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Martina, Roni, Eyal, Klaus | BAH-460 | add api to search patients wit…
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…h similar name, gender and birthdate/age
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@mduemcke
mduemcke committed Aug 20, 2018
1 parent 89fc7a5 commit 117df8f
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Showing 11 changed files with 384 additions and 59 deletions.
36 changes: 36 additions & 0 deletions .../src/main/java/org/bahmni/module/bahmnicore/contract/patient/PatientSearchParameters.java
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Expand Up @@ -3,12 +3,18 @@
import org.apache.commons.lang.StringUtils;
import org.openmrs.module.webservices.rest.web.RequestContext;

import java.sql.Timestamp;
import java.util.Date;
import java.util.Map;

public class PatientSearchParameters {
private final String MIDNIGHT = "00:00:00";

private Boolean filterPatientsByLocation;
private String identifier;
private String name;
private String gender;
private Date birthdate;
private String addressFieldName;
private String addressFieldValue;
private Integer start;
Expand Down Expand Up @@ -43,6 +49,8 @@ public PatientSearchParameters(RequestContext context) {
} else {
this.setAddressFieldName("city_village");
}
this.setGender(context.getParameter("gender"));
this.setBirthdate(context.getParameter("birthdate"));
this.setAddressFieldValue(context.getParameter("addressFieldValue"));
Map parameterMap = context.getRequest().getParameterMap();
this.setAddressSearchResultFields((String[]) parameterMap.get("addressSearchResultsConfig"));
Expand Down Expand Up @@ -71,6 +79,26 @@ public void setName(String name) {
this.name = name;
}

public String getGender() {
return gender;
}

public void setGender(String gender) {
this.gender = gender;
}

public void setBirthdate(String birthdate) {
if(StringUtils.isEmpty(birthdate)) {
return;
}

this.birthdate = Timestamp.valueOf(setToMidnight(birthdate));
}

public Date getBirthdate() {
return birthdate;
}

public String getAddressFieldName() {
return addressFieldName;
}
Expand Down Expand Up @@ -174,4 +202,12 @@ public void setFilterOnAllIdentifiers(Boolean filterOnAllIdentifiers) {
public Boolean getFilterOnAllIdentifiers() {
return filterOnAllIdentifiers;
}

private String setToMidnight(String birthdate) {
if(StringUtils.isNotEmpty(birthdate) && birthdate.matches("\\d{4}-\\d{2}-\\d{2}")) {
return birthdate + " " + MIDNIGHT;
} else {
return birthdate;
}
}
}
13 changes: 8 additions & 5 deletions ...main/java/org/bahmni/module/bahmnicore/contract/patient/mapper/PatientResponseMapper.java
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@@ -1,6 +1,5 @@
package org.bahmni.module.bahmnicore.contract.patient.mapper;

import java.util.Objects;
import org.apache.commons.beanutils.PropertyUtils;
import org.apache.commons.lang3.StringUtils;
import org.bahmni.module.bahmnicore.contract.patient.response.PatientResponse;
Expand All @@ -21,11 +20,13 @@

import java.lang.reflect.InvocationTargetException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Objects;
import java.util.Set;
import java.util.stream.Collectors;

import static java.util.Arrays.asList;

public class PatientResponseMapper {
private PatientResponse patientResponse;
private VisitService visitService;
Expand All @@ -38,8 +39,8 @@ public PatientResponseMapper(VisitService visitService, BahmniVisitLocationServi
}

public PatientResponse map(Patient patient, String loginLocationUuid, String[] searchResultFields, String[] addressResultFields, Object programAttributeValue) {
List<String> patientSearchResultFields = searchResultFields != null ? Arrays.asList(searchResultFields) : new ArrayList<>();
List<String> addressSearchResultFields = addressResultFields != null ? Arrays.asList(addressResultFields) : new ArrayList<>();
List<String> patientSearchResultFields = searchResultFields != null ? asList(searchResultFields) : new ArrayList<>();
List<String> addressSearchResultFields = addressResultFields != null ? asList(addressResultFields) : new ArrayList<>();

