Example usage for java.util Set clear

List of usage examples for java.util Set clear

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Introduction

In this page you can find the example usage for java.util Set clear.

Prototype

void clear();

Source Link

Document

Removes all of the elements from this set (optional operation).

Usage

From source file:com.netflix.genie.core.jpa.services.JpaClusterServiceImplIntegrationTests.java

/**
 * Test the get clusters method./*from   w  w w  .ja va  2  s  .  c om*/
 */
@Test
public void testGetClustersByTags() {
    final Set<String> tags = Sets.newHashSet("prod");
    Page<Cluster> clusters = this.service.getClusters(null, null, tags, null, null, PAGE);
    Assert.assertEquals(1, clusters.getNumberOfElements());
    Assert.assertEquals(CLUSTER_1_ID,
            clusters.getContent().get(0).getId().orElseThrow(IllegalArgumentException::new));

    tags.clear();
    tags.add("hive");
    clusters = this.service.getClusters(null, null, tags, null, null, PAGE);
    Assert.assertEquals(2, clusters.getNumberOfElements());
    Assert.assertEquals(CLUSTER_2_ID,
            clusters.getContent().get(0).getId().orElseThrow(IllegalArgumentException::new));
    Assert.assertEquals(CLUSTER_1_ID,
            clusters.getContent().get(1).getId().orElseThrow(IllegalArgumentException::new));

    tags.add("somethingThatWouldNeverReallyExist");
    clusters = this.service.getClusters(null, null, tags, null, null, PAGE);
    Assert.assertTrue(clusters.getContent().isEmpty());

    tags.clear();
    clusters = this.service.getClusters(null, null, tags, null, null, PAGE);
    Assert.assertEquals(2, clusters.getNumberOfElements());
    Assert.assertEquals(CLUSTER_2_ID,
            clusters.getContent().get(0).getId().orElseThrow(IllegalArgumentException::new));
    Assert.assertEquals(CLUSTER_1_ID,
            clusters.getContent().get(1).getId().orElseThrow(IllegalArgumentException::new));
}

From source file:gaffer.accumulostore.operation.spark.handler.GetJavaRDDOfElementsHandlerTest.java

@Test
public void checkGetCorrectElementsInRDDForEdgeSeed() throws OperationException, IOException {
    final Graph graph1 = new Graph.Builder()
            .addSchema(getClass().getResourceAsStream("/schema/dataSchema.json"))
            .addSchema(getClass().getResourceAsStream("/schema/dataTypes.json"))
            .addSchema(getClass().getResourceAsStream("/schema/storeTypes.json"))
            .storeProperties(getClass().getResourceAsStream("/store.properties")).build();

    final List<Element> elements = new ArrayList<>();
    for (int i = 0; i < 10; i++) {
        final Entity entity = new Entity(ENTITY_GROUP);
        entity.setVertex("" + i);

        final Edge edge1 = new Edge(EDGE_GROUP);
        edge1.setSource("" + i);
        edge1.setDestination("B");
        edge1.setDirected(false);/*from  w w  w .j a v  a2s  . c om*/
        edge1.putProperty("count", 2);

        final Edge edge2 = new Edge(EDGE_GROUP);
        edge2.setSource("" + i);
        edge2.setDestination("C");
        edge2.setDirected(false);
        edge2.putProperty("count", 4);

        elements.add(edge1);
        elements.add(edge2);
        elements.add(entity);
    }
    final User user = new User();
    graph1.execute(new AddElements(elements), user);

    final SparkConf sparkConf = new SparkConf().setMaster("local")
            .setAppName("testCheckGetCorrectElementsInJavaRDDForEdgeSeed")
            .set("spark.serializer", "org.apache.spark.serializer.KryoSerializer")
            .set("spark.kryo.registrator", "gaffer.serialisation.kryo.Registrator")
            .set("spark.driver.allowMultipleContexts", "true");
    final JavaSparkContext sparkContext = new JavaSparkContext(sparkConf);

    // Create Hadoop configuration and serialise to a string
    final Configuration configuration = new Configuration();
    final ByteArrayOutputStream baos = new ByteArrayOutputStream();
    configuration.write(new DataOutputStream(baos));
    final String configurationString = new String(baos.toByteArray(), CommonConstants.UTF_8);

