Example usage for java.util LinkedHashSet add

List of usage examples for java.util LinkedHashSet add

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Introduction

In this page you can find the example usage for java.util LinkedHashSet add.

Prototype

boolean add(E e);

Source Link

Document

Adds the specified element to this set if it is not already present (optional operation).

Usage

From source file:org.apache.tajo.plan.rewrite.rules.ProjectionPushDownRule.java

public LogicalNode visitJoin(Context context, LogicalPlan plan, LogicalPlan.QueryBlock block, JoinNode node,
        Stack<LogicalNode> stack) throws TajoException {
    Context newContext = new Context(context);

    String joinQualReference = null;
    if (node.hasJoinQual()) {
        for (EvalNode eachQual : AlgebraicUtil.toConjunctiveNormalFormArray(node.getJoinQual())) {
            if (eachQual instanceof BinaryEval) {
                BinaryEval binaryQual = (BinaryEval) eachQual;

                for (int i = 0; i < 2; i++) {
                    EvalNode term = binaryQual.getChild(i);
                    pushDownIfComplexTermInJoinCondition(newContext, eachQual, term);
                }/*  ww w.  jav a2s. c  o m*/
            }
        }

        joinQualReference = newContext.addExpr(node.getJoinQual());
        newContext.addNecessaryReferences(node.getJoinQual());
    }

    String[] referenceNames = null;
    if (node.hasTargets()) {
        referenceNames = new String[node.getTargets().size()];
        int i = 0;
        for (Iterator<Target> it = getFilteredTarget(node.getTargets(), context.requiredSet); it.hasNext();) {
            Target target = it.next();
            referenceNames[i++] = newContext.addExpr(target);
        }
    }

    stack.push(node);
    LogicalNode left = visit(newContext, plan, block, node.getLeftChild(), stack);
    LogicalNode right = visit(newContext, plan, block, node.getRightChild(), stack);
    stack.pop();

    Schema merged = SchemaUtil.merge(left.getOutSchema(), right.getOutSchema());

    node.setInSchema(merged);

    if (node.hasJoinQual()) {
        Target target = context.targetListMgr.getTarget(joinQualReference);
        if (newContext.targetListMgr.isEvaluated(joinQualReference)) {
            throw new TajoInternalError(
                    "Join condition must be evaluated in the proper Join Node: " + joinQualReference);
        } else {
            node.setJoinQual(target.getEvalTree());
            newContext.targetListMgr.markAsEvaluated(target);
        }
    }

    LinkedHashSet<Target> projectedTargets = Sets.newLinkedHashSet();
    for (Iterator<String> it = getFilteredReferences(context.targetListMgr.getNames(), context.requiredSet); it
            .hasNext();) {
        String referenceName = it.next();
        Target target = context.targetListMgr.getTarget(referenceName);

        if (context.targetListMgr.isEvaluated(referenceName)) {
            Target fieldReference = new Target(new FieldEval(target.getNamedColumn()));
            // here, we assume that every exprs are specified at the on clause
            // because all filters have been moved to appropriate logical nodes during the filter push down phase
            if (LogicalPlanner.checkIfBeEvaluatedAtJoin(block, fieldReference.getEvalTree(), node,
                    stack.peek().getType() != NodeType.JOIN)) {
                projectedTargets.add(fieldReference);
            }
        } else if (LogicalPlanner.checkIfBeEvaluatedAtJoin(block, target.getEvalTree(), node,
                stack.peek().getType() != NodeType.JOIN)) {
            projectedTargets.add(target);
            context.targetListMgr.markAsEvaluated(target);
        }
    }

    node.setTargets(new ArrayList<>(projectedTargets));
    LogicalPlanner.verifyProjectedFields(block, node);
    return node;
}

From source file:org.apache.ws.scout.registry.BusinessLifeCycleManagerImpl.java

public BulkResponse saveServices(Collection services) throws JAXRException {
    BulkResponseImpl bulk = new BulkResponseImpl();
    BusinessService[] sarr = new BusinessService[services.size()];

    LinkedHashSet<Key> coll = new LinkedHashSet<Key>();
    Collection<Exception> exceptions = new ArrayList<Exception>();

    Iterator iter = services.iterator();
    int currLoc = 0;
    while (iter.hasNext()) {
        try {//from   ww  w .ja  va2s .co  m
            BusinessService bs = ScoutJaxrUddiHelper.getBusinessServiceFromJAXRService((Service) iter.next());
            sarr[currLoc] = bs;
            currLoc++;
        } catch (ClassCastException ce) {
            throw new UnexpectedObjectException();
        }
    }
    // Save Service
    ServiceDetail sd = null;
    try {
        sd = (ServiceDetail) executeOperation(sarr, "SAVE_SERVICE");
    } catch (RegistryException e) {
        exceptions.add(new SaveException(e.getLocalizedMessage()));
        bulk.setStatus(JAXRResponse.STATUS_FAILURE);
        return bulk;
    }

