org.apache.logging.log4j.util.Strings Java Examples

The following examples show how to use org.apache.logging.log4j.util.Strings. You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example. You may check out the related API usage on the sidebar.
Example #1
Source File: KVMHost.java    From zstack with Apache License 2.0 6 votes vote down vote up
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);
}
 
Example #2
Source File: MockTlsSyslogServer.java    From logging-log4j2 with Apache License 2.0 6 votes vote down vote up
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);
    }
}
 
Example #3
Source File: PatientReporterTestFactory.java    From hmftools with GNU General Public License v3.0 6 votes vote down vote up
@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);
}
 
Example #4
Source File: PatientReporterTestFactory.java    From hmftools with GNU General Public License v3.0 6 votes vote down vote up
@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);
}
 
Example #5
Source File: CertificateSignRequest.java    From hadoop-ozone with Apache License 2.0 6 votes vote down vote up
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());
  }
}
 
Example #6
Source File: JdbcDatabaseManager.java    From logging-log4j2 with Apache License 2.0 6 votes vote down vote up
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++;
        }
    }
}
 
Example #7
Source File: DataSourceConnectionSource.java    From logging-log4j2 with Apache License 2.0 6 votes vote down vote up
/**
 * 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;
    }
}
 
Example #8
Source File: PatientReporterTestFactory.java    From hmftools with GNU General Public License v3.0 6 votes vote down vote up
@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();
}
 
Example #9
Source File: PostgresqlSerializer.java    From hugegraph with Apache License 2.0 6 votes vote down vote up
@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;
}
 
Example #10
Source File: ExampleAnalysisTestFactory.java    From hmftools with GNU General Public License v3.0 6 votes vote down vote up
@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();
}
 
Example #11
Source File: ColumnConfigTest.java    From logging-log4j2 with Apache License 2.0 6 votes vote down vote up
@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());
}
 
Example #12
Source File: TumorCharacteristicsChapter.java    From hmftools with GNU General Public License v3.0 6 votes vote down vote up
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));
}
 
Example #13
Source File: PatternSelectorTest.java    From logging-log4j2 with Apache License 2.0 6 votes vote down vote up
@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();
}
 
Example #14
Source File: PatternSelectorTest.java    From logging-log4j2 with Apache License 2.0 6 votes vote down vote up
@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();
}
 
Example #15
Source File: VariantHotspotEvidenceFactory.java    From hmftools with GNU General Public License v3.0 6 votes vote down vote up
@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);
}
 
Example #16
Source File: LoggerTest.java    From logging-log4j2 with Apache License 2.0 5 votes vote down vote up
@Test
public void testLog() {
    final Log logger = LogFactory.getLog("LoggerTest");
    logger.debug("Test message");
    verify("List", "o.a.l.l.j.LoggerTest Test message MDC{}" + Strings.LINE_SEPARATOR);
    logger.debug("Exception: " , new NullPointerException("Test"));
    verify("List", "o.a.l.l.j.LoggerTest Exception:  MDC{}" + Strings.LINE_SEPARATOR);
    logger.info("Info Message");
    verify("List", "o.a.l.l.j.LoggerTest Info Message MDC{}" + Strings.LINE_SEPARATOR);
    logger.info("Info Message {}");
    verify("List", "o.a.l.l.j.LoggerTest Info Message {} MDC{}" + Strings.LINE_SEPARATOR);
}
 
Example #17
Source File: LevelAttributeConverter.java    From logging-log4j2 with Apache License 2.0 5 votes vote down vote up
@Override
public Level convertToEntityAttribute(final String s) {
    if (Strings.isEmpty(s)) {
        return null;
    }

    return Level.toLevel(s, null);
}
 
Example #18
Source File: K8SController.java    From logging-log4j2 with Apache License 2.0 5 votes vote down vote up
private Pod getCurrentPod(KubernetesClient kubernetesClient) {
    String hostName = System.getenv(HOSTNAME);
    try {
        if (isServiceAccount() && Strings.isNotBlank(hostName)) {
            return kubernetesClient.pods().withName(hostName).get();
        }
    } catch (Throwable t) {
        LOGGER.debug("Unable to locate pod with name {}.", hostName);
    }
    return null;
}
 
Example #19
Source File: LoggerTest.java    From logging-log4j2 with Apache License 2.0 5 votes vote down vote up
@Test
public void simpleFlow() {
    xlogger.entry(CONFIG);
    verify("List", "o.a.l.s.LoggerTest entry with (log4j-test1.xml) MDC{}" + Strings.LINE_SEPARATOR);
    xlogger.exit(0);
    verify("List", "o.a.l.s.LoggerTest exit with (0) MDC{}" + Strings.LINE_SEPARATOR);
}
 
Example #20
Source File: ExampleAnalysisTestFactory.java    From hmftools with GNU General Public License v3.0 5 votes vote down vote up
@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;
}
 
Example #21
Source File: LoggerConfig.java    From logging-log4j2 with Apache License 2.0 5 votes vote down vote up
/**
 * Default constructor.
 */
public LoggerConfig() {
    this.logEventFactory = LOG_EVENT_FACTORY;
    this.level = Level.ERROR;
    this.name = Strings.EMPTY;
    this.properties = null;
    this.propertiesRequireLookup = false;
    this.config = null;
    this.reliabilityStrategy = new DefaultReliabilityStrategy(this);
}
 
