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Merged the rel_5_3_0 branch into this Branch to pick up the MDM changes.

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This commit is contained in:
Kevin Dougan
2021-01-07 09:12:52 -05:00
parent a83927aa0c
commit 3954f6a3f4
18 changed files with 338 additions and 262 deletions
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45
src/main/java/ca/uhn/fhir/jpa/mdm/MdmConfig.java Normal file
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@@ -0,0 +1,45 @@
package ca.uhn.fhir.jpa.mdm;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.mdm.config.MdmConsumerConfig;
import ca.uhn.fhir.jpa.mdm.config.MdmSubmitterConfig;
import ca.uhn.fhir.jpa.starter.AppProperties;
import ca.uhn.fhir.mdm.api.IMdmSettings;
import ca.uhn.fhir.mdm.rules.config.MdmRuleValidator;
import ca.uhn.fhir.mdm.rules.config.MdmSettings;
import ca.uhn.fhir.rest.server.util.ISearchParamRetriever;
import com.google.common.base.Charsets;
import org.apache.commons.io.IOUtils;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Conditional;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
import org.springframework.core.io.DefaultResourceLoader;
import org.springframework.core.io.Resource;
import java.io.IOException;
/**
* TODO: Move this to package "ca.uhn.fhir.jpa.starter" in HAPI FHIR 5.2.0+. The lousy component scan
* in 5.1.0 picks this up even if MDM is disabled currently.
*/
@Configuration
@Conditional(MdmConfigCondition.class)
@Import({MdmConsumerConfig.class, MdmSubmitterConfig.class})
public class MdmConfig {
@Bean
MdmRuleValidator mdmRuleValidator(FhirContext theFhirContext, ISearchParamRetriever theSearchParamRetriever) {
return new MdmRuleValidator(theFhirContext, theSearchParamRetriever);
}
@Bean
IMdmSettings mdmSettings(@Autowired MdmRuleValidator theMdmRuleValidator, AppProperties appProperties) throws IOException {
DefaultResourceLoader resourceLoader = new DefaultResourceLoader();
Resource resource = resourceLoader.getResource("mdm-rules.json");
String json = IOUtils.toString(resource.getInputStream(), Charsets.UTF_8);
return new MdmSettings(theMdmRuleValidator).setEnabled(appProperties.getMdm_enabled()).setScriptText(json);
}
}

13
src/main/java/ca/uhn/fhir/jpa/mdm/MdmConfigCondition.java Normal file
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@@ -0,0 +1,13 @@
package ca.uhn.fhir.jpa.mdm;
import org.springframework.context.annotation.Condition;
import org.springframework.context.annotation.ConditionContext;
import org.springframework.core.type.AnnotatedTypeMetadata;
public class MdmConfigCondition implements Condition {
@Override
public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
String property = conditionContext.getEnvironment().getProperty("hapi.fhir.mdm_enabled");
return Boolean.parseBoolean(property);
}
}

20
src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java
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@@ -23,6 +23,7 @@ import org.springframework.context.annotation.Configuration;
public class AppProperties {
private Boolean cql_enabled = false;
private Boolean mdm_enabled = false;
private Boolean allow_cascading_deletes = false;
private Boolean allow_contains_searches = true;
private Boolean allow_external_references = false;
@@ -31,6 +32,7 @@ public class AppProperties {
private Boolean allow_placeholder_references = true;
private Boolean auto_create_placeholder_reference_targets = true;
private Boolean enable_index_missing_fields = false;
private Boolean enable_repository_validating_interceptor = false;
private Boolean enforce_referential_integrity_on_delete = true;
private Boolean enforce_referential_integrity_on_write = true;
private Boolean etag_support_enabled = true;
@@ -97,6 +99,14 @@ public class AppProperties {
this.cql_enabled = cql_enabled;
}
public Boolean getMdm_enabled() {
return mdm_enabled;
}
public void setMdm_enabled(Boolean mdm_enabled) {
this.mdm_enabled = mdm_enabled;
}
public Cors getCors() {
return cors;
}
@@ -244,7 +254,15 @@ public class AppProperties {
this.enable_index_missing_fields = enable_index_missing_fields;
}
public Boolean getEnforce_referential_integrity_on_delete() {
public Boolean getEnable_repository_validating_interceptor() {
return enable_repository_validating_interceptor;
}
public void setEnable_repository_validating_interceptor(Boolean theEnable_repository_validating_interceptor) {
enable_repository_validating_interceptor = theEnable_repository_validating_interceptor;
}
public Boolean getEnforce_referential_integrity_on_delete() {
return enforce_referential_integrity_on_delete;
}