    List<BusinessService> bizServiceList = sd.getBusinessService();
    sarr = new BusinessService[bizServiceList.size()];
    bizServiceList.toArray(sarr);

    for (int i = 0; sarr != null && i < sarr.length; i++) {
        BusinessService entity = (BusinessService) sarr[i];
        coll.add(new KeyImpl(entity.getServiceKey()));
    }
    bulk.setCollection(coll);
    bulk.setExceptions(exceptions);

    return bulk;
}

From source file:cross.io.InputDataFactory.java

/**
 * Create a collection of files from the given string resource paths.
 *
 * @param input the string resource paths
 * @return a collection of files/*from w w  w  . j a  v a 2  s.  co  m*/
 */
@Override
public Collection<File> getInputFiles(String[] input) {
    LinkedHashSet<File> files = new LinkedHashSet<>();
    for (String inputString : input) {
        log.debug("Processing input string {}", inputString);
        //separate wildcards from plain files
        String name = FilenameUtils.getName(inputString);
        boolean isWildcard = name.contains("?") || name.contains("*");
        String fullPath = FilenameUtils.getFullPath(inputString);
        File path = new File(fullPath);
        File baseDirFile = new File(this.basedir);
        if (!baseDirFile.exists()) {
            throw new ExitVmException("Input base directory '" + baseDirFile + "' does not exist!");
        }
        if (!baseDirFile.isDirectory()) {
            throw new ExitVmException("Input base directory '" + baseDirFile + "' is not a directory!");
        }
        log.debug("Path is absolute: {}", path.isAbsolute());
        //identify absolute and relative files
        if (!path.isAbsolute()) {
            log.info("Resolving relative file against basedir: {}", this.basedir);
            path = new File(this.basedir, fullPath);
        }
        //normalize filenames
        fullPath = FilenameUtils.normalize(path.getAbsolutePath());
        log.debug("After normalization: {}", fullPath);
        IOFileFilter dirFilter = this.recurse ? TrueFileFilter.INSTANCE : null;
        if (isWildcard) {
            log.debug("Using wildcard matcher for {}", name);
            files.addAll(FileUtils.listFiles(new File(fullPath),
                    new WildcardFileFilter(name, IOCase.INSENSITIVE), dirFilter));
        } else {
            log.debug("Using name for {}", name);
            File f = new File(fullPath, name);
            if (!f.exists()) {
                throw new ExitVmException("Input file '" + f + "' does not exist!");
            }
            files.add(f);
        }
    }
    return files;
}

From source file:org.apache.ws.scout.registry.BusinessLifeCycleManagerV3Impl.java

public BulkResponse saveServices(Collection services) throws JAXRException {
    BulkResponseImpl bulk = new BulkResponseImpl();
    BusinessService[] sarr = new BusinessService[services.size()];

    LinkedHashSet<Key> coll = new LinkedHashSet<Key>();
    Collection<Exception> exceptions = new ArrayList<Exception>();

    Iterator iter = services.iterator();
    int currLoc = 0;
    while (iter.hasNext()) {
        try {// w ww .j  ava2  s  .com
            BusinessService bs = ScoutJaxrUddiV3Helper.getBusinessServiceFromJAXRService((Service) iter.next());
            sarr[currLoc] = bs;
            currLoc++;
        } catch (ClassCastException ce) {
            throw new UnexpectedObjectException();
        }
    }
    // Save Service
    ServiceDetail sd = null;
    try {
        sd = (ServiceDetail) executeOperation(sarr, "SAVE_SERVICE");
    } catch (RegistryV3Exception e) {
        exceptions.add(new SaveException(e.getLocalizedMessage()));
        bulk.setStatus(JAXRResponse.STATUS_FAILURE);
        return bulk;
    }

    List<BusinessService> bizServiceList = sd.getBusinessService();
    sarr = new BusinessService[bizServiceList.size()];
    bizServiceList.toArray(sarr);

    for (int i = 0; sarr != null && i < sarr.length; i++) {
        BusinessService entity = (BusinessService) sarr[i];
        coll.add(new KeyImpl(entity.getServiceKey()));
    }
    bulk.setCollection(coll);
    bulk.setExceptions(exceptions);

    return bulk;
}

From source file:org.apache.ws.scout.registry.BusinessLifeCycleManagerImpl.java

public BulkResponse saveServiceBindings(Collection bindings) throws JAXRException {
    BulkResponseImpl bulk = new BulkResponseImpl();
    BindingTemplate[] sbarr = new BindingTemplate[bindings.size()];

