/**
* 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 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;
import java.util.ArrayList;
import java.util.List;
import java.util.Vector;
/**
* @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 = readPatient(patient.getId());
try {
AuditTrailDAO auditDAO = new AuditTrailDAOImpl();
String sysUserId = patient.getSysUserId();
String event = IActionConstants.AUDIT_TRAIL_UPDATE;
String tableName = "PATIENT";
auditDAO.saveHistory(patient,oldData,sysUserId,event,tableName);
} catch (Exception e) {
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) {
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) {
if (pat.getBirthDate() != null && pat.getBirthDateForDisplay() == null)
pat.setBirthDateForDisplay(DateUtil.convertTimestampToStringDate(pat.getBirthDate()));
if (pat.getBirthTime() != null)
pat.setBirthTimeForDisplay(DateUtil.convertSqlDateToStringDate(pat.getBirthTime()));
if (pat.getDeathDate() != null)
pat.setDeathDateForDisplay(DateUtil.convertSqlDateToStringDate(pat.getDeathDate()));
}
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 propertyValue) {
List<Patient> patients;
try {
String sql = "From Patient p where p." + propertyName + " = :" + propertyName;
Query query = HibernateUtil.getSession().createQuery(sql);
query.setString(propertyName, propertyValue);
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.isEmpty() ? null : patients.get(0);
}
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>();
}
}