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[BAH-460][Roni/Martina] Add api for search similar patient using Pers…
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…onService and Lucene
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@mduemcke
mduemcke committed May 24, 2018
1 parent 140a6db commit 7ee46a5
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Showing 16 changed files with 228 additions and 53 deletions.
10 changes: 10 additions & 0 deletions .../src/main/java/org/bahmni/module/bahmnicore/contract/patient/PatientSearchParameters.java
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Expand Up @@ -9,6 +9,7 @@ public class PatientSearchParameters {
private Boolean filterPatientsByLocation;
private String identifier;
private String name;
private String gender;
private String addressFieldName;
private String addressFieldValue;
private Integer start;
Expand Down Expand Up @@ -43,6 +44,7 @@ public PatientSearchParameters(RequestContext context) {
} else {
this.setAddressFieldName("city_village");
}
this.setGender(context.getParameter("gender"));
this.setAddressFieldValue(context.getParameter("addressFieldValue"));
Map parameterMap = context.getRequest().getParameterMap();
this.setAddressSearchResultFields((String[]) parameterMap.get("addressSearchResultsConfig"));
Expand Down Expand Up @@ -71,6 +73,14 @@ public void setName(String name) {
this.name = name;
}

public String getGender() {
return gender;
}

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

public String getAddressFieldName() {
return addressFieldName;
}
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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 @@ -17,11 +16,13 @@

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 @@ -34,8 +35,8 @@ 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 @@ -51,7 +52,9 @@ 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);
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2 changes: 2 additions & 0 deletions bahmnicore-api/src/main/java/org/bahmni/module/bahmnicore/dao/PatientDao.java
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Expand Up @@ -19,6 +19,8 @@ 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, String loginLocationUuid, Integer length);

public Patient getPatient(String identifier);

public List<Patient> getPatients(String partialIdentifier, boolean shouldMatchExactPatientId);
Expand Down
5 changes: 3 additions & 2 deletions bahmnicore-api/src/main/java/org/bahmni/module/bahmnicore/dao/impl/OrderDaoImpl.java
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Expand Up @@ -31,14 +31,15 @@
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;

import static java.util.Arrays.asList;

@Component
public class OrderDaoImpl implements OrderDao {
private static final String ORDER_TEMPLATES_DIRECTORY = "ordertemplates";
Expand Down Expand Up @@ -364,7 +365,7 @@ public List<Order> getAllOrders(Patient patientByUuid, OrderType drugOrderTypeUu

return getAllOrders(patientByUuid, drugOrderTypeUuid, null, null, encounters);
}
return getAllOrders(patientByUuid, Arrays.asList(drugOrderTypeUuid), offset, limit);
return getAllOrders(patientByUuid, asList(drugOrderTypeUuid), offset, limit);
}

@Override
Expand Down
72 changes: 60 additions & 12 deletions bahmnicore-api/src/main/java/org/bahmni/module/bahmnicore/dao/impl/PatientDaoImpl.java
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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.HashMap;
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 +94,60 @@ 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, String loginLocationUuid, Integer length) {
PatientResponseMapper patientResponseMapper = new PatientResponseMapper(Context.getVisitService(),new BahmniVisitLocationServiceImpl(Context.getLocationService()));
List<Patient> patients = getPatientsByNameAndGender(name, gender, 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> getPatientsByNameAndGender(String name, String gender, Integer length) {
HibernatePatientDAO patientDAO = new HibernatePatientDAO();
patientDAO.setSessionFactory(sessionFactory);
List<Patient> patients = new ArrayList<Patient>();
String query = LuceneQuery.escapeQuery(name);
PersonLuceneQuery personLuceneQuery = new PersonLuceneQuery(sessionFactory);
LuceneQuery<PersonName> nameQuery = personLuceneQuery.getPatientNameQueryWithOrParser(query, false);
List<PersonName> persons = nameQuery.list().stream()
.filter(
personName ->
personName.getPreferred()
&& checkGender(personName.getPerson(), gender)
).collect(toList());
persons = persons.subList(0, Math.min(length, persons.size()));
persons.forEach(person -> patients.add(new Patient(person.getPerson())));
return patients;
}


