Personal-Twin/hapi-fhir-jpaserver-starter
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Merge remote-tracking branch 'origin/master' into do-20230731-bump-to-hapi-6-8-0

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This commit is contained in:
dotasek
2023-07-31 15:23:57 -04:00
parent aafd4fa0d9 8ef50832d3
commit bf7698bf0b
31 changed files with 213 additions and 160 deletions
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14
src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java
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@@ -5,16 +5,17 @@ import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings.ClientIdStrategyEnum;
import ca.uhn.fhir.jpa.model.entity.NormalizedQuantitySearchLevel;
import ca.uhn.fhir.rest.api.EncodingEnum;
import com.google.common.collect.ImmutableList;
import org.hl7.fhir.r4.model.Bundle;
import org.springframework.boot.context.properties.ConfigurationProperties;
import org.springframework.boot.context.properties.EnableConfigurationProperties;
import org.springframework.context.annotation.Configuration;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.Set;
@ConfigurationProperties(prefix = "hapi.fhir")
@Configuration
@@ -33,6 +34,7 @@ public class AppProperties {
private Boolean allow_multiple_delete = false;
private Boolean allow_override_default_search_params = true;
private Boolean auto_create_placeholder_reference_targets = false;
private final Set<String> auto_version_reference_at_paths = new HashSet<>();
private Boolean dao_scheduling_enabled = true;
private Boolean delete_expunge_enabled = false;
private Boolean enable_index_missing_fields = false;
@@ -85,7 +87,7 @@ public class AppProperties {
private Integer bundle_batch_pool_size = 20;
private Integer bundle_batch_pool_max_size = 100;
private final List<String> local_base_urls = new ArrayList<>();
private final Set<String> local_base_urls = new HashSet<>();
private final List<String> custom_interceptor_classes = new ArrayList<>();
@@ -307,6 +309,10 @@ public class AppProperties {
this.auto_create_placeholder_reference_targets = auto_create_placeholder_reference_targets;
}
public Set<String> getAuto_version_reference_at_paths() {
return auto_version_reference_at_paths;
}
public Integer getDefault_page_size() {
return default_page_size;
}
@@ -571,13 +577,13 @@ public class AppProperties {
this.bundle_batch_pool_max_size = bundle_batch_pool_max_size;
}
public List<String> getLocal_base_urls() {
public Set<String> getLocal_base_urls() {
return local_base_urls;
}
public static class Cors {
private Boolean allow_Credentials = true;
private List<String> allowed_origin = ImmutableList.of("*");
private List<String> allowed_origin = List.of("*");
public List<String> getAllowed_origin() {
return allowed_origin;