    // Check get correct edges for EdgeSeed 1 -> B
    GetJavaRDDOfElements<EdgeSeed> rddQuery = new GetJavaRDDOfElements.Builder<EdgeSeed>()
            .javaSparkContext(sparkContext).seeds(Collections.singleton(new EdgeSeed("1", "B", false)))
            .setIncludeEdges(GetOperation.IncludeEdgeType.ALL).setIncludeEntities(false).build();
    rddQuery.addOption(AbstractGetRDDOperationHandler.HADOOP_CONFIGURATION_KEY, configurationString);
    JavaRDD<Element> rdd = graph1.execute(rddQuery, user);
    if (rdd == null) {
        fail("No RDD returned");
    }
    final Set<Element> results = new HashSet<>();
    results.addAll(rdd.collect());
    final Set<Element> expectedElements = new HashSet<>();
    final Edge edge1B = new Edge(EDGE_GROUP);
    edge1B.setSource("1");
    edge1B.setDestination("B");
    edge1B.setDirected(false);
    edge1B.putProperty("count", 2);
    expectedElements.add(edge1B);
    assertEquals(expectedElements, results);

    // Check get entity for 1 when query for 1 -> B and specify entities only
    rddQuery = new GetJavaRDDOfElements.Builder<EdgeSeed>().javaSparkContext(sparkContext)
            .seeds(Collections.singleton(new EdgeSeed("1", "B", false))).setIncludeEntities(true)
            .setIncludeEdges(GetOperation.IncludeEdgeType.NONE).build();
    rddQuery.addOption(AbstractGetRDDOperationHandler.HADOOP_CONFIGURATION_KEY, configurationString);
    rdd = graph1.execute(rddQuery, user);
    if (rdd == null) {
        fail("No RDD returned");
    }
    results.clear();
    results.addAll(rdd.collect());
    expectedElements.clear();
    final Entity entity1 = new Entity(ENTITY_GROUP);
    entity1.setVertex("1");
    expectedElements.add(entity1);
    assertEquals(expectedElements, results);

    // Check get correct edges for 1 -> B when specify edges only
    rddQuery = new GetJavaRDDOfElements.Builder<EdgeSeed>().javaSparkContext(sparkContext)
            .seeds(Collections.singleton(new EdgeSeed("1", "B", false)))
            .view(new View.Builder().edge(EDGE_GROUP).build()).setIncludeEntities(false)
            .setIncludeEdges(GetOperation.IncludeEdgeType.ALL).build();
    rddQuery.addOption(AbstractGetRDDOperationHandler.HADOOP_CONFIGURATION_KEY, configurationString);
    rdd = graph1.execute(rddQuery, user);
    if (rdd == null) {
        fail("No RDD returned");
    }
    results.clear();
    results.addAll(rdd.collect());
    expectedElements.clear();
    expectedElements.add(edge1B);
    assertEquals(expectedElements, results);

    // Check get correct edges for 1 -> B and 5 -> C
    Set<EdgeSeed> seeds = new HashSet<>();
    seeds.add(new EdgeSeed("1", "B", false));
    seeds.add(new EdgeSeed("5", "C", false));
    rddQuery = new GetJavaRDDOfElements.Builder<EdgeSeed>().javaSparkContext(sparkContext)
            .setIncludeEntities(false).seeds(seeds).build();
    rddQuery.addOption(AbstractGetRDDOperationHandler.HADOOP_CONFIGURATION_KEY, configurationString);
    rdd = graph1.execute(rddQuery, user);
    if (rdd == null) {
        fail("No RDD returned");
    }
    results.clear();
    results.addAll(rdd.collect());
    final Edge edge5C = new Edge(EDGE_GROUP);
    edge5C.setSource("5");
    edge5C.setDestination("C");
    edge5C.setDirected(false);
    edge5C.putProperty("count", 4);
    expectedElements.clear();
    expectedElements.add(edge1B);
    expectedElements.add(edge5C);
    assertEquals(expectedElements, results);

    sparkContext.stop();
}

From source file:control.ExperimentImportController.java

protected void initMissingInfoListener(SamplePreparator prep, Map<String, List<String>> missingCategoryToValues,
        Map<String, List<String>> catToVocabulary) {
    extCodeToBarcode = new HashMap<String, String>();

    // TODO where is this added? does it need to be added?
    ProjectInformationComponent projectInfoComponent = new ProjectInformationComponent(vocabs.getSpaces(),
            vocabs.getPeople().keySet());

