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: * Raj Kuttan * Lori Phillips */ package edu.harvard.i2b2.ontology.ws; import org.apache.axiom.om.OMElement; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import edu.harvard.i2b2.common.exception.I2B2Exception; import edu.harvard.i2b2.ontology.datavo.i2b2message.ResponseMessageType; import edu.harvard.i2b2.ontology.delegate.AddChildHandler; import edu.harvard.i2b2.ontology.delegate.AddModifierHandler; import edu.harvard.i2b2.ontology.delegate.CRCConceptUpdateHandler; import edu.harvard.i2b2.ontology.delegate.DeleteChildHandler; import edu.harvard.i2b2.ontology.delegate.ExcludeModifierHandler; import edu.harvard.i2b2.ontology.delegate.GetCategoriesHandler; import edu.harvard.i2b2.ontology.delegate.GetChildrenHandler; import edu.harvard.i2b2.ontology.delegate.GetCodeInfoHandler; import edu.harvard.i2b2.ontology.delegate.GetDirtyStateHandler; import edu.harvard.i2b2.ontology.delegate.GetModifierChildrenHandler; import edu.harvard.i2b2.ontology.delegate.GetModifierCodeInfoHandler; import edu.harvard.i2b2.ontology.delegate.GetModifierInfoHandler; import edu.harvard.i2b2.ontology.delegate.GetModifierNameInfoHandler; import edu.harvard.i2b2.ontology.delegate.GetModifiersHandler; import edu.harvard.i2b2.ontology.delegate.GetNameInfoHandler; import edu.harvard.i2b2.ontology.delegate.GetOntProcessStatusHandler; import edu.harvard.i2b2.ontology.delegate.GetSchemesHandler; import edu.harvard.i2b2.ontology.delegate.GetTermInfoHandler; import edu.harvard.i2b2.ontology.delegate.ModifyChildHandler; import edu.harvard.i2b2.ontology.delegate.RequestHandler; import edu.harvard.i2b2.ontology.delegate.UpdateTotalNumHandler; /** * This is webservice skeleton class. It parses incoming Ontology service * requests and generates responses in the Vocab Data Object XML format. * */ public class OntologyService { private static Log log = LogFactory.getLog(OntologyService.class); /** * This function is main webservice interface to get vocab data for a query. * It uses AXIOM elements(OMElement) to conveniently parse xml messages. * * It excepts incoming request in i2b2 message format, which wraps an * Ontology query inside a vocab query request object. The response is also * will be in i2b2 message format, which will wrap vocab data object. Vocab * data object will have all the results returned by the query. * * * @param getChildren * @return OMElement in i2b2message format * @throws Exception */ public OMElement getChildren(OMElement getChildrenElement) throws I2B2Exception { OMElement returnElement = null; String ontologyDataResponse = null; String unknownErrorMessage = "Error message delivered from the remote server \n" + "You may wish to retry your last action"; if (getChildrenElement == null) { log.error("Incoming Ontology request is null"); ResponseMessageType responseMsgType = MessageFactory.doBuildErrorResponse(null, unknownErrorMessage); ontologyDataResponse = MessageFactory.convertToXMLString(responseMsgType); return MessageFactory.createResponseOMElementFromString(ontologyDataResponse); } String requestElementString = getChildrenElement.toString(); GetChildrenDataMessage childrenDataMsg = new GetChildrenDataMessage(requestElementString); long waitTime = 0; if (childrenDataMsg.getRequestMessageType() != null) { if (childrenDataMsg.getRequestMessageType().getRequestHeader() != null) { waitTime = childrenDataMsg.getRequestMessageType().getRequestHeader().getResultWaittimeMs(); } } // do Ontology query processing inside thread, so that // service could sends back message with timeout error. // ExecutorRunnable er = new ExecutorRunnable(); return execute(new GetChildrenHandler(childrenDataMsg), waitTime); } /** * This function is main webservice interface to get vocab data for a query. * It uses AXIOM elements(OMElement) to conveniently parse xml messages. * * It excepts incoming request in i2b2 message format, which wraps an * Ontology query inside a vocab query request object. The response is also * will be in i2b2 message format, which will wrap vocab data object. Vocab * data object will have all the results returned by the query. * * * @param OMElement * getCategoriesElement * @return OMElement in i2b2message format * @throws Exception */ public OMElement getCategories(OMElement getCategoriesElement) throws I2B2Exception { OMElement returnElement = null; String ontologyDataResponse = null; String unknownErrorMessage = "Error message delivered from the remote server \n" + "You may