Merge pull request #51 from hapifhir/allowedBundleTypes

Allowed bundle types

.editorconfig

@@ -0,0 +1,5 @@
+[*.java]
+charset = utf-8
+indent_style = space
+indent_size = 2
+

.gitignore

@@ -1,7 +1,6 @@
-target/
-.idea/
-*.iml
 *.orig
+target/
+*.iml
 
 # Compiled class file
 *.class
@@ -26,3 +25,136 @@ target/
 
 # virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
 hs_err_pid*
+### Windows template
+# Windows thumbnail cache files
+Thumbs.db
+Thumbs.db:encryptable
+ehthumbs.db
+ehthumbs_vista.db
+
+# Dump file
+*.stackdump
+
+# Folder config file
+[Dd]esktop.ini
+
+# Recycle Bin used on file shares
+$RECYCLE.BIN/
+
+# Windows Installer files
+*.cab
+*.msi
+*.msix
+*.msm
+*.msp
+
+# Windows shortcuts
+*.lnk
+
+### JetBrains template
+# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio and WebStorm
+# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
+.idea/
+
+# CMake
+cmake-build-*/
+
+# File-based project format
+*.iws
+
+# IntelliJ
+out/
+
+# JIRA plugin
+atlassian-ide-plugin.xml
+
+# Crashlytics plugin (for Android Studio and IntelliJ)
+com_crashlytics_export_strings.xml
+crashlytics.properties
+crashlytics-build.properties
+fabric.properties
+
+### Eclipse template
+.metadata
+bin/
+tmp/
+*.tmp
+*.bak
+*.swp
+*~.nib
+local.properties
+.settings/
+.loadpath
+.recommenders
+
+# External tool builders
+.externalToolBuilders/
+
+# Locally stored "Eclipse launch configurations"
+*.launch
+
+# PyDev specific (Python IDE for Eclipse)
+*.pydevproject
+
+# CDT-specific (C/C++ Development Tooling)
+.cproject
+
+# CDT- autotools
+.autotools
+
+# Java annotation processor (APT)
+.factorypath
+
+# PDT-specific (PHP Development Tools)
+.buildpath
+
+# sbteclipse plugin
+.target
+
+# Tern plugin
+.tern-project
+
+# TeXlipse plugin
+.texlipse
+
+# STS (Spring Tool Suite)
+.springBeans
+
+# Code Recommenders
+.recommenders/
+
+# Annotation Processing
+.apt_generated/
+
+# Scala IDE specific (Scala & Java development for Eclipse)
+.cache-main
+.scala_dependencies
+.worksheet
+
+### macOS template
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk

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

@@ -45,6 +45,7 @@ public class HapiProperties {
     static final String SUBSCRIPTION_EMAIL_ENABLED = "subscription.email.enabled";
     static final String SUBSCRIPTION_RESTHOOK_ENABLED = "subscription.resthook.enabled";
     static final String SUBSCRIPTION_WEBSOCKET_ENABLED = "subscription.websocket.enabled";
+    static final String ALLOWED_BUNDLE_TYPES = "allowed_bundle_types";
     static final String TEST_PORT = "test.port";
     static final String TESTER_CONFIG_REFUSE_TO_FETCH_THIRD_PARTY_URLS = "tester.config.refuse_to_fetch_third_party_urls";
     static final String CORS_ENABLED = "cors.enabled";
@@ -286,6 +287,10 @@ public class HapiProperties {
         return HapiProperties.getProperty(CORS_ALLOWED_ORIGIN, "*");
     }
 
+    public static  String getAllowedBundleTypes() {
+        return HapiProperties.getProperty(ALLOWED_BUNDLE_TYPES, "");
+    }
+
     public static Set<String> getSupportedResourceTypes() {
         String[] types = defaultString(getProperty("supported_resource_types")).split(",");
         return Arrays.stream(types)

