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Feature/elastic back in green (#893)

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* Getting automated tests back into green

* using native API's

* formatting

* refactoring

* getting 8.X ES working

* Removed sleep

* Update src/test/java/ca/uhn/fhir/jpa/starter/ElasticsearchLastNR4IT.java

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* Reintroduced sleep as indicies are a bit slow ?

* Using the production bean instead of a test one

* updating default parameters for es

* Making separate profile for ES

* works from here

* remove all not needed code anymore

* removing parent defined version

* fixed tests

---------

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
This commit is contained in:
Jens Kristian Villadsen
2026-02-08 17:18:28 +01:00
committed by GitHub
parent c5fd867efc
commit 78a068ab45
6 changed files with 142 additions and 75 deletions
Download Patch File Download Diff File Expand all files Collapse all files

15
pom.xml
View File

@@ -307,25 +307,18 @@
<dependency>
<groupId>org.testcontainers</groupId>
<artifactId>testcontainers</artifactId>
<version>2.0.3</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.testcontainers</groupId>
<artifactId>elasticsearch</artifactId>
<version>1.21.4</version>
<artifactId>testcontainers-elasticsearch</artifactId>
<version>2.0.2</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.testcontainers</groupId>
<artifactId>postgresql</artifactId>
<version>1.21.4</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.testcontainers</groupId>
<artifactId>junit-jupiter</artifactId>
<version>1.21.4</version>
<artifactId>testcontainers-junit-jupiter</artifactId>
<version>2.0.2</version>
<scope>test</scope>
</dependency>

2
src/main/java/ca/uhn/fhir/jpa/starter/common/StarterJpaConfig.java
View File

@@ -50,6 +50,7 @@ import ca.uhn.fhir.jpa.starter.AppProperties;
import ca.uhn.fhir.jpa.starter.annotations.OnCorsPresent;
import ca.uhn.fhir.jpa.starter.annotations.OnImplementationGuidesPresent;
import ca.uhn.fhir.jpa.starter.common.validation.IRepositoryValidationInterceptorFactory;
import ca.uhn.fhir.jpa.starter.elastic.ElasticsearchBootSvcImpl;
import ca.uhn.fhir.jpa.starter.ig.ExtendedPackageInstallationSpec;
import ca.uhn.fhir.jpa.starter.ig.IImplementationGuideOperationProvider;
import ca.uhn.fhir.jpa.subscription.util.SubscriptionDebugLogInterceptor;
@@ -149,6 +150,7 @@ public class StarterJpaConfig {
@Primary
@Bean
public LocalContainerEntityManagerFactoryBean entityManagerFactory(
Optional<ElasticsearchBootSvcImpl> elasticsearchSvc,
JpaProperties theJpaProperties,
DataSource myDataSource,
ConfigurableListableBeanFactory myConfigurableListableBeanFactory,