    ValueChangeListener missingInfoFilledListener = new ValueChangeListener() {

        @Override/*from  ww  w .  j  ava 2  s.c  o m*/
        public void valueChange(ValueChangeEvent event) {
            boolean overflow = false;
            boolean infoComplete = questionaire.isValid();
            boolean samplesToRegister = false;
            if (infoComplete) {
                List<SampleSummaryBean> summaries = prep.getSummary();
                for (SampleSummaryBean b : summaries) {
                    String cat = "";
                    if (b.getSampleType().contains("Source"))
                        cat = "Species";
                    else if (b.getSampleType().contains("Sample Extract"))
                        cat = "Tissues";
                    else if (b.getSampleType().contains("Preparations"))
                        cat = "Analytes";
                    if (missingCategoryToValues.containsKey(cat)) {
                        String val = b.getFullSampleContent();
                        List<String> newVal = new ArrayList<String>();
                        for (String v : val.split(", ")) {
                            v = v.trim();
                            String translation = questionaire.getVocabularyLabelForValue(cat, v);
                            if (translation == null)
                                translation = reverseTissueMap.get(v);
                            if (translation == null)
                                translation = v;
                            newVal.add(translation);
                        }
                        b.setSampleContent(StringUtils.join(newVal, ", "));
                    }
                }
                view.setSummary(summaries);
                projectInfo = projectInfoComponent.getProjectInfo();
                String space = questionaire.getSpaceCode();
                String project = questionaire.getProjectCode();
                try {
                    countExistingOpenbisEntities(space, project);
                } catch (TooManySamplesException e1) {
                    // TODO Auto-generated catch block
                    overflow = true;
                }

                int entityNum = firstFreeEntityID;
                nextBarcode = null;

                List<List<ISampleBean>> processed = prep.getProcessed();
                Set<String> msCodes = new HashSet<String>();
                dnaSampleCodeToMHCType = new HashMap<String, MHCTyping>();
                Map<String, String> specialExpToExpCode = new HashMap<String, String>();
                for (List<ISampleBean> level : processed) {
                    String type = level.get(0).getType();
                    String exp = "";
                    if (!type.equals("Q_MS_RUN") && !type.equals("Q_MHC_LIGAND_EXTRACT"))
                        exp = getNextExperiment(project);
                    // list of existing samples to be removed before registration
                    List<ISampleBean> existing = new ArrayList<ISampleBean>();
                    for (ISampleBean b : level) {
                        TSVSampleBean t = (TSVSampleBean) b;
                        String extID = (String) t.getMetadata().get("Q_EXTERNALDB_ID");
                        if (extIDToSample.containsKey(extID)) {
                            existing.add(t);
                            extCodeToBarcode.put(extID, extIDToSample.get(extID).getCode());
                        } else {
                            t.setProject(project);
                            t.setSpace(space);
                            String code = "";
                            Map<String, Object> props = t.getMetadata();
                            switch (t.getType()) {
                            case "Q_BIOLOGICAL_ENTITY":
                                code = project + "ENTITY-" + entityNum;
                                String newVal = questionaire.getVocabularyLabelForValue("Species",
                                        props.get("Q_NCBI_ORGANISM"));
                                props.put("Q_NCBI_ORGANISM", taxMap.get(newVal));
                                entityNum++;
                                break;
                            case "Q_BIOLOGICAL_SAMPLE":
                                try {
                                    incrementOrCreateBarcode(project);
                                } catch (TooManySamplesException e) {
                                    overflow = true;
                                }
                                code = nextBarcode;
                                newVal = questionaire.getVocabularyLabelForValue("Tissues",
                                        props.get("Q_PRIMARY_TISSUE"));
                                props.put("Q_PRIMARY_TISSUE", tissueMap.get(newVal));
                                break;
                            case "Q_TEST_SAMPLE":
                                try {
                                    incrementOrCreateBarcode(project);
                                } catch (TooManySamplesException e) {
                                    overflow = true;
                                }
                                code = nextBarcode;
                                newVal = questionaire.getVocabularyLabelForValue("Analytes",
                                        props.get("Q_SAMPLE_TYPE"));
                                props.put("Q_SAMPLE_TYPE", newVal);
                                if (getImportType().equals(DesignType.MHC_Ligands_Finished)) {
                                    if ("DNA".equals(newVal)) {
                                        List<String> c1 = (List<String>) props.get("MHC_I");
                                        List<String> c2 = (List<String>) props.get("MHC_II");
                                        dnaSampleCodeToMHCType.put(code, new MHCTyping(c1, c2));
                                        props.remove("MHC_I");
                                        props.remove("MHC_II");
                                    }
                                }
                                break;
                            case "Q_MHC_LIGAND_EXTRACT":
                                try {
                                    incrementOrCreateBarcode(project);
                                } catch (TooManySamplesException e) {
                                    overflow = true;
                                }
                                code = nextBarcode;
                                if (!specialExpToExpCode.containsKey(t.getExperiment())) {
                                    specialExpToExpCode.put(t.getExperiment(), getNextExperiment(project));
                                }
                                exp = specialExpToExpCode.get(t.getExperiment());
                                break;
                            case "Q_MS_RUN":
                                // get ms experiment to connect it correctly
                                if (!specialExpToExpCode.containsKey(t.getExperiment())) {
                                    specialExpToExpCode.put(t.getExperiment(), getNextExperiment(project));
                                }
                                exp = specialExpToExpCode.get(t.getExperiment());
                                // get parent sample for code
                                String parentExtID = t.fetchParentIDs().get(0);
                                String parentCode = extCodeToBarcode.get(parentExtID);// .getCode();
                                int msRun = 1;
                                code = "";
                                while (code.isEmpty() || msCodes.contains(code)) {
                                    code = "MS" + Integer.toString(msRun) + parentCode;
                                    msRun++;
                                }
                                msCodes.add(code);
                                break;
                            }
                            t.setExperiment(exp);
                            t.setCode(code);
                            extCodeToBarcode.put((String) props.get("Q_EXTERNALDB_ID"), code);// t);
                            List<String> parents = t.fetchParentIDs();
                            t.setParents("");
                            for (String parentExtID : parents) {
                                if (extCodeToBarcode.containsKey(parentExtID))
                                    t.addParent(extCodeToBarcode.get(parentExtID));// .getCode());
                                else
                                    logger.warn(
                                            "Parent could not be translated, because no ext id to code mapping was found for ext id "
                                                    + parentExtID);
                            }
                        }
                    }
                    // remove existing samples from registration process
                    level.removeAll(existing);
                    samplesToRegister |= !level.isEmpty();
                }
                fixSpecialExperiments(specialExpToExpCode);
                view.setProcessed(processed);
            }
            view.setRegEnabled(infoComplete && samplesToRegister && !overflow);
            if (infoComplete) {
                if (!samplesToRegister) {
                    Styles.notification("Samples already exist.",
                            "Every Analyte ID was already found in existing samples of this project.",
                            NotificationType.DEFAULT);
                }
                if (overflow) {
                    Styles.notification("Too many samples.",
                            "This experiment exceeds the maximum number of samples for one project.",
                            NotificationType.ERROR);
                }
            }
        }

