Example usage for java.lang InternalError InternalError

List of usage examples for java.lang InternalError InternalError

Introduction

In this page you can find the example usage for java.lang InternalError InternalError.

Prototype

public InternalError(Throwable cause) 

Source Link

Document

Constructs an InternalError with the specified cause and a detail message of (cause==null ?

Usage

From source file:com.citrix.cpbm.portal.fragment.controllers.AbstractAuthenticationController.java

@RequestMapping({ "/login", "/portal", "/" })
public String login(HttpServletRequest request, ModelMap map, HttpSession session) {
    logger.debug("###Entering in login(req,map,session) method");

    boolean loginFailed = request.getParameter(LOGIN_FAILED_PARAM) != null;

    if (!loginFailed && request.getUserPrincipal() != null) {
        map.clear();// w  w  w  .ja  va 2s  .c  om
        return "redirect:/portal/home";
    }

    if (session.getAttribute("email_verified") != null) {
        map.addAttribute("email_verified", session.getAttribute("email_verified"));
        session.removeAttribute("email_verified");
    }
    String showSuffixControl = "false";
    String suffixControlType = "textbox";
    List<String> suffixList = null;
    if (config.getValue(Names.com_citrix_cpbm_username_duplicate_allowed).equals("true")) {
        showSuffixControl = "true";
        if (config.getValue(Names.com_citrix_cpbm_login_screen_tenant_suffix_dropdown_enabled).equals("true")) {
            suffixControlType = "dropdown";
            suffixList = tenantService.getSuffixList();
        }
    }
    map.addAttribute("showSuffixControl", showSuffixControl);
    map.addAttribute("suffixControlType", suffixControlType);
    map.addAttribute("suffixList", suffixList);
    if (config.getBooleanValue(Configuration.Names.com_citrix_cpbm_portal_directory_service_enabled)
            && config.getValue(Names.com_citrix_cpbm_directory_mode).equals("pull")) {
        map.addAttribute("directoryServiceAuthenticationEnabled", "true");
    }
    if (config.getValue(Names.com_citrix_cpbm_public_catalog_display).equals("true")
            && channelService.getDefaultServiceProviderChannel() != null) {
        map.addAttribute("showAnonymousCatalogBrowsing", "true");
    }
    map.addAttribute("showLanguageSelection", "true");
    map.addAttribute("supportedLocaleList", this.getLocaleDisplayName(listSupportedLocales()));
    map.addAttribute("selected_language", request.getParameter("lang"));
    String redirect = null;
    boolean loggedOut = request.getParameter(LOGOUT_PARAM) != null;
    final Throwable ex = (Throwable) session.getAttribute(WebAttributes.AUTHENTICATION_EXCEPTION);

    // capture previous CAPTCHA position
    Boolean captchaRequiredSessionObj = (Boolean) session
            .getAttribute(CaptchaAuthenticationFilter.CAPTCHA_REQUIRED);

    // Get last user
    String username = (String) session
            .getAttribute(UsernamePasswordAuthenticationFilter.SPRING_SECURITY_LAST_USERNAME_KEY);

    // this as spring does a text-escape when it saves this attribute
    final String uUsername = HtmlUtils.htmlUnescape(username);

    if (loginFailed) {
        String error = " "
                + messageSource.getMessage("error.auth.username.password.invalid", null, request.getLocale());

        try {
            User user = privilegeService.runAsPortal(new PrivilegedAction<User>() {

                @Override
                public User run() {
                    User user = userService.getUserByParam("username", uUsername, false);

                    // All user writes here.
                    // Every time there is a login failure but not invalid CAPTCHA,
                    // we update failed login attempts for the user
                    if (!(ex instanceof CaptchaValidationException) && !(ex instanceof LockedException)
                            && !(ex instanceof IpRangeValidationException)) {
                        user.setFailedLoginAttempts(user.getFailedLoginAttempts() + 1);
                    }

                    int attempts = user.getFailedLoginAttempts();

                    // Also locking the root user and quite easily too. Clearly this
                    // needs an eye!
                    if (attempts >= config.getIntValue(
                            Names.com_citrix_cpbm_accountManagement_security_logins_lockThreshold)) {
                        user.setEnabled(false);
                    }

                    return user;
                }
            });

            int attempts = user.getFailedLoginAttempts();
            if (attempts >= config
                    .getIntValue(Names.com_citrix_cpbm_accountManagement_security_logins_captchaThreshold)) {
                session.setAttribute(CaptchaAuthenticationFilter.CAPTCHA_REQUIRED, true);
            }
        } catch (NoSuchUserException e) {
            // map.addAttribute("showCaptcha", true);
        }

        captchaRequiredSessionObj = (Boolean) session
                .getAttribute(CaptchaAuthenticationFilter.CAPTCHA_REQUIRED);

        map.addAttribute("loginFailed", loginFailed);
        String lastUsername = uUsername;

        if (config.getValue(Names.com_citrix_cpbm_username_duplicate_allowed).equals("true")) {
            if (!lastUsername.equals("root") && !lastUsername.equals("")) {
                lastUsername = lastUsername.substring(0, lastUsername.lastIndexOf('@'));
            }
        }
        map.addAttribute("lastUser", lastUsername);

