Personal-Twin/hapi-fhir-jpaserver-starter
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Add Elasticsearch index prefix configuration (#891)

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* Add Elasticsearch configuration section to application.yaml

* Add configuration for reindexing resources upon search parameter change

* Add Elasticsearch client configuration for testing

* Update logback dependencies because of a security issue and enable resource filtering in pom.xml

* Add application name and tester configuration to application.yaml. Refactor hibernate properties

* Add custom Elasticsearch configuration to create ElasticsearchClient bean

* Add index prefix configuration for Elasticsearch indices

* Fix Elasticsearch URI format in test initialization

* Refactor ElasticsearchConfig for improved readability and code style consistency (spotless:apply)

* Refactor ElasticsearchConfig for improved readability and code style consistency (spotless:apply)

* Update index prefix in application.yaml for Elasticsearch configuration

* Enhance index prefix validation and add sanitization method for Elasticsearch index names

* Merged with master in upstream

* Refactor ElasticsearchBootSvcImpl and ElasticsearchConfig for improved readability (mvn spotless)

* Comment out custom_content_path in application.yaml for clarity

* - Refactor application.yaml for improved structure and readability;
- Add PostgresLucenePatientIT integration test; and
- Update testcontainers dependencies to avoid compatibility issues with newer Docker APIs.

* Refactor PostgresLucenePatientIT to use external configuration file for test properties

* Add integration tests for PostgreSQL and Elasticsearch with dynamic configuration

* Increase socket timeout in CdsHooksServletIT for improved stability during tests

* Remove deprecated tester configuration from application.yaml
This commit is contained in:
darth.cav
2026-01-20 15:32:24 +01:00
committed by GitHub
parent bf7f6a3b6a
commit b81e2abe81
12 changed files with 476 additions and 19 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
src/test/java/ca/uhn/fhir/jpa/starter/CdsHooksServletIT.java
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@@ -72,7 +72,7 @@ class CdsHooksServletIT implements IServerSupport {
@BeforeEach
void beforeEach() {
ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 3000);
ourServerBase = "http://localhost:" + port + "/fhir/";
ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
ourCdsBase = "http://localhost:" + port + "/cds-services";

29
src/test/java/ca/uhn/fhir/jpa/starter/ElasticsearchLastNR4IT.java
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@@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.starter;
import static org.junit.jupiter.api.Assertions.assertEquals;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.search.lastn.ElasticsearchRestClientFactory;
import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl;
import ca.uhn.fhir.jpa.starter.elastic.ElasticsearchBootSvcImpl;
import ca.uhn.fhir.jpa.test.config.TestElasticsearchContainerHelper;
@@ -14,6 +15,8 @@ import java.io.IOException;
import java.util.Date;
import java.util.GregorianCalendar;
import co.elastic.clients.elasticsearch.ElasticsearchClient;
import co.elastic.clients.elasticsearch.indices.IndexSettings;
import jakarta.annotation.PreDestroy;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Bundle;
@@ -25,7 +28,6 @@ import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.StringType;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.springframework.beans.factory.annotation.Autowired;
@@ -35,6 +37,8 @@ import org.springframework.boot.test.web.server.LocalServerPort;
import org.springframework.context.ApplicationContextInitializer;
import org.springframework.context.ConfigurableApplicationContext;
import org.springframework.test.context.ActiveProfiles;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.junit.jupiter.SpringExtension;
import org.testcontainers.elasticsearch.ElasticsearchContainer;
@@ -43,9 +47,8 @@ import org.testcontainers.junit.jupiter.Testcontainers;
@ExtendWith(SpringExtension.class)
@Testcontainers
@Disabled
@ActiveProfiles("test")
@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = {Application.class}, properties =
@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = {Application.class, ElasticsearchLastNR4IT.TestConfig.class}, properties =
{
"spring.datasource.url=jdbc:h2:mem:dbr4",
"hapi.fhir.fhir_version=r4",
@@ -81,21 +84,20 @@ class ElasticsearchLastNR4IT {
@BeforeAll
public static void beforeClass() throws IOException {
//Given
// ElasticsearchClient elasticsearchHighLevelRestClient = ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient(
// "http", embeddedElastic.getHost() + ":" + embeddedElastic.getMappedPort(9200), "", "");
ElasticsearchClient elasticsearchHighLevelRestClient = ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient(
"http", embeddedElastic.getHost() + ":" + embeddedElastic.getMappedPort(9200), "", "");
/* As of 2023-08-10, HAPI FHIR sets SubscriptionConstants.MAX_SUBSCRIPTION_RESULTS to 50000
which is in excess of elastic's default max_result_window. If MAX_SUBSCRIPTION_RESULTS is changed
to a value <= 10000, the following will no longer be necessary. - dotasek
*/
/* elasticsearchHighLevelRestClient.indices().putTemplate(t->{
elasticsearchHighLevelRestClient.indices().putTemplate(t->{
t.name("hapi_fhir_template");
t.indexPatterns("*");
t.settings(new IndexSettings.Builder().maxResultWindow(50000).build());
t.settings(new IndexSettings.Builder().maxNgramDiff(50).maxResultWindow(50000).build());
return t;
});
*/
}
@PreDestroy
@@ -151,6 +153,15 @@ class ElasticsearchLastNR4IT {
}
@Configuration
static class TestConfig {
@Bean
public ElasticsearchClient elasticsearchClient() throws IOException {
return ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient(
"http", embeddedElastic.getHost() + ":" + embeddedElastic.getMappedPort(9200), "", "");
}
}
static class Initializer
implements ApplicationContextInitializer<ConfigurableApplicationContext> {
@@ -158,7 +169,7 @@ class ElasticsearchLastNR4IT {
public void initialize(
ConfigurableApplicationContext configurableApplicationContext) {
// Since the port is dynamically generated, replace the URL with one that has the correct port
TestPropertyValues.of("spring.elasticsearch.uris=" + embeddedElastic.getHost() +":" + embeddedElastic.getMappedPort(9200))
TestPropertyValues.of("spring.elasticsearch.uris=http://" + embeddedElastic.getHost() + ":" + embeddedElastic.getMappedPort(9200))
.applyTo(configurableApplicationContext.getEnvironment());
TestPropertyValues.of("spring.jpa.properties.hibernate.search.backend.hosts=" + embeddedElastic.getHost() +":" + embeddedElastic.getMappedPort(9200))
.applyTo(configurableApplicationContext.getEnvironment());

