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FM2-649: Implementation of _has parameter for patients #545

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merged 5 commits into from
Dec 3, 2024
+441 −104
Merged

FM2-649: Implementation of _has parameter for patients #545

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fa21503
(feat) _has parameter added for patients
icrc-jofrancisco Jul 19, 2024
4c35de8
(test) patient dao tests
icrc-jofrancisco Jul 19, 2024
055c60d
(test) add more patient dao tests
icrc-jofrancisco Jul 19, 2024
827ccdb
(chore) (tests) Update _has parameter in patient provider and tests.
Oct 17, 2024
0621277
Merge branch 'master' into feat/has-parameter
icrc-jofrancisco Nov 27, 2024
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5 changes: 5 additions & 0 deletions api/src/main/java/org/openmrs/module/fhir2/FhirConstants.java
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Original file line number Diff line number Diff line change
Expand Up @@ -137,6 +137,8 @@ private FhirConstants() {

public static final String MEDICATION = "Medication";

public static final String GROUP = "Group";

public static final String MEDICATION_DISPENSE = "MedicationDispense";

public static final String MEDICATION_REQUEST = "MedicationRequest";
Expand Down Expand Up @@ -356,4 +358,7 @@ private FhirConstants() {
public static final String EXACT_TOTAL_SEARCH_PARAMETER = "_exactTotal";

public static final String COUNT_QUERY_CACHE = "countQueryCache";

public static final String INCLUDE_MEMBER_PARAM = "member";

}
57 changes: 57 additions & 0 deletions api/src/main/java/org/openmrs/module/fhir2/api/dao/impl/FhirPatientDaoImpl.java
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Expand Up @@ -19,11 +19,16 @@

import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.NoSuchElementException;
import java.util.Optional;
import java.util.Set;
import java.util.stream.Collectors;

import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.HasAndListParam;
import ca.uhn.fhir.rest.param.StringAndListParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenAndListParam;
Expand All @@ -33,17 +38,24 @@
import org.hibernate.Criteria;
import org.hibernate.criterion.Criterion;
import org.hibernate.sql.JoinType;
import org.openmrs.Cohort;
import org.openmrs.CohortMembership;
import org.openmrs.Patient;
import org.openmrs.PatientIdentifierType;
import org.openmrs.module.fhir2.FhirConstants;
import org.openmrs.module.fhir2.api.dao.FhirGroupDao;
import org.openmrs.module.fhir2.api.dao.FhirPatientDao;
import org.openmrs.module.fhir2.api.search.param.SearchParameterMap;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;

@Component
@Setter(AccessLevel.PACKAGE)
public class FhirPatientDaoImpl extends BasePersonDao<Patient> implements FhirPatientDao {

@Autowired
private FhirGroupDao groupDao;

@Override
public Patient getPatientById(@Nonnull Integer id) {
return (Patient) getSessionFactory().getCurrentSession().createCriteria(Patient.class).add(eq("patientId", id))
Expand Down Expand Up @@ -111,10 +123,55 @@ protected void setupSearchParams(Criteria criteria, SearchParameterMap theParams
case FhirConstants.COMMON_SEARCH_HANDLER:
handleCommonSearchParameters(entry.getValue()).ifPresent(criteria::add);
break;
case FhirConstants.HAS_SEARCH_HANDLER:
entry.getValue().forEach(param -> handleHasAndListParam(criteria, (HasAndListParam) param.getParam()));
break;
}
});
}

protected void handleHasAndListParam(Criteria criteria, HasAndListParam hasAndListParam) {
if (hasAndListParam != null) {
List<String> groupIds = new ArrayList<>();
hasAndListParam.getValuesAsQueryTokens().forEach(hasOrListParam -> {
hasOrListParam.getValuesAsQueryTokens().forEach(hasParam -> {
if (hasParam != null) {
String paramValue = hasParam.getParameterValue();
switch (hasParam.getTargetResourceType()) {
case FhirConstants.GROUP:
switch (hasParam.getReferenceFieldName()) {
case FhirConstants.INCLUDE_MEMBER_PARAM:
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Shouldn't we also have some sort of check for the :id part mentioned in the PR comments?

