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.sample.action; import java.util.ArrayList; import java.util.Calendar; import java.util.Date; import java.util.List; import java.util.Locale; import javax.servlet.http.HttpServletRequest; import javax.servlet.http.HttpServletResponse; 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.hibernate.StaleObjectStateException; import org.hibernate.Transaction; import us.mn.state.health.lims.analysis.dao.AnalysisDAO; import us.mn.state.health.lims.analysis.daoimpl.AnalysisDAOImpl; import us.mn.state.health.lims.analysis.valueholder.Analysis; import us.mn.state.health.lims.analysisqaevent.dao.AnalysisQaEventDAO; import us.mn.state.health.lims.analysisqaevent.daoimpl.AnalysisQaEventDAOImpl; import us.mn.state.health.lims.analysisqaevent.valueholder.AnalysisQaEvent; import us.mn.state.health.lims.common.action.BaseActionForm; 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.provider.validation.QuickEntryAccessionNumberValidationProvider; import us.mn.state.health.lims.common.provider.validation.QuickEntrySampleSourceValidationProvider; import us.mn.state.health.lims.common.provider.validation.QuickEntrySampleTypeValidationProvider; import us.mn.state.health.lims.common.services.StatusService; import us.mn.state.health.lims.common.services.StatusService.SampleStatus; 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.hibernate.HibernateUtil; import us.mn.state.health.lims.login.valueholder.UserSessionData; import us.mn.state.health.lims.qaevent.dao.QaEventDAO; import us.mn.state.health.lims.qaevent.daoimpl.QaEventDAOImpl; import us.mn.state.health.lims.qaevent.valueholder.QaEvent; 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.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.sourceofsample.dao.SourceOfSampleDAO; import us.mn.state.health.lims.sourceofsample.daoimpl.SourceOfSampleDAOImpl; import us.mn.state.health.lims.sourceofsample.valueholder.SourceOfSample; import us.mn.state.health.lims.test.dao.TestDAO; import us.mn.state.health.lims.test.daoimpl.TestDAOImpl; import us.mn.state.health.lims.test.valueholder.Test; import us.mn.state.health.lims.typeofsample.dao.TypeOfSampleDAO; import us.mn.state.health.lims.typeofsample.daoimpl.TypeOfSampleDAOImpl; import us.mn.state.health.lims.typeofsample.valueholder.TypeOfSample; /** * The QuickEntryUpdateAction class represents the Update Action for the * QuickEntry form of the application. * * @author - Ken Rosha 08/29/2006 02/21/2007 - bugzilla 1757: clean up overly * complex code and fix bug with received date 08/02/2007 - bugzilla * 1813 add batch functionality */ public class QuickEntryUpdateAction extends BatchSampleProcessingBaseAction { protected ActionForward performAction(ActionMapping mapping, ActionForm form, HttpServletRequest request, HttpServletResponse response) throws Exception { String forward = FWD_SUCCESS; request.setAttribute(ALLOW_EDITS_KEY, "true"); BaseActionForm dynaForm = (BaseActionForm) form; // Perform server-side validation (validation.xml) ActionMessages errors = dynaForm.validate(mapping, request); try { errors = validateAll(request, errors, dynaForm); } catch (Exception e) { //bugzilla 2154 LogEvent.logError("QuickEntryUpdateAction", "performAction()", e.toString()); ActionError error = new ActionError("errors.ValidationException", null, null); errors.add(ActionMessages.GLOBAL_MESSAGE, error); } if ((errors != null) && (errors.size() > 0)) { saveErrors(request, errors); return mapping.findForward(FWD_FAIL); } String accessionNumber = (String) dynaForm.get("accessionNumber"); String accessionNumber2 = (String) dynaForm.get("accessionNumber2"); String receivedDate = (String) dynaForm.get("receivedDateForDisplay"); String typeOfSample = (String) dynaForm.get("typeOfSampleDesc"); String sourceOfSample = (String) dynaForm.get("sourceOfSampleDesc"); //bugzilla 1778 String sourceOther = (String) dynaForm.get("sourceOther"); String stringOfTestIds = (String) dynaForm.get("selectedTestIds"); Sample sample = null; List accessionNumbers = populateAccessionNumberList(accessionNumber, accessionNumber2, null); SampleItem sampleItem = new SampleItem(); sampleItem.setStatusId(StatusService.getInstance().getStatusID(SampleStatus.Entered)); // 1926 get sysUserId from login module UserSessionData usd = (UserSessionData) request.getSession().getAttribute(USER_SESSION_DATA); String sysUserId = String.valueOf(usd.getSystemUserId()); Transaction tx = HibernateUtil.getSession().beginTransaction(); try { SampleDAO sampleDAO = new SampleDAOImpl(); SampleItemDAO sampleItemDAO = new SampleItemDAOImpl(); AnalysisDAO analysisDAO = new AnalysisDAOImpl(); TypeOfSampleDAO typeOfSampleDAO = new TypeOfSampleDAOImpl(); SourceOfSampleDAO sourceOfSampleDAO = new SourceOfSampleDAOImpl(); AnalysisQaEventDAO analysisQaEventDAO = new AnalysisQaEventDAOImpl(); QaEventDAO qaEventDAO = new QaEventDAOImpl(); for (int j = 0; j < accessionNumbers.size(); j++) { sample = new Sample(); sample.setAccessionNumber((String) accessionNumbers.get(j)); sampleDAO.getSampleByAccessionNumber(sample); // if we are in batch mode we need to make // sure that the samples being updated are // in the correct status if (SystemConfiguration.getInstance().getSampleStatusLabelPrinted().equals(sample.getStatus())) { String[] listOfTestIds = stringOfTestIds .split(SystemConfiguration.getInstance().getDefaultIdSeparator(), -1); List analyses = new ArrayList(); for (int i = 0; i < listOfTestIds.length; i++) { if (!StringUtil.isNullorNill(listOfTestIds[i])) { Analysis analysis = new Analysis(); Test test = new Test(); String testId = (String) listOfTestIds[i]; test.setId(testId); TestDAO testDAO = new TestDAOImpl(); testDAO.getData(test); analysis.setTest(test); // bgm - bugzilla 1495 setting analysis status here // from // above analysis.setStatus(SystemConfiguration.getInstance().getAnalysisStatusAssigned()); //bugzilla 1942 analysis.setIsReportable(test.getIsReportable()); /** TODO: need to populate this with actual data!!! */ analysis.setAnalysisType("TEST"); analyses.add(analysis); } } sample.setAccessionNumber((String) accessionNumbers.get(j)); sample.setStatus(SystemConfiguration.getInstance().getSampleStatusQuickEntryComplete()); sample.setReceivedDateForDisplay(receivedDate); sample.setCollectionTimeForDisplay("00:00"); // Set entered date to today's date Date today = Calendar.getInstance().getTime(); Locale locale = (Locale) request.getSession().getAttribute("org.apache.struts.action.LOCALE"); String dateAsText = DateUtil.formatDateAsText(today, locale); sample.setEnteredDateForDisplay(dateAsText); //bugzilla 2528 String newbornTypeOfSample = SystemConfiguration.getInstance().getNewbornTypeOfSample(); if (typeOfSample.equals(newbornTypeOfSample)) sample.setDomain(SystemConfiguration.getInstance().getNewbornDomain()); else sample.setDomain(SystemConfiguration.getInstance().getHumanDomain()); sampleItem.setSortOrder("1"); if (!StringUtil.isNullorNill(typeOfSample)) { TypeOfSample typeOfSamp = new TypeOfSample(); typeOfSamp.setDescription(typeOfSample); typeOfSamp.setDomain(SystemConfiguration.getInstance().getHumanDomain()); typeOfSamp = typeOfSampleDAO.getTypeOfSampleByDescriptionAndDomain(typeOfSamp, true); sampleItem.setTypeOfSample(typeOfSamp); } if (!StringUtil.isNullorNill(sourceOfSample)) { SourceOfSample sourceOfSamp = new SourceOfSample(); sourceOfSamp.setDescription(sourceOfSample); //bugzilla 2528 if (typeOfSample.equals(newbornTypeOfSample)) sourceOfSamp.setDomain(SystemConfiguration.getInstance().getNewbornDomain()); else sourceOfSamp.setDomain(SystemConfiguration.getInstance().getHumanDomain()); String sourceOfSampleId = dynaForm.getString("sourceOfSampleId"); sourceOfSamp = sourceOfSampleDAO.getSourceOfSampleByDescriptionAndDomain(sourceOfSamp, true); sampleItem.setSourceOfSampleId(sourceOfSampleId); } //bugzilla 1778 if (!StringUtil.isNullorNill(sourceOther)) { sampleItem.setSourceOther(sourceOther); } // bugzilla 1926 sample.setSysUserId(sysUserId); sampleItem.setSysUserId(sysUserId); if (!StringUtil.isNullorNill(sample.getId())) { // Now update sampleDAO.updateData(sample); // bugzilla 1773 need to store sample not sampleId for // use in sorting sampleItem.setSample(sample); } else { sampleDAO.insertDataWithAccessionNumber(sample); // bugzilla 1773 need to store sample not sampleId for // use in sorting sampleItem.setSample(sample); } sampleItemDAO.insertData(sampleItem); // Analysis table for (int i = 0; i < analyses.size(); i++) { Analysis analysis = (Analysis) analyses.get(i); analysis.setSampleItem(sampleItem); // bugizlla 1926 analysis.setSysUserId(sysUserId); //bugzilla 2064 analysis.setRevision(SystemConfiguration.getInstance().getAnalysisDefaultRevision()); //bugzilla 2013 added duplicateCheck parameter analysisDAO.insertData(analysis, false); //bugzilla 2028: If Sample Type NOT GIVE then create ANALYSIS_QA_EVENT for each added test if (typeOfSample.equals(SAMPLE_TYPE_NOT_GIVEN)) { QaEvent qaEvent = new