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) CIRG, University of Washington, Seattle WA. All Rights Reserved. * */ package us.mn.state.health.lims.referral.action; import org.apache.commons.beanutils.PropertyUtils; import org.apache.commons.validator.GenericValidator; import org.apache.struts.Globals; import org.apache.struts.action.*; import org.dom4j.Document; import org.dom4j.DocumentException; import org.dom4j.DocumentHelper; import org.dom4j.Element; import org.hibernate.StaleObjectStateException; import org.hibernate.Transaction; import org.json.simple.JSONObject; import org.json.simple.parser.JSONParser; import org.json.simple.parser.ParseException; 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.common.action.BaseAction; 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.services.*; import us.mn.state.health.lims.common.services.StatusService.AnalysisStatus; import us.mn.state.health.lims.common.services.StatusService.OrderStatus; import us.mn.state.health.lims.common.util.DateUtil; import us.mn.state.health.lims.common.util.validator.ActionError; import us.mn.state.health.lims.hibernate.HibernateUtil; import us.mn.state.health.lims.note.dao.NoteDAO; import us.mn.state.health.lims.note.daoimpl.NoteDAOImpl; import us.mn.state.health.lims.note.valueholder.Note; import us.mn.state.health.lims.organization.dao.OrganizationDAO; import us.mn.state.health.lims.organization.daoimpl.OrganizationDAOImpl; import us.mn.state.health.lims.patient.valueholder.Patient; import us.mn.state.health.lims.referral.action.beanitems.IReferralResultTest; import us.mn.state.health.lims.referral.action.beanitems.ReferralItem; import us.mn.state.health.lims.referral.action.beanitems.ReferredTest; import us.mn.state.health.lims.referral.dao.ReferralDAO; import us.mn.state.health.lims.referral.dao.ReferralResultDAO; import us.mn.state.health.lims.referral.daoimpl.ReferralDAOImpl; import us.mn.state.health.lims.referral.daoimpl.ReferralResultDAOImpl; import us.mn.state.health.lims.referral.valueholder.Referral; import us.mn.state.health.lims.referral.valueholder.ReferralResult; import us.mn.state.health.lims.result.dao.ResultDAO; import us.mn.state.health.lims.result.daoimpl.ResultDAOImpl; import us.mn.state.health.lims.result.valueholder.Result; import us.mn.state.health.lims.resultlimits.valueholder.ResultLimit; 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.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.testresult.dao.TestResultDAO; import us.mn.state.health.lims.testresult.daoimpl.TestResultDAOImpl; import us.mn.state.health.lims.testresult.valueholder.TestResult; import us.mn.state.health.lims.typeoftestresult.valueholder.TypeOfTestResult.ResultType; import javax.servlet.http.HttpServletRequest; import javax.servlet.http.HttpServletResponse; import java.util.*; public class ReferredOutUpdateAction extends BaseAction { private List<ReferralSet> referralSetList; private List<ReferralResult> removableReferralResults; private List<ReferralItem> modifiedItems; private List<ReferralItem> canceledItems; private Set<Sample> parentSamples; private List<Sample> modifiedSamples; private ActionMessages errors; private final ReferralDAO referralDAO = new ReferralDAOImpl(); private final ReferralResultDAO referralResultDAO = new ReferralResultDAOImpl(); private final OrganizationDAO organizationDAO = new OrganizationDAOImpl(); private final ResultDAO resultDAO = new ResultDAOImpl(); private final SampleDAO sampleDAO = new SampleDAOImpl(); private final AnalysisDAO analysisDAO = new AnalysisDAOImpl(); private final NoteDAO noteDAO = new NoteDAOImpl(); private final TestResultDAO testResultDAO = new TestResultDAOImpl(); private static final String RESULT_SUBJECT = "Result Note"; private TestDAO testDAO = new TestDAOImpl(); private SampleHumanDAO sampleHumanDAO = new SampleHumanDAOImpl(); @Override protected String getPageSubtitleKey() { return "referral.out.manage"; } @Override protected