3
src/main/java/ca/uhn/fhir/jpa/starter/Application.java
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@@ -1,5 +1,6 @@
package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.jpa.mdm.MdmConfig;
import ca.uhn.fhir.jpa.starter.annotations.OnEitherVersion;
import ca.uhn.fhir.jpa.subscription.channel.config.SubscriptionChannelConfig;
import ca.uhn.fhir.jpa.subscription.match.config.SubscriptionProcessorConfig;
@@ -23,7 +24,7 @@ import org.springframework.web.servlet.DispatcherServlet;
@ServletComponentScan(basePackageClasses = {
JpaRestfulServer.class})
@SpringBootApplication(exclude = {ElasticsearchRestClientAutoConfiguration.class})
@Import({SubscriptionSubmitterConfig.class, SubscriptionProcessorConfig.class, SubscriptionChannelConfig.class, WebsocketDispatcherConfig.class})
@Import({SubscriptionSubmitterConfig.class, SubscriptionProcessorConfig.class, SubscriptionChannelConfig.class, WebsocketDispatcherConfig.class, MdmConfig.class})
public class Application extends SpringBootServletInitializer {
public static void main(String[] args) {

7
src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java
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@@ -11,6 +11,7 @@ import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.binstore.BinaryStorageInterceptor;
import ca.uhn.fhir.jpa.bulk.provider.BulkDataExportProvider;
import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
import ca.uhn.fhir.jpa.interceptor.validation.RepositoryValidatingInterceptor;
import ca.uhn.fhir.jpa.packages.IPackageInstallerSvc;
import ca.uhn.fhir.jpa.packages.PackageInstallationSpec;
import ca.uhn.fhir.jpa.partition.PartitionManagementProvider;
@@ -365,6 +366,12 @@ public class BaseJpaRestfulServer extends RestfulServer {
daoConfig.setLastNEnabled(true);
}
// Repository Validating Interceptor
if (Boolean.TRUE.equals(appProperties.getEnable_repository_validating_interceptor())) {
RepositoryValidationInterceptorFactory repositoryValidationInterceptorFactory = myApplicationContext.getBean(RepositoryValidationInterceptorFactory.class);
RepositoryValidatingInterceptor interceptor = repositoryValidationInterceptorFactory.build();
interceptorService.registerInterceptor(interceptor);
}
}

