fix: serialization issue with fhir consent and embedding research consent

src/main/java/dev/dnpm/etl/processor/consent/GicsConsentService.java

@@ -8,7 +8,6 @@ import java.util.Date;
 import java.util.Optional;
 import org.apache.commons.lang3.NotImplementedException;
 import org.apache.commons.lang3.StringUtils;
-import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r4.model.BooleanType;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Coding;
@@ -185,7 +184,7 @@ public class GicsConsentService implements ICheckConsent {
             throw new IllegalStateException(
                 "consent data request failed - stopping processing! - try again or fix other problems first.");
         }
-        IBaseResource iBaseResource = fhirContext.newXmlParser()
+        var iBaseResource = fhirContext.newJsonParser()
             .parseResource(consentDataSerialized);
         if (iBaseResource instanceof OperationOutcome) {
             // log error  - very likely a configuration error

src/main/kotlin/dev/dnpm/etl/processor/config/ConsentResourceDeserializer.kt

@@ -1,20 +1,18 @@
 package dev.dnpm.etl.processor.config
 
-import ca.uhn.fhir.context.FhirContext
 import com.fasterxml.jackson.core.JsonParser
 
 import com.fasterxml.jackson.databind.DeserializationContext
 import com.fasterxml.jackson.databind.JsonDeserializer
 import com.fasterxml.jackson.databind.JsonNode
-import org.hl7.fhir.instance.model.api.IBaseResource
+import org.hl7.fhir.r4.model.Consent
 
-class IBaseResourceDeserializer : JsonDeserializer<IBaseResource>() {
+class ConsentResourceDeserializer : JsonDeserializer<Consent>() {
-    override fun deserialize(p: JsonParser?, ctxt: DeserializationContext?): IBaseResource {
+    override fun deserialize(p: JsonParser?, ctxt: DeserializationContext?): Consent {
-        val fhirContext = FhirContext.forR4()
 
         val jsonNode = p?.readValueAsTree<JsonNode>()
         val json = jsonNode?.toString()
 
-        return fhirContext.newJsonParser().parseResource(json) as IBaseResource
+        return JacksonConfig.fhirContext().newJsonParser().parseResource(json) as Consent
     }
 }

src/main/kotlin/dev/dnpm/etl/processor/config/ConsentResourceSerializer.kt

@@ -0,0 +1,15 @@
+package dev.dnpm.etl.processor.config
+
+import com.fasterxml.jackson.core.JsonGenerator
+import com.fasterxml.jackson.databind.JsonSerializer
+import com.fasterxml.jackson.databind.SerializerProvider
+import org.hl7.fhir.r4.model.Consent
+
+class ConsentResourceSerializer : JsonSerializer<Consent>() {
+    override fun serialize(
+        value: Consent, gen: JsonGenerator, serializers: SerializerProvider
+    ) {
+        val json = JacksonConfig.fhirContext().newJsonParser().encodeResourceToString(value)
+        gen.writeRawValue(json)
+    }
+}

src/main/kotlin/dev/dnpm/etl/processor/config/FhirResourceModule.kt

@@ -2,11 +2,11 @@ package dev.dnpm.etl.processor.config
 
 
 import com.fasterxml.jackson.databind.module.SimpleModule
-import org.hl7.fhir.instance.model.api.IBaseResource
+import org.hl7.fhir.r4.model.Consent
 
 class FhirResourceModule : SimpleModule() {
     init {
-        addSerializer(IBaseResource::class.java, IBaseResourceSerializer())
+        addSerializer(Consent::class.java, ConsentResourceSerializer())
-        addDeserializer(IBaseResource::class.java, IBaseResourceDeserializer())
+        addDeserializer(Consent::class.java, ConsentResourceDeserializer())
     }
 }