11
src/main/java/ca/uhn/fhir/jpa/starter/common/FhirServerConfigCommon.java
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@@ -9,7 +9,6 @@ import ca.uhn.fhir.jpa.model.config.PartitionSettings.CrossPartitionReferenceMod
import ca.uhn.fhir.jpa.model.entity.StorageSettings;
import ca.uhn.fhir.jpa.starter.AppProperties;
import ca.uhn.fhir.jpa.starter.util.JpaHibernatePropertiesProvider;
import ca.uhn.fhir.jpa.subscription.channel.subscription.SubscriptionDeliveryHandlerFactory;
import ca.uhn.fhir.jpa.subscription.match.deliver.email.EmailSenderImpl;
import ca.uhn.fhir.jpa.subscription.match.deliver.email.IEmailSender;
import ca.uhn.fhir.rest.server.mail.IMailSvc;
@@ -26,8 +25,6 @@ import org.springframework.context.annotation.Primary;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.transaction.annotation.EnableTransactionManagement;
import java.util.HashSet;
import java.util.Optional;
import java.util.stream.Collectors;
/**
@@ -49,6 +46,7 @@ public class FhirServerConfigCommon {
ourLog.info("Server configured to " + (appProperties.getExpunge_enabled() ? "enable" : "disable") + " expunges");
ourLog.info("Server configured to " + (appProperties.getAllow_override_default_search_params() ? "allow" : "deny") + " overriding default search params");
ourLog.info("Server configured to " + (appProperties.getAuto_create_placeholder_reference_targets() ? "allow" : "disable") + " auto-creating placeholder references");
ourLog.info("Server configured to auto-version references at paths {}", appProperties.getAuto_version_reference_at_paths());
if (appProperties.getSubscription().getEmail() != null) {
AppProperties.Subscription.Email email = appProperties.getSubscription().getEmail();
@@ -84,8 +82,9 @@ public class FhirServerConfigCommon {
public JpaStorageSettings jpaStorageSettings(AppProperties appProperties) {
JpaStorageSettings jpaStorageSettings = new JpaStorageSettings();
jpaStorageSettings.setIndexMissingFields(appProperties.getEnable_index_missing_fields() ? JpaStorageSettings.IndexEnabledEnum.ENABLED : JpaStorageSettings.IndexEnabledEnum.DISABLED);
jpaStorageSettings.setIndexMissingFields(appProperties.getEnable_index_missing_fields() ? StorageSettings.IndexEnabledEnum.ENABLED : StorageSettings.IndexEnabledEnum.DISABLED);
jpaStorageSettings.setAutoCreatePlaceholderReferenceTargets(appProperties.getAuto_create_placeholder_reference_targets());
jpaStorageSettings.setAutoVersionReferenceAtPaths(appProperties.getAuto_version_reference_at_paths());
jpaStorageSettings.setEnforceReferentialIntegrityOnWrite(appProperties.getEnforce_referential_integrity_on_write());
jpaStorageSettings.setEnforceReferentialIntegrityOnDelete(appProperties.getEnforce_referential_integrity_on_delete());
jpaStorageSettings.setAllowContainsSearches(appProperties.getAllow_contains_searches());
@@ -127,9 +126,9 @@ public class FhirServerConfigCommon {
jpaStorageSettings.setFilterParameterEnabled(appProperties.getFilter_search_enabled());
jpaStorageSettings.setAdvancedHSearchIndexing(appProperties.getAdvanced_lucene_indexing());
jpaStorageSettings.setTreatBaseUrlsAsLocal(new HashSet<>(appProperties.getLocal_base_urls()));
jpaStorageSettings.setTreatBaseUrlsAsLocal(appProperties.getLocal_base_urls());
if (appProperties.getLastn_enabled()) {
if (appProperties.getLastn_enabled()) {
jpaStorageSettings.setLastNEnabled(true);
}

2
src/main/java/ca/uhn/fhir/jpa/starter/common/FhirTesterConfig.java
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@@ -26,7 +26,7 @@ public class FhirTesterConfig {
* server, as well as one public server. If you are creating a project to
* deploy somewhere else, you might choose to only put your own server's
* address here.
*
* <p>
* Note the use of the ${serverBase} variable below. This will be replaced with
* the base URL as reported by the server itself. Often for a simple Tomcat
* (or other container) installation, this will end up being something

6
src/main/java/ca/uhn/fhir/jpa/starter/common/StarterJpaConfig.java
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@@ -24,7 +24,6 @@ import ca.uhn.fhir.jpa.config.util.ResourceCountCacheUtil;
import ca.uhn.fhir.jpa.config.util.ValidationSupportConfigUtil;
import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.dao.mdm.MdmLinkDaoJpaImpl;
import ca.uhn.fhir.jpa.dao.search.HSearchSortHelperImpl;
import ca.uhn.fhir.jpa.dao.search.IHSearchSortHelper;
import ca.uhn.fhir.jpa.delete.ThreadSafeResourceDeleterSvc;
@@ -44,12 +43,10 @@ import ca.uhn.fhir.jpa.starter.AppProperties;
import ca.uhn.fhir.jpa.starter.annotations.OnCorsPresent;
import ca.uhn.fhir.jpa.starter.annotations.OnImplementationGuidesPresent;
import ca.uhn.fhir.jpa.starter.common.validation.IRepositoryValidationInterceptorFactory;
import ca.uhn.fhir.jpa.starter.ips.IpsConfigCondition;
import ca.uhn.fhir.jpa.starter.util.EnvironmentHelper;
import ca.uhn.fhir.jpa.subscription.util.SubscriptionDebugLogInterceptor;
import ca.uhn.fhir.jpa.util.ResourceCountCache;
import ca.uhn.fhir.jpa.validation.JpaValidationSupportChain;
import ca.uhn.fhir.mdm.dao.IMdmLinkDao;
import ca.uhn.fhir.mdm.provider.MdmProviderLoader;
import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
import ca.uhn.fhir.narrative2.NullNarrativeGenerator;
@@ -64,7 +61,6 @@ import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import ca.uhn.fhir.validation.IValidatorModule;
import ca.uhn.fhir.validation.ResultSeverityEnum;
import com.google.common.base.Strings;
import com.google.common.collect.ImmutableList;
import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
import org.springframework.beans.factory.NoSuchBeanDefinitionException;
import org.springframework.beans.factory.annotation.Autowired;
@@ -205,7 +201,7 @@ public class StarterJpaConfig {
packageInstallationSpec.setReloadExisting(appProperties.getReload_existing_implementationguides());
if (appProperties.getInstall_transitive_ig_dependencies()) {
packageInstallationSpec.setFetchDependencies(true);
packageInstallationSpec.setDependencyExcludes(ImmutableList.of("hl7.fhir.r2.core", "hl7.fhir.r3.core", "hl7.fhir.r4.core", "hl7.fhir.r5.core"));
packageInstallationSpec.setDependencyExcludes(List.of("hl7.fhir.r2.core", "hl7.fhir.r3.core", "hl7.fhir.r4.core", "hl7.fhir.r5.core"));
}
packageInstallerSvc.install(packageInstallationSpec);
}