        private void fixSpecialExperiments(Map<String, String> specialExpToExpCode) {
            Set<String> codes = new HashSet<String>();
            if (mhcProperties != null) {
                codes.addAll(mhcProperties.keySet());
                for (String code : codes) {
                    mhcProperties.put(specialExpToExpCode.get(code), mhcProperties.get(code));
                    mhcProperties.remove(code);
                }
            }
            codes.clear();
            if (msProperties != null) {
                codes.addAll(msProperties.keySet());
                for (String code : codes) {
                    msProperties.put(specialExpToExpCode.get(code), msProperties.get(code));
                    msProperties.remove(code);
                }
            }
        }
    };
    questionaire = view.initMissingInfoComponent(projectInfoComponent, missingCategoryToValues, catToVocabulary,
            missingInfoFilledListener);
    // view.addComponent(questionaire);

    // add project code validators
    TextField f = projectInfoComponent.getProjectField();
    CompositeValidator vd = new CompositeValidator();
    RegexpValidator p = new RegexpValidator("Q[A-Xa-x0-9]{4}",
            "Project must have length of 5, start with Q and not contain Y or Z");
    vd.addValidator(p);
    vd.addValidator(new ProjectNameValidator(openbis));
    f.addValidator(vd);
    f.setImmediate(true);
    f.setValidationVisible(true);

    FocusListener fListener = new FocusListener() {
        private static final long serialVersionUID = 8721337946386845992L;

        @Override
        public void focus(FocusEvent event) {
            TextField pr = projectInfoComponent.getProjectField();
            if (!pr.isValid() || pr.isEmpty()) {
                // new project selected...keep generating codes until one is valid
                projectInfoComponent.tryEnableCustomProject(generateUnusedProjectCode());
            }
        }
    };
    projectInfoComponent.getProjectField().addFocusListener(fListener);

    Button.ClickListener projCL = new Button.ClickListener() {

        /**
         * 
         */
        private static final long serialVersionUID = -6646294420820222646L;

        @Override
        public void buttonClick(ClickEvent event) {
            String existingProject = (String) projectInfoComponent.getProjectBox().getValue();
            if (existingProject == null || existingProject.isEmpty()) {
                projectInfoComponent.tryEnableCustomProject(generateUnusedProjectCode());
            }
        }
    };
    projectInfoComponent.getProjectReloadButton().addClickListener(projCL);

    questionaire.getSpaceBox().addValueChangeListener(new ValueChangeListener() {

        @Override
        public void valueChange(ValueChangeEvent event) {
            questionaire.resetProjects();
            String space = questionaire.getSpaceCode();
            if (space != null) {
                List<String> projects = new ArrayList<String>();
                for (Project p : openbis.getProjectsOfSpace(space)) {
                    String code = p.getCode();
                    // String name = dbm.getProjectName("/" + space + "/" + code);
                    // if (name != null && name.length() > 0) {
                    // if (name.length() >= 80)
                    // name = name.substring(0, 80) + "...";
                    // code += " (" + name + ")";
                    // }
                    projects.add(code);
                }
                questionaire.setProjectCodes(projects);
            }
        }
    });
}