wish to retry your last action"; if (getCategoriesElement == null) { log.error("Incoming Ontology request is null"); ResponseMessageType responseMsgType = MessageFactory.doBuildErrorResponse(null, unknownErrorMessage); ontologyDataResponse = MessageFactory.convertToXMLString(responseMsgType); return MessageFactory.createResponseOMElementFromString(ontologyDataResponse); } String requestElementString = getCategoriesElement.toString(); GetCategoriesDataMessage categoriesDataMsg = new GetCategoriesDataMessage(requestElementString); long waitTime = 0; if (categoriesDataMsg.getRequestMessageType() != null) { if (categoriesDataMsg.getRequestMessageType().getRequestHeader() != null) { waitTime = categoriesDataMsg.getRequestMessageType().getRequestHeader().getResultWaittimeMs(); } } // do Ontology query processing inside thread, so that // service could sends back message with timeout error. // ExecutorRunnable er = new ExecutorRunnable(); return execute(new GetCategoriesHandler(categoriesDataMsg), waitTime); } /** * This function is main webservice interface to get vocab data for a query. * It uses AXIOM elements(OMElement) to conveniently parse xml messages. * * It excepts incoming request in i2b2 message format, which wraps an * Ontology query inside a vocab query request object. The response is also * will be in i2b2 message format, which will wrap vocab data object. Vocab * data object will have all the results returned by the query. * * * @param OMElement * geSchemesElement * @return OMElement in i2b2message format * @throws Exception */ public OMElement getSchemes(OMElement getSchemesElement) throws I2B2Exception { OMElement returnElement = null; String ontologyDataResponse = null; String unknownErrorMessage = "Error message delivered from the remote server \n" + "You may wish to retry your last action"; if (getSchemesElement == null) { log.error("Incoming Ontology request is null"); ResponseMessageType responseMsgType = MessageFactory.doBuildErrorResponse(null, unknownErrorMessage); ontologyDataResponse = MessageFactory.convertToXMLString(responseMsgType); return MessageFactory.createResponseOMElementFromString(ontologyDataResponse); } String requestElementString = getSchemesElement.toString(); GetSchemesDataMessage schemesDataMsg = new GetSchemesDataMessage(requestElementString); long waitTime = 0; if (schemesDataMsg.getRequestMessageType() != null) { if (schemesDataMsg.getRequestMessageType().getRequestHeader() != null) { waitTime = schemesDataMsg.getRequestMessageType().getRequestHeader().getResultWaittimeMs(); } } // do Ontology query processing inside thread, so that // service could sends back message with timeout error. // ExecutorRunnable er = new ExecutorRunnable(); return execute(new GetSchemesHandler(schemesDataMsg), waitTime); } /** * This function is main webservice interface to get vocab data for a query. * It uses AXIOM elements(OMElement) to conveniently parse xml messages. * * It excepts incoming request in i2b2 message format, which wraps an * Ontology query inside a vocab query request object. The response is also * will be in i2b2 message format, which will wrap vocab data object. Vocab * data object will have all the results returned by the query. * * * @param OMElement * getCodeInfoElement * @return OMElement in i2b2message format * @throws Exception */ public OMElement getCodeInfo(OMElement getCodeInfoElement) throws I2B2Exception { OMElement returnElement = null; String ontologyDataResponse = null; String unknownErrorMessage = "Error message delivered from the remote server \n" + "You may wish to retry your last action"; if (getCodeInfoElement == null) { log.error("Incoming Ontology request is null"); ResponseMessageType responseMsgType = MessageFactory.doBuildErrorResponse(null, unknownErrorMessage); ontologyDataResponse = MessageFactory.convertToXMLString(responseMsgType); return MessageFactory.createResponseOMElementFromString(ontologyDataResponse); } String requestElementString = getCodeInfoElement.toString(); GetCodeInfoDataMessage codeInfoDataMsg = new GetCodeInfoDataMessage(requestElementString); long waitTime = 0; if (codeInfoDataMsg.getRequestMessageType() != null) { if (codeInfoDataMsg.getRequestMessageType().getRequestHeader() != null) { waitTime = codeInfoDataMsg.getRequestMessageType().getRequestHeader().getResultWaittimeMs(); } } // do Ontology query processing inside thread, so that // service could sends back message with timeout error. // ExecutorRunnable er = new