String getPageTitleKey() { return "referral.out.manage"; } @SuppressWarnings("unchecked") @Override protected ActionForward performAction(ActionMapping mapping, ActionForm form, HttpServletRequest request, HttpServletResponse response) throws Exception { parentSamples = new HashSet<Sample>(); modifiedSamples = new ArrayList<Sample>(); errors = new ActionMessages(); request.getSession().setAttribute(SAVE_DISABLED, TRUE); DynaActionForm dynaForm = (DynaActionForm) form; List<ReferralItem> referralItems = (List<ReferralItem>) PropertyUtils.getProperty(dynaForm, "referralItems"); selectModifiedAndCanceledItems(referralItems); validateModifedItems(); if (errors.size() > 0) { saveErrors(request, errors); request.setAttribute(Globals.ERROR_KEY, errors); return mapping.findForward(IActionConstants.FWD_VALIDATION_ERROR); } try { createReferralSets(); } catch (LIMSRuntimeException e) { saveErrors(request, errors); request.setAttribute(Globals.ERROR_KEY, errors); return mapping.findForward(IActionConstants.FWD_VALIDATION_ERROR); } Transaction tx = HibernateUtil.getSession().beginTransaction(); try { for (ReferralSet referralSet : referralSetList) { referralDAO.updateData(referralSet.referral); for (ReferralResult referralResult : referralSet.updatableReferralResults) { Result result = referralResult.getResult(); if (result != null) { if (result.getId() == null) { resultDAO.insertData(result); } else { result.setSysUserId(currentUserId); resultDAO.updateData(result); } } if (referralResult.getId() == null) { referralResultDAO.insertData(referralResult); } else { referralResultDAO.updateData(referralResult); } } if (referralSet.note != null) { if (referralSet.note.getId() == null) { noteDAO.insertData(referralSet.note); } else { noteDAO.updateData(referralSet.note); } } } for (ReferralResult referralResult : removableReferralResults) { referralResult.setSysUserId(currentUserId); referralResultDAO.deleteData(referralResult); if (referralResult.getResult() != null && referralResult.getResult().getId() != null) { referralResult.getResult().setSysUserId(currentUserId); resultDAO.deleteData(referralResult.getResult()); } } setStatusOfParentSamples(); for (Sample sample : modifiedSamples) { sampleDAO.updateData(sample); } tx.commit(); } catch (LIMSRuntimeException lre) { tx.rollback(); ActionError error; if (lre.getException() instanceof StaleObjectStateException) { error = new ActionError("errors.OptimisticLockException", null, null); } else { lre.printStackTrace(); error = new ActionError("error.system", 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(); } return mapping.findForward(IActionConstants.FWD_SUCCESS); } private void selectModifiedAndCanceledItems(List<ReferralItem> referralItems) { modifiedItems = new ArrayList<ReferralItem>(); canceledItems = new ArrayList<ReferralItem>(); for (ReferralItem item : referralItems) { if (item.isCanceled()) { canceledItems.add(item); } else if (item.isModified()) { modifiedItems.add(item); } } } private void validateModifedItems() { for (ReferralItem referralItem : modifiedItems) { validateModifedItem(referralItem); } } private void validateModifedItem(ReferralItem referralItem) { // if an institution has not been entered then there may not be a test if (!institutionEntered(referralItem) && testEntered(referralItem)) { ActionError error = new ActionError("error.referral.missingInstitution", referralItem.getAccessionNumber(), null); errors.add(ActionErrors.GLOBAL_MESSAGE, error); } // if a test has not been entered then there can not be a result or // report date if (!testEntered(referralItem) && (reportDateEntered(referralItem) || resultEntered(referralItem))) { ActionError error = new ActionError("error.referral.missingTest", referralItem.getAccessionNumber(), null); errors.add(ActionErrors.GLOBAL_MESSAGE, error); } } private boolean institutionEntered(ReferralItem referralItem) { return !"0".equals(referralItem.getReferredInstituteId()); } private boolean testEntered(IReferralResultTest resultTest) { return !"0".equals(resultTest.getReferredTestId()); } private boolean reportDateEntered(IReferralResultTest resultTest) { return !GenericValidator.isBlankOrNull(resultTest.getReferredReportDate()); } private boolean resultEntered(IReferralResultTest resultTest) { return !