groupIds.add(paramValue);
break;
}
break;
}
}
});
});

if (!groupIds.isEmpty()) {
verifyPatientInGroups(criteria, groupIds);
}
}
}

private void verifyPatientInGroups(Criteria criteria, List<String> groupIds) {
Set<Integer> patientIds = new HashSet<>();
groupIds.forEach(groupId -> patientIds.addAll(getGroupMemberIds(groupId)));

criteria.add(in("patientId", patientIds.isEmpty() ? Collections.emptyList() : patientIds));
}

private List<Integer> getGroupMemberIds(String groupId) {
Cohort cohort = groupDao.get(groupId);
if (cohort != null) {
return cohort.getMemberships().stream().map(CohortMembership::getPatientId).collect(Collectors.toList());
} else {
return Collections.emptyList();
}
}
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Can we reformulate this as a subquery?


private void handlePatientQuery(Criteria criteria, @Nonnull StringAndListParam query) {
if (query == null) {
return;
Expand Down
11 changes: 8 additions & 3 deletions api/src/main/java/org/openmrs/module/fhir2/api/search/param/OpenmrsPatientSearchParams.java
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Expand Up @@ -14,6 +14,7 @@
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.HasAndListParam;
import ca.uhn.fhir.rest.param.StringAndListParam;
import ca.uhn.fhir.rest.param.TokenAndListParam;
import lombok.Builder;
Expand Down Expand Up @@ -45,11 +46,13 @@ public class OpenmrsPatientSearchParams extends BaseResourceSearchParams {

private StringAndListParam country;

private HasAndListParam hasAndListParam;

@Builder
public OpenmrsPatientSearchParams(StringAndListParam query, TokenAndListParam gender, DateRangeParam birthDate,
DateRangeParam deathDate, TokenAndListParam deceased, StringAndListParam city, StringAndListParam state,
StringAndListParam postalCode, StringAndListParam country, TokenAndListParam id, DateRangeParam lastUpdated,
SortSpec sort, HashSet<Include> revIncludes) {
StringAndListParam postalCode, StringAndListParam country, TokenAndListParam id, HasAndListParam hasAndListParam,
DateRangeParam lastUpdated, SortSpec sort, HashSet<Include> revIncludes) {

super(id, lastUpdated, sort, null, revIncludes);

Expand All @@ -62,6 +65,7 @@ public OpenmrsPatientSearchParams(StringAndListParam query, TokenAndListParam ge
this.state = state;
this.postalCode = postalCode;
this.country = country;
this.hasAndListParam = hasAndListParam;
}

@Override
Expand All @@ -74,6 +78,7 @@ public SearchParameterMap toSearchParameterMap() {
.addParameter(FhirConstants.ADDRESS_SEARCH_HANDLER, FhirConstants.CITY_PROPERTY, getCity())
.addParameter(FhirConstants.ADDRESS_SEARCH_HANDLER, FhirConstants.STATE_PROPERTY, getState())
.addParameter(FhirConstants.ADDRESS_SEARCH_HANDLER, FhirConstants.POSTAL_CODE_PROPERTY, getPostalCode())
.addParameter(FhirConstants.ADDRESS_SEARCH_HANDLER, FhirConstants.COUNTRY_PROPERTY, getCountry());
.addParameter(FhirConstants.ADDRESS_SEARCH_HANDLER, FhirConstants.COUNTRY_PROPERTY, getCountry())
.addParameter(FhirConstants.HAS_SEARCH_HANDLER, getHasAndListParam());
}
}
11 changes: 8 additions & 3 deletions api/src/main/java/org/openmrs/module/fhir2/api/search/param/PatientSearchParams.java
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Expand Up @@ -14,6 +14,7 @@
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.HasAndListParam;
import ca.uhn.fhir.rest.param.StringAndListParam;
import ca.uhn.fhir.rest.param.TokenAndListParam;
import lombok.Builder;
Expand Down Expand Up @@ -51,12 +52,14 @@ public class PatientSearchParams extends BaseResourceSearchParams {

private StringAndListParam country;

private HasAndListParam hasAndListParam;

@Builder
public PatientSearchParams(StringAndListParam name, StringAndListParam given, StringAndListParam family,
TokenAndListParam identifier, TokenAndListParam gender, DateRangeParam birthDate, DateRangeParam deathDate,
TokenAndListParam deceased, StringAndListParam city, StringAndListParam state, StringAndListParam postalCode,
StringAndListParam country, TokenAndListParam id, DateRangeParam lastUpdated, SortSpec sort,
HashSet<Include> revIncludes) {
StringAndListParam country, TokenAndListParam id, HasAndListParam hasAndListParam, DateRangeParam lastUpdated,
SortSpec sort, HashSet<Include> revIncludes) {

super(id, lastUpdated, sort, null, revIncludes);

