0.8.5

pom.xml

@@ -8,7 +8,7 @@
 
   <groupId>de.difuture.uds</groupId>
   <artifactId>odm2fhir</artifactId>
-  <version>0.8.4</version>
+  <version>0.8.5</version>
 
   <name>ODM2FHIR</name>
   <description>Mapper for GECCO based study/patient data in CDISC ODM to HL7 FHIR</description>
@@ -25,13 +25,13 @@
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
 
-    <hapi-fhir.version>6.1.3</hapi-fhir.version>
-    <jackson.version>2.13.4</jackson.version>
+    <hapi-fhir.version>6.2.0</hapi-fhir.version>
+    <jackson.version>2.14.0</jackson.version>
     <kafka-fhir-serializer.version>1.0.2</kafka-fhir-serializer.version>
     <lombok.version>1.18.24</lombok.version>
     <spring-kafka.version>2.9.2</spring-kafka.version>
     <spring-retry.version>1.3.4</spring-retry.version>
-    <woodstox.version>6.3.1</woodstox.version>
+    <woodstox.version>6.4.0</woodstox.version>
 
     <maven-antrun-plugin.version>3.1.0</maven-antrun-plugin.version>
     <maven-compiler-plugin.version>3.10.1</maven-compiler-plugin.version>

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/anamnesis/item/OrganRecipient.java

@@ -68,21 +68,16 @@ private Condition createCondition(ItemData transplantCoding) {
 
     for (var coding : createCodings(transplantCoding)) {
       switch (coding.getCode()) {
-        case "410605003": //YES
-          condition.setClinicalStatus(ACTIVE).setVerificationStatus(CONFIRMED);
-          break;
-        case "410594000": //NO
-          condition.setVerificationStatus(REFUTED);
-          break;
-        case "261665006": //UNKNOWN
-          condition.addModifierExtension(DATA_PRESENCE_UNKNOWN);
-          break;
-        default:
+        case "410605003" -> condition.setClinicalStatus(ACTIVE).setVerificationStatus(CONFIRMED); //YES
+        case "410594000" -> condition.setVerificationStatus(REFUTED); //NO
+        case "261665006" -> condition.addModifierExtension(DATA_PRESENCE_UNKNOWN); //UNKNOWN
+        default -> {
           if (ICD_10_GM.getUrl().equals(coding.getSystem())) { //add ICD Code
             codeCodeableConcept.addCoding(coding);
           } else if (SNOMED_CT.getUrl().equals(coding.getSystem())) { //add SNOMED Code of bodySite
             bodySiteCodeableConcept.addCoding(coding);
           }
+        }
       }
     }
 

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/consent/item/BroadConsent.java

@@ -123,30 +123,25 @@ private Consent createConsent(FormData formData) {
         .setMeta(createMeta(GERMAN_CONSENT));
 
     switch (formData.getItemData("miibc_consent_status").getValue()) {
-      case "1": //agreed
-        consent.setStatus(ConsentState.ACTIVE);
-        break;
-      case "2": //rejected
-        consent.setStatus(REJECTED);
-        break;
-      case "3": //revoked
+      case "1" -> consent.setStatus(ConsentState.ACTIVE); //agreed
+      case "2" -> consent.setStatus(REJECTED); //rejected
+      case "3" -> { //revoked
         var revocationDateItem = formData.getItemData("miibc_w_dat_dok");
         switch (formData.getItemData("miibc_widerruf").getValue()) {
-          case "1": //fully revoked
-            consent.setStatus(INACTIVE)
-              .setDateTimeElement(createDateTimeType(revocationDateItem)); //revocation -> replace 'consentDate' by 'revocationDate'
-            break;
-          case "2": //partly revoked
-            consent.setDateTimeElement(createDateTimeType(revocationDateItem)); //revocation -> replace 'consentDate' by 'revocationDate'
+          case "1" -> //fully revoked
+            consent.setStatus(INACTIVE).setDateTimeElement(
+                createDateTimeType(revocationDateItem)); //revocation -> replace 'consentDate' by 'revocationDate'
+          case "2" -> //partly revoked
+            consent.setDateTimeElement(
+                createDateTimeType(revocationDateItem)); //revocation -> replace 'consentDate' by 'revocationDate'
             //purposely no 'break;'
-          case "3": //not revoked
-          case "4": //unknown (REVOCATION-Status, not CONSENT-Status!)
+          case "3", "4" -> //not revoked, //unknown (REVOCATION-Status, not CONSENT-Status!)
             consent.setStatus(ConsentState.ACTIVE); //default if not revoked
-            break;
         }
-        break;
-      case "4": //unknown
+      }
+      case "4" -> { //unknown
         return new Consent(); //skip if general CONSENT-Status is 'unknown'
+      }
     }
 