(GenericValidator.isBlankOrNull(resultTest.getReferredResult()) && "0".equals(resultTest.getReferredDictionaryResult())); } private void createReferralSets() throws LIMSRuntimeException { referralSetList = new ArrayList<ReferralSet>(); removableReferralResults = new ArrayList<ReferralResult>(); for (ReferralItem item : canceledItems) { referralSetList.add(createCanceledReferralSet(item)); } for (ReferralItem item : modifiedItems) { referralSetList.add(createModifiedSet(item)); } } private ReferralSet createCanceledReferralSet(ReferralItem item) { ReferralSet referralSet = new ReferralSet(); Referral referral = referralDAO.getReferralById(item.getReferralId()); referralSet.referral = referral; referral.setSysUserId(currentUserId); referral.setCanceled(true); setStatusForCanceledReferrals(referral); return referralSet; } @SuppressWarnings("unchecked") private void setStatusForCanceledReferrals(Referral referral) { Analysis analysis = referral.getAnalysis(); analysis.setReferredOut(false); Sample sample = analysis.getSampleItem().getSample(); parentSamples.add(sample); } private ReferralSet createModifiedSet(ReferralItem referralItem) throws LIMSRuntimeException { // place all existing referral results in list ReferralSet referralSet = new ReferralSet(); referralSet.setExistingReferralResults( referralResultDAO.getReferralResultsForReferral(referralItem.getReferralId())); Referral referral = referralDAO.getReferralById(referralItem.getReferralId()); referral.setCanceled(false); referral.setSysUserId(currentUserId); referral.setOrganization(organizationDAO.getOrganizationById(referralItem.getReferredInstituteId())); referral.setSentDate(DateUtil.convertStringDateToTruncatedTimestamp(referralItem.getReferredSendDate())); referral.setRequesterName(referralItem.getReferrer()); referralSet.referral = referral; referralSet.note = new NoteService(referral.getAnalysis()).createSavableNote(NoteService.NoteType.INTERNAL, referralItem.getNote(), RESULT_SUBJECT, currentUserId); createReferralResults(referralItem, referralSet); if (referralItem.getAdditionalTests() != null) { for (ReferredTest existingAdditionalTest : referralItem.getAdditionalTests()) { if (!existingAdditionalTest.isRemove()) { // nothing to do if isRemove, because on insert we reused what we could // then deleted all old referralResults (see below). // removableReferralResults.add(getRemovableReferralableResults(existingAdditionalTest)); createReferralResults(existingAdditionalTest, referralSet); } } } List<ReferredTest> newAdditionalTests = getNewTests(referralItem.getAdditionalTestsXMLWad()); for (ReferredTest newReferralTest : newAdditionalTests) { newReferralTest.setReferralId(referralItem.getReferralId()); createReferralResults(newReferralTest, referralSet); } // any leftovers get deleted this.removableReferralResults.addAll(referralSet.getExistingReferralResults()); return referralSet; } /** * Reuse any existing referrableResults, placing the submitted results in * them. Then any remaining referral results are removable. ***/ private void createReferralResults(IReferralResultTest referralItem, ReferralSet referralSet) { if (referralItem.getReferredTestIdShadow() != null && !referralItem.getReferredTestId().equals(referralItem.getReferredTestIdShadow())) { referralSet.updateTest(referralItem.getReferredTestIdShadow(), referralItem.getReferredTestId(), currentUserId); } else { String referredResultType = getReferredResultType(referralItem, null); if (ResultType.isMultiSelectVariant(referredResultType)) { if (!GenericValidator.isBlankOrNull(referralItem.getMultiSelectResultValues()) && !"