        // Compose error string
        if (ex instanceof DisabledException) {
            error = " " + messageSource.getMessage("error.auth.username.password.invalid", null,
                    request.getLocale());
        } else if (ex instanceof CaptchaValidationException) {
            error = " " + messageSource.getMessage("error.auth.captcha.invalid", null, request.getLocale());
        } else if (ex instanceof IpRangeValidationException) {
            error = " " + messageSource.getMessage("error.auth.username.password.invalid", null,
                    request.getLocale());
        } else if (ex instanceof LockedException) {
            error = " " + messageSource.getMessage("error.auth.username.password.invalid", null,
                    request.getLocale());
        } else if (ex instanceof BadCredentialsException) {
            if (ex.getMessage() != null && ex.getMessage().length() > 0) {
                // error = " " + ex.getMessage();
                error = " " + messageSource.getMessage("error.auth.username.password.invalid", null,
                        request.getLocale());
            }
        } else if (ex instanceof AuthenticationException) {
            error = " " + messageSource.getMessage("error.auth.username.password.invalid", null,
                    request.getLocale());
        } else {
            logger.error("Error occurred in authentication", ex);
            error = " " + messageSource.getMessage("error.auth.unknown", null, request.getLocale());
        }

        if (captchaRequiredSessionObj != null && captchaRequiredSessionObj == true
                && !(ex instanceof CaptchaValidationException) && !(ex instanceof LockedException)) {
            error += " " + messageSource.getMessage("error.auth.account.may.locked", null, request.getLocale());
        }

        map.addAttribute("error", error);

    }

    if (loggedOut) {
        map.addAttribute("logout", loggedOut);
    }

    // This could come from session or from user
    if (captchaRequiredSessionObj != null && captchaRequiredSessionObj.booleanValue()
            && !Boolean.valueOf(config.getValue(Names.com_citrix_cpbm_use_intranet_only))) {
        map.addAttribute("showCaptcha", true);
        map.addAttribute("recaptchaPublicKey", config.getRecaptchaPublicKey());
    }

    map.addAttribute(TIME_OUT, request.getParameter(TIME_OUT) != null);
    map.addAttribute(VERIFY, request.getParameter(VERIFY) != null);
    logger.debug("###Exiting login(req,map,session) method");

    if (config.getAuthenticationService().compareToIgnoreCase(CAS) == 0) {
        try {
            redirect = StringUtils.isEmpty(config.getCasLoginUrl()) ? null
                    : config.getCasLoginUrl() + "?service="
                            + URLEncoder.encode(config.getCasServiceUrl(), "UTF-8");
        } catch (UnsupportedEncodingException e) {
            logger.error("Exception encoding: " + redirect, e);
        }
        if (redirect == null) {
            throw new InternalError("CAS authentication required, but login url not set");
        }
    }
    return redirect == null ? "auth.login" : "redirect:" + redirect;
}

From source file:org.projectforge.core.AbstractBaseDO.java

/**
 * //ww w .j  a  v a  2 s . com
 * @param srcClazz
 * @param src
 * @param dest
 * @param ignoreFields
 * @return true, if any modifications are detected, otherwise false;
 */
@SuppressWarnings("unchecked")
private static ModificationStatus copyDeclaredFields(final Class<?> srcClazz, final BaseDO<?> src,
        final BaseDO<?> dest, final String... ignoreFields) {
    final Field[] fields = srcClazz.getDeclaredFields();
    AccessibleObject.setAccessible(fields, true);
    ModificationStatus modificationStatus = null;
    for (final Field field : fields) {
        final String fieldName = field.getName();
        if ((ignoreFields != null && ArrayUtils.contains(ignoreFields, fieldName) == true)
                || accept(field) == false) {
            continue;
        }
        try {
            final Object srcFieldValue = field.get(src);
            final Object destFieldValue = field.get(dest);
            if (field.getType().isPrimitive() == true) {
                if (ObjectUtils.equals(destFieldValue, srcFieldValue) == false) {
                    field.set(dest, srcFieldValue);
                    modificationStatus = getModificationStatus(modificationStatus, src, fieldName);
                }
                continue;
            } else if (srcFieldValue == null) {
                if (field.getType() == String.class) {
                    if (StringUtils.isNotEmpty((String) destFieldValue) == true) {
                        field.set(dest, null);
                        modificationStatus = getModificationStatus(modificationStatus, src, fieldName);
                    }
                } else if (destFieldValue != null) {
                    field.set(dest, null);
                    modificationStatus = getModificationStatus(modificationStatus, src, fieldName);
                } else {
                    // dest was already null
                }
            } else if (srcFieldValue instanceof Collection) {
                Collection<Object> destColl = (Collection<Object>) destFieldValue;
                final Collection<Object> srcColl = (Collection<Object>) srcFieldValue;
                final Collection<Object> toRemove = new ArrayList<Object>();
                if (srcColl != null && destColl == null) {
                    if (srcColl instanceof TreeSet) {
                        destColl = new TreeSet<Object>();
                    } else if (srcColl instanceof HashSet) {
                        destColl = new HashSet<Object>();
                    } else if (srcColl instanceof List) {
                        destColl = new ArrayList<Object>();
                    } else if (srcColl instanceof PersistentSet) {
                        destColl = new HashSet<Object>();
                    } else {
                        log.error("Unsupported collection type: " + srcColl.getClass().getName());
                    }
                    field.set(dest, destColl);
                }
                for (final Object o : destColl) {
                    if (srcColl.contains(o) == false) {
                        toRemove.add(o);
                    }
                }
                for (final Object o : toRemove) {
                    if (log.isDebugEnabled() == true) {
                        log.debug("Removing collection entry: " + o);
                    }
                    destColl.remove(o);
                    modificationStatus = getModificationStatus(modificationStatus, src, fieldName);
                }
                for (final Object srcEntry : srcColl) {
                    if (destColl.contains(srcEntry) == false) {
                        if (log.isDebugEnabled() == true) {
                            log.debug("Adding new collection entry: " + srcEntry);
                        }
                        destColl.add(srcEntry);
                        modificationStatus = getModificationStatus(modificationStatus, src, fieldName);
                    } else if (srcEntry instanceof BaseDO) {
                        final PFPersistancyBehavior behavior = field.getAnnotation(PFPersistancyBehavior.class);
                        if (behavior != null && behavior.autoUpdateCollectionEntries() == true) {
                            BaseDO<?> destEntry = null;
                            for (final Object entry : destColl) {
                                if (entry.equals(srcEntry) == true) {
                                    destEntry = (BaseDO<?>) entry;
                                    break;
                                }
                            }
                            Validate.notNull(destEntry);
                            final ModificationStatus st = destEntry.copyValuesFrom((BaseDO<?>) srcEntry);
                            modificationStatus = getModificationStatus(modificationStatus, st);
                        }
                    }
                }
            } else if (srcFieldValue instanceof BaseDO) {
                final Serializable srcFieldValueId = HibernateUtils.getIdentifier((BaseDO<?>) srcFieldValue);
                if (srcFieldValueId != null) {
                    if (destFieldValue == null || ObjectUtils.equals(srcFieldValueId,
                            ((BaseDO<?>) destFieldValue).getId()) == false) {
                        field.set(dest, srcFieldValue);
                        modificationStatus = getModificationStatus(modificationStatus, src, fieldName);
                    }
                } else {
                    log.error(
                            "Can't get id though can't copy the BaseDO (see error message above about HHH-3502).");
                }
            } else if (srcFieldValue instanceof java.sql.Date) {
                if (destFieldValue == null) {
                    field.set(dest, srcFieldValue);
                    modificationStatus = getModificationStatus(modificationStatus, src, fieldName);
                } else {
                    final DayHolder srcDay = new DayHolder((Date) srcFieldValue);
                    final DayHolder destDay = new DayHolder((Date) destFieldValue);
                    if (srcDay.isSameDay(destDay) == false) {
                        field.set(dest, srcDay.getSQLDate());
                        modificationStatus = getModificationStatus(modificationStatus, src, fieldName);
                    }
                }
            } else if (srcFieldValue instanceof Date) {
                if (destFieldValue == null
                        || ((Date) srcFieldValue).getTime() != ((Date) destFieldValue).getTime()) {
                    field.set(dest, srcFieldValue);
                    modificationStatus = getModificationStatus(modificationStatus, src, fieldName);
                }
            } else if (srcFieldValue instanceof BigDecimal) {
                if (destFieldValue == null
                        || ((BigDecimal) srcFieldValue).compareTo((BigDecimal) destFieldValue) != 0) {
                    field.set(dest, srcFieldValue);
                    modificationStatus = getModificationStatus(modificationStatus, src, fieldName);
                }
            } else if (ObjectUtils.equals(destFieldValue, srcFieldValue) == false) {
                field.set(dest, srcFieldValue);
                modificationStatus = getModificationStatus(modificationStatus, src, fieldName);
            }
        } catch (final IllegalAccessException ex) {
            throw new InternalError("Unexpected IllegalAccessException: " + ex.getMessage());
        }
    }
    final Class<?> superClazz = srcClazz.getSuperclass();
    if (superClazz != null) {
        final ModificationStatus st = copyDeclaredFields(superClazz, src, dest, ignoreFields);
        modificationStatus = getModificationStatus(modificationStatus, st);
    }
    return modificationStatus;
}

From source file:org.shredzone.cilla.view.FeedView.java

/**
 * Builds a taxonomy URL.// ww w.  j  a va 2  s . c  om
 *
 * @param prefix
 *            URI prefix for this web site
 * @param type
 *            feed type (e.g. "author")
 * @param id
 *            unique id String of the feed's entity
 * @return generated URI
 */
private String buildTaxonomyUri(String prefix, String type, String id) {
    try {
        return prefix + type + '-' + URLEncoder.encode(id, "utf-8");
    } catch (UnsupportedEncodingException ex) {
        throw new InternalError("utf-8 missing");
    }
}

