Personal-Twin/hapi-fhir-jpaserver-starter
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Merge branch 'master' into search-coord-thread-pool

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Conflicts:
	src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java
This commit is contained in:
xluandc
2021-03-08 10:32:18 -05:00
parent c142e6bdfa b5c34033c0
commit f5e5739363
5 changed files with 181 additions and 123 deletions
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16
pom.xml
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@@ -126,7 +126,6 @@
<artifactId>hapi-fhir-testpage-overlay</artifactId>
<version>${project.version}</version>
<classifier>classes</classifier>
</dependency>
<!-- 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
@@ -312,6 +311,21 @@
<build>
<pluginManagement>
<plugins>
<!--
There is a bug in 3.1.2 that prevents go-offline from working
Reported here:
https://issues.apache.org/jira/browse/MDEP-739
-->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>3.1.1</version>
</plugin>
</plugins>
</pluginManagement>
<!-- Tells Maven to name the generated WAR file as ROOT.war -->
<finalName>ROOT</finalName>

18
src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java
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@@ -70,6 +70,24 @@ public class AppProperties {
private Integer search_coord_core_pool_size = 20;
private Integer search_coord_max_pool_size = 100;
private Integer search_coord_queue_capacity = 200;
private Boolean use_apache_address_strategy = false;
private Boolean use_apache_address_strategy_https = false;
public Boolean getUse_apache_address_strategy() {
return use_apache_address_strategy;
}
public void setUse_apache_address_strategy(Boolean use_apache_address_strategy) {
this.use_apache_address_strategy = use_apache_address_strategy;
}
public Boolean getUse_apache_address_strategy_https() {
return use_apache_address_strategy_https;
}
public void setUse_apache_address_strategy_https(Boolean use_apache_address_strategy_https) {
this.use_apache_address_strategy_https = use_apache_address_strategy_https;
}
public Integer getDefer_indexing_for_codesystems_of_size() {
return defer_indexing_for_codesystems_of_size;

8
src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java
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@@ -27,6 +27,8 @@ import ca.uhn.fhir.narrative.INarrativeGenerator;
import ca.uhn.fhir.narrative2.NullNarrativeGenerator;
import ca.uhn.fhir.rest.server.ETagSupportEnum;
import ca.uhn.fhir.rest.server.HardcodedServerAddressStrategy;
import ca.uhn.fhir.rest.server.ApacheProxyAddressStrategy;
import ca.uhn.fhir.rest.server.IncomingRequestAddressStrategy;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.interceptor.*;
import ca.uhn.fhir.rest.server.interceptor.partition.RequestTenantPartitionInterceptor;
@@ -239,6 +241,12 @@ public class BaseJpaRestfulServer extends RestfulServer {
String serverAddress = appProperties.getServer_address();
if (!Strings.isNullOrEmpty(serverAddress)) {
setServerAddressStrategy(new HardcodedServerAddressStrategy(serverAddress));
} else if (appProperties.getUse_apache_address_strategy()) {
boolean useHttps = appProperties.getUse_apache_address_strategy_https();
setServerAddressStrategy(useHttps ? ApacheProxyAddressStrategy.forHttps() :
ApacheProxyAddressStrategy.forHttp());
} else {
setServerAddressStrategy(new IncomingRequestAddressStrategy());
}
/*

