fix: do not re-anonymize diagnosis ID (#179)

(cherry picked from commit 30ad7c299cb5c6e70a934df885efe82501fe5172)

2 files changed, 86 insertions, 24 deletions

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 8460293..c302362 100644
--- a/src/test/kotlin/dev/dnpm/etl/processