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.patient.daoimpl; import java.util.ArrayList; import java.util.List; import java.util.Vector; import org.apache.commons.beanutils.PropertyUtils; import org.hibernate.HibernateException; import org.hibernate.Query; 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.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.SystemConfiguration; import us.mn.state.health.lims.hibernate.HibernateUtil; import us.mn.state.health.lims.patient.dao.PatientDAO; import us.mn.state.health.lims.patient.valueholder.Patient; import us.mn.state.health.lims.person.valueholder.Person; /** * @author diane benz */ public class PatientDAOImpl extends BaseDAOImpl implements PatientDAO { public void deleteData(List patients) throws LIMSRuntimeException { //add to audit trail try { AuditTrailDAO auditDAO = new AuditTrailDAOImpl(); for (int i = 0; i < patients.size(); i++) { Patient data = (Patient) patients.get(i); Patient oldData = (Patient) readPatient(data.getId()); Patient newData = new Patient(); String sysUserId = data.getSysUserId(); String event = IActionConstants.AUDIT_TRAIL_DELETE; String tableName = "PATIENT"; auditDAO.saveHistory(newData, oldData, sysUserId, event, tableName); } } catch (Exception e) { //bugzilla 2154 LogEvent.logError("PatientDAOImpl", "AuditTrail deleteData()", e.toString()); throw new LIMSRuntimeException("Error in Patient AuditTrail deleteData()", e); } try { for (int i = 0; i < patients.size(); i++) { Patient data = (Patient) patients.get(i); //bugzilla 2206 data = (Patient) readPatient(data.getId()); HibernateUtil.getSession().delete(data); HibernateUtil.getSession().flush(); HibernateUtil.getSession().clear(); } } catch (Exception e) { //bugzilla 2154 LogEvent.logError("PatientDAOImpl", "deleteData()", e.toString()); throw new LIMSRuntimeException("Error in Patient deleteData()", e); } } public boolean insertData(Patient patient) throws LIMSRuntimeException { try { String id = (String) HibernateUtil.getSession().save(patient); patient.setId(id); //bugzilla 1824 inserts will be logged in history table AuditTrailDAO auditDAO = new AuditTrailDAOImpl(); String sysUserId = patient.getSysUserId(); String tableName = "PATIENT"; auditDAO.saveNewHistory(patient, sysUserId, tableName); HibernateUtil.getSession().flush(); HibernateUtil.getSession().clear(); } catch (Exception e) { //bugzilla 2154 LogEvent.logError("PatientDAOImpl", "insertData()", e.toString()); throw new LIMSRuntimeException("Error in Patient insertData()", e); } return true; } public void updateData(Patient patient) throws LIMSRuntimeException { Patient oldData = (Patient) readPatient(patient.getId()); Patient newData = patient; //add to audit trail try { AuditTrailDAO auditDAO = new AuditTrailDAOImpl(); String sysUserId = patient.getSysUserId(); String event = IActionConstants.AUDIT_TRAIL_UPDATE; String tableName = "PATIENT"; auditDAO.saveHistory(newData, oldData, sysUserId, event, tableName); } catch (Exception e) { //bugzilla 2154 LogEvent.logError("PatientDAOImpl", "AuditTrail updateData()", e.toString()); throw new LIMSRuntimeException("Error in Patient AuditTrail updateData()", e); } try { HibernateUtil.getSession().merge(patient); HibernateUtil.getSession().flush(); HibernateUtil.getSession().clear(); HibernateUtil.getSession().evict(patient); HibernateUtil.getSession().refresh(patient); } catch (Exception e) { //bugzilla 2154 LogEvent.logError("PatientDAOImpl", "updateData()", e.toString()); throw new LIMSRuntimeException("Error in Patient updateData()", e); } } @Override public Patient getData(String patientId) throws LIMSRuntimeException { try { Patient pat = (Patient) HibernateUtil.getSession().get(Patient.class, patientId); closeSession(); if (pat != null) { updateDisplayValues(pat); } return pat; } catch (HibernateException e) { handleException(e, "getData(patientId)"); } return null; } public void getData(Patient patient) throws LIMSRuntimeException { try { Patient pat = (Patient) HibernateUtil.getSession().get(Patient.class, patient.getId()); HibernateUtil.getSession().flush(); HibernateUtil.getSession().clear(); if (pat != null) { updateDisplayValues(pat); PropertyUtils.copyProperties(patient, pat); } else { patient.setId(null); } } catch (Exception e) { LogEvent.logError("PatientDAOImpl", "getData()", e.toString()); throw new LIMSRuntimeException("Error in Patient getData()", e); } } private void updateDisplayValues(Patient pat) { // set the display dates for STARTED_DATE, COMPLETED_DATE String locale = SystemConfiguration.getInstance().getDefaultLocale().toString(); if (pat.getBirthDate() != null && pat.getBirthDateForDisplay() == null) pat.setBirthDateForDisplay(DateUtil.convertTimestampToStringDate(pat.getBirthDate(), locale)); if (pat.getBirthTime() != null) pat.setBirthTimeForDisplay(DateUtil.convertSqlDateToStringDate(pat.getBirthTime(), locale)); if (pat.getDeathDate() != null) pat.setDeathDateForDisplay(DateUtil.convertSqlDateToStringDate(pat.getDeathDate(), locale)); } public List getAllPatients() throws LIMSRuntimeException { List list = new Vector(); try { String sql = "from Patient"; org.hibernate.Query query = HibernateUtil.getSession().createQuery(sql); list = query.list(); HibernateUtil.getSession().flush(); HibernateUtil.getSession().clear(); } catch (Exception e) { //bugzilla 2154 LogEvent.logError("PatientDAOImpl", "getAllPatients()", e.toString()); throw new LIMSRuntimeException("Error in Patient getAllPatients()", e); } return list; } public List getPageOfPatients(int startingRecNo) throws LIMSRuntimeException { List patients = new Vector(); try { // calculate maxRow to be one more than the page size int endingRecNo = startingRecNo + (SystemConfiguration.getInstance().getDefaultPageSize() + 1); String sql = "from Patient t order by t.id"; org.hibernate.Query query = HibernateUtil.getSession().createQuery(sql); query.setFirstResult(startingRecNo - 1); query.setMaxResults(endingRecNo - 1); patients = query.list(); HibernateUtil.getSession().flush(); HibernateUtil.getSession().clear(); } catch (Exception e) { //bugzilla 2154 LogEvent.logError("PatientDAOImpl", "getPageOfPatients()", e.toString()); throw new LIMSRuntimeException("Error in Patient getPageOfPatients()", e); } return patients; } public Patient readPatient(String idString) { Patient pat = null; try { pat = (Patient) HibernateUtil.getSession().get(Patient.class, idString); HibernateUtil.getSession().flush(); HibernateUtil.getSession().clear(); } catch (Exception e) { //bugzilla 2154 LogEvent.logError("PatientDAOImpl", "readPatient()", e.toString()); throw new LIMSRuntimeException("Error in Patient readPatient()", e); } return pat; } public List getNextPatientRecord(String id) throws LIMSRuntimeException { return getNextRecord(id, "Patient", Patient.class); } public List getPreviousPatientRecord(String id) throws LIMSRuntimeException { return getPreviousRecord(id, "Patient", Patient.class); } public boolean externalIDExists(String patientExternalID) { List results; try { String sql = "From Patient where external_id = :patientID"; Query query = HibernateUtil.getSession().createQuery(sql); query.setParameter("patientID", patientExternalID); results = query.list(); HibernateUtil.getSession().flush(); HibernateUtil.getSession().clear(); } catch (Exception e) { e.printStackTrace(); throw new LIMSRuntimeException("Error in Patient readPatient()", e); } return !results.isEmpty(); } @SuppressWarnings("unchecked") protected Patient getPatientByStringProperty(String propertyName, String nationalId) { List<Patient> patients; try { String sql = "From Patient p where p." + propertyName + " = :" + propertyName; Query query = HibernateUtil.getSession().createQuery(sql); query.setString(propertyName, nationalId); patients = query.list(); HibernateUtil.getSession().flush(); HibernateUtil.getSession().clear(); } catch (Exception e) { e.printStackTrace(); throw new LIMSRuntimeException("Error in Patient getPatientByStringProperty(" + propertyName + "\", ) ", e); } return patients.size() > 0 ? patients.get(0) : null; } public Patient getPatientByNationalId(String nationalId) { return getPatientByStringProperty("nationalId", nationalId); } @SuppressWarnings("unchecked") @Override public List<Patient> getPatientsByNationalId(String nationalId) throws LIMSRuntimeException { try { String sql = "From Patient p where p.nationalId = :nationalId"; Query query = HibernateUtil.getSession().createQuery(sql); query.setString("nationalId", nationalId); List<Patient> patients = query.list(); closeSession(); return patients; } catch (Exception e) { handleException(e, "getPatientsByNationalId"); } return null; } public Patient getPatientByExternalId(String externalId) { return getPatientByStringProperty("externalId", externalId); } @SuppressWarnings("unchecked") public Patient getPatientByPerson(Person person) throws LIMSRuntimeException { List<Patient> patients; try { String sql = "From Patient p where p.person.id = :personID"; Query query = HibernateUtil.getSession().createQuery(sql); query.setInteger("personID", Integer.parseInt(person.getId())); patients = query.list(); HibernateUtil.getSession().flush(); HibernateUtil.getSession().clear(); } catch (Exception e) { e.printStackTrace(); throw new LIMSRuntimeException("Error in Patient getPatientByPerson()", e); } return patients.size() > 0 ? patients.get(0) : null; } public List<String> getPatientIdentityBySampleStatusIdAndProject(List<Integer> inclusiveStatusIdList, String project) throws LIMSRuntimeException { boolean useIdList = inclusiveStatusIdList != null && inclusiveStatusIdList.size() > 0; StringBuilder sqlBuilder = new StringBuilder(); sqlBuilder.append("select COALESCE(pat.national_id, pat.external_id) as subjectNo from clinlims.sample s "); sqlBuilder.append("join clinlims.sample_projects sp on sp.samp_id = s.id "); sqlBuilder.append("join clinlims.project p on sp.proj_id = p.id "); sqlBuilder.append("join clinlims.sample_human sh on sh.samp_id = s.id "); sqlBuilder.append("join clinlims.patient pat on pat.id = sh.patient_id "); sqlBuilder.append("where p.name = :project "); if (useIdList) { sqlBuilder.append("and s.status_id in(:statusIdList) "); } try { Query query = HibernateUtil.getSession().createSQLQuery(sqlBuilder.toString()); if (useIdList) { query.setParameterList("statusIdList", inclusiveStatusIdList); } query.setString("project", project); List<String> subjectList = query.list(); closeSession(); return subjectList; } catch (Exception e) { handleException(e, "getPatientIdentityBySampleStatusIdAndProject"); } return new ArrayList<String>(); } }