110
src/main/java/ca/uhn/fhir/jpa/starter/EnvironmentHelper.java
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@@ -1,97 +1,109 @@
package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.jpa.config.HapiFhirLocalContainerEntityManagerFactoryBean;
import ca.uhn.fhir.jpa.search.HapiLuceneAnalysisConfigurer;
import ca.uhn.fhir.jpa.search.elastic.ElasticsearchHibernatePropertiesBuilder;
import org.apache.commons.lang3.StringUtils;
import org.elasticsearch.action.admin.indices.stats.IndexStats;
import org.apache.lucene.util.Version;
import org.hibernate.cfg.AvailableSettings;
import org.hibernate.search.backend.elasticsearch.cfg.ElasticsearchBackendSettings;
import org.hibernate.search.backend.elasticsearch.index.IndexStatus;
import org.hibernate.search.backend.lucene.cfg.LuceneBackendSettings;
import org.hibernate.search.backend.lucene.cfg.LuceneIndexSettings;
import org.hibernate.search.backend.lucene.lowlevel.directory.impl.LocalFileSystemDirectoryProvider;
import org.hibernate.search.engine.cfg.BackendSettings;
import org.hibernate.search.mapper.orm.automaticindexing.session.AutomaticIndexingSynchronizationStrategyNames;
import org.hibernate.search.mapper.orm.cfg.HibernateOrmMapperSettings;
import org.hibernate.search.mapper.orm.schema.management.SchemaManagementStrategyName;
import org.springframework.boot.orm.jpa.hibernate.SpringImplicitNamingStrategy;
import org.springframework.boot.orm.jpa.hibernate.SpringPhysicalNamingStrategy;
import org.springframework.core.env.CompositePropertySource;
import org.springframework.core.env.ConfigurableEnvironment;
import org.springframework.core.env.EnumerablePropertySource;
import org.springframework.core.env.PropertySource;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Map;
import java.util.Properties;
import java.util.*;
public class EnvironmentHelper {
public static Properties getHibernateProperties(ConfigurableEnvironment environment) {
Properties properties = new Properties();
Map<String, Object> jpaProps = getPropertiesStartingWith(environment, "spring.jpa.properties");
properties.putIfAbsent("hibernate.format_sql", "false");
properties.putIfAbsent("hibernate.show_sql", "false");
properties.putIfAbsent("hibernate.hbm2ddl.auto", "update");
properties.putIfAbsent("hibernate.jdbc.batch_size", "20");
properties.putIfAbsent("hibernate.cache.use_query_cache", "false");
properties.putIfAbsent("hibernate.cache.use_second_level_cache", "false");
properties.putIfAbsent("hibernate.cache.use_structured_entries", "false");
properties.putIfAbsent("hibernate.cache.use_minimal_puts", "false");
if (jpaProps.getOrDefault("spring.jpa.properties.hibernate.search.enabled", "false").toString() == "true") {
properties.putIfAbsent(HibernateOrmMapperSettings.ENABLED, true);
properties.putIfAbsent(BackendSettings.backendKey(LuceneIndexSettings.DIRECTORY_TYPE), "local-filesystem");
properties.putIfAbsent(BackendSettings.backendKey(LuceneIndexSettings.DIRECTORY_ROOT), "target/lucenefiles");
properties.putIfAbsent(BackendSettings.backendKey(BackendSettings.TYPE), "lucene");
properties.putIfAbsent(BackendSettings.backendKey(LuceneBackendSettings.ANALYSIS_CONFIGURER), HapiLuceneAnalysisConfigurer.class.getName());
properties.putIfAbsent(BackendSettings.backendKey(LuceneBackendSettings.LUCENE_VERSION), "LUCENE_CURRENT");
} else {
properties.putIfAbsent(HibernateOrmMapperSettings.ENABLED, false);
}
for (Map.Entry<String, Object> entry : jpaProps.entrySet()) {
String strippedKey = entry.getKey().replace("spring.jpa.properties.", "");
properties.put(strippedKey, entry.getValue().toString());
}
//Spring Boot Autoconfiguration defaults
properties.putIfAbsent(AvailableSettings.SCANNER, "org.hibernate.boot.archive.scan.internal.DisabledScanner");
properties.putIfAbsent(AvailableSettings.IMPLICIT_NAMING_STRATEGY, SpringImplicitNamingStrategy.class.getName());
properties.putIfAbsent(AvailableSettings.PHYSICAL_NAMING_STRATEGY, SpringPhysicalNamingStrategy.class.getName());
//TODO The bean factory should be added as parameter but that requires that it can be injected from the entityManagerFactory bean from xBaseConfig
//properties.putIfAbsent(AvailableSettings.BEAN_CONTAINER, new SpringBeanContainer(beanFactory));
if (environment.getProperty("elasticsearch.enabled", Boolean.class) != null
&& environment.getProperty("elasticsearch.enabled", Boolean.class) == true) {
//hapi-fhir-jpaserver-base "sensible defaults"
Map<String, Object> hapiJpaPropertyMap = new HapiFhirLocalContainerEntityManagerFactoryBean().getJpaPropertyMap();
hapiJpaPropertyMap.forEach(properties::putIfAbsent);
//hapi-fhir-jpaserver-starter defaults
properties.putIfAbsent(AvailableSettings.FORMAT_SQL, false);
properties.putIfAbsent(AvailableSettings.SHOW_SQL, false);
properties.putIfAbsent(AvailableSettings.HBM2DDL_AUTO, "update");
