Merge branch 'master' into cr-6.9.6-snapshot

.github/workflows/maven.yml

@@ -20,10 +20,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up JDK 17
-      uses: actions/setup-java@v1
+      uses: actions/setup-java@v3
       with:
         java-version: 17
+        distribution: zulu
     - name: Build with Maven
       run: mvn -B package --file pom.xml verify

.github/workflows/smoke-tests.yml

@@ -21,11 +21,12 @@ jobs:
 
     steps:
     - name: Checkout project
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
     - name: Set up JDK 17
-      uses: actions/setup-java@v1
+      uses: actions/setup-java@v3
       with:
         java-version: 17
+        distribution: zulu
     - name: Build with Maven
       run: mvn -B package --file pom.xml -Dmaven.test.skip=true
     - name: Docker Pull HTTP client

README.md

@@ -515,6 +515,32 @@ To add a custom operation, refer to the documentation in the core hapi-fhir libr
 
 Within `hapi-fhir-jpaserver-starter`, create a generic class (that does not extend or implement any classes or interfaces), add the `@Operation` as a method within the generic class, and then register the class as a provider using `RestfulServer.registerProvider()`.
 
+## Runtime package install
+
+It's possible to install a FHIR Implementation Guide package (`package.tgz`) either from a published package or from a local package with the `$install` operation, without having to restart the server. This is available for R4 and R5.
+
+This feature must be enabled in the application.yaml (or docker command line):
+
+```yaml
+hapi:
+  fhir:
+    ig_runtime_upload_enabled: true
+```
+
+The `$install` operation is triggered with a POST to `[server]/ImplementationGuide/$install`, with the payload below:
+
+```json
+{
+  "resourceType": "Parameters",
+  "parameter": [
+    {
+      "name": "npmContent",
+      "valueBase64Binary": "[BASE64_ENCODED_NPM_PACKAGE_DATA]"
+    }
+  ]
+}
+```
+
 ## Enable OpenTelemetry auto-instrumentation
 
 The container image includes the [OpenTelemetry Java auto-instrumentation](https://github.com/open-telemetry/opentelemetry-java-instrumentation)

src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java

@@ -76,6 +76,18 @@ public class AppProperties {
 	private Boolean reload_existing_implementationguides = false;
 	private Map<String, PackageInstallationSpec> implementationGuides = null;
 	private Boolean cr_enabled = false;
+
+  private Boolean ig_runtime_upload_enabled = false;
+
+  private Validation validation = new Validation();
+  private Map<String, Tester> tester = null;
+  private Logger logger = new Logger();
+  private Subscription subscription = new Subscription();
+  private Cors cors = null;
+  private Partitioning partitioning = null;
+  private Boolean install_transitive_ig_dependencies = true;
+  private Map<String, PackageInstallationSpec> implementationGuides = null;
+
 	private String staticLocation = null;
 	private String staticLocationPrefix = "/static";
 	private Boolean lastn_enabled = false;
@@ -579,6 +591,14 @@ public class AppProperties {
 		return local_base_urls;
 	}
 
+	public Boolean getIg_runtime_upload_enabled() {
+		return ig_runtime_upload_enabled;
+	}
+
+	public void setIg_runtime_upload_enabled(Boolean ig_runtime_upload_enabled) {
+		this.ig_runtime_upload_enabled = ig_runtime_upload_enabled;
+	}
+
 	public static class Cors {
 		private Boolean allow_Credentials = true;
 		private List<String> allowed_origin = List.of("*");

src/main/java/ca/uhn/fhir/jpa/starter/common/StarterJpaConfig.java

@@ -44,6 +44,7 @@ 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.util.EnvironmentHelper;
+import ca.uhn.fhir.jpa.starter.ig.IImplementationGuideOperationProvider;
 import ca.uhn.fhir.jpa.subscription.util.SubscriptionDebugLogInterceptor;
 import ca.uhn.fhir.jpa.util.ResourceCountCache;
 import ca.uhn.fhir.jpa.validation.JpaValidationSupportChain;
@@ -241,7 +242,7 @@ public class StarterJpaConfig {
 	}
 
