fix: pseudonymize patient reference at embedded consent resources

src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt

@@ -21,7 +21,9 @@ package dev.dnpm.etl.processor.pseudonym
 
 import de.ukw.ccc.bwhc.dto.MtbFile
 import dev.dnpm.etl.processor.PatientId
+import dev.pcvolkmer.mv64e.mtb.ModelProjectConsent
 import dev.pcvolkmer.mv64e.mtb.Mtb
+import dev.pcvolkmer.mv64e.mtb.MvhMetadata
 import org.apache.commons.codec.digest.DigestUtils
 import org.hl7.fhir.r4.model.Consent
 
@@ -291,12 +293,13 @@ infix fun Mtb.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
         it.patient.id = patientPseudonym
     }
 
-    // FIXME: MUST CREATE TESTCASE  - NEEDS TESTING!!
-    this.metadata?.researchConsents?.forEach {  it  -> {
-        val consent = it as? Consent
-        consent?.patient?.reference = "Patient/$patientPseudonym"
-        consent?.patient?.display = null
-        }
+    this.metadata?.researchConsents?.forEach { it ->
+        val entry = it ?: return@forEach
+        val key = entry.keys.first()
+        val consent = entry[key] as? Consent ?: return@forEach
+            val patRef= "Patient/$patientPseudonym"
+            consent.patient?.setReference(patRef)
+            consent.patient?.display = null
     }
 }
 
@@ -326,3 +329,23 @@ infix fun Mtb.anonymizeContentWith(pseudonymizeService: PseudonymizeService) {
 
     // TODO all other properties
 }
+
+fun Mtb.ensureMetaDataIsInitialized() {
+    // init metadata if necessary
+    if (this.metadata == null) {
+        val mvhMetadata = MvhMetadata.builder().build()
+        this.metadata = mvhMetadata
+    }
+    if (this.metadata.researchConsents == null) {
+        this.metadata.researchConsents = mutableListOf()
+    }
+    if (this.metadata.modelProjectConsent == null) {
+        this.metadata.modelProjectConsent = ModelProjectConsent()
+        this.metadata.modelProjectConsent.provisions = mutableListOf()
+    } else
+        if (this.metadata.modelProjectConsent.provisions != null) {
+            // make sure list can be changed
+            this.metadata.modelProjectConsent.provisions =
+                this.metadata.modelProjectConsent.provisions.toMutableList()
+        }
+}

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

@@ -33,10 +33,9 @@ import dev.dnpm.etl.processor.monitoring.RequestType
 import dev.dnpm.etl.processor.output.*
 import dev.dnpm.etl.processor.pseudonym.PseudonymizeService
 import dev.dnpm.etl.processor.pseudonym.anonymizeContentWith
+import dev.dnpm.etl.processor.pseudonym.ensureMetaDataIsInitialized
 import dev.dnpm.etl.processor.pseudonym.pseudonymizeWith
-import dev.pcvolkmer.mv64e.mtb.ModelProjectConsent
 import dev.pcvolkmer.mv64e.mtb.Mtb
-import dev.pcvolkmer.mv64e.mtb.MvhMetadata
 import org.apache.commons.codec.binary.Base32
 import org.apache.commons.codec.digest.DigestUtils
 import org.hl7.fhir.r4.model.Consent
@@ -97,7 +96,7 @@ class RequestProcessor(
             return true
         }
 
-        initMetaDataAtMtbFile(mtbFile)
+        mtbFile.ensureMetaDataIsInitialized()
 
         val personIdentifierValue = extractPatientIdentifier(mtbFile)
         val requestDate = Date.from(Instant.now(Clock.systemUTC()))
@@ -146,27 +145,6 @@ class RequestProcessor(
         return false
     }
 
-
-    private fun initMetaDataAtMtbFile(mtbFile: Mtb) {
-        // init metadata if necessary
-        if (mtbFile.metadata == null) {
-            val mvhMetadata = MvhMetadata.builder().build()
-            mtbFile.metadata = mvhMetadata
-        }
-        if (mtbFile.metadata.researchConsents == null) {
-            mtbFile.metadata.researchConsents = mutableListOf()
-        }
-        if (mtbFile.metadata.modelProjectConsent == null) {
-            mtbFile.metadata.modelProjectConsent = ModelProjectConsent()
-            mtbFile.metadata.modelProjectConsent.provisions = mutableListOf()
-        } else
-            if (mtbFile.metadata.modelProjectConsent.provisions != null) {
-                // make sure list can be changed
-                mtbFile.metadata.modelProjectConsent.provisions =
-                    mtbFile.metadata.modelProjectConsent.provisions.toMutableList()
-            }
-    }
-
     fun processMtbFile(mtbFile: Mtb, requestId: RequestId) {
         val pid = PatientId(extractPatientIdentifier(mtbFile))
 