properties.putIfAbsent(AvailableSettings.STATEMENT_BATCH_SIZE, 20);
properties.putIfAbsent(AvailableSettings.USE_QUERY_CACHE, false);
properties.putIfAbsent(AvailableSettings.USE_SECOND_LEVEL_CACHE, false);
properties.putIfAbsent(AvailableSettings.USE_STRUCTURED_CACHE, false);
properties.putIfAbsent(AvailableSettings.USE_MINIMAL_PUTS, false);
//Hibernate Search defaults
properties.putIfAbsent(HibernateOrmMapperSettings.ENABLED, true);
if (Boolean.parseBoolean(String.valueOf(properties.get(HibernateOrmMapperSettings.ENABLED)))) {
properties.putIfAbsent(BackendSettings.backendKey(BackendSettings.TYPE), LuceneBackendSettings.TYPE_NAME);
if (properties.get(BackendSettings.backendKey(BackendSettings.TYPE)).equals(LuceneBackendSettings.TYPE_NAME)) {
properties.putIfAbsent(BackendSettings.backendKey(LuceneIndexSettings.DIRECTORY_TYPE), LocalFileSystemDirectoryProvider.NAME);
properties.putIfAbsent(BackendSettings.backendKey(LuceneIndexSettings.DIRECTORY_ROOT), "target/lucenefiles");
properties.putIfAbsent(BackendSettings.backendKey(LuceneBackendSettings.ANALYSIS_CONFIGURER), HapiLuceneAnalysisConfigurer.class.getName());
properties.putIfAbsent(BackendSettings.backendKey(LuceneBackendSettings.LUCENE_VERSION), Version.LATEST);
} else if (properties.get(BackendSettings.backendKey(BackendSettings.TYPE)).equals(ElasticsearchBackendSettings.TYPE_NAME)) {
ElasticsearchHibernatePropertiesBuilder builder = new ElasticsearchHibernatePropertiesBuilder();
IndexStatus requiredIndexStatus = environment.getProperty("elasticsearch.required_index_status", IndexStatus.class);
if (requiredIndexStatus == null) {
builder.setRequiredIndexStatus(IndexStatus.YELLOW);
} else {
builder.setRequiredIndexStatus(requiredIndexStatus);
}
builder.setRequiredIndexStatus(requireNonNullElse(requiredIndexStatus, IndexStatus.YELLOW));
builder.setRestUrl(getElasticsearchServerUrl(environment));
builder.setUsername(getElasticsearchServerUsername(environment));
builder.setPassword(getElasticsearchServerPassword(environment));
builder.setProtocol(getElasticsearchServerProtocol(environment));
SchemaManagementStrategyName indexSchemaManagementStrategy = environment.getProperty("elasticsearch.schema_management_strategy", SchemaManagementStrategyName.class);
if (indexSchemaManagementStrategy == null) {
builder.setIndexSchemaManagementStrategy(SchemaManagementStrategyName.CREATE);
} else {
builder.setIndexSchemaManagementStrategy(indexSchemaManagementStrategy);
}
// pretty_print_json_log: false
builder.setIndexSchemaManagementStrategy(requireNonNullElse(indexSchemaManagementStrategy, SchemaManagementStrategyName.CREATE));
Boolean refreshAfterWrite = environment.getProperty("elasticsearch.debug.refresh_after_write", Boolean.class);
if (refreshAfterWrite == null || refreshAfterWrite == false) {
if (refreshAfterWrite == null || !refreshAfterWrite) {
builder.setDebugIndexSyncStrategy(AutomaticIndexingSynchronizationStrategyNames.ASYNC);
} else {
builder.setDebugIndexSyncStrategy(AutomaticIndexingSynchronizationStrategyNames.READ_SYNC);
}
// pretty_print_json_log: false
Boolean prettyPrintJsonLog = environment.getProperty("elasticsearch.debug.pretty_print_json_log", Boolean.class);
if (prettyPrintJsonLog == null) {
builder.setDebugPrettyPrintJsonLog(false);
} else {
builder.setDebugPrettyPrintJsonLog(prettyPrintJsonLog);
}
builder.setDebugPrettyPrintJsonLog(requireNonNullElse(environment.getProperty("elasticsearch.debug.pretty_print_json_log", Boolean.class), false));
builder.apply(properties);
} else {
throw new UnsupportedOperationException("Unsupported Hibernate Search backend: " + properties.get(BackendSettings.backendKey(BackendSettings.TYPE)));
}
}
return properties;
}
//TODO Removed when we're up on Java 11
private static <T> T requireNonNullElse(T obj, T defaultObj) {
return (obj != null) ? obj : requireNonNull(defaultObj, "defaultObj");
}
//TODO Removed when we're up on Java 11
private static <T> T requireNonNull(T obj, String message) {
if (obj == null)
throw new NullPointerException(message);
return obj;
}
public static String getElasticsearchServerUrl(ConfigurableEnvironment environment) {
return environment.getProperty("elasticsearch.rest_url", String.class);
}

6
src/main/resources/application.yaml
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@@ -36,6 +36,12 @@ spring:
hapi:
fhir:
### enable to use the ApacheProxyAddressStrategy which uses X-Forwarded-* headers
### to determine the FHIR server address
# use_apache_address_strategy: false
### forces the use of the https:// protocol for the returned server address.
### alternatively, it may be set using the X-Forwarded-Proto header.
# use_apache_address_strategy_https: false
### enable to set the Server URL
# server_address: http://hapi.fhir.org/baseR4
### This is the FHIR version. Choose between, DSTU2, DSTU3, R4 or R5