4
src/main/java/ca/uhn/fhir/jpa/starter/common/validation/RepositoryValidationInterceptorFactoryDstu3.java
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@@ -47,12 +47,12 @@ public class RepositoryValidationInterceptorFactoryDstu3 implements IRepositoryV
public RepositoryValidatingInterceptor buildUsingStoredStructureDefinitions() {
IBundleProvider results = structureDefinitionResourceProvider.search(new SearchParameterMap().add(StructureDefinition.SP_KIND, new TokenParam("resource")));
Map<String, List<StructureDefinition>> structureDefintions = results.getResources(0, results.size())
Map<String, List<StructureDefinition>> structureDefinitions = results.getResources(0, results.size())
.stream()
.map(StructureDefinition.class::cast)
.collect(Collectors.groupingBy(StructureDefinition::getType));
structureDefintions.forEach((key, value) -> {
structureDefinitions.forEach((key, value) -> {
String[] urls = value.stream().map(StructureDefinition::getUrl).toArray(String[]::new);
repositoryValidatingRuleBuilder.forResourcesOfType(key).requireAtLeastOneProfileOf(urls).and().requireValidationToDeclaredProfiles();
});

6
src/main/java/ca/uhn/fhir/jpa/starter/ips/StarterIpsConfig.java
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@@ -15,18 +15,18 @@ import ca.uhn.fhir.jpa.ips.generator.IpsGeneratorSvcImpl;
@Conditional(IpsConfigCondition.class)
public class StarterIpsConfig {
@Bean
IIpsGenerationStrategy IpsGenerationStrategy()
IIpsGenerationStrategy ipsGenerationStrategy()
{
return new DefaultIpsGenerationStrategy();
}
@Bean
public IpsOperationProvider IpsOperationProvider(IIpsGeneratorSvc theIpsGeneratorSvc){
public IpsOperationProvider ipsOperationProvider(IIpsGeneratorSvc theIpsGeneratorSvc){
return new IpsOperationProvider(theIpsGeneratorSvc);
}
@Bean
public IIpsGeneratorSvc IpsGeneratorSvcImpl(FhirContext theFhirContext, IIpsGenerationStrategy theGenerationStrategy, DaoRegistry theDaoRegistry)
public IIpsGeneratorSvc ipsGeneratorSvcImpl(FhirContext theFhirContext, IIpsGenerationStrategy theGenerationStrategy, DaoRegistry theDaoRegistry)
{
return new IpsGeneratorSvcImpl(theFhirContext, theGenerationStrategy, theDaoRegistry);
}

4
src/main/java/ca/uhn/fhir/jpa/starter/mdm/MdmConfig.java
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@@ -6,7 +6,6 @@ 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 com.google.common.base.Charsets;
import org.apache.commons.io.IOUtils;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
@@ -17,6 +16,7 @@ import org.springframework.core.io.DefaultResourceLoader;
import org.springframework.core.io.Resource;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
@Configuration
@Conditional(MdmConfigCondition.class)
@@ -27,7 +27,7 @@ public class MdmConfig {
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);
String json = IOUtils.toString(resource.getInputStream(), StandardCharsets.UTF_8);
return new MdmSettings(theMdmRuleValidator).setEnabled(appProperties.getMdm_enabled()).setScriptText(json);
}
}

1
src/main/java/ca/uhn/fhir/jpa/starter/util/EnvironmentHelper.java
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@@ -17,7 +17,6 @@ import org.hibernate.search.mapper.orm.cfg.HibernateOrmMapperSettings;
import org.hibernate.search.mapper.orm.schema.management.SchemaManagementStrategyName;
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
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;