50
src/main/java/ca/uhn/fhir/jpa/starter/EnvironmentHelper.java
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@@ -1,8 +1,16 @@
package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.jpa.search.HapiLuceneAnalysisConfigurer;
import ca.uhn.fhir.jpa.search.elastic.ElasticsearchHibernatePropertiesBuilder;
import org.hibernate.search.elasticsearch.cfg.ElasticsearchIndexStatus;
import org.hibernate.search.elasticsearch.cfg.IndexSchemaManagementStrategy;
import org.apache.commons.lang3.StringUtils;
import org.elasticsearch.action.admin.indices.stats.IndexStats;
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.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.core.env.CompositePropertySource;
import org.springframework.core.env.ConfigurableEnvironment;
import org.springframework.core.env.EnumerablePropertySource;
@@ -19,7 +27,6 @@ public class EnvironmentHelper {
Properties properties = new Properties();
if (environment.getProperty("spring.jpa.properties", String.class) == null) {
properties.put("hibernate.search.model_mapping", "ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory");
properties.put("hibernate.format_sql", "false");
properties.put("hibernate.show_sql", "false");
properties.put("hibernate.hbm2ddl.auto", "update");
@@ -28,11 +35,18 @@ public class EnvironmentHelper {
properties.put("hibernate.cache.use_second_level_cache", "false");
properties.put("hibernate.cache.use_structured_entries", "false");
properties.put("hibernate.cache.use_minimal_puts", "false");
properties.put("hibernate.search.default.directory_provider", "filesystem");
properties.put("hibernate.search.default.indexBase", "target/lucenefiles");
properties.put("hibernate.search.lucene_version", "LUCENE_CURRENT");
properties.put(BackendSettings.backendKey(LuceneIndexSettings.DIRECTORY_TYPE), "local-filesystem");
properties.put(BackendSettings.backendKey(LuceneIndexSettings.DIRECTORY_ROOT), "target/lucenefiles");
properties.put(BackendSettings.backendKey(BackendSettings.TYPE), "lucene");
properties.put(BackendSettings.backendKey(LuceneBackendSettings.ANALYSIS_CONFIGURER), HapiLuceneAnalysisConfigurer.class.getName());
properties.put(BackendSettings.backendKey(LuceneBackendSettings.LUCENE_VERSION), "LUCENE_CURRENT");
//Set this value to true in the properties to enable lucene.
properties.put(HibernateOrmMapperSettings.ENABLED, environment.getProperty("spring.jpa.properties.hibernate.search.enabled", "false"));
} else {
Arrays.asList(environment.getProperty("spring.jpa.properties", String.class).split(" ")).stream().forEach(s ->
Arrays.asList(environment.getProperty("spring.jpa.properties", String.class).split(" ")).stream().filter(s -> !StringUtils.isEmpty(s)).forEach(s ->
{
String[] values = s.split("=");
properties.put(values[0], values[1]);
@@ -42,9 +56,9 @@ public class EnvironmentHelper {
if (environment.getProperty("elasticsearch.enabled", Boolean.class) != null
&& environment.getProperty("elasticsearch.enabled", Boolean.class) == true ){
ElasticsearchHibernatePropertiesBuilder builder = new ElasticsearchHibernatePropertiesBuilder();
ElasticsearchIndexStatus requiredIndexStatus = environment.getProperty("elasticsearch.required_index_status", ElasticsearchIndexStatus.class);
IndexStatus requiredIndexStatus = environment.getProperty("elasticsearch.required_index_status", IndexStatus.class);
if (requiredIndexStatus == null) {
builder.setRequiredIndexStatus(ElasticsearchIndexStatus.YELLOW);
builder.setRequiredIndexStatus(IndexStatus.YELLOW);
} else {
builder.setRequiredIndexStatus(requiredIndexStatus);
}
@@ -52,18 +66,19 @@ public class EnvironmentHelper {
builder.setRestUrl(getElasticsearchServerUrl(environment));
builder.setUsername(getElasticsearchServerUsername(environment));
builder.setPassword(getElasticsearchServerPassword(environment));
IndexSchemaManagementStrategy indexSchemaManagementStrategy = environment.getProperty("elasticsearch.schema_management_strategy", IndexSchemaManagementStrategy.class);
builder.setProtocol(getElasticsearchServerProtocol(environment));
SchemaManagementStrategyName indexSchemaManagementStrategy = environment.getProperty("elasticsearch.schema_management_strategy", SchemaManagementStrategyName.class);
if (indexSchemaManagementStrategy == null) {
builder.setIndexSchemaManagementStrategy(IndexSchemaManagementStrategy.CREATE);
builder.setIndexSchemaManagementStrategy(SchemaManagementStrategyName.CREATE);
} else {
builder.setIndexSchemaManagementStrategy(indexSchemaManagementStrategy);
}
// pretty_print_json_log: false
Boolean refreshAfterWrite = environment.getProperty("elasticsearch.debug.refresh_after_write", Boolean.class);
if (refreshAfterWrite == null) {
builder.setDebugRefreshAfterWrite(false);
if (refreshAfterWrite == null || refreshAfterWrite == false) {
builder.setDebugIndexSyncStrategy(AutomaticIndexingSynchronizationStrategyNames.ASYNC);
} else {
builder.setDebugRefreshAfterWrite(refreshAfterWrite);
builder.setDebugIndexSyncStrategy(AutomaticIndexingSynchronizationStrategyNames.READ_SYNC);
}
// pretty_print_json_log: false
Boolean prettyPrintJsonLog = environment.getProperty("elasticsearch.debug.pretty_print_json_log", Boolean.class);
@@ -74,7 +89,6 @@ public class EnvironmentHelper {
}
builder.apply(properties);
}
return properties;
}
@@ -82,7 +96,11 @@ public class EnvironmentHelper {
return environment.getProperty("elasticsearch.rest_url", String.class);
}
public static String getElasticsearchServerUsername(ConfigurableEnvironment environment) {
public static String getElasticsearchServerProtocol(ConfigurableEnvironment environment) {
return environment.getProperty("elasticsearch.protocol", String.class, "http");
}
public static String getElasticsearchServerUsername(ConfigurableEnvironment environment) {
return environment.getProperty("elasticsearch.username");
}