src/test/kotlin/dev/dnpm/etl/processor/pseudonym/ExtensionsTest.kt

@@ -22,9 +22,15 @@ package dev.dnpm.etl.processor.pseudonym
 import com.fasterxml.jackson.databind.ObjectMapper
 import de.ukw.ccc.bwhc.dto.*
 import de.ukw.ccc.bwhc.dto.Patient
+import dev.dnpm.etl.processor.config.GIcsConfigProperties
 import dev.dnpm.etl.processor.config.JacksonConfig
+import dev.dnpm.etl.processor.consent.BaseConsentService
+import dev.dnpm.etl.processor.consent.ConsentDomain
+import dev.dnpm.etl.processor.consent.TtpConsentStatus
+import dev.dnpm.etl.processor.services.TransformationServiceTest
 import dev.pcvolkmer.mv64e.mtb.*
 import org.assertj.core.api.Assertions.assertThat
+import org.hl7.fhir.r4.model.Bundle
 import org.junit.jupiter.api.Nested
 import org.junit.jupiter.api.Test
 import org.junit.jupiter.api.assertThrows
@@ -231,6 +237,8 @@ class ExtensionsTest {
             }.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
 
             val mtbFile = fakeMtbFile()
+            mtbFile.ensureMetaDataIsInitialized()
+            addConsentData(CLEAN_PATIENT_ID,mtbFile)
 
             mtbFile.pseudonymizeWith(pseudonymizeService)
 
@@ -238,6 +246,39 @@ class ExtensionsTest {
             assertThat(mtbFile.serialized()).doesNotContain(CLEAN_PATIENT_ID)
         }
 
+        private fun addConsentData(cleanPatientId: String, mtbFile: Mtb) {
+            val gIcsConfigProperties = GIcsConfigProperties("","","", true)
+
+            val baseConsentService =  object: BaseConsentService(gIcsConfigProperties){
+                override fun getTtpBroadConsentStatus(personIdentifierValue: String?): TtpConsentStatus? {
+                   throw NotImplementedError("dummy")
+                }
+
+                override fun currentConsentForPersonAndTemplate(
+                    personIdentifierValue: String?,
+                    targetConsentDomain: ConsentDomain?,
+                    requestDate: Date?
+                ): Bundle? {
+                    throw NotImplementedError("dummy")
+                }
+
+                override fun getProvisionTypeByPolicyCode(
+                    consentBundle: Bundle?,
+                    requestDate: Date?,
+                    consentDomain: ConsentDomain?
+                ): org.hl7.fhir.r4.model.Consent.ConsentProvisionType? {
+                    throw NotImplementedError("dummy")
+                }
+            }
+
+            val bundle = Bundle()
+            val dummyConsent = TransformationServiceTest.getDummyConsent()
+            dummyConsent.patient.reference = "Patient/$cleanPatientId"
+            bundle.addEntry().resource= dummyConsent
+
+            baseConsentService.embedBroadConsentResources(mtbFile,bundle)
+        }
+
         @Test
         fun shouldNotThrowExceptionOnNullValues(@Mock pseudonymizeService: PseudonymizeService) {
             doAnswer {

src/test/kotlin/dev/dnpm/etl/processor/services/TransformationServiceTest.kt

@@ -133,18 +133,18 @@ class TransformationServiceTest {
         mvhMetadata.modelProjectConsent =
             ModelProjectConsent.builder().date(Date.from(Instant.parse("2025-06-23T00:00:00.00Z")))
                 .version("1").provisions(
-                listOf(
-                    Provision.builder().type(ConsentProvision.PERMIT)
-                        .purpose(ModelProjectConsentPurpose.SEQUENCING)
-                        .date(Date.from(Instant.parse("2025-06-23T00:00:00.00Z"))).build(),
-                    Provision.builder().type(ConsentProvision.PERMIT)
-                        .purpose(ModelProjectConsentPurpose.REIDENTIFICATION)
-                        .date(Date.from(Instant.parse("2025-06-23T00:00:00.00Z"))).build(),
-                    Provision.builder().type(ConsentProvision.DENY)
-                        .purpose(ModelProjectConsentPurpose.CASE_IDENTIFICATION)
-                        .date(Date.from(Instant.parse("2025-06-23T00:00:00.00Z"))).build()
-                )
-            ).build()
+                    listOf(
+                        Provision.builder().type(ConsentProvision.PERMIT)
+                            .purpose(ModelProjectConsentPurpose.SEQUENCING)
+                            .date(Date.from(Instant.parse("2025-06-23T00:00:00.00Z"))).build(),
+                        Provision.builder().type(ConsentProvision.PERMIT)
+                            .purpose(ModelProjectConsentPurpose.REIDENTIFICATION)
+                            .date(Date.from(Instant.parse("2025-06-23T00:00:00.00Z"))).build(),
+                        Provision.builder().type(ConsentProvision.DENY)
+                            .purpose(ModelProjectConsentPurpose.CASE_IDENTIFICATION)
+                            .date(Date.from(Instant.parse("2025-06-23T00:00:00.00Z"))).build()
+                    )
+                ).build()
         val consent = getDummyConsent()
 
         mvhMetadata.researchConsents = mutableListOf()
@@ -156,49 +156,52 @@ class TransformationServiceTest {
         assertThat(transformed.metadata.modelProjectConsent.date).isNotNull
 