ExecutorRunnable(); return execute(new GetCodeInfoHandler(codeInfoDataMsg), waitTime); } /** * This function is main webservice interface to get vocab data for a query. * It uses AXIOM elements(OMElement) to conveniently parse xml messages. * * It excepts incoming request in i2b2 message format, which wraps an * Ontology query inside a vocab query request object. The response is also * will be in i2b2 message format, which will wrap vocab data object. Vocab * data object will have all the results returned by the query. * * * @param OMElement * getCodeInfoElement * @return OMElement in i2b2message format * @throws Exception */ public OMElement getNameInfo(OMElement getNameInfoElement) throws I2B2Exception { OMElement returnElement = null; String ontologyDataResponse = null; String unknownErrorMessage = "Error message delivered from the remote server \n" + "You may wish to retry your last action"; if (getNameInfoElement == null) { log.error("Incoming Ontology request is null"); ResponseMessageType responseMsgType = MessageFactory.doBuildErrorResponse(null, unknownErrorMessage); ontologyDataResponse = MessageFactory.convertToXMLString(responseMsgType); return MessageFactory.createResponseOMElementFromString(ontologyDataResponse); } String requestElementString = getNameInfoElement.toString(); GetNameInfoDataMessage nameInfoDataMsg = new GetNameInfoDataMessage(requestElementString); long waitTime = 0; if (nameInfoDataMsg.getRequestMessageType() != null) { if (nameInfoDataMsg.getRequestMessageType().getRequestHeader() != null) { waitTime = nameInfoDataMsg.getRequestMessageType().getRequestHeader().getResultWaittimeMs(); } } // do Ontology query processing inside thread, so that // service could sends back message with timeout error. // ExecutorRunnable er = new ExecutorRunnable(); return execute(new GetNameInfoHandler(nameInfoDataMsg), waitTime); } /** * This function is main webservice interface to get vocab data for a query. * It uses AXIOM elements(OMElement) to conveniently parse xml messages. * * It excepts incoming request in i2b2 message format, which wraps an * Ontology query inside a vocab query request object. The response is also * will be in i2b2 message format, which will wrap vocab data object. Vocab * data object will have all the results returned by the query. * * * @param getChildren * @return OMElement in i2b2message format * @throws Exception */ public OMElement getTermInfo(OMElement getTermInfoElement) throws I2B2Exception { OMElement returnElement = null; String ontologyDataResponse = null; String unknownErrorMessage = "Error message delivered from the remote server \n" + "You may wish to retry your last action"; if (getTermInfoElement == null) { log.error("Incoming Ontology request is null"); ResponseMessageType responseMsgType = MessageFactory.doBuildErrorResponse(null, unknownErrorMessage); ontologyDataResponse = MessageFactory.convertToXMLString(responseMsgType); return MessageFactory.createResponseOMElementFromString(ontologyDataResponse); } String requestElementString = getTermInfoElement.toString(); GetTermInfoDataMessage termInfoDataMsg = new GetTermInfoDataMessage(requestElementString); long waitTime = 0; if (termInfoDataMsg.getRequestMessageType() != null) { if (termInfoDataMsg.getRequestMessageType().getRequestHeader() != null) { waitTime = termInfoDataMsg.getRequestMessageType().getRequestHeader().getResultWaittimeMs(); } } // do Ontology query processing inside thread, so that // service could sends back message with timeout error. // ExecutorRunnable er = new ExecutorRunnable(); return execute(new GetTermInfoHandler(termInfoDataMsg), waitTime); } private OMElement execute(RequestHandler handler, long waitTime) throws I2B2Exception { // do Ontology query processing inside thread, so that // service could sends back message with timeout error. OMElement returnElement = null; String unknownErrorMessage = "Error message delivered from the remote server \n" + "You may wish to retry your last action"; ExecutorRunnable er = new ExecutorRunnable(); er.setRequestHandler(handler); Thread t = new Thread(er); String ontologyDataResponse = null; synchronized (t) { t.start(); // try { // if (waitTime > 0) { // t.wait(waitTime); // } else { // t.wait(); // } try { long startTime = System.currentTimeMillis(); long deltaTime = -1; while ((er.isJobCompleteFlag() == false) && (deltaTime < waitTime)) { if (waitTime > 0) { t.wait(waitTime - deltaTime); deltaTime = System.currentTimeMillis() - startTime; } else { t.wait(); } } ontologyDataResponse = er.getOutputString(); if (ontologyDataResponse == null) { if (er.getJobException() != null) { log.error("er.jobException is " + er.getJobException().getMessage()); log.info("waitTime is " + waitTime); ResponseMessageType responseMsgType = MessageFactory.doBuildErrorResponse(null, unknownErrorMessage); ontologyDataResponse = MessageFactory.convertToXMLString(responseMsgType); } else if (er.isJobCompleteFlag() == false) { // <result_waittime_ms>5000</result_waittime_ms> String timeOuterror = "Remote server timed out \n" + "Result waittime = " + waitTime + " ms elapsed,\nPlease try again"; log.error(timeOuterror); log.debug("ontology waited " + deltaTime + "ms for " + er.getRequestHandler().getClass().getName()); ResponseMessageType responseMsgType = MessageFactory.doBuildErrorResponse(null, timeOuterror); ontologyDataResponse = MessageFactory.convertToXMLString(responseMsgType); } else { log.error("ontology data response is null"); log.info("waitTime is " + waitTime); log.debug("ontology waited " + deltaTime + "ms for " + er.getRequestHandler().getClass().getName()); ResponseMessageType responseMsgType = MessageFactory.doBuildErrorResponse(null, unknownErrorMessage); ontologyDataResponse = MessageFactory.convertToXMLString(responseMsgType); } } } catch (InterruptedException e) { log.error(e.getMessage()); throw new I2B2Exception("Thread error while running Ontology job "); } finally { t.interrupt(); er = null; t = null; } } returnElement = MessageFactory.createResponseOMElementFromString(ontologyDataResponse); return returnElement; } public OMElement addChild(OMElement addChildElement) throws I2B2Exception { OMElement returnElement = null; String ontologyDataResponse = null; String unknownErrorMessage = "Error message delivered from the remote server \n" + "You may wish to retry your last action"; if (addChildElement == null) { log.error("Incoming Ontology request is null"); ResponseMessageType responseMsgType = MessageFactory.doBuildErrorResponse(null, unknownErrorMessage); ontologyDataResponse = MessageFactory.convertToXMLString(responseMsgType); return MessageFactory.createResponseOMElementFromString(ontologyDataResponse); } String requestElementString = addChildElement.toString(); AddChildDataMessage childDataMsg = new AddChildDataMessage(requestElementString); long waitTime = 0; if (childDataMsg.getRequestMessageType() != null) { if (childDataMsg.getRequestMessageType().getRequestHeader() != null) { waitTime = childDataMsg.getRequestMessageType().getRequestHeader().getResultWaittimeMs(); } } // do Ontology query processing inside thread, so that // service could sends back message with timeout error. // ExecutorRunnable er = new ExecutorRunnable(); return execute(new AddChildHandler(childDataMsg), waitTime); } public OMElement modifyChild(OMElement modifyChildElement) throws I2B2Exception { OMElement returnElement = null; String ontologyDataResponse = null; String unknownErrorMessage = "Error message delivered from the remote server \n" + "You may wish to retry your last action"; if (modifyChildElement == null) { log.error("Incoming Ontology request is null"); ResponseMessageType responseMsgType = MessageFactory.doBuildErrorResponse(null, unknownErrorMessage); ontologyDataResponse = MessageFactory.convertToXMLString(responseMsgType); return MessageFactory.createResponseOMElementFromString(ontologyDataResponse); } String requestElementString = modifyChildElement.toString(); log.debug(requestElementString); ModifyChildDataMessage childDataMsg = new ModifyChildDataMessage(requestElementString); long waitTime = 0; if (childDataMsg.getRequestMessageType() != null) { if (childDataMsg.getRequestMessageType().getRequestHeader() != null) { waitTime = childDataMsg.getRequestMessageType().getRequestHeader().getResultWaittimeMs(); } } // do Ontology query processing inside thread, so that // service could sends back message with timeout error. // ExecutorRunnable er = new ExecutorRunnable(); return execute(new ModifyChildHandler(childDataMsg), waitTime); } public OMElement deleteChild(OMElement deleteNodeElement) throws Exception { OMElement returnElement = null; String ontologyDataResponse = null; String unknownErrorMessage = "Error message delivered from the remote server \n" + "You may wish to retry your last action"; if (deleteNodeElement == null) { log.error("Incoming Ontology request is null"); ResponseMessageType responseMsgType = MessageFactory.doBuildErrorResponse(null, unknownErrorMessage); ontologyDataResponse = MessageFactory.convertToXMLString(responseMsgType); return MessageFactory.createResponseOMElementFromString(ontologyDataResponse); } String requestElementString = deleteNodeElement.toString(); DeleteChildDataMessage deleteDataMsg = new DeleteChildDataMessage(requestElementString); // log.info(requestElementString); // deleteDataMsg.setRequestMessageType(requestElementString); long waitTime = 0; if (deleteDataMsg.getRequestMessageType() != null) { if (deleteDataMsg.getRequestMessageType().getRequestHeader() != null) { waitTime = deleteDataMsg.getRequestMessageType().getRequestHeader().getResultWaittimeMs(); } } // do Workplace query processing inside thread, so that // service could send back message with timeout error. // ExecutorRunnable er = new ExecutorRunnable(); return execute(new DeleteChildHandler(deleteDataMsg), waitTime); } public OMElement updateCRCConcept(OMElement updateCRCConceptElement) throws I2B2Exception { OMElement returnElement = null; String ontologyDataResponse = null; String unknownErrorMessage = "Error message delivered from the remote server \n" + "You may wish to retry your last action"; if (updateCRCConceptElement == null) { log.error("Incoming Ontology request is null"); ResponseMessageType responseMsgType = MessageFactory.doBuildErrorResponse(null, unknownErrorMessage); ontologyDataResponse = MessageFactory.convertToXMLString(responseMsgType); return MessageFactory.createResponseOMElementFromString(ontologyDataResponse); } String requestElementString = updateCRCConceptElement.toString(); CRCUpdateConceptMessage childDataMsg = new CRCUpdateConceptMessage(requestElementString); long waitTime = 0; if (childDataMsg.getRequestMessageType() != null) { if (childDataMsg.getRequestMessageType().getRequestHeader() != null) { waitTime = childDataMsg.getRequestMessageType().getRequestHeader().getResultWaittimeMs(); } } // do Ontology query processing inside thread, so that // service could sends back message with timeout error. // ExecutorRunnable er = new ExecutorRunnable(); return execute(new CRCConceptUpdateHandler(childDataMsg), waitTime); } public OMElement updateConceptTotalNum(OMElement updateConceptTotalNumElement) throws I2B2Exception { OMElement returnElement = null; String ontologyDataResponse = null; String unknownErrorMessage = "Error message delivered from the remote server \n" + "You may wish to retry your last action"; if (updateConceptTotalNumElement == null) { log.error("Incoming Ontology request is null"); ResponseMessageType responseMsgType = MessageFactory.doBuildErrorResponse(null, unknownErrorMessage); ontologyDataResponse = MessageFactory.convertToXMLString(responseMsgType); return MessageFactory.createResponseOMElementFromString(ontologyDataResponse); } String requestElementString = updateConceptTotalNumElement.toString(); UpdateTotalNumMessage childDataMsg = new UpdateTotalNumMessage(requestElementString); long waitTime = 0; if (childDataMsg.getRequestMessageType() != null) { if (childDataMsg.getRequestMessageType().getRequestHeader() != null) { waitTime = childDataMsg.getRequestMessageType().getRequestHeader().getResultWaittimeMs(); } } // do Ontology query processing inside thread, so that // service could sends back message with timeout error. // ExecutorRunnable er = new ExecutorRunnable(); return execute(new UpdateTotalNumHandler(childDataMsg), waitTime); } public OMElement getProcessStatus(OMElement getOntProcessStatus) throws I2B2Exception { OMElement returnElement = null; String ontologyDataResponse = null; String unknownErrorMessage = "Error message delivered from the remote server \n" + "You may wish to retry your last action"; if (getOntProcessStatus == null) { log.error("Incoming Ontology request is null"); ResponseMessageType responseMsgType = MessageFactory.doBuildErrorResponse(null, unknownErrorMessage); ontologyDataResponse = MessageFactory.convertToXMLString(responseMsgType); return MessageFactory.createResponseOMElementFromString(ontologyDataResponse); } String requestElementString = getOntProcessStatus.toString(); GetOntProcessStatusMessage childDataMsg = new GetOntProcessStatusMessage(requestElementString); long waitTime = 0; if (childDataMsg.getRequestMessageType() != null) { if (childDataMsg.getRequestMessageType().getRequestHeader() != null) { waitTime = childDataMsg.getRequestMessageType().getRequestHeader().getResultWaittimeMs(); } } // do Ontology query processing inside thread, so that // service could sends back message with