private Boolean checkGender(Person person, String gender) {
if(gender != null && !gender.isEmpty()){
return gender.equals(person.getGender());
} 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 Down Expand Up @@ -179,7 +227,7 @@ 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 +249,7 @@ 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 +277,7 @@ 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
7 changes: 4 additions & 3 deletions ...icore-api/src/main/java/org/bahmni/module/bahmnicore/matcher/EncounterSessionMatcher.java
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Expand Up @@ -22,13 +22,14 @@
import org.springframework.stereotype.Component;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.Calendar;
import java.util.Collection;
import java.util.Date;
import java.util.List;
import java.util.Map;

import static java.util.Arrays.asList;

@Component
public class EncounterSessionMatcher implements BaseEncounterMatcher {

Expand Down Expand Up @@ -79,7 +80,7 @@ private Encounter findMatchingEncounter(Visit visit, EncounterParameters encount
if (visit.getId() == null) { // To handle new Visit scenario where visit will not be persisted in DB and we get a visit obj (Called from emr-api).
return null;
}
visits = Arrays.asList(visit);
visits = asList(visit);
}

if (null == encounterParameters.getEncounterDateTime()) {
Expand All @@ -90,7 +91,7 @@ private Encounter findMatchingEncounter(Visit visit, EncounterParameters encount
Collection<Encounter> encounters = this.encounterService.getEncounters(encounterParameters.getPatient(), null,
getSearchStartDate(encounterParameters.getEncounterDateTime()),
encounterParameters.getEncounterDateTime(), new ArrayList<Form>(),
Arrays.asList(encounterParameters.getEncounterType()),
asList(encounterParameters.getEncounterType()),
encounterParameters.getProviders(), null, visits, false);

Map<String, Object> context = encounterParameters.getContext();
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
12 changes: 7 additions & 5 deletions ...i/src/main/java/org/bahmni/module/bahmnicore/service/impl/BahmniDiagnosisServiceImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,8 @@
import java.util.Iterator;
import java.util.List;

import static java.util.Arrays.*;

@Component
public class BahmniDiagnosisServiceImpl implements BahmniDiagnosisService {
private EncounterService encounterService;
Expand Down Expand Up @@ -80,8 +82,8 @@ private void voidAllDiagnosisWithSameInitialDiagnosis(String initialVisitDiagnos
private List<Diagnosis> getDiagnosisByPatient(Patient patient, Visit visit) {
List<Diagnosis> diagnoses = new ArrayList<Diagnosis>();

List<Obs> observations = obsService.getObservations(Arrays.asList((Person) patient), new ArrayList<>(visit.getEncounters()),
Arrays.asList(bahmniDiagnosisMetadata.getDiagnosisSetConcept()), null, null, null, Arrays.asList("obsDatetime"),
List<Obs> observations = obsService.getObservations(asList((Person) patient), new ArrayList<>(visit.getEncounters()),
asList(bahmniDiagnosisMetadata.getDiagnosisSetConcept()), null, null, null, asList("obsDatetime"),
null, null, null, null, false);

Collection<Concept> nonDiagnosisConcepts = emrApiProperties.getSuppressedDiagnosisConcepts();
Expand Down Expand Up @@ -150,9 +152,9 @@ public List<BahmniDiagnosisRequest> getBahmniDiagnosisByPatientAndVisit(String p
private Obs getLatestObsGroupBasedOnAnyDiagnosis(Diagnosis diagnosis, Concept bahmniDiagnosisRevised) {
String initialDiagnosisUuid = bahmniDiagnosisMetadata.findInitialDiagnosisUuid(diagnosis.getExistingObs());

List<Obs> observations = obsService.getObservations(Arrays.asList(diagnosis.getExistingObs().getPerson()), null,
Arrays.asList(bahmniDiagnosisRevised),
Arrays.asList(conceptService.getFalseConcept()), null, null, null,
List<Obs> observations = obsService.getObservations(asList(diagnosis.getExistingObs().getPerson()), null,
asList(bahmniDiagnosisRevised),
asList(conceptService.getFalseConcept()), null, null, null,
null, null, null, null, false);

for (Obs obs : observations) {
Expand Down
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