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Merge branch 'master' into rel_8_7-tracking

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This commit is contained in:
dotasek
2026-01-21 15:05:45 -05:00
parent 392df7f377 b81e2abe81
commit 15e018a453
12 changed files with 468 additions and 19 deletions
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25
pom.xml
View File

@@ -204,13 +204,16 @@
<!-- HAPI-FHIR uses Logback for logging support. The logback library is included automatically by Maven as a part of the hapi-fhir-base dependency, but you also need to include a logging library. Logback
is used here, but log4j would also be fine. -->
<!-- Fixes CVE-2025-11226 -->
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<version>1.5.19</version>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-core</artifactId>
<version>1.5.19</version>
</dependency>
<!-- Needed for JEE/Servlet support -->
@@ -308,6 +311,7 @@
<dependency>
<groupId>org.testcontainers</groupId>
<artifactId>testcontainers</artifactId>
<version>2.0.3</version>
<scope>test</scope>
</dependency>
<dependency>
@@ -443,6 +447,14 @@
<build>
<!-- Enabling resource filtering -->
<resources>
<resource>
<directory>src/main/resources</directory>
<filtering>true</filtering>
</resource>
</resources>
<pluginManagement>
<plugins>
<plugin>
@@ -485,6 +497,19 @@
</executions>
</plugin>
<!-- Resources plugin: sets custom delimiter '@' for placeholder substitutions -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<version>3.3.1</version>
<configuration>
<delimiters>
<delimiter>@</delimiter>
</delimiters>
<useDefaultDelimiters>false</useDefaultDelimiters>
</configuration>
</plugin>
<!-- Tell Maven which Java source version you want to use -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>

22
src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java
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@@ -129,6 +129,7 @@ public class AppProperties {
private Boolean mark_resources_for_reindexing_upon_search_parameter_change = true;
private Integer reindex_thread_count = null;
private Integer expunge_thread_count = null;
private Elasticsearch elasticsearch = null;
public List<String> getCustomInterceptorClasses() {
return custom_interceptor_classes;
@@ -847,6 +848,14 @@ public class AppProperties {
this.store_meta_source_information = store_meta_source_information;
}
public Elasticsearch getElasticsearch() {
return elasticsearch;
}
public void setElasticsearch(Elasticsearch elasticsearch) {
this.elasticsearch = elasticsearch;
}
public static class Cors {
private Boolean allow_Credentials = true;
private List<String> allowed_origin = List.of("*");
@@ -1196,4 +1205,17 @@ public class AppProperties {
}
}
}
public static class Elasticsearch {
private String index_prefix = "";
public String getIndex_prefix() {
return index_prefix;
}
public void setIndex_prefix(String index_prefix) {
this.index_prefix = index_prefix;
}
}
}

6
src/main/java/ca/uhn/fhir/jpa/starter/common/FhirServerConfigCommon.java
View File

@@ -296,6 +296,12 @@ public class FhirServerConfigCommon {
appProperties.getExpunge_thread_count());
}
// Determine index prefix from configuration
if (appProperties.getElasticsearch() != null) {
String indexPrefix = appProperties.getElasticsearch().getIndex_prefix();
jpaStorageSettings.setHSearchIndexPrefix(indexPrefix != null ? indexPrefix : "");
}
return jpaStorageSettings;
}

76
src/main/java/ca/uhn/fhir/jpa/starter/elastic/ElasticsearchBootSvcImpl.java
View File