From source file:com.commsen.apropos.core.PropertiesManager.java

/**
 * Updates existing {@link Property} called <code>oldPropertyName</code> in
 * {@link PropertyPackage} called <code>packageName</code> with values from
 * <code>property</code>. The actual update is handled by
 * {@link PropertyPackage#updateProperty(Property)}.
 * //from  w ww. ja  v  a 2  s .c o  m
 * @param packageName the name of the package. Can not be <code>null</code> or empty.
 * @param oldPropertyName the name of the property to be updated
 * @param property the {@link Property} object to get the values from. Can not be
 *        <code>null</code>
 * @return a new clone of the {@link PropertyPackage} made after the property is updated
 * @throws PropertiesException if no package called <code>packageName</code> found or if no
 *         such {@link Property} exists in this package
 * @throws IllegalArgumentException if any of the arguments is <code>null</code>
 */
public static synchronized PropertyPackage updateProperty(String packageName, String oldPropertyName,
        Property property) throws PropertiesException {
    if (StringUtils.isBlank(packageName))
        throw new IllegalArgumentException("package name can not be null nor empty string");
    if (property == null)
        throw new IllegalArgumentException("property can not be null");
    if (!allPackages.containsKey(packageName))
        throw new PropertiesException("No package called " + packageName + " found ");
    PropertyPackage propertyPackage = allPackages.get(packageName);
    try {
        propertyPackage.updateProperty(oldPropertyName, (Property) property.clone());
        save();
        return (PropertyPackage) propertyPackage.clone();
    } catch (CloneNotSupportedException e) {
        throw new InternalError(e.toString());
    }
}

From source file:org.apache.tajo.master.exec.DDLExecutor.java

/**
 * Drop a given named table/*from   ww  w  .  ja  va  2s .  c om*/
 *
 * @param tableName to be dropped
 * @param purge     Remove all data if purge is true.
 */
public void dropTable(QueryContext queryContext, String tableName, boolean ifExists, boolean purge)
        throws TajoException {

    String databaseName;
    String simpleTableName;
    if (IdentifierUtil.isFQTableName(tableName)) {
        String[] splitted = IdentifierUtil.splitFQTableName(tableName);
        databaseName = splitted[0];
        simpleTableName = splitted[1];
    } else {
        databaseName = queryContext.getCurrentDatabase();
        simpleTableName = tableName;
    }
    String qualifiedName = IdentifierUtil.buildFQName(databaseName, simpleTableName);

    boolean exists = catalog.existsTable(qualifiedName);
    if (!exists) {
        if (ifExists) { // DROP TABLE IF EXISTS
            LOG.info("relation \"" + qualifiedName + "\" is already exists.");
            return;
        } else { // Otherwise, it causes an exception.
            throw new UndefinedTableException(qualifiedName);
        }
    }

    TableDesc tableDesc = catalog.getTableDesc(qualifiedName);
    catalog.dropTable(qualifiedName);

    if (purge) {
        try {
            TablespaceManager.get(tableDesc.getUri()).purgeTable(tableDesc);
        } catch (IOException e) {
            throw new InternalError(e.getMessage());
        }
    }
    LOG.info(String.format("relation \"%s\" is " + (purge ? " purged." : " dropped."), qualifiedName));
}

From source file:FullThreadDump.java

private void parseMBeanInfo() throws IOException {
    try {//from   w ww. ja  va2  s  .c o m
        MBeanOperationInfo[] mopis = server.getMBeanInfo(objname).getOperations();

        // look for findDeadlockedThreads operations;
        boolean found = false;
        for (MBeanOperationInfo op : mopis) {
            if (op.getName().equals(findDeadlocksMethodName)) {
                found = true;
                break;
            }
        }
        if (!found) {
            // if findDeadlockedThreads operation doesn't exist,
            // the target VM is running on JDK 5 and details about
            // synchronizers and locks cannot be dumped.
            findDeadlocksMethodName = "findMonitorDeadlockedThreads";
            canDumpLocks = false;
        }
    } catch (IntrospectionException e) {
        InternalError ie = new InternalError(e.getMessage());
        ie.initCause(e);
        throw ie;
    } catch (InstanceNotFoundException e) {
        InternalError ie = new InternalError(e.getMessage());
        ie.initCause(e);
        throw ie;
    } catch (ReflectionException e) {
        InternalError ie = new InternalError(e.getMessage());
        ie.initCause(e);
        throw ie;
    }
}

From source file:edu.cornell.med.icb.goby.modes.DiscoverSequenceVariantsMode.java

/**
 * Configure./*from  ww w .  j  a  v  a  2  s.  c  om*/
 *
 * @param args command line arguments
 * @return this object for chaining
 * @throws java.io.IOException error parsing
 * @throws com.martiansoftware.jsap.JSAPException
 *                             error parsing
 */
@Override
public AbstractCommandLineMode configure(final String[] args) throws IOException, JSAPException {

    final JSAPResult jsapResult = parseJsapArguments(args);

    inputFilenames = jsapResult.getStringArray("input");

    String outputFile = jsapResult.getString("output");
    outputInfo = new OutputInfo(outputFile);
    String groupsDefinition = jsapResult.getString("groups");
    String groupsDefinitionFile = jsapResult.getString("group-file");
    if (groupsDefinition != null && groupsDefinitionFile != null) {
        System.err.println(
                "--groups and --groups-file are mutually exclusive. Please provide only once such parameter.");
        System.exit(1);
    }
    if (groupsDefinitionFile != null) {
        groupsDefinition = parseGroupFile(groupsDefinitionFile, inputFilenames);
    }
    String compare = jsapResult.getString("compare");
    /*if (compare == null) {
    // make default groups and group definitions.  Each sample becomes its own group, compare group1 and group2.
            