12
src/main/java/ca/uhn/fhir/jpa/starter/elastic/ElasticsearchBootSvcImpl.java
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@@ -50,7 +50,7 @@ public class ElasticsearchBootSvcImpl implements IElasticsearchSvc {
private static final String OBSERVATION_RESOURCE_NAME = "Observation";
private final ElasticsearchClient myRestHighLevelClient;
private final ElasticsearchClient myElasticsearchClient;
private final FhirContext myContext;
@@ -61,7 +61,7 @@ public class ElasticsearchBootSvcImpl implements IElasticsearchSvc {
public ElasticsearchBootSvcImpl(ElasticsearchClient client, FhirContext fhirContext, AppProperties appProperties) {
myContext = fhirContext;
myRestHighLevelClient = client;
myElasticsearchClient = client;
// Determine index prefix from configuration
if (appProperties.getElasticsearch() != null) {
@@ -144,7 +144,7 @@ public class ElasticsearchBootSvcImpl implements IElasticsearchSvc {
}
private boolean createIndex(String theIndexName, String theMapping) throws IOException {
return myRestHighLevelClient
return myElasticsearchClient
.indices()
.create(cir -> cir.index(theIndexName).withJson(new StringReader(theMapping)))
.acknowledged();
@@ -152,7 +152,7 @@ public class ElasticsearchBootSvcImpl implements IElasticsearchSvc {
private boolean indexExists(String theIndexName) throws IOException {
ExistsRequest request = new ExistsRequest.Builder().index(theIndexName).build();
return myRestHighLevelClient.indices().exists(request).value();
return myElasticsearchClient.indices().exists(request).value();
}
@Override
@@ -165,7 +165,7 @@ public class ElasticsearchBootSvcImpl implements IElasticsearchSvc {
SearchRequest searchRequest = buildObservationResourceSearchRequest(thePids);
try {
SearchResponse<ObservationJson> observationDocumentResponse =
myRestHighLevelClient.search(searchRequest, ObservationJson.class);
myElasticsearchClient.search(searchRequest, ObservationJson.class);
List<Hit<ObservationJson>> observationDocumentHits =
observationDocumentResponse.hits().hits();
IParser parser = TolerantJsonParser.createWithLenientErrorHandling(myContext, null);
@@ -202,7 +202,7 @@ public class ElasticsearchBootSvcImpl implements IElasticsearchSvc {
@VisibleForTesting
public void refreshIndex(String theIndexName) throws IOException {
myRestHighLevelClient.indices().refresh(fn -> fn.index(theIndexName));
myElasticsearchClient.indices().refresh(fn -> fn.index(theIndexName));
}
/**

50
src/main/resources/application-elastic.yaml Normal file
View File

@@ -0,0 +1,50 @@
spring:
elasticsearch:
uris: http://localhost:9200
username: elastic
password: elastic
autoconfigure:
# This empty exclude is needed to override the default exclusion of the Elasticsearch configuration.
exclude:
jpa:
properties:
hibernate:
# --- Hibernate Search (Lucene/Elasticsearch) ---
# Note: the following values should be kept in sync with ca.uhn.fhir.jpa.search.elastic.ElasticsearchHibernatePropertiesBuilder
search:
schema_management:
strategy: CREATE
enabled: true
backend:
layout:
strategy: ca.uhn.fhir.jpa.search.elastic.IndexNamePrefixLayoutStrategy
type: elasticsearch
protocol: http
analysis:
configurer: ca.uhn.fhir.jpa.search.HapiHSearchAnalysisConfigurers$HapiElasticsearchAnalysisConfigurer
scroll_timeout: 60
schema_management:
settings_file: ca/uhn/fhir/jpa/elastic/index-settings.json
minimal_required_status_wait_timeout: 10000
minimal_required_status: YELLOW
dynamic_mapping: true
indexing:
plan:
synchronization:
strategy: async
# -------------------------------------------------------------------------------------
# HAPI FHIR — grouped by domain
# -------------------------------------------------------------------------------------
hapi:
fhir:
# -------------------------------------------------------------------------------
# D. Search & Indexing
# -------------------------------------------------------------------------------
# NOTE: Extended Lucene/Elasticsearch indexing is experimental.
# See https://hapifhir.io/hapi-fhir/docs/server_jpa/elastic.html
advanced_lucene_indexing: true
search_index_full_text_enabled: true