@@ -6,6 +6,7 @@ import ca.uhn.fhir.jpa.dao.TolerantJsonParser;
import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl;
import ca.uhn.fhir.jpa.search.lastn.IElasticsearchSvc;
import ca.uhn.fhir.jpa.search.lastn.json.ObservationJson;
import ca.uhn.fhir.jpa.starter.AppProperties;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@@ -33,8 +34,8 @@ import java.util.stream.Collectors;
public class ElasticsearchBootSvcImpl implements IElasticsearchSvc {
// Index Constants
public static final String OBSERVATION_INDEX = "observation_index";
public static final String OBSERVATION_CODE_INDEX = "code_index";
public static final String OBSERVATION_INDEX_BASE_NAME = "observation_index";
public static final String OBSERVATION_CODE_INDEX_BASE_NAME = "code_index";
public static final String OBSERVATION_INDEX_SCHEMA_FILE = "ObservationIndexSchema.json";
public static final String OBSERVATION_CODE_INDEX_SCHEMA_FILE = "ObservationCodeIndexSchema.json";
@@ -53,11 +54,26 @@ public class ElasticsearchBootSvcImpl implements IElasticsearchSvc {
private final FhirContext myContext;
public ElasticsearchBootSvcImpl(ElasticsearchClient client, FhirContext fhirContext) {
// Prefixed index names
private String observationIndexName = OBSERVATION_INDEX_BASE_NAME;
private String observationCodeIndexName = OBSERVATION_CODE_INDEX_BASE_NAME;
public ElasticsearchBootSvcImpl(ElasticsearchClient client, FhirContext fhirContext, AppProperties appProperties) {
myContext = fhirContext;
myRestHighLevelClient = client;
// Determine index prefix from configuration
if (appProperties.getElasticsearch() != null) {
String indexPrefix = appProperties.getElasticsearch().getIndex_prefix();
if (indexPrefix != null
&& !sanitizeElasticsearchIndexName(indexPrefix).isEmpty()) {
// Set prefixed index names
this.observationIndexName = indexPrefix + "-" + OBSERVATION_INDEX_BASE_NAME;
this.observationCodeIndexName = indexPrefix + "-" + OBSERVATION_CODE_INDEX_BASE_NAME;
}
}
try {
createObservationIndexIfMissing();
createObservationCodeIndexIfMissing();
@@ -66,6 +82,34 @@ public class ElasticsearchBootSvcImpl implements IElasticsearchSvc {
}
}
/**
* Sanitizes a string to be a valid Elasticsearch index name.
* <p>
* Elasticsearch index name requirements:
* - Must be lowercase
* - Can only contain: lowercase letters, numbers, hyphens (-), and underscores (_)
* - Cannot start with: -, _, or +
* - Cannot exceed 255 characters
* <p>
* This method performs the following transformations:
* 1. Converts to lowercase
* 2. Replaces any invalid characters with underscores
* 3. Removes leading -, _, or + characters
* 4. Truncates to 255 characters if necessary
* 5. Trims any remaining whitespace
*
* @param name the string to sanitize
* @return a valid Elasticsearch index name
*/
private String sanitizeElasticsearchIndexName(String name) {
String cleaned = name.toLowerCase().replaceAll("[^a-z0-9\\-_]", "_");
cleaned = cleaned.replaceAll("^[\\-_.]+", "");
if (cleaned.length() > 255) {
cleaned = cleaned.substring(0, 255);
}
return cleaned.trim();
}
private String getIndexSchema(String theSchemaFileName) throws IOException {
InputStreamReader input =
new InputStreamReader(ElasticsearchSvcImpl.class.getResourceAsStream(theSchemaFileName));
@@ -80,21 +124,21 @@ public class ElasticsearchBootSvcImpl implements IElasticsearchSvc {
}
private void createObservationIndexIfMissing() throws IOException {
if (indexExists(OBSERVATION_INDEX)) {
if (indexExists(observationIndexName)) {
return;
}
String observationMapping = getIndexSchema(OBSERVATION_INDEX_SCHEMA_FILE);
if (!createIndex(OBSERVATION_INDEX, observationMapping)) {
if (!createIndex(observationIndexName, observationMapping)) {
throw new RuntimeException(Msg.code(1176) + "Failed to create observation index");
}
}
private void createObservationCodeIndexIfMissing() throws IOException {
if (indexExists(OBSERVATION_CODE_INDEX)) {
if (indexExists(observationCodeIndexName)) {
return;
}
String observationCodeMapping = getIndexSchema(OBSERVATION_CODE_INDEX_SCHEMA_FILE);
if (!createIndex(OBSERVATION_CODE_INDEX, observationCodeMapping)) {
if (!createIndex(observationCodeIndexName, observationCodeMapping)) {
throw new RuntimeException(Msg.code(1177) + "Failed to create observation code index");
}
}
@@ -147,7 +191,7 @@ public class ElasticsearchBootSvcImpl implements IElasticsearchSvc {
.map(v -> FieldValue.of(v))
.collect(Collectors.toList());
return SearchRequest.of(sr -> sr.index(OBSERVATION_INDEX)
return SearchRequest.of(sr -> sr.index(observationIndexName)
.query(qb -> qb.bool(bb -> bb.must(bbm -> {
bbm.terms(terms ->
terms.field(OBSERVATION_IDENTIFIER_FIELD_NAME).terms(termsb -> termsb.value(values)));
@@ -160,4 +204,20 @@ public class ElasticsearchBootSvcImpl implements IElasticsearchSvc {
public void refreshIndex(String theIndexName) throws IOException {
myRestHighLevelClient.indices().refresh(fn -> fn.index(theIndexName));
}
/**
* Get the observation index name (with prefix if configured)
* @return the observation index name
*/
public String getObservationIndexName() {
return observationIndexName;
}
/**
* Get the observation code index name (with prefix if configured)
* @return the observation code index name
*/
public String getObservationCodeIndexName() {
return observationCodeIndexName;
}
}