Expand All @@ -72,6 +75,7 @@ public PatientSearchParams(StringAndListParam name, StringAndListParam given, St
this.state = state;
this.postalCode = postalCode;
this.country = country;
this.hasAndListParam = hasAndListParam;
}

@Override
Expand All @@ -88,6 +92,7 @@ public SearchParameterMap toSearchParameterMap() {
.addParameter(FhirConstants.ADDRESS_SEARCH_HANDLER, FhirConstants.CITY_PROPERTY, getCity())
.addParameter(FhirConstants.ADDRESS_SEARCH_HANDLER, FhirConstants.STATE_PROPERTY, getState())
.addParameter(FhirConstants.ADDRESS_SEARCH_HANDLER, FhirConstants.POSTAL_CODE_PROPERTY, getPostalCode())
.addParameter(FhirConstants.ADDRESS_SEARCH_HANDLER, FhirConstants.COUNTRY_PROPERTY, getCountry());
.addParameter(FhirConstants.ADDRESS_SEARCH_HANDLER, FhirConstants.COUNTRY_PROPERTY, getCountry())
.addParameter(FhirConstants.HAS_SEARCH_HANDLER, getHasAndListParam());
}
}
12 changes: 8 additions & 4 deletions api/src/main/java/org/openmrs/module/fhir2/providers/r3/PatientFhirResourceProvider.java
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Expand Up @@ -32,6 +32,7 @@
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.HasAndListParam;
import ca.uhn.fhir.rest.param.StringAndListParam;
import ca.uhn.fhir.rest.param.TokenAndListParam;
import ca.uhn.fhir.rest.param.TokenParam;
Expand All @@ -53,6 +54,7 @@
import org.hl7.fhir.dstu3.model.ProcedureRequest;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.ServiceRequest;
import org.openmrs.module.fhir2.FhirConstants;
import org.openmrs.module.fhir2.api.FhirPatientService;
import org.openmrs.module.fhir2.api.annotations.R3Provider;
import org.openmrs.module.fhir2.api.search.SearchQueryBundleProviderR3Wrapper;
Expand Down Expand Up @@ -128,6 +130,7 @@ public IBundleProvider searchPatients(@OptionalParam(name = Patient.SP_NAME) Str
@OptionalParam(name = Patient.SP_ADDRESS_POSTALCODE) StringAndListParam postalCode,
@OptionalParam(name = Patient.SP_ADDRESS_COUNTRY) StringAndListParam country,
@OptionalParam(name = Patient.SP_RES_ID) TokenAndListParam id,
@OptionalParam(name = FhirConstants.HAS_SEARCH_HANDLER) HasAndListParam hasAndListParam,
@OptionalParam(name = "_lastUpdated") DateRangeParam lastUpdated, @Sort SortSpec sort,
@IncludeParam(reverse = true, allow = { "Observation:" + Observation.SP_PATIENT,
"AllergyIntolerance:" + AllergyIntolerance.SP_PATIENT, "DiagnosticReport:" + DiagnosticReport.SP_PATIENT,
Expand All @@ -138,9 +141,9 @@ public IBundleProvider searchPatients(@OptionalParam(name = Patient.SP_NAME) Str
revIncludes = null;
}

return new SearchQueryBundleProviderR3Wrapper(
patientService.searchForPatients(new PatientSearchParams(name, given, family, identifier, gender, birthDate,
deathDate, deceased, city, state, postalCode, country, id, lastUpdated, sort, revIncludes)));
return new SearchQueryBundleProviderR3Wrapper(patientService
.searchForPatients(new PatientSearchParams(name, given, family, identifier, gender, birthDate, deathDate,
deceased, city, state, postalCode, country, id, hasAndListParam, lastUpdated, sort, revIncludes)));
}

