Example usage for javax.xml.bind JAXBElement getValue

List of usage examples for javax.xml.bind JAXBElement getValue

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Introduction

In this page you can find the example usage for javax.xml.bind JAXBElement getValue.

Prototype

public T getValue()

Source Link

Document

Return the content model and attribute values for this element.

See #isNil() for a description of a property constraint when this value is null

Usage

From source file:com.evolveum.midpoint.prism.util.JaxbTestUtil.java

public <T> T unmarshalToObject(Node node, Class<T> type) throws JAXBException, SchemaException {
    JAXBElement<T> element = unmarshalElement(node, type);
    if (element == null) {
        return null;
    }//ww  w.ja  v  a2  s. c o  m
    adopt(element);
    return element.getValue();
}

From source file:com.evolveum.midpoint.prism.util.JaxbTestUtil.java

private <T extends Containerable> PrismContainer<T> unmarshalSingleValueContainer(JAXBElement<T> element)
        throws JAXBException, SchemaException {
    if (element == null) {
        return null;
    }//w w  w.j a  v a2s  .  c  om
    T value = element.getValue();

    // this is a bit tricky - we have to create a container and put the newly obtained value into it
    PrismContainerValue<T> containerValue = value.asPrismContainerValue();
    containerValue.revive(prismContext);
    PrismContainerDefinition definition = prismContext.getSchemaRegistry()
            .findContainerDefinitionByElementName(element.getName());
    if (definition == null) {
        throw new IllegalStateException(
                "There's no container definition for element name " + element.getName());
    }
    containerValue.applyDefinition(definition, false);
    PrismContainer container = definition.instantiate();
    container.add(containerValue);
    return container;
}

From source file:edu.harvard.i2b2.crc.delegate.setfinder.QueryRequestDelegate.java

/**
 * @see edu.harvard.i2b2.crc.delegate.RequestHandlerDelegate#handleRequest(java.lang.String)
 */// ww  w  .  j a  va 2 s .c om
public String handleRequest(String requestXml) throws I2B2Exception {
    PsmQryHeaderType headerType = null;
    String response = null;
    JAXBUtil jaxbUtil = CRCJAXBUtil.getJAXBUtil();

    try {
        JAXBElement jaxbElement = jaxbUtil.unMashallFromString(requestXml);

        if (jaxbElement == null) {
            throw new I2B2Exception("Request is null after unmashall" + requestXml);
        }

        RequestMessageType requestMessageType = (RequestMessageType) jaxbElement.getValue();
        BodyType bodyType = requestMessageType.getMessageBody();

        if (bodyType == null) {
            log.error("null value in body type");
            throw new I2B2Exception("null value in body type");
        }
        // Call PM cell to validate user
        ProjectType projectType = null;
        StatusType procStatus = null;
        try {
            SecurityType securityType = null;
            String projectId = null;
            if (requestMessageType.getMessageHeader() != null) {
                if (requestMessageType.getMessageHeader().getSecurity() != null) {
                    securityType = requestMessageType.getMessageHeader().getSecurity();
                }
                projectId = requestMessageType.getMessageHeader().getProjectId();
            }
            if (securityType == null) {
                procStatus = new StatusType();
                procStatus.setType("ERROR");
                procStatus.setValue("Request message missing user/password");
                response = I2B2MessageResponseFactory.buildResponseMessage(requestXml, procStatus, bodyType);
                return response;
            }

            // String pmResponse =
            // PMServiceDriver.checkValidUser(securityType);
            PMServiceDriver pmServiceDriver = new PMServiceDriver();
            projectType = pmServiceDriver.checkValidUser(securityType, projectId);

            if (projectType == null) {
                procStatus = new StatusType();
                procStatus.setType("ERROR");
                procStatus.setValue("Invalid user/password for the given project[" + projectId + "]");
                response = I2B2MessageResponseFactory.buildResponseMessage(requestXml, procStatus, bodyType);
                return response;
            }

            log.debug("project name from PM " + projectType.getName());
            log.debug("project id from PM " + projectType.getId());

            if (projectType.getRole() != null) {
                log.debug("project role from PM " + projectType.getRole().get(0));

                this.putRoles(projectId, securityType.getUsername(), securityType.getDomain(),
                        projectType.getRole());