From source file:org.asqatasun.service.command.AuditCommandImpl.java

@Override
public void process() {
    audit = auditDataService.getAuditWithTest(audit.getId());
    if (!audit.getStatus().equals(AuditStatus.PROCESSING)) {
        LOGGER.warn(//from  w ww .  j  av a  2  s  . c o  m
                new StringBuilder(AUDIT_STATUS_IS_LOGGER_STR).append(audit.getStatus()).append(WHILE_LOGGER_STR)
                        .append(AuditStatus.PROCESSING).append(WAS_REQUIRED_LOGGER_STR).toString());
        return;
    }
    if (LOGGER.isInfoEnabled()) {
        LOGGER.info("Processing " + audit.getSubject().getURL());
    }
    // debug tools
    Date beginProcessDate = null;
    Date endProcessDate = null;
    Date endPersistDate;
    Long persistenceDuration = (long) 0;

    Long i = (long) 0;
    Long webResourceId = audit.getSubject().getId();
    Long nbOfContent = contentDataService.getNumberOfSSPFromWebResource(audit.getSubject(), HttpStatus.SC_OK);

    Set<ProcessResult> processResultSet = new HashSet<>();

    while (i.compareTo(nbOfContent) < 0) {
        if (LOGGER.isDebugEnabled()) {
            LOGGER.debug(new StringBuilder("Processing from ").append(i).append(TO_LOGGER_STR)
                    .append(i + processingTreatmentWindow).append("for ").append(audit.getSubject().getURL())
                    .toString());
            beginProcessDate = Calendar.getInstance().getTime();
        }
        Collection<Content> contentList = contentDataService
                .getSSPWithRelatedContentFromWebResource(webResourceId, i, processingTreatmentWindow, false);
        processResultSet.clear();
        processResultSet.addAll(processorService.process(contentList, audit.getTestList()));
        for (ProcessResult processResult : processResultSet) {
            processResult.setGrossResultAudit(audit);
        }

        if (LOGGER.isDebugEnabled()) {
            endProcessDate = Calendar.getInstance().getTime();
            LOGGER.debug(new StringBuilder("Processing of ").append(processingTreatmentWindow)
                    .append(" elements took ").append(endProcessDate.getTime() - beginProcessDate.getTime())
                    .append(MS_LOGGER_STR).append("for ").append(audit.getSubject().getURL()).toString());
        }
        if (LOGGER.isDebugEnabled()) {
            for (Content content : contentList) {
                LOGGER.debug("Persisting result for page " + content.getURI());
            }
        }
        processResultDataService.saveOrUpdate(processResultSet);
        if (LOGGER.isDebugEnabled()) {
            endPersistDate = Calendar.getInstance().getTime();
            LOGGER.debug(new StringBuilder("Persist processing of ").append(processingTreatmentWindow)
                    .append(" elements took ").append(endPersistDate.getTime() - endProcessDate.getTime())
                    .append(MS_LOGGER_STR).append("for ").append(audit.getSubject().getURL()).toString());
            persistenceDuration = persistenceDuration + (endPersistDate.getTime() - endProcessDate.getTime());
        }
        i = i + processingTreatmentWindow;
        System.gc();
    }

    if (LOGGER.isDebugEnabled()) {
        LOGGER.debug(new StringBuilder("Application spent ").append(persistenceDuration)
                .append(" ms to write in Disk while processing").toString());
    }

    if (processResultDataService.getNumberOfGrossResultFromAudit(audit) > 0) {
        setStatusToAudit(AuditStatus.CONSOLIDATION);
    } else {
        LOGGER.error("Audit has no gross result");
        setStatusToAudit(AuditStatus.ERROR);
    }
    if (LOGGER.isInfoEnabled()) {
        LOGGER.info(audit.getSubject().getURL() + " has been processed");
    }
}

From source file:tools.xor.logic.DefaultUpdate4Set.java

public void testCase22() {
    C = taskDao.findById(C.getId());// w  ww . j  a v a  2  s  .  c  o m
    Set<Task> children = new HashSet<Task>();
    children.add(C);

    // Setup the bi-directional link
    A = taskDao.findById(A.getId());
    A.setTaskChildren(children);
    C.setTaskParent(A);
    taskDao.saveOrUpdate(A);

    A = (Task) aggregateService.read(A, getSettings());
    C = A.getTaskChildren().iterator().next();
    assert (C.getTaskParent() != null);

    // Remove child1 and add child2
    children = A.getTaskChildren();
    children.clear();
    children.add(B);
    children.add(D);
    A.setAlternateTask(C);
    C.setTaskParent(null);
    B.setTaskParent(A);
    D.setTaskParent(A);