 	@Bean
-	public RestfulServer restfulServer(IFhirSystemDao<?, ?> fhirSystemDao, AppProperties appProperties, DaoRegistry daoRegistry, Optional<MdmProviderLoader> mdmProviderProvider, IJpaSystemProvider jpaSystemProvider, ResourceProviderFactory resourceProviderFactory, JpaStorageSettings jpaStorageSettings, ISearchParamRegistry searchParamRegistry, IValidationSupport theValidationSupport, DatabaseBackedPagingProvider databaseBackedPagingProvider, LoggingInterceptor loggingInterceptor, Optional<TerminologyUploaderProvider> terminologyUploaderProvider, Optional<SubscriptionTriggeringProvider> subscriptionTriggeringProvider, Optional<CorsInterceptor> corsInterceptor, IInterceptorBroadcaster interceptorBroadcaster, Optional<BinaryAccessProvider> binaryAccessProvider, BinaryStorageInterceptor binaryStorageInterceptor, IValidatorModule validatorModule, Optional<GraphQLProvider> graphQLProvider, BulkDataExportProvider bulkDataExportProvider, BulkDataImportProvider bulkDataImportProvider, ValueSetOperationProvider theValueSetOperationProvider, ReindexProvider reindexProvider, PartitionManagementProvider partitionManagementProvider, Optional<RepositoryValidatingInterceptor> repositoryValidatingInterceptor, IPackageInstallerSvc packageInstallerSvc, ThreadSafeResourceDeleterSvc theThreadSafeResourceDeleterSvc, ApplicationContext appContext, Optional<IpsOperationProvider> theIpsOperationProvider) {
+	public RestfulServer restfulServer(IFhirSystemDao<?, ?> fhirSystemDao, AppProperties appProperties, DaoRegistry daoRegistry, Optional<MdmProviderLoader> mdmProviderProvider, IJpaSystemProvider jpaSystemProvider, ResourceProviderFactory resourceProviderFactory, JpaStorageSettings jpaStorageSettings, ISearchParamRegistry searchParamRegistry, IValidationSupport theValidationSupport, DatabaseBackedPagingProvider databaseBackedPagingProvider, LoggingInterceptor loggingInterceptor, Optional<TerminologyUploaderProvider> terminologyUploaderProvider, Optional<SubscriptionTriggeringProvider> subscriptionTriggeringProvider, Optional<CorsInterceptor> corsInterceptor, IInterceptorBroadcaster interceptorBroadcaster, Optional<BinaryAccessProvider> binaryAccessProvider, BinaryStorageInterceptor binaryStorageInterceptor, IValidatorModule validatorModule, Optional<GraphQLProvider> graphQLProvider, BulkDataExportProvider bulkDataExportProvider, BulkDataImportProvider bulkDataImportProvider, ValueSetOperationProvider theValueSetOperationProvider, ReindexProvider reindexProvider, PartitionManagementProvider partitionManagementProvider, Optional<RepositoryValidatingInterceptor> repositoryValidatingInterceptor, IPackageInstallerSvc packageInstallerSvc, ThreadSafeResourceDeleterSvc theThreadSafeResourceDeleterSvc, ApplicationContext appContext, Optional<IpsOperationProvider> theIpsOperationProvider, Optional<IImplementationGuideOperationProvider> implementationGuideOperationProvider) {
 		RestfulServer fhirServer = new RestfulServer(fhirSystemDao.getContext());
 
 		List<String> supportedResourceTypes = appProperties.getSupported_resource_types();
@@ -304,6 +305,8 @@ public class StarterJpaConfig {
 
 		fhirServer.registerInterceptor(loggingInterceptor);
 
+		implementationGuideOperationProvider.ifPresent(fhirServer::registerProvider);
+
 		/*
 		 * If you are hosting this server at a specific DNS name, the server will try to
 		 * figure out the FHIR base URL based on what the web container tells it, but

src/main/java/ca/uhn/fhir/jpa/starter/ig/IImplementationGuideOperationProvider.java

@@ -0,0 +1,18 @@
+package ca.uhn.fhir.jpa.starter.ig;
+
+import ca.uhn.fhir.jpa.packages.PackageInstallationSpec;
+import org.hl7.fhir.utilities.npm.NpmPackage;
+
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+
+public interface IImplementationGuideOperationProvider {
+	static PackageInstallationSpec toPackageInstallationSpec(byte[] npmPackageAsByteArray) throws IOException {
+		NpmPackage npmPackage = NpmPackage.fromPackage(new ByteArrayInputStream(npmPackageAsByteArray));
+		return new PackageInstallationSpec().setName(npmPackage.name()).setPackageContents(npmPackageAsByteArray).setVersion(npmPackage.version()).setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL).setFetchDependencies(false);
+	}
+
+	//The following declaration is the one that counts but cannot be used across different versions as stating Base64BinaryType would bind to a separate version
+	//@Operation(name = "$install", typeName = "ImplementationGuide")
+	//Parameters install(@OperationParam(name = "npmContent",min = 1, max = 1) Base64BinaryType implementationGuide);
+}

src/main/java/ca/uhn/fhir/jpa/starter/ig/IgConfigCondition.java

@@ -0,0 +1,14 @@
+package ca.uhn.fhir.jpa.starter.ig;
+
+import org.springframework.context.annotation.Condition;
+import org.springframework.context.annotation.ConditionContext;
+import org.springframework.core.type.AnnotatedTypeMetadata;
+
+public class IgConfigCondition implements Condition {
+
+	@Override
+	public boolean matches(ConditionContext theConditionContext, AnnotatedTypeMetadata theAnnotatedTypeMetadata) {
+		String property = theConditionContext.getEnvironment().getProperty("hapi.fhir.ig_runtime_upload_enabled");
+		return Boolean.parseBoolean(property);
+	}
+}

src/main/java/ca/uhn/fhir/jpa/starter/ig/ImplementationGuideR4OperationProvider.java