    compare = "group1/group2";
    MutableString buffer = new MutableString();
    int groupIndex = 1;
    for (String inputFilename : inputFilenames) {
        buffer.append("group").append(String.valueOf(groupIndex++));
        buffer.append("=");
        buffer.append(AlignmentReaderImpl.getBasename(inputFilename));
        buffer.append('/');
    }
    groupsDefinition = buffer.substring(0, buffer.length() - 1).toString();
    System.out.println(groupsDefinition);
    } else {
    groupsAreDefined = true;
    }     */
    deAnalyzer.parseGroupsDefinition(groupsDefinition, deCalculator, inputFilenames);
    groupComparisonsList = deAnalyzer.parseCompare(compare);

    boolean parallel = jsapResult.getBoolean("parallel", false);
    deAnalyzer.setRunInParallel(parallel);
    Map<String, String> sampleToGroupMap = deCalculator.getSampleToGroupMap();
    readerIndexToGroupIndex = new int[inputFilenames.length];

    groups = deAnalyzer.getGroups();
    numberOfGroups = groups.length;
    IndexedIdentifier groupIds = new IndexedIdentifier();
    for (String group : groups) {
        groupIds.registerIdentifier(new MutableString(group));
    }
    maxThresholdPerSite = jsapResult.getInt("max-coverage-per-site");
    minimumVariationSupport = jsapResult.getInt("minimum-variation-support");
    thresholdDistinctReadIndices = jsapResult.getInt("threshold-distinct-read-indices");
    CompactAlignmentToAnnotationCountsMode.parseEval(jsapResult, deAnalyzer);

    for (String sample : sampleToGroupMap.keySet()) {
        final String group = sampleToGroupMap.get(sample);
        System.out.printf("sample: %s group %s%n", sample, group);
        for (int readerIndex = 0; readerIndex < inputFilenames.length; readerIndex++) {
            if (AlignmentReaderImpl.getBasename(inputFilenames[readerIndex]).endsWith(sample)) {
                readerIndexToGroupIndex[readerIndex] = groupIds.get(new MutableString(group));

            }
        }
    }
    File statFile = jsapResult.getFile("variation-stats");
    if (statFile != null) {
        loadStatFile(statFile);
    } else {
        if (deAnalyzer.eval("within-groups")) {
            System.err.println(
                    "To evaluate statistics within-groups you must provide a --variation-stats argument.");
            System.exit(1);
        }

    }
    callIndels = jsapResult.getBoolean("call-indels");
    diploid = jsapResult.getBoolean("diploid");

    realignmentFactory = configureProcessor(jsapResult);
    final String formatString = jsapResult.getString("format");

    final OutputFormat format = OutputFormat.valueOf(formatString.toUpperCase());

    SequenceVariationOutputFormat formatter = null;
    switch (format) {
    case VARIANT_DISCOVERY:
    case BETWEEN_GROUPS:
        stopWhenDefaultGroupOptions();
        formatter = new BetweenGroupSequenceVariationOutputFormat();
        break;
    case COMPARE_GROUPS:
        stopWhenDefaultGroupOptions();
        formatter = new CompareGroupsVCFOutputFormat();
        break;
    case ALLELE_FREQUENCIES:
        stopWhenDefaultGroupOptions();
        formatter = new AlleleFrequencyOutputFormat();
        break;
    case GENOTYPES:
        formatter = new GenotypesOutputFormat();
        break;
    case METHYLATION_REGIONS:
        formatter = new MethylationRegionsOutputFormat();
        methylFormat((MethylationFormat) formatter);
        break;
    case METHYLATION:
        formatter = new MethylationRateVCFOutputFormat();
        methylFormat((MethylationFormat) formatter);
        break;
    case INDEL_COUNTS:
        formatter = new IndelCountOutputFormat();
        callIndels = true;
        break;
    default:
        ObjectArrayList<OutputFormat> values = ObjectArrayList.wrap(OutputFormat.values());
        System.err.printf("The format argument is not recognized. Allowed values include %s",
                values.toString());
        System.exit(1);
    }

    // set base filters according to output format:
    genotypeFilters = new ObjectArrayList<GenotypeFilter>();
    switch (format) {

    case METHYLATION:
    case METHYLATION_REGIONS:
        // no filters at all for methylation. It seems that in some dataset quality scores are much lower for
        //bases that are not methylated and therefore converted. We don't want to filter these bases and therefore
        // do not install the quality score filter.
        if (callIndels) {
            genotypeFilters.add(new RemoveIndelArtifactsFilter());
        }
        break;
    case COMPARE_GROUPS:
    case ALLELE_FREQUENCIES:
    case BETWEEN_GROUPS:
    case VARIANT_DISCOVERY:

        genotypeFilters.add(new QualityScoreFilter());
        genotypeFilters.add(new LeftOverFilter());
        if (callIndels) {
            genotypeFilters.add(new RemoveIndelArtifactsFilter());
        }
        if (!disableAtLeastQuarterFilter && callIndels) {
            System.out.println("Active: AtLeastAQuarterFilter.");

            genotypeFilters.add(new AtLeastAQuarterFilter());
        }
        if (diploid) {
            genotypeFilters.add(new DiploidFilter());
        }

        break;
    case GENOTYPES:

        genotypeFilters.add(new QualityScoreFilter());
        genotypeFilters.add(new LeftOverFilter());

