0.7.7

pom.xml

@@ -8,15 +8,15 @@
 
   <groupId>de.difuture.uds</groupId>
   <artifactId>odm2fhir</artifactId>
-  <version>0.7.6</version>
+  <version>0.7.7</version>
 
   <name>ODM2FHIR</name>
   <description>Mapper for GECCO based study/patient data in CDISC ODM to HL7 FHIR</description>
 
   <parent>
     <groupId>org.springframework.boot</groupId>
     <artifactId>spring-boot-starter-parent</artifactId>
-    <version>2.6.4</version>
+    <version>2.6.6</version>
   </parent>
 
   <properties>
@@ -25,18 +25,17 @@
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
 
-    <hapi-fhir.version>5.7.0</hapi-fhir.version>
+    <hapi-fhir.version>5.7.2</hapi-fhir.version>
     <jackson.version>2.13.2</jackson.version>
-    <kafka-fhir-serializer.version>1.0.2</kafka-fhir-serializer.version>
     <lombok.version>1.18.22</lombok.version>
     <spring-boot.version>${project.parent.version}</spring-boot.version>
     <spring-retry.version>1.3.2</spring-retry.version>
     <woodstox.version>6.2.8</woodstox.version>
 
     <maven-antrun-plugin.version>3.0.0</maven-antrun-plugin.version>
-    <maven-compiler-plugin.version>3.9.0</maven-compiler-plugin.version>
-    <maven-project-info-reports-plugin.version>3.1.2</maven-project-info-reports-plugin.version>
-    <maven-site-plugin.version>3.10.0</maven-site-plugin.version>
+    <maven-compiler-plugin.version>3.10.1</maven-compiler-plugin.version>
+    <maven-project-info-reports-plugin.version>3.2.2</maven-project-info-reports-plugin.version>
+    <maven-site-plugin.version>3.11.0</maven-site-plugin.version>
   </properties>
 
   <dependencies>

src/main/java/de/difuture/uds/odm2fhir/fhir/writer/FHIRBundleWriter.java

@@ -18,7 +18,6 @@
  * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.parser.StrictErrorHandler;
 
@@ -30,15 +29,16 @@
 import java.util.concurrent.atomic.AtomicInteger;
 import javax.annotation.PostConstruct;
 
+import static ca.uhn.fhir.context.FhirContext.forR4Cached;
+
 import static de.difuture.uds.odm2fhir.util.HTTPHelper.HTTP_CLIENT;
 
 public abstract class FHIRBundleWriter {
 
   @Value("${fhir.errorhandling.strict:false}")
   protected boolean errorhandlingStrict;
 
-  protected static final FhirContext FHIR_CONTEXT = FhirContext.forR4();
-  protected static final IParser JSON_PARSER = FHIR_CONTEXT.newJsonParser().setPrettyPrint(true);
+  protected static final IParser JSON_PARSER = forR4Cached().newJsonParser().setPrettyPrint(true);
 
   public static final AtomicInteger RESOURCES_NUMBER = new AtomicInteger();
   public static final AtomicInteger BUNDLES_NUMBER = new AtomicInteger();
@@ -50,7 +50,7 @@ private void init() {
     if (errorhandlingStrict) {
       JSON_PARSER.setParserErrorHandler(new StrictErrorHandler());
     }
-    FHIR_CONTEXT.getRestfulClientFactory().setHttpClient(HTTP_CLIENT);
+    forR4Cached().getRestfulClientFactory().setHttpClient(HTTP_CLIENT);
   }
 
 }

src/main/java/de/difuture/uds/odm2fhir/fhir/writer/FHIRBundler.java

@@ -58,6 +58,7 @@
 import javax.annotation.Nullable;
 import javax.annotation.PostConstruct;
 
+import static ca.uhn.fhir.context.FhirContext.forR4Cached;
 import static ca.uhn.fhir.validation.ResultSeverityEnum.ERROR;
 import static ca.uhn.fhir.validation.ResultSeverityEnum.WARNING;
 
@@ -66,7 +67,6 @@
 import static de.difuture.uds.odm2fhir.fhir.util.CommonCodeSystem.SNOMED_CT;
 import static de.difuture.uds.odm2fhir.fhir.util.IdentifierHelper.getIdentifierSystem;
 import static de.difuture.uds.odm2fhir.fhir.util.NUMStructureDefinition.GECCO_BUNDLE;
-import static de.difuture.uds.odm2fhir.fhir.writer.FHIRBundleWriter.FHIR_CONTEXT;
 import static de.difuture.uds.odm2fhir.fhir.writer.FHIRBundleWriter.JSON_PARSER;
 import static de.difuture.uds.odm2fhir.util.HTTPHelper.createAuthInterceptor;
 