37
src/main/resources/application.yaml
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@@ -37,6 +37,10 @@ management:
enabled: true
spring:
# elasticsearch:
# uris: http://localhost:9200
# username: elastic
# password: elastic
# -------------------------------------------------------------------------------
# Application Name
# -------------------------------------------------------------------------------
@@ -130,8 +134,10 @@ spring:
use_minimal_puts: false
# --- Hibernate Search (Lucene/Elasticsearch) ---
search:
enabled: false
#search:
# schema_management:
# strategy: CREATE
# enabled: true
# Lucene backend (default example)
# backend:
# type: lucene
@@ -142,10 +148,25 @@ spring:
# root: target/lucenefiles
# lucene_version: lucene_current
# Elasticsearch backend (alternative) — see also hapi.fhir.elasticsearch section in docs
# backend:
# type: elasticsearch
# analysis:
# configurer: ca.uhn.fhir.jpa.search.HapiHSearchAnalysisConfigurers$HapiElasticAnalysisConfigurer
# backend:
# layout:
# strategy: ca.uhn.fhir.jpa.search.elastic.IndexNamePrefixLayoutStrategy
# type: elasticsearch
# protocol: http
# analysis:
# configurer: ca.uhn.fhir.jpa.search.HapiHSearchAnalysisConfigurers$HapiElasticsearchAnalysisConfigurer
# scroll_timeout: 60
# schema_management:
# settings_file: ca/uhn/fhir/jpa/elastic/index-settings.json
# minimal_required_status_wait_timeout: 10000
# minimal_required_status: YELLOW
#
# dynamic_mapping: true
# indexing:
# plan:
# synchronization:
# strategy: async
# -------------------------------------------------------------------------------------
# HAPI FHIR — grouped by domain
@@ -249,8 +270,8 @@ hapi:
# -------------------------------------------------------------------------------
# NOTE: Extended Lucene/Elasticsearch indexing is experimental.
# See https://hapifhir.io/hapi-fhir/docs/server_jpa/elastic.html
advanced_lucene_indexing: false
search_index_full_text_enabled: false
# advanced_lucene_indexing: true
# search_index_full_text_enabled: true
# language_search_parameter_enabled: true
# upliftedRefchains_enabled: true
# index_storage_optimized: false

