Java tutorial
/* * PatientView * * Copyright (c) Worth Solutions Limited 2004-2013 * * This file is part of PatientView. * * PatientView is free software: you can redistribute it and/or modify it under the terms of the * GNU General Public License as published by the Free Software Foundation, either version 3 of the License, * or (at your option) any later version. * PatientView is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even * the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * You should have received a copy of the GNU General Public License along with PatientView in a file * titled COPYING. If not, see <http://www.gnu.org/licenses/>. * * @package PatientView * @link http://www.patientview.org * @author PatientView <info@patientview.org> * @copyright Copyright (c) 2004-2013, Worth Solutions Limited * @license http://www.gnu.org/licenses/gpl-3.0.html The GNU General Public License V3.0 */ package org.patientview.radar.dao.impl; import org.apache.commons.collections.CollectionUtils; import org.apache.commons.lang.StringUtils; import org.patientview.model.Clinician; import org.patientview.model.Ethnicity; import org.patientview.model.Patient; import org.patientview.model.Sex; import org.patientview.model.Status; import org.patientview.model.enums.NhsNumberType; import org.patientview.model.enums.SourceType; import org.patientview.model.generic.DiseaseGroup; import org.patientview.model.generic.GenericDiagnosis; import org.patientview.radar.dao.PatientDao; import org.patientview.radar.dao.UserDao; import org.patientview.radar.dao.UtilityDao; import org.patientview.radar.dao.generic.DiseaseGroupDao; import org.patientview.radar.dao.generic.GenericDiagnosisDao; import org.patientview.util.CommonUtils; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.beans.factory.InitializingBean; import org.springframework.dao.EmptyResultDataAccessException; import org.springframework.jdbc.core.RowMapper; import org.springframework.jdbc.core.simple.SimpleJdbcInsert; import javax.sql.DataSource; import java.sql.ResultSet; import java.sql.SQLException; import java.text.SimpleDateFormat; import java.util.HashMap; import java.util.List; /** * User: james@solidstategroup.com * Date: 06/11/13 * Time: 10:13 */ public class PatientDaoImpl extends BaseDaoImpl implements PatientDao, InitializingBean { private SimpleJdbcInsert patientInsert; private SimpleJdbcInsert radarNumberInsert; private static final Logger LOGGER = LoggerFactory.getLogger(DemographicsDaoImpl.class); private static final String DATE_FORMAT = "yyyy-MM-dd"; // Static data private Sex unSpecifiedSex; private List<Sex> sexes; private List<Status> statuses; private List<DiseaseGroup> diseaseGroups; private List<GenericDiagnosis> genericDiagnoses; private List<Ethnicity> ethnicities; private UtilityDao utilityDao; private DiseaseGroupDao diseaseGroupDao; private GenericDiagnosisDao genericDiagnosisDao; private UserDao userDao; @Override public void setDataSource(DataSource dataSource) { // Call super super.setDataSource(dataSource); // Initialise a simple JDBC insert to be able to get the allocated ID patientInsert = new SimpleJdbcInsert(dataSource).withTableName("patient").usingGeneratedKeyColumns("id") .usingColumns("rrNo", "dateReg", "nhsno", "nhsNoType", "hospitalnumber", "uktNo", "surname", "surnameAlias", "forename", "dateofbirth", "AGE", "SEX", "ethnicGp", "address1", "address2", "address3", "address4", "POSTCODE", "radarConsentConfirmedByUserId", "postcodeOld", "CONSENT", "dateBapnReg", "consNeph", "unitcode", "STATUS", "emailAddress", "telephone1", "telephone2", "mobile", "rrtModality", "genericDiagnosis", "dateOfGenericDiagnosis", "otherClinicianAndContactInfo", "comments", "republicOfIrelandId", "isleOfManId", "channelIslandsId", "indiaId", "generic", "sourceType", "patientLinkId"); radarNumberInsert = new SimpleJdbcInsert(dataSource).withTableName("rdr_radar_number") .usingGeneratedKeyColumns("id"); } public void afterPropertiesSet() throws Exception { sexes = jdbcTemplate.query("SELECT * FROM tbl_Sex", new SexRowMapper()); statuses = jdbcTemplate.query("SELECT * FROM tbl_Status ", new StatusRowMapper()); diseaseGroups = diseaseGroupDao.getAll(); genericDiagnoses = genericDiagnosisDao.getAll(); ethnicities = utilityDao.getEthnicities(); for (Sex sex : sexes) { if (!sex.getType().toLowerCase().startsWith("m") && !sex.getType().toLowerCase().startsWith("f")) { unSpecifiedSex = sex; } } } public List<Patient> getPatientsByNhsNumber(final String nhsNo) { StringBuilder query = new StringBuilder(); query.append("SELECT id "); query.append(", nhsno "); query.append(", forename "); query.append(", surname "); query.append(", dateofbirth "); query.append(", unitcode "); query.append(", mostRecentTestResultDateRangeStopDate "); query.append("FROM patient "); query.append("WHERE nhsNo = ? "); query.append("ORDER BY mostRecentTestResultDateRangeStopDate DESC "); return jdbcTemplate.query(query.toString(), new Object[] { nhsNo }, new PatientSearchMapper()); } public List<Patient> getPatientsWithRadarSourceType() { StringBuilder query = new StringBuilder(); query.append("SELECT * "); query.append("FROM patient "); query.append("WHERE sourceType = ? "); return jdbcTemplate.query(query.toString(), new Object[] { "Radar" }, new EnhancedPatientSearchMapper()); } public Patient getByRadarNumber(Long radarNumber) { Patient patient = null; try { StringBuilder query = new StringBuilder(); query.append("SELECT * "); query.append("FROM patient "); query.append("WHERE radarNo = ? "); patient = jdbcTemplate.queryForObject(query.toString(), new Object[] { radarNumber }, new PatientRowMapper()); } catch (EmptyResultDataAccessException e) { // Can't find the patient by id LOGGER.debug("Cannot find patient with radar number {}", radarNumber); } return patient; } public Patient getById(final Long id) { Patient patient = null; try { StringBuilder query = new StringBuilder(); query.append("SELECT * "); query.append("FROM patient "); query.append("WHERE id = ? "); patient = jdbcTemplate.queryForObject(query.toString(), new Object[] { id }, new PatientRowMapper()); } catch (EmptyResultDataAccessException e) { // Can't find the patient by id LOGGER.debug("Cannot find patient with id {}", id); } return patient; } private Long getNextRadarNumber() { return radarNumberInsert.executeAndReturnKey(new HashMap<String, Object>() { }).longValue(); } private class PatientSearchMapper implements RowMapper<Patient> { public Patient mapRow(ResultSet resultSet, int i) throws SQLException { Patient patient = new Patient(); patient.setId(resultSet.getLong("id")); patient.setNhsno(resultSet.getString("nhsno")); patient.setSurname(resultSet.getString("surname")); patient.setForename(resultSet.getString("forename")); patient.setDateofbirth(resultSet.getDate("dateofbirth")); patient.setUnitcode(resultSet.getString("unitcode")); patient.setMostRecentTestResultDateRangeStopDate( resultSet.getDate("mostRecentTestResultDateRangeStopDate")); return patient; } } private class EnhancedPatientSearchMapper implements RowMapper<Patient> { public Patient mapRow(ResultSet resultSet, int i) throws SQLException { Patient patient = new Patient(); patient.setId(resultSet.getLong("id")); patient.setNhsno(resultSet.getString("nhsno")); patient.setSurname(resultSet.getString("surname")); patient.setForename(resultSet.getString("forename")); patient.setDateofbirth(resultSet.getDate("dateofbirth")); patient.setUnitcode(resultSet.getString("unitcode")); patient.setMostRecentTestResultDateRangeStopDate( resultSet.getDate("mostRecentTestResultDateRangeStopDate")); patient.setRadarNo(resultSet.getLong("radarNo")); return patient; } } public void save(final Patient patient) { // Sex fix if (patient.getSexModel() != null) { if (patient.getSexModel().getType().equalsIgnoreCase("male")) { patient.setSex("M"); } else if (patient.getSexModel().getType().equalsIgnoreCase("female")) { patient.setSex("F"); } } // If we have an ID then update, otherwise insert new and set the ID if (patient.hasValidId()) { jdbcTemplate.update( "UPDATE patient SET " + "rrNo = ?, " + "dateReg = ?, " + "nhsno = ?, " + "nhsNoType = ?, " + "hospitalnumber = ?, " + "uktNo = ?, " + "surname = ?, " + "surnameAlias = ?, " + "forename = ?, " + "dateofbirth = ?, " + "AGE = ?, " + "SEX = ?, " + "ethnicGp = ?, " + "address1 = ?, " + "address2 = ?, " + "address3 = ?, " + "address4 = ?, " + "POSTCODE = ?, " + "postcodeOld = ?," + "CONSENT = ?, " + "dateBapnReg = ?, " + "consNeph = ?, " + "STATUS = ?, " + "emailAddress = ?, " + "telephone1 = ?, " + "telephone2 = ?, " + "mobile = ?, " + "rrtModality = ?, " + "genericDiagnosis = ?, " + "dateOfGenericDiagnosis = ?, " + "otherClinicianAndContactInfo = ?, " + "comments = ?, " + "republicOfIrelandId = ?, " + "isleOfManId = ?, " + "channelIslandsId = ?, " + "indiaId = ?, " + "radarConsentConfirmedByUserId = ?, " + "generic = ?, " + "patientLinkId = ? " + " WHERE id = ?", patient.getRrNo(), patient.getDateReg(), patient.getNhsno(), patient.getNhsNumberType() != null ? patient.getNhsNumberType().getId() : 1, patient.getHospitalnumber(), patient.getUktNo(), patient.getSurname(), patient.getSurnameAlias(), patient.getForename(), patient.getDob() != null ? new SimpleDateFormat(DATE_FORMAT).format(patient.getDob()) : null, patient.getAge(), patient.getSex(), patient.getEthnicity() != null ? patient.getEthnicity().getCode() : null, patient.getAddress1(), patient.getAddress2(), patient.getAddress3(), patient.getAddress4(), patient.getPostcode(), patient.getPostcodeOld(), patient.isConsent(), patient.getDateReg(), patient.getClinician() != null ? patient.getClinician().getId() : null, patient.getStatusModel() != null ? patient.getStatusModel().getId() : null, patient.getEmailAddress(), patient.getTelephone1(), patient.getTelephone2(), patient.getMobile(), patient.getRrtModalityEunm() != null ? patient.getRrtModalityEunm().getId() : null, patient.getGenericDiagnosisModel() != null ? patient.getGenericDiagnosisModel().getId() : null, patient.getDateOfGenericDiagnosis(), patient.getOtherClinicianAndContactInfo(), patient.getComments(), patient.getRepublicOfIrelandId(), patient.getIsleOfManId(), patient.getChannelIslandsId(), patient.getIndiaId(), patient.getRadarConsentConfirmedByUserId(), patient.isGeneric(), patient.getPatientLinkId() == null ? null : patient.getPatientLinkId(), patient.getId()); } else { Number id = patientInsert.executeAndReturnKey(new HashMap<String, Object>() { { put("rrNo", patient.getRrNo()); put("dateReg", patient.getDateReg()); put("nhsno", patient.getNhsno()); put("nhsNoType", patient.getNhsNumberType() != null ? patient.getNhsNumberType().getId() : null); put("hospitalnumber", patient.getHospitalnumber()); put("uktNo", patient.getUktNo()); put("surname", patient.getSurname()); put("surnameAlias", patient.getSurnameAlias()); put("forename", patient.getForename()); put("dateofbirth", patient.getDob() != null ? new SimpleDateFormat(DATE_FORMAT).format(patient.getDob()) : null); put("AGE", patient.getAge()); put("SEX", patient.getSex()); put("ethnicGp", patient.getEthnicity() != null ? patient.getEthnicity().getCode() : null); put("address1", patient.getAddress1()); put("address2", patient.getAddress2()); put("address3", patient.getAddress3()); put("address4", patient.getAddress4()); put("POSTCODE", patient.getPostcode()); put("postcodeOld", patient.getPostcodeOld()); put("CONSENT", patient.isConsent()); put("dateBapnReg", null); put("consNeph", patient.getClinician() != null ? patient.getClinician().getId() : null); put("unitcode", patient.getUnitcode() != null ? patient.getUnitcode() : patient.getRenalUnit().getUnitCode()); put("STATUS", patient.getStatusModel() != null ? patient.getStatusModel().getId() : null); put("emailAddress", patient.getEmailAddress()); put("telephone1", patient.getTelephone1()); put("telephone2", patient.getTelephone2()); put("mobile", patient.getMobile()); put("rrtModality", patient.getRrtModalityEunm() != null ? patient.getRrtModalityEunm().getId() : null); put("genericDiagnosis", patient.getGenericDiagnosisModel() != null ? patient.getGenericDiagnosisModel().getId() : null); put("dateOfGenericDiagnosis", patient.getDateOfGenericDiagnosis()); put("otherClinicianAndContactInfo", patient.getOtherClinicianAndContactInfo()); put("comments", patient.getComments()); put("republicOfIrelandId", patient.getRepublicOfIrelandId()); put("isleOfManId", patient.getIsleOfManId()); put("channelIslandsId", patient.getChannelIslandsId()); put("indiaId", patient.getIndiaId()); put("generic", patient.isGeneric()); put("radarConsentConfirmedByUserId", patient.getRadarConsentConfirmedByUserId()); put("sourceType", SourceType.RADAR.getName()); put("patientLinkId", patient.getPatientLinkId() == null ? null : patient.getPatientLinkId()); } }); patient.setId(id.longValue()); //The id of the patient record is now the new radar number Long radarNumber = getNextRadarNumber(); jdbcTemplate.update("UPDATE patient set radarNo = ? WHERE id = ? ", radarNumber, id.longValue()); patient.setRadarNo(radarNumber); // Sex fix if (patient.getSexModel() != null) { if (patient.getSexModel().getType().equalsIgnoreCase("m")) { patient.setSex("Male"); } else if (patient.getSexModel().getType().equalsIgnoreCase("f")) { patient.setSex("Female"); } } } } public List<Patient> getPatientsByUnitCode(List<String> unitCodes) { String unitCodeValues = buildValueList(unitCodes); StringBuilder query = new StringBuilder(); query.append("SELECT DISTINCT p.* "); query.append("FROM user u "); query.append("INNER JOIN patient p "); query.append("INNER JOIN usermapping m "); query.append("WHERE m.nhsno = p.nhsno "); query.append("AND u.username NOT LIKE '%-GP%' "); query.append("AND u.username = m.username "); query.append("AND m.unitcode <> 'PATIENT' "); query.append("AND m.unitcode IN ("); query.append(unitCodeValues); query.append(")"); query.append("AND p.sourceType = '"); query.append(SourceType.RADAR.getName()); query.append("'"); if (StringUtils.isNotEmpty(unitCodeValues)) { return jdbcTemplate.query(query.toString(), new PatientRowMapper()); } else { return null; } } // This is here to move away from the old Demographic Dao Class and clean the mapping up. public class PatientRowMapper implements RowMapper<Patient> { public Patient mapRow(ResultSet resultSet, int i) throws SQLException { // Construct object and set radar number Patient patient = new Patient(); Long radarId = resultSet.getLong("radarNo"); patient.setRadarNo(radarId); patient.setId(resultSet.getLong("id")); patient.setDateReg(resultSet.getDate("dateReg")); patient.setRrNo(resultSet.getString("rrNo")); patient.setUktNo(resultSet.getString("uktNo")); patient.setNhsno(resultSet.getString("nhsno")); patient.setNhsNumberType(NhsNumberType.getNhsNumberType(resultSet.getLong("nhsNoType"))); patient.setHospitalnumber(resultSet.getString("hospitalnumber")); patient.setSurname(resultSet.getString("surname")); patient.setSurnameAlias(resultSet.getString("surnameAlias")); patient.setForename(resultSet.getString("forename")); patient.setDob(CommonUtils.parseDate(resultSet.getString("dateofbirth"))); // Addresses patient.setAddress1(resultSet.getString("address1")); patient.setAddress2(resultSet.getString("address2")); patient.setAddress3(resultSet.getString("address3")); patient.setAddress4(resultSet.getString("address4")); patient.setPostcode(resultSet.getString("POSTCODE")); patient.setPostcodeOld(resultSet.getString("postcodeOld")); patient.setSexModel(getSex(resultSet.getString("SEX"))); patient.setSex(resultSet.getString("SEX")); patient.setEthnicity(getEthnicity(resultSet.getString("ethnicGp"))); patient.setConsent(resultSet.getBoolean("CONSENT")); patient.setStatusModel(getStatus(resultSet.getLong("STATUS"))); // Not sure on the why this field is called this patient.setClinician(getClinician(resultSet.getLong("consNeph"))); patient.setUnitcode(resultSet.getString("unitCode")); patient.setRenalUnit(utilityDao.getCentre(patient.getUnitcode())); patient.setEmailAddress(resultSet.getString("emailAddress")); patient.setTelephone1(resultSet.getString("telephone1")); patient.setTelephone2(resultSet.getString("telephone2")); patient.setMobile(resultSet.getString("mobile")); Integer rrtModalityId = getIntegerWithNullCheck("rrtModality", resultSet); if (rrtModalityId != null) { patient.setRrtModalityEunm(getEnumValue(Patient.RRTModality.class, rrtModalityId)); } patient.setDiseaseGroup(getDiseaseGroup(patient.getNhsno())); patient.setDateOfGenericDiagnosis(resultSet.getDate("dateOfGenericDiagnosis")); patient.setOtherClinicianAndContactInfo(resultSet.getString("otherClinicianAndContactInfo")); patient.setComments(resultSet.getString("comments")); //comments, patient.setRepublicOfIrelandId(resultSet.getString("republicOfIrelandId")); patient.setIsleOfManId(resultSet.getString("isleOfManId")); patient.setChannelIslandsId(resultSet.getString("channelIslandsId")); patient.setIndiaId(resultSet.getString("indiaId")); patient.setGeneric(resultSet.getBoolean("generic")); patient.setEthnicGp(resultSet.getString("ethnicGp")); // Needs fixing into getting a Enum patient.setSourceType(resultSet.getString("sourceType")); patient.setPatientLinkId(resultSet.getLong("patientLinkId")); if (patient.getPatientLinkId() == 0) { patient.setPatientLinkId(null); } patient.setRadarConsentConfirmedByUserId(resultSet.getLong("radarConsentConfirmedByUserId")); patient.setGenericDiagnosisModel( getGenericDiagnosis(resultSet.getString("genericDiagnosis"), patient.getDiseaseGroup())); return patient; } } //// Helper methods for the Row Mapper private Ethnicity getEthnicity(String ethnicityCode) { if (StringUtils.isNotEmpty(ethnicityCode)) { for (Ethnicity ethnicity : ethnicities) { if (ethnicity.getCode().equals(ethnicityCode)) { return ethnicity; } } } return null; } private GenericDiagnosis getGenericDiagnosis(String genericDiagnosisId, DiseaseGroup diseaseGroupId) { if (diseaseGroupId != null && StringUtils.isNotEmpty(genericDiagnosisId) && StringUtils.isNotEmpty(diseaseGroupId.getId())) { for (GenericDiagnosis genericDiagnosis : genericDiagnoses) { if (genericDiagnosis.getPrdCode().equals(genericDiagnosisId) && genericDiagnosis.getWorkingGroup().equals(diseaseGroupId.getId())) { return genericDiagnosis; } } } return null; } private DiseaseGroup getDiseaseGroup(String nhsNo) { String diseaseGroupId = null; List<String> radarMappings = userDao.getPatientRadarMappings(nhsNo); if (CollectionUtils.isNotEmpty(radarMappings)) { diseaseGroupId = radarMappings.get(0); } for (DiseaseGroup diseaseGroup : diseaseGroups) { if (diseaseGroup.getId().equals(diseaseGroupId)) { return diseaseGroup; } } return null; } private Clinician getClinician(Long consultantId) { if (consultantId != null) { try { Clinician clinician = utilityDao.getClinician(consultantId); return clinician; } catch (Exception e) { LOGGER.error("Error return clinician", e); return null; } } return null; } private Status getStatus(Long statusId) { if (statusId != null) { for (Status status : statuses) { if (status.getId().equals(statusId)) { return status; } } } return null; } private Sex getSex(String sexType) { if (StringUtils.isNotEmpty(sexType)) { for (Sex sex : sexes) { if (sex.getType().toLowerCase().startsWith(sexType.toLowerCase())) { return sex; } } } return unSpecifiedSex; } private class SexRowMapper implements RowMapper<Sex> { public Sex mapRow(ResultSet resultSet, int i) throws SQLException { Sex sex = new Sex(); sex.setId(resultSet.getLong("sID")); sex.setType(resultSet.getString("sType")); return sex; } } private class StatusRowMapper implements RowMapper<Status> { public Status mapRow(ResultSet resultSet, int i) throws SQLException { // Cosntruct new status object Status status = new Status(); status.setId(resultSet.getLong("sID")); status.setDescription(resultSet.getString("sDesc")); status.setAbbreviation(resultSet.getString("sAbbrev")); return status; } } public void setUtilityDao(UtilityDao utilityDao) { this.utilityDao = utilityDao; } public void setDiseaseGroupDao(DiseaseGroupDao diseaseGroupDao) { this.diseaseGroupDao = diseaseGroupDao; } public void setGenericDiagnosisDao(GenericDiagnosisDao genericDiagnosisDao) { this.genericDiagnosisDao = genericDiagnosisDao; } public void setUserDao(UserDao userDao) { this.userDao = userDao; } public List<Sex> getSexes() { return sexes; } public List<Status> getStatuses() { return statuses; } public List<DiseaseGroup> getDiseaseGroups() { return diseaseGroups; } public List<GenericDiagnosis> getGenericDiagnoses() { return genericDiagnoses; } public List<Ethnicity> getEthnicities() { return ethnicities; } }