     var mainProvisionComponent = new Consent.provisionComponent().setType(DENY);

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/medication/item/Anticoagulation.java

@@ -75,26 +75,20 @@ private MedicationStatement createMedicationStatement(ItemData generalCoding, It
     var medicationCodeableConcept = createCodeableConcept(generalCoding);
     for (var coding : createCodings(specificCoding)) {
       switch (coding.getCode()) {
-        case "410605003": //Answer = YES
-          medicationStatement.setStatus(MedicationStatementStatus.ACTIVE);
-          break;
-        case "410594000": //Answer = NO
-          medicationStatement.setStatus(NOTTAKEN);
-          break;
-        case "261665006": //Answer = Unknown
-          medicationStatement.setStatus(MedicationStatementStatus.UNKNOWN);
-          break;
-        case "74964007": //Answer = Sonstige/Other
+        case "410605003" -> medicationStatement.setStatus(MedicationStatementStatus.ACTIVE); //Answer = YES
+        case "410594000" -> medicationStatement.setStatus(NOTTAKEN); //Answer = NO
+        case "261665006" -> medicationStatement.setStatus(MedicationStatementStatus.UNKNOWN); //Answer = Unknown
+        case "74964007" -> { //Answer = Sonstige/Other
           medicationCodeableConcept.addCoding(coding.setDisplay("Other (qualifier value)"));
           if (endsWith(accurateCodingOrText.getItemOID(), "_textfeld") && !accurateCodingOrText.isEmpty()) {
             medicationCodeableConcept.setText(accurateCodingOrText.getValue());
           }
-          break;
-        default: //add Medication Codes
+        }
+        default -> { //add Medication Codes
           if (accurateCodingOrText.isEmpty()) {
             medicationCodeableConcept.addCoding(coding);
           }
-          break;
+        }
       }
     }
 

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/medication/item/COVID19Therapy.java

@@ -68,26 +68,20 @@ private MedicationStatement createMedicationStatement(ItemData specificCoding, I
     var medicationCodeableConcept = new CodeableConcept();
     for (var coding : createCodings(specificCoding)) {
       switch (coding.getCode()) {
-        case "410605003":
-          medicationStatement.setStatus(MedicationStatementStatus.ACTIVE);
-          break;
-        case "410594000":
-          medicationStatement.setStatus(NOTTAKEN);
-          break;
-        case "261665006":
-          medicationStatement.setStatus(MedicationStatementStatus.UNKNOWN);
-          break;
-        case "74964007": //Answer = Sonstige/Other
+        case "410605003" -> medicationStatement.setStatus(MedicationStatementStatus.ACTIVE);
+        case "410594000" -> medicationStatement.setStatus(NOTTAKEN);
+        case "261665006" -> medicationStatement.setStatus(MedicationStatementStatus.UNKNOWN);
+        case "74964007" -> { //Answer = Sonstige/Other
           medicationCodeableConcept.addCoding(coding.setDisplay("Other (qualifier value)"));
           if (endsWith(accurateCodingOrText.getItemOID(), "_textfeld") && !accurateCodingOrText.isEmpty()) {
             medicationCodeableConcept.setText(accurateCodingOrText.getValue());
           }
-          break;
-        default: //add Medication Codes
+        }
+        default -> { //add Medication Codes
           if (accurateCodingOrText.isEmpty()) {
             medicationCodeableConcept.addCoding(coding);
           }
-          break;
+        }
       }
     }
 

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/symptoms/item/SymptomConditions.java

