Java tutorial
/* * Copyright (c) 2006-2007 Massachusetts General Hospital * All rights reserved. This program and the accompanying materials * are made available under the terms of the i2b2 Software License v1.0 * which accompanies this distribution. * * Contributors: * Rajesh Kuttan */ package edu.harvard.i2b2.crc.ejb; import java.io.StringWriter; import java.rmi.RemoteException; import java.sql.SQLException; import java.util.ArrayList; import java.util.Arrays; import java.util.Date; import java.util.HashMap; import java.util.List; import java.util.Map; //import javax.ejb.CreateException; //import javax.ejb.EJBException; //import javax.ejb.SessionBean; //import javax.ejb.SessionContext; import javax.xml.bind.JAXBElement; import javax.xml.stream.XMLStreamException; import org.apache.axis2.AxisFault; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import edu.harvard.i2b2.common.exception.I2B2DAOException; import edu.harvard.i2b2.common.exception.I2B2Exception; import edu.harvard.i2b2.common.exception.StackTraceUtil; import edu.harvard.i2b2.common.util.jaxb.JAXBUtil; import edu.harvard.i2b2.common.util.jaxb.JAXBUtilException; import edu.harvard.i2b2.crc.dao.DAOFactoryHelper; import edu.harvard.i2b2.crc.dao.IDAOFactory; import edu.harvard.i2b2.crc.dao.PatientDataDAOFactory; import edu.harvard.i2b2.crc.dao.pdo.DimensionTable; import edu.harvard.i2b2.crc.dao.pdo.IMetadataDao; import edu.harvard.i2b2.crc.dao.pdo.IObservationFactDao; import edu.harvard.i2b2.crc.dao.pdo.MetaDataTypeMapper; import edu.harvard.i2b2.crc.dao.pdo.MetadataDao; import edu.harvard.i2b2.crc.dao.pdo.MetadataDao.TableMetaData; import edu.harvard.i2b2.crc.dao.pdo.PdoQueryHandler; import edu.harvard.i2b2.crc.dao.pdo.input.IInputOptionListHandler; import edu.harvard.i2b2.crc.dao.pdo.input.OutputOptionFactRelatedHelper; import edu.harvard.i2b2.crc.dao.pdo.input.PDOFactory; import edu.harvard.i2b2.crc.dao.pdo.input.PagingHandler; import edu.harvard.i2b2.crc.dao.setfinder.IQueryPdoMasterDao; import edu.harvard.i2b2.crc.dao.setfinder.querybuilder.ItemMetaDataHandler; import edu.harvard.i2b2.crc.datavo.CRCJAXBUtil; import edu.harvard.i2b2.crc.datavo.db.DataSourceLookup; import edu.harvard.i2b2.crc.datavo.db.QtQueryMaster; import edu.harvard.i2b2.crc.datavo.i2b2message.PasswordType; import edu.harvard.i2b2.crc.datavo.i2b2message.RequestMessageType; import edu.harvard.i2b2.crc.datavo.i2b2message.SecurityType; import edu.harvard.i2b2.crc.datavo.ontology.ConceptType; import edu.harvard.i2b2.crc.datavo.ontology.ModifierType; import edu.harvard.i2b2.crc.datavo.ontology.XmlValueType; import edu.harvard.i2b2.crc.datavo.pdo.ParamType; import edu.harvard.i2b2.crc.datavo.pdo.PatientDataType; import edu.harvard.i2b2.crc.datavo.pdo.query.FilterListType; import edu.harvard.i2b2.crc.datavo.pdo.query.GetObservationFactByPrimaryKeyRequestType; import edu.harvard.i2b2.crc.datavo.pdo.query.GetPDOFromInputListRequestType; import edu.harvard.i2b2.crc.datavo.pdo.query.InputOptionListType; import edu.harvard.i2b2.crc.datavo.pdo.query.ItemType; import edu.harvard.i2b2.crc.datavo.pdo.query.MetadataxmlValueType; import edu.harvard.i2b2.crc.datavo.pdo.query.OutputOptionNameType; import edu.harvard.i2b2.crc.datavo.pdo.query.PageByPatientType; import edu.harvard.i2b2.crc.datavo.pdo.query.PageRangeType; import edu.harvard.i2b2.crc.datavo.pdo.query.PageType; import edu.harvard.i2b2.crc.datavo.pdo.query.PanelType; import edu.harvard.i2b2.crc.datavo.pdo.query.PatientDataResponseType; import