        if (callIndels) {
            genotypeFilters.add(new RemoveIndelArtifactsFilter());
        }
        if (!disableAtLeastQuarterFilter) {
            genotypeFilters.add(new AtLeastAQuarterFilter());
        }
        if (diploid) {
            genotypeFilters.add(new DiploidFilter());
        }
        break;
    case INDEL_COUNTS:
        genotypeFilters.add(new QualityScoreFilter());
        genotypeFilters.add(new LeftOverFilter());
        genotypeFilters.add(new RemoveIndelArtifactsFilter());
        if (!disableAtLeastQuarterFilter) {
            genotypeFilters.add(new AtLeastAQuarterFilter());
        }
        if (diploid) {
            genotypeFilters.add(new DiploidFilter());
        }
        break;
    default:
        throw new InternalError("Filters must be configured for new output format.");
    }
    System.out.println("Filtering reads that have these criteria:");
    for (final GenotypeFilter filter : genotypeFilters) {
        System.out.println(filter.describe());
    }

    final RandomAccessSequenceInterface genome = configureGenome(testGenome, jsapResult);

    final int startFlapSize = jsapResult.getInt("start-flap-size", 100);
    if (callIndels) {
        System.err.println("Indel calling was activated.");
    }
    formatConfigurator.configureFormatter(formatter);
    sortedPositionIterator = new DiscoverVariantIterateSortedAlignments(formatter);
    sortedPositionIterator.setCallIndels(callIndels);
    sortedPositionIterator.setGenome(genome);
    sortedPositionIterator.setStartFlapLength(startFlapSize);
    sortedPositionIterator.parseIncludeReferenceArgument(jsapResult);
    sortedPositionIterator.setMinimumVariationSupport(minimumVariationSupport);
    sortedPositionIterator.setThresholdDistinctReadIndices(thresholdDistinctReadIndices);
    return this;
}

From source file:net.sf.gazpachoquest.rest.auth.TokenStore.java

/**
 * Creates a byte array of entry from the current state of the system:
 * <ul>//w w w .j a  v  a  2  s  .co m
 * <li>The current system time in milliseconds since the epoch</li>
 * <li>The number of nanoseconds since system startup</li>
 * <li>The name, size and last modification time of the files in the
 * <code>java.io.tmpdir</code> folder.</li>
 * </ul>
 * <p>
 * <b>NOTE</b> This method generates entropy fast but not necessarily
 * secure enough for seeding the random number generator.
 *
 * @return bytes of entropy
 */
private static byte[] getFastEntropy() {
    final MessageDigest md;

    try {
        md = MessageDigest.getInstance("SHA");
    } catch (NoSuchAlgorithmException nsae) {
        throw new InternalError("internal error: SHA-1 not available.");
    }

    // update with XorShifted time values
    update(md, System.currentTimeMillis());
    update(md, System.nanoTime());

    // scan the temp file system
    File file = new File(System.getProperty("java.io.tmpdir"));
    File[] entries = file.listFiles();
    if (entries != null) {
        for (File entry : entries) {
            md.update(entry.getName().getBytes());
            update(md, entry.lastModified());
            update(md, entry.length());
        }
    }

    return md.digest();
}

From source file:com.clustercontrol.winevent.dialog.WinEventDialog.java

/**
 * ????//from ww  w . ja  v a 2  s  .  c o m
 *
 * @param parent ?
 */
@Override
protected void customizeDialog(Composite parent) {

    super.customizeDialog(parent);

    // 
    shell.setText(Messages.getString("dialog.winevent.create.modify"));

    // ????
    Label label = null;
    // ????
    GridData gridData = null;

    /*
     * ????
     */
    Group groupCheckRule = new Group(groupRule, SWT.NONE);
    WidgetTestUtil.setTestId(this, "checkrule", groupCheckRule);
    GridLayout layout = new GridLayout(1, true);
    layout.marginWidth = 5;
    layout.marginHeight = 5;
    layout.numColumns = BASIC_UNIT;
    groupCheckRule.setLayout(layout);
    gridData = new GridData();
    gridData.horizontalSpan = BASIC_UNIT;
    gridData.horizontalAlignment = GridData.FILL;
    gridData.grabExcessHorizontalSpace = true;
    groupCheckRule.setLayoutData(gridData);
    groupCheckRule.setText(Messages.getString("check.rule"));

    /*
     * 
     */
    // 
    label = new Label(groupCheckRule, SWT.NONE);
    WidgetTestUtil.setTestId(this, "wineventlevel", label);
    gridData = new GridData();
    gridData.horizontalSpan = WIDTH_TITLE_LONG;
    gridData.horizontalAlignment = GridData.FILL;
    gridData.grabExcessHorizontalSpace = true;
    label.setLayoutData(gridData);
    label.setText(Messages.getString("winevent.level") + " : ");

    // (?)
    this.levelCritical = new Button(groupCheckRule, SWT.CHECK);
    WidgetTestUtil.setTestId(this, "criticalcheck", levelCritical);
    gridData = new GridData();
    gridData.horizontalSpan = WIDTH_VALUE_LONG;
    gridData.horizontalAlignment = GridData.FILL;
    gridData.grabExcessHorizontalSpace = true;
    this.levelCritical.setLayoutData(gridData);
    this.levelCritical.setText(Messages.getString("winevent.level.critical"));

