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.testreflex.daoimpl; import org.apache.commons.beanutils.PropertyUtils; import org.apache.commons.validator.GenericValidator; import org.hibernate.Query; import us.mn.state.health.lims.analysis.valueholder.Analysis; import us.mn.state.health.lims.audittrail.dao.AuditTrailDAO; import us.mn.state.health.lims.audittrail.daoimpl.AuditTrailDAOImpl; import us.mn.state.health.lims.common.action.IActionConstants; import us.mn.state.health.lims.common.daoimpl.BaseDAOImpl; import us.mn.state.health.lims.common.exception.LIMSDuplicateRecordException; 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.services.TestService; import us.mn.state.health.lims.common.util.StringUtil; import us.mn.state.health.lims.common.util.SystemConfiguration; import us.mn.state.health.lims.hibernate.HibernateUtil; import us.mn.state.health.lims.testanalyte.valueholder.TestAnalyte; import us.mn.state.health.lims.testreflex.dao.TestReflexDAO; import us.mn.state.health.lims.testreflex.valueholder.TestReflex; import us.mn.state.health.lims.testresult.valueholder.TestResult; import java.util.ArrayList; import java.util.List; import java.util.Vector; /** * @author diane benz 11/17/2007 instead of printing StackTrace log error */ public class TestReflexDAOImpl extends BaseDAOImpl implements TestReflexDAO { public void deleteData(List testReflexs) throws LIMSRuntimeException { // add to audit trail try { AuditTrailDAO auditDAO = new AuditTrailDAOImpl(); for (int i = 0; i < testReflexs.size(); i++) { TestReflex data = (TestReflex) testReflexs.get(i); TestReflex oldData = (TestReflex) readTestReflex(data.getId()); TestReflex newData = new TestReflex(); String sysUserId = data.getSysUserId(); String event = IActionConstants.AUDIT_TRAIL_DELETE; String tableName = "TEST_REFLEX"; auditDAO.saveHistory(newData, oldData, sysUserId, event, tableName); } } catch (Exception e) { // bugzilla 2154 LogEvent.logError("TestReflexDAOImpl", "AuditTrail deleteData()", e.toString()); throw new LIMSRuntimeException("Error in TestReflex AuditTrail deleteData()", e); } try { for (int i = 0; i < testReflexs.size(); i++) { TestReflex data = (TestReflex) testReflexs.get(i); // bugzilla 2206 data = (TestReflex) readTestReflex(data.getId()); HibernateUtil.getSession().delete(data); HibernateUtil.getSession().flush(); HibernateUtil.getSession().clear(); } } catch (Exception e) { // bugzilla 2154 LogEvent.logError("TestReflexDAOImpl", "deleteData()", e.toString()); throw new LIMSRuntimeException("Error in TestReflex deleteData()", e); } } public boolean insertData(TestReflex testReflex) throws LIMSRuntimeException { try { // bugzilla 1482 throw Exception if record already exists if (duplicateTestReflexExists(testReflex)) { throw new LIMSDuplicateRecordException( "Duplicate record exists for " + TestService.getLocalizedTestName(testReflex.getTest()) + BLANK + testReflex.getTestAnalyte().getAnalyte().getAnalyteName() + BLANK + testReflex.getTestResult().getValue() + BLANK + TestService.getLocalizedTestName(testReflex.getAddedTest())); } String id = (String) HibernateUtil.getSession().save(testReflex); testReflex.setId(id); // bugzilla 1824 inserts will be logged in history table AuditTrailDAO auditDAO = new AuditTrailDAOImpl(); String sysUserId = testReflex.getSysUserId(); String tableName = "TEST_REFLEX"; auditDAO.saveNewHistory(testReflex, sysUserId, tableName); HibernateUtil.getSession().flush(); HibernateUtil.getSession().clear(); } catch (Exception e) { // bugzilla 2154 LogEvent.logError("TestReflexDAOImpl", "insertData()", e.toString()); throw new LIMSRuntimeException("Error in TestReflex insertData()", e); } return true; } public void