public PKCS10CertificationRequest build() throws SCMSecurityException {
  Preconditions.checkNotNull(key, "KeyPair cannot be null");
  Preconditions.checkArgument(Strings.isNotBlank(subject), "Subject " +
      "cannot be blank");

  try {
    CertificateSignRequest csr = new CertificateSignRequest(subject, scmID,
        clusterID, key, config, createExtensions());
    return csr.generateCSR();
  } catch (IOException ioe) {
    throw new CertificateException(String.format("Unable to create " +
        "extension for certificate sign request for %s.", SecurityUtil
        .getDistinguishedName(subject, scmID, clusterID)), ioe.getCause());
  } catch (OperatorCreationException ex) {
    throw new CertificateException(String.format("Unable to create " +
        "certificate sign request for %s.", SecurityUtil
        .getDistinguishedName(subject, scmID, clusterID)),
        ex.getCause());
  }
}
 

private synchronized void processFrames() throws IOException {
    try {
        int count = 0;
        while (!shutdown) {
            String message = Strings.EMPTY;
            message = syslogReader.read();
            messageList.add(message);
            count++;
            if (isEndOfMessages(count)) {
                break;
            }
        }
        this.notify();
    }
    catch(final Exception e) {
        this.notify();
        throw new IOException(e);
    }
}
 

private void setFields(final MapMessage<?, ?> mapMessage) throws SQLException {
    final IndexedReadOnlyStringMap map = mapMessage.getIndexedReadOnlyStringMap();
    final String simpleName = statement.getClass().getName();
    int j = 1; // JDBC indices start at 1
    for (final ColumnMapping mapping : this.factoryData.columnMappings) {
        if (mapping.getLiteralValue() == null) {
            final String source = mapping.getSource();
            final String key = Strings.isEmpty(source) ? mapping.getName() : source;
            final Object value = map.getValue(key);
            if (logger().isTraceEnabled()) {
                final String valueStr = value instanceof String ? "\"" + value + "\""
                        : Objects.toString(value, null);
                logger().trace("{} setObject({}, {}) for key '{}' and mapping '{}'", simpleName, j, valueStr, key,
                        mapping.getName());
            }
            setStatementObject(j, mapping.getNameKey(), value);
            j++;
        }
    }
}
 

/**
 * Factory method for creating a connection source within the plugin manager.
 *
 * @param jndiName The full JNDI path where the data source is bound. Should start with java:/comp/env or
 *                 environment-equivalent.
 * @return the created connection source.
 */
@PluginFactory
public static DataSourceConnectionSource createConnectionSource(@PluginAttribute final String jndiName) {
    if (Strings.isEmpty(jndiName)) {
        LOGGER.error("No JNDI name provided.");
        return null;
    }

    try {
        final InitialContext context = new InitialContext();
        final DataSource dataSource = (DataSource) context.lookup(jndiName);
        if (dataSource == null) {
            LOGGER.error("No data source found with JNDI name [" + jndiName + "].");
            return null;
        }

        return new DataSourceConnectionSource(jndiName, dataSource);
    } catch (final NamingException e) {
        LOGGER.error(e.getMessage(), e);
        return null;
    }
}
 

@NotNull
public static DriverCatalog createTestDriverCatalogEntry(@NotNull String gene) {
    return ImmutableDriverCatalog.builder()
            .gene(gene)
            .chromosome(Strings.EMPTY)
            .chromosomeBand(Strings.EMPTY)
            .category(DriverCategory.ONCO)
            .driver(DriverType.MUTATION)
            .likelihoodMethod(LikelihoodMethod.NONE)
            .driverLikelihood(0D)
            .dndsLikelihood(0D)
            .missense(0)
            .nonsense(0)
            .splice(0)
            .inframe(0)
            .frameshift(0)
            .biallelic(false)
            .minCopyNumber(0)
            .maxCopyNumber(0)
            .build();
}
 