timeout error. // ExecutorRunnable er = new ExecutorRunnable(); return execute(new GetOntProcessStatusHandler(childDataMsg), waitTime); } /** * This function is main webservice interface to get vocab data for a query. * It uses AXIOM elements(OMElement) to conveniently parse xml messages. * * It excepts incoming request in i2b2 message format, which wraps an * Ontology query inside a vocab query request object. The response is also * will be in i2b2 message format, which will wrap vocab data object. Vocab * data object will have all the results returned by the query. * * * @param OMElement * getDirtyStateElement * @return OMElement in i2b2message format * @throws Exception */ public OMElement getDirtyState(OMElement getDirtyStateElement) throws I2B2Exception { OMElement returnElement = null; String ontologyDataResponse = null; String unknownErrorMessage = "Error message delivered from the remote server \n" + "You may wish to retry your last action"; if (getDirtyStateElement == null) { log.error("Incoming Ontology request is null"); ResponseMessageType responseMsgType = MessageFactory.doBuildErrorResponse(null, unknownErrorMessage); ontologyDataResponse = MessageFactory.convertToXMLString(responseMsgType); return MessageFactory.createResponseOMElementFromString(ontologyDataResponse); } String requestElementString = getDirtyStateElement.toString(); GetDirtyStateDataMessage dirtyStateDataMsg = new GetDirtyStateDataMessage(requestElementString); long waitTime = 0; if (dirtyStateDataMsg.getRequestMessageType() != null) { if (dirtyStateDataMsg.getRequestMessageType().getRequestHeader() != null) { waitTime = dirtyStateDataMsg.getRequestMessageType().getRequestHeader().getResultWaittimeMs(); } } // do Ontology query processing inside thread, so that // service could sends back message with timeout error. // ExecutorRunnable er = new ExecutorRunnable(); return execute(new GetDirtyStateHandler(dirtyStateDataMsg), waitTime); } /** * This function is main webservice interface to get modifier data for a query. * It uses AXIOM elements(OMElement) to conveniently parse xml messages. * * It excepts incoming request in i2b2 message format, which wraps an * Ontology query inside a modifier query request object. The response is also * will be in i2b2 message format, which will wrap modifier data object. Modifier * data object will have all the results returned by the query. * * * @param getModifiers * @return OMElement in i2b2message format * @throws Exception */ public OMElement getModifiers(OMElement getModifiersElement) throws I2B2Exception { OMElement returnElement = null; String ontologyDataResponse = null; String unknownErrorMessage = "Error message delivered from the remote server \n" + "You may wish to retry your last action"; if (getModifiersElement == null) { log.error("Incoming Ontology request is null"); ResponseMessageType responseMsgType = MessageFactory.doBuildErrorResponse(null, unknownErrorMessage); ontologyDataResponse = MessageFactory.convertToXMLString(responseMsgType); return MessageFactory.createResponseOMElementFromString(ontologyDataResponse); } String requestElementString = getModifiersElement.toString(); GetModifiersDataMessage modifiersDataMsg = new GetModifiersDataMessage(requestElementString); long waitTime = 0; if (modifiersDataMsg.getRequestMessageType() != null) { if (modifiersDataMsg.getRequestMessageType().getRequestHeader() != null) { waitTime = modifiersDataMsg.getRequestMessageType().getRequestHeader().getResultWaittimeMs(); } } // do Ontology query processing inside thread, so that // service could sends back message with timeout error. // ExecutorRunnable er = new ExecutorRunnable(); return execute(new GetModifiersHandler(modifiersDataMsg), waitTime); } /** * This function is main webservice interface to get modifier data for a query. * It uses AXIOM elements(OMElement) to conveniently parse xml messages. * * It excepts incoming request in i2b2 message format, which wraps an * Ontology query inside a modifier query request object. The response is also * will be in i2b2 message format, which will wrap modifier data object. Modifier * data object will have all the results returned by the query. * * * @param getModifierInfo * @return OMElement in i2b2message format * @throws Exception */ public OMElement getModifierInfo(OMElement getModifierInfoElement) throws I2B2Exception { OMElement returnElement = null; String ontologyDataResponse = null; String unknownErrorMessage = "Error message delivered from