feat: add pseudonymization for patient IDs (#107)

1 files changed, 228 insertions, 145 deletions

diff --git a/src/test/kotlin/dev/dnpm/etl/processor/pseudonym/ExtensionsTest.kt b/src/test/kotlin/dev/dnpm/etl/processor/pseudonym/ExtensionsTest.kt
index 0acf7db..d0ccb2b 100644
--- a/src/test/kotlin/dev/dnpm/etl/processor/pseudonym/ExtensionsTest.kt
+++ b/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
@@ -32,167 +37,245 @@ 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 {
 
-    private fun fakeMtbFile(): MtbFile {
-        val mtbFile = ClassPathResource(FAKE_MTB_FILE_PATH).inputStream
-        return ObjectMapper().readValue(mtbFile, MtbFile::class.java)
-    }
+    @Nested
+    inner class UsingBwhcDatamodel {
 
-    private fun MtbFile.serialized(): String {
-        return ObjectMapper().writeValueAsString(this)
-    }
+        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)
+        }
 
-    @Test
-    fun shouldNotContainCleanPatientId(@Mock pseudonymizeService: PseudonymizeService) {
-        doAnswer {
-            it.arguments[0]
-            "PSEUDO-ID"
-        }.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
+        private fun MtbFile.serialized(): String {
+            return ObjectMapper().writeValueAsString(this)
+        }
 
-        val mtbFile = fakeMtbFile()
+        @Test
+        fun shouldNotContainCleanPatientId(@Mock pseudonymizeService: PseudonymizeService) {
+            doAnswer {
+                it.arguments[0]
+                "PSEUDO-ID"
+            }.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
 
-        mtbFile.pseudonymizeWith(pseudonymizeService)
+            val mtbFile = fakeMtbFile()
 
-        assertThat(mtbFile.patient.id).isEqualTo("PSEUDO-ID")
-        assertThat(mtbFile.serialized()).doesNotContain(CLEAN_PATIENT_ID)
-    }
+            mtbFile.pseudonymizeWith(pseudonymizeService)
+
+            assertThat(mtbFile.patient.id).isEqualTo("PSEUDO-ID")
+            assertThat(mtbFile.serialized()).doesNotContain(CLEAN_PATIENT_ID)
+        }
+
+        @Test
+        fun shouldNotContainAnyUuidAfterRehashingOfIds(@Mock pseudonymizeService: PseudonymizeService) {
+            doAnswer {
+                it.arguments[0]
+                "PSEUDO-ID"
+            }.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
 
-    @Test
-    fun shouldNotContainAnyUuidAfterRehashingOfIds(@Mock pseudonymizeService: PseudonymizeService) {
-        doAnswer {
-            it.arguments[0]
-            "PSEUDO-ID"
-        }.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
+            doAnswer {
+                "TESTDOMAIN"
+            }.whenever(pseudonymizeService).prefix()
 
-        doAnswer {
-            "TESTDOMAIN"
-        }.whenever(pseudonymizeService).prefix()
+            val mtbFile = fakeMtbFile()
 
-        val mtbFile = fakeMtbFile()
+            mtbFile.pseudonymizeWith(pseudonymizeService)
+            mtbFile.anonymizeContentWith(pseudonymizeService)
 
-        mtbFile.pseudonymizeWith(pseudonymizeService)
-        mtbFile.anonymizeContentWith(pseudonymizeService)
+            val pattern = "\"[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}\"".toRegex().toPattern()
+            val matcher = pattern.matcher(mtbFile.serialized())
 
-        val pattern = "\"[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}\"".toRegex().toPattern()
-        val matcher = pattern.matcher(mtbFile.serialized())
+            assertThrows<IllegalStateException> {
+                matcher.find()
+                matcher.group()
+            }.also {
+                assertThat(it.message).isEqualTo("No match found")
+            }
 
-        assertThrows<IllegalStateException> {
-            matcher.find()
-            matcher.group()
-        }.also {
-            assertThat(it.message).isEqualTo("No match found")
         }
 
-    }
+        @Test
+        fun shouldRehashIdsWithPrefix(@Mock pseudonymizeService: PseudonymizeService) {
+            doAnswer {
+                it.arguments[0]
+                "PSEUDO-ID"
+            }.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
 