@@ -69,26 +69,20 @@ private Stream<DomainResource> createConditions(FormData formData, ItemData gene
     var codeCodeableConcept = new CodeableConcept();
     for (var coding : specificCodings) {
       switch (coding.getCode()) {
-        case "410605003": //PRESENT
-          condition.setClinicalStatus(ACTIVE).setVerificationStatus(CONFIRMED);
-          break;
-        case "410594000": //ABSENT
-          condition.setVerificationStatus(REFUTED);
-          break;
-        case "261665006": //UNKNOWN
-          condition.addModifierExtension(DATA_PRESENCE_UNKNOWN);
-          break;
-        case "74964007": //Answer = Sonstige/Other
+        case "410605003" -> condition.setClinicalStatus(ACTIVE).setVerificationStatus(CONFIRMED); //PRESENT
+        case "410594000" -> condition.setVerificationStatus(REFUTED); //ABSENT
+        case "261665006" -> condition.addModifierExtension(DATA_PRESENCE_UNKNOWN); //UNKNOWN
+        case "74964007" -> { //Answer = Sonstige/Other
           codeCodeableConcept.addCoding(coding.setDisplay("Other (qualifier value)"));
           if (!formData.getItemData("symptome_andere_symptome_textfeld").isEmpty()) {
             codeCodeableConcept.setText(formData.getItemData("symptome_andere_symptome_textfeld").getValue());
           }
-          break;
-        default: //SYMPTOM CODING
+        }
+        default -> { //SYMPTOM CODING
           if (!"symptome_geruchs_bzw_geschmacksstoerungen".equals(specificCoding.getItemOID())) {
             codeCodeableConcept.addCoding(coding);
           }
-          break;
+        }
       }
     }
 

src/main/java/de/difuture/uds/odm2fhir/fhir/util/NUMCodeSystem.java

@@ -24,7 +24,6 @@ public enum NUMCodeSystem {
 
   ECRF_PARAMETER_CODES,
   FRAILTY_SCORE,
-  SNOMED_PCE_SUPPLEMENT,
   SOFA_SCORE;
 
   private static final String BASE = "https://www.netzwerk-universitaetsmedizin.de/fhir/CodeSystem/";

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

@@ -50,6 +50,7 @@
 import static org.springframework.util.ReflectionUtils.invokeMethod;
 
 import static java.lang.String.format;
+import static java.util.function.Predicate.not;
 
 @Slf4j
 @Service
@@ -88,6 +89,7 @@ public Bundle bundle(Stream<DomainResource> domainResources) {
     var bundle = (Bundle) new Bundle().setType(TRANSACTION).setMeta(new Meta().addProfile(GECCO_BUNDLE.getUrl()));
 
     domainResources
+        .filter(not(DomainResource::isEmpty))
         .peek(this::removeCodingDisplays)
         .filter(domainResource -> resourceValidator == null || resourceValidator.validate(domainResource))
         .forEach(domainResource -> {

src/main/java/de/difuture/uds/odm2fhir/odm/processor/ODMProcessor.java

@@ -120,7 +120,7 @@ private void process(InputStream inputStream) throws Exception {
 
       if (xmlStreamReader.isStartElement()) {
         switch (xmlStreamReader.getLocalName()) {
-          case "ODM":
+          case "ODM" -> {
             if (subjectODMHashes != null && initialODMInRun) {
               var creationDateTime = xmlStreamReader.getAttributeValue(null, "CreationDateTime");
               try {
@@ -129,19 +129,18 @@ private void process(InputStream inputStream) throws Exception {
                 previousRunDateTime = ZonedDateTime.parse(creationDateTime).toLocalDateTime();
               }
             }
-            break;
-          case "SubjectData":
+          }
+          case "SubjectData" -> {
             var subjectData = xmlMapper.readValue(xmlStreamReader, SubjectData.class);
-
             var hash = subjectODMHashes != null ? subjectData.hashCode() : null;
-
             if (hash == null || !hash.equals(subjectODMHashes.get(subjectData.getSubjectKey()))) {
               fhirBundleWriter.write(fhirBundler.bundle(new Subject().map(subjectData)));
 
               if (subjectODMHashes != null) {
                 subjectODMHashes.put(subjectData.getSubjectKey(), hash);
               }
             }
+          }
         }
       }
     }