From 30ad7c299cb5c6e70a934df885efe82501fe5172 Mon Sep 17 00:00:00 2001
From: Paul-Christian Volkmer
Date: Mon, 3 Nov 2025 11:43:19 +0100
Subject: fix: do not re-anonymize diagnosis ID (#179)

---
 .../dev/dnpm/etl/processor/pseudonym/extensions.kt | 36 +++++++++-------------
 .../dnpm/etl/processor/pseudonym/ExtensionsTest.kt | 11 +++++++
 2 files changed, 25 insertions(+), 22 deletions(-)

(limited to 'src')

diff --git a/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt b/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt
index 21d49c2..8721cbe 100644
--- a/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt
@@ -125,35 +125,32 @@ infix fun Mtb.anonymizeContentWith(pseudonymizeService: PseudonymizeService) {
 
     this.carePlans?.onEach { carePlan ->
         carePlan?.apply {
-            id = id?.let { anonymize(it) }
+            this.id = id?.let { anonymize(it) }
 
-            diagnoses?.forEach { it -> it?.id = it.id?.let(::anonymize) }
-            geneticCounselingRecommendation?.apply {
-                id = geneticCounselingRecommendation.id?.let(::anonymize)
+            this.geneticCounselingRecommendation?.apply {
+                this.id = this.id?.let(::anonymize)
             }
-            rebiopsyRequests?.forEach { it ->
+            this.rebiopsyRequests?.forEach { it ->
                 it.id = it.id?.let(::anonymize)
                 it.tumorEntity?.id = it.tumorEntity?.id?.let(::anonymize)
             }
-            histologyReevaluationRequests?.forEach { it ->
+            this.histologyReevaluationRequests?.forEach { it ->
                 it.id = it?.id?.let(::anonymize)
                 it.specimen?.id = it.specimen?.id?.let(::anonymize)
             }
 
-            medicationRecommendations?.forEach { it ->
+            this.medicationRecommendations?.forEach { it ->
                 it.id = it?.id?.let(::anonymize)
                 it.supportingVariants?.forEach { it ->
                     it.variant?.id = it.variant?.id?.let(::anonymize)
                 }
                 it.reason?.id = it.reason?.id?.let(::anonymize)
             }
-            reason?.id = reason?.id?.let(::anonymize)
-            studyEnrollmentRecommendations?.forEach { it ->
+            this.reason?.id = this.reason?.id?.let(::anonymize)
+            this.studyEnrollmentRecommendations?.forEach { it ->
                 it?.reason?.id = it.reason?.id?.let(::anonymize)
             }
-
-            procedureRecommendations?.forEach { it ->
-
+            this.procedureRecommendations?.forEach { it ->
                 it.id = it?.id?.let(::anonymize)
                 it.supportingVariants?.forEach { it ->
                     it.variant?.id = it.variant?.id?.let(::anonymize)
@@ -161,16 +158,11 @@ infix fun Mtb.anonymizeContentWith(pseudonymizeService: PseudonymizeService) {
 
                 it.reason?.id = it.reason?.id?.let(::anonymize)
 
-                studyEnrollmentRecommendations?.forEach { it ->
-
-                    it.id = it?.id?.let(::anonymize)
-                    it.supportingVariants.forEach { it ->
-                        it.variant?.id = it?.variant?.id?.let(::anonymize)
-                    }
-                    responses?.forEach { it ->
-                        it.id = it?.id?.let(::anonymize)
-                        it.id = it?.id?.let(::anonymize)
-                    }
+            }
+            this.studyEnrollmentRecommendations?.forEach { it ->
+                it.id = it?.id?.let(::anonymize)
+                it.supportingVariants.forEach { it ->
+                    it.variant?.id = it?.variant?.id?.let(::anonymize)
                 }
             }
         }
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 8e4cde7..c302362 100644
--- a/src/test/kotlin/dev/dnpm/etl/processor/pseudonym/ExtensionsTest.kt
+++ b/src/test/kotlin/dev/dnpm/etl/processor/pseudonym/ExtensionsTest.kt
@@ -223,6 +223,16 @@ class ExtensionsTest {
                     this.id = "Diagnosis-1"
                 }
             )
+            this.episodesOfCare = listOf(
+                MtbEpisodeOfCare().apply {
+                    this.id = "Episode-1"
+                    this.diagnoses = listOf(
+                        Reference().apply {
+                            this.id = "Diagnosis-1"
+                        }
+                    )
+                }
+            )
             this.guidelineTherapies = listOf(
                 MtbSystemicTherapy().apply {
                     this.id = "Systemic-Therapy-1"
@@ -252,6 +262,7 @@ class ExtensionsTest {
         mtbFile.pseudonymizeWith(pseudonymizeService)
         mtbFile.anonymizeContentWith(pseudonymizeService)
 
+        assertThat(mtbFile.diagnoses.first().id).isEqualTo(mtbFile.episodesOfCare.first().diagnoses.first().id)
         assertThat(mtbFile.diagnoses.first().id).isEqualTo(mtbFile.guidelineTherapies.first().reason.id)
         assertThat(mtbFile.diagnoses.first().id).isEqualTo(mtbFile.guidelineProcedures.first().reason.id)
         assertThat(mtbFile.diagnoses.first().id).isEqualTo(mtbFile.specimens.first().diagnosis.id)
-- 
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