Merged the rel_5_3_0 branch into this Branch to pick up the MDM changes.
This commit is contained in:
Kevin Dougan
45
src/main/java/ca/uhn/fhir/jpa/mdm/MdmConfig.java
Normal file
45
src/main/java/ca/uhn/fhir/jpa/mdm/MdmConfig.java
Normal file
@@ -0,0 +1,45 @@
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package ca.uhn.fhir.jpa.mdm;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.jpa.mdm.config.MdmConsumerConfig;
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import ca.uhn.fhir.jpa.mdm.config.MdmSubmitterConfig;
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import ca.uhn.fhir.jpa.starter.AppProperties;
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import ca.uhn.fhir.mdm.api.IMdmSettings;
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import ca.uhn.fhir.mdm.rules.config.MdmRuleValidator;
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import ca.uhn.fhir.mdm.rules.config.MdmSettings;
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import ca.uhn.fhir.rest.server.util.ISearchParamRetriever;
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import com.google.common.base.Charsets;
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import org.apache.commons.io.IOUtils;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.context.annotation.Bean;
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import org.springframework.context.annotation.Conditional;
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import org.springframework.context.annotation.Configuration;
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import org.springframework.context.annotation.Import;
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import org.springframework.core.io.DefaultResourceLoader;
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import org.springframework.core.io.Resource;
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import java.io.IOException;
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/**
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* TODO: Move this to package "ca.uhn.fhir.jpa.starter" in HAPI FHIR 5.2.0+. The lousy component scan
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* in 5.1.0 picks this up even if MDM is disabled currently.
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*/
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@Configuration
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@Conditional(MdmConfigCondition.class)
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@Import({MdmConsumerConfig.class, MdmSubmitterConfig.class})
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public class MdmConfig {
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@Bean
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MdmRuleValidator mdmRuleValidator(FhirContext theFhirContext, ISearchParamRetriever theSearchParamRetriever) {
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return new MdmRuleValidator(theFhirContext, theSearchParamRetriever);
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}
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@Bean
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IMdmSettings mdmSettings(@Autowired MdmRuleValidator theMdmRuleValidator, AppProperties appProperties) throws IOException {
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DefaultResourceLoader resourceLoader = new DefaultResourceLoader();
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Resource resource = resourceLoader.getResource("mdm-rules.json");
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String json = IOUtils.toString(resource.getInputStream(), Charsets.UTF_8);
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return new MdmSettings(theMdmRuleValidator).setEnabled(appProperties.getMdm_enabled()).setScriptText(json);
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}
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}
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13
src/main/java/ca/uhn/fhir/jpa/mdm/MdmConfigCondition.java
Normal file
13
src/main/java/ca/uhn/fhir/jpa/mdm/MdmConfigCondition.java
Normal file
@@ -0,0 +1,13 @@
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package ca.uhn.fhir.jpa.mdm;
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import org.springframework.context.annotation.Condition;
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import org.springframework.context.annotation.ConditionContext;
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import org.springframework.core.type.AnnotatedTypeMetadata;
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public class MdmConfigCondition implements Condition {
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@Override
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public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
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String property = conditionContext.getEnvironment().getProperty("hapi.fhir.mdm_enabled");
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return Boolean.parseBoolean(property);
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}
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}
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@@ -23,6 +23,7 @@ import org.springframework.context.annotation.Configuration;
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public class AppProperties {
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private Boolean cql_enabled = false;
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private Boolean mdm_enabled = false;
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private Boolean allow_cascading_deletes = false;
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private Boolean allow_contains_searches = true;
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private Boolean allow_external_references = false;
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@@ -31,6 +32,7 @@ public class AppProperties {
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private Boolean allow_placeholder_references = true;
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private Boolean auto_create_placeholder_reference_targets = true;
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private Boolean enable_index_missing_fields = false;
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private Boolean enable_repository_validating_interceptor = false;
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private Boolean enforce_referential_integrity_on_delete = true;
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private Boolean enforce_referential_integrity_on_write = true;
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private Boolean etag_support_enabled = true;
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@@ -97,6 +99,14 @@ public class AppProperties {
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this.cql_enabled = cql_enabled;
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}
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public Boolean getMdm_enabled() {
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return mdm_enabled;
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}
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public void setMdm_enabled(Boolean mdm_enabled) {
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this.mdm_enabled = mdm_enabled;
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}
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public Cors getCors() {
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return cors;
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}
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@@ -244,7 +254,15 @@ public class AppProperties {
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this.enable_index_missing_fields = enable_index_missing_fields;
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}
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public Boolean getEnforce_referential_integrity_on_delete() {
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public Boolean getEnable_repository_validating_interceptor() {
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return enable_repository_validating_interceptor;
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}
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public void setEnable_repository_validating_interceptor(Boolean theEnable_repository_validating_interceptor) {
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enable_repository_validating_interceptor = theEnable_repository_validating_interceptor;