108
src/test/java/ca/uhn/fhir/jpa/starter/PostgresElasticsearchPatientIT.java Normal file
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@@ -0,0 +1,108 @@
package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Patient;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.springframework.boot.test.context.SpringBootTest;
import org.springframework.boot.test.web.server.LocalServerPort;
import org.springframework.test.context.ActiveProfiles;
import org.springframework.test.context.DynamicPropertyRegistry;
import org.springframework.test.context.DynamicPropertySource;
import org.springframework.test.context.TestPropertySource;
import org.testcontainers.containers.PostgreSQLContainer;
import org.testcontainers.elasticsearch.ElasticsearchContainer;
import org.testcontainers.junit.jupiter.Container;
import org.testcontainers.junit.jupiter.Testcontainers;
import java.time.Duration;
import static org.awaitility.Awaitility.await;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
@Testcontainers
@ActiveProfiles("test")
@TestPropertySource(locations = "classpath:test-postgres-elasticsearch.yaml")
@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = {Application.class})
class PostgresElasticsearchPatientIT {
@Container
private static final PostgreSQLContainer<?> POSTGRES = new PostgreSQLContainer<>("postgres:16-alpine")
.withDatabaseName("hapi")
.withUsername("fhiruser")
.withPassword("fhirpass");
@Container
private static final ElasticsearchContainer ELASTICSEARCH = new ElasticsearchContainer(
"docker.elastic.co/elasticsearch/elasticsearch:8.11.0"
)
.withEnv("xpack.security.enabled", "false")
.withEnv("discovery.type", "single-node")
.withEnv("ES_JAVA_OPTS", "-Xms512m -Xmx512m");
@DynamicPropertySource
static void registerDatasourceProperties(DynamicPropertyRegistry registry) {
// PostgreSQL configuration
registry.add("spring.datasource.url", POSTGRES::getJdbcUrl);
registry.add("spring.datasource.username", POSTGRES::getUsername);
registry.add("spring.datasource.password", POSTGRES::getPassword);
registry.add("spring.datasource.driver-class-name", POSTGRES::getDriverClassName);
registry.add("spring.jpa.properties.hibernate.dialect", () -> "ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgresDialect");
// Elasticsearch configuration
registry.add("spring.jpa.properties.hibernate.search.backend.hosts", ELASTICSEARCH::getHttpHostAddress);
registry.add("spring.jpa.properties.hibernate.search.backend.protocol", () -> "http");
registry.add("spring.jpa.properties.hibernate.search.backend.username", () -> "");
registry.add("spring.jpa.properties.hibernate.search.backend.password", () -> "");
}
@LocalServerPort
private int port;
private IGenericClient ourClient;
private FhirContext ourCtx;
@BeforeEach
void beforeEach() {
ourCtx = FhirContext.forR4();
ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
ourCtx.getRestfulClientFactory().setSocketTimeout((int) Duration.ofMinutes(20).toMillis());
String ourServerBase = "http://localhost:" + port + "/fhir/";
ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
ourClient.registerInterceptor(new LoggingInterceptor(true));
}
@Test
void testCreateAndSearchPatientByFamilyName() {
String givenName = "Jane";
String familyName = "Smith Doe";
Patient patient = new Patient();
patient.addName().setFamily(familyName).addGiven(givenName);
IIdType id = ourClient.create().resource(patient).execute().getId().toUnqualifiedVersionless();
assertNotNull(id);
await().atMost(Duration.ofSeconds(30)).until(() -> searchByFamily(familyName).getTotal() == 1);
Bundle results = searchByFamily(familyName);
assertEquals(1, results.getTotal());
Patient found = (Patient) results.getEntry().get(0).getResource();
assertEquals(familyName, found.getNameFirstRep().getFamily());
assertEquals(id, found.getIdElement().toUnqualifiedVersionless());
}
private Bundle searchByFamily(String family) {
return ourClient
.search()
.forResource(Patient.class)
.where(Patient.FAMILY.matches().value(family))
.returnBundle(Bundle.class)
.execute();
}
}