                //TODO removed cache
                //   Node rootNode = CacheUtil.getCache().getRoot();
                //List<String> roles = (List<String>) rootNode
                //      .get(securityType.getDomain() + "/" + projectId
                //            + "/" + securityType.getUsername());
                List<String> roles = (List<String>) CacheUtil
                        .get(securityType.getDomain() + "/" + projectId + "/" + securityType.getUsername());
                if (roles != null) {
                    log.debug("User Roles count " + roles.size());
                }
            } else {
                log.error("Project role not set for the user ");

            }

            //check if process_timing_flag is set
            log.debug("check if process_timing_flag is set");
            LogTimingUtil.clearPocessTiming(projectId, securityType.getUsername(), securityType.getDomain());
            ParamUtil paramUtil = new ParamUtil();
            paramUtil.clearParam(projectId, securityType.getUsername(), securityType.getDomain(),
                    ParamUtil.CRC_ENABLE_UNITCD_CONVERSION);
            if (projectType.getParam() != null) {
                for (ParamType param : projectType.getParam()) {
                    if (param.getName() != null && param.getName().trim()
                            .equalsIgnoreCase(LogTimingUtil.PM_ENABLE_PROCESS_TIMING)) {
                        //this.putPocessTiming(projectId, securityType.getUsername(), securityType.getDomain(), param);
                        LogTimingUtil.putPocessTiming(projectId, securityType.getUsername(),
                                securityType.getDomain(), param);
                        String cacheValue = LogTimingUtil.getPocessTiming(projectId, securityType.getUsername(),
                                securityType.getDomain());
                        log.debug("CRC param stored in the cache Project Id [" + projectId + "] user ["
                                + securityType.getUsername() + "] domain [" + securityType.getDomain() + "] "
                                + ParamUtil.PM_ENABLE_PROCESS_TIMING + "[" + cacheValue + "]");

                    } else if (param.getName() != null && param.getName().trim()
                            .equalsIgnoreCase(ParamUtil.CRC_ENABLE_UNITCD_CONVERSION)) {
                        paramUtil.putParam(projectId, securityType.getUsername(), securityType.getDomain(),
                                ParamUtil.CRC_ENABLE_UNITCD_CONVERSION, param);
                        String unitCdCache = paramUtil.getParam(projectId, securityType.getUsername(),
                                securityType.getDomain(), ParamUtil.CRC_ENABLE_UNITCD_CONVERSION);
                        log.debug("CRC param stored in the cache Project Id [" + projectId + "] user ["
                                + securityType.getUsername() + "] domain [" + securityType.getDomain() + "] "
                                + ParamUtil.CRC_ENABLE_UNITCD_CONVERSION + "[" + unitCdCache + "]");
                    }
                }
            }

        } catch (AxisFault e) {
            procStatus = new StatusType();
            procStatus.setType("ERROR");
            procStatus.setValue("Could not connect to server");
            response = I2B2MessageResponseFactory.buildResponseMessage(requestXml, procStatus, bodyType);
            return response;
        } catch (I2B2Exception e) {
            procStatus = new StatusType();
            procStatus.setType("ERROR");
            procStatus.setValue("Message error connecting Project Management cell");
            response = I2B2MessageResponseFactory.buildResponseMessage(requestXml, procStatus, bodyType);
            return response;
        } catch (JAXBUtilException e) {
            procStatus = new StatusType();
            procStatus.setType("ERROR");
            procStatus.setValue("Message error from Project Management cell");
            response = I2B2MessageResponseFactory.buildResponseMessage(requestXml, procStatus, bodyType);
            return response;
        }