@Search(queryName = "openmrsPatients")
Expand All @@ -155,6 +158,7 @@ public IBundleProvider searchOpenmrsPatients(@OptionalParam(name = "q") StringAn
@OptionalParam(name = org.hl7.fhir.r4.model.Patient.SP_ADDRESS_POSTALCODE) StringAndListParam postalCode,
@OptionalParam(name = org.hl7.fhir.r4.model.Patient.SP_ADDRESS_COUNTRY) StringAndListParam country,
@OptionalParam(name = org.hl7.fhir.r4.model.Patient.SP_RES_ID) TokenAndListParam id,
@OptionalParam(name = FhirConstants.HAS_SEARCH_HANDLER) HasAndListParam hasAndListParam,
@OptionalParam(name = "_lastUpdated") DateRangeParam lastUpdated, @Sort SortSpec sort,
@IncludeParam(reverse = true, allow = { "Observation:" + org.hl7.fhir.r4.model.Observation.SP_PATIENT,
"AllergyIntolerance:" + org.hl7.fhir.r4.model.AllergyIntolerance.SP_PATIENT,
Expand All @@ -169,7 +173,7 @@ public IBundleProvider searchOpenmrsPatients(@OptionalParam(name = "q") StringAn

return new SearchQueryBundleProviderR3Wrapper(
patientService.searchForPatients(new OpenmrsPatientSearchParams(query, gender, birthDate, deathDate,
deceased, city, state, postalCode, country, id, lastUpdated, sort, revIncludes)));
deceased, city, state, postalCode, country, id, hasAndListParam, lastUpdated, sort, revIncludes)));
}

/**
Expand Down
8 changes: 6 additions & 2 deletions api/src/main/java/org/openmrs/module/fhir2/providers/r4/PatientFhirResourceProvider.java
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Expand Up @@ -35,6 +35,7 @@
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.HasAndListParam;
import ca.uhn.fhir.rest.param.StringAndListParam;
import ca.uhn.fhir.rest.param.TokenAndListParam;
import ca.uhn.fhir.rest.param.TokenParam;
Expand All @@ -54,6 +55,7 @@
import org.hl7.fhir.r4.model.OperationOutcome;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.ServiceRequest;
import org.openmrs.module.fhir2.FhirConstants;
import org.openmrs.module.fhir2.api.FhirPatientService;
import org.openmrs.module.fhir2.api.annotations.R4Provider;
import org.openmrs.module.fhir2.api.search.param.OpenmrsPatientSearchParams;
Expand Down Expand Up @@ -136,6 +138,7 @@ public IBundleProvider searchPatients(@OptionalParam(name = Patient.SP_NAME) Str
@OptionalParam(name = Patient.SP_ADDRESS_POSTALCODE) StringAndListParam postalCode,
@OptionalParam(name = Patient.SP_ADDRESS_COUNTRY) StringAndListParam country,
@OptionalParam(name = Patient.SP_RES_ID) TokenAndListParam id,
@OptionalParam(name = FhirConstants.HAS_SEARCH_HANDLER) HasAndListParam hasAndListParam,
@OptionalParam(name = "_lastUpdated") DateRangeParam lastUpdated, @Sort SortSpec sort,
@IncludeParam(reverse = true, allow = { "Observation:" + Observation.SP_PATIENT,
"AllergyIntolerance:" + AllergyIntolerance.SP_PATIENT, "DiagnosticReport:" + DiagnosticReport.SP_PATIENT,
Expand All @@ -147,7 +150,7 @@ public IBundleProvider searchPatients(@OptionalParam(name = Patient.SP_NAME) Str
}

return patientService.searchForPatients(new PatientSearchParams(name, given, family, identifier, gender, birthDate,
deathDate, deceased, city, state, postalCode, country, id, lastUpdated, sort, revIncludes));
deathDate, deceased, city, state, postalCode, country, id, hasAndListParam, lastUpdated, sort, revIncludes));
}

@Search(queryName = "openmrsPatients")
Expand All @@ -162,6 +165,7 @@ public IBundleProvider searchOpenmrsPatients(@OptionalParam(name = "q") StringAn
@OptionalParam(name = Patient.SP_ADDRESS_POSTALCODE) StringAndListParam postalCode,
@OptionalParam(name = Patient.SP_ADDRESS_COUNTRY) StringAndListParam country,
@OptionalParam(name = Patient.SP_RES_ID) TokenAndListParam id,
@OptionalParam(name = FhirConstants.HAS_SEARCH_HANDLER) HasAndListParam hasAndListParam,
@OptionalParam(name = "_lastUpdated") DateRangeParam lastUpdated, @Sort SortSpec sort,
@IncludeParam(reverse = true, allow = { "Observation:" + Observation.SP_PATIENT,
"AllergyIntolerance:" + AllergyIntolerance.SP_PATIENT, "DiagnosticReport:" + DiagnosticReport.SP_PATIENT,
Expand All @@ -173,7 +177,7 @@ public IBundleProvider searchOpenmrsPatients(@OptionalParam(name = "q") StringAn
}

return patientService.searchForPatients(new OpenmrsPatientSearchParams(query, gender, birthDate, deathDate, deceased,
city, state, postalCode, country, id, lastUpdated, sort, revIncludes));
city, state, postalCode, country, id, hasAndListParam, lastUpdated, sort, revIncludes));
}