    LinkedHashSet<Key> coll = new LinkedHashSet<Key>();
    Collection<Exception> exceptions = new ArrayList<Exception>();

    Iterator iter = bindings.iterator();
    int currLoc = 0;
    while (iter.hasNext()) {
        try {/*from  w ww .  ja v  a2  s. com*/
            BindingTemplate bs = ScoutJaxrUddiHelper.getBindingTemplateFromJAXRSB((ServiceBinding) iter.next());
            sbarr[currLoc] = bs;
            currLoc++;
        } catch (ClassCastException ce) {
            throw new UnexpectedObjectException();
        }
    }
    // Save ServiceBinding
    BindingDetail bd = null;
    try {
        bd = (BindingDetail) executeOperation(sbarr, "SAVE_SERVICE_BINDING");
    } catch (RegistryException e) {
        exceptions.add(new SaveException(e.getLocalizedMessage()));
        bulk.setStatus(JAXRResponse.STATUS_FAILURE);
        return bulk;
    }

    List<BindingTemplate> bindingTemplateList = bd.getBindingTemplate();
    sbarr = new BindingTemplate[bindingTemplateList.size()];
    bindingTemplateList.toArray(sbarr);

    for (int i = 0; sbarr != null && i < sbarr.length; i++) {
        BindingTemplate bt = (BindingTemplate) sbarr[i];
        coll.add(new KeyImpl(bt.getBindingKey()));
    }
    if (coll.size() > 0) {
        bulk.setCollection(coll);
    }
    bulk.setExceptions(exceptions);

    return bulk;
}

From source file:org.apache.tajo.engine.planner.LogicalPlanner.java

public TableSubQueryNode visitTableSubQuery(PlanContext context, Stack<Expr> stack, TablePrimarySubQuery expr)
        throws PlanningException {
    QueryBlock block = context.queryBlock;

    QueryBlock childBlock = context.plan.getBlock(context.plan.getBlockNameByExpr(expr.getSubQuery()));
    PlanContext newContext = new PlanContext(context, childBlock);
    LogicalNode child = visit(newContext, new Stack<Expr>(), expr.getSubQuery());
    TableSubQueryNode subQueryNode = context.queryBlock.getNodeFromExpr(expr);
    context.plan.connectBlocks(childBlock, context.queryBlock, BlockType.TableSubQuery);
    subQueryNode.setSubQuery(child);//from www .  ja v  a 2s.  co  m

    // Add additional expressions required in upper nodes.
    Set<String> newlyEvaluatedExprs = TUtil.newHashSet();
    for (NamedExpr rawTarget : block.namedExprsMgr.getAllNamedExprs()) {
        try {
            EvalNode evalNode = exprAnnotator.createEvalNode(context, rawTarget.getExpr(),
                    NameResolvingMode.RELS_ONLY);
            if (checkIfBeEvaluatedAtRelation(block, evalNode, subQueryNode)) {
                block.namedExprsMgr.markAsEvaluated(rawTarget.getAlias(), evalNode);
                newlyEvaluatedExprs.add(rawTarget.getAlias()); // newly added exr
            }
        } catch (VerifyException ve) {
        }
    }

    // Assume that each unique expr is evaluated once.
    LinkedHashSet<Target> targets = createFieldTargetsFromRelation(block, subQueryNode, newlyEvaluatedExprs);

    for (String newAddedExpr : newlyEvaluatedExprs) {
        targets.add(block.namedExprsMgr.getTarget(newAddedExpr, true));
    }

    subQueryNode.setTargets(targets.toArray(new Target[targets.size()]));

    return subQueryNode;
}

From source file:org.apache.ws.scout.registry.BusinessLifeCycleManagerV3Impl.java

public BulkResponse saveServiceBindings(Collection bindings) throws JAXRException {
    BulkResponseImpl bulk = new BulkResponseImpl();
    BindingTemplate[] sbarr = new BindingTemplate[bindings.size()];

    LinkedHashSet<Key> coll = new LinkedHashSet<Key>();
    Collection<Exception> exceptions = new ArrayList<Exception>();