@Override
public BackendEntry writeIndex(HugeIndex index) {
    TableBackendEntry entry = newBackendEntry(index);
    /*
     * When field-values is null and elementIds size is 0, it is
     * meaningful for deletion of index data in secondary/range index.
     */
    if (index.fieldValues() == null && index.elementIds().size() == 0) {
        entry.column(HugeKeys.INDEX_LABEL_ID, index.indexLabel().longId());
    } else {
        Object value = index.fieldValues();
        if (value != null && "\u0000".equals(value)) {
            value = Strings.EMPTY;
        }
        entry.column(HugeKeys.FIELD_VALUES, value);
        entry.column(HugeKeys.INDEX_LABEL_ID, index.indexLabel().longId());
        entry.column(HugeKeys.ELEMENT_IDS,
                     IdUtil.writeStoredString(index.elementId()));
        entry.column(HugeKeys.EXPIRED_TIME, index.expiredTime());
        entry.subId(index.elementId());
    }
    return entry;
}
 

@Test
public void testPatternColumn03() {
    final ColumnConfig config = ColumnConfig.newBuilder()
        .setName("col3")
        .setPattern("%X{id} %level")
        .setLiteral(Strings.EMPTY)
        .setEventTimestamp(false)
        .setUnicode(true)
        .setClob(false)
        .build();

    assertNotNull("The result should not be null.", config);
    assertEquals("The column name is not correct.", "col3", config.getColumnName());
    assertNotNull("The pattern should not be null.", config.getLayout());
    assertEquals("The pattern is not correct.", "%X{id} %level", config.getLayout().toString());
    assertNull("The literal value should be null.", config.getLiteralValue());
    assertFalse("The timestamp flag should be false.", config.isEventTimestamp());
    assertTrue("The unicode flag should be true.", config.isUnicode());
    assertFalse("The clob flag should be false.", config.isClob());
}
 

@Test
public void testJavaScriptPatternSelector() throws Exception {
    final org.apache.logging.log4j.Logger logger = LogManager.getLogger("TestJavaScriptPatternSelector");
    final org.apache.logging.log4j.Logger logger2 = LogManager.getLogger("JavascriptNoLocation");
    logger.traceEntry();
    logger.info("Hello World");
    logger2.info("No location information");
    logger.traceExit();
    final ListAppender app = (ListAppender) context.getRequiredAppender("List3");
    assertNotNull("No ListAppender", app);
    final List<String> messages = app.getMessages();
    assertNotNull("No Messages", messages);
    assertTrue("Incorrect number of messages. Expected 4, Actual " + messages.size() + ": " + messages, messages.size() == 4);
    String expect = "[TRACE] TestJavaScriptPatternSelector ====== " +
            "o.a.l.l.c.PatternSelectorTest.testJavaScriptPatternSelector:85 Enter ======" + Strings.LINE_SEPARATOR;
    assertEquals(expect, messages.get(0));
    expect = "[INFO ] TestJavaScriptPatternSelector " +
            "o.a.l.l.c.PatternSelectorTest.testJavaScriptPatternSelector.86 Hello World" + Strings.LINE_SEPARATOR;
    assertEquals(expect, messages.get(1));
    assertEquals("[INFO ] JavascriptNoLocation No location information" + Strings.LINE_SEPARATOR, messages.get(2));
    app.clear();
}
 

@Test
public void testMarkerPatternSelector() throws Exception {
    final org.apache.logging.log4j.Logger logger = LogManager.getLogger("TestMarkerPatternSelector");
    logger.traceEntry();
    logger.info("Hello World");
    logger.traceExit();
    final ListAppender app = (ListAppender) context.getRequiredAppender("List");
    assertNotNull("No ListAppender", app);
    final List<String> messages = app.getMessages();
    assertNotNull("No Messages", messages);
    assertTrue("Incorrect number of messages. Expected 3, Actual " + messages.size() + ": " + messages, messages.size() == 3);
    final String expect = String.format("[TRACE] TestMarkerPatternSelector ====== "
            + "o.a.l.l.c.PatternSelectorTest.testMarkerPatternSelector:43 Enter ======%n");
    assertEquals(expect, messages.get(0));
    assertEquals("[INFO ] TestMarkerPatternSelector Hello World" + Strings.LINE_SEPARATOR, messages.get(1));
    app.clear();
}
 