Integer visitLocationId = bahmniVisitLocationService.getVisitLocation(loginLocationUuid).getLocationId();
List<Visit> activeVisitsByPatient = visitService.getActiveVisitsByPatient(patient);
Expand All @@ -55,7 +56,9 @@ public PatientResponse map(Patient patient, String loginLocationUuid, String[] s
patientResponse.setFamilyName(patient.getFamilyName());
patientResponse.setGender(patient.getGender());
PatientIdentifier primaryIdentifier = patient.getPatientIdentifier();
patientResponse.setIdentifier(primaryIdentifier.getIdentifier());
if(primaryIdentifier != null) {
patientResponse.setIdentifier(primaryIdentifier.getIdentifier());
}
patientResponse.setPatientProgramAttributeValue(programAttributeValue);

mapExtraIdentifiers(patient, primaryIdentifier);
Expand Down
3 changes: 3 additions & 0 deletions bahmnicore-api/src/main/java/org/bahmni/module/bahmnicore/dao/PatientDao.java
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Expand Up @@ -4,6 +4,7 @@
import org.openmrs.Patient;
import org.openmrs.RelationshipType;

import java.util.Date;
import java.util.List;

public interface PatientDao {
Expand All @@ -19,6 +20,8 @@ List<PatientResponse> getPatientsUsingLuceneSearch(String identifier, String nam
String programAttributeFieldName, String[] addressSearchResultFields,
String[] patientSearchResultFields, String loginLocationUuid, Boolean filterPatientsByLocation, Boolean filterOnAllIdentifiers);

List<PatientResponse> getSimilarPatientsUsingLuceneSearch(String name, String gender, Date birthdate, String loginLocationUuid, Integer length);

public Patient getPatient(String identifier);

public List<Patient> getPatients(String partialIdentifier, boolean shouldMatchExactPatientId);
Expand Down
90 changes: 76 additions & 14 deletions bahmnicore-api/src/main/java/org/bahmni/module/bahmnicore/dao/impl/PatientDaoImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -22,20 +22,26 @@
import org.openmrs.Patient;
import org.openmrs.PatientIdentifier;
import org.openmrs.PatientIdentifierType;
import org.openmrs.Person;
import org.openmrs.PersonName;
import org.openmrs.RelationshipType;
import org.openmrs.api.context.Context;
import org.openmrs.api.db.hibernate.HibernatePatientDAO;
import org.openmrs.api.db.hibernate.PersonLuceneQuery;
import org.openmrs.api.db.hibernate.search.LuceneQuery;
import org.openmrs.module.bahmniemrapi.visitlocation.BahmniVisitLocationServiceImpl;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Repository;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.Set;

import static java.util.stream.Collectors.reducing;
import static java.util.Arrays.asList;
import static java.util.stream.Collectors.toList;

@Repository
Expand Down Expand Up @@ -88,18 +94,74 @@ public List<PatientResponse> getPatientsUsingLuceneSearch(String identifier, Str
List<PatientResponse> patientResponses = patientIdentifiers.stream()
.map(patientIdentifier -> {
Patient patient = patientIdentifier.getPatient();
if(!uniquePatientIds.contains(patient.getPatientId())) {
PatientResponse patientResponse = patientResponseMapper.map(patient, loginLocationUuid, patientSearchResultFields, addressSearchResultFields,
programAttributes.get(patient.getPatientId()));
uniquePatientIds.add(patient.getPatientId());
return patientResponse;
}else
return null;
return toPatientResponse(patientResponseMapper, patient, loginLocationUuid, addressSearchResultFields, patientSearchResultFields, programAttributes, uniquePatientIds);
}).filter(Objects::nonNull)
.collect(toList());
return patientResponses;
}

@Override
public List<PatientResponse> getSimilarPatientsUsingLuceneSearch(String name, String gender, Date birthdate, String loginLocationUuid, Integer length) {
PatientResponseMapper patientResponseMapper = new PatientResponseMapper(Context.getVisitService(),new BahmniVisitLocationServiceImpl(Context.getLocationService()));
List<Patient> patients = getPatientsByNameGenderAndBirthdate(name, gender, birthdate, length);
List<PatientResponse> patientResponses = patients.stream()
.map(patient -> {return patientResponseMapper.map(patient, loginLocationUuid, null, null,null);}).filter(Objects::nonNull)
.collect(toList());
return patientResponses;
}

private PatientResponse toPatientResponse(PatientResponseMapper patientResponseMapper, Patient patient, String loginLocationUuid, String[] addressSearchResultFields, String[] patientSearchResultFields, Map<Object, Object> programAttributes, Set<Integer> uniquePatientIds) {
if(!uniquePatientIds.contains(patient.getPatientId())) {
PatientResponse patientResponse = patientResponseMapper.map(patient, loginLocationUuid, patientSearchResultFields, addressSearchResultFields,
programAttributes.get(patient.getPatientId()));
uniquePatientIds.add(patient.getPatientId());
return patientResponse;
} else {
return null;
}
}

private List<Patient> getPatientsByNameGenderAndBirthdate(String name, String gender, Date birthdate, Integer length) {
if(isAllNullOrEmpty(name, gender, birthdate)) {
return new ArrayList<>();
}