@@ -0,0 +1,35 @@
+package ca.uhn.fhir.jpa.starter.ig;
+
+import ca.uhn.fhir.jpa.packages.IPackageInstallerSvc;
+import ca.uhn.fhir.jpa.starter.annotations.OnR4Condition;
+import ca.uhn.fhir.rest.annotation.Operation;
+import ca.uhn.fhir.rest.annotation.OperationParam;
+import org.hl7.fhir.r4.model.Base64BinaryType;
+import org.hl7.fhir.r4.model.Parameters;
+import org.springframework.context.annotation.Conditional;
+import org.springframework.stereotype.Service;
+
+import java.io.IOException;
+
+@Conditional({OnR4Condition.class, IgConfigCondition.class})
+@Service
+public class ImplementationGuideR4OperationProvider implements IImplementationGuideOperationProvider {
+
+	IPackageInstallerSvc packageInstallerSvc;
+
+	public ImplementationGuideR4OperationProvider(IPackageInstallerSvc packageInstallerSvc) {
+		this.packageInstallerSvc = packageInstallerSvc;
+	}
+
+	@Operation(name = "$install", typeName = "ImplementationGuide")
+	public Parameters install(@OperationParam(name = "npmContent", min = 1, max = 1) Base64BinaryType implementationGuide) {
+		try {
+
+			packageInstallerSvc.install(IImplementationGuideOperationProvider.toPackageInstallationSpec(implementationGuide.getValue()));
+		} catch (IOException e) {
+			throw new RuntimeException(e);
+		}
+		return new Parameters();
+	}
+
+}

src/main/java/ca/uhn/fhir/jpa/starter/ig/ImplementationGuideR5OperationProvider.java

@@ -0,0 +1,36 @@
+package ca.uhn.fhir.jpa.starter.ig;
+
+import ca.uhn.fhir.jpa.packages.IPackageInstallerSvc;
+import ca.uhn.fhir.jpa.starter.annotations.OnR5Condition;
+import ca.uhn.fhir.rest.annotation.Operation;
+import ca.uhn.fhir.rest.annotation.OperationParam;
+import org.hl7.fhir.r5.model.Base64BinaryType;
+import org.hl7.fhir.r5.model.Parameters;
+import org.springframework.context.annotation.Conditional;
+import org.springframework.stereotype.Service;
+
+import java.io.IOException;
+
+@Conditional({OnR5Condition.class, IgConfigCondition.class})
+@Service
+public class ImplementationGuideR5OperationProvider {
+
+	IPackageInstallerSvc packageInstallerSvc;
+
+	public ImplementationGuideR5OperationProvider(IPackageInstallerSvc packageInstallerSvc) {
+		this.packageInstallerSvc = packageInstallerSvc;
+	}
+
+	@Operation(name = "$install", typeName = "ImplementationGuide")
+	public Parameters install(@OperationParam(name = "npmContent", min = 1, max = 1) Base64BinaryType implementationGuide) {
+		try {
+
+			packageInstallerSvc.install(IImplementationGuideOperationProvider.toPackageInstallationSpec(implementationGuide.getValue()));
+		} catch (IOException e) {
+			throw new RuntimeException(e);
+		}
+		return new Parameters();
+	}
+
+
+}

src/main/resources/application.yaml

@@ -56,7 +56,7 @@ hapi:
     ### This flag when enabled to true, will avail evaluate measure operations from CR Module.
     ### Flag is false by default, can be passed as command line argument to override.
     cr:
-      enabled: true
+      enabled: false
 
     cdshooks:
       enabled: true
@@ -66,6 +66,9 @@ hapi:
     openapi_enabled: true
     ### This is the FHIR version. Choose between, DSTU2, DSTU3, R4 or R5
     fhir_version: R4
+    ### Flag is false by default. This flag enables runtime installation of IG's.
+    ig_runtime_upload_enabled: false
+    ### This flag when enabled to true, will avail evaluate measure operations from CR Module.
 
     ### enable to use the ApacheProxyAddressStrategy which uses X-Forwarded-* headers
     ### to determine the FHIR server address