fix: serialization issue with fhir consent and embedding research consent

2025-07-17 12:52:54 +00:00 · 2025-07-09 19:08:42 +02:00
parent 357abe2b05
commit 3a2f37c34c
8 changed files with 40 additions and 41 deletions
--- a/src/main/java/dev/dnpm/etl/processor/consent/GicsConsentService.java
+++ b/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
--- a/src/main/kotlin/dev/dnpm/etl/processor/config/ConsentResourceDeserializer.kt
+++ b/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>() {
-    override fun deserialize(p: JsonParser?, ctxt: DeserializationContext?): IBaseResource {
-        val fhirContext = FhirContext.forR4()
+class ConsentResourceDeserializer : JsonDeserializer<Consent>() {
+    override fun deserialize(p: JsonParser?, ctxt: DeserializationContext?): Consent {

        val jsonNode = p?.readValueAsTree<JsonNode>()
        val json = jsonNode?.toString()

-        return fhirContext.newJsonParser().parseResource(json) as IBaseResource
+        return JacksonConfig.fhirContext().newJsonParser().parseResource(json) as Consent
    }
 }
--- a/src/main/kotlin/dev/dnpm/etl/processor/config/ConsentResourceSerializer.kt
+++ b/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)
+    }
+}
--- a/src/main/kotlin/dev/dnpm/etl/processor/config/FhirResourceModule.kt
+++ b/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())
-        addDeserializer(IBaseResource::class.java, IBaseResourceDeserializer())
+        addSerializer(Consent::class.java, ConsentResourceSerializer())
+        addDeserializer(Consent::class.java, ConsentResourceDeserializer())
    }
 }
--- a/src/main/kotlin/dev/dnpm/etl/processor/config/IBaseResourceSerializer.kt
+++ b/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)
-    }
-}
--- a/src/main/kotlin/dev/dnpm/etl/processor/config/JacksonConfig.kt
+++ b/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 =
-        ObjectMapper()
-            .registerModule(FhirResourceModule())
+    fun objectMapper(): ObjectMapper = ObjectMapper().registerModule(FhirResourceModule())
        .disable(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS).registerModule(
            JavaTimeModule()
-            );
+        )
 }
--- a/src/main/kotlin/dev/dnpm/etl/processor/monitoring/ConnectionCheckService.kt
+++ b/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()
--- a/src/main/kotlin/dev/dnpm/etl/processor/services/RequestProcessor.kt
+++ b/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))
        }
    }