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}
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public Boolean getEnforce_referential_integrity_on_delete() {
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return enforce_referential_integrity_on_delete;
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}
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@@ -1,5 +1,6 @@
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package ca.uhn.fhir.jpa.starter;
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import ca.uhn.fhir.jpa.mdm.MdmConfig;
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import ca.uhn.fhir.jpa.starter.annotations.OnEitherVersion;
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import ca.uhn.fhir.jpa.subscription.channel.config.SubscriptionChannelConfig;
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import ca.uhn.fhir.jpa.subscription.match.config.SubscriptionProcessorConfig;
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@@ -23,7 +24,7 @@ import org.springframework.web.servlet.DispatcherServlet;
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@ServletComponentScan(basePackageClasses = {
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JpaRestfulServer.class})
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@SpringBootApplication(exclude = {ElasticsearchRestClientAutoConfiguration.class})
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@Import({SubscriptionSubmitterConfig.class, SubscriptionProcessorConfig.class, SubscriptionChannelConfig.class, WebsocketDispatcherConfig.class})
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@Import({SubscriptionSubmitterConfig.class, SubscriptionProcessorConfig.class, SubscriptionChannelConfig.class, WebsocketDispatcherConfig.class, MdmConfig.class})
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public class Application extends SpringBootServletInitializer {
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public static void main(String[] args) {
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@@ -11,6 +11,7 @@ import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
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import ca.uhn.fhir.jpa.binstore.BinaryStorageInterceptor;
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import ca.uhn.fhir.jpa.bulk.provider.BulkDataExportProvider;
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import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
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import ca.uhn.fhir.jpa.interceptor.validation.RepositoryValidatingInterceptor;
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import ca.uhn.fhir.jpa.packages.IPackageInstallerSvc;
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import ca.uhn.fhir.jpa.packages.PackageInstallationSpec;
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import ca.uhn.fhir.jpa.partition.PartitionManagementProvider;
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@@ -365,6 +366,12 @@ public class BaseJpaRestfulServer extends RestfulServer {
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daoConfig.setLastNEnabled(true);
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}
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// Repository Validating Interceptor
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if (Boolean.TRUE.equals(appProperties.getEnable_repository_validating_interceptor())) {
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RepositoryValidationInterceptorFactory repositoryValidationInterceptorFactory = myApplicationContext.getBean(RepositoryValidationInterceptorFactory.class);
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RepositoryValidatingInterceptor interceptor = repositoryValidationInterceptorFactory.build();
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interceptorService.registerInterceptor(interceptor);
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}
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}
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@@ -1,8 +1,16 @@
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package ca.uhn.fhir.jpa.starter;
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import ca.uhn.fhir.jpa.search.HapiLuceneAnalysisConfigurer;
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import ca.uhn.fhir.jpa.search.elastic.ElasticsearchHibernatePropertiesBuilder;
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import org.hibernate.search.elasticsearch.cfg.ElasticsearchIndexStatus;
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import org.hibernate.search.elasticsearch.cfg.IndexSchemaManagementStrategy;
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import org.apache.commons.lang3.StringUtils;
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import org.elasticsearch.action.admin.indices.stats.IndexStats;
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import org.hibernate.search.backend.elasticsearch.index.IndexStatus;
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import org.hibernate.search.backend.lucene.cfg.LuceneBackendSettings;
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import org.hibernate.search.backend.lucene.cfg.LuceneIndexSettings;
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import org.hibernate.search.engine.cfg.BackendSettings;
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import org.hibernate.search.mapper.orm.automaticindexing.session.AutomaticIndexingSynchronizationStrategyNames;
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import org.hibernate.search.mapper.orm.cfg.HibernateOrmMapperSettings;
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import org.hibernate.search.mapper.orm.schema.management.SchemaManagementStrategyName;
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import org.springframework.core.env.CompositePropertySource;
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import org.springframework.core.env.ConfigurableEnvironment;
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import org.springframework.core.env.EnumerablePropertySource;
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@@ -19,7 +27,6 @@ public class EnvironmentHelper {
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Properties properties = new Properties();
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if (environment.getProperty("spring.jpa.properties", String.class) == null) {
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properties.put("hibernate.search.model_mapping", "ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory");
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properties.put("hibernate.format_sql", "false");
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properties.put("hibernate.show_sql", "false");
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properties.put("hibernate.hbm2ddl.auto", "update");
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@@ -28,11 +35,18 @@ public class EnvironmentHelper {
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properties.put("hibernate.cache.use_second_level_cache", "false");
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properties.put("hibernate.cache.use_structured_entries", "false");
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properties.put("hibernate.cache.use_minimal_puts", "false");
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properties.put("hibernate.search.default.directory_provider", "filesystem");
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properties.put("hibernate.search.default.indexBase", "target/lucenefiles");
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properties.put("hibernate.search.lucene_version", "LUCENE_CURRENT");
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properties.put(BackendSettings.backendKey(LuceneIndexSettings.DIRECTORY_TYPE), "local-filesystem");
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properties.put(BackendSettings.backendKey(LuceneIndexSettings.DIRECTORY_ROOT), "target/lucenefiles");
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properties.put(BackendSettings.backendKey(BackendSettings.TYPE), "lucene");
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properties.put(BackendSettings.backendKey(LuceneBackendSettings.ANALYSIS_CONFIGURER), HapiLuceneAnalysisConfigurer.class.getName());
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properties.put(BackendSettings.backendKey(LuceneBackendSettings.LUCENE_VERSION), "LUCENE_CURRENT");
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//Set this value to true in the properties to enable lucene.