    Settings settings = getSettings();
    settings.setInterceptor(new Interceptor() {
        // check the number of actions in each object
        private void checkNumber(BusinessObject dataObject, List<Executable> actions) {
            Task task = (Task) dataObject.getInstance();
            if (task.getName().equals(A_NAME)) {
                assert (actions.size() == 1); // SetUpdateAction
                assert (SetUpdateAction.class.isAssignableFrom(actions.get(0).getClass()));
            } else
                assert (actions.size() == 2);
        }

        @Override
        public void preBiDirActionStage(Map<PropertyKey, List<Executable>> actions) {
            // check the action queue to see if the correct number of actions are present
            assert (actions.size() == 4);

            for (Map.Entry<PropertyKey, List<Executable>> entry : actions.entrySet())
                checkNumber(entry.getKey().getDataObject(), entry.getValue());
        }
    });
    A = (Task) aggregateService.update(A, settings);

    A = taskDao.findById(A.getId());
    B = taskDao.findById(B.getId());
    D = taskDao.findById(D.getId());

    A = (Task) aggregateService.read(A, getSettings());
    B = (Task) aggregateService.read(B, getSettings());
    D = (Task) aggregateService.read(D, getSettings());

    assert (A.getTaskChildren() != null && A.getTaskChildren().size() == 2);
}

From source file:org.carewebframework.maven.plugin.theme.CSSTransform.java

@Override
public void process() throws Exception {
    int c = 0;/*w  w  w  . j  a v a2 s. c o  m*/
    int state = 0;
    StringBuilder sb = new StringBuilder();
    Set<String> matches = new HashSet<String>();
    Map<String, String> refMap = new LinkedHashMap<String, String>();
    Map<String, String> styles = new HashMap<String, String>();
    String prop = null;
    checkForMatch("@before@", matches, refMap);

    while (c != -1) {
        c = inputStream.read();

        if (c == -1) {
            state = -1;
        } else {
            outputStream.write(c);
        }

        switch (state) {
        case -1: // Process template
            for (String match : matches) {
                String template = refMap.get(match);

                if (!template.contains(DELIM)) {
                    continue;
                }

                for (Entry<String, String> entry : styles.entrySet()) {
                    String replace = DELIM + entry.getKey() + DELIM;
                    template = template.replace(replace, entry.getValue());
                }

                refMap.put(match, template);
            }

            matches.clear();
            styles.clear();

            if (c == -1) {
                continue;
            }

            state = 0;
            // Fall through intended

        case 0: // Baseline
            switch (c) {
            case '/': // Possible comment start
                state = 1;
                break;

            case '<': // Directive start
                state = 10;
                break;

            case '{': // Declaration block
                state = 20;
                break;

            case ',': // Selector separator
                break;

            case '}': // Don't know why these occur, but ignore them.
                continue;

            default:
                sb.append((char) c);
                continue;
            }

            checkForMatch(sb.toString(), matches, refMap);
            sb.setLength(0);
            break;

        case 1: // Possible comment
            state = c == '*' ? 2 : 0;
            break;

        case 2: // Possible comment end
            state = c == '*' ? 3 : state;
            break;

        case 3: // Comment end
            state = c == '/' ? 0 : c == '*' ? state : 2;
            break;

        case 10: // Directive end
            state = c == '>' ? 0 : state;
            break;

        case 20: // Declaration block
            switch (c) {
            case '}': // End block
                state = -1;
                break;

            case ':': // Start of property value
                prop = sb.toString().trim();
                sb.setLength(0);
                state = 30;
                break;

            default: // Build property name
                sb.append((char) c);
                break;
            }
            break;

        case 30: // Property value
            switch (c) {
            case ';': // Property separator
            case '}': // Block terminator
                styles.put(prop, sb.toString());
                sb.setLength(0);
                state = c == ';' ? 20 : -1;
                break;

            default: // Build property value
                sb.append((char) c);
                break;
            }
            break;
        }

    }

    checkForMatch("@after@", matches, defMap);
    writeMap(refMap);
    writeMap(defMap);

    if (!srcMap.isEmpty()) {
        mojo.getLog().warn("The following entries failed to match and were ignored:");

        for (Entry<String, String> entry : srcMap.entrySet()) {
            mojo.getLog().warn("   " + entry);
        }
    }
}

From source file:gov.nih.nci.ispy.web.taglib.CorrScatterPlotTag.java

public int doStartTag() {
    chart = null;//  w  w w  .j av  a2 s  .  co m
    plotPoints.clear();

    ServletRequest request = pageContext.getRequest();
    HttpSession session = pageContext.getSession();
    Object o = request.getAttribute(beanName);
    JspWriter out = pageContext.getOut();
    ServletResponse response = pageContext.getResponse();

    try {
        //retrieve the Finding from cache and build the list of PCAData points
        ISPYCorrelationFinding corrFinding = (ISPYCorrelationFinding) businessTierCache
                .getSessionFinding(session.getId(), taskId);