        // check if the role is DATA_AGG to proceed
        log.debug("check if the role is DATA_AGG to proceed");
        boolean errorFlag = false;
        JAXBUnWrapHelper unWrapHelper = new JAXBUnWrapHelper();
        headerType = (PsmQryHeaderType) unWrapHelper.getObjectByClass(bodyType.getAny(),
                edu.harvard.i2b2.crc.datavo.setfinder.query.PsmQryHeaderType.class);
        BodyType responseBodyType = null;
        if (headerType.getRequestType().equals(PsmRequestTypeType.CRC_QRY_GET_QUERY_MASTER_LIST_FROM_USER_ID)) {
            GetQueryMasterListFromUserIdHandler handler = new GetQueryMasterListFromUserIdHandler(requestXml);
            responseBodyType = handler.execute();
        } else if (headerType.getRequestType()
                .equals(PsmRequestTypeType.CRC_QRY_GET_QUERY_MASTER_LIST_FROM_GROUP_ID)) {
            // check if user have right permission to access this request
            if (projectType != null && projectType.getRole().size() > 0) {
                if ((!projectType.getRole().contains("MANAGER"))) {
                    // Not authorized
                    procStatus = new StatusType();
                    procStatus.setType("ERROR");
                    procStatus.setValue("Authorization failure, should have MANAGER  role");
                    response = I2B2MessageResponseFactory.buildResponseMessage(requestXml, procStatus,
                            bodyType);
                    return response;
                }
            } else {
                // Not authorized
                procStatus = new StatusType();
                procStatus.setType("ERROR");
                procStatus.setValue("Authorization failure, should have MANAGER role");
                response = I2B2MessageResponseFactory.buildResponseMessage(requestXml, procStatus, bodyType);
                return response;
            }

            GetQueryMasterListFromGroupIdHandler handler = new GetQueryMasterListFromGroupIdHandler(requestXml);
            responseBodyType = handler.execute();
        } else if (headerType.getRequestType()
                .equals(PsmRequestTypeType.CRC_QRY_RUN_QUERY_INSTANCE_FROM_QUERY_DEFINITION)) {
            log.debug("Running in " + PsmRequestTypeType.CRC_QRY_RUN_QUERY_INSTANCE_FROM_QUERY_DEFINITION);
            ParamType lockedParamType = null;
            List<ParamType> paramList = projectType.getParam();
            for (ParamType paramType : paramList) {
                if (paramType.getName().equals(EJBPMUtil.LOCKEDOUT)) {
                    lockedParamType = paramType;
                    break;
                }
            }
            log.debug("Check if user is locked out");
            if (lockedParamType != null) {
                // Not authorized
                procStatus = new StatusType();
                procStatus.setType("ERROR");
                procStatus.setValue("LOCKEDOUT error: The user account is lockedout at ["
                        + lockedParamType.getValue() + "]");
                bodyType = new BodyType();
                response = I2B2MessageResponseFactory.buildResponseMessage(requestXml, procStatus, bodyType);
                return response;
            } else {
                RunQueryInstanceFromQueryDefinitionHandler handler = new RunQueryInstanceFromQueryDefinitionHandler(
                        requestXml);
                responseBodyType = handler.execute();

                // check if the response body type has lockedout error
                if (handler.getLockedoutFlag()) {
                    procStatus = new StatusType();
                    procStatus.setType("ERROR");
                    procStatus.setValue("LOCKEDOUT error: The user account is lockedout at ["
                            + new Date(System.currentTimeMillis()) + "]");
                    response = I2B2MessageResponseFactory.buildResponseMessage(requestXml, procStatus,
                            responseBodyType);
                    return response;
                }

                //if (handler.getErrorFlag()) { 
                //   errorFlag = true;
                //}