101
src/test/java/ca/uhn/fhir/jpa/starter/ElasticsearchLastNR4IT.java
View File

@@ -1,7 +1,5 @@
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.ElasticsearchSvcImpl;
import ca.uhn.fhir.jpa.starter.common.TestContainerHelper;
@@ -36,69 +34,72 @@ import org.testcontainers.elasticsearch.ElasticsearchContainer;
import org.testcontainers.junit.jupiter.Container;
import org.testcontainers.junit.jupiter.Testcontainers;
import static org.junit.jupiter.api.Assertions.assertEquals;
@Testcontainers
@ActiveProfiles("test")
@TestPropertySource(locations = "classpath:test-elasticsearch-lastn.yaml")
@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = {Application.class})
class ElasticsearchLastNR4IT {
private IGenericClient ourClient;
private IGenericClient ourClient;
@Container
private static final ElasticsearchContainer ELASTICSEARCH = TestContainerHelper.newElasticsearchContainer()
// Set index defaults to handle HAPI FHIR's MAX_SUBSCRIPTION_RESULTS (50000)
.withEnv("indices.query.bool.max_clause_count", "50000");
@Container
private static final ElasticsearchContainer ELASTICSEARCH = TestContainerHelper.newElasticsearchContainer()
// Set index defaults to handle HAPI FHIR's MAX_SUBSCRIPTION_RESULTS (50000)
.withEnv("indices.query.bool.max_clause_count", "50000");
@DynamicPropertySource
static void registerElasticsearchProperties(DynamicPropertyRegistry registry) {
TestContainerHelper.registerElasticsearchProperties(registry, ELASTICSEARCH);
// Also register spring.elasticsearch.uris for ElasticConfigCondition to enable ElasticsearchBootSvcImpl
registry.add("spring.elasticsearch.uris", () -> TestContainerHelper.getElasticsearchHttpUrl(ELASTICSEARCH));
}
@DynamicPropertySource
static void registerElasticsearchProperties(DynamicPropertyRegistry registry) {
TestContainerHelper.registerElasticsearchProperties(registry, ELASTICSEARCH);
// Also register spring.elasticsearch.uris for ElasticConfigCondition to enable ElasticsearchBootSvcImpl
registry.add("spring.elasticsearch.uris", () -> TestContainerHelper.getElasticsearchHttpUrl(ELASTICSEARCH));
@Autowired
private ElasticsearchBootSvcImpl myElasticsearchSvc;
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;
@Autowired
private ElasticsearchBootSvcImpl myElasticsearchSvc;
@Test
void testLastN() throws IOException, InterruptedException {
Thread.sleep(2000);
@LocalServerPort
private int port;
Patient pt = new Patient();
pt.addName().setFamily("Lastn").addGiven("Arthur");
IIdType id = ourClient.create().resource(pt).execute().getId().toUnqualifiedVersionless();
@Test
void testLastN() throws IOException, InterruptedException {
Patient pt = new Patient();
pt.addName().setFamily("Lastn").addGiven("Arthur");
IIdType id = ourClient.create().resource(pt).execute().getId().toUnqualifiedVersionless();
Observation obs = new Observation();
obs.getSubject().setReferenceElement(id);
String observationCode = "testobservationcode";
Observation obs = new Observation();
obs.getSubject().setReferenceElement(id);
String observationCode = "testobservationcode";
obs.getCode().addCoding().setCode(observationCode).setSystem("http://testobservationcodesystem");
obs.setValue(new StringType(observationCode));
Date effectiveDtm = new GregorianCalendar().getTime();
obs.setEffective(new DateTimeType(effectiveDtm));
obs.getCategoryFirstRep().addCoding().setCode("testcategorycode").setSystem("http://testcategorycodesystem");
IIdType obsId = ourClient.create().resource(obs).execute().getId().toUnqualifiedVersionless();
obs.getCode().addCoding().setCode(observationCode).setSystem("http://testobservationcodesystem");
obs.setValue(new StringType(observationCode));
myElasticsearchSvc.refreshIndex(ElasticsearchSvcImpl.OBSERVATION_INDEX);
Thread.sleep(2000);
Date effectiveDtm = new GregorianCalendar().getTime();
obs.setEffective(new DateTimeType(effectiveDtm));
obs.getCategoryFirstRep().addCoding().setCode("testcategorycode").setSystem("http://testcategorycodesystem");
IIdType obsId = ourClient.create().resource(obs).execute().getId().toUnqualifiedVersionless();
Parameters output = ourClient.operation().onType(Observation.class).named("lastn")
.withParameter(Parameters.class, "max", new IntegerType(1))
.andParameter("subject", new StringType("Patient/" + id.getIdPart()))
.execute();
Bundle b = (Bundle) output.getParameter().get(0).getResource();
assertEquals(1, b.getTotal());
assertEquals(obsId, b.getEntry().get(0).getResource().getIdElement().toUnqualifiedVersionless());
}
myElasticsearchSvc.refreshIndex(ElasticsearchSvcImpl.OBSERVATION_INDEX);
@BeforeEach
void beforeEach() {
FhirContext ctx = FhirContext.forR4();
ctx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
ctx.getRestfulClientFactory().setSocketTimeout((int) Duration.ofMinutes(20).toMillis());
ourClient = ctx.newRestfulGenericClient("http://localhost:" + port + "/fhir/");
ourClient.registerInterceptor(new LoggingInterceptor(true));
}
Thread.sleep(2000);
Parameters output = ourClient.operation().onType(Observation.class).named("lastn").withParameter(Parameters.class, "max", new IntegerType(1)).andParameter("subject", new StringType("Patient/" + id.getIdPart())).execute();
Bundle b = (Bundle) output.getParameter().get(0).getResource();
assertEquals(1, b.getTotal());
assertEquals(obsId, b.getEntry().get(0).getResource().getIdElement().toUnqualifiedVersionless());
}
@BeforeEach
void beforeEach() {
FhirContext ctx = FhirContext.forR4();
ctx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
ctx.getRestfulClientFactory().setSocketTimeout((int) Duration.ofMinutes(20).toMillis());
ourClient = ctx.newRestfulGenericClient("http://localhost:" + port + "/fhir/");
ourClient.registerInterceptor(new LoggingInterceptor(true));
}
}