92
src/test/java/ca/uhn/fhir/jpa/starter/PostgresLucenePatientIT.java Normal file
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@@ -0,0 +1,92 @@
package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Patient;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.springframework.boot.test.context.SpringBootTest;
import org.springframework.boot.test.web.server.LocalServerPort;
import org.springframework.test.context.ActiveProfiles;
import org.springframework.test.context.DynamicPropertyRegistry;
import org.springframework.test.context.DynamicPropertySource;
import org.springframework.test.context.TestPropertySource;
import org.testcontainers.containers.PostgreSQLContainer;
import org.testcontainers.junit.jupiter.Container;
import org.testcontainers.junit.jupiter.Testcontainers;
import java.time.Duration;
import static org.awaitility.Awaitility.await;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
@Testcontainers
@ActiveProfiles("test")
@TestPropertySource(locations = "classpath:test-postgres-lucene.yaml")
@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = {Application.class})
class PostgresLucenePatientIT {
@Container
private static final PostgreSQLContainer<?> POSTGRES = new PostgreSQLContainer<>("postgres:16-alpine")
.withDatabaseName("hapi")
.withUsername("fhiruser")
.withPassword("fhirpass");
@DynamicPropertySource
static void registerDatasourceProperties(DynamicPropertyRegistry registry) {
registry.add("spring.datasource.url", POSTGRES::getJdbcUrl);
registry.add("spring.datasource.username", POSTGRES::getUsername);
registry.add("spring.datasource.password", POSTGRES::getPassword);
registry.add("spring.datasource.driver-class-name", POSTGRES::getDriverClassName);
registry.add("spring.jpa.properties.hibernate.dialect", () -> "ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgresDialect");
}
@LocalServerPort
private int port;
private IGenericClient ourClient;
private FhirContext ourCtx;
@BeforeEach
void beforeEach() {
ourCtx = FhirContext.forR4();
ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
ourCtx.getRestfulClientFactory().setSocketTimeout((int) Duration.ofMinutes(20).toMillis());
String ourServerBase = "http://localhost:" + port + "/fhir/";
ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
ourClient.registerInterceptor(new LoggingInterceptor(true));
}
@Test
void testCreateAndSearchPatientByFamilyName() {
String givenName = "Jane";
String familyName = "Smith Doe";
Patient patient = new Patient();
patient.addName().setFamily(familyName).addGiven(givenName);
IIdType id = ourClient.create().resource(patient).execute().getId().toUnqualifiedVersionless();
assertNotNull(id);
await().atMost(Duration.ofSeconds(30)).until(() -> searchByFamily(familyName).getTotal() == 1);
Bundle results = searchByFamily(familyName);
assertEquals(1, results.getTotal());
Patient found = (Patient) results.getEntry().get(0).getResource();
assertEquals(familyName, found.getNameFirstRep().getFamily());
assertEquals(id, found.getIdElement().toUnqualifiedVersionless());
}
private Bundle searchByFamily(String family) {
return ourClient
.search()
.forResource(Patient.class)
.where(Patient.FAMILY.matches().value(family))
.returnBundle(Bundle.class)
.execute();
}
}