edu.harvard.i2b2.crc.datavo.pdo.query.RangeType; import edu.harvard.i2b2.crc.datavo.setfinder.query.QueryDefinitionType; import edu.harvard.i2b2.crc.delegate.ontology.CallOntologyUtil; import edu.harvard.i2b2.crc.role.AuthrizationHelper; import edu.harvard.i2b2.crc.util.I2B2RequestMessageHelper; import edu.harvard.i2b2.crc.util.PMServiceAccountUtil; import edu.harvard.i2b2.crc.util.ParamUtil; import edu.harvard.i2b2.crc.util.QueryProcessorUtil; /** * This is the PDO Query ejb class. It passes pdo query request's to the * appropriate dao classes to get response in pdo format. * * @ejb.bean description="Patient data Query bean" * display-name="Patient data Query" * jndi-name="ejb.querytool.PdoQuery" * local-jndi-name="ejb.querytool.PdoQueryLocal" * name="querytool.PdoQuery" type="Stateless" view-type="both" * transaction-type="Container" * * @ejb.interface remote-class="edu.harvard.i2b2.crc.ejb.PdoQueryRemote" * * @author rkuttan */ public class PdoQueryBean { //implements SessionBean { // RunQuery /** log **/ protected final Log log = LogFactory.getLog(getClass()); /** * Function to get plain pdo from the given pdo request * * @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; } /** * Function to get plain pdo from the given pdo request * * @ejb.interface-method view-type="both" * @ejb.transaction type="Required" */ public List<ParamType> getPDOTemplate(String dimensionTableName, DataSourceLookup dataSourceLookup, boolean tablePDOFlag) throws I2B2Exception { List<ParamType> paramList = new ArrayList<ParamType>(); DAOFactoryHelper helper = new DAOFactoryHelper(dataSourceLookup.getDomainId(), dataSourceLookup.getProjectPath(), dataSourceLookup.getOwnerId()); IDAOFactory daoFactory = helper.getDAOFactory(); // MetaDataTypeMapper metaDataTypeMapper = new MetaDataTypeMapper(); IMetadataDao metadataDao = daoFactory.getPatientDataDAOFactory().getMetadataDAO(); try { Map optionalFieldMap = metadataDao.getMetadataForOptionalField(dimensionTableName); MetadataDao.TableMetaData[] tableMetaDataList = (TableMetaData[]) optionalFieldMap.values() .toArray(new MetadataDao.TableMetaData[] {}); metaDataTypeMapper.fillXmlDataType(tableMetaDataList, tablePDOFlag); for (int i = 0; i < tableMetaDataList.length; i++) { ParamType paramType = new ParamType(); paramType.setColumn(tableMetaDataList[i].column_name); paramType.setColumnDescriptor(tableMetaDataList[i].column_comment); paramType.setType(tableMetaDataList[i].column_xml_type); paramList.add(paramType); } } catch (Exception i2b2DaoEx) { i2b2DaoEx.printStackTrace(); throw new I2B2Exception(i2b2DaoEx.getMessage(), i2b2DaoEx); } return paramList; } private PageType buildPageType(int requestedMinIndex, int requestedMaxIndex, int maxInputIndex, long totalSize, long pageSize) { PageType pageType = new PageType(); PageByPatientType pageByPatientType = new PageByPatientType(); pageByPatientType.setPageSize(pageSize); pageByPatientType.setFactsTotal(totalSize); PageRangeType requestedPageRangeType = new PageRangeType(); requestedPageRangeType.setFirstIndex(requestedMinIndex); requestedPageRangeType.setLastIndex(requestedMaxIndex); pageByPatientType.setPatientsRequested(requestedPageRangeType); PageRangeType returnedPageRangeType = new PageRangeType(); returnedPageRangeType.setFirstIndex(requestedMinIndex); int maxReturnedIndex = requestedMinIndex + maxInputIndex - 1; returnedPageRangeType.setLastIndex(maxReturnedIndex); pageByPatientType.setPatientsReturned(returnedPageRangeType); PageRangeType