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properties.put(HibernateOrmMapperSettings.ENABLED, environment.getProperty("spring.jpa.properties.hibernate.search.enabled", "false"));
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|
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} else {
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Arrays.asList(environment.getProperty("spring.jpa.properties", String.class).split(" ")).stream().forEach(s ->
|
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Arrays.asList(environment.getProperty("spring.jpa.properties", String.class).split(" ")).stream().filter(s -> !StringUtils.isEmpty(s)).forEach(s ->
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{
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String[] values = s.split("=");
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properties.put(values[0], values[1]);
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@@ -42,9 +56,9 @@ public class EnvironmentHelper {
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if (environment.getProperty("elasticsearch.enabled", Boolean.class) != null
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&& environment.getProperty("elasticsearch.enabled", Boolean.class) == true ){
|
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ElasticsearchHibernatePropertiesBuilder builder = new ElasticsearchHibernatePropertiesBuilder();
|
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ElasticsearchIndexStatus requiredIndexStatus = environment.getProperty("elasticsearch.required_index_status", ElasticsearchIndexStatus.class);
|
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IndexStatus requiredIndexStatus = environment.getProperty("elasticsearch.required_index_status", IndexStatus.class);
|
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if (requiredIndexStatus == null) {
|
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builder.setRequiredIndexStatus(ElasticsearchIndexStatus.YELLOW);
|
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builder.setRequiredIndexStatus(IndexStatus.YELLOW);
|
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} else {
|
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builder.setRequiredIndexStatus(requiredIndexStatus);
|
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}
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@@ -52,18 +66,19 @@ public class EnvironmentHelper {
|
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builder.setRestUrl(getElasticsearchServerUrl(environment));
|
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builder.setUsername(getElasticsearchServerUsername(environment));
|
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builder.setPassword(getElasticsearchServerPassword(environment));
|
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IndexSchemaManagementStrategy indexSchemaManagementStrategy = environment.getProperty("elasticsearch.schema_management_strategy", IndexSchemaManagementStrategy.class);
|
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builder.setProtocol(getElasticsearchServerProtocol(environment));
|
||||
SchemaManagementStrategyName indexSchemaManagementStrategy = environment.getProperty("elasticsearch.schema_management_strategy", SchemaManagementStrategyName.class);
|
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if (indexSchemaManagementStrategy == null) {
|
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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");
|
||||
}
|
||||
|
||||
|
||||
@@ -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
|
||||
|
||||
@@ -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));
|
||||
|
||||
@@ -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()
|
||||
@@ -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);
|
||||
}
|
||||
|
||||
}
|
||||
@@ -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
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
{
|
||||
"version": "1",
|
||||
"mdmTypes": ["Patient", "Practitioner"],
|
||||
"candidateSearchParams": [
|
||||
{
|
||||
"resourceType": "Patient",
|
||||
@@ -26,11 +26,13 @@ import org.springframework.context.ApplicationContextInitializer;
|
||||
import org.springframework.context.ConfigurableApplicationContext;
|
||||
import org.springframework.test.context.ContextConfiguration;
|
||||
import org.springframework.test.context.junit.jupiter.SpringExtension;
|
||||
import pl.allegro.tech.embeddedelasticsearch.EmbeddedElastic;
|
||||
import pl.allegro.tech.embeddedelasticsearch.PopularProperties;
|
||||
import org.testcontainers.elasticsearch.ElasticsearchContainer;
|
||||
import org.testcontainers.junit.jupiter.Container;
|
||||
|
||||
import javax.annotation.PreDestroy;
|
||||
import java.io.IOException;
|
||||
import java.time.Duration;
|
||||
import java.time.temporal.ChronoUnit;
|
||||
import java.util.Date;
|
||||
import java.util.GregorianCalendar;
|
||||
import java.util.UUID;
|
||||
@@ -49,7 +51,8 @@ import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
// Because the port is set randomly, we will set the rest_url using the Initializer.
