/**
* 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.
*
* Contributor(s): CIRG, University of Washington, Seattle WA.
*/
package us.mn.state.health.lims.analyte.daoimpl;
import java.util.ArrayList;
import java.util.List;
import java.util.Vector;
import org.apache.commons.beanutils.PropertyUtils;
import us.mn.state.health.lims.analyte.dao.AnalyteDAO;
import us.mn.state.health.lims.analyte.valueholder.Analyte;
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.util.StringUtil;
import us.mn.state.health.lims.common.util.SystemConfiguration;
import us.mn.state.health.lims.hibernate.HibernateUtil;
/**
* @author diane benz
*/
public class AnalyteDAOImpl extends BaseDAOImpl implements AnalyteDAO {
public void deleteData(List analytes) throws LIMSRuntimeException {
// add to audit trail
try {
AuditTrailDAO auditDAO = new AuditTrailDAOImpl();
for (int i = 0; i < analytes.size(); i++) {
Analyte data = (Analyte) analytes.get(i);
Analyte oldData = (Analyte) readAnalyte(data.getId());
Analyte newData = new Analyte();
String sysUserId = data.getSysUserId();
String event = IActionConstants.AUDIT_TRAIL_DELETE;
String tableName = "ANALYTE";
auditDAO.saveHistory(newData, oldData, sysUserId, event,
tableName);
}
} catch (Exception e) {
//buzilla 2154
LogEvent.logError("AnalyteDAOImpl","AuditTrail deleteData()",e.toString());
throw new LIMSRuntimeException(
"Error in Analyte AuditTrail deleteData()", e);
}
try {
for (int i = 0; i < analytes.size(); i++) {
Analyte data = (Analyte) analytes.get(i);
Analyte cloneData = (Analyte) readAnalyte(data.getId());
cloneData.setIsActive(IActionConstants.NO);
HibernateUtil.getSession().merge(cloneData);
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
HibernateUtil.getSession().evict(cloneData);
HibernateUtil.getSession().refresh(cloneData);
}
} catch (Exception e) {
//buzilla 2154
LogEvent.logError("AnalyteDAOImpl","deleteData()",e.toString());
throw new LIMSRuntimeException("Error in Analyte deleteData()", e);
}
}
public boolean insertData(Analyte analyte) throws LIMSRuntimeException {
try {
// bugzilla 1482 throw Exception if record already exists
if (duplicateAnalyteExists(analyte)) {
throw new LIMSDuplicateRecordException(
"Duplicate record exists for " + analyte.getAnalyteName());
}
String id = (String) HibernateUtil.getSession().save(analyte);
analyte.setId(id);
//bugzilla 1824 inserts will be logged in history table
AuditTrailDAO auditDAO = new AuditTrailDAOImpl();
String sysUserId = analyte.getSysUserId();
String tableName = "ANALYTE";
auditDAO.saveNewHistory(analyte,sysUserId,tableName);
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
} catch (Exception e) {
//buzilla 2154
LogEvent.logError("AnalyteDAOImpl","insertData()",e.toString());
throw new LIMSRuntimeException("Error in Analyte insertData()", e);
}
return true;
}
public void updateData(Analyte analyte) throws LIMSRuntimeException {
// bugzilla 1482 throw Exception if record already exists
try {
if ( duplicateAnalyteExists(analyte)) {
throw new LIMSDuplicateRecordException(
"Duplicate record exists for " + analyte.getAnalyteName());
}
} catch (Exception e) {
//buzilla 2154
LogEvent.logError("AnalyteDAOImpl","updateData()",e.toString());
throw new LIMSRuntimeException("Error in Analyte updateData()", e);
}
Analyte oldData = (Analyte) readAnalyte(analyte.getId());
Analyte newData = analyte;
// add to audit trail
try {
AuditTrailDAO auditDAO = new AuditTrailDAOImpl();
String sysUserId = analyte.getSysUserId();
String event = IActionConstants.AUDIT_TRAIL_UPDATE;
String tableName = "ANALYTE";
auditDAO.saveHistory(newData, oldData, sysUserId, event, tableName);
} catch (Exception e) {
//buzilla 2154
LogEvent.logError("AnalyteDAOImpl","updateData()",e.toString());
throw new LIMSRuntimeException(
"Error in Analyte AuditTrail updateData()", e);
}
try {
HibernateUtil.getSession().merge(analyte);
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
HibernateUtil.getSession().evict(analyte);
HibernateUtil.getSession().refresh(analyte);
} catch (Exception e) {
//buzilla 2154
LogEvent.logError("AnalyteDAOImpl","updateData()",e.toString());
throw new LIMSRuntimeException("Error in Analyte updateData()", e);
}
}
public void getData(Analyte analyte) throws LIMSRuntimeException {
try {