HibernatePatientDAO patientDAO = new HibernatePatientDAO();
patientDAO.setSessionFactory(sessionFactory);
String query = LuceneQuery.escapeQuery(name);
PersonLuceneQuery personLuceneQuery = new PersonLuceneQuery(sessionFactory);
LuceneQuery<PersonName> nameQuery = personLuceneQuery.getPatientNameQuery(query, false);
List<Patient> patients = nameQuery.list().stream()
.filter(patient -> patient.getPreferred() && checkGender(patient.getPerson(), gender)
&& checkBirthdate(patient.getPerson(), birthdate)
)
.limit(length)
.map(patient -> new Patient(patient.getPerson()))
.collect(toList());
return patients;
}

private Boolean isAllNullOrEmpty(String name, String gender, Date birthdate) {
return (name == null || name.trim().isEmpty()) && (gender == null || gender.isEmpty()) && birthdate == null;
}


private Boolean checkGender(Person person, String gender) {
if(gender != null && !gender.isEmpty()){
return gender.equals(person.getGender());
} else {
return true;
}
}

private Boolean checkBirthdate(Person person, Date birthdate) {
if(birthdate != null) {
return birthdate.equals(person.getBirthdate());
} else {
return true;
}
}

private List<PatientIdentifier> getPatientIdentifiers(String identifier, Boolean filterOnAllIdentifiers, Integer offset, Integer length) {
FullTextSession fullTextSession = Search.getFullTextSession(sessionFactory.getCurrentSession());
QueryBuilder queryBuilder = fullTextSession.getSearchFactory().buildQueryBuilder().forEntity(PatientIdentifier.class).get();
Expand All @@ -108,7 +170,7 @@ private List<PatientIdentifier> getPatientIdentifiers(String identifier, Boolean
.wildcard().onField("identifierAnywhere").matching("*" + identifier.toLowerCase() + "*").createQuery();
org.apache.lucene.search.Query nonVoidedIdentifiers = queryBuilder.keyword().onField("voided").matching(false).createQuery();
org.apache.lucene.search.Query nonVoidedPatients = queryBuilder.keyword().onField("patient.voided").matching(false).createQuery();

List<String> identifierTypeNames = getIdentifierTypeNames(filterOnAllIdentifiers);

BooleanJunction identifierTypeShouldJunction = queryBuilder.bool();
Expand All @@ -132,7 +194,7 @@ private List<PatientIdentifier> getPatientIdentifiers(String identifier, Boolean
fullTextQuery.setMaxResults(length);
return (List<PatientIdentifier>) fullTextQuery.list();
}

private List<String> getIdentifierTypeNames(Boolean filterOnAllIdentifiers) {
List<String> identifierTypeNames = new ArrayList<>();
addIdentifierTypeName(identifierTypeNames,"bahmni.primaryIdentifierType");
Expand Down Expand Up @@ -179,7 +241,7 @@ private boolean isValidAddressField(String addressFieldName) {
"LOWER (TABLE_NAME) ='person_address' and LOWER(COLUMN_NAME) IN " +
"( :personAddressField)";
Query queryToGetAddressFields = sessionFactory.getCurrentSession().createSQLQuery(query);
queryToGetAddressFields.setParameterList("personAddressField", Arrays.asList(addressFieldName.toLowerCase()));
queryToGetAddressFields.setParameterList("personAddressField", asList(addressFieldName.toLowerCase()));
List list = queryToGetAddressFields.list();
return list.size() > 0;
}
Expand All @@ -201,7 +263,7 @@ private List<Integer> getPersonAttributeIds(String[] patientAttributes) {
String query = "select person_attribute_type_id from person_attribute_type where name in " +
"( :personAttributeTypeNames)";
Query queryToGetAttributeIds = sessionFactory.getCurrentSession().createSQLQuery(query);
queryToGetAttributeIds.setParameterList("personAttributeTypeNames", Arrays.asList(patientAttributes));
queryToGetAttributeIds.setParameterList("personAttributeTypeNames", asList(patientAttributes));
List list = queryToGetAttributeIds.list();
return (List<Integer>) list;
}
Expand Down Expand Up @@ -229,7 +291,7 @@ public List<Patient> getPatients(String patientIdentifier, boolean shouldMatchEx
}