13
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigCommon.java
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@@ -3,7 +3,7 @@ package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.binstore.DatabaseBlobBinaryStorageSvcImpl;
import ca.uhn.fhir.jpa.binstore.IBinaryStorageSvc;
import ca.uhn.fhir.jpa.config.HibernateDialectProvider;
import ca.uhn.fhir.jpa.config.HibernatePropertiesProvider;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.subscription.channel.subscription.SubscriptionDeliveryHandlerFactory;
@@ -132,10 +132,17 @@ public class FhirServerConfigCommon {
}
@Bean
@Lazy
public RepositoryValidationInterceptorFactory repositoryValidationInterceptorFactory() {
return new RepositoryValidationInterceptorFactory();
}
@Primary
@Bean
public HibernateDialectProvider jpaStarterDialectProvider(LocalContainerEntityManagerFactoryBean myEntityManagerFactory) {
return new JpaHibernateDialectProvider(myEntityManagerFactory);
public HibernatePropertiesProvider jpaStarterDialectProvider(LocalContainerEntityManagerFactoryBean myEntityManagerFactory) {
return new JpaHibernatePropertiesProvider(myEntityManagerFactory);
}
@Bean

10
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR4.java
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@@ -69,8 +69,14 @@ public class FhirServerConfigR4 extends BaseJavaConfigR4 {
@Bean()
public ElasticsearchSvcImpl elasticsearchSvc() {
if (EnvironmentHelper.isElasticsearchEnabled(configurableEnvironment)) {
String elasticsearchUrl = EnvironmentHelper.getElasticsearchServerUrl(configurableEnvironment);
String elasticsearchHost = elasticsearchUrl.substring(elasticsearchUrl.indexOf("://")+3, elasticsearchUrl.lastIndexOf(":"));
String elasticsearchUrl = EnvironmentHelper.getElasticsearchServerUrl(configurableEnvironment);
String elasticsearchHost;
if (elasticsearchUrl.startsWith("http")) {
elasticsearchHost = elasticsearchUrl.substring(elasticsearchUrl.indexOf("://") + 3, elasticsearchUrl.lastIndexOf(":"));
} else {
elasticsearchHost = elasticsearchUrl.substring(0, elasticsearchUrl.indexOf(":"));
}
String elasticsearchUsername = EnvironmentHelper.getElasticsearchServerUsername(configurableEnvironment);
String elasticsearchPassword = EnvironmentHelper.getElasticsearchServerPassword(configurableEnvironment);
int elasticsearchPort = Integer.parseInt(elasticsearchUrl.substring(elasticsearchUrl.lastIndexOf(":")+1));