Analyte anal = (Analyte) HibernateUtil.getSession().get(
Analyte.class, analyte.getId());
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
if (anal != null) {
PropertyUtils.copyProperties(analyte, anal);
} else {
analyte.setId(null);
}
} catch (Exception e) {
//buzilla 2154
LogEvent.logError("AnalyteDAOImpl","getData()",e.toString());
throw new LIMSRuntimeException("Error in Analyte getData()", e);
}
}
public List getAllAnalytes() throws LIMSRuntimeException {
List list = new Vector();
try {
String sql = "from Analyte";
org.hibernate.Query query = HibernateUtil.getSession().createQuery(
sql);
list = query.list();
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
} catch (Exception e) {
//buzilla 2154
LogEvent.logError("AnalyteDAOImpl","getAllAnalytes()",e.toString());
throw new LIMSRuntimeException("Error in Analyte getAllAnalytes()",
e);
}
return list;
}
public List getPageOfAnalytes(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
String sql = "from Analyte a order by a.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) {
//buzilla 2154
LogEvent.logError("AnalyteDAOImpl","getPageOfAnalytes()",e.toString());
throw new LIMSRuntimeException(
"Error in Analyte getPageOfAnalytes()", e);
}
return list;
}
// bugzilla 2370
public List getPagesOfSearchedAnalytes(int startingRecNo, String searchString)
throws LIMSRuntimeException {
List list = new Vector();
String wildCard = "*";
String newSearchStr;
String sql;
try {
int endingRecNo = startingRecNo
+ (SystemConfiguration.getInstance().getDefaultPageSize() + 1);
int wCdPosition = searchString.indexOf (wildCard);
if (wCdPosition == -1) // no wild card looking for exact match
{
newSearchStr = searchString.toLowerCase().trim();
sql = "from Analyte a where trim(lower (a.analyteName)) = :param order by a.analyteName ";
}
else
{
newSearchStr = searchString.replace(wildCard, "%").toLowerCase().trim();
sql = "from Analyte a where trim(lower (a.analyteName)) like :param order by a.analyteName";
}
org.hibernate.Query query = HibernateUtil.getSession().createQuery(sql);
query.setParameter("param", newSearchStr);
query.setFirstResult(startingRecNo - 1);
query.setMaxResults(endingRecNo - 1);
list = query.list();
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
} catch (Exception e) {
e.printStackTrace();
throw new LIMSRuntimeException(
"Error in AnalyteDAOImpl getPagesOfSearchedAnalytes()", e);
}
return list;
}
//end bugzilla 2370
public Analyte readAnalyte(String idString) {
Analyte analyte = null;
try {
analyte = (Analyte) HibernateUtil.getSession().get(Analyte.class,
idString);
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
} catch (Exception e) {
//buzilla 2154
LogEvent.logError("AnalyteDAOImpl","readAnalyte()",e.toString());
throw new LIMSRuntimeException("Error in Analyte readAnalyte()", e);
}
return analyte;
}
// this is for autocomplete
public List getAnalytes(String filter) throws LIMSRuntimeException {
List list = new Vector();
try {
String sql = "from Analyte a where upper(a.analyteName) like upper(:param) and a.isActive='Y' order by upper(a.analyteName)";
org.hibernate.Query query = HibernateUtil.getSession().createQuery(
sql);
query.setParameter("param", filter + "%");
list = query.list();
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
} catch (Exception e) {
//buzilla 2154
LogEvent.logError("AnalyteDAOImpl","getAnalytes()",e.toString());
throw new LIMSRuntimeException(
"Error in Analyte getAnalytes(String filter)", e);
}
return list;
}
public List getNextAnalyteRecord(String id) throws LIMSRuntimeException {
return getNextRecord(id, "Analyte", Analyte.class);
}
public List getPreviousAnalyteRecord(String id) throws LIMSRuntimeException {
return getPreviousRecord(id, "Analyte", Analyte.class);
}
//bugzilla 1367 added ignoreCase
public Analyte getAnalyteByName(Analyte analyte, boolean ignoreCase)
throws LIMSRuntimeException {
try {
String sql = null;
if (ignoreCase) {
sql = "from Analyte a where trim(lower(a.analyteName)) = :param and a.isActive='Y'";
} else {
sql = "from Analyte a where a.analyteName = :param and a.isActive='Y'";
}
org.hibernate.Query query = HibernateUtil.getSession().createQuery(
sql);
if (ignoreCase) {
query.setString("param", analyte.getAnalyteName().trim()
.toLowerCase());