|
||||
// "elasticsearch.rest_url='http://localhost:9200'",
|
||||
"elasticsearch.username=SomeUsername",
|
||||
"elasticsearch.password=SomePassword"
|
||||
"elasticsearch.password=SomePassword",
|
||||
"elasticsearch.protocol=http"
|
||||
})
|
||||
@ContextConfiguration(initializers = ElasticsearchLastNR4IT.Initializer.class)
|
||||
public class ElasticsearchLastNR4IT {
|
||||
@@ -57,30 +60,20 @@ public class ElasticsearchLastNR4IT {
|
||||
private IGenericClient ourClient;
|
||||
private FhirContext ourCtx;
|
||||
|
||||
private static final String ELASTIC_VERSION = "6.5.4";
|
||||
private static EmbeddedElastic embeddedElastic;
|
||||
private static final String ELASTIC_VERSION = "7.10.0";
|
||||
private static final String ELASTIC_IMAGE = "docker.elastic.co/elasticsearch/elasticsearch:" + ELASTIC_VERSION;
|
||||
|
||||
private static ElasticsearchContainer embeddedElastic;
|
||||
|
||||
@Autowired
|
||||
private ElasticsearchSvcImpl myElasticsearchSvc;
|
||||
|
||||
@BeforeAll
|
||||
public static void beforeClass() {
|
||||
|
||||
embeddedElastic = null;
|
||||
try {
|
||||
embeddedElastic = EmbeddedElastic.builder()
|
||||
.withElasticVersion(ELASTIC_VERSION)
|
||||
.withSetting(PopularProperties.TRANSPORT_TCP_PORT, 0)
|
||||
.withSetting(PopularProperties.HTTP_PORT, 0)
|
||||
.withSetting(PopularProperties.CLUSTER_NAME, UUID.randomUUID())
|
||||
.withStartTimeout(60, TimeUnit.SECONDS)
|
||||
.build()
|
||||
.start();
|
||||
} catch (IOException | InterruptedException e) {
|
||||
throw new ConfigurationException(e);
|
||||
}
|
||||
embeddedElastic = new ElasticsearchContainer(ELASTIC_IMAGE).withStartupTimeout(Duration.of(300, ChronoUnit.SECONDS));
|
||||
embeddedElastic.start();
|
||||
}
|
||||
|
||||
|
||||
@PreDestroy
|
||||
public void stop() {
|
||||
embeddedElastic.stop();
|
||||
@@ -136,7 +129,7 @@ public 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("elasticsearch.rest_url=http://localhost:" + embeddedElastic.getHttpPort())
|
||||
TestPropertyValues.of("elasticsearch.rest_url=" + embeddedElastic.getHost() +":" + embeddedElastic.getMappedPort(9200))
|
||||
.applyTo(configurableApplicationContext.getEnvironment());
|
||||
}
|
||||
|
||||
|
||||
@@ -14,10 +14,12 @@ import org.eclipse.jetty.websocket.api.Session;
|
||||
import org.eclipse.jetty.websocket.client.ClientUpgradeRequest;
|
||||
import org.eclipse.jetty.websocket.client.WebSocketClient;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.hl7.fhir.r4.model.*;
|
||||
import org.junit.Assert;
|
||||
import org.junit.jupiter.api.AfterEach;
|
||||
import org.hl7.fhir.r4.model.Bundle;
|
||||
import org.hl7.fhir.r4.model.Observation;
|
||||
import org.hl7.fhir.r4.model.Patient;
|
||||
import org.hl7.fhir.r4.model.Subscription;
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
import org.junit.jupiter.api.Order;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.junit.jupiter.api.extension.ExtendWith;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
@@ -27,246 +29,145 @@ import org.springframework.test.context.junit.jupiter.SpringExtension;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.net.URI;
|
||||
import java.util.Collection;
|
||||
import java.util.List;
|
||||
import java.util.Optional;
|
||||
import java.util.concurrent.Future;
|
||||
import java.util.concurrent.TimeUnit;
|
||||
|
||||
import static ca.uhn.fhir.util.TestUtil.waitForSize;
|
||||
import static java.util.Comparator.comparing;
|
||||
import static org.awaitility.Awaitility.await;
|
||||
import static org.hamcrest.Matchers.equalTo;
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
import static org.junit.jupiter.api.Assertions.assertNotNull;
|
||||
|
||||
@ExtendWith(SpringExtension.class)
|
||||
@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = Application.class, properties =
|
||||
{
|
||||
"spring.batch.job.enabled=false",
|
||||
"spring.datasource.url=jdbc:h2:mem:dbr4",
|
||||
"hapi.fhir.fhir_version=R4",