6
src/main/java/ca/uhn/fhir/jpa/starter/JpaHibernateDialectProvider.java → src/main/java/ca/uhn/fhir/jpa/starter/JpaHibernatePropertiesProvider.java
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@@ -1,7 +1,7 @@
package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.jpa.config.HibernateDialectProvider;
import ca.uhn.fhir.jpa.config.HibernatePropertiesProvider;
import org.hibernate.dialect.Dialect;
import org.hibernate.engine.jdbc.dialect.internal.StandardDialectResolver;
import org.hibernate.engine.jdbc.dialect.spi.DatabaseMetaDataDialectResolutionInfoAdapter;
@@ -10,11 +10,11 @@ import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import javax.sql.DataSource;
import java.sql.SQLException;
public class JpaHibernateDialectProvider extends HibernateDialectProvider {
public class JpaHibernatePropertiesProvider extends HibernatePropertiesProvider {
private final Dialect dialect;
public JpaHibernateDialectProvider(LocalContainerEntityManagerFactoryBean myEntityManagerFactory) {
public JpaHibernatePropertiesProvider(LocalContainerEntityManagerFactoryBean myEntityManagerFactory) {
DataSource connection = myEntityManagerFactory.getDataSource();
try {
dialect = new StandardDialectResolver()

38
src/main/java/ca/uhn/fhir/jpa/starter/RepositoryValidationInterceptorFactory.java Normal file
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@@ -0,0 +1,38 @@
package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.interceptor.validation.IRepositoryValidatingRule;
import ca.uhn.fhir.jpa.interceptor.validation.RepositoryValidatingInterceptor;
import ca.uhn.fhir.jpa.interceptor.validation.RepositoryValidatingRuleBuilder;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationContext;
import java.util.List;
/**
* This class can be customized to enable the {@link ca.uhn.fhir.jpa.interceptor.validation.RepositoryValidatingInterceptor}
* on this server.
*
* The <code>enable_repository_validating_interceptor</code> property must be enabled in <code>application.yaml</code>
* in order to use this class.
*/
public class RepositoryValidationInterceptorFactory {
@Autowired
private ApplicationContext myApplicationContext;
@Autowired
private FhirContext myFhirContext;
public RepositoryValidatingInterceptor build() {
RepositoryValidatingRuleBuilder ruleBuilder = myApplicationContext.getBean(RepositoryValidatingRuleBuilder.class);
// Customize the ruleBuilder here to have the rules you want! We will give a simple example
// of enabling validation for all Patient resources
ruleBuilder.forResourcesOfType("Patient").requireValidationToDeclaredProfiles();
// Do not customize below this line
List<IRepositoryValidatingRule> rules = ruleBuilder.build();
return new RepositoryValidatingInterceptor(myFhirContext, rules);
}
}

5
src/main/resources/application.yaml
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@@ -18,6 +18,7 @@ spring:
# hibernate.cache.use_second_level_cache: false
# hibernate.cache.use_structured_entries: false
# hibernate.cache.use_minimal_puts: false
# hibernate.search.enabled: true
# hibernate.search.default.directory_provider: filesystem
# hibernate.search.default.indexbase: target/lucenefiles
# hibernate.search.lucene_version: lucene_current
@@ -58,6 +59,7 @@ hapi:
# default_encoding: JSON
# default_pretty_print: true
# default_page_size: 20
# enable_repository_validating_interceptor: false
# enable_index_missing_fields: false
# enforce_referential_integrity_on_delete: false
# enforce_referential_integrity_on_write: false
@@ -135,6 +137,7 @@ hapi:
# enabled: false
# password: SomePassword
# required_index_status: YELLOW
# rest_url: 'http://localhost:9200'
# rest_url: 'localhost:9200'
# protocol: 'http'
# schema_management_strategy: CREATE
# username: SomeUsername

1
src/main/resources/empi-rules.json → src/main/resources/mdm-rules.json
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@@ -1,5 +1,6 @@
{
"version": "1",
"mdmTypes": ["Patient", "Practitioner"],
"candidateSearchParams": [
{
"resourceType": "Patient",