src/main/kotlin/dev/dnpm/etl/processor/config/IBaseResourceSerializer.kt

@@ -1,19 +0,0 @@
-package dev.dnpm.etl.processor.config
-
-import ca.uhn.fhir.context.FhirContext
-import com.fasterxml.jackson.core.JsonGenerator
-import com.fasterxml.jackson.databind.JsonSerializer
-import com.fasterxml.jackson.databind.SerializerProvider
-import org.hl7.fhir.instance.model.api.IBaseResource
-
-class IBaseResourceSerializer : JsonSerializer<IBaseResource>() {
-    override fun serialize(
-        value: IBaseResource,
-        gen: JsonGenerator,
-        serializers: SerializerProvider
-    ) {
-        val fhirContext = FhirContext.forR4()
-        val json = fhirContext.newJsonParser().encodeResourceToString(value)
-        gen.writeRawValue(json)
-    }
-}

src/main/kotlin/dev/dnpm/etl/processor/config/JacksonConfig.kt

@@ -1,5 +1,6 @@
 package dev.dnpm.etl.processor.config
 
+import ca.uhn.fhir.context.FhirContext
 import org.springframework.context.annotation.Bean
 import org.springframework.context.annotation.Configuration
 import com.fasterxml.jackson.databind.ObjectMapper
@@ -9,11 +10,18 @@ import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule
 @Configuration
 class JacksonConfig {
 
+    companion object {
+        var fhirContext: FhirContext = FhirContext.forR4()
+
+        @JvmStatic
+        fun fhirContext(): FhirContext {
+            return fhirContext
+        }
+    }
+
     @Bean
-    fun objectMapper(): ObjectMapper =
+    fun objectMapper(): ObjectMapper = ObjectMapper().registerModule(FhirResourceModule())
-        ObjectMapper()
+        .disable(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS).registerModule(
-            .registerModule(FhirResourceModule())
+            JavaTimeModule()
-            .disable(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS).registerModule(
+        )
-                JavaTimeModule()
-            );
 }

src/main/kotlin/dev/dnpm/etl/processor/monitoring/ConnectionCheckService.kt

@@ -177,7 +177,7 @@ class GPasConnectionCheckService(
     fun check() {
         result = try {
             val uri = UriComponentsBuilder.fromUriString(
-                gPasConfigProperties.uri?.replace("/\$\$pseudonymizeAllowCreate", "/metadata").toString()
+                gPasConfigProperties.uri?.replace("/\$pseudonymizeAllowCreate", "/metadata").toString()
             ).build().toUri()
 
             val headers = HttpHeaders()

src/main/kotlin/dev/dnpm/etl/processor/services/RequestProcessor.kt

@@ -42,7 +42,6 @@ import dev.pcvolkmer.mv64e.mtb.MvhMetadata
 import dev.pcvolkmer.mv64e.mtb.Provision
 import org.apache.commons.codec.binary.Base32
 import org.apache.commons.codec.digest.DigestUtils
-import org.hl7.fhir.instance.model.api.IBaseResource
 import org.hl7.fhir.r4.model.Bundle
 import org.hl7.fhir.r4.model.Consent
 import org.slf4j.Logger
@@ -53,7 +52,6 @@ import java.io.IOException
 import java.lang.RuntimeException
 import java.time.Clock
 import java.time.Instant
-import java.time.ZoneId
 import java.util.*
 
 @Service
@@ -107,7 +105,7 @@ class RequestProcessor(
         initMetaDataAtMtbFile(mtbFile)
 
         val personIdentifierValue = extractPatientIdentifier(mtbFile)
-        val requestDate = Date.from(Instant.now(Clock.system(ZoneId.of("ECT"))))
+        val requestDate = Date.from(Instant.now(Clock.systemUTC()))
 
         // 1. Broad consent Entry exists?
         // 1.1. -> yes and research consent is given -> send mtb file
@@ -192,7 +190,7 @@ class RequestProcessor(
         mtbFile: Mtb, broadConsent: Bundle
     ) {
         broadConsent.entry.forEach { it ->
-            mtbFile.metadata.researchConsents.add(mapOf(it.resource.id to it as IBaseResource))
+            mtbFile.metadata.researchConsents.add(mapOf(it.resource.id to it.resource as Consent))
         }
     }