|
||||
"hapi.fhir.cql_enabled=true",
|
||||
"hapi.fhir.subscription.websocket_enabled=true",
|
||||
//Override is currently required when using Empi as the construction of the Empi beans are ambiguous as they are constructed multiple places. This is evident when running in a spring boot environment
|
||||
"spring.main.allow-bean-definition-overriding=true"
|
||||
})
|
||||
public class ExampleServerR4IT implements IServerSupport {
|
||||
{
|
||||
"spring.batch.job.enabled=false",
|
||||
"spring.datasource.url=jdbc:h2:mem:dbr4",
|
||||
"hapi.fhir.enable_repository_validating_interceptor=true",
|
||||
"hapi.fhir.fhir_version=r4",
|
||||
"hapi.fhir.subscription.websocket_enabled=true",
|
||||
"hapi.fhir.mdm_enabled=true",
|
||||
//Override is currently required when using MDM as the construction of the MDM beans are ambiguous as they are constructed multiple places. This is evident when running in a spring boot environment
|
||||
"spring.main.allow-bean-definition-overriding=true"
|
||||
})
|
||||
public class ExampleServerR4IT {
|
||||
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerDstu2IT.class);
|
||||
private IGenericClient ourClient;
|
||||
private FhirContext ourCtx;
|
||||
private String ourServerBaseURL;
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerDstu2IT.class);
|
||||
private IGenericClient ourClient;
|
||||
private FhirContext ourCtx;
|
||||
|
||||
@Autowired
|
||||
DaoRegistry myDaoRegistry;
|
||||
@LocalServerPort
|
||||
private int port;
|
||||
|
||||
@LocalServerPort
|
||||
private int port;
|
||||
|
||||
@BeforeEach
|
||||
void beforeEach() {
|
||||
ourCtx = FhirContext.forR4();
|
||||
ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
|
||||
ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
|
||||
ourServerBaseURL = "http://localhost:" + port + "/fhir/";
|
||||
ourClient = ourCtx.newRestfulGenericClient(ourServerBaseURL);
|
||||
ourClient.registerInterceptor(new LoggingInterceptor(true));
|
||||
}
|
||||
@Test
|
||||
@Order(0)
|
||||
void testCreateAndRead() {
|
||||
|
||||
@AfterEach
|
||||
void afterEach() {
|
||||
ourLog.info("Finished running a test...");
|
||||
}
|
||||
String methodName = "testCreateResourceConditional";
|
||||
|
||||
@Test
|
||||
public void testCQLEXM104EvaluateMeasure() throws IOException {
|
||||
String measureId = "measure-EXM104-8.2.000";
|
||||
Patient pt = new Patient();
|
||||
pt.setActive(true);
|
||||
pt.getBirthDateElement().setValueAsString("2020-01-01");
|
||||
pt.addIdentifier().setSystem("http://foo").setValue("12345");
|
||||
pt.addName().setFamily(methodName);
|
||||
IIdType id = ourClient.create().resource(pt).execute().getId();
|
||||
|
||||
loadBundle("r4/EXM104/EXM104-8.2.000-bundle.json", ourCtx, ourClient);
|
||||
Patient pt2 = ourClient.read().resource(Patient.class).withId(id).execute();
|
||||
assertEquals(methodName, pt2.getName().get(0).getFamily());
|
||||
|
||||
// http://localhost:8080/fhir/Measure/measure-EXM104-8.2.000/$evaluate-measure?periodStart=2019-01-01&periodEnd=2019-12-31
|
||||
Parameters inParams = new Parameters();
|
||||
inParams.addParameter().setName("periodStart").setValue(new StringType("2019-01-01"));
|
||||
inParams.addParameter().setName("periodEnd").setValue(new StringType("2019-12-31"));
|
||||
// Test MDM
|
||||
|
||||
Parameters outParams = ourClient
|
||||
.operation()
|
||||
.onInstance(new IdDt("Measure", measureId))
|
||||
.named("$evaluate-measure")
|
||||
.withParameters(inParams)
|
||||
.cacheControl(new CacheControlDirective().setNoCache(true))
|
||||
.withAdditionalHeader("Content-Type", "application/json")
|
||||
.useHttpGet()
|
||||
.execute();
|
||||
// Wait until the MDM message has been processed
|
||||
await().until(() -> getPatients().size(), equalTo(2));
|
||||
List<Patient> persons = getPatients();
|
||||
Patient goldenRecord = persons.get(0);
|
||||
|
||||
List<Parameters.ParametersParameterComponent> response = outParams.getParameter();
