Java tutorial
/* * Copyright (c) 2006-2012 Massachusetts General Hospital * All rights reserved. This program and the accompanying materials * are made available under the terms of the i2b2 Software License v2.1 * which accompanies this distribution. * * Contributors: * Lori Phillips */ package edu.harvard.i2b2.patientSet.data; import java.io.IOException; import java.io.StringReader; import java.io.StringWriter; import java.util.ArrayList; import javax.xml.bind.JAXBContext; import javax.xml.bind.JAXBElement; import javax.xml.bind.Unmarshaller; import org.jdom.JDOMException; import org.jdom.input.SAXBuilder; import org.jdom.output.DOMOutputter; import org.w3c.dom.Document; import org.w3c.dom.Element; import org.w3c.dom.Node; import org.w3c.dom.NodeList; import edu.harvard.i2b2.crcxmljaxb.datavo.i2b2message.BodyType; import edu.harvard.i2b2.crcxmljaxb.datavo.i2b2message.InfoType; import edu.harvard.i2b2.crcxmljaxb.datavo.i2b2message.MessageHeaderType; import edu.harvard.i2b2.crcxmljaxb.datavo.i2b2message.RequestHeaderType; import edu.harvard.i2b2.crcxmljaxb.datavo.i2b2message.RequestMessageType; import edu.harvard.i2b2.crcxmljaxb.datavo.i2b2message.SecurityType; import edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.ItemType; import edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.PanelType; import edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.PsmQryHeaderType; import edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.PsmRequestTypeType; import edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.QueryDefinitionRequestType; import edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.QueryDefinitionType; import edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.ResultOutputOptionListType; import edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.ResultOutputOptionType; import edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.UserType; import edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.ItemType.ConstrainByDate; import edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.ItemType.ConstrainByModifier; import edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.ItemType.ConstrainByValue; import edu.harvard.i2b2.eclipse.UserInfoBean; import edu.harvard.i2b2.eclipse.plugins.patientSet.workplaceMessaging.ExportChildRequestMessage; import edu.harvard.i2b2.eclipse.plugins.patientSet.workplaceMessaging.WorkplaceRequestData; import edu.harvard.i2b2.patientSet.datavo.PatientSetJAXBUtil; import edu.harvard.i2b2.crcxmljaxb.datavo.wdo.XmlValueType; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; public class XmlUtil { //to make this class singleton private static XmlUtil thisInstance; private static Log log = LogFactory.getLog(XmlUtil.class.getName()); static { thisInstance = new XmlUtil(); } public static XmlUtil getInstance() { return thisInstance; } public String writeQueryXML(String resultOptions) throws Exception { // String domString = edu.harvard.i2b2.common.util.xml.XMLUtil // .convertDOMElementToString(element); JAXBContext jc1 = JAXBContext.newInstance(edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.ObjectFactory.class); Unmarshaller unMarshaller = jc1.createUnmarshaller(); JAXBElement queryDefinitionJaxbElement = (JAXBElement) unMarshaller .unmarshal(new StringReader(resultOptions)); QueryDefinitionType queryDefinitionType = (QueryDefinitionType) queryDefinitionJaxbElement.getValue(); //Document queryDefinitionType = edu.harvard.i2b2.common.util.xml.XMLUtil..convertStringToDOM(resultOptions); //new QueryDefinitionType(); ResultOutputOptionListType resultOutputOptionListType = new ResultOutputOptionListType(); // /loop thru the options ResultOutputOptionType resultOutputOptionType = new ResultOutputOptionType(); resultOutputOptionType.setName("patient_count_xml"); // ); resultOutputOptionType.setPriorityIndex(1); resultOutputOptionListType.getResultOutput().add(resultOutputOptionType); QueryDefinitionRequestType queryDefinitionRequestType = new QueryDefinitionRequestType(); // create header PsmQryHeaderType headerType = new PsmQryHeaderType(); UserType userType = new UserType(); // userType.setLogin(UserInfoBean.getInstance().getUserName()); // userType.setGroup(System.getProperty("projectName")); // userType.setValue(UserInfoBean.getInstance().getUserName()); headerType.setUser(userType); headerType.setRequestType(PsmRequestTypeType.CRC_QRY_RUN_QUERY_INSTANCE_FROM_QUERY_DEFINITION); queryDefinitionRequestType.setQueryDefinition(queryDefinitionType); queryDefinitionRequestType.setResultOutputList(resultOutputOptionListType); RequestHeaderType requestHeader = new RequestHeaderType(); if (System.getProperty("QueryToolMaxWaitingTime") != null) { requestHeader .setResultWaittimeMs((Integer.parseInt(System.getProperty("QueryToolMaxWaitingTime"))) * 1000); } else { requestHeader.setResultWaittimeMs(180000); } BodyType bodyType = new BodyType(); edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.ObjectFactory psmOf = new edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.ObjectFactory(); bodyType.getAny().add(psmOf.createPsmheader(headerType)); bodyType.getAny().add(psmOf.createRequest(queryDefinitionRequestType)); ExportChildRequestMessage reqMsg = new ExportChildRequestMessage(); MessageHeaderType messageHeader = reqMsg.getMessageHeader(); SecurityType security = messageHeader.getSecurity(); security.setPassword(null); messageHeader.setSecurity(security); RequestMessageType requestMessageType = new RequestMessageType(); requestMessageType.setMessageBody(bodyType); requestMessageType.setMessageHeader(messageHeader); requestMessageType.setRequestHeader(requestHeader); edu.harvard.i2b2.common.util.jaxb.JAXBUtil jaxbUtil = PatientSetJAXBUtil.getJAXBUtil(); StringWriter strWriter = new StringWriter(); try { edu.harvard.i2b2.crcxmljaxb.datavo.i2b2message.ObjectFactory of = new edu.harvard.i2b2.crcxmljaxb.datavo.i2b2message.ObjectFactory(); jaxbUtil.marshaller(of.createRequest(requestMessageType), strWriter); } catch (Exception e) { e.printStackTrace(); } return strWriter.toString(); } public static XmlValueType stringToXml(String c_xml) { if (c_xml == null) return null; else { // convert SAXBuilder parser = new SAXBuilder(); java.io.StringReader xmlStringReader = new java.io.StringReader(c_xml); Element rootElement = null; try { org.jdom.Document metadataDoc = parser.build(xmlStringReader); org.jdom.output.DOMOutputter out = new DOMOutputter(); Document doc = out.output(metadataDoc); rootElement = doc.getDocumentElement(); } catch (JDOMException e) { log.error(e.getMessage()); return null; } catch (IOException e1) { log.error(e1.getMessage()); return null; } if (rootElement != null) { XmlValueType xml = new XmlValueType(); xml.getAny().add(rootElement); return xml; } } return null; } public static String getName(XmlValueType xml) { String name = null; Element rootElement = xml.getAny().get(0); NodeList nameElements = rootElement.getElementsByTagName("name"); // Group templates dont have tag 'name' if (nameElements.getLength() == 0) { nameElements = rootElement.getElementsByTagNameNS("*", "panel"); if (nameElements.getLength() == 0) { nameElements = rootElement.getElementsByTagName("query_name"); if (nameElements.getLength() == 0) { // if we get to here and no name has been found then its a PDO. // return generically -- change to obs or event etc one level up. return "PDO"; } else { name = nameElements.item(0).getTextContent(); } } else { name = nameElements.item(0).getAttributes().getNamedItem("name").getNodeValue(); } if (name != null) return name; // Default to ABC if we cant find a name at all. else return "ABC" + MessageUtil.getInstance().getTimestamp(); } // append result_instance_id to PATIENT_COUNT_XML <name> to create unique name else if ((nameElements.item(0).getTextContent().equals("PATIENT_COUNT_XML"))) { NodeList resultElements = rootElement.getElementsByTagName("result_instance_id"); if (resultElements.getLength() > 0) { String resultInstanceId = resultElements.item(0).getTextContent(); return nameElements.item(0).getTextContent() + "_" + resultInstanceId; } } else if ((nameElements.item(0).getTextContent().equals("PATIENTSET")) || (nameElements.item(0).getTextContent().equals("PATIENT_ENCOUNTER_SET")) || (nameElements.item(0).getTextContent().equals("PATIENT_GENDER_COUNT_XML")) || (nameElements.item(0).getTextContent().equals("PATIENT_AGE_COUNT_XML")) || (nameElements.item(0).getTextContent().equals("PATIENT_VITALSTATUS_COUNT_XML")) || (nameElements.item(0).getTextContent().equals("PATIENT_RACE_COUNT_XML"))) { NodeList resultElements = rootElement.getElementsByTagName("description"); if (resultElements.getLength() > 0) { return resultElements.item(0).getTextContent(); } } return nameElements.item(0).getTextContent(); } public static String getPatientId(XmlValueType xml) { Element rootElement = xml.getAny().get(0); NodeList nameElements = rootElement.getElementsByTagName("patient_id"); if (nameElements.getLength() != 0) { return nameElements.item(0).getTextContent(); } else return MessageUtil.getInstance().getTimestamp(); } public static String getSiteId(XmlValueType xml) { Element rootElement = xml.getAny().get(0); NodeList nameElements = rootElement.getElementsByTagName("patient_id"); if (nameElements.getLength() != 0 && nameElements.item(0).getAttributes().getLength() != 0) { return nameElements.item(0).getAttributes().item(0).getTextContent(); } else return "";//MessageUtil.getInstance().getTimestamp(); } public static String