            }
        } else if (headerType.getRequestType()
                .equals(PsmRequestTypeType.CRC_QRY_RUN_QUERY_INSTANCE_FROM_QUERY_MASTER_ID)) {
            RunQueryInstanceFromQueryMasterHandler handler = new RunQueryInstanceFromQueryMasterHandler(
                    requestXml);
            responseBodyType = handler.execute();
        } else if (headerType.getRequestType()
                .equals(PsmRequestTypeType.CRC_QRY_GET_QUERY_RESULT_INSTANCE_LIST_FROM_QUERY_INSTANCE_ID)) {
            GetQueryResultInstanceListFromQueryInstanceIdHandler handler = new GetQueryResultInstanceListFromQueryInstanceIdHandler(
                    requestXml);
            responseBodyType = handler.execute();
        } else if (headerType.getRequestType()
                .equals(PsmRequestTypeType.CRC_QRY_GET_QUERY_INSTANCE_LIST_FROM_QUERY_MASTER_ID)) {
            GetQueryInstanceListFromMasterIdHandler handler = new GetQueryInstanceListFromMasterIdHandler(
                    requestXml);
            responseBodyType = handler.execute();
        } else if (headerType.getRequestType()
                .equals(PsmRequestTypeType.CRC_QRY_GET_REQUEST_XML_FROM_QUERY_MASTER_ID)) {
            GetRequestXmlFromQueryMasterIdHandler handler = new GetRequestXmlFromQueryMasterIdHandler(
                    requestXml);
            responseBodyType = handler.execute();
        } else if (headerType.getRequestType().equals(PsmRequestTypeType.CRC_QRY_DELETE_QUERY_MASTER)) {
            DeleteQueryMasterHandler handler = new DeleteQueryMasterHandler(requestXml);
            responseBodyType = handler.execute();
        } else if (headerType.getRequestType().equals(PsmRequestTypeType.CRC_QRY_RENAME_QUERY_MASTER)) {
            RenameQueryMasterHandler handler = new RenameQueryMasterHandler(requestXml);
            responseBodyType = handler.execute();
        } else if (headerType.getRequestType()
                .equals(PsmRequestTypeType.CRC_QRY_UPDATE_RESULT_INSTANCE_DESCRIPTION)) {
            UpdateQueryResultInstanceDescriptionHandler handler = new UpdateQueryResultInstanceDescriptionHandler(
                    requestXml);
            responseBodyType = handler.execute();
        } else if (headerType.getRequestType()
                .equals(PsmRequestTypeType.CRC_QRY_GET_RESULT_DOCUMENT_FROM_RESULT_INSTANCE_ID)) {
            GetXmlResultFromQueryResultIdHandler handler = new GetXmlResultFromQueryResultIdHandler(requestXml);
            responseBodyType = handler.execute();
        } else if (headerType.getRequestType().equals(PsmRequestTypeType.CRC_QRY_GET_RESULT_TYPE)) {
            GetAllQueryResultTypeHandler handler = new GetAllQueryResultTypeHandler(requestXml);
            responseBodyType = handler.execute();
        } else if (headerType.getRequestType()
                .equals(PsmRequestTypeType.CRC_QRY_RUN_QUERY_INSTANCE_FROM_ANALYSIS_DEFINITION)) {

            RunQueryInstanceFromAnalysisDefinitionHandler handler = new RunQueryInstanceFromAnalysisDefinitionHandler(
                    requestXml);
            responseBodyType = handler.execute();

        } else if (headerType.getRequestType().equals(PsmRequestTypeType.CRC_QRY_CANCEL_QUERY)) {
            CancelQueryInstanceHandler handler = new CancelQueryInstanceHandler(requestXml);
            responseBodyType = handler.execute();
        } else if (headerType.getRequestType()
                .equals(PsmRequestTypeType.CRC_QRY_GET_ANALYSIS_PLUGIN_METADATA)) {
            GetAnalysisPluginMetadataTypeHandler handler = new GetAnalysisPluginMetadataTypeHandler(requestXml);
            responseBodyType = handler.execute();
        }

        procStatus = new StatusType();
        if (errorFlag == false) {
            procStatus.setType("DONE");
            procStatus.setValue("DONE");
        } else {
            procStatus.setType("ERROR");
            procStatus.setValue("ERROR");
        }

        response = I2B2MessageResponseFactory.buildResponseMessage(requestXml, procStatus, responseBodyType);

    } catch (JAXBUtilException e) {
        log.error("JAXBUtilException", e);
        StatusType procStatus = new StatusType();
        procStatus.setType("ERROR");
        procStatus.setValue(requestXml + "\n\n" + StackTraceUtil.getStackTrace(e));
        try {
            response = I2B2MessageResponseFactory.buildResponseMessage(null, procStatus, null);
        } catch (JAXBUtilException e1) {
            e1.printStackTrace();
        }
        // throw new I2B2Exception("JAXBUtil exception",e);
    } catch (I2B2Exception e) {
        log.error("I2B2Exception", e);
        StatusType procStatus = new StatusType();
        procStatus.setType("ERROR");
        procStatus.setValue(StackTraceUtil.getStackTrace(e));
        try {
            response = I2B2MessageResponseFactory.buildResponseMessage(requestXml, procStatus, null);
        } catch (JAXBUtilException e1) {
            e1.printStackTrace();
        }
    } catch (Throwable e) {
        log.error("Throwable", e);
        StatusType procStatus = new StatusType();
        procStatus.setType("ERROR");
        procStatus.setValue(StackTraceUtil.getStackTrace(e));
        try {
            response = I2B2MessageResponseFactory.buildResponseMessage(requestXml, procStatus, null);
        } catch (JAXBUtilException e1) {
            e1.printStackTrace();
        }
    }

