feat: add pseudonymization for patient IDs (#107)

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

@@ -21,12 +21,12 @@ package dev.dnpm.etl.processor.pseudonym
 
 import de.ukw.ccc.bwhc.dto.MtbFile
 import dev.dnpm.etl.processor.PatientId
+import dev.pcvolkmer.mv64e.mtb.Mtb
 import org.apache.commons.codec.digest.DigestUtils
 
 /** Replaces patient ID with generated patient pseudonym
  *
  * @param pseudonymizeService The pseudonymizeService to be used
- *
  * @return The MTB file containing patient pseudonymes
  */
 infix fun MtbFile.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
@@ -49,7 +49,11 @@ infix fun MtbFile.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
     }
     this.lastGuidelineTherapies?.forEach { it.patient = patientPseudonym }
     this.molecularPathologyFindings?.forEach { it.patient = patientPseudonym }
-    this.molecularTherapies?.forEach { molecularTherapy -> molecularTherapy.history.forEach { it.patient = patientPseudonym } }
+    this.molecularTherapies?.forEach { molecularTherapy ->
+        molecularTherapy.history.forEach {
+            it.patient = patientPseudonym
+        }
+    }
     this.ngsReports?.forEach { it.patient = patientPseudonym }
     this.previousGuidelineTherapies?.forEach { it.patient = patientPseudonym }
     this.rebiopsyRequests?.forEach { it.patient = patientPseudonym }
@@ -63,7 +67,6 @@ infix fun MtbFile.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
  * Creates new hash of content IDs with given prefix except for patient IDs
  *
  * @param pseudonymizeService The pseudonymizeService to be used
- *
  * @return The MTB file containing rehashed content IDs
  */
 infix fun MtbFile.anonymizeContentWith(pseudonymizeService: PseudonymizeService) {
@@ -224,3 +227,89 @@ infix fun MtbFile.anonymizeContentWith(pseudonymizeService: PseudonymizeService)
         }
     }
 }
+
+/** Replaces patient ID with generated patient pseudonym
+ *
+ * @since 0.11.0
+ *
+ * @param pseudonymizeService The pseudonymizeService to be used
+ * @return The MTB file containing patient pseudonymes
+ */
+infix fun Mtb.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
+    val patientPseudonym = pseudonymizeService.patientPseudonym(PatientId(this.patient.id)).value
+
+    this.episodesOfCare?.forEach { it.patient.id = patientPseudonym }
+    this.carePlans?.forEach {
+        it.patient.id = patientPseudonym
+        it.rebiopsyRequests?.forEach { it.patient.id = patientPseudonym }
+        it.histologyReevaluationRequests?.forEach { it.patient.id = patientPseudonym }
+        it.medicationRecommendations.forEach { it.patient.id = patientPseudonym }
+        it.studyEnrollmentRecommendations?.forEach { it.patient.id = patientPseudonym }
+        it.procedureRecommendations?.forEach { it.patient.id = patientPseudonym }
+        it.geneticCounselingRecommendation.patient.id = patientPseudonym
+    }
+    this.diagnoses?.forEach { it.patient.id = patientPseudonym }
+    this.guidelineTherapies?.forEach { it.patient.id = patientPseudonym }
+    this.guidelineProcedures?.forEach { it.patient.id = patientPseudonym }
+    this.patient.id = patientPseudonym
+    this.claims?.forEach { it.patient.id = patientPseudonym }
+    this.claimResponses?.forEach { it.patient.id = patientPseudonym }
+    this.diagnoses?.forEach { it.patient.id = patientPseudonym }
+    this.histologyReports?.forEach {
+        it.patient.id = patientPseudonym
+        it.results.tumorMorphology?.patient?.id = patientPseudonym
+        it.results.tumorCellContent?.patient?.id = patientPseudonym
+    }
+    this.ngsReports?.forEach {
+        it.patient.id = patientPseudonym
+        it.results.simpleVariants?.forEach { it.patient.id = patientPseudonym }
+        it.results.copyNumberVariants?.forEach { it.patient.id = patientPseudonym }
+        it.results.dnaFusions?.forEach { it.patient.id = patientPseudonym }
+        it.results.rnaFusions?.forEach { it.patient.id = patientPseudonym }
+        it.results.tumorCellContent?.patient?.id = patientPseudonym
+        it.results.brcaness?.patient?.id = patientPseudonym
+        it.results.tmb?.patient?.id = patientPseudonym
+        it.results.hrdScore?.patient?.id = patientPseudonym
+    }
+    this.ihcReports?.forEach {
+        it.patient.id = patientPseudonym
+        it.results.msiMmr?.forEach { it.patient.id = patientPseudonym }
+        it.results.proteinExpression?.forEach { it.patient.id = patientPseudonym }
+    }
+    this.responses?.forEach { it.patient.id = patientPseudonym }
+    this.specimens?.forEach { it.patient.id = patientPseudonym }
+    this.priorDiagnosticReports?.forEach { it.patient.id = patientPseudonym }
+    this.performanceStatus.forEach { it.patient.id = patientPseudonym }
+    this.systemicTherapies.forEach {
+        it.history?.forEach {
+            it.patient.id = patientPseudonym
+        }
+    }
+}
+
+/**
+ * Creates new hash of content IDs with given prefix except for patient IDs
+ *
+ * @since 0.11.0
+ *
+ * @param pseudonymizeService The pseudonymizeService to be used
+ * @return The MTB file containing rehashed content IDs
+ */
+infix fun Mtb.anonymizeContentWith(pseudonymizeService: PseudonymizeService) {
+    val prefix = pseudonymizeService.prefix()
+
+    fun anonymize(id: String): String {
+        val hash = DigestUtils.sha256Hex("$prefix-$id").substring(0, 41).lowercase()
+        return "$prefix$hash"
+    }
+
+    this.episodesOfCare?.forEach {
+        it?.apply {
+            id = id?.let {
+                anonymize(it)
+            }
+        }
+    }
+
+    // TODO all other properties
+}