skippedPageRangeType = new PageRangeType(); skippedPageRangeType.setFirstIndex(0); skippedPageRangeType.setLastIndex(requestedMinIndex); pageByPatientType.setPatientsSkipped(skippedPageRangeType); pageType.setPagingByPatients(pageByPatientType); return pageType; } /** * Function to get observation fact by its primary key * * @ejb.interface-method view-type="both" * @ejb.transaction type="Required" */ public PatientDataType getObservationFactByPrimaryKey(DataSourceLookup dataSourceLookup, GetObservationFactByPrimaryKeyRequestType getObservationFactByPrimaryKeyRequestType) throws I2B2Exception { PatientDataType patientDataType = null; try { PatientDataDAOFactory pdoDaoFactory = getPatientDataDaoFactory(dataSourceLookup.getDomainId(), dataSourceLookup.getProjectPath(), dataSourceLookup.getOwnerId()); IObservationFactDao observationFactDao = pdoDaoFactory.getObservationFactDAO(); patientDataType = observationFactDao.getObservationFactByPrimaryKey( getObservationFactByPrimaryKeyRequestType.getFactPrimaryKey(), getObservationFactByPrimaryKeyRequestType.getFactOutputOption()); } catch (I2B2DAOException ex) { ex.printStackTrace(); log.error(ex.getMessage(), ex); throw new I2B2Exception(ex.getMessage(), ex); } return patientDataType; } private PatientDataDAOFactory getPatientDataDaoFactory(String domainId, String projectPath, String ownerId) throws I2B2DAOException { DAOFactoryHelper helper = new DAOFactoryHelper(domainId, projectPath, ownerId); PatientDataDAOFactory pdoDaoFactory = helper.getDAOFactory().getPatientDataDAOFactory(); return pdoDaoFactory; } private boolean checkForBlob(GetPDOFromInputListRequestType getPDOFromInputListReqType) { boolean booleanConcept = true, booleanEid = true, booleanEvent = true, booleanObservation = true, booleanObserver = true, booleanPatient = true; boolean booleanPid = true; if (getPDOFromInputListReqType.getOutputOption().getConceptSetUsingFilterList() != null) { booleanConcept = getPDOFromInputListReqType.getOutputOption().getConceptSetUsingFilterList().isBlob(); if (booleanConcept) { booleanConcept = false; } else { booleanConcept = true; } } if (getPDOFromInputListReqType.getOutputOption().getEidSet() != null) { booleanEid = getPDOFromInputListReqType.getOutputOption().getEidSet().isBlob(); if (booleanEid) { booleanEid = false; } else { booleanEid = true; } } if (getPDOFromInputListReqType.getOutputOption().getEventSet() != null) { booleanEvent = getPDOFromInputListReqType.getOutputOption().getEventSet().isBlob(); if (booleanEvent) { booleanEvent = false; } else { booleanEvent = true; } } if (getPDOFromInputListReqType.getOutputOption().getObservationSet() != null) { booleanObservation = getPDOFromInputListReqType.getOutputOption().getObservationSet().isBlob(); if (booleanObservation) { booleanObservation = false; } else { booleanObservation = true; } } if (getPDOFromInputListReqType.getOutputOption().getObserverSetUsingFilterList() != null) { booleanObserver = getPDOFromInputListReqType.getOutputOption().getObserverSetUsingFilterList().isBlob(); if (booleanObserver) { booleanObserver = false; } else { booleanObserver = true; } } if (getPDOFromInputListReqType.getOutputOption().getPatientSet() != null) { booleanPatient = getPDOFromInputListReqType.getOutputOption().getPatientSet().isBlob(); if (booleanPatient) { booleanPatient = false; } else { booleanPatient = true; } } if (getPDOFromInputListReqType.getOutputOption().getPidSet() != null) { booleanPid = getPDOFromInputListReqType.getOutputOption().getPidSet().isBlob(); if (booleanPid) { booleanPid = false; } else { booleanPid = true; } } if (booleanConcept && booleanEid && booleanEvent && booleanObservation && booleanObserver && booleanPatient && booleanPid) { return false; } else { return true; } } private void savePdoQueryMaster(IQueryPdoMasterDao queryPdoMasterDao, String requestXml) throws I2B2Exception { QtQueryMaster queryMaster = new QtQueryMaster(); I2B2RequestMessageHelper requestMessageHelper = new I2B2RequestMessageHelper(requestXml); SecurityType securityType = requestMessageHelper.getSecurityType(); String userId = securityType.getUsername(); String groupId = requestMessageHelper.getProjectId(); QueryDefinitionType queryDefType = null; try { queryDefType = requestMessageHelper.getQueryDefinition(); } catch (JAXBUtilException e) { throw new I2B2Exception("Error reading the query definition [" + StackTraceUtil.getStackTrace(e) + "]"); } edu.harvard.i2b2.crc.datavo.setfinder.query.ObjectFactory of = new edu.harvard.i2b2.crc.datavo.setfinder.query.ObjectFactory(); queryMaster.setUserId(userId); StringWriter queryDefWriter = new StringWriter(); try { CRCJAXBUtil.getQueryDefJAXBUtil().marshaller(of.createQueryDefinition(queryDefType), queryDefWriter); } catch (JAXBUtilException e) { throw new I2B2Exception( "Error marshalling the query definition [" + StackTraceUtil.getStackTrace(e) + "]"); } queryMaster.setRequestXml(queryDefWriter.toString()); queryMaster.setGroupId(groupId); queryMaster.setCreateDate(new Date(System.currentTimeMillis())); queryMaster.setI2b2RequestXml(requestXml); queryMaster.setRequestXml(requestXml); //remove user password from the request RequestMessageType i2b2RequestMsgType = requestMessageHelper.getI2B2RequestMessageType(); PasswordType passType = i2b2RequestMsgType.getMessageHeader().getSecurity().getPassword(); passType.setValue("password not stored"); passType.setIsToken(false); JAXBUtil util = CRCJAXBUtil.getJAXBUtil(); StringWriter strWriter = new StringWriter(); edu.harvard.i2b2.crc.datavo.i2b2message.ObjectFactory i2b2ObjFactory = new edu.harvard.i2b2.crc.datavo.i2b2message.ObjectFactory(); try { util.marshaller(i2b2ObjFactory.createRequest(i2b2RequestMsgType), strWriter); } catch (JAXBUtilException e) { throw new I2B2Exception("Error marshalling the request after resetting the password [" + StackTraceUtil.getStackTrace(e) + "]"); } queryPdoMasterDao.createPdoQueryMaster(queryMaster, strWriter.toString()); } private String getVersion(IQueryPdoMasterDao queryPdoMasterDao, String requestXml) throws I2B2Exception { QtQueryMaster queryMaster = new QtQueryMaster(); I2B2RequestMessageHelper requestMessageHelper = new I2B2RequestMessageHelper(requestXml); return requestMessageHelper.getVersion(); } private void copyModifierToItem(ItemType itemType, ModifierType modifierType) { ItemType.ConstrainByModifier modifierConstrain = itemType.getConstrainByModifier(); modifierConstrain.setAppliedPath(modifierType.getAppliedPath()); modifierConstrain.setDimColumndatatype(modifierType.getColumndatatype()); modifierConstrain.setDimColumnname(modifierType.getColumnname()); modifierConstrain.setDimDimcode(modifierType.getDimcode()); modifierConstrain.setDimOperator(modifierType.getOperator()); modifierConstrain.setDimTablename(modifierType.getTablename()); modifierConstrain.setFacttablecolumn(modifierType.getFacttablecolumn()); modifierConstrain.setModifierKey(modifierType.getKey()); modifierConstrain.setModifierName(modifierType.getName()); } }