Patient patient = getPatient(patientIdentifier);
List<Patient> result = (patient == null ? new ArrayList<Patient>() : Arrays.asList(patient));
List<Patient> result = (patient == null ? new ArrayList<Patient>() : asList(patient));
return result;
}

Expand Down
4 changes: 4 additions & 0 deletions bahmnicore-api/src/main/java/org/bahmni/module/bahmnicore/service/BahmniPatientService.java
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Original file line number Diff line number Diff line change
@@ -1,9 +1,11 @@
package org.bahmni.module.bahmnicore.service;

import org.bahmni.module.bahmnicore.contract.patient.PatientSearchParameters;
import org.bahmni.module.bahmnicore.contract.patient.mapper.PatientResponseMapper;
import org.bahmni.module.bahmnicore.contract.patient.response.PatientConfigResponse;
import org.bahmni.module.bahmnicore.contract.patient.response.PatientResponse;
import org.openmrs.Patient;
import org.openmrs.Person;
import org.openmrs.RelationshipType;

import java.util.List;
Expand All @@ -15,6 +17,8 @@ public interface BahmniPatientService {

List<PatientResponse> luceneSearch(PatientSearchParameters searchParameters);

List<PatientResponse> searchSimilarPatients(PatientSearchParameters searchParameters);

public List<Patient> get(String partialIdentifier, boolean shouldMatchExactPatientId);

public List<RelationshipType> getByAIsToB(String aIsToB);
Expand Down
10 changes: 10 additions & 0 deletions ...api/src/main/java/org/bahmni/module/bahmnicore/service/impl/BahmniPatientServiceImpl.java
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Expand Up @@ -20,6 +20,7 @@
@Service
@Lazy //to get rid of cyclic dependencies
public class BahmniPatientServiceImpl implements BahmniPatientService {
private static final int SIMILAR_PATIENT_RESULT_LENGTH = 5;
private PersonService personService;
private ConceptService conceptService;
private PatientDao patientDao;
Expand Down Expand Up @@ -83,6 +84,15 @@ public List<PatientResponse> luceneSearch(PatientSearchParameters searchParamete
searchParameters.getFilterPatientsByLocation(), searchParameters.getFilterOnAllIdentifiers());
}

@Override
public List<PatientResponse> searchSimilarPatients(PatientSearchParameters searchParameters) {
return patientDao.getSimilarPatientsUsingLuceneSearch(searchParameters.getName(),
searchParameters.getGender(),
searchParameters.getBirthdate(),
searchParameters.getLoginLocationUuid(),
SIMILAR_PATIENT_RESULT_LENGTH);
}

@Override
public List<Patient> get(String partialIdentifier, boolean shouldMatchExactPatientId) {
return patientDao.getPatients(partialIdentifier, shouldMatchExactPatientId);
Expand Down
46 changes: 46 additions & 0 deletions .../test/java/org/bahmni/module/bahmnicore/contract/patient/PatientSearchParametersTest.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,46 @@
package org.bahmni.module.bahmnicore.contract.patient;

import org.junit.Before;
import org.junit.Test;
import org.mockito.Mock;
import org.openmrs.module.webservices.rest.web.RequestContext;

import javax.servlet.http.HttpServletRequest;
import java.sql.Timestamp;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNull;
import static org.mockito.Mockito.when;
import static org.mockito.MockitoAnnotations.initMocks;


public class PatientSearchParametersTest {

@Mock
RequestContext requestContext;

@Mock
HttpServletRequest request;

@Before
public void setup() {
initMocks(this);
when(requestContext.getRequest()).thenReturn(request);
}

@Test
public void shouldIgnoreEmptyBirthdate () {
when(requestContext.getParameter("birthdate")).thenReturn("");
PatientSearchParameters patientSearchParameters = new PatientSearchParameters(requestContext);

assertNull(patientSearchParameters.getBirthdate());
}

@Test
public void shouldParseBirthdateFromStringAndSetToMidnight () {
when(requestContext.getParameter("birthdate")).thenReturn("1983-01-30");
PatientSearchParameters patientSearchParameters = new PatientSearchParameters(requestContext);

assertEquals(Timestamp.valueOf("1983-01-30 00:00:00"), patientSearchParameters.getBirthdate());
}
}
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