|
||||
Assert.assertTrue(!response.isEmpty());
|
||||
Parameters.ParametersParameterComponent component = response.get(0);
|
||||
Assert.assertTrue(component.getResource() instanceof MeasureReport);
|
||||
MeasureReport report = (MeasureReport) component.getResource();
|
||||
Assert.assertEquals("Measure/"+measureId, report.getMeasure());
|
||||
}
|
||||
// Verify that a golden record Patient was created
|
||||
assertNotNull(goldenRecord.getMeta().getTag("http://hapifhir.io/fhir/NamingSystem/mdm-record-status", "GOLDEN_RECORD"));
|
||||
}
|
||||
|
||||
private Bundle loadBundle(String theLocation, FhirContext theCtx, IGenericClient theClient) throws IOException {
|
||||
String json = stringFromResource(theLocation);
|
||||
Bundle bundle = (Bundle) theCtx.newJsonParser().parseResource(json);
|
||||
Bundle result = (Bundle) theClient.transaction().withBundle(bundle).execute();
|
||||
return result;
|
||||
}
|
||||
private List<Patient> getPatients() {
|
||||
Bundle bundle = ourClient.search().forResource(Patient.class).cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute();
|
||||
List<Patient> retVal = BundleUtil.toListOfResourcesOfType(ourCtx, bundle, Patient.class);
|
||||
retVal.sort(comparing(o -> ((Patient) o).getMeta().getLastUpdated()).reversed());
|
||||
return retVal;
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testCQLEXM130EvaluateMeasure() throws IOException {
|
||||
String measureId = "measure-EXM130-7.3.000";
|
||||
@Test
|
||||
@Order(1)
|
||||
public void testWebsocketSubscription() throws Exception {
|
||||
/*
|
||||
* Create subscription
|
||||
*/
|
||||
Subscription subscription = new Subscription();
|
||||
subscription.setReason("Monitor new neonatal function (note, age will be determined by the monitor)");
|
||||
subscription.setStatus(Subscription.SubscriptionStatus.REQUESTED);
|
||||
subscription.setCriteria("Observation?status=final");
|
||||
|
||||
loadBundle("r4/EXM130/EXM130-7.3.000-bundle.json", ourCtx, ourClient);
|
||||
Subscription.SubscriptionChannelComponent channel = new Subscription.SubscriptionChannelComponent();
|
||||
channel.setType(Subscription.SubscriptionChannelType.WEBSOCKET);
|
||||
channel.setPayload("application/json");
|
||||
subscription.setChannel(channel);
|
||||
|
||||
// http://localhost:8080/fhir/Measure/measure-EXM130-FHIR4-7.2.000/$evaluate-measure?periodStart=2019-01-01&periodEnd=2019-12-31
|
||||
Parameters inParams = new Parameters();
|
||||
// inParams.addParameter().setName("measure").setValue(new StringType("Measure/measure-EXM104-8.2.000"));
|
||||
// inParams.addParameter().setName("patient").setValue(new StringType("Patient/numer-EXM104-FHIR3"));
|
||||
inParams.addParameter().setName("periodStart").setValue(new StringType("2019-01-01"));
|
||||
inParams.addParameter().setName("periodEnd").setValue(new StringType("2019-12-31"));
|
||||
MethodOutcome methodOutcome = ourClient.create().resource(subscription).execute();
|
||||
IIdType mySubscriptionId = methodOutcome.getId();
|
||||
|
||||
Parameters outParams = ourClient
|
||||
.operation()
|
||||
.onInstance(new IdDt("Measure", measureId))
|
||||
.named("$evaluate-measure")
|
||||
.withParameters(inParams)
|
||||
.cacheControl(new CacheControlDirective().setNoCache(true))
|
||||
.withAdditionalHeader("Content-Type", "application/json")
|
||||
.useHttpGet()
|
||||
.execute();
|
||||
// Wait for the subscription to be activated
|
||||
await().until(() -> activeSubscriptionCount() == 3);
|
||||
|
||||
List<Parameters.ParametersParameterComponent> response = outParams.getParameter();
|
||||
Assert.assertTrue(!response.isEmpty());
|
||||
Parameters.ParametersParameterComponent component = response.get(0);
|
||||
Assert.assertTrue(component.getResource() instanceof MeasureReport);
|
||||
MeasureReport report = (MeasureReport) component.getResource();
|
||||
Assert.assertEquals("Measure/"+measureId, report.getMeasure());
|
||||