@NotNull
static ModifiableVariantHotspotEvidence create(@NotNull final VariantHotspot hotspot) {
    return ModifiableVariantHotspotEvidence.create()
            .from(hotspot)
            .setRef(hotspot.ref())
            .setAlt(hotspot.alt())
            .setAltQuality(0)
            .setAltSupport(0)
            .setRefSupport(0)
            .setRefQuality(0)
            .setIndelSupport(0)
            .setReadDepth(0)
            .setAltMapQuality(0)
            .setAltMinQuality(0)
            .setAltDistanceFromRecordStart(0)
            .setAltMinDistanceFromAlignment(0)
            .setSubprimeReadDepth(0)
            .setReadContext(Strings.EMPTY)
            .setReadContextCount(0)
            .setReadContextCountOther(0);
}
 

private void renderMicrosatelliteStabilityCharacteristic(@NotNull Document reportDocument) {
    boolean hasReliablePurity = patientReport.hasReliablePurity();
    double microSatelliteStability = patientReport.microsatelliteIndelsPerMb();
    String microSatelliteStabilityString = hasReliablePurity ? patientReport.microsatelliteStatus().display() + " "
            + DOUBLE_DECIMAL_FORMAT.format(patientReport.microsatelliteIndelsPerMb()) : DataUtil.NA_STRING;

    BarChart satelliteChart =
            new BarChart(microSatelliteStability, MicroSatelliteStatus.RANGE_MIN, MicroSatelliteStatus.RANGE_MAX, "MSS", "MSI", false);
    satelliteChart.enabled(hasReliablePurity);
    satelliteChart.scale(InlineBarChart.LOG10_SCALE);
    satelliteChart.setTickMarks(new double[] { MicroSatelliteStatus.RANGE_MIN, 10, MicroSatelliteStatus.RANGE_MAX },
            DOUBLE_DECIMAL_FORMAT);
    satelliteChart.enableUndershoot(NO_DECIMAL_FORMAT.format(0));
    satelliteChart.enableOvershoot(">" + NO_DECIMAL_FORMAT.format(satelliteChart.max()));
    satelliteChart.setIndicator(MicroSatelliteStatus.THRESHOLD,
            "Microsatellite \ninstability (" + DOUBLE_DECIMAL_FORMAT.format(MicroSatelliteStatus.THRESHOLD) + ")");
    reportDocument.add(createCharacteristicDiv("Microsatellite status",
            microSatelliteStabilityString,
            "The microsatellite stability score represents the number of somatic inserts and deletes in "
                    + "(short) repeat sections across the whole genome of the tumor per Mb. This metric can be "
                    + "considered as a good marker for instability in microsatellite repeat regions. Tumors with a "
                    + "score greater than 4.0 are considered microsatellite unstable (MSI).",
            satelliteChart,
            Strings.EMPTY,
            false));
}
 

@NotNull
private static SampleReport createSkinMelanomaSampleReport(@NotNull String sample) {
    SampleMetadata sampleMetadata = ImmutableSampleMetadata.builder()
            .refSampleId(Strings.EMPTY)
            .refSampleBarcode("FR12123488")
            .tumorSampleId(sample)
            .tumorSampleBarcode("FR12345678")
            .build();

    return ImmutableSampleReport.builder()
            .sampleMetadata(sampleMetadata)
            .patientTumorLocation(ImmutablePatientTumorLocation.of(Strings.EMPTY, "Skin", "Melanoma"))
            .refArrivalDate(LocalDate.parse("01-Jan-2020", DATE_FORMATTER))
            .tumorArrivalDate(LocalDate.parse("05-Jan-2020", DATE_FORMATTER))
            .shallowSeqPurityString(Lims.NOT_PERFORMED_STRING)
            .labProcedures("PREP013V23-QC037V20-SEQ008V25")
            .cohort("TEST")
            .projectName("TEST-001-002")
            .submissionId("SUBM")
            .hospitalContactData(createTestHospitalContactData())
            .hospitalPatientId("HOSP1")
            .hospitalPathologySampleId("PA1")
            .build();
}
 

private void handle(GetKVMHostDownloadCredentialMsg msg) {
    final GetKVMHostDownloadCredentialReply reply = new GetKVMHostDownloadCredentialReply();