QaEvent(); qaEvent.setQaEventName( SystemConfiguration.getInstance().getQaEventCodeForRequestNoSampleType()); qaEvent = qaEventDAO.getQaEventByName(qaEvent); AnalysisQaEvent analysisQaEvent = new AnalysisQaEvent(); analysisQaEvent.setAnalysis(analysis); analysisQaEvent.setQaEvent(qaEvent); analysisQaEvent.setCompletedDate(null); analysisQaEvent.setSysUserId(sysUserId); analysisQaEventDAO.insertData(analysisQaEvent); } } } } tx.commit(); } catch (LIMSRuntimeException lre) { //bugzilla 2154 LogEvent.logError("QuickEntryUpdateAction", "performAction()", lre.toString()); tx.rollback(); errors = new ActionMessages(); ActionError error = null; if (lre.getException() instanceof StaleObjectStateException) { error = new ActionError("errors.OptimisticLockException", null, null); } else { //bugzilla 2154 LogEvent.logError("QuickEntryUpdateAction", "performAction()", lre.toString()); error = new ActionError("errors.UpdateException", 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); } finally { HibernateUtil.closeSession(); } // initialize the form dynaForm.initialize(mapping); PropertyUtils.copyProperties(dynaForm, sample); dynaForm.set("accessionNumber", accessionNumber); dynaForm.set("accessionNumber2", accessionNumber2); // PropertyUtils.setProperty(dynaForm, "sysUsers", sysUsers); if ("true".equalsIgnoreCase(request.getParameter("close"))) { forward = FWD_CLOSE; } if (forward.equals(FWD_SUCCESS)) { request.setAttribute("menuDefinition", "default"); } return mapping.findForward(forward); } // ============================================================== protected String getPageTitleKey() { return "quick.entry.add.title"; } // ============================================================== protected String getPageSubtitleKey() { return "quick.entry.add.title"; } // ============================================================== protected ActionMessages validateAll(HttpServletRequest request, ActionMessages errors, BaseActionForm dynaForm) throws Exception { String result; String messageKey; // Accession number validation against database (reusing ajax validation // logic) // The specified accession number SHOULD NOT exist in the database. QuickEntryAccessionNumberValidationProvider accessionValidator = new QuickEntryAccessionNumberValidationProvider(); result = accessionValidator.validate((String) dynaForm.get("accessionNumber")); messageKey = "quick.entry.accession.number"; if (result.equals("invalid")) { ActionError error = new ActionError("errors.invalid", getMessageForKey(messageKey), null); errors.add(ActionMessages.GLOBAL_MESSAGE, error); } //only validate if not null or blank (this is not a required field) if (!StringUtil.isNullorNill((String) dynaForm.get("accessionNumber2"))) { result = accessionValidator.validate((String) dynaForm.get("accessionNumber2")); messageKey = "quick.entry.accession.number.2"; if (result.equals("invalid") || !fromAccessionLessThanThruAccession((String) dynaForm.get("accessionNumber"), (String) dynaForm.get("accessionNumber2"))) { ActionError error = new ActionError("errors.invalid", getMessageForKey(messageKey), null); errors.add(ActionMessages.GLOBAL_MESSAGE, error); } } // Sample type validation against database (reusing ajax validation // logic) QuickEntrySampleTypeValidationProvider typeValidator = new QuickEntrySampleTypeValidationProvider(); result = typeValidator.validate((String) dynaForm.get("typeOfSampleDesc")); messageKey = "quick.entry.sample.type"; if (result.equals("invalid")) { ActionError error = new ActionError("errors.invalid", getMessageForKey(messageKey), null); errors.add(ActionMessages.GLOBAL_MESSAGE, error); } /* * AIS - bugzilla 1396 Added if constraint-- to check if it is invalid, * only when it is filled in */ if (!dynaForm.get("sourceOfSampleDesc").equals("")) { // Sample source validation against database (reusing ajax // validation logic) QuickEntrySampleSourceValidationProvider sourceValidator = new QuickEntrySampleSourceValidationProvider(); result = sourceValidator.validate((String) dynaForm.get("sourceOfSampleDesc")); messageKey = "quick.entry.sample.source"; if (result.equals("invalid")) { ActionError error = new ActionError("errors.invalid", getMessageForKey(messageKey), null); errors.add(ActionMessages.GLOBAL_MESSAGE, error); } } return errors; } private boolean fromAccessionLessThanThruAccession(String from, String thru) { int fromInt = Integer.parseInt(from); int thruInt = Integer.parseInt(thru); if (fromInt < thruInt) { return true; } return false; } }