}
|
||||
/*
|
||||
* Attach websocket
|
||||
*/
|
||||
|
||||
@Test
|
||||
public void testCQLEXM349EvaluateMeasure() throws IOException {
|
||||
String measureId = "measure-EXM349-2.10.000";
|
||||
WebSocketClient myWebSocketClient = new WebSocketClient();
|
||||
SocketImplementation mySocketImplementation = new SocketImplementation(mySubscriptionId.getIdPart(), EncodingEnum.JSON);
|
||||
|
||||
loadBundle("r4/EXM349/EXM349-2.10.000-bundle.json.manuallyeditedtoremovesupplementaldata", ourCtx, ourClient);
|
||||
myWebSocketClient.start();
|
||||
URI echoUri = new URI("ws://localhost:" + port + "/websocket");
|
||||
ClientUpgradeRequest request = new ClientUpgradeRequest();
|
||||
ourLog.info("Connecting to : {}", echoUri);
|
||||
Future<Session> connection = myWebSocketClient.connect(mySocketImplementation, echoUri, request);
|
||||
Session session = connection.get(2, TimeUnit.SECONDS);
|
||||
|
||||
// http://localhost:8080/fhir/Measure/measure-EXM349-2.10.000/$evaluate-measure?periodStart=2019-01-01&periodEnd=2019-12-31
|
||||
Parameters inParams = new Parameters();
|
||||
inParams.addParameter().setName("periodStart").setValue(new StringType("2019-01-01"));
|
||||
inParams.addParameter().setName("periodEnd").setValue(new StringType("2019-12-31"));
|
||||
ourLog.info("Connected to WS: {}", session.isOpen());
|
||||
|
||||
Parameters outParams = ourClient
|
||||
.operation()
|
||||
.onInstance(new IdDt("Measure", measureId))
|
||||
.named("$evaluate-measure")
|
||||
.withParameters(inParams)
|
||||
.cacheControl(new CacheControlDirective().setNoCache(true))
|
||||
.withAdditionalHeader("Content-Type", "application/json")
|
||||
.useHttpGet()
|
||||
.execute();
|
||||
/*
|
||||
* Create a matching resource
|
||||
*/
|
||||
Observation obs = new Observation();
|
||||
obs.setStatus(Observation.ObservationStatus.FINAL);
|
||||
ourClient.create().resource(obs).execute();
|
||||
|
||||
List<Parameters.ParametersParameterComponent> response = outParams.getParameter();
|
||||
Assert.assertTrue(!response.isEmpty());
|
||||
Parameters.ParametersParameterComponent component = response.get(0);
|
||||
Assert.assertTrue(component.getResource() instanceof MeasureReport);
|
||||
MeasureReport report = (MeasureReport) component.getResource();
|
||||
Assert.assertEquals("Measure/"+measureId, report.getMeasure());
|
||||
}
|
||||
// Give some time for the subscription to deliver
|
||||
Thread.sleep(2000);
|
||||
|
||||
//@Test
|
||||
void testCreateAndRead() {
|
||||
/*
|
||||
* Ensure that we receive a ping on the websocket
|
||||
*/
|
||||
waitForSize(1, () -> mySocketImplementation.myPingCount);
|
||||
|
||||
String methodName = "testCreateResourceConditional";
|
||||
/*
|
||||
* Clean up
|
||||
*/
|
||||
ourClient.delete().resourceById(mySubscriptionId).execute();
|
||||
}
|
||||
|
||||
Patient pt = new Patient();
|
||||
pt.setActive(true);
|
||||
pt.getBirthDateElement().setValueAsString("2020-01-01");
|
||||
pt.addIdentifier().setSystem("http://foo").setValue("12345");
|
||||
pt.addName().setFamily(methodName);
|
||||
IIdType id = ourClient.create().resource(pt).execute().getId();
|
||||
private int activeSubscriptionCount() {
|
||||
return ourClient.search().forResource(Subscription.class).where(Subscription.STATUS.exactly().code("active")).cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute().getEntry().size();
|
||||
}
|
||||
|
||||
Patient pt2 = ourClient.read().resource(Patient.class).withId(id).execute();
|
||||
assertEquals(methodName, pt2.getName().get(0).getFamily());
|
||||
|
||||
// Wait until the message has been processed
|
||||
await().until(() -> getPeople().size() > 0);
|
||||
List<Person> persons = getPeople();
|
||||
@BeforeEach
|
||||
void beforeEach() {
|
||||
|
||||
// Verify a Person was created that links to our Patient
|
||||
Optional<String> personLinkToCreatedPatient = persons.stream()
|
||||
.map(Person::getLink)
|
||||
.flatMap(Collection::stream)
