classConcept.primordialUuid);
            concepts_.put(temp.primordialUuid, temp);
        }

        // And the axis metadata
        EConcept axisConcept = conceptUtility_.createConcept(pt_SkipAxis_.getPropertyTypeUUID(),
                pt_SkipAxis_.getPropertyTypeDescription(), rootConcept.primordialUuid);
        concepts_.put(axisConcept.primordialUuid, axisConcept);

        for (String property : pt_SkipAxis_.getPropertyNames()) {
            EConcept temp = conceptUtility_.createConcept(pt_SkipAxis_.getProperty(property).getUUID(),
                    property, axisConcept.primordialUuid);
            concepts_.put(temp.primordialUuid, temp);
        }

        // load the data
        ConsoleUtil.println("Reading data file into memory.");

        int dataRows = 0;
        {
            String[] line = loincData.readLine();
            dataRows++;
            while (line != null) {
                if (line.length > 0) {
                    processDataLine(line);
                }
                line = loincData.readLine();
                dataRows++;
                if (dataRows % 1000 == 0) {
                    ConsoleUtil.showProgress();
                }
            }
        }
        loincData.close();

        ConsoleUtil.println("Read " + dataRows + " data lines from file");

        ConsoleUtil.println("Processing multi-axial file");

        {
            // header - PATH_TO_ROOT,SEQUENCE,IMMEDIATE_PARENT,CODE,CODE_TEXT
            int lineCount = 0;
            String[] line = loincMultiData.readLine();
            while (line != null) {
                lineCount++;
                if (line.length > 0) {
                    processMultiAxialData(rootConcept.getPrimordialUuid(), line);
                }
                line = loincMultiData.readLine();
                if (lineCount % 1000 == 0) {
                    ConsoleUtil.showProgress();
                }
            }
            loincMultiData.close();
            ConsoleUtil.println("Read " + lineCount + " data lines from file");
        }

        ConsoleUtil.println("Writing jbin file");

        int conCounter = 0;
        for (EConcept concept : concepts_.values()) {
            conceptUtility_.addRefsetMember(loincRefset, concept.getPrimordialUuid(), null, true, null);
            concept.writeExternal(dos_);
            conCounter++;

            if (conCounter % 10 == 0) {
                ConsoleUtil.showProgress();
            }
            if ((conCounter % 10000) == 0) {
                ConsoleUtil.println("Processed: " + conCounter + " - just completed "
                        + concept.getDescriptions().get(0).getText());
            }
        }

        ConsoleUtil.println("Processed " + conCounter + " concepts total");

        conceptUtility_.storeRefsetConcepts(pt_refsets_, dos_);

        ConsoleUtil.println("Data Load Summary:");
        for (String s : conceptUtility_.getLoadStats().getSummary()) {
            ConsoleUtil.println("  " + s);
        }

        ConsoleUtil.println("Skipped " + skippedDeletedItems
                + " Loinc codes because they were flagged as DELETED and they had no desriptions.");

        // this could be removed from final release. Just added to help debug editor problems.
        ConsoleUtil.println("Dumping UUID Debug File");
        ConverterUUID.dump(outputDirectory, "loincUuid");
        ConsoleUtil.println("LOINC Processing Completes " + new Date().toString());
        ConsoleUtil.writeOutputToFile(new File(outputDirectory, "ConsoleOutput.txt").toPath());
    } catch (Exception ex) {
        throw new MojoExecutionException(ex.getLocalizedMessage(), ex);
    } finally {
        if (dos_ != null) {
            try {
                dos_.flush();
                dos_.close();
                loincData.close();
                loincMultiData.close();
                if (mapTo != null) {
                    mapTo.close();
                }
                if (sourceOrg != null) {
                    sourceOrg.close();
                }
            } catch (IOException e) {
                throw new MojoExecutionException(e.getLocalizedMessage(), e);
            }
        }
    }
}

From source file:net.sf.logsaw.index.internal.LuceneIndexServiceImpl.java

@Override
public ResultPage query(IQueryContext context, final List<ARestriction<?>> restrictions, final int offset,
        final int limit) throws CoreException {
    Assert.isNotNull(context, "context"); //$NON-NLS-1$
    Assert.isTrue(context instanceof LuceneQueryContextImpl,
            "Query context must be of type net.sf.logsaw.index.impl.LuceneQueryContextImpl"); //$NON-NLS-1$
    Assert.isTrue(context.isOpen(), "Query context must be open"); //$NON-NLS-1$
    Assert.isNotNull(restrictions, "restrictions"); //$NON-NLS-1$

    ARunWithIndexReader<ResultPage> runnable = new ARunWithIndexReader<ResultPage>() {

        /* (non-Javadoc)
         * @see net.sf.logsaw.index.impl.ARunWithIndexReader#doRunWithIndexReader(org.apache.lucene.index.IndexReader, net.sf.logsaw.core.framework.ILogResource)
         *///from   w w  w.j  a  v  a  2 s. c om
        @Override
        protected ResultPage doRunWithIndexReader(IndexReader reader, ILogResource log) throws CoreException {
            if (reader == null) {
                // Index does not exist yet
                return new ResultPage();
            }

            try {
                IndexSearcher searcher = new IndexSearcher(reader);
                Sort sort = new Sort(new SortField[] { SortField.FIELD_DOC });
                TopFieldCollector collector = TopFieldCollector.create(sort, offset + limit, false, false,
                        false, true);
                // TODO Investigate use of searchAfter
                searcher.search(convertToQuery(restrictions), collector);
                List<LogEntry> result = new LinkedList<LogEntry>();
                collectHits(searcher, collector.topDocs(offset), log.getDialect(), result);
                return new ResultPage(result, offset, collector.getTotalHits());
            } catch (IOException e) {
                // Unexpected exception; wrap with CoreException
                throw new CoreException(new Status(IStatus.ERROR, IndexPlugin.PLUGIN_ID,
                        NLS.bind(Messages.LuceneIndexService_error_failedToReadIndex,
                                new Object[] { log.getName(), e.getLocalizedMessage() }),
                        e));
            }
        }
    };
    runnable.setQueryContext((LuceneQueryContextImpl) context);
    return runnable.runWithIndexReader(context.getLogResource());
}