     }
-}
 
-fun getDummyConsent(): org.hl7.fhir.r4.model.Consent {
-    val modelVorhabenConsent = org.hl7.fhir.r4.model.Consent()
-    modelVorhabenConsent.id = "consent 1 id"
-    modelVorhabenConsent.patient.reference = "Patient/1234-pat1"
+    companion object {
+        fun getDummyConsent(): org.hl7.fhir.r4.model.Consent {
+            val modelVorhabenConsent = org.hl7.fhir.r4.model.Consent()
+            modelVorhabenConsent.id = "consent 1 id"
+            modelVorhabenConsent.patient.reference = "Patient/1234-pat1"
 
-    modelVorhabenConsent.provision.setType(
-        org.hl7.fhir.r4.model.Consent.ConsentProvisionType.fromCode(
-            "deny"
-        )
-    )
-    modelVorhabenConsent.provision.period.start =
-        Date.from(Instant.parse("2025-06-23T00:00:00.00Z"))
-    modelVorhabenConsent.provision.period.end = Date.from(Instant.parse("3000-01-01T00:00:00.00Z"))
-
-
-    val addProvision1 = modelVorhabenConsent.provision.addProvision()
-    addProvision1.setType(org.hl7.fhir.r4.model.Consent.ConsentProvisionType.fromCode("permit"))
-    addProvision1.period.start = Date.from(Instant.parse("2025-06-23T00:00:00.00Z"))
-    addProvision1.period.end = Date.from(Instant.parse("3000-01-01T00:00:00.00Z"))
-    addProvision1.code.addLast(
-        CodeableConcept(
-            Coding(
-                "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
-                "Teilnahme",
-                "Teilnahme am Modellvorhaben und Einwilligung zur Genomsequenzierung"
+            modelVorhabenConsent.provision.setType(
+                org.hl7.fhir.r4.model.Consent.ConsentProvisionType.fromCode(
+                    "deny"
+                )
             )
-        )
-    )
+            modelVorhabenConsent.provision.period.start =
+                Date.from(Instant.parse("2025-06-23T00:00:00.00Z"))
+            modelVorhabenConsent.provision.period.end =
+                Date.from(Instant.parse("3000-01-01T00:00:00.00Z"))
 
-    val addProvision2 = modelVorhabenConsent.provision.addProvision()
-    addProvision2.setType(org.hl7.fhir.r4.model.Consent.ConsentProvisionType.fromCode("deny"))
-    addProvision2.period.start = Date.from(Instant.parse("2025-06-23T00:00:00.00Z"))
-    addProvision2.period.end = Date.from(Instant.parse("3000-01-01T00:00:00.00Z"))
-    addProvision2.code.addLast(
-        CodeableConcept(
-            Coding(
-                "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
-                "Rekontaktierung",
-                "Re-Identifizierung meiner Daten über die Vertrauensstelle beim Robert Koch-Institut und in die erneute Kontaktaufnahme durch meine behandelnde Ärztin oder meinen behandelnden Arzt"
+
+            val addProvision1 = modelVorhabenConsent.provision.addProvision()
+            addProvision1.setType(org.hl7.fhir.r4.model.Consent.ConsentProvisionType.fromCode("permit"))
+            addProvision1.period.start = Date.from(Instant.parse("2025-06-23T00:00:00.00Z"))
+            addProvision1.period.end = Date.from(Instant.parse("3000-01-01T00:00:00.00Z"))
+            addProvision1.code.addLast(
+                CodeableConcept(
+                    Coding(
+                        "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
+                        "Teilnahme",
+                        "Teilnahme am Modellvorhaben und Einwilligung zur Genomsequenzierung"
+                    )
+                )
             )
-        )
-    )
-    return modelVorhabenConsent
+
+            val addProvision2 = modelVorhabenConsent.provision.addProvision()
+            addProvision2.setType(org.hl7.fhir.r4.model.Consent.ConsentProvisionType.fromCode("deny"))
+            addProvision2.period.start = Date.from(Instant.parse("2025-06-23T00:00:00.00Z"))
+            addProvision2.period.end = Date.from(Instant.parse("3000-01-01T00:00:00.00Z"))
+            addProvision2.code.addLast(
+                CodeableConcept(
+                    Coding(
+                        "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
+                        "Rekontaktierung",
+                        "Re-Identifizierung meiner Daten über die Vertrauensstelle beim Robert Koch-Institut und in die erneute Kontaktaufnahme durch meine behandelnde Ärztin oder meinen behandelnden Arzt"
+                    )
+                )
+            )
+            return modelVorhabenConsent
+        }
+    }
 }