    return response;
}

From source file:de.extra.client.plugins.dataplugin.helper.DataPluginHelper.java

/**
 * Hilfsklasse zum unmarshalling des Auftragssatzes.
 * /*from  w  w w.  j  a va  2 s  .  c  om*/
 * @param auftragssatzName
 * @return JaxB-Element vom Typ AuftragssatzType
 */
public AuftragssatzType unmarshalAuftragssatz(final String auftragssatzName) {
    JAXBContext jc;
    JAXBElement<?> element = null;
    try {
        // Initialisieren des JaxB-Contextes
        jc = JAXBContext.newInstance("de.extra.client.plugins.dataPlugin.auftragssatz");

        // Aufruf des Unmarshallers
        final Unmarshaller u = jc.createUnmarshaller();
        final File auftragsFile = new File(auftragssatzName);
        element = (JAXBElement<?>) u.unmarshal(auftragsFile);
    } catch (final JAXBException e) {
        LOG.error("Fehler beim Verarbeiten des XML", e);
    } catch (final Exception e) {
        LOG.error("Fehler beim Verarbeiten des XML", e);
    }

    return (AuftragssatzType) element.getValue();
}

From source file:com.evolveum.midpoint.prism.util.JaxbTestUtil.java

public <T> T unmarshalObject(InputStream input, Class<T> type) throws JAXBException, SchemaException {
    Object object = getUnmarshaller().unmarshal(input);
    JAXBElement<T> jaxbElement = (JAXBElement<T>) object;
    adopt(jaxbElement);//from w  w w.  j av a  2 s .co  m

    if (jaxbElement == null) {
        return null;
    }
    T value = jaxbElement.getValue();
    // adopt not needed, already adopted in unmarshalElement call above
    return value;

}

From source file:com.evolveum.midpoint.prism.util.JaxbTestUtil.java

public <T> T unmarshalObject(InputStream input) throws JAXBException, SchemaException {
    Object object = getUnmarshaller().unmarshal(input);
    JAXBElement<T> jaxbElement = (JAXBElement<T>) object;
    adopt(jaxbElement);//from   w ww.j  a  v  a 2  s.c om

    if (jaxbElement == null) {
        return null;
    }
    T value = jaxbElement.getValue();
    // adopt not needed, already adopted in unmarshalElement call above
    return value;

}

From source file:org.castor.jaxb.CastorUnmarshallerTest.java

/**
 * Tests the passed {@link JAXBElement}.
 *
 * @param jaxbElement the {@link JAXBElement} to test
 *//*from   www. java2s . com*/
private void testJAXBElement(JAXBElement<Entity> jaxbElement) {
    assertNotNull("Entity can not be null.", jaxbElement);
    testEntity(jaxbElement.getValue());
}

From source file:ca.phon.session.io.xml.v12.XMLSessionReader_v12.java

@Override
public Session read(Document doc, Element ele) throws IOException {
    Session retVal = null;//  w  w w  . j  a  va  2s . c  o  m

    final ObjectFactory xmlFactory = new ObjectFactory();

    try {
        // TODO JAXB is good enough for reading in this type of session
        final JAXBContext context = JAXBContext.newInstance(xmlFactory.getClass());
        final Unmarshaller unmarshaller = context.createUnmarshaller();
        final JAXBElement<SessionType> sessionTypeEle = unmarshaller.unmarshal(doc.getDocumentElement(),
                SessionType.class);

        if (sessionTypeEle != null && sessionTypeEle.getValue() != null) {
            final SessionType sessionType = sessionTypeEle.getValue();
            retVal = readSessionType(sessionType);
        }
    } catch (JAXBException e) {
        throw new IOException(e);
    }

    return retVal;
}

From source file:com.inmobi.grill.client.GrillMetadataClient.java

public XStorageTableElement getStorageOfDimension(String dimName, String storage) {
    WebTarget target = getMetastoreWebTarget();
    JAXBElement<XStorageTableElement> result = target.path("dimensions").path(dimName).path("storages")
            .path(storage).queryParam("sessionid", this.connection.getSessionHandle())
            .request(MediaType.APPLICATION_XML).get(new GenericType<JAXBElement<XStorageTableElement>>() {
            });/*ww  w  . j av a 2 s.co  m*/
    return result.getValue();
}

