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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

22
src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java
View File

@@ -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
View File

@@ -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);
}
}