getIndex(XmlValueType xml) { Element rootElement = xml.getAny().get(0); NodeList indexElements = rootElement.getElementsByTagName("index"); if (indexElements.getLength() == 0) return null; return indexElements.item(0).getTextContent(); } public static Boolean hasConceptTag(XmlValueType xml) { Element rootElement = xml.getAny().get(0); NodeList conceptElements = rootElement.getElementsByTagNameNS("*", "concepts"); if (conceptElements.getLength() == 0) return false; else return true; } public static Boolean hasFolderTag(XmlValueType xml) { Element rootElement = xml.getAny().get(0); NodeList folderElements = rootElement.getElementsByTagName("folder"); if (folderElements.getLength() == 0) return false; else return true; } public static Boolean hasBreakdownTag(XmlValueType xml) { Element rootElement = xml.getAny().get(0); // <name>PATIENTSET</name> NodeList psElements = rootElement.getElementsByTagName("name"); if (psElements.getLength() == 0) return false; else { Boolean result = false; for (int i = 0; i < psElements.getLength(); i++) { String resultTypeName = psElements.item(i).getTextContent(); // log.info(resultTypeName); if (resultTypeName.equals("PATIENT_GENDER_COUNT_XML") || resultTypeName.equals("PATIENT_AGE_COUNT_XML") || resultTypeName.equals("PATIENT_VITALSTATUS_COUNT_XML") || resultTypeName.equals("PATIENT_RACE_COUNT_XML")) { result = true; } } return result; } } public static Boolean hasPatientSetTag(XmlValueType xml) { Element rootElement = xml.getAny().get(0); // <name>PATIENTSET</name> NodeList psElements = rootElement.getElementsByTagName("name"); if (psElements.getLength() == 0) return false; else { Boolean result = false; for (int i = 0; i < psElements.getLength(); i++) { String resultTypeName = psElements.item(i).getTextContent(); // log.info(resultTypeName); if (resultTypeName.equals("PATIENTSET")) { result = true; } } return result; } } public static String getXmlI2B2Type(XmlValueType xml) { Element rootElement = xml.getAny().get(0); // <name>PATIENTSET</name> NodeList pcElements = rootElement.getElementsByTagName("name"); if (pcElements.getLength() == 0) return null; else { return pcElements.item(0).getTextContent(); } } public static Boolean hasPatientCountTag(XmlValueType xml) { Element rootElement = xml.getAny().get(0); // <name>PATIENTSET</name> NodeList pcElements = rootElement.getElementsByTagName("name"); if (pcElements.getLength() == 0) return false; else { Boolean result = false; for (int i = 0; i < pcElements.getLength(); i++) { String resultTypeName = pcElements.item(i).getTextContent(); // log.info(resultTypeName); if (resultTypeName.equals("PATIENT_COUNT_XML")) { result = true; } } return result; } } public static Boolean hasEncounterSetTag(XmlValueType xml) { Element rootElement = xml.getAny().get(0); // <name>PATIENTSET</name> NodeList psElements = rootElement.getElementsByTagName("name"); if (psElements.getLength() == 0) return false; else { Boolean result = false; for (int i = 0; i < psElements.getLength(); i++) { String resultTypeName = psElements.item(i).getTextContent(); // log.info(resultTypeName); if (resultTypeName.equals("PATIENT_ENCOUNTER_SET")) { result = true; } } return result; } } public static Boolean hasPrevQueryTag(XmlValueType xml) { Element rootElement = xml.getAny().get(0); // <query_master_id> indicates PrevQuery NodeList pqElements = rootElement.getElementsByTagNameNS("*", "query_master"); if (pqElements.getLength() == 0) return false; else return true; } public static Boolean hasGroupTemplateTag(XmlValueType xml) { Element rootElement = xml.getAny().get(0); // <query_master_id> indicates PrevQuery NodeList gtElements = rootElement.getElementsByTagNameNS("*", "panel"); if (gtElements.getLength() == 0) return false; else return true; } public static Boolean hasQueryDefinitionTag(XmlValueType xml) { Element rootElement = xml.getAny().get(0); NodeList gtElements = rootElement.getElementsByTagNameNS("*", "query_definition"); if (gtElements.getLength() == 0) return false; else return true; } public static Boolean hasObservationTag(XmlValueType xml) { Element rootElement = xml.getAny().get(0); NodeList gtElements = rootElement.getElementsByTagNameNS("*", "observation_set"); if (gtElements.getLength() == 0) return false; else return true; } public static Boolean hasPatientDataTag(XmlValueType xml) { Element rootElement = xml.getAny().get(0); NodeList gtElements = rootElement.getElementsByTagNameNS("*", "patient_data"); if (gtElements.getLength() == 0) return false; else return true; } public static Boolean hasPatientTag(XmlValueType xml) { Element rootElement = xml.getAny().get(0); NodeList gtElements = rootElement.getElementsByTagNameNS("*", "patient_set"); if (gtElements.getLength() == 0) return false; else return true; } }