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

@@ -27,7 +27,10 @@ import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.rest.server.interceptor.*;
 import ca.uhn.fhir.validation.IValidatorModule;
 import ca.uhn.fhir.validation.ResultSeverityEnum;
+import java.util.HashSet;
+import java.util.TreeSet;
 import org.hl7.fhir.dstu3.model.Bundle;
+import org.hl7.fhir.r4.model.Bundle.BundleType;
 import org.hl7.fhir.dstu3.model.Meta;
 import org.springframework.context.ApplicationContext;
 import org.springframework.http.HttpHeaders;
@@ -51,7 +54,8 @@ public class JpaRestfulServer extends RestfulServer {
      * Create a FhirContext object that uses the version of FHIR
      * specified in the properties file.
      */
-        ApplicationContext appCtx = (ApplicationContext) getServletContext().getAttribute("org.springframework.web.context.WebApplicationContext.ROOT");
+    ApplicationContext appCtx = (ApplicationContext) getServletContext()
+        .getAttribute("org.springframework.web.context.WebApplicationContext.ROOT");
     // Customize supported resource types
     Set<String> supportedResourceTypes = HapiProperties.getSupportedResourceTypes();
     if (!supportedResourceTypes.isEmpty()) {
@@ -95,23 +99,31 @@ public class JpaRestfulServer extends RestfulServer {
      * provide further customization of your server's CapabilityStatement
      */
     if (fhirVersion == FhirVersionEnum.DSTU2) {
-            IFhirSystemDao<ca.uhn.fhir.model.dstu2.resource.Bundle, MetaDt> systemDao = appCtx.getBean("mySystemDaoDstu2", IFhirSystemDao.class);
-            JpaConformanceProviderDstu2 confProvider = new JpaConformanceProviderDstu2(this, systemDao, appCtx.getBean(DaoConfig.class));
+      IFhirSystemDao<ca.uhn.fhir.model.dstu2.resource.Bundle, MetaDt> systemDao = appCtx
+          .getBean("mySystemDaoDstu2", IFhirSystemDao.class);
+      JpaConformanceProviderDstu2 confProvider = new JpaConformanceProviderDstu2(this, systemDao,
+          appCtx.getBean(DaoConfig.class));
       confProvider.setImplementationDescription("HAPI FHIR DSTU2 Server");
       setServerConformanceProvider(confProvider);
     } else if (fhirVersion == FhirVersionEnum.DSTU3) {
-            IFhirSystemDao<Bundle, Meta> systemDao = appCtx.getBean("mySystemDaoDstu3", IFhirSystemDao.class);
-            JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(this, systemDao, appCtx.getBean(DaoConfig.class));
+      IFhirSystemDao<Bundle, Meta> systemDao = appCtx
+          .getBean("mySystemDaoDstu3", IFhirSystemDao.class);
+      JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(this, systemDao,
+          appCtx.getBean(DaoConfig.class));
       confProvider.setImplementationDescription("HAPI FHIR DSTU3 Server");
       setServerConformanceProvider(confProvider);
     } else if (fhirVersion == FhirVersionEnum.R4) {
-            IFhirSystemDao<org.hl7.fhir.r4.model.Bundle, org.hl7.fhir.r4.model.Meta> systemDao = appCtx.getBean("mySystemDaoR4", IFhirSystemDao.class);
-            JpaConformanceProviderR4 confProvider = new JpaConformanceProviderR4(this, systemDao, appCtx.getBean(DaoConfig.class));
+      IFhirSystemDao<org.hl7.fhir.r4.model.Bundle, org.hl7.fhir.r4.model.Meta> systemDao = appCtx
+          .getBean("mySystemDaoR4", IFhirSystemDao.class);
+      JpaConformanceProviderR4 confProvider = new JpaConformanceProviderR4(this, systemDao,
+          appCtx.getBean(DaoConfig.class));
       confProvider.setImplementationDescription("HAPI FHIR R4 Server");
       setServerConformanceProvider(confProvider);
     } else if (fhirVersion == FhirVersionEnum.R5) {
-            IFhirSystemDao<org.hl7.fhir.r5.model.Bundle, org.hl7.fhir.r5.model.Meta> systemDao = appCtx.getBean("mySystemDaoR5", IFhirSystemDao.class);
-            JpaConformanceProviderR5 confProvider = new JpaConformanceProviderR5(this, systemDao, appCtx.getBean(DaoConfig.class));
+      IFhirSystemDao<org.hl7.fhir.r5.model.Bundle, org.hl7.fhir.r5.model.Meta> systemDao = appCtx
+          .getBean("mySystemDaoR5", IFhirSystemDao.class);
+      JpaConformanceProviderR5 confProvider = new JpaConformanceProviderR5(this, systemDao,
+          appCtx.getBean(DaoConfig.class));
       confProvider.setImplementationDescription("HAPI FHIR R5 Server");
       setServerConformanceProvider(confProvider);
     } else {
@@ -191,7 +203,8 @@ public class JpaRestfulServer extends RestfulServer {
     // If you want to enable the $trigger-subscription operation to allow
     // manual triggering of a subscription delivery, enable this provider
     if (false) { // <-- DISABLED RIGHT NOW
-            SubscriptionTriggeringProvider retriggeringProvider = appCtx.getBean(SubscriptionTriggeringProvider.class);
+      SubscriptionTriggeringProvider retriggeringProvider = appCtx
+          .getBean(SubscriptionTriggeringProvider.class);
       registerProvider(retriggeringProvider);
     }
 
