Java tutorial
/** * The contents of this file are subject to the Mozilla Public License * Version 1.1 (the "License"); you may not use this file except in * compliance with the License. You may obtain a copy of the License at * http://www.mozilla.org/MPL/ * * Software distributed under the License is distributed on an "AS IS" * basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the * License for the specific language governing rights and limitations under * the License. * * The Original Code is OpenELIS code. * * Copyright (C) The Minnesota Department of Health. All Rights Reserved. */ package us.mn.state.health.lims.reports.action; import java.io.ByteArrayOutputStream; import java.io.File; import java.io.IOException; import java.io.InputStream; import java.io.StringReader; import java.sql.Timestamp; import java.util.ArrayList; import java.util.Collections; import java.util.List; import java.util.Properties; import javax.servlet.ServletContext; import javax.servlet.http.HttpServletRequest; import javax.servlet.http.HttpServletResponse; import javax.servlet.http.HttpSession; import javax.xml.parsers.DocumentBuilder; import javax.xml.parsers.DocumentBuilderFactory; import javax.xml.parsers.ParserConfigurationException; import javax.xml.transform.Source; import javax.xml.transform.Transformer; import javax.xml.transform.TransformerConfigurationException; import javax.xml.transform.TransformerException; import javax.xml.transform.TransformerFactory; import javax.xml.transform.stream.StreamResult; import javax.xml.transform.stream.StreamSource; import org.apache.commons.beanutils.PropertyUtils; import org.apache.struts.Globals; import org.apache.struts.action.ActionForm; import org.apache.struts.action.ActionForward; import org.apache.struts.action.ActionMapping; import org.apache.struts.action.ActionMessages; import org.w3c.dom.Document; import org.xml.sax.InputSource; import org.xml.sax.SAXException; import us.mn.state.health.lims.audittrail.dao.AuditTrailDAO; import us.mn.state.health.lims.audittrail.daoimpl.AuditTrailDAOImpl; import us.mn.state.health.lims.audittrail.valueholder.History; import us.mn.state.health.lims.common.action.BaseAction; import us.mn.state.health.lims.common.action.BaseActionForm; import us.mn.state.health.lims.common.action.IActionConstants; import us.mn.state.health.lims.common.exception.LIMSRuntimeException; import us.mn.state.health.lims.common.log.LogEvent; import us.mn.state.health.lims.common.util.DateUtil; import us.mn.state.health.lims.common.util.StringUtil; import us.mn.state.health.lims.common.util.SystemConfiguration; import us.mn.state.health.lims.common.util.validator.ActionError; import us.mn.state.health.lims.organization.valueholder.Organization; import us.mn.state.health.lims.patient.dao.PatientDAO; import us.mn.state.health.lims.patient.daoimpl.PatientDAOImpl; import us.mn.state.health.lims.patient.valueholder.Patient; import us.mn.state.health.lims.person.valueholder.Person; import us.mn.state.health.lims.project.valueholder.Project; import us.mn.state.health.lims.provider.dao.ProviderDAO; import us.mn.state.health.lims.provider.daoimpl.ProviderDAOImpl; import us.mn.state.health.lims.provider.valueholder.Provider; import us.mn.state.health.lims.referencetables.dao.ReferenceTablesDAO; import us.mn.state.health.lims.referencetables.daoimpl.ReferenceTablesDAOImpl; import us.mn.state.health.lims.referencetables.valueholder.ReferenceTables; import us.mn.state.health.lims.reports.valueholder.audittrail.HistoryComparator; import us.mn.state.health.lims.reports.valueholder.audittrail.HistoryXmlHelper; import us.mn.state.health.lims.reports.valueholder.audittrail.SampleXmlHelper; import