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

@@ -1,7 +1,7 @@
 /*
  * This file is part of ETL-Processor
  *
- * Copyright (c) 2023  Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
+ * Copyright (c) 2025  Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
  *
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU Affero General Public License as published
@@ -21,7 +21,12 @@ package dev.dnpm.etl.processor.pseudonym
 
 import com.fasterxml.jackson.databind.ObjectMapper
 import de.ukw.ccc.bwhc.dto.*
+import dev.pcvolkmer.mv64e.mtb.MTBEpisodeOfCare
+import dev.pcvolkmer.mv64e.mtb.Mtb
+import dev.pcvolkmer.mv64e.mtb.PeriodDate
+import dev.pcvolkmer.mv64e.mtb.Reference
 import org.assertj.core.api.Assertions.assertThat
+import org.junit.jupiter.api.Nested
 import org.junit.jupiter.api.Test
 import org.junit.jupiter.api.assertThrows
 import org.junit.jupiter.api.extension.ExtendWith
@@ -32,12 +37,15 @@ import org.mockito.kotlin.doAnswer
 import org.mockito.kotlin.whenever
 import org.springframework.core.io.ClassPathResource
 
-const val FAKE_MTB_FILE_PATH = "fake_MTBFile.json"
-const val CLEAN_PATIENT_ID = "5dad2f0b-49c6-47d8-a952-7b9e9e0f7549"
-
 @ExtendWith(MockitoExtension::class)
 class ExtensionsTest {
 
+    @Nested
+    inner class UsingBwhcDatamodel {
+
+        val FAKE_MTB_FILE_PATH = "fake_MTBFile.json"
+        val CLEAN_PATIENT_ID = "5dad2f0b-49c6-47d8-a952-7b9e9e0f7549"
+
         private fun fakeMtbFile(): MtbFile {
             val mtbFile = ClassPathResource(FAKE_MTB_FILE_PATH).inputStream
             return ObjectMapper().readValue(mtbFile, MtbFile::class.java)
@@ -191,8 +199,83 @@ class ExtensionsTest {
             mtbFile.pseudonymizeWith(pseudonymizeService)
             mtbFile.anonymizeContentWith(pseudonymizeService)
 
-
             assertThat(mtbFile.episode.id).isNotNull()
         }
+    }
 
+    @Nested
+    inner class UsingDnpmV2Datamodel {
+
+        val FAKE_MTB_FILE_PATH = "mv64e-mtb-fake-patient.json"
+        val CLEAN_PATIENT_ID = "63f8fd7b-8127-4f3c-8843-aa9199e21c29"
+
+        private fun fakeMtbFile(): Mtb {
+            val mtbFile = ClassPathResource(FAKE_MTB_FILE_PATH).inputStream
+            return ObjectMapper().readValue(mtbFile, Mtb::class.java)
+        }
+
+        private fun Mtb.serialized(): String {
+            return ObjectMapper().writeValueAsString(this)
+        }
+
+        @Test
+        fun shouldNotContainCleanPatientId(@Mock pseudonymizeService: PseudonymizeService) {
+            doAnswer {
+                it.arguments[0]
+                "PSEUDO-ID"
+            }.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
+
+            val mtbFile = fakeMtbFile()
+
+            mtbFile.pseudonymizeWith(pseudonymizeService)
+
+            assertThat(mtbFile.patient.id).isEqualTo("PSEUDO-ID")
+            assertThat(mtbFile.serialized()).doesNotContain(CLEAN_PATIENT_ID)
+        }
+
+        @Test
+        fun shouldNotThrowExceptionOnNullValues(@Mock pseudonymizeService: PseudonymizeService) {
+            doAnswer {
+                it.arguments[0]
+                "PSEUDO-ID"
+            }.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
+
+            doAnswer {
+                "TESTDOMAIN"
+            }.whenever(pseudonymizeService).prefix()
+
+            val mtbFile = Mtb.builder()
+                .withPatient(
+                    dev.pcvolkmer.mv64e.mtb.Patient.builder()
+                        .withId("1")
+                        .withBirthDate("2000-08-08")
+                        .withGender(null)
+                        .build()
+                )
+                .withEpisodesOfCare(
+                    listOf(
+                        MTBEpisodeOfCare.builder()
+                            .withId("1")
+                            .withPatient(Reference("1"))
+                            .withPeriod(PeriodDate.builder().withStart("2023-08-08").build())
+                            .build()
+                    )
+                )
+                .withClaims(null)
+                .withDiagnoses(null)
+                .withCarePlans(null)
+                .withClaimResponses(null)
+                .withHistologyReports(null)
+                .withNgsReports(null)
+                .withResponses(null)
+                .withSpecimens(null)
+                .build()
+
+            mtbFile.pseudonymizeWith(pseudonymizeService)
+            mtbFile.anonymizeContentWith(pseudonymizeService)
+
+            assertThat(mtbFile.episodesOfCare).hasSize(1)
+            assertThat(mtbFile.episodesOfCare.map { it.id }).isNotNull
+        }
+    }
 }