@@ -232,7 +245,8 @@ public class JpaRestfulServer extends RestfulServer {
         HapiProperties.getSubscriptionRestHookEnabled()) {
       // Loads subscription interceptors (SubscriptionActivatingInterceptor, SubscriptionMatcherInterceptor)
       // with activation of scheduled subscription
-            SubscriptionInterceptorLoader subscriptionInterceptorLoader = appCtx.getBean(SubscriptionInterceptorLoader.class);
+      SubscriptionInterceptorLoader subscriptionInterceptorLoader = appCtx
+          .getBean(SubscriptionInterceptorLoader.class);
       subscriptionInterceptorLoader.registerInterceptors();
 
       // Subscription debug logging
@@ -244,13 +258,15 @@ public class JpaRestfulServer extends RestfulServer {
     DaoRegistry daoRegistry = appCtx.getBean(DaoRegistry.class);
     IInterceptorBroadcaster interceptorBroadcaster = appCtx.getBean(IInterceptorBroadcaster.class);
     if (HapiProperties.getAllowCascadingDeletes()) {
-            CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(daoRegistry, interceptorBroadcaster);
+      CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(
+          daoRegistry, interceptorBroadcaster);
       getInterceptorService().registerInterceptor(cascadingDeleteInterceptor);
     }
 
     // Binary Storage
     if (HapiProperties.isBinaryStorageEnabled()) {
-            BinaryStorageInterceptor binaryStorageInterceptor = appCtx.getBean(BinaryStorageInterceptor.class);
+      BinaryStorageInterceptor binaryStorageInterceptor = appCtx
+          .getBean(BinaryStorageInterceptor.class);
       getInterceptorService().registerInterceptor(binaryStorageInterceptor);
     }
 
@@ -292,6 +308,16 @@ public class JpaRestfulServer extends RestfulServer {
       }
     }
 
+    if (!HapiProperties.getAllowedBundleTypes().isEmpty()) {
+      String allowedBundleTypesString = HapiProperties.getAllowedBundleTypes();
+      Set<String> allowedBundleTypes = new HashSet<>();
+      Arrays.stream(allowedBundleTypesString.split(",")).forEach(o -> {
+        BundleType type = BundleType.valueOf(o);
+        allowedBundleTypes.add(type.toCode());
+      });
+      DaoConfig config = appCtx.getBean(DaoConfig.class);
+      config.setBundleTypesAllowedForStorage(
+          Collections.unmodifiableSet(new TreeSet<>(allowedBundleTypes)));
+    }
   }
-
 }

src/main/resources/hapi.properties

@@ -92,6 +92,11 @@ cors.allowCredentials=true
 # cors.allowed_origin=http://localhost:8080,https://localhost:8080,https://fhirtest.uhn.ca
 cors.allow_origin=*
 
+##################################################
+# Allowed Bundle Types for persistence (defaults are: COLLECTION,DOCUMENT,MESSAGE)
+##################################################
+#allowed_bundle_types=COLLECTION,DOCUMENT,MESSAGE,TRANSACTION,TRANSACTIONRESPONSE,BATCH,BATCHRESPONSE,HISTORY,SEARCHSET
+
 ##################################################
 # Subscriptions
 ##################################################