From source file:edu.harvard.i2b2.crc.ejb.PdoQueryBean.java

/**
 * Function to get plain pdo from the given pdo request
 * /* w w  w.j  a va  2 s. c o m*/
 * @ejb.interface-method view-type="both"
 * @ejb.transaction type="Required"
 */
public PatientDataResponseType getPlainPatientData(DataSourceLookup dataSourceLookup,
        GetPDOFromInputListRequestType getPDOFromInputListReqType, String requestXml) throws I2B2Exception {
    PatientDataType patientDataType = null;

    DAOFactoryHelper helper = new DAOFactoryHelper(dataSourceLookup.getDomainId(),
            dataSourceLookup.getProjectPath(), dataSourceLookup.getOwnerId());
    IDAOFactory daoFactory = helper.getDAOFactory();

    IQueryPdoMasterDao queryPdoMasterDao = daoFactory.getSetFinderDAOFactory().getQueryPdoMasterDAO();

    savePdoQueryMaster(queryPdoMasterDao, requestXml);

    String version = getVersion(queryPdoMasterDao, requestXml);
    // check if the user have the blob permission
    boolean blobFlag = checkForBlob(getPDOFromInputListReqType);
    if (blobFlag) {
        //
        String domainId = dataSourceLookup.getDomainId();
        String projectId = dataSourceLookup.getProjectPath();
        String userId = dataSourceLookup.getOwnerId();
        daoFactory = helper.getDAOFactory();
        AuthrizationHelper authHelper = new AuthrizationHelper(domainId, projectId, userId, daoFactory);
        authHelper.checkRoleForProtectionLabel("PDO_WITH_BLOB");
    }

    // get unit cd conversion project param from cache 
    ParamUtil paramUtil = new ParamUtil();
    DataSourceLookup origDataSourceLookup = daoFactory.getPatientDataDAOFactory().getOriginalDataSourceLookup();
    String unitCdConversionParam = paramUtil.getParam(origDataSourceLookup.getProjectPath(),
            origDataSourceLookup.getOwnerId(), origDataSourceLookup.getDomainId(),
            ParamUtil.CRC_ENABLE_UNITCD_CONVERSION);

    Map projectParamMap = null;
    if (unitCdConversionParam != null) {
        projectParamMap = new HashMap();
        projectParamMap.put(ParamUtil.CRC_ENABLE_UNITCD_CONVERSION, unitCdConversionParam.trim());

    }

    // call ontology cell to get the item's metadata to build the query sql
    FilterListType filterList = getPDOFromInputListReqType.getFilterList();
    Map<String, XmlValueType> modifierMetadataXmlMap = new HashMap<String, XmlValueType>();
    if (filterList != null) {
        try {
            //CallOntologyUtil ontologyUtil = new CallOntologyUtil(requestXml);

            JAXBElement responseJaxb = CRCJAXBUtil.getJAXBUtil().unMashallFromString(requestXml);
            RequestMessageType request = (RequestMessageType) responseJaxb.getValue();
            String projectId = request.getMessageHeader().getProjectId();
            SecurityType tempSecurityType = request.getMessageHeader().getSecurity();
            SecurityType securityType = PMServiceAccountUtil
                    .getServiceSecurityType(tempSecurityType.getDomain());

            // if regular concepts
            for (PanelType panel : filterList.getPanel()) {
                for (ItemType item : panel.getItem()) {
                    //ConceptType conceptType = ontologyUtil.callOntology(item.getItemKey());
                    ConceptType conceptType = CallOntologyUtil.callOntology(item.getItemKey(), securityType,
                            projectId, QueryProcessorUtil.getInstance().getOntologyUrl());

                    log.debug("fetching the metadata information from ontology [" + item.getItemKey() + "]");
                    if (conceptType != null) {
                        item.setDimDimcode(conceptType.getDimcode());
                        item.setDimColumnname(conceptType.getColumnname());
                        item.setDimOperator(conceptType.getOperator());
                        item.setDimTablename(conceptType.getTablename());
                        item.setFacttablecolumn(conceptType.getFacttablecolumn());
                        item.setDimColumndatatype(conceptType.getColumndatatype());