the remote server \n" + "You may wish to retry your last action"; if (getModifierInfoElement == null) { log.error("Incoming Ontology request is null"); ResponseMessageType responseMsgType = MessageFactory.doBuildErrorResponse(null, unknownErrorMessage); ontologyDataResponse = MessageFactory.convertToXMLString(responseMsgType); return MessageFactory.createResponseOMElementFromString(ontologyDataResponse); } String requestElementString = getModifierInfoElement.toString(); GetModifierInfoDataMessage modifierInfoDataMsg = new GetModifierInfoDataMessage(requestElementString); long waitTime = 0; if (modifierInfoDataMsg.getRequestMessageType() != null) { if (modifierInfoDataMsg.getRequestMessageType().getRequestHeader() != null) { waitTime = modifierInfoDataMsg.getRequestMessageType().getRequestHeader().getResultWaittimeMs(); } } // do Ontology query processing inside thread, so that // service could sends back message with timeout error. // ExecutorRunnable er = new ExecutorRunnable(); return execute(new GetModifierInfoHandler(modifierInfoDataMsg), waitTime); } /** * This function is main webservice interface to get modifier data for a query. * It uses AXIOM elements(OMElement) to conveniently parse xml messages. * * It excepts incoming request in i2b2 message format, which wraps an * Ontology query inside a modifier query request object. The response is also * will be in i2b2 message format, which will wrap modifier data object. Modifier * data object will have all the results returned by the query. * * * @param getModifierInfo * @return OMElement in i2b2message format * @throws Exception */ public OMElement getModifierChildren(OMElement getModifierChildrenElement) throws I2B2Exception { OMElement returnElement = null; String ontologyDataResponse = null; String unknownErrorMessage = "Error message delivered from the remote server \n" + "You may wish to retry your last action"; if (getModifierChildrenElement == null) { log.error("Incoming Ontology request is null"); ResponseMessageType responseMsgType = MessageFactory.doBuildErrorResponse(null, unknownErrorMessage); ontologyDataResponse = MessageFactory.convertToXMLString(responseMsgType); return MessageFactory.createResponseOMElementFromString(ontologyDataResponse); } String requestElementString = getModifierChildrenElement.toString(); GetModifierChildrenDataMessage modifierChildrenDataMsg = new GetModifierChildrenDataMessage( requestElementString); long waitTime = 0; if (modifierChildrenDataMsg.getRequestMessageType() != null) { if (modifierChildrenDataMsg.getRequestMessageType().getRequestHeader() != null) { waitTime = modifierChildrenDataMsg.getRequestMessageType().getRequestHeader().getResultWaittimeMs(); } } // do Ontology query processing inside thread, so that // service could sends back message with timeout error. // ExecutorRunnable er = new ExecutorRunnable(); return execute(new GetModifierChildrenHandler(modifierChildrenDataMsg), waitTime); } public OMElement addModifier(OMElement addChildElement) throws I2B2Exception { OMElement returnElement = null; String ontologyDataResponse = null; String unknownErrorMessage = "Error message delivered from the remote server \n" + "You may wish to retry your last action"; if (addChildElement == null) { log.error("Incoming Ontology request is null"); ResponseMessageType responseMsgType = MessageFactory.doBuildErrorResponse(null, unknownErrorMessage); ontologyDataResponse = MessageFactory.convertToXMLString(responseMsgType); return MessageFactory.createResponseOMElementFromString(ontologyDataResponse); } String requestElementString = addChildElement.toString(); AddChildDataMessage childDataMsg = new AddChildDataMessage(requestElementString); long waitTime = 0; if (childDataMsg.getRequestMessageType() != null) { if (childDataMsg.getRequestMessageType().getRequestHeader() != null) { waitTime = childDataMsg.getRequestMessageType().getRequestHeader().getResultWaittimeMs(); } } // do Ontology query processing inside thread, so that // service could sends back message with timeout error. // ExecutorRunnable er = new ExecutorRunnable(); return execute(new AddModifierHandler(childDataMsg), waitTime); } public OMElement excludeModifier(OMElement addChildElement) throws I2B2Exception { OMElement returnElement = null; String ontologyDataResponse = null; String unknownErrorMessage = "Error message delivered from the remote server \n" + "You may wish to retry your last action"; if (addChildElement == null) { log.error("Incoming Ontology