} else {
query.setString("param", analyte.getAnalyteName());
}
List list = query.list();
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
Analyte ana = null;
if (list.size() > 0)
ana = (Analyte) list.get(0);
return ana;
} catch (Exception e) {
//buzilla 2154
LogEvent.logError("AnalyteDAOImpl","getAnalyteByName()",e.toString());
throw new LIMSRuntimeException(
"Error in Analyte getAnalyteByName()", e);
}
}
// bugzilla 1411
public Integer getTotalAnalyteCount() throws LIMSRuntimeException {
return getTotalCount("Analyte", Analyte.class);
}
// overriding BaseDAOImpl bugzilla 1427 pass in name not id
public List getNextRecord(String id, String table, Class clazz)
throws LIMSRuntimeException {
List list = new Vector();
try {
String sql = "from " + table + " t where name >= " + enquote(id)
+ " order by t.analyteName";
org.hibernate.Query query = HibernateUtil.getSession().createQuery(
sql);
query.setFirstResult(1);
query.setMaxResults(2);
list = query.list();
} catch (Exception e) {
//buzilla 2154
LogEvent.logError("AnalyteDAOImpl","getNextRecord()",e.toString());
throw new LIMSRuntimeException("Error in getNextRecord() for "
+ table, e);
}
return list;
}
// overriding BaseDAOImpl bugzilla 1427 pass in name not id
public List getPreviousRecord(String id, String table, Class clazz)
throws LIMSRuntimeException {
List list = new Vector();
try {
String sql = "from " + table
+ " t order by t.analyteName desc where name <= "
+ enquote(id);
org.hibernate.Query query = HibernateUtil.getSession().createQuery(
sql);
query.setFirstResult(1);
query.setMaxResults(2);
list = query.list();
} catch (Exception e) {
//buzilla 2154
LogEvent.logError("AnalyteDAOImpl","getPreviousRecord()",e.toString());
throw new LIMSRuntimeException("Error in getPreviousRecord() for "
+ table, e);
}
return list;
}
//bugzilla 1482
private boolean duplicateAnalyteExists(Analyte analyte) throws LIMSRuntimeException {
try {
List list = new ArrayList();
// not case sensitive hemolysis and Hemolysis are considered
// duplicates
// bugzilla 2432 add check for local abbreviation
String sql = "";
if (analyte.getLocalAbbreviation() != null) {
sql = "from Analyte a where (trim(lower(a.analyteName)) = :name and a.id != :id)" +
" or (trim(lower(a.localAbbreviation)) = :abbreviation and a.id != :id)";
} else {
sql = "from Analyte a where trim(lower(a.analyteName)) = :name and a.id != :id";
}
org.hibernate.Query query = HibernateUtil.getSession().createQuery(sql);
query.setString("name", analyte.getAnalyteName().toLowerCase().trim());
//bugzilla 2432
if (analyte.getLocalAbbreviation() != null) {
query.setString("abbreviation", analyte.getLocalAbbreviation().toLowerCase().trim());
}
String analyteId = !StringUtil.isNullorNill(analyte.getId()) ? analyte.getId() : "0";
query.setInteger("id", Integer.parseInt(analyteId));
list = query.list();
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
return list.size() > 0;
} catch (Exception e) {
//buzilla 2154
LogEvent.logError("AnalyteDAOImpl","duplicateAnalyteExists()",e.toString());
throw new LIMSRuntimeException("Error in duplicateAnalyteExists()", e);
}
}
// bugzilla 2370 get total searched results
public Integer getTotalSearchedAnalyteCount( String searchString )
throws LIMSRuntimeException{
String wildCard = "*";
String newSearchStr;
String sql;
Integer count = null;
try {
int wCdPosition = searchString.indexOf (wildCard);
if (wCdPosition == -1) // no wild card looking for exact match
{
newSearchStr = searchString.toLowerCase().trim();
sql = "select count (*) from Analyte a where trim(lower (a.analyteName)) = :param ";
}
else
{
newSearchStr = searchString.replace(wildCard, "%").toLowerCase().trim();
sql = "select count (*) from Analyte a where trim(lower (a.analyteName)) like :param ";
}
org.hibernate.Query query = HibernateUtil.getSession().createQuery(sql);
query.setParameter("param", newSearchStr);
List results = query.list();
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
if (results != null && results.get(0) != null) {
if (results.get(0) != null) {
count = (Integer)results.get(0);
}
}
} catch (Exception e) {
e.printStackTrace();
throw new LIMSRuntimeException(
"Error in AnalyteDAOImpl getTotalSearchedAnalyteCount()", e);
}
return count;
}
//end bugzilla 2370
}