    // ()
    this.levelWarning = new Button(groupCheckRule, SWT.CHECK);
    WidgetTestUtil.setTestId(this, "warningcheck", levelWarning);
    gridData = new GridData();
    gridData.horizontalSpan = WIDTH_VALUE_LONG;
    gridData.horizontalAlignment = GridData.FILL;
    gridData.grabExcessHorizontalSpace = true;
    this.levelWarning.setLayoutData(gridData);
    this.levelWarning.setText(Messages.getString("winevent.level.warning"));

    // ()
    this.levelVerbose = new Button(groupCheckRule, SWT.CHECK);
    WidgetTestUtil.setTestId(this, "verbosecheck", levelVerbose);
    gridData = new GridData();
    gridData.horizontalSpan = WIDTH_VALUE_LONG;
    gridData.horizontalAlignment = GridData.FILL;
    gridData.grabExcessHorizontalSpace = true;
    this.levelVerbose.setLayoutData(gridData);
    this.levelVerbose.setText(Messages.getString("winevent.level.verbose"));

    // ()
    this.levelError = new Button(groupCheckRule, SWT.CHECK);
    WidgetTestUtil.setTestId(this, "errorcheck", levelError);
    gridData = new GridData();
    gridData.horizontalSpan = WIDTH_VALUE_LONG;
    gridData.horizontalAlignment = GridData.FILL;
    gridData.grabExcessHorizontalSpace = true;
    this.levelError.setLayoutData(gridData);
    this.levelError.setText(Messages.getString("winevent.level.error"));

    // ()
    this.levelInformational = new Button(groupCheckRule, SWT.CHECK);
    WidgetTestUtil.setTestId(this, "infomationalcheck", levelInformational);
    gridData = new GridData();
    gridData.horizontalSpan = WIDTH_VALUE_LONG;
    gridData.horizontalAlignment = GridData.FILL;
    gridData.grabExcessHorizontalSpace = true;
    this.levelInformational.setLayoutData(gridData);
    this.levelInformational.setText(Messages.getString("winevent.level.informational"));

    /*
     *  
     */
    // 
    label = new Label(groupCheckRule, SWT.NONE);
    WidgetTestUtil.setTestId(this, "wineveltlog", label);
    gridData = new GridData();
    gridData.horizontalSpan = WIDTH_TITLE_LONG;
    gridData.horizontalAlignment = GridData.FILL;
    gridData.grabExcessHorizontalSpace = true;
    label.setLayoutData(gridData);
    label.setText(Messages.getString("winevent.log") + " : ");
    // 
    this.logName = new Text(groupCheckRule, SWT.BORDER | SWT.LEFT);
    WidgetTestUtil.setTestId(this, "logname", logName);
    gridData = new GridData();
    gridData.horizontalSpan = WIDTH_TEXT_LONG;
    gridData.horizontalAlignment = GridData.FILL;
    gridData.grabExcessHorizontalSpace = true;
    this.logName.setLayoutData(gridData);
    this.logName.addModifyListener(new ModifyListener() {
        @Override
        public void modifyText(ModifyEvent arg0) {
            update();
        }
    });

    /*
     *  
     */
    // 
    label = new Label(groupCheckRule, SWT.NONE);
    WidgetTestUtil.setTestId(this, "wineventsource", label);
    gridData = new GridData();
    gridData.horizontalSpan = WIDTH_TITLE_LONG;
    gridData.horizontalAlignment = GridData.FILL;
    gridData.grabExcessHorizontalSpace = true;
    label.setLayoutData(gridData);
    label.setText(Messages.getString("winevent.source") + " : ");
    // 
    this.source = new Text(groupCheckRule, SWT.BORDER | SWT.LEFT);
    WidgetTestUtil.setTestId(this, "source", source);
    gridData = new GridData();
    gridData.horizontalSpan = WIDTH_TEXT_LONG;
    gridData.horizontalAlignment = GridData.FILL;
    gridData.grabExcessHorizontalSpace = true;
    this.source.setLayoutData(gridData);
    this.source.setMessage(Messages.getString("message.winevent.1"));

    /*
     * ID
     */
    // 
    label = new Label(groupCheckRule, SWT.NONE);
    WidgetTestUtil.setTestId(this, "wineventid", label);
    gridData = new GridData();
    gridData.horizontalSpan = WIDTH_TITLE_LONG;
    gridData.horizontalAlignment = GridData.FILL;
    gridData.grabExcessHorizontalSpace = true;
    label.setLayoutData(gridData);
    label.setText(Messages.getString("winevent.id") + " : ");
    // 
    this.eventId = new Text(groupCheckRule, SWT.BORDER | SWT.LEFT);
    WidgetTestUtil.setTestId(this, "eventid", eventId);
    gridData = new GridData();
    gridData.horizontalSpan = WIDTH_TEXT_LONG;
    gridData.horizontalAlignment = GridData.FILL;
    gridData.grabExcessHorizontalSpace = true;
    this.eventId.setLayoutData(gridData);
    this.eventId.setMessage(Messages.getString("message.winevent.2"));