{}".equals(referralItem.getMultiSelectResultValues())) { JSONParser parser = new JSONParser(); try { JSONObject jsonResult = (JSONObject) parser .parse(referralItem.getMultiSelectResultValues()); for (Object key : jsonResult.keySet()) { String[] ids = ((String) jsonResult.get(key)).trim().split(","); //This will populate a result for each item in the multiselect referral result for (String id : ids) { ReferralResult referralResult = referralSet.getNextReferralResult(); referralItem.setReferredDictionaryResult(id); // move particular multi result into (single) dictionary result. fillReferralResultResult(referralItem, referralResult, Integer.parseInt((String) key)); } } } catch (ParseException e) { e.printStackTrace(); } } else { ReferralResult referralResult = referralSet.getNextReferralResult(); fillReferralResultResult(referralItem, referralResult, 0); } } else { ReferralResult referralResult = referralSet.getNextReferralResult(); fillReferralResultResult(referralItem, referralResult, 0); } } } private void fillReferralResultResult(IReferralResultTest referralItem, ReferralResult referralResult, int grouping) { referralResult.setSysUserId(currentUserId); setReferredResultReportDate(referralItem, referralResult); setReferredResultTestId(referralItem, referralResult); referralResult.setReferralId(referralItem.getReferralId()); Result result = referralResult.getResult(); if (result == null && !GenericValidator.isBlankOrNull(referralItem.getReferredResultType())) { result = new Result(); } if (result != null) { setResultValuesForReferralResult(referralItem, result, grouping); referralResult.setResult(result); } } /** * If the referredTest.referredResultType is "M" the particular value to * translate into the result should already be loaded in * referredTest.referredDictionaryResult * */ private void setResultValuesForReferralResult(IReferralResultTest referredTest, Result result, int grouping) { result.setSysUserId(currentUserId); result.setSortOrder("0"); Test test = testDAO.getTestById(referredTest.getReferredTestId()); Sample sample = referralDAO.getReferralById(referredTest.getReferralId()).getAnalysis().getSampleItem() .getSample(); Patient patient = sampleHumanDAO.getPatientForSample(sample); ResultLimit limit = new ResultLimitService().getResultLimitForTestAndPatient(test, patient); result.setMinNormal(limit != null ? limit.getLowNormal() : 0.0); result.setMaxNormal(limit != null ? limit.getHighNormal() : 0.0); result.setGrouping(grouping); String referredResultType = getReferredResultType(referredTest, test); result.setResultType(referredResultType); if (ResultType.isDictionaryVariant(referredResultType)) { String dicResult = referredTest.getReferredDictionaryResult(); if (!(GenericValidator.isBlankOrNull(dicResult) || "0".equals(dicResult))) { result.setValue(dicResult); } } else { result.setValue(referredTest.getReferredResult()); } } private String getReferredResultType(IReferralResultTest referredTest, Test test) { //N.B. this should not be corrected here. It should be done on load /* referredTest.getReferredResultType() is not always accurate * alpha-numeric and numeric are not differentiated */ String referredResultType = referredTest.getReferredResultType(); if (!ResultType.isDictionaryVariant(referredResultType) && test != null) { @SuppressWarnings("unchecked") List<TestResult> testResults = testResultDAO.getAllActiveTestResultsPerTest(test); if (!testResults.isEmpty()) { referredResultType = testResults.get(0).getTestResultType(); } } return referredResultType; } private void setReferredResultTestId(IReferralResultTest referralTest, ReferralResult referralResult) { if (!"0".equals(referralTest.getReferredTestId())) { referralResult.setTestId(referralTest.getReferredTestId()); } } private void setReferredResultReportDate(IReferralResultTest referralTest, ReferralResult referralResult) throws LIMSRuntimeException { if (!GenericValidator.isBlankOrNull(referralTest.getReferredReportDate())) { try { referralResult.setReferralReportDate( DateUtil.convertStringDateToTruncatedTimestamp(referralTest.getReferredReportDate())); } catch (LIMSRuntimeException e) { ActionError error = new ActionError("errors.date", referralTest.getReferredReportDate(), null); errors.add(ActionErrors.GLOBAL_MESSAGE, error); throw e; } } } @SuppressWarnings("unchecked") private List<ReferredTest> getNewTests(String xml) { List<ReferredTest> newTestList = new ArrayList<ReferredTest>(); if (GenericValidator.isBlankOrNull(xml)) { return newTestList; } try { Document testsDom = DocumentHelper.parseText(xml); for (Iterator<Element> i = testsDom.getRootElement().elementIterator("test"); i.hasNext();) { Element testItem = i.next(); String testId = testItem.attribute("testId").getValue(); ReferredTest referralTest = new ReferredTest(); referralTest.setReferredTestId(testId); referralTest.setReferredResultType(new TestService(testId).getResultType()); referralTest.setReferredResult(""); referralTest.setReferredDictionaryResult(""); referralTest.setReferredMultiDictionaryResult(""); referralTest.setReferredReportDate(""); newTestList.add(referralTest); } } catch (DocumentException e) { e.printStackTrace(); throw new LIMSRuntimeException(e); } return newTestList; } private void setStatusOfParentSamples() { for (Sample sample : parentSamples) { List<Analysis> analysisList = analysisDAO.getAnalysesBySampleId(sample.getId()); String finalizedId = StatusService.getInstance().getStatusID(AnalysisStatus.Finalized); boolean allAnalysisFinished = true; if (analysisList != null) { for (Analysis childAnalysis : analysisList) { Referral referral = referralDAO.getReferralByAnalysisId(childAnalysis.getId()); List<ReferralResult> referralResultList; if (referral == null || referral.getId() == null) { referralResultList = new ArrayList<ReferralResult>(); } else { referralResultList = referralResultDAO.getReferralResultsForReferral(referral.getId()); } if (referralResultList.isEmpty()) { if (!finalizedId.equals(childAnalysis.getStatusId())) { allAnalysisFinished = false; break; } } else { for (ReferralResult referralResult : referralResultList) { if (referralResult.getResult() == null || GenericValidator.isBlankOrNull(referralResult.getResult().getValue())) { if (!(referral.isCanceled() && finalizedId.equals(childAnalysis.getStatusId()))) { allAnalysisFinished = false; break; } } } } } } if (allAnalysisFinished) { sample.setStatusId(StatusService.getInstance().getStatusID(OrderStatus.Finished)); sample.setSysUserId(currentUserId); modifiedSamples.add(sample); } } } static class ReferralSet { Referral referral; Note note; List<ReferralResult> updatableReferralResults = new ArrayList<ReferralResult>(); private List<ReferralResult> existingReferralResults = new ArrayList<ReferralResult>(); public List<ReferralResult> getExistingReferralResults() { return existingReferralResults; } public void setExistingReferralResults(List<ReferralResult> existingReferralResults) { this.existingReferralResults = existingReferralResults; } ReferralResult getNextReferralResult() { ReferralResult referralResult = existingReferralResults.isEmpty() ? new ReferralResult() : existingReferralResults.remove(0); updatableReferralResults.add(referralResult); return referralResult; } public void updateTest(String oldTestId, String newTestId, String currentUserId) { ReferralResult updatedReferralResult = null; for (ReferralResult referralResult : existingReferralResults) { if (referralResult.getTestId().equals(oldTestId)) { Result result = referralResult.getResult(); result.setSysUserId(currentUserId); if (updatedReferralResult == null) { referralResult.setTestId(newTestId); referralResult.setSysUserId(currentUserId); result.setResultType(new TestService(newTestId).getResultType()); result.setValue(""); updatedReferralResult = referralResult; updatableReferralResults.add(referralResult); } } } existingReferralResults.remove(updatedReferralResult); } } }