@@ -132,7 +132,7 @@ private void init() throws IOException {
       Locale.setDefault(ENGLISH);
 
       @SuppressWarnings("unchecked")
-      var prePopulatedValidationSupport = new PrePopulatedValidationSupport(FHIR_CONTEXT) {
+      var prePopulatedValidationSupport = new PrePopulatedValidationSupport(forR4Cached()) {
         @Override
         public ValueSetExpansionOutcome expandValueSet(ValidationSupportContext validationSupportContext,
                                                        @Nullable ValueSetExpansionOptions valueSetExpansionOptions,
@@ -150,27 +150,27 @@ public ValueSetExpansionOutcome expandValueSet(ValidationSupportContext validati
           .map(JSON_PARSER::parseResource)
           .forEach(prePopulatedValidationSupport::addResource);
 
-      var unknownCodeSystemWarningValidationSupport = new UnknownCodeSystemWarningValidationSupport(FHIR_CONTEXT);
+      var unknownCodeSystemWarningValidationSupport = new UnknownCodeSystemWarningValidationSupport(forR4Cached());
       unknownCodeSystemWarningValidationSupport.setNonExistentCodeSystemSeverity(IssueSeverity.WARNING);
 
       var validationSupportChain = new ValidationSupportChain(
-          new DefaultProfileValidationSupport(FHIR_CONTEXT),
-          new CommonCodeSystemsTerminologyService(FHIR_CONTEXT),
-          new InMemoryTerminologyServerValidationSupport(FHIR_CONTEXT),
+          new DefaultProfileValidationSupport(forR4Cached()),
+          new CommonCodeSystemsTerminologyService(forR4Cached()),
+          new InMemoryTerminologyServerValidationSupport(forR4Cached()),
           unknownCodeSystemWarningValidationSupport,
-          new SnapshotGeneratingValidationSupport(FHIR_CONTEXT),
+          new SnapshotGeneratingValidationSupport(forR4Cached()),
           prePopulatedValidationSupport);
 
       if (terminologyserverUrl.isAbsolute()) {
-        var remoteTerminologyServiceValidationSupport = new RemoteTerminologyServiceValidationSupport(FHIR_CONTEXT);
+        var remoteTerminologyServiceValidationSupport = new RemoteTerminologyServiceValidationSupport(forR4Cached());
         remoteTerminologyServiceValidationSupport.setBaseUrl(terminologyserverUrl.toString());
         remoteTerminologyServiceValidationSupport.addClientInterceptor(
             createAuthInterceptor(terminologyserverBasicauthUsername, terminologyserverBasicauthPassword,
                                   terminologyserverOauth2TokenURL, terminologyserverOauth2ClientId, terminologyserverOauth2ClientSecret));
         validationSupportChain.addValidationSupport(remoteTerminologyServiceValidationSupport);
       }
 
-      fhirValidator = FHIR_CONTEXT.newValidator()
+      fhirValidator = forR4Cached().newValidator()
           .registerValidatorModule(new FhirInstanceValidator(new CachingValidationSupport(validationSupportChain)));
     }
   }

src/main/java/de/difuture/uds/odm2fhir/fhir/writer/ServerFHIRBundleWriter.java

@@ -39,6 +39,8 @@
 
 import static de.difuture.uds.odm2fhir.util.HTTPHelper.createAuthInterceptor;
 
+import static ca.uhn.fhir.context.FhirContext.forR4Cached;
+
 @ConditionalOnExpression("!'${fhir.server.url:}'.empty")
 @Service
 @Slf4j
@@ -66,7 +68,7 @@ public class ServerFHIRBundleWriter extends FHIRBundleWriter {
   private RetryTemplate retryTemplate;
 
   private void init() throws IOException {
-    genericClient = FHIR_CONTEXT.getRestfulClientFactory().newGenericClient(url.toString());
+    genericClient = forR4Cached().getRestfulClientFactory().newGenericClient(url.toString());
     genericClient.registerInterceptor(
         createAuthInterceptor(basicauthUsername, basicauthPassword, oauth2TokenURL, oauth2ClientId, oauth2ClientSecret));
 

src/main/java/de/difuture/uds/odm2fhir/util/HTTPHelper.java

@@ -64,8 +64,6 @@ public void setHttpClient(Environment environment) throws Exception {
 
     HTTP_CLIENT = HttpClientBuilder.create()
                                    .useSystemProperties()
-                                   .setMaxConnTotal(100)
-                                   .setMaxConnPerRoute(100)
                                    .setSSLContext(sslContextBuilder.build())
                                    .setSSLHostnameVerifier(new NoopHostnameVerifier())
                                    .build();