                        if (conceptType.getMetadataxml() != null
                                && conceptType.getMetadataxml().getAny().get(0) != null) {
                            MetadataxmlValueType metadataXmlType = new MetadataxmlValueType();
                            metadataXmlType.getContent().add(conceptType.getMetadataxml().getAny().get(0));
                            item.setMetadataxml(metadataXmlType);
                        }

                        log.debug("metadata from ontology received for [" + item.getItemKey() + "]"
                                + conceptType.getTablename());

                        //check for modifier constrain and get modifier metadata
                        ItemType.ConstrainByModifier modifierConstrain = item.getConstrainByModifier();
                        if (modifierConstrain != null) {
                            ItemMetaDataHandler itemMetaDataHandler = new ItemMetaDataHandler(requestXml);
                            String modifierKey = modifierConstrain.getModifierKey();
                            String modifierAppliedPath = modifierConstrain.getAppliedPath();
                            ModifierType modifierType = itemMetaDataHandler.getModifierDataFromOntologyCell(
                                    modifierKey, modifierAppliedPath,
                                    helper.getDataSourceLookup().getServerType());
                            copyModifierToItem(item, modifierType);

                            //cache the modifier metadat in the map
                            if (projectParamMap != null) {
                                String unitConversionFlag = (String) projectParamMap
                                        .get(ParamUtil.CRC_ENABLE_UNITCD_CONVERSION);
                                if (unitConversionFlag != null && unitConversionFlag.equals("ON")) {
                                    if (modifierType.getMetadataxml() != null) {
                                        log.debug("Adding modifier metadata xml to lookup map for modifier key"
                                                + modifierType.getKey() + modifierType.getAppliedPath());
                                        modifierMetadataXmlMap.put(
                                                modifierType.getKey() + modifierType.getAppliedPath(),
                                                modifierType.getMetadataxml());
                                    }
                                }
                            }
                        }

                    } else {
                        log.debug(
                                "Unable to get item's metadata from ontology cell [" + item.getItemKey() + "]");
                    }
                }
            }
        } catch (JAXBUtilException jaxEx) {
            jaxEx.printStackTrace();
            throw new I2B2Exception(
                    "Error in getting item's metadata from the ontology : " + jaxEx.getMessage(), jaxEx);
        } catch (AxisFault e) {
            e.printStackTrace();
            throw new I2B2Exception("Error in getting item's metadata from the ontology : " + e.getMessage(),
                    e);
        } catch (XMLStreamException e) {
            e.printStackTrace();
            throw new I2B2Exception("Error in getting item's metadata from the ontology : " + e.getMessage(),
                    e);
        }
    }

    PatientDataDAOFactory pdoDaoFactory = daoFactory.getPatientDataDAOFactory();

    PatientDataResponseType patientDataResponseType = new PatientDataResponseType();
    try {
        OutputOptionNameType ot = getPDOFromInputListReqType.getOutputOption().getNames();

        QueryProcessorUtil qpUtil = QueryProcessorUtil.getInstance();
        String pageMethod = qpUtil.getPagingMethod();
        log.debug("PageMethod value [" + pageMethod + "]");

        InputOptionListType origInputList = getPDOFromInputListReqType.getInputList();
        InputOptionListType inputList = getPDOFromInputListReqType.getInputList();
        IInputOptionListHandler inputListHandler = PDOFactory.buildInputListHandler(inputList,
                helper.getDataSourceLookup());

        int requestedMinIndex = inputListHandler.getMinIndex();
        int requestedMaxIndex = inputListHandler.getMaxIndex();
        // if the request missing the max index, then default the maxindex
        // to size of the input list
        if (requestedMaxIndex < 1) {
            requestedMaxIndex = inputListHandler.getInputSize();
            RangeType rangeType = PDOFactory.getRangeType(inputList);
            rangeType.setMax(requestedMaxIndex);
        }