    Iterator iter = bindings.iterator();
    int currLoc = 0;
    while (iter.hasNext()) {
        try {// w ww .  j  a v a  2 s  . c o m
            BindingTemplate bs = ScoutJaxrUddiV3Helper
                    .getBindingTemplateFromJAXRSB((ServiceBinding) iter.next());
            sbarr[currLoc] = bs;
            currLoc++;
        } catch (ClassCastException ce) {
            throw new UnexpectedObjectException();
        }
    }
    // Save ServiceBinding
    BindingDetail bd = null;
    try {
        bd = (BindingDetail) executeOperation(sbarr, "SAVE_SERVICE_BINDING");
    } catch (RegistryV3Exception e) {
        exceptions.add(new SaveException(e.getLocalizedMessage()));
        bulk.setStatus(JAXRResponse.STATUS_FAILURE);
        return bulk;
    }

    List<BindingTemplate> bindingTemplateList = bd.getBindingTemplate();
    sbarr = new BindingTemplate[bindingTemplateList.size()];
    bindingTemplateList.toArray(sbarr);

    for (int i = 0; sbarr != null && i < sbarr.length; i++) {
        BindingTemplate bt = (BindingTemplate) sbarr[i];
        coll.add(new KeyImpl(bt.getBindingKey()));
    }
    if (coll.size() > 0) {
        bulk.setCollection(coll);
    }
    bulk.setExceptions(exceptions);

    return bulk;
}

From source file:org.opencb.opencga.storage.core.variant.io.VariantVcfDataWriter.java

@Override
public boolean pre() {
    LinkedHashSet<VCFHeaderLine> meta = new LinkedHashSet<>();
    sampleNames.clear();/*from w w w . j a  va 2  s.co m*/
    sampleNames.addAll(getSamples());
    logger.info("Use {} samples for export ... ", this.sampleNames.size());
    sampleNameMapping.putAll(
            sampleNames.stream().collect(Collectors.toMap(s -> s, s -> sampleNameConverter.get().apply(s))));

    List<String> names = sampleNames.stream().map(s -> sampleNameMapping.get(s)).collect(Collectors.toList());
    logger.info("Samples mapped: {} ... ", names.size());

    //        Iterator<VariantSource> iterator = sourceDBAdaptor.iterator(
    //                new Query(VariantStorageEngine.Options.STUDY_ID.key(), studyConfiguration.getStudyId()),
    //                new QueryOptions());
    //        if (iterator.hasNext()) {
    //            VariantSource source = iterator.next();
    //            fileHeader = source.getMetadata().get(VariantFileUtils.VARIANT_FILE_HEADER).toString();
    //        } else {
    //            throw new IllegalStateException("file headers not available for study " + studyConfiguration.getStudyName()
    //                    + ". note: check files: " + studyConfiguration.getFileIds().values().toString());
    //        }

    /* FILTER */
    meta.add(new VCFFilterHeaderLine("PASS", "Valid variant"));
    meta.add(new VCFFilterHeaderLine(".", "No FILTER info"));

    /* INFO */
    meta.add(new VCFInfoHeaderLine("PR", 1, VCFHeaderLineType.Float, "Pass rate"));
    meta.add(new VCFInfoHeaderLine("CR", 1, VCFHeaderLineType.Float, "Call rate"));
    meta.add(new VCFInfoHeaderLine("OPR", 1, VCFHeaderLineType.Float, "Overall Pass rate"));
    addCohortInfo(meta);
    addAnnotationInfo(meta);

    /* FORMAT */
    meta.add(new VCFFormatHeaderLine("GT", 1, VCFHeaderLineType.String, "Genotype"));
    meta.add(new VCFFormatHeaderLine("PF", 1, VCFHeaderLineType.Integer,
            "Variant was PASS (1) filter in original vcf"));

    final VCFHeader header = new VCFHeader(meta, names);
    final SAMSequenceDictionary sequenceDictionary = header.getSequenceDictionary();

    // setup writer
    VariantContextWriterBuilder builder = new VariantContextWriterBuilder().setOutputStream(outputStream)
            .setReferenceDictionary(sequenceDictionary).unsetOption(Options.INDEX_ON_THE_FLY);
    if (sampleNames.isEmpty() || !this.exportGenotype.get()) {
        builder.setOption(Options.DO_NOT_WRITE_GENOTYPES);
    }
    List<String> formatFields = studyConfiguration.getAttributes()
            .getAsStringList(VariantStorageEngine.Options.EXTRA_GENOTYPE_FIELDS.key());
    List<String> formatFieldsType = studyConfiguration.getAttributes()
            .getAsStringList(VariantStorageEngine.Options.EXTRA_GENOTYPE_FIELDS_TYPE.key());
    for (int i = 0; i < formatFields.size(); i++) {
        String id = formatFields.get(i);
        if (header.getFormatHeaderLine(id) == null) {
            header.addMetaDataLine(
                    new VCFFormatHeaderLine(id, 1, VCFHeaderLineType.valueOf(formatFieldsType.get(i)), ""));
        }
    }

    writer = builder.build();
    writer.writeHeader(header);
    return true;
}

From source file:org.apache.ws.scout.registry.BusinessLifeCycleManagerImpl.java

public BulkResponse saveConcepts(Collection concepts) throws JAXRException {
    //Now we need to convert the collection into a vector for juddi
    BulkResponseImpl bulk = new BulkResponseImpl();
    TModel[] entityarr = new TModel[concepts.size()];