    String key = asf.getPrivateKey();

    String hostname = null;
    if (Strings.isNotEmpty(msg.getDataNetworkCidr())) {
        String dataNetworkAddress = getDataNetworkAddress(self.getUuid(), msg.getDataNetworkCidr());

        if (dataNetworkAddress != null) {
            hostname = dataNetworkAddress;
        }
    }

    reply.setHostname(hostname == null ? getSelf().getManagementIp() : hostname);
    reply.setUsername(getSelf().getUsername());
    reply.setSshPort(getSelf().getPort());
    reply.setSshKey(key);
    bus.reply(msg, reply);
}
 

@NotNull
public static ImmutableGermlineVariant.Builder createTestGermlineVariantBuilder() {
    return ImmutableGermlineVariant.builder()
            .passFilter(true)
            .gene(Strings.EMPTY)
            .ref(Strings.EMPTY)
            .alt(Strings.EMPTY)
            .codingEffect(CodingEffect.UNDEFINED)
            .chromosome(Strings.EMPTY)
            .position(0)
            .hgvsCodingImpact(Strings.EMPTY)
            .hgvsProteinImpact(Strings.EMPTY)
            .totalReadCount(0)
            .alleleReadCount(0)
            .adjustedCopyNumber(0)
            .adjustedVAF(0)
            .biallelic(false);
}
 

@NotNull
public static ImmutableReportableVariant.Builder createTestReportableVariantBuilder() {
    return ImmutableReportableVariant.builder()
            .gene(Strings.EMPTY)
            .position(0)
            .chromosome(Strings.EMPTY)
            .ref(Strings.EMPTY)
            .alt(Strings.EMPTY)
            .canonicalCodingEffect(CodingEffect.UNDEFINED)
            .canonicalHgvsCodingImpact(Strings.EMPTY)
            .canonicalHgvsProteinImpact(Strings.EMPTY)
            .gDNA(Strings.EMPTY)
            .hotspot(Hotspot.HOTSPOT)
            .clonalLikelihood(1D)
            .alleleReadCount(0)
            .totalReadCount(0)
            .allelePloidy(0D)
            .totalPloidy(0)
            .biallelic(false)
            .driverCategory(DriverCategory.ONCO)
            .driverLikelihood(0D)
            .notifyClinicalGeneticist(false);
}
 

@NotNull
private static List<ClinicalTrial> createCOLO829ClinicalTrials() {
    List<ClinicalTrial> trials = Lists.newArrayList();
    ImmutableClinicalTrial.Builder iclusionBuilder =
            ImmutableClinicalTrial.builder().cancerType(Strings.EMPTY).isOnLabel(true).source(ActionabilitySource.ICLUSION);

    trials.add(iclusionBuilder.event("BRAF p.Val600Glu")
            .scope(EvidenceScope.GENE_LEVEL)
            .acronym("CLXH254X2101")
            .reference("EXT10453 (NL55506.078.15)")
            .build());
    trials.add(iclusionBuilder.event("BRAF p.Val600Glu")
            .scope(EvidenceScope.SPECIFIC)
            .acronym("COWBOY")
            .reference("EXT12301 (NL71732.091.19)")
            .build());
    trials.add(iclusionBuilder.event("BRAF p.Val600Glu")
            .scope(EvidenceScope.GENE_LEVEL)
            .acronym("DRUP")
            .reference("EXT10299 (NL54757.031.16)")
            .build());
    trials.add(iclusionBuilder.event("BRAF p.Val600Glu")
            .scope(EvidenceScope.GENE_LEVEL)
            .acronym("EBIN (EORTC-1612-MG)")
            .reference("EXT11284 (NL67202.031.18)")
            .build());
    trials.add(iclusionBuilder.event("BRAF p.Val600Glu")
            .scope(EvidenceScope.GENE_LEVEL)
            .acronym("POLARIS")
            .reference("EXT11388 (NL69569.028.19)")
            .build());
    trials.add(iclusionBuilder.event("CDKN2A p.Ala68fs")
            .scope(EvidenceScope.GENE_LEVEL)
            .acronym("DRUP")
            .reference("EXT10299 (NL54757.031.16)")
            .build());