        Collection<ClinicalFactorType> clinicalFactors = new ArrayList<ClinicalFactorType>();
        List<String> sampleIds = new ArrayList<String>();

        List<DataPoint> points = corrFinding.getDataPoints();

        ClinicalDataService cqs = ClinicalDataServiceFactory.getInstance();
        IdMapperFileBasedService idMapper = IdMapperFileBasedService.getInstance();

        List<ISPYPlotPoint> plotPoints = new ArrayList<ISPYPlotPoint>();
        ISPYPlotPoint pp;
        SampleInfo si;
        ISPYclinicalDataQueryDTO dto;
        Set<String> sampleHolder = new HashSet<String>(); //set just holds one entry need this for the dto
        Set<PatientData> dataHolder = new HashSet<PatientData>();
        PatientData pd = null;
        for (DataPoint p : points) {
            pp = new ISPYPlotPoint(p.getId());
            pp.setX(p.getX());
            pp.setY(p.getY());
            pp.setZ(p.getZ());

            String patientId = null;

            if (corrFinding.isSampleBased()) {
                si = idMapper.getSampleInfoForLabtrackId(p.getId());
                if (si != null) {
                    pp.setSampleInfo(si);
                    patientId = si.getISPYId();
                } else {
                    logger.warn("Could not get sample info for DataPoint=" + p.getId());
                }
            } else if (corrFinding.isPatientBased()) {
                patientId = p.getId();
            }

            if (patientId != null) {
                dto = new ISPYclinicalDataQueryDTO();
                sampleHolder.clear();
                sampleHolder.add(patientId);
                dto.setRestrainingSamples(sampleHolder);
                dataHolder.clear();
                dataHolder = cqs.getClinicalData(dto);

                if (dataHolder.size() == 1) {
                    Iterator i = dataHolder.iterator();
                    pd = (PatientData) i.next();
                    pp.setPatientData(pd);
                } else {
                    logger.error("Internal Error. Did not get back correct patient data for  patientId="
                            + patientId);
                }
            }

            plotPoints.add(pp);
        }

        ISPYCorrelationScatterPlot plot = new ISPYCorrelationScatterPlot(plotPoints,
                corrFinding.getGroup1Name(), corrFinding.getGroup2Name(), corrFinding.getContinuousType1(),
                corrFinding.getContinuousType2(), corrFinding.getCorrelationValue(),
                ColorByType.valueOf(ColorByType.class, colorBy.toUpperCase()));
        chart = plot.getChart();
        ISPYImageFileHandler imageHandler = new ISPYImageFileHandler(session.getId(), "png", 650, 600);
        //The final complete path to be used by the webapplication
        String finalPath = imageHandler.getSessionTempFolder();
        String finalURLpath = imageHandler.getFinalURLPath();
        /*
         * Create the actual charts, writing it to the session temp folder
        */
        ChartRenderingInfo info = new ChartRenderingInfo(new StandardEntityCollection());
        String mapName = imageHandler.createUniqueMapName();
        //PrintWriter writer = new PrintWriter(new FileWriter(mapName));
        ChartUtilities.writeChartAsPNG(new FileOutputStream(finalPath), chart, 650, 600, info);
        //ImageMapUtil.writeBoundingRectImageMap(writer,"PCAimageMap",info,true);
        //writer.close();

        /*   This is here to put the thread into a loop while it waits for the
         *   image to be available.  It has an unsophisticated timer but at 
         *   least it is something to avoid an endless loop.
         **/
        boolean imageReady = false;
        int timeout = 1000;
        FileInputStream inputStream = null;
        while (!imageReady) {
            timeout--;
            try {
                inputStream = new FileInputStream(finalPath);
                inputStream.available();
                imageReady = true;
                inputStream.close();
            } catch (IOException ioe) {
                imageReady = false;
                if (inputStream != null) {
                    inputStream.close();
                }
            }
            if (timeout <= 1) {

                break;
            }
        }

        out.print(ImageMapUtil.getBoundingRectImageMapTag(mapName, true, info));
        finalURLpath = finalURLpath.replace("\\", "/");
        long randomness = System.currentTimeMillis(); //prevent image caching
        out.print("<img id=\"geneChart\" name=\"geneChart\" src=\"" + finalURLpath + "?" + randomness
                + "\" usemap=\"#" + mapName + "\" border=\"0\" />");

        //(imageHandler.getImageTag(mapFileName));