|
||||
.map(Person.PersonLinkComponent::getTarget)
|
||||
.map(Reference::getReference)
|
||||
.filter(pid -> id.toUnqualifiedVersionless().getValue().equals(pid))
|
||||
.findAny();
|
||||
assertTrue(personLinkToCreatedPatient.isPresent());
|
||||
}
|
||||
|
||||
private List<Person> getPeople() {
|
||||
Bundle bundle = ourClient.search().forResource(Person.class).cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute();
|
||||
return BundleUtil.toListOfResourcesOfType(ourCtx, bundle, Person.class);
|
||||
}
|
||||
|
||||
//@Test
|
||||
public void testWebsocketSubscription() throws Exception {
|
||||
/*
|
||||
* Create subscription
|
||||
*/
|
||||
Subscription subscription = new Subscription();
|
||||
subscription.setReason("Monitor new neonatal function (note, age will be determined by the monitor)");
|
||||
subscription.setStatus(Subscription.SubscriptionStatus.REQUESTED);
|
||||
subscription.setCriteria("Observation?status=final");
|
||||
|
||||
Subscription.SubscriptionChannelComponent channel = new Subscription.SubscriptionChannelComponent();
|
||||
channel.setType(Subscription.SubscriptionChannelType.WEBSOCKET);
|
||||
channel.setPayload("application/json");
|
||||
subscription.setChannel(channel);
|
||||
|
||||
MethodOutcome methodOutcome = ourClient.create().resource(subscription).execute();
|
||||
IIdType mySubscriptionId = methodOutcome.getId();
|
||||
|
||||
// Wait for the subscription to be activated
|
||||
await().until(() -> activeSubscriptionCount() == 3);
|
||||
|
||||
/*
|
||||
* Attach websocket
|
||||
*/
|
||||
|
||||
WebSocketClient myWebSocketClient = new WebSocketClient();
|
||||
SocketImplementation mySocketImplementation = new SocketImplementation(mySubscriptionId.getIdPart(), EncodingEnum.JSON);
|
||||
|
||||
myWebSocketClient.start();
|
||||
URI echoUri = new URI("ws://localhost:" + port + "/websocket");
|
||||
ClientUpgradeRequest request = new ClientUpgradeRequest();
|
||||
ourLog.info("Connecting to : {}", echoUri);
|
||||
Future<Session> connection = myWebSocketClient.connect(mySocketImplementation, echoUri, request);
|
||||
Session session = connection.get(2, TimeUnit.SECONDS);
|
||||
|
||||
ourLog.info("Connected to WS: {}", session.isOpen());
|
||||
|
||||
/*
|
||||
* Create a matching resource
|
||||
*/
|
||||
Observation obs = new Observation();
|
||||
obs.setStatus(Observation.ObservationStatus.FINAL);
|
||||
ourClient.create().resource(obs).execute();
|
||||
|
||||
// Give some time for the subscription to deliver
|
||||
Thread.sleep(2000);
|
||||
|
||||
/*
|
||||
* Ensure that we receive a ping on the websocket
|
||||
*/
|
||||
waitForSize(1, () -> mySocketImplementation.myPingCount);
|
||||
|
||||
/*
|
||||
* Clean up
|
||||
*/
|
||||
ourClient.delete().resourceById(mySubscriptionId).execute();
|
||||
}
|
||||
|
||||
private int activeSubscriptionCount() {
|
||||
return ourClient.search().forResource(Subscription.class).where(Subscription.STATUS.exactly().code("active")).cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute().getEntry().size();
|
||||
}
|
||||
ourCtx = FhirContext.forR4();
|
||||
ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
|
||||
ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
|
||||
String ourServerBase = "http://localhost:" + port + "/fhir/";
|
||||
ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
|
||||
ourClient.registerInterceptor(new LoggingInterceptor(true));
|
||||
}
|
||||
}
|
||||
|
||||
@@ -37,7 +37,8 @@ import org.springframework.test.context.junit.jupiter.SpringExtension;
|
||||
"spring.batch.job.enabled=false",
|
||||
"spring.datasource.url=jdbc:h2:mem:dbr5",
|
||||
"hapi.fhir.fhir_version=r5",
|
||||
"hapi.fhir.subscription.websocket_enabled=true"
|
||||
"hapi.fhir.subscription.websocket_enabled=true",
|
||||
"hapi.fhir.subscription.websocket_enabled=true"
|
||||
})
|
||||
public class ExampleServerR5IT {
|
||||
|
||||
|
||||
Reference in New Issue
Block a user