updateData(TestReflex testReflex) throws LIMSRuntimeException { // bugzilla 1482 throw Exception if record already exists try { if (duplicateTestReflexExists(testReflex)) { throw new LIMSDuplicateRecordException( "Duplicate record exists for " + TestService.getLocalizedTestName(testReflex.getTest()) + BLANK + testReflex.getTestAnalyte().getAnalyte().getAnalyteName() + BLANK + testReflex.getTestResult().getValue() + BLANK + TestService.getLocalizedTestName(testReflex.getAddedTest())); } } catch (Exception e) { // bugzilla 2154 LogEvent.logError("TestReflexDAOImpl", "updateData()", e.toString()); throw new LIMSRuntimeException("Error in TestReflex updateData()", e); } TestReflex oldData = (TestReflex) readTestReflex(testReflex.getId()); TestReflex newData = testReflex; // add to audit trail try { AuditTrailDAO auditDAO = new AuditTrailDAOImpl(); String sysUserId = testReflex.getSysUserId(); String event = IActionConstants.AUDIT_TRAIL_UPDATE; String tableName = "TEST_REFLEX"; auditDAO.saveHistory(newData, oldData, sysUserId, event, tableName); } catch (Exception e) { // bugzilla 2154 LogEvent.logError("TestReflexDAOImpl", "AuditTrail updateData()", e.toString()); throw new LIMSRuntimeException("Error in TestReflex AuditTrail updateData()", e); } try { HibernateUtil.getSession().merge(testReflex); HibernateUtil.getSession().flush(); HibernateUtil.getSession().clear(); HibernateUtil.getSession().evict(testReflex); HibernateUtil.getSession().refresh(testReflex); } catch (Exception e) { // bugzilla 2154 LogEvent.logError("TestReflexDAOImpl", "updateData()", e.toString()); throw new LIMSRuntimeException("Error in TestReflex updateData()", e); } } public void getData(TestReflex testReflex) throws LIMSRuntimeException { try { TestReflex tr = (TestReflex) HibernateUtil.getSession().get(TestReflex.class, testReflex.getId()); HibernateUtil.getSession().flush(); HibernateUtil.getSession().clear(); if (tr != null) { PropertyUtils.copyProperties(testReflex, tr); } else { testReflex.setId(null); } } catch (Exception e) { // bugzilla 2154 LogEvent.logError("TestReflexDAOImpl", "getData()", e.toString()); throw new LIMSRuntimeException("Error in TestReflex getData()", e); } } public List getAllTestReflexs() throws LIMSRuntimeException { List list = null; try { String sql = "from TestReflex t order by t.test.testName, t.testAnalyte.analyte.analyteName"; org.hibernate.Query query = HibernateUtil.getSession().createQuery(sql); // query.setMaxResults(10); // query.setFirstResult(3); list = query.list(); HibernateUtil.getSession().flush(); HibernateUtil.getSession().clear(); } catch (Exception e) { // bugzilla 2154 LogEvent.logError("TestReflexDAOImpl", "getAllTestReflexs()", e.toString()); throw new LIMSRuntimeException("Error in TestReflex getAllTestReflexs()", e); } return list; } public List getPageOfTestReflexs(int startingRecNo) throws LIMSRuntimeException { List list = new Vector(); try { // calculate maxRow to be one more than the page size int endingRecNo = startingRecNo + (SystemConfiguration.getInstance().getDefaultPageSize() + 1); // bugzilla 1399 - still need to figure out how to sort (3rd sort // column) for dictionary values - requires further step of getting // value from dictionary table before sorting String sql = "from TestReflex t order by t.test.testName, t.testAnalyte.analyte.analyteName"; org.hibernate.Query query = HibernateUtil.getSession().createQuery(sql); query.setFirstResult(startingRecNo - 1); query.setMaxResults(endingRecNo - 1); list = query.list(); HibernateUtil.getSession().flush(); HibernateUtil.getSession().clear(); } catch (Exception e) { // bugzilla 2154 LogEvent.logError("TestReflexDAOImpl", "getPageOfTestReflexs()", e.toString()); throw