    return trials;
}
 

@Test
public void mdc() {

    MDC.put("TestYear", "2010");
    logger.debug("Debug message");
    verify("List", "o.a.l.s.LoggerTest Debug message MDC{TestYear=2010}" + Strings.LINE_SEPARATOR);
    MDC.clear();
    logger.debug("Debug message");
    verify("List", "o.a.l.s.LoggerTest Debug message MDC{}" + Strings.LINE_SEPARATOR);
}
 

private String getRequestUrl(){
    HttpServletRequest request = ((ServletRequestAttributes) RequestContextHolder.currentRequestAttributes()).getRequest();
    if(request == null){
        return Strings.EMPTY;
    }

    return request.getRequestURL().toString();
}
 

@ExceptionHandler(GeneralException.class)
public ResponseEntity generalException(GeneralException e, HttpServletRequest request) {
    log.error("{}", getStackTrace(e));
    ExceptionType exceptionType = e.getExceptionType();
    setHttpResponseErrorCode(request, exceptionType.getCode());
    String message = messageManager.getProperty(exceptionType.getCode());
    if (Strings.isNotEmpty(e.getMessage())) message = String.format("%s %s", message, e.getMessage());
    CommonResponseEntity response = CommonResponseEntity.generateException(e.getExceptionType().getCode(), message);
    return HttpHelper.newResponseEntityWithId(e.getExceptionType().getHttpStatus(), response);
}
 

private List<String> getGuidFromMapList(List value) {
    List<String> guids;
    guids = (List<String>) value.stream().map(e -> {
        if (e instanceof Map) {
            return (String) ((Map) e).get("guid");
        } else {
            return Strings.EMPTY;
        }
    }).collect(Collectors.toList());
    return guids;
}
 

public static Map<String, String> getValuesToMask(Object o) {
    Map<String, String> results = new HashMap<>();
    maskFields.getOrDefault(o.getClass(), Collections.emptySet()).forEach(f -> {
        Object obj = f.getValue(o);
        if (obj instanceof Collection) {
            ((Collection<?>) obj).forEach(v -> results.put(v.toString(), f.getMaskedValue(v.toString())));
        } else if (obj != null) {
            results.put(obj.toString(), f.getMaskedValue(obj.toString()));
        }
    });

    autoFields.getOrDefault(o.getClass(), Collections.emptySet()).forEach(f -> {
        Object si = f.getValue(o);
        if (mayHasSensitiveInfo(si)) {
            results.putAll(getValuesToMask(si));
        } else if (si instanceof Collection) {
            ((Collection<?>) si).forEach(v -> {
                if (mayHasSensitiveInfo(v)) {
                    results.put(v.toString(), f.getMaskedValue(v.toString()));
                }
            });
        }
    });

    results.remove(Strings.EMPTY);
    return results;
}
 

@Test
public void testBothCentreMatches() {
    ReadContext victim1 = new ReadContext(Strings.EMPTY, 1000, 4, 4, 4, 4, "AAAATGGGG".getBytes(), Strings.EMPTY);
    ReadContext victim2 = new ReadContext(Strings.EMPTY, 1005, 5, 5, 5, 4,     "TGGGGACCCC".getBytes(), Strings.EMPTY);
    assertFalse(victim1.phased(-5, victim2));
    assertFalse(victim2.phased(5, victim1));
}
 

public String getBindingMessage() {
    String bindingMessage = null;

    if (Strings.isNotBlank(getAuthReqId())) {
        final CibaRequestCacheControl cibaRequestCacheControl = cibaRequestService.getCibaRequest(authReqId);

        if (cibaRequestCacheControl != null) {
            bindingMessage = cibaRequestCacheControl.getBindingMessage();
        }
    }

    return bindingMessage;
}
 

@Test
public void testPhasedMNV() {
    ReadContext victim1 = new ReadContext(Strings.EMPTY, 1000, 4, 4, 4, 4, "GATCTTGAT".getBytes(), Strings.EMPTY);
    ReadContext victim2 = new ReadContext(Strings.EMPTY, 1001, 5, 5, 5, 4, "GATCTTGATC".getBytes(), Strings.EMPTY);

    assertTrue(victim1.phased(-1, victim2));
    assertTrue(victim2.phased(1, victim1));
}
 