69
src/main/java/ca/uhn/fhir/jpa/starter/elastic/ElasticsearchConfig.java Normal file
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@@ -0,0 +1,69 @@
package ca.uhn.fhir.jpa.starter.elastic;
import co.elastic.clients.elasticsearch.ElasticsearchClient;
import co.elastic.clients.json.jackson.JacksonJsonpMapper;
import co.elastic.clients.transport.rest_client.RestClientTransport;
import org.apache.http.HttpHost;
import org.apache.http.auth.AuthScope;
import org.apache.http.auth.UsernamePasswordCredentials;
import org.apache.http.impl.client.BasicCredentialsProvider;
import org.elasticsearch.client.RestClient;
import org.elasticsearch.client.RestClientBuilder;
import org.springframework.boot.autoconfigure.elasticsearch.ElasticsearchProperties;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Conditional;
import org.springframework.context.annotation.Configuration;
import java.net.URI;
import java.util.List;
/**
* Custom Elasticsearch configuration that creates the ElasticsearchClient bean
* without the sniffer. This is used when the default Spring Boot autoconfiguration
* is excluded.
*/
@Configuration
@Conditional(ElasticConfigCondition.class)
public class ElasticsearchConfig {
@Bean
public RestClient elasticsearchRestClient(ElasticsearchProperties properties) {
List<String> uris = properties.getUris();
HttpHost[] hosts = uris.stream()
.map(URI::create)
.map(uri -> new HttpHost(uri.getHost(), uri.getPort(), uri.getScheme()))
.toArray(HttpHost[]::new);
RestClientBuilder builder = RestClient.builder(hosts);
// Configure authentication if credentials are provided
if (properties.getUsername() != null && properties.getPassword() != null) {
BasicCredentialsProvider credentialsProvider = new BasicCredentialsProvider();
credentialsProvider.setCredentials(
AuthScope.ANY, new UsernamePasswordCredentials(properties.getUsername(), properties.getPassword()));
builder.setHttpClientConfigCallback(
httpClientBuilder -> httpClientBuilder.setDefaultCredentialsProvider(credentialsProvider));
}
// Configure connection and socket timeouts if needed
builder.setRequestConfigCallback(requestConfigBuilder -> requestConfigBuilder
.setConnectTimeout(
properties.getConnectionTimeout() != null
? (int) properties.getConnectionTimeout().toMillis()
: 5000)
.setSocketTimeout(
properties.getSocketTimeout() != null
? (int) properties.getSocketTimeout().toMillis()
: 60000));
return builder.build();
}
@Bean
public ElasticsearchClient elasticsearchClient(RestClient restClient) {
RestClientTransport transport = new RestClientTransport(restClient, new JacksonJsonpMapper());
return new ElasticsearchClient(transport);
}
}

13
src/main/resources/application.yaml
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@@ -37,6 +37,12 @@ management:
enabled: true
spring:
# -------------------------------------------------------------------------------
# Application Name
# -------------------------------------------------------------------------------
application:
name: "@project.artifactId@"
# -------------------------------------------------------------------------------
# A. Spring AI — Model Context Protocol (MCP)
# -------------------------------------------------------------------------------
@@ -81,6 +87,7 @@ spring:
main:
allow-bean-definition-overriding: false
allow-circular-references: true
banner-mode: off
autoconfigure:
# This exclude is only needed for setups not using Elasticsearch where the elasticsearch sniff is not needed.
@@ -252,6 +259,12 @@ hapi:
# enable_index_contained_resource: false
# store_resource_in_lucene_index_enabled: true
# -------------------------------------------------------------------------------
# Elasticsearch Configuration
# -------------------------------------------------------------------------------
# elasticsearch:
# index_prefix: "myprefix" # Prefix for all Elasticsearch indexes (e.g., myprefix_observation_index)
# -------------------------------------------------------------------------------
# E. Bulk Operations
# -------------------------------------------------------------------------------

2
src/test/java/ca/uhn/fhir/jpa/starter/CdsHooksServletIT.java
View File

@@ -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
View File

@@ -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
View File

@@ -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
View File

@@ -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();
}
}

21
src/test/resources/test-postgres-elasticsearch.yaml Normal file
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@@ -0,0 +1,21 @@
hapi:
fhir:
fhir_version: r4
cr_enabled: false
advanced_lucene_indexing: true
store_resource_in_lucene_index_enabled: true
search_index_full_text_enabled: true
spring:
main:
allow-bean-definition-overriding: true
jpa:
properties:
hibernate:
search:
enabled: true
backend:
type: elasticsearch
analysis:
configurer: ca.uhn.fhir.jpa.search.HapiHSearchAnalysisConfigurers$HapiElasticAnalysisConfigurer
# Connection properties will be set dynamically by the test via @DynamicPropertySource

22
src/test/resources/test-postgres-lucene.yaml Normal file
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hapi:
fhir:
fhir_version: r4
cr_enabled: false
advanced_lucene_indexing: true
store_resource_in_lucene_index_enabled: true
search_index_full_text_enabled: true
spring:
main:
allow-bean-definition-overriding: true
jpa:
properties:
hibernate:
search:
enabled: true
backend:
type: lucene
analysis:
configurer: ca.uhn.fhir.jpa.search.HapiHSearchAnalysisConfigurers$HapiLuceneAnalysisConfigurer
directory:
type: local-heap