/**
Expand Down
43 changes: 43 additions & 0 deletions api/src/test/java/org/openmrs/module/fhir2/api/dao/impl/FhirPatientDaoImplTest.java
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Expand Up @@ -10,15 +10,23 @@
package org.openmrs.module.fhir2.api.dao.impl;

import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.equalTo;
import static org.hamcrest.Matchers.notNullValue;
import static org.hamcrest.Matchers.nullValue;

import java.util.List;

import ca.uhn.fhir.rest.param.HasAndListParam;
import ca.uhn.fhir.rest.param.HasOrListParam;
import ca.uhn.fhir.rest.param.HasParam;
import org.hibernate.SessionFactory;
import org.junit.Before;
import org.junit.Test;
import org.openmrs.Patient;
import org.openmrs.module.fhir2.FhirConstants;
import org.openmrs.module.fhir2.TestFhirSpringConfiguration;
import org.openmrs.module.fhir2.api.search.param.SearchParameterMap;
import org.openmrs.test.BaseModuleContextSensitiveTest;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.context.ContextConfiguration;
Expand All @@ -30,19 +38,30 @@ public class FhirPatientDaoImplTest extends BaseModuleContextSensitiveTest {

private static final String BAD_PATIENT_UUID = "282390a6-3608-496d-9025-aecbc1235670";

private static final String GROUP_A = "dfb29c44-2e39-46c4-8cd7-18f21c6d47b1";

private static final String GROUP_B = "a25ce1d7-326c-43ff-a87f-63d9d2f60f11";

private static final String PATIENT_GROUP_A = "61b38324-e2fd-4feb-95b7-9e9a2a4400df";

private static final String[] PATIENT_SEARCH_DATA_FILES = {
"org/openmrs/module/fhir2/api/dao/impl/FhirPatientDaoImplTest_initial_data.xml",
"org/openmrs/module/fhir2/api/dao/impl/FhirPatientDaoImplTest_address_data.xml" };

private FhirPatientDaoImpl dao;

private FhirGroupDaoImpl groupDao;

@Autowired
private SessionFactory sessionFactory;

@Before
public void setup() throws Exception {
groupDao = new FhirGroupDaoImpl();
groupDao.setSessionFactory(sessionFactory);
dao = new FhirPatientDaoImpl();
dao.setSessionFactory(sessionFactory);
dao.setGroupDao(groupDao);
for (String search_data : PATIENT_SEARCH_DATA_FILES) {
executeDataSet(search_data);
}
Expand Down Expand Up @@ -76,4 +95,28 @@ public void getPatientByUuid_shouldReturnNullIfPatientNotFound() {

assertThat(result, nullValue());
}

@Test
public void getSearchResults_shouldReturnPatientSearchResults() {
HasAndListParam groupParam = new HasAndListParam().addAnd(
new HasOrListParam().add(new HasParam(FhirConstants.GROUP, FhirConstants.INCLUDE_MEMBER_PARAM, "id", GROUP_A)));

SearchParameterMap theParams = new SearchParameterMap().addParameter(FhirConstants.HAS_SEARCH_HANDLER, groupParam);
List<Patient> result = dao.getSearchResults(theParams);

assertThat(result, notNullValue());
assertThat(result.get(0).getUuid(), equalTo(PATIENT_GROUP_A));
}

@Test
public void getSearchResults_shouldReturnEmptyList() {
HasAndListParam groupParam = new HasAndListParam().addAnd(
new HasOrListParam().add(new HasParam(FhirConstants.GROUP, FhirConstants.INCLUDE_MEMBER_PARAM, "id", GROUP_B)));

SearchParameterMap theParams = new SearchParameterMap().addParameter(FhirConstants.HAS_SEARCH_HANDLER, groupParam);
List<Patient> result = dao.getSearchResults(theParams);

assertThat(result, notNullValue());
assertThat(result, empty());
}
}
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