new LIMSRuntimeException("Error in TestReflex getPageOfTestReflexs()", e); } return list; } /* * (non-Javadoc) * * @seeus.mn.state.health.lims.testreflex.dao.TestReflexDAO# * getTestReflexesByTestResult * (us.mn.state.health.lims.testreflex.valueholder.TestReflex, * us.mn.state.health.lims.testresult.valueholder.TestResult) */ public List getTestReflexesByTestResult(TestResult testResult) throws LIMSRuntimeException { try { String sql = "from TestReflex t where t.testResult.id = :testResultId"; org.hibernate.Query query = HibernateUtil.getSession().createQuery(sql); query.setInteger("testResultId", Integer.parseInt(testResult.getId())); List list = query.list(); HibernateUtil.getSession().flush(); HibernateUtil.getSession().clear(); return list; } catch (Exception e) { // bugzilla 2154 LogEvent.logError("TestReflexDAOImpl", "getTestReflexesByTestResult()", e.toString()); throw new LIMSRuntimeException("Error in TestReflex getTestReflexesByTestResult(TestResult testResult)", e); } } /* * (non-Javadoc) * * @seeus.mn.state.health.lims.testreflex.dao.TestReflexDAO# * getTestReflexesByTestResult * (us.mn.state.health.lims.testreflex.valueholder.TestReflex, * us.mn.state.health.lims.testresult.valueholder.TestResult) */ public List getTestReflexesByTestResultAndTestAnalyte(TestResult testResult, TestAnalyte testAnalyte) throws LIMSRuntimeException { try { // bugzilla 1404 testResultId is mapped as testResult.id now String sql = "from TestReflex t where t.testResult.id = :param and t.testAnalyte.id = :param2"; org.hibernate.Query query = HibernateUtil.getSession().createQuery(sql); query.setParameter("param", testResult.getId()); query.setParameter("param2", testAnalyte.getId()); List list = query.list(); HibernateUtil.getSession().flush(); HibernateUtil.getSession().clear(); return list; } catch (Exception e) { // bugzilla 2154 LogEvent.logError("TestReflexDAOImpl", "getTestReflexesByTestResult()", e.toString()); throw new LIMSRuntimeException("Error in TestReflex getTestReflexesByTestResult(TestResult testResult)", e); } } /* * (non-Javadoc) * * @seeus.mn.state.health.lims.testreflex.dao.TestReflexDAO# * getTestReflexesByTestResult * (us.mn.state.health.lims.testreflex.valueholder.TestReflex, * us.mn.state.health.lims.testresult.valueholder.TestResult) bugzilla 1798 * find out if a test with a parent was reflexed or linked */ public boolean isReflexedTest(Analysis analysis) throws LIMSRuntimeException { try { List list = null; if (analysis.getParentAnalysis() != null && analysis.getParentResult() != null) { String sql = "from TestReflex t where t.testResult.id = :param and t.testAnalyte.analyte.id = :param2 and t.test.id = :param3 and t.addedTest.id = :param4"; org.hibernate.Query query = HibernateUtil.getSession().createQuery(sql); query.setParameter("param", analysis.getParentResult().getTestResult().getId()); query.setParameter("param2", analysis.getParentResult().getAnalyte().getId()); query.setParameter("param3", analysis.getParentAnalysis().getTest().getId()); query.setParameter("param4", analysis.getTest().getId()); list = query.list(); HibernateUtil.getSession().flush(); HibernateUtil.getSession().clear(); } return list != null && list.size() > 0; } catch (Exception e) { // bugzilla 2154 LogEvent.logError("TestReflexDAOImpl", "getTestReflexesByTestResult()", e.toString()); throw new LIMSRuntimeException("Error in TestReflex getTestReflexesByTestResult(TestResult testResult)", e); } } @SuppressWarnings("unchecked") public List<TestReflex> getTestReflexsByTestResultAnalyteTest(String testResultId, String analyteId, String testId) throws LIMSRuntimeException { if (!GenericValidator.isBlankOrNull(testResultId) && !GenericValidator.isBlankOrNull(analyteId) && !GenericValidator.isBlankOrNull(testId)) { try { List<TestReflex> list = null; String sql = "from TestReflex t where t.testResult.id = :testResultId and t.testAnalyte.analyte.id = :analyteId and t.test.id = :testId"; org.hibernate.Query query = HibernateUtil.getSession().createQuery(sql); query.setInteger("testResultId", Integer.parseInt(testResultId)); query.setInteger("analyteId", Integer.parseInt(analyteId)); query.setInteger("testId", Integer.parseInt(testId)); list = query.list(); HibernateUtil.getSession().flush(); HibernateUtil.getSession().clear(); return list; } catch (Exception e) { LogEvent.logError("TestReflexDAOImpl", "getTestReflexByTestResultAnalyteTest", e.toString()); throw new LIMSRuntimeException( "Error in TestReflex getTestReflexByTestResultAnalyteTest(String testResultId, String analyteId, String testId)", e); } } return new ArrayList<TestReflex>(); } public TestReflex readTestReflex(String idString) { TestReflex tr = null; try { tr = (TestReflex) HibernateUtil.getSession().get(TestReflex.class, idString); HibernateUtil.getSession().flush(); HibernateUtil.getSession().clear(); } catch (Exception e) { // bugzilla 2154 LogEvent.logError("TestReflexDAOImpl", "readTestReflex()", e.toString()); throw new LIMSRuntimeException("Error in TestReflex readTestReflex()", e); } return tr; } public List getNextTestReflexRecord(String id) throws LIMSRuntimeException { return getNextRecord(id, "TestReflex", TestReflex.class); } public List getPreviousTestReflexRecord(String id) throws LIMSRuntimeException { return getPreviousRecord(id, "TestReflex", TestReflex.class); } // bugzilla 1411 public Integer getTotalTestReflexCount() throws LIMSRuntimeException { return getTotalCount("TestReflex", TestReflex.class); } // bugzilla 1427 public List getNextRecord(String id, String table, Class clazz) throws LIMSRuntimeException { int currentId = (Integer.valueOf(id)).intValue(); String tablePrefix = getTablePrefix(table); List list = new Vector(); // bugzilla 1908 int rrn = 0; try { //bugzilla 1908 cannot use named query for postgres because of oracle ROWNUM //instead get the list in this sortorder and determine the index of record with id = currentId String sql = "select tr.id from TestReflex tr " + " order by tr.test.testName, tr.testAnalyte.analyte.analyteName"; org.hibernate.Query query = HibernateUtil.getSession().createQuery(sql); list = query.list(); HibernateUtil.getSession().flush(); HibernateUtil.getSession().clear(); rrn = list.indexOf(String.valueOf(currentId)); list = HibernateUtil.getSession().getNamedQuery(tablePrefix + "getNext").setFirstResult(rrn + 1) .setMaxResults(2).list(); } catch (Exception e) { // bugzilla 2154 LogEvent.logError("TestReflexDAOImpl", "getNextRecord()", e.toString()); throw new LIMSRuntimeException("Error in getNextRecord() for " + table, e); } return list; } // bugzilla 1427 public List getPreviousRecord(String id, String table, Class clazz) throws LIMSRuntimeException { int currentId = (Integer.valueOf(id)).intValue(); String tablePrefix = getTablePrefix(table); List list = new Vector(); // bugzilla 1908 int rrn = 0; try { //bugzilla 1908 cannot use named query for postgres because of oracle ROWNUM //instead get the list in this sortorder and determine the index of record with id = currentId String sql = "select tr.id from TestReflex tr " + " order by tr.test.testName desc, tr.testAnalyte.analyte.analyteName desc"; org.hibernate.Query query = HibernateUtil.getSession().createQuery(sql); list = query.list(); HibernateUtil.getSession().flush(); HibernateUtil.getSession().clear(); rrn = list.indexOf(String.valueOf(currentId)); list = HibernateUtil.getSession().getNamedQuery(tablePrefix + "getPrevious").setFirstResult(rrn + 1) .setMaxResults(2).list(); } catch (Exception e) { // bugzilla 2154 LogEvent.logError("TestReflexDAOImpl", "getPreviousRecord()", e.toString()); throw new LIMSRuntimeException("Error in getPreviousRecord() for " + table, e); } return list; } // bugzilla 1482 private boolean duplicateTestReflexExists(TestReflex testReflex) throws LIMSRuntimeException { try { List list = new ArrayList(); // not case sensitive hemolysis and Hemolysis are considered // duplicates String sql = "from TestReflex t where t.test.localizedTestName = :localizedTestNameId and " + "trim(lower(t.testAnalyte.analyte.analyteName)) = :analyteName and " + "t.testResult.id = :resultId and " + "t.addedTest.localizedTestName = :addedTestNameId or " + "trim(lower(t.actionScriptlet.scriptletName)) = :scriptletName ) and " + " t.id != :testId"; Query query = HibernateUtil.getSession().createQuery(sql); query.setInteger("localizedTestName", Integer.parseInt(testReflex.getTest().getLocalizedTestName().getId())); query.setString("analyteName", testReflex.getTestAnalyte().getAnalyte().getAnalyteName().toLowerCase().trim()); query.setInteger("resultId", Integer.parseInt(testReflex.getTestResult().getId())); query.setInteger("addedTestNameId", testReflex.getAddedTest() == null ? -1 : Integer.parseInt(testReflex.getAddedTest().getLocalizedTestName().getId())); query.setString("scriptletName", testReflex.getActionScriptlet() == null ? null : testReflex.getActionScriptlet().getScriptletName().toLowerCase().trim()); String testReflexId = StringUtil.isNullorNill(testReflex.getId()) ? "0" : testReflex.getId(); query.setInteger("testId", Integer.parseInt(testReflexId)); list = query.list(); HibernateUtil.getSession().flush(); HibernateUtil.getSession().clear(); if (list.size() > 0) { return true; } else { return false; } } catch (Exception e) { LogEvent.logError("TestReflexDAOImpl", "duplicateTestReflexExists()", e.toString()); throw new LIMSRuntimeException("Error in duplicateTestReflexExists()", e); } } @SuppressWarnings("unchecked") public List<TestReflex> getTestReflexsByTestAndFlag(String testId, String flag) throws LIMSRuntimeException { if (GenericValidator.isBlankOrNull(testId)) { return new ArrayList<TestReflex>(); } List<TestReflex> reflexList = null; try { Query query = null; if (GenericValidator.isBlankOrNull(flag)) { String sql = "from TestReflex tr where tr.testResult.test.id = :id"; query = HibernateUtil.getSession().createQuery(sql); query.setInteger("id", Integer.parseInt(testId)); } else { String sql = "from TestReflex tr where tr.testResult.test.id = :id and tr.flags = :flag"; query = HibernateUtil.getSession().createQuery(sql); query.setInteger("id", Integer.parseInt(testId)); query.setString("flag", flag); } reflexList = query.list(); HibernateUtil.getSession().flush(); HibernateUtil.getSession().clear(); } catch (Exception e) { handleException(e, "getTestReflexsByTestAndFlag()"); } return reflexList; } @SuppressWarnings("unchecked") @Override public List<TestReflex> getFlaggedTestReflexesByTestResult(TestResult testResult, String flag) throws LIMSRuntimeException { if (GenericValidator.isBlankOrNull(flag)) { return new ArrayList<TestReflex>(); } try { String sql = "from TestReflex t where t.testResult.id = :testResultId and t.flags = :flag"; Query query = HibernateUtil.getSession().createQuery(sql); query.setInteger("testResultId", Integer.parseInt(testResult.getId())); query.setString("flag", flag); List<TestReflex> list = query.list(); closeSession(); return list; } catch (Exception e) { handleException(e, "getFlaggedTestReflexesByTestResult"); } return null; } }