us.mn.state.health.lims.sample.dao.SampleDAO; import us.mn.state.health.lims.sample.daoimpl.SampleDAOImpl; import us.mn.state.health.lims.sample.valueholder.Sample; import us.mn.state.health.lims.samplehuman.dao.SampleHumanDAO; import us.mn.state.health.lims.samplehuman.daoimpl.SampleHumanDAOImpl; import us.mn.state.health.lims.samplehuman.valueholder.SampleHuman; import us.mn.state.health.lims.sampleitem.dao.SampleItemDAO; import us.mn.state.health.lims.sampleitem.daoimpl.SampleItemDAOImpl; import us.mn.state.health.lims.sampleitem.valueholder.SampleItem; import us.mn.state.health.lims.sampleorganization.dao.SampleOrganizationDAO; import us.mn.state.health.lims.sampleorganization.daoimpl.SampleOrganizationDAOImpl; import us.mn.state.health.lims.sampleorganization.valueholder.SampleOrganization; import us.mn.state.health.lims.sampleproject.valueholder.SampleProject; import us.mn.state.health.lims.sourceofsample.valueholder.SourceOfSample; import us.mn.state.health.lims.systemuser.dao.SystemUserDAO; import us.mn.state.health.lims.systemuser.daoimpl.SystemUserDAOImpl; import us.mn.state.health.lims.systemuser.valueholder.SystemUser; import us.mn.state.health.lims.typeofsample.valueholder.TypeOfSample; /** * @author diane benz * * To change this generated comment edit the template variable "typecomment": * Window>Preferences>Java>Templates. To enable and disable the creation of type * comments go to Window>Preferences>Java>Code Generation. * bugzilla 2569 */ public class AuditTrailReportBySampleProcessAction extends BaseAction { Properties transmissionMap = null; InputStream propertyStream = null; protected ActionForward performAction(ActionMapping mapping, ActionForm form, HttpServletRequest request, HttpServletResponse response) throws Exception { String forward = FWD_SUCCESS; BaseActionForm dynaForm = (BaseActionForm) form; ActionMessages errors = null; request.setAttribute(ALLOW_EDITS_KEY, "false"); request.setAttribute(PREVIOUS_DISABLED, "true"); request.setAttribute(NEXT_DISABLED, "true"); String accessionNumber = (String) dynaForm.getString("accessionNumber"); SampleXmlHelper sampleXmlHelper = new SampleXmlHelper(); if (!StringUtil.isNullorNill(accessionNumber)) { Sample sample = new Sample(); SampleDAO sampleDAO = new SampleDAOImpl(); sample.setAccessionNumber(accessionNumber); List testTestAnalytes = new ArrayList(); try { sampleDAO.getSampleByAccessionNumber(sample); if (!StringUtil.isNullorNill(sample.getStatus()) && sample.getStatus() .equals(SystemConfiguration.getInstance().getSampleStatusLabelPrinted())) { dynaForm.set("accessionNumber", accessionNumber); request.setAttribute(ALLOW_EDITS_KEY, "false"); return mapping.findForward(FWD_FAIL); } } catch (LIMSRuntimeException lre) { LogEvent.logError("AuditTrailReportBySampleProcessAction", "performAction()", lre.toString()); errors = new ActionMessages(); ActionError error = null; error = new ActionError("errors.GetException", null, null); errors.add(ActionMessages.GLOBAL_MESSAGE, error); saveErrors(request, errors); request.setAttribute(Globals.ERROR_KEY, errors); request.setAttribute(ALLOW_EDITS_KEY, "false"); return mapping.findForward(FWD_FAIL); } String domain = sample.getDomain(); String humanDomain = SystemConfiguration.getInstance().getHumanDomain(); String animalDomain = SystemConfiguration.getInstance().getAnimalDomain(); if (domain != null && domain.equals(humanDomain)) { // go to human view Patient patient = new Patient(); Person patientPerson = new Person(); Provider provider = new Provider(); Person providerPerson = new Person(); SampleHuman sampleHuman = new SampleHuman(); SampleOrganization sampleOrganization = new SampleOrganization(); Organization organization = new Organization(); List sampleProjects = new ArrayList(); Project project = new Project(); Project project2 = new Project(); SampleItem sampleItem = new SampleItem(); try { PatientDAO patientDAO = new PatientDAOImpl(); ProviderDAO providerDAO = new ProviderDAOImpl(); SampleItemDAO sampleItemDAO = new SampleItemDAOImpl(); SampleHumanDAO sampleHumanDAO = new SampleHumanDAOImpl(); SampleOrganizationDAO sampleOrganizationDAO = new SampleOrganizationDAOImpl(); AuditTrailDAO auditTrailDAO = new AuditTrailDAOImpl(); SystemUserDAO systemUserDAO = new SystemUserDAOImpl(); if (!StringUtil.isNullorNill(sample.getId())) { sampleHuman.setSampleId(sample.getId()); sampleHumanDAO.getDataBySample(sampleHuman); sampleOrganization.setSampleId(sample.getId()); sampleOrganizationDAO.getDataBySample(sampleOrganization); sampleItem.setSample(sample); sampleItemDAO.getDataBySample(sampleItem); if (sampleHuman != null) { if (sampleHuman.getPatientId() != null) { patient.setId(sampleHuman.getPatientId()); patientDAO.getData(patient); patientPerson = patient.getPerson(); provider.setId(sampleHuman.getProviderId()); providerDAO.getData(provider); providerPerson = provider.getPerson(); } } } organization = (Organization) sampleOrganization.getOrganization(); sampleProjects = sample.getSampleProjects(); if (sampleProjects != null && sampleProjects.size() > 0) { SampleProject sampleProject = (SampleProject) sampleProjects.get(0); project = sampleProject.getProject(); if (sampleProjects.size() > 1) { SampleProject sampleProject2 = (SampleProject) sampleProjects.get(1); project2 = sampleProject2.getProject(); } } String tableName = "SAMPLE"; ReferenceTablesDAO referenceTablesDAO = new ReferenceTablesDAOImpl(); ReferenceTables referenceTables = new ReferenceTables(); referenceTables.setTableName(tableName); ReferenceTables rt = referenceTablesDAO.getReferenceTableByName(referenceTables); PropertyUtils.copyProperties(sampleXmlHelper, sample); //String data = auditTrailDAO.retrieveBlobData(sample.getId()); //String data = auditTrailDAO.retrieveBlobData("9446"); History history = new History(); history.setReferenceId(sample.getId()); history.setReferenceTable(rt.getId()); List historyRecords = auditTrailDAO.getHistoryByRefIdAndRefTableId(history); List sampleHistoryRecords = populateHistoryList(request, historyRecords, "sample", "sampleHistoryMapping.xsl"); sampleXmlHelper.setHistoryRecords((ArrayList) sampleHistoryRecords); tableName = "SAMPLE_ITEM"; referenceTables = new ReferenceTables(); referenceTables.setTableName(tableName); rt = referenceTablesDAO.getReferenceTableByName(referenceTables); history = new History(); history.setReferenceId(sampleItem.getId()); history.setReferenceTable(rt.getId()); historyRecords = auditTrailDAO.getHistoryByRefIdAndRefTableId(history); List sampleItemHistoryRecords = populateHistoryList(request, historyRecords, "sampleItem", "sampleItemHistoryMapping.xsl"); sampleXmlHelper.addHistoryRecords((ArrayList) sampleItemHistoryRecords); tableName = "PATIENT"; referenceTables = new ReferenceTables(); referenceTables.setTableName(tableName); rt = referenceTablesDAO.getReferenceTableByName(referenceTables); history = new History(); history.setReferenceId(patient.getId()); history.setReferenceTable(rt.getId()); historyRecords = auditTrailDAO.getHistoryByRefIdAndRefTableId(history); List patientHistoryRecords = populateHistoryList(request, historyRecords, "patient", "patientHistoryMapping.xsl"); sampleXmlHelper.addHistoryRecords((ArrayList) patientHistoryRecords); tableName = "PERSON"; referenceTables = new ReferenceTables(); referenceTables.setTableName(tableName); rt = referenceTablesDAO.getReferenceTableByName(referenceTables); history = new History(); history.setReferenceId(patientPerson.getId()); history.setReferenceTable(rt.getId()); historyRecords = auditTrailDAO.getHistoryByRefIdAndRefTableId(history); //List patientPersonHistoryRecords = populateHistoryList(request, historyRecords, "person", "personHistoryMapping.xsl"); //sampleXmlHelper.addHistoryRecords((ArrayList)patientPersonHistoryRecords); tableName = "PERSON"; referenceTables = new ReferenceTables(); referenceTables.setTableName(tableName); rt = referenceTablesDAO.getReferenceTableByName(referenceTables); history = new History(); history.setReferenceId(providerPerson.getId()); history.setReferenceTable(rt.getId()); historyRecords = auditTrailDAO.getHistoryByRefIdAndRefTableId(history); //List providerPersonHistoryRecords = populateHistoryList(request, historyRecords, "person", "personHistoryMapping.xsl"); //sampleXmlHelper.addHistoryRecords((ArrayList)providerPersonHistoryRecords); tableName = "SAMPLE_PROJECTS"; referenceTables = new ReferenceTables(); referenceTables.setTableName(tableName); rt = referenceTablesDAO.getReferenceTableByName(referenceTables); history = new History(); history.setReferenceId(providerPerson.getId()); history.setReferenceTable(rt.getId()); historyRecords = auditTrailDAO.getHistoryByRefIdAndRefTableId(history); List sampleProjectHistoryRecords = populateHistoryList(request, historyRecords, "sampleProject", "sampleProjectHistoryMapping.xsl"); sampleXmlHelper.addHistoryRecords((ArrayList) sampleProjectHistoryRecords); // initialize the form dynaForm.initialize(mapping); tableName = "SAMPLE_ORGANIZATION"; referenceTables = new ReferenceTables(); referenceTables.setTableName(tableName); rt = referenceTablesDAO.getReferenceTableByName(referenceTables); history = new History(); history.setReferenceId(sampleOrganization.getId()); history.setReferenceTable(rt.getId()); historyRecords = auditTrailDAO.getHistoryByRefIdAndRefTableId(history); List sampleOrganizationHistoryRecords = populateHistoryList(request, historyRecords, "sampleOrganization", "sampleOrganizationHistoryMapping.xsl"); sampleXmlHelper.addHistoryRecords((ArrayList) sampleOrganizationHistoryRecords); List historyRecordsForSorting = sampleXmlHelper.getHistoryRecords(); Collections.sort(historyRecordsForSorting, HistoryComparator.NAME_COMPARATOR); String savedUserName = ""; List dateSortList = new ArrayList(); List finalList = new ArrayList(); //now within name sort by date desc for (int i = 0; i < historyRecordsForSorting.size(); i++) { //break down into chunks by name HistoryXmlHelper hist = (HistoryXmlHelper) historyRecordsForSorting.get(i); if (i > 0 && !hist.getUserName().equals(savedUserName)) { //now sort chunk so far Collections.sort(dateSortList, HistoryComparator.DATE_COMPARATOR); finalList.addAll(dateSortList); dateSortList.clear(); } dateSortList.add(hist); savedUserName = hist.getUserName(); } if (dateSortList != null && dateSortList.size() > 0) { Collections.sort(dateSortList, HistoryComparator.DATE_COMPARATOR); finalList.addAll(dateSortList); dateSortList.clear(); } sampleXmlHelper.setHistoryRecords((ArrayList) finalList); // initialize the form dynaForm.initialize(mapping); } catch (LIMSRuntimeException lre) { // if error then forward to fail and don't update to blank // page // = false //bugzilla 2154 LogEvent.logError("ResultsEntryViewAction", "performAction()", lre.toString()); errors = new ActionMessages(); ActionError error = null; error = new ActionError("errors.GetException", null, null); errors.add(ActionMessages.GLOBAL_MESSAGE, error); saveErrors(request, errors); request.setAttribute(Globals.ERROR_KEY, errors); request.setAttribute(ALLOW_EDITS_KEY, "false"); return