request is null"); ResponseMessageType responseMsgType = MessageFactory.doBuildErrorResponse(null, unknownErrorMessage); ontologyDataResponse = MessageFactory.convertToXMLString(responseMsgType); return MessageFactory.createResponseOMElementFromString(ontologyDataResponse); } String requestElementString = addChildElement.toString(); AddChildDataMessage childDataMsg = new AddChildDataMessage(requestElementString); long waitTime = 0; if (childDataMsg.getRequestMessageType() != null) { if (childDataMsg.getRequestMessageType().getRequestHeader() != null) { waitTime = childDataMsg.getRequestMessageType().getRequestHeader().getResultWaittimeMs(); } } // do Ontology query processing inside thread, so that // service could sends back message with timeout error. // ExecutorRunnable er = new ExecutorRunnable(); return execute(new ExcludeModifierHandler(childDataMsg), waitTime); } /** * This function is main webservice interface to get vocab data for a query. * It uses AXIOM elements(OMElement) to conveniently parse xml messages. * * It excepts incoming request in i2b2 message format, which wraps an * Ontology query inside a vocab query request object. The response is also * will be in i2b2 message format, which will wrap vocab data object. Vocab * data object will have all the results returned by the query. * * * @param OMElement * getModifierNameInfoElement * @return OMElement in i2b2message format * @throws Exception */ public OMElement getModifierNameInfo(OMElement getNameInfoElement) throws I2B2Exception { OMElement returnElement = null; String ontologyDataResponse = null; String unknownErrorMessage = "Error message delivered from the remote server \n" + "You may wish to retry your last action"; if (getNameInfoElement == null) { log.error("Incoming Ontology request is null"); ResponseMessageType responseMsgType = MessageFactory.doBuildErrorResponse(null, unknownErrorMessage); ontologyDataResponse = MessageFactory.convertToXMLString(responseMsgType); return MessageFactory.createResponseOMElementFromString(ontologyDataResponse); } String requestElementString = getNameInfoElement.toString(); GetNameInfoDataMessage nameInfoDataMsg = new GetNameInfoDataMessage(requestElementString); long waitTime = 0; if (nameInfoDataMsg.getRequestMessageType() != null) { if (nameInfoDataMsg.getRequestMessageType().getRequestHeader() != null) { waitTime = nameInfoDataMsg.getRequestMessageType().getRequestHeader().getResultWaittimeMs(); } } // do Ontology query processing inside thread, so that // service could sends back message with timeout error. // ExecutorRunnable er = new ExecutorRunnable(); return execute(new GetModifierNameInfoHandler(nameInfoDataMsg), waitTime); } /** * This function is main webservice interface to get vocab data for a query. * It uses AXIOM elements(OMElement) to conveniently parse xml messages. * * It excepts incoming request in i2b2 message format, which wraps an * Ontology query inside a vocab query request object. The response is also * will be in i2b2 message format, which will wrap vocab data object. Vocab * data object will have all the results returned by the query. * * * @param OMElement * getModifierCodeInfoElement * @return OMElement in i2b2message format * @throws Exception */ public OMElement getModifierCodeInfo(OMElement getCodeInfoElement) throws I2B2Exception { OMElement returnElement = null; String ontologyDataResponse = null; String unknownErrorMessage = "Error message delivered from the remote server \n" + "You may wish to retry your last action"; if (getCodeInfoElement == null) { log.error("Incoming Ontology request is null"); ResponseMessageType responseMsgType = MessageFactory.doBuildErrorResponse(null, unknownErrorMessage); ontologyDataResponse = MessageFactory.convertToXMLString(responseMsgType); return MessageFactory.createResponseOMElementFromString(ontologyDataResponse); } String requestElementString = getCodeInfoElement.toString(); GetCodeInfoDataMessage codeInfoDataMsg = new GetCodeInfoDataMessage(requestElementString); long waitTime = 0; if (codeInfoDataMsg.getRequestMessageType() != null) { if (codeInfoDataMsg.getRequestMessageType().getRequestHeader() != null) { waitTime = codeInfoDataMsg.getRequestMessageType().getRequestHeader().getResultWaittimeMs(); } } // do Ontology query processing inside thread, so that // service could sends back message with timeout error. // ExecutorRunnable er = new ExecutorRunnable(); return execute(new GetModifierCodeInfoHandler(codeInfoDataMsg), waitTime); } }