    /*
     * ?
     */
    // 
    label = new Label(groupCheckRule, SWT.NONE);
    WidgetTestUtil.setTestId(this, "wineventcategory", label);
    gridData = new GridData();
    gridData.horizontalSpan = WIDTH_TITLE_LONG;
    gridData.horizontalAlignment = GridData.FILL;
    gridData.grabExcessHorizontalSpace = true;
    label.setLayoutData(gridData);
    label.setText(Messages.getString("winevent.category") + " : ");
    // 
    this.category = new Text(groupCheckRule, SWT.BORDER | SWT.LEFT);
    WidgetTestUtil.setTestId(this, "category", category);
    gridData = new GridData();
    gridData.horizontalSpan = WIDTH_TEXT_LONG;
    gridData.horizontalAlignment = GridData.FILL;
    gridData.grabExcessHorizontalSpace = true;
    this.category.setLayoutData(gridData);
    this.category.setMessage(Messages.getString("message.winevent.3"));

    /*
     * 
     */
    // 
    label = new Label(groupCheckRule, SWT.NONE);
    WidgetTestUtil.setTestId(this, "keywords", label);
    gridData = new GridData();
    gridData.horizontalSpan = WIDTH_TITLE_LONG;
    gridData.horizontalAlignment = GridData.FILL;
    gridData.grabExcessHorizontalSpace = true;
    label.setLayoutData(gridData);
    label.setText(Messages.getString("winevent.keywords") + " : ");
    // 
    this.keywords = new Text(groupCheckRule, SWT.BORDER | SWT.LEFT);
    WidgetTestUtil.setTestId(this, "keywords", keywords);
    gridData = new GridData();
    gridData.horizontalSpan = WIDTH_TEXT_LONG;
    gridData.horizontalAlignment = GridData.FILL;
    gridData.grabExcessHorizontalSpace = true;
    this.keywords.setLayoutData(gridData);
    this.keywords.setMessage(Messages.getString("message.winevent.4"));

    // ?????
    this.m_monitorRule.setRunIntervalEnabled(false);

    // 
    this.adjustDialog();

    // ?
    MonitorInfo info = null;
    if (this.monitorId == null) {
        // ???
        info = new MonitorInfo();
        this.setInfoInitialValue(info);
    } else {
        // ????
        try {
            MonitorSettingEndpointWrapper wrapper = MonitorSettingEndpointWrapper.getWrapper(managerName);
            info = wrapper.getMonitor(this.monitorId);
        } catch (InvalidRole_Exception e) {
            // ??????
            MessageDialog.openInformation(null, Messages.getString("message"),
                    Messages.getString("message.accesscontrol.16"));
            throw new InternalError(e.getMessage());
        } catch (Exception e) {
            // ?
            m_log.warn("customizeDialog(), " + HinemosMessage.replace(e.getMessage()), e);
            MessageDialog.openInformation(null, Messages.getString("message"),
                    Messages.getString("message.hinemos.failure.unexpected") + ", "
                            + HinemosMessage.replace(e.getMessage()));
            throw new InternalError(e.getMessage());
        }
    }
    this.setInputData(info);
    this.update();
}

From source file:org.projectforge.framework.configuration.ConfigXml.java

/**
 * Copies only not null values of the configuration.
 *///w w  w .  ja  v a  2s . c  o  m
private static void copyDeclaredFields(final String prefix, final Class<?> srcClazz, final Object src,
        final Object dest, final String... ignoreFields) {
    final Field[] fields = srcClazz.getDeclaredFields();
    AccessibleObject.setAccessible(fields, true);
    for (final Field field : fields) {
        if (ignoreFields != null && ArrayUtils.contains(ignoreFields, field.getName()) == false
                && accept(field)) {
            try {
                final Object srcFieldValue = field.get(src);
                if (srcFieldValue == null) {
                    // Do nothing
                } else if (srcFieldValue instanceof ConfigurationData) {
                    final Object destFieldValue = field.get(dest);
                    Validate.notNull(destFieldValue);
                    final StringBuffer buf = new StringBuffer();
                    if (prefix != null) {
                        buf.append(prefix);
                    }
                    String alias = null;
                    if (field.isAnnotationPresent(XmlField.class)) {
                        final XmlField xmlFieldAnn = field.getAnnotation(XmlField.class);
                        if (xmlFieldAnn != null) {
                            alias = xmlFieldAnn.alias();
                        }
                    }
                    if (alias != null) {
                        buf.append(alias);
                    } else {
                        buf.append(field.getClass().getName());
                    }
                    buf.append(".");
                    copyDeclaredFields(buf.toString(), srcFieldValue.getClass(), srcFieldValue, destFieldValue,
                            ignoreFields);
                } else if (PLUGIN_CONFIGS_FIELD_NAME.equals(field.getName()) == true) {
                    // Do nothing.
                } else {
                    field.set(dest, srcFieldValue);
                    if (field.isAnnotationPresent(ConfigXmlSecretField.class) == true) {
                        log.info(StringUtils.defaultString(prefix) + field.getName() + " = "
                                + SECRET_PROPERTY_STRING);
                    } else {
                        log.info(StringUtils.defaultString(prefix) + field.getName() + " = " + srcFieldValue);
                    }
                }
            } catch (final IllegalAccessException ex) {
                throw new InternalError("Unexpected IllegalAccessException: " + ex.getMessage());
            }
        }
    }
    final Class<?> superClazz = srcClazz.getSuperclass();
    if (superClazz != null) {
        copyDeclaredFields(prefix, superClazz, src, dest, ignoreFields);
    }
}