    } catch (IOException e) {
        logger.error(e);
    } catch (Exception e) {
        StringWriter sw = new StringWriter();
        PrintWriter pw = new PrintWriter(sw);
        e.printStackTrace(pw);
        logger.error(sw.toString());
    } catch (Throwable t) {
        logger.error(t);
    }

    return EVAL_BODY_INCLUDE;
}

From source file:com.google.gwt.emultest.java.util.TreeSetTest.java

/**
 * Test method for 'java.util.Set.clear()'.
 *
 * @see java.util.Set#clear()//from   ww w . j av a 2s  .  c  o m
 */
public void testClear_throwsUnsupportedOperationException() {
    Set<E> set = createSet();
    if (!isClearSupported) {
        try {
            set.clear();
            fail("expected exception");
        } catch (UnsupportedOperationException e) {
            // expected outcome
        }
    }
}

From source file:org.apache.camel.util.IntrospectionSupport.java

private static Set<Method> findSetterMethods(TypeConverter typeConverter, Class<?> clazz, String name,
        Object value) {/*from w  ww  .ja  va 2 s.c o m*/
    Set<Method> candidates = new LinkedHashSet<Method>();

    // Build the method name.
    name = "set" + ObjectHelper.capitalize(name);
    while (clazz != Object.class) {
        // Since Object.class.isInstance all the objects,
        // here we just make sure it will be add to the bottom of the set.
        Method objectSetMethod = null;
        Method[] methods = clazz.getMethods();
        for (Method method : methods) {
            Class<?> params[] = method.getParameterTypes();
            if (method.getName().equals(name) && params.length == 1) {
                Class<?> paramType = params[0];
                if (paramType.equals(Object.class)) {
                    objectSetMethod = method;
                } else if (typeConverter != null || isSetter(method) || paramType.isInstance(value)) {
                    candidates.add(method);
                }
            }
        }
        if (objectSetMethod != null) {
            candidates.add(objectSetMethod);
        }
        clazz = clazz.getSuperclass();
    }

    if (candidates.isEmpty()) {
        return candidates;
    } else if (candidates.size() == 1) {
        // only one
        return candidates;
    } else {
        // find the best match if possible
        if (LOG.isTraceEnabled()) {
            LOG.trace("Found " + candidates.size() + " suitable setter methods for setting " + name);
        }
        // prefer to use the one with the same instance if any exists
        for (Method method : candidates) {
            if (method.getParameterTypes()[0].isInstance(value)) {
                if (LOG.isTraceEnabled()) {
                    LOG.trace("Method " + method
                            + " is the best candidate as it has parameter with same instance type");
                }
                // retain only this method in the answer
                candidates.clear();
                candidates.add(method);
                return candidates;
            }
        }
        // fallback to return what we have found as candidates so far
        return candidates;
    }
}

From source file:org.apache.hadoop.hdfs.server.blockmanagement.TestReplicationPolicyWithNodeGroup.java

/**
 * In this testcase, client is dataNodes[0], but the dataNodes[1] is
 * not allowed to be chosen. So the 1st replica should be
 * placed on dataNodes[0], the 2nd replica should be placed on a different
 * rack, the 3rd should be on same rack as the 2nd replica but in different
 * node group, and the rest should be placed on a third rack.
 * @throws Exception/*from ww  w .ja va2 s.  c o m*/
 */
@Test
public void testChooseTarget2() throws Exception {
    DatanodeStorageInfo[] targets;
    BlockPlacementPolicyDefault repl = (BlockPlacementPolicyDefault) replicator;
    List<DatanodeStorageInfo> chosenNodes = new ArrayList<DatanodeStorageInfo>();

    Set<Node> excludedNodes = new HashSet<Node>();
    excludedNodes.add(dataNodes[1]);
    targets = repl.chooseTarget(filename, 4, dataNodes[0], chosenNodes, false, excludedNodes, BLOCK_SIZE,
            TestBlockStoragePolicy.DEFAULT_STORAGE_POLICY);
    assertEquals(targets.length, 4);
    assertEquals(storages[0], targets[0]);

    assertTrue(cluster.isNodeGroupAware());
    // Make sure no replicas are on the same nodegroup 
    for (int i = 1; i < 4; i++) {
        assertFalse(isOnSameNodeGroup(targets[0], targets[i]));
    }
    assertTrue(isOnSameRack(targets[1], targets[2]) || isOnSameRack(targets[2], targets[3]));
    assertFalse(isOnSameRack(targets[1], targets[3]));

    excludedNodes.clear();
    chosenNodes.clear();
    excludedNodes.add(dataNodes[1]);
    chosenNodes.add(storages[2]);
    targets = repl.chooseTarget(filename, 1, dataNodes[0], chosenNodes, true, excludedNodes, BLOCK_SIZE,
            TestBlockStoragePolicy.DEFAULT_STORAGE_POLICY);
    System.out.println("targets=" + Arrays.asList(targets));
    assertEquals(2, targets.length);
    //make sure that the chosen node is in the target.
    int i = 0;
    for (; i < targets.length && !storages[2].equals(targets[i]); i++)
        ;
    assertTrue(i < targets.length);
}