    LinkedHashSet<Key> coll = new LinkedHashSet<Key>();
    Collection<Exception> exceptions = new ArrayList<Exception>();

    Iterator iter = concepts.iterator();
    int currLoc = 0;
    while (iter.hasNext()) {
        try {/*from   ww  w  .ja  v a2s . c o  m*/
            TModel en = ScoutJaxrUddiHelper.getTModelFromJAXRConcept((Concept) iter.next());
            entityarr[currLoc] = en;
            currLoc++;
        } catch (ClassCastException ce) {
            throw new UnexpectedObjectException();
        }
    }
    log.debug("Method:save_concept: ENlength=" + entityarr.length);
    // Save business
    TModelDetail td = null;
    try {
        td = (TModelDetail) executeOperation(entityarr, "SAVE_TMODEL");
    } catch (RegistryException e) {
        exceptions.add(new SaveException(e.getLocalizedMessage()));
        bulk.setStatus(JAXRResponse.STATUS_FAILURE);
        return bulk;
    }

    List<TModel> tmodelList = td.getTModel();
    entityarr = new TModel[tmodelList.size()];
    tmodelList.toArray(entityarr);

    log.debug("After Saving TModel. Obtained vector size:" + entityarr != null ? entityarr.length : 0);
    for (int i = 0; entityarr != null && i < entityarr.length; i++) {
        TModel tm = (TModel) entityarr[i];
        coll.add(new KeyImpl(tm.getTModelKey()));
    }

    bulk.setCollection(coll);
    bulk.setExceptions(exceptions);

    return bulk;
}

From source file:org.apache.ws.scout.registry.BusinessQueryManagerImpl.java

public BulkResponse findAssociations(Collection findQualifiers, String sourceObjectId, String targetObjectId,
        Collection associationTypes) throws JAXRException {
    //TODO: Currently we just return all the Association objects owned by the caller
    IRegistry registry = (IRegistry) registryService.getRegistry();
    try {//from  ww w . jav  a 2 s  . c  o  m
        ConnectionImpl con = ((RegistryServiceImpl) getRegistryService()).getConnection();
        AuthToken auth = this.getAuthToken(con, registry);
        PublisherAssertions result = null;
        try {
            result = registry.getPublisherAssertions(auth.getAuthInfo());
        } catch (RegistryException rve) {
            String username = getUsernameFromCredentials(con.getCredentials());
            if (AuthTokenSingleton.getToken(username) != null) {
                AuthTokenSingleton.deleteAuthToken(username);
            }
            auth = getAuthToken(con, registry);
            result = registry.getPublisherAssertions(auth.getAuthInfo());
        }

        List<PublisherAssertion> publisherAssertionList = result.getPublisherAssertion();
        LinkedHashSet<Association> col = new LinkedHashSet<Association>();
        for (PublisherAssertion pas : publisherAssertionList) {
            String sourceKey = pas.getFromKey();
            String targetKey = pas.getToKey();

            if ((sourceObjectId == null || sourceObjectId.equals(sourceKey))
                    && (targetObjectId == null || targetObjectId.equals(targetKey))) {
                Collection<Key> orgcol = new ArrayList<Key>();
                orgcol.add(new KeyImpl(sourceKey));
                orgcol.add(new KeyImpl(targetKey));
                BulkResponse bl = getRegistryObjects(orgcol, LifeCycleManager.ORGANIZATION);
                Association asso = ScoutUddiJaxrHelper.getAssociation(bl.getCollection(),
                        registryService.getBusinessLifeCycleManager());
                KeyedReference keyr = pas.getKeyedReference();
                Concept c = new ConceptImpl(getRegistryService().getBusinessLifeCycleManager());
                c.setName(new InternationalStringImpl(keyr.getKeyName()));
                c.setKey(new KeyImpl(keyr.getTModelKey()));
                c.setValue(keyr.getKeyValue());
                asso.setAssociationType(c);
                col.add(asso);
            }

        }
        return new BulkResponseImpl(col);
    } catch (RegistryException e) {
        throw new JAXRException(e);
    }
}