Example #22
Source File: DetermineEventOfGenomicMutation.java    From hmftools with GNU General Public License v3.0 5 votes vote down vote up
@NotNull
public static KnownFusions checkFusionPromiscuous(@NotNull ViccEntry viccEntry, @NotNull String gene, @NotNull String event) {
    String function =
            viccEntry.association().evidence().description() == null ? Strings.EMPTY : viccEntry.association().evidence().description();

    if (FUSIONS_PROMISCUOUS.contains(event)) {
        GenomicEvents typeEvent = GenomicEvents.genomicEvents("fusion promiscuous");
        return FusionExtractor.determinePromiscuousFusions(viccEntry.source(), typeEvent.toString(), gene, function);
    }
    return ImmutableKnownFusions.builder().gene("").eventType("").source("").sourceLink("").build();
}
 
Example #23
Source File: DocumentConverter.java    From baleen with Apache License 2.0 5 votes vote down vote up
private void addMetadataToProperties(final List<BaleenDocumentMetadata> list, final JCas jCas) {
  for (final Metadata metadata : JCasUtil.select(jCas, Metadata.class)) {
    String key = metadata.getKey();
    if (key.contains(".")) {
      // Field names can't contain a "." in Mongo, so replace with a _
      key = key.replaceAll("\\.", "_");
    }

    final String value = metadata.getValue();
    if (!Strings.isEmpty(key) && !Strings.isEmpty(value)) {
      list.add(new BaleenDocumentMetadata(key, value));
    }
  }
}
 
Example #24
Source File: PluginManager.java    From logging-log4j2 with Apache License 2.0 5 votes vote down vote up
/**
 * Adds a list of package names to be scanned for plugins. Convenience method for {@link #addPackage(String)}.
 *
 * @param packages collection of package names to add. Empty and null package names are ignored.
 */
public static void addPackages(final Collection<String> packages) {
    for (final String pkg : packages) {
        if (Strings.isNotBlank(pkg)) {
            PACKAGES.addIfAbsent(pkg);
        }
    }
}
 
Example #25
Source File: LoggerTest.java    From logging-log4j2 with Apache License 2.0 5 votes vote down vote up
@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);
}
 
Example #26
Source File: AsyncLoggerConfig.java    From logging-log4j2 with Apache License 2.0 5 votes vote down vote up
/**
 * Factory method to create a LoggerConfig.
 *
 * @param additivity True if additive, false otherwise.
 * @param level The Level to be associated with the Logger.
 * @param loggerName The name of the Logger.
 * @param includeLocation "true" if location should be passed downstream
 * @param refs An array of Appender names.
 * @param properties Properties to pass to the Logger.
 * @param config The Configuration.
 * @param filter A Filter.
 * @return A new LoggerConfig.
 * @since 3.0
 */
@PluginFactory
public static LoggerConfig createLogger(
        @PluginAttribute(defaultBoolean = true) final boolean additivity,
        @PluginAttribute final Level level,
        @Required(message = "Loggers cannot be configured without a name") @PluginAttribute("name") final String loggerName,
        @PluginAttribute final String includeLocation,
        @PluginElement final AppenderRef[] refs,
        @PluginElement final Property[] properties,
        @PluginConfiguration final Configuration config,
        @PluginElement final Filter filter) {
    final String name = loggerName.equals(ROOT) ? Strings.EMPTY : loggerName;
    return new AsyncLoggerConfig(name, Arrays.asList(refs), filter, level, additivity, properties, config,
            includeLocation(includeLocation));
}
 
Example #27
Source File: PurpleDatamodelTest.java    From hmftools with GNU General Public License v3.0 5 votes vote down vote up
@NotNull
public static ImmutableStructuralVariantImpl.Builder createStructuralVariantSingleBreakend(@NotNull final String startChromosome,
       final long startPosition, double startVaf) {
    return ImmutableStructuralVariantImpl.builder()
            .id(Strings.EMPTY)
            .insertSequence(Strings.EMPTY)
            .insertSequenceAlignments(Strings.EMPTY)
            .qualityScore(0)
            .recovered(false)
            .type(StructuralVariantType.BND)
            .start(createStartLeg(startChromosome, startPosition, StructuralVariantType.BND).alleleFrequency(startVaf).build())
            .startContext(dummyContext())
            .imprecise(false);
}
 
Example #28
Source File: LoggerTest.java    From logging-log4j2 with Apache License 2.0 5 votes vote down vote up
@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);
}
 
Example #29
Source File: OperationLogAspect.java    From we-cmdb with Apache License 2.0 5 votes vote down vote up
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;
}
 
Example #30
Source File: StatusLogger.java    From logging-log4j2 with Apache License 2.0 5 votes vote down vote up
private StatusLogger(final String name, final MessageFactory messageFactory) {
    super(name, messageFactory);
    final String dateFormat = PROPS.getStringProperty(STATUS_DATE_FORMAT, Strings.EMPTY);
    final boolean showDateTime = !Strings.isEmpty(dateFormat);
    this.logger = new SimpleLogger("StatusLogger", Level.ERROR, false, true, showDateTime, false,
            dateFormat, messageFactory, PROPS, System.err);
    this.listenersLevel = Level.toLevel(DEFAULT_STATUS_LEVEL, Level.WARN).intLevel();

    // LOG4J2-1813 if system property "log4j2.debug" is defined, print all status logging
    if (isDebugPropertyEnabled()) {
        logger.setLevel(Level.TRACE);
    }
}