chore: beta -> master

.github/workflows/ci.yml

@@ -6,11 +6,13 @@ on:
       - master
       - beta
   release:
-    types: [created]
+    types:
+      - created
   pull_request:
     branches:
       - master
       - beta
+  workflow_dispatch: {}
 
 permissions: read-all
 

.gitignore

@@ -64,3 +64,6 @@ package-lock.json
 tests/k8s/**/charts
 
 node_modules/
+
+# generated code
+src/generated/

build.gradle

@@ -8,14 +8,15 @@ plugins {
 }
 
 group = 'org.miracum.streams.ume'
-version = '2.2.1'
+version = '2.3.0-beta.1'
 sourceCompatibility = '21'
 targetCompatibility = '21'
 
 configurations {
 	compileOnly {
 		extendsFrom annotationProcessor
 	}
+	xsd2java
 }
 
 repositories {
@@ -25,6 +26,15 @@ repositories {
 ext {
 	set('springCloudVersion', "2023.0.3")
 	set('hapiVersion', "7.4.0")
+	jaxbTargetDir = file("src/generated/java")
+}
+
+sourceSets {
+	main {
+		java {
+			srcDirs jaxbTargetDir
+		}
+	}
 }
 
 dependencies {
@@ -44,7 +54,11 @@ dependencies {
 	// Jackson v3 supports Optional out-of-the-box but isn't yet provided by Spring Boot by default
 	// <https://github.com/FasterXML/jackson-modules-java8>
 	implementation 'com.fasterxml.jackson.datatype:jackson-datatype-jdk8'
+	implementation 'com.fasterxml.jackson.module:jackson-module-jakarta-xmlbind-annotations'
 
+	// JAXB code generation
+	xsd2java "com.sun.xml.bind:jaxb-xjc:4.0.5"
+	xsd2java "com.sun.xml.bind:jaxb-impl:4.0.5"
 
 	annotationProcessor "org.springframework.boot:spring-boot-configuration-processor"
 
@@ -71,6 +85,8 @@ jacoco {
 
 spotless {
 	java {
+		target("**/*.java")
+		targetExclude("src/generated/java/**/*.*")
 		importOrder()
 		removeUnusedImports()
 		googleJavaFormat()
@@ -88,3 +104,22 @@ jacocoTestReport {
 jar {
 	enabled = false
 }
+
+tasks.register('xsd2java') {
+
+	doLast {
+		jaxbTargetDir.mkdirs()
+
+		ant.taskdef(name: 'xjc', classname: 'com.sun.tools.xjc.XJCTask', classpath: configurations.xsd2java.asPath)
+		ant.jaxbTargetDir = jaxbTargetDir
+
+
+		ant.xjc(
+				destdir: "${jaxbTargetDir}",
+				package: 'de.basisdatensatz.obds.v3',
+				schema: 'src/main/resources/schema/oBDS_v3.0.3.xsd'
+		)
+
+	}
+}
+compileJava.dependsOn xsd2java

gradle.properties

@@ -0,0 +1 @@
+org.gradle.jvmargs=-Dfile.enconding=UTF-8

package.json

@@ -5,7 +5,8 @@
   "dependencies": {
     "hl7.fhir.r4.core": "4.0.1",
     "de.dktk.oncology": "1.6.0",
-    "de.medizininformatikinitiative.kerndatensatz.person": "2024.0.0"
+    "de.medizininformatikinitiative.kerndatensatz.person": "2024.0.0",
+    "de.medizininformatikinitiative.kerndatensatz.onkologie": "2024.0.0-beta-2"
   },
   "fhirVersions": [
     "4.0.1"

src/main/java/org/miracum/streams/ume/obdstofhir/FhirProperties.java

@@ -81,6 +81,7 @@ public static class FhirProfiles {
     private String systMedStatement;
     private String miiPatientPseudonymisiert;
     private String deathObservation;
+    private String miiPrOnkoDiagnosePrimaertumor;
   }
 