mapping.findForward(FWD_FAIL); } // populate form from valueholder //PropertyUtils.setProperty(dynaForm, "sampleLastupdated", sample //.getLastupdated()); PropertyUtils.setProperty(dynaForm, "patientFirstName", patientPerson.getFirstName()); PropertyUtils.setProperty(dynaForm, "patientLastName", patientPerson.getLastName()); PropertyUtils.setProperty(dynaForm, "patientId", patient.getExternalId()); PropertyUtils.setProperty(dynaForm, "gender", patient.getGender()); PropertyUtils.setProperty(dynaForm, "chartNumber", patient.getChartNumber()); PropertyUtils.setProperty(dynaForm, "birthDateForDisplay", (String) patient.getBirthDateForDisplay()); TypeOfSample typeOfSample = sampleItem.getTypeOfSample(); SourceOfSample sourceOfSample = sampleItem.getSourceOfSample(); if (typeOfSample == null) { PropertyUtils.setProperty(dynaForm, "typeOfSample", new TypeOfSample()); } else { PropertyUtils.setProperty(dynaForm, "typeOfSample", typeOfSample); } if (sourceOfSample == null) { PropertyUtils.setProperty(dynaForm, "sourceOfSample", new SourceOfSample()); } else { PropertyUtils.setProperty(dynaForm, "sourceOfSample", sourceOfSample); } PropertyUtils.setProperty(dynaForm, "sourceOther", sampleItem.getSourceOther()); PropertyUtils.setProperty(dynaForm, "receivedDateForDisplay", (String) sample.getReceivedDateForDisplay()); PropertyUtils.setProperty(dynaForm, "collectionDateForDisplay", (String) sample.getCollectionDateForDisplay()); PropertyUtils.setProperty(dynaForm, "collectionTimeForDisplay", (String) sample.getCollectionTimeForDisplay()); PropertyUtils.setProperty(dynaForm, "referredCultureFlag", (String) sample.getReferredCultureFlag()); PropertyUtils.setProperty(dynaForm, "stickerReceivedFlag", (String) sample.getStickerReceivedFlag()); if (organization == null) { PropertyUtils.setProperty(dynaForm, "organization", new Organization()); } else { PropertyUtils.setProperty(dynaForm, "organization", organization); } if (project == null) { PropertyUtils.setProperty(dynaForm, "project", new Project()); } else { PropertyUtils.setProperty(dynaForm, "project", project); } if (project2 == null) { PropertyUtils.setProperty(dynaForm, "project2", new Project()); } else { PropertyUtils.setProperty(dynaForm, "project2", project2); } // reload accession number PropertyUtils.setProperty(dynaForm, "accessionNumber", accessionNumber); PropertyUtils.setProperty(dynaForm, "domain", domain); PropertyUtils.setProperty(dynaForm, "sampleXmlHelper", sampleXmlHelper); forward = FWD_SUCCESS_HUMAN; } else if (domain != null && domain.equals(animalDomain)) { // go to animal view // System.out.println("Going to animal view"); forward = FWD_SUCCESS_ANIMAL; } else { forward = FWD_SUCCESS; } } return mapping.findForward(forward); } protected String getPageTitleKey() { return "report.audit.trail.sample.title"; } protected String getPageSubtitleKey() { return "report.audit.trail.sample.subtitle"; } protected String convertToDisplayableXML(String xml) { if (!StringUtil.isNullorNill(xml)) { xml = xml.replaceAll("<", "<"); xml = xml.replaceAll(">", ">"); // the following 2 lines are for display on page (not for system // out) xml = xml.replaceAll("\n", "<br>"); xml = xml.replaceAll(" ", " "); } return xml; } private void parseXmlFile(String xml) { //get the factory DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance(); try { //Using factory get an instance of document builder DocumentBuilder db = dbf.newDocumentBuilder(); //parse using builder to get DOM representation of the XML file Document dom = db.parse(xml); System.out.println("This is parsed xml getting changes " + dom.getElementById("accessionNumber")); } catch (ParserConfigurationException pce) { pce.printStackTrace(); } catch (SAXException se) { se.printStackTrace(); } catch (IOException ioe) { ioe.printStackTrace(); } } protected InputSource getSource(String castorMappingName) { InputStream mappingStream = null; // System.out.println("This is classpath " + // System.getProperty("java.class.path")); InputStream mappingXml = Thread.currentThread().getContextClassLoader() .getResourceAsStream(castorMappingName); // System.out.println("this is mappingXml " + mappingXml); InputSource source = new InputSource(mappingXml); return source; } protected List populateHistoryList(HttpServletRequest request, List historyRecords, String rootNodeName, String xslMappingFileName) throws LIMSRuntimeException { List list = new ArrayList(); try { SystemUserDAO systemUserDAO = new SystemUserDAOImpl(); AuditTrailDAO auditTrailDAO = new AuditTrailDAOImpl(); for (int i = 0; i < historyRecords.size(); i++) { History historyRecord = (History) historyRecords.get(i); Timestamp date = historyRecord.getTimestamp(); String stringLocale = SystemConfiguration.getInstance().getDefaultLocale().toString(); String dateForDisplay = DateUtil.convertTimestampToStringDateAndTime(date, stringLocale); SystemUser systemUser = new SystemUser(); systemUser.setId(historyRecord.getSysUserId()); systemUserDAO.getData(systemUser); String blob = null; if (!historyRecord.getActivity().equals(AUDIT_TRAIL_INSERT)) { blob = auditTrailDAO.retrieveBlobData(historyRecord.getId()); } //this is temporary until 2593 has been completed if (historyRecord.getActivity().equals(IActionConstants.AUDIT_TRAIL_UPDATE)) { blob = "<" + rootNodeName + ">" + blob + "</" + rootNodeName + ">"; } if (!StringUtil.isNullorNill(blob)) { HistoryXmlHelper historyXmlHelper = new HistoryXmlHelper(); historyXmlHelper.setActivity(historyRecord.getActivity()); historyXmlHelper.setUserName(systemUser.getNameForDisplay()); String media = null, title = null, charset = null, xsldata = ""; ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); try { // NOTE!!!! // in order to run this in oc4j I needed to do the following: // add this to OC4J startup: -Djavax.xml.transform.TransformerFactory=org.apache.xalan.processor.TransformerFactoryImpl //to make sure that oc4j uses correct XSL processor (else it could not handle "function extensions" used to bring in MessageResources labels //place xalan.jar, xml-apis.jar, XercesImpl.jar into the applib folder of the oc4j installation TransformerFactory tFactory = TransformerFactory.newInstance(); HttpSession session = request.getSession(); ServletContext context = session.getServletContext(); File xslFile = new File( context.getRealPath("/WEB-INF/transformation/" + xslMappingFileName)); Source stylesheet = new StreamSource(xslFile); Transformer transformer = tFactory.newTransformer(stylesheet); System.out.println("This is blob " + blob); transformer.transform(new StreamSource(new StringReader(blob)), new StreamResult(outputStream)); } catch (TransformerConfigurationException tce) { tce.printStackTrace(); } catch (TransformerException te) { te.printStackTrace(); } catch (Exception e) { e.printStackTrace(); } System.out.println("This is xml " + outputStream.toString()); historyXmlHelper.setChange(outputStream.toString()); historyXmlHelper.setDate(dateForDisplay); if (!StringUtil.isNullorNill(historyXmlHelper.getChange())) { historyXmlHelper.setChange(historyXmlHelper.getChange().trim()); } if (!StringUtil.isNullorNill(historyXmlHelper.getChange())) { list.add(historyXmlHelper); } } } } catch (Exception e) { throw new LIMSRuntimeException(e); } return list; } }