/**
 * Formats the stack trace including packaging information.
 *
 * @param src            ThrowableProxy instance to format
 * @param sb             Destination.
 * @param ignorePackages List of packages to be ignored in the trace.
 * @param textRenderer   The message renderer.
 * @param suffix         Append this to the end of each stack frame.
 * @param lineSeparator  The end-of-line separator.
 */
static void formatExtendedStackTraceTo(ThrowableProxy src, final StringBuilder sb, final List<String> ignorePackages, final TextRenderer textRenderer, final String suffix, final String lineSeparator) {
    textRenderer.render(src.getName(), sb, "Name");
    textRenderer.render(": ", sb, "NameMessageSeparator");
    textRenderer.render(src.getMessage(), sb, "Message");
    renderSuffix(suffix, sb, textRenderer);
    textRenderer.render(lineSeparator, sb, "Text");
    final StackTraceElement[] causedTrace = src.getThrowable() != null ? src.getThrowable().getStackTrace() : null;
    formatElements(sb, Strings.EMPTY, 0, causedTrace, src.getExtendedStackTrace(), ignorePackages, textRenderer, suffix, lineSeparator);
    formatSuppressed(sb, TAB, src.getSuppressedProxies(), ignorePackages, textRenderer, suffix, lineSeparator);
    formatCause(sb, Strings.EMPTY, src.getCauseProxy(), ignorePackages, textRenderer, suffix, lineSeparator);
}
 

private static boolean isForwardCandidate(@NotNull final VariantContext context) {
    final boolean altMatch =
            context.getAlternateAlleles().stream().anyMatch(x -> x.getBaseString().equals("T") || x.getBaseString().equals("G"));

    final String triContext = context.getAttributeAsString(SomaticRefContextEnrichment.TRINUCLEOTIDE_FLAG, Strings.EMPTY);
    final boolean triMatch = triContext.startsWith("TC");

    return isNotFiltered(context) && triMatch && altMatch;
}
 

@Test
public void test() {
    Assert.assertEquals(".dev", LogEnvUtils.getLogConfEnvSuffix("app"));
    Assert.assertEquals(".test", LogEnvUtils.getLogConfEnvSuffix("app2"));
    Assert.assertEquals(Strings.EMPTY, LogEnvUtils.getLogConfEnvSuffix("app3"));
    Assert.assertEquals(Strings.EMPTY, LogEnvUtils.getLogConfEnvSuffix("app4"));
}
 

@Test
public void basicFlow() {
    xlogger.entry();
    verify("List", "o.a.l.s.LoggerTest entry MDC{}" + Strings.LINE_SEPARATOR);
    xlogger.exit();
    verify("List", "o.a.l.s.LoggerTest exit MDC{}" + Strings.LINE_SEPARATOR);
}
 

@Override
public Instant convertToEntityAttribute(final String s) {
    if (Strings.isEmpty(s)) {
        return null;
    }

    int pos = s.indexOf(",");
    long epochSecond = Long.parseLong(s.substring(0, pos));
    int nanos = Integer.parseInt(s.substring(pos + 1, s.length()));

    MutableInstant result = new MutableInstant();
    result.initFromEpochSecond(epochSecond, nanos);
    return result;
}
 

@Test
public void debugNoParms() {
    logger.debug("Debug message {}");
    verify("List", "o.a.l.s.LoggerTest Debug message {} MDC{}" + Strings.LINE_SEPARATOR);
    logger.debug("Debug message {}", (Object[]) null);
    verify("List", "o.a.l.s.LoggerTest Debug message {} MDC{}" + Strings.LINE_SEPARATOR);
    ((LocationAwareLogger)logger).log(null, Log4jLogger.class.getName(), LocationAwareLogger.DEBUG_INT,
        "Debug message {}", null, null);
    verify("List", "o.a.l.s.LoggerTest Debug message {} MDC{}" + Strings.LINE_SEPARATOR);
}