-    @Test
-    fun shouldRehashIdsWithPrefix(@Mock pseudonymizeService: PseudonymizeService) {
-        doAnswer {
-            it.arguments[0]
-            "PSEUDO-ID"
-        }.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
-
-        doAnswer {
-            "TESTDOMAIN"
-        }.whenever(pseudonymizeService).prefix()
-
-        val mtbFile = MtbFile.builder()
-            .withPatient(
-                Patient.builder()
-                    .withId("1")
-                    .withBirthDate("2000-08-08")
-                    .withGender(Patient.Gender.MALE)
-                    .build()
-            )
-            .withConsent(
-                Consent.builder()
-                    .withId("1")
-                    .withStatus(Consent.Status.ACTIVE)
-                    .withPatient("123")
-                    .build()
-            )
-            .withEpisode(
-                Episode.builder()
-                    .withId("1")
-                    .withPatient("1")
-                    .withPeriod(PeriodStart("2023-08-08"))
-                    .build()
-            )
-            .build()
-
-        mtbFile.pseudonymizeWith(pseudonymizeService)
-        mtbFile.anonymizeContentWith(pseudonymizeService)
-
-
-       assertThat(mtbFile.episode.id)
-           // TESTDOMAIN<sha256(TESTDOMAIN-1)[0-41]>
-           .isEqualTo("TESTDOMAIN44e20a53bbbf9f3ae39626d05df7014dcd77d6098")
-    }
+            doAnswer {
+                "TESTDOMAIN"
+            }.whenever(pseudonymizeService).prefix()
+
+            val mtbFile = MtbFile.builder()
+                .withPatient(
+                    Patient.builder()
+                        .withId("1")
+                        .withBirthDate("2000-08-08")
+                        .withGender(Patient.Gender.MALE)
+                        .build()
+                )
+                .withConsent(
+                    Consent.builder()
+                        .withId("1")
+                        .withStatus(Consent.Status.ACTIVE)
+                        .withPatient("123")
+                        .build()
+                )
+                .withEpisode(
+                    Episode.builder()
+                        .withId("1")
+                        .withPatient("1")
+                        .withPeriod(PeriodStart("2023-08-08"))
+                        .build()
+                )
+                .build()
+
+            mtbFile.pseudonymizeWith(pseudonymizeService)
+            mtbFile.anonymizeContentWith(pseudonymizeService)
+
+
+            assertThat(mtbFile.episode.id)
+                // TESTDOMAIN<sha256(TESTDOMAIN-1)[0-41]>
+                .isEqualTo("TESTDOMAIN44e20a53bbbf9f3ae39626d05df7014dcd77d6098")
+        }
+
+        @Test
+        fun shouldNotThrowExceptionOnNullValues(@Mock pseudonymizeService: PseudonymizeService) {
+            doAnswer {
+                it.arguments[0]
+                "PSEUDO-ID"
+            }.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
+
+            doAnswer {
+                "TESTDOMAIN"
+            }.whenever(pseudonymizeService).prefix()
+
+            val mtbFile = MtbFile.builder()
+                .withPatient(
+                    Patient.builder()
+                        .withId("1")
+                        .withBirthDate("2000-08-08")
+                        .withGender(Patient.Gender.MALE)
+                        .build()
+                )
+                .withConsent(
+                    Consent.builder()
+                        .withId("1")
+                        .withStatus(Consent.Status.ACTIVE)
+                        .withPatient("123")
+                        .build()
+                )
+                .withEpisode(
+                    Episode.builder()
+                        .withId("1")
+                        .withPatient("1")
+                        .withPeriod(PeriodStart("2023-08-08"))
+                        .build()
+                )
+                .withClaims(null)
+                .withDiagnoses(null)
+                .withCarePlans(null)
+                .withClaimResponses(null)
+                .withEcogStatus(null)
+                .withFamilyMemberDiagnoses(null)
+                .withGeneticCounsellingRequests(null)
+                .withHistologyReevaluationRequests(null)
+                .withHistologyReports(null)
+                .withLastGuidelineTherapies(null)
+                .withMolecularPathologyFindings(null)
+                .withMolecularTherapies(null)
+                .withNgsReports(null)
+                .withPreviousGuidelineTherapies(null)
+                .withRebiopsyRequests(null)
+                .withRecommendations(null)
+                .withResponses(null)
+                .withStudyInclusionRequests(null)
+                .withSpecimens(null)
+                .build()
 
-    @Test
-    fun shouldNotThrowExceptionOnNullValues(@Mock pseudonymizeService: PseudonymizeService) {
-        doAnswer {
-            it.arguments[0]
-            "PSEUDO-ID"
-        }.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
-
-        doAnswer {
-            "TESTDOMAIN"
-        }.whenever(pseudonymizeService).prefix()
-
-        val mtbFile = MtbFile.builder()
-            .withPatient(
-                Patient.builder()
-                    .withId("1")
-                    .withBirthDate("2000-08-08")
-                    .withGender(Patient.Gender.MALE)
-                    .build()
-            )
-            .withConsent(
-                Consent.builder()
-                    .withId("1")
-                    .withStatus(Consent.Status.ACTIVE)
-                    .withPatient("123")
-                    .build()
-            )
-            .withEpisode(
-                Episode.builder()
-                    .withId("1")
-                    .withPatient("1")
-                    .withPeriod(PeriodStart("2023-08-08"))
-                    .build()
-            )
-            .withClaims(null)
-            .withDiagnoses(null)
-            .withCarePlans(null)
-            .withClaimResponses(null)
-            .withEcogStatus(null)
-            .withFamilyMemberDiagnoses(null)
-            .withGeneticCounsellingRequests(null)
-            .withHistologyReevaluationRequests(null)
-            .withHistologyReports(null)
-            .withLastGuidelineTherapies(null)
-            .withMolecularPathologyFindings(null)
-            .withMolecularTherapies(null)
-            .withNgsReports(null)
-            .withPreviousGuidelineTherapies(null)
-            .withRebiopsyRequests(null)
-            .withRecommendations(null)
-            .withResponses(null)
-            .withStudyInclusionRequests(null)
-            .withSpecimens(null)
-            .build()
-
-        mtbFile.pseudonymizeWith(pseudonymizeService)
-        mtbFile.anonymizeContentWith(pseudonymizeService)
-
-
-        assertThat(mtbFile.episode.id).isNotNull()
+            mtbFile.pseudonymizeWith(pseudonymizeService)
+            mtbFile.anonymizeContentWith(pseudonymizeService)
+
+            assertThat(mtbFile.episode.id).isNotNull()
+        }
     }
 
-}
\ No newline at end of file
+    @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
+        }
+    }
+}