        // before doing the paging, check if the output option list has
        // observaion
        OutputOptionFactRelatedHelper opFactRelatedHelper = new OutputOptionFactRelatedHelper(
                getPDOFromInputListReqType.getOutputOption());
        boolean pagingNeeded = opFactRelatedHelper.isFactRelated();
        if (pagingNeeded) {
            PagingHandler ph = new PagingHandler(helper, getPDOFromInputListReqType.getInputList(),
                    getPDOFromInputListReqType.getFilterList(), pageMethod);
            ph.setProjectParamMap(projectParamMap);
            ph.setModifierMetadataXmlMap(modifierMetadataXmlMap);
            HashMap calculatedValueMap = ph.calculateMaxPageInputList();

            // do paging if required
            if ((Boolean) calculatedValueMap.get(PagingHandler.PAGING_REQUIRED_FLAG)) {

                long totalSize = (Long) calculatedValueMap.get(PagingHandler.TOTAL_OBSERVATION);
                int maxInputSize = (Integer) calculatedValueMap.get(PagingHandler.MAX_INPUT_LIST);
                long pageSize = ph.getPageSize();

                // build page type
                PageType pageType = buildPageType(requestedMinIndex, requestedMaxIndex, maxInputSize, totalSize,
                        pageSize);
                patientDataResponseType.setPage(pageType);

                RangeType rangeType = PDOFactory.getRangeType(inputList);
                rangeType.setMax(requestedMinIndex + maxInputSize - 1);

                // inputList.getPatientList().setMax(
                // requestedMinIndex + maxInputSize);
            }
        }
        boolean tablePDO = false;
        if (getPDOFromInputListReqType.getOutputOption().getNames() != null) {
            if (getPDOFromInputListReqType.getOutputOption().getNames().name()
                    .equalsIgnoreCase(OutputOptionNameType.ASATTRIBUTES.name())) {
                tablePDO = true;
            }
        }
        log.debug("PDO reading metadat for patient_dimension table");
        //get patient dimension metadata
        List<ParamType> patientMetaDataList = getPDOTemplate("patient_dimension", dataSourceLookup, tablePDO);
        //get visit dimension metadata
        log.debug("PDO reading metadat for visit_dimension table");
        List<ParamType> visitMetaDataList = getPDOTemplate("visit_dimension", dataSourceLookup, tablePDO);

        if ((ot != null) && ot.name().equalsIgnoreCase(OutputOptionNameType.ASATTRIBUTES.name())) {
            PdoQueryHandler pdoQueryHandler = new PdoQueryHandler(pdoDaoFactory, PdoQueryHandler.TABLE_PDO_TYPE,
                    origInputList, inputList, // /getPDOFromInputListReqType.getInputList(),
                    getPDOFromInputListReqType.getFilterList(), getPDOFromInputListReqType.getOutputOption());
            pdoQueryHandler.setProjectParamMap(projectParamMap);
            pdoQueryHandler.setModifierMetadataXmlMap(modifierMetadataXmlMap);
            pdoQueryHandler.setRequestVersion(version);
            pdoQueryHandler.setDimensionMetaDataParamList(patientMetaDataList, visitMetaDataList);
            pdoQueryHandler.processPDORequest();
            patientDataType = pdoQueryHandler.getTablePdo();
        } else {
            PdoQueryHandler pdoQueryHandler = new PdoQueryHandler(pdoDaoFactory, PdoQueryHandler.PLAIN_PDO_TYPE,
                    origInputList, inputList, // getPDOFromInputListReqType.getInputList(),
                    getPDOFromInputListReqType.getFilterList(), getPDOFromInputListReqType.getOutputOption());
            pdoQueryHandler.setProjectParamMap(projectParamMap);
            pdoQueryHandler.setModifierMetadataXmlMap(modifierMetadataXmlMap);
            pdoQueryHandler.setRequestVersion(version);
            pdoQueryHandler.setDimensionMetaDataParamList(patientMetaDataList, visitMetaDataList);
            pdoQueryHandler.processPDORequest();
            patientDataType = pdoQueryHandler.getPlainPdo();
        }
    } catch (Exception ex) {
        ex.printStackTrace();
        log.error(ex.getMessage(), ex);
        throw new I2B2Exception(ex.getMessage(), ex);
    }
    patientDataResponseType.setPatientData(patientDataType);

    return patientDataResponseType;
}