   @Data

src/main/java/org/miracum/streams/ume/obdstofhir/mapper/mii/ConditionMapper.java

@@ -0,0 +1,41 @@
+package org.miracum.streams.ume.obdstofhir.mapper.mii;
+
+import de.basisdatensatz.obds.v3.OBDS;
+import org.hl7.fhir.r4.model.*;
+import org.miracum.streams.ume.obdstofhir.FhirProperties;
+import org.miracum.streams.ume.obdstofhir.mapper.ObdsToFhirMapper;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+
+@Service
+public class ConditionMapper extends ObdsToFhirMapper {
+
+  private static final Logger LOG = LoggerFactory.getLogger(ConditionMapper.class);
+
+  @Autowired
+  public ConditionMapper(FhirProperties fhirProperties) {
+    super(fhirProperties);
+  }
+
+  public Condition map(OBDS.MengePatient.Patient.MengeMeldung.Meldung meldung, Reference patient) {
+    var condition = new Condition();
+    condition.setSubject(patient);
+    condition.getMeta().addProfile(fhirProperties.getProfiles().getMiiPrOnkoDiagnosePrimaertumor());
+    var tumorzuordnung = meldung.getTumorzuordnung();
+    if (tumorzuordnung == null) {
+      throw new RuntimeException("tumorzuordnung ist null");
+    }
+    condition.setRecordedDate(
+        tumorzuordnung.getDiagnosedatum().getValue().toGregorianCalendar().getTime());
+
+    condition.setCode(
+        new CodeableConcept(
+            new Coding(
+                fhirProperties.getSystems().getIcd10gm(),
+                tumorzuordnung.getPrimaertumorICD().getCode(),
+                "")));
+    return condition;
+  }
+}

src/main/java/org/miracum/streams/ume/obdstofhir/mapper/mii/PatientMapper.java

@@ -0,0 +1,31 @@
+package org.miracum.streams.ume.obdstofhir.mapper.mii;
+
+import de.basisdatensatz.obds.v3.OBDS;
+import de.basisdatensatz.obds.v3.PatientenStammdatenMelderTyp;
+import java.util.List;
+import org.hl7.fhir.r4.model.*;
+import org.miracum.streams.ume.obdstofhir.FhirProperties;
+import org.miracum.streams.ume.obdstofhir.mapper.ObdsToFhirMapper;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+
+@Service
+public class PatientMapper extends ObdsToFhirMapper {
+
+  private static final Logger LOG = LoggerFactory.getLogger(PatientMapper.class);
+
+  @Autowired
+  public PatientMapper(FhirProperties fhirProperties) {
+    super(fhirProperties);
+  }
+
+  public Patient map(
+      PatientenStammdatenMelderTyp stammdaten,
+      List<OBDS.MengePatient.Patient.MengeMeldung.Meldung> meldungen) {
+    var patient = new Patient();
+    patient.getMeta().addProfile(fhirProperties.getProfiles().getMiiPatientPseudonymisiert());
+    return patient;
+  }
+}

src/main/resources/application.yml

@@ -1,5 +1,5 @@
 app:
-  version: 2.2.1
+  version: 2.3.0-beta.1
   enableCheckDigitConv: ${CHECK_DIGIT_CONVERSION:false}
   patient-id-pattern: "[^0]\\d{8}"
 
@@ -62,8 +62,10 @@ fhir:
     opProcedure: "http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Procedure-Operation"
     stProcedure: "http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Procedure-Strahlentherapie"
     systMedStatement: "http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-MedicationStatement-Systemtherapie"
-    miiPatientPseudonymisiert: "https://www.medizininformatik-initiative.de/fhir/core/modul-person/StructureDefinition/PatientPseudonymisiert"
     deathObservation: "http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Observation-TodUrsache"
+    # MII
+    miiPatientPseudonymisiert: "https://www.medizininformatik-initiative.de/fhir/core/modul-person/StructureDefinition/PatientPseudonymisiert"
+    mii-pr-onko-diagnose-primaertumor: https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-pr-onko-diagnose-primaertumor
   display:
     histologyLoinc: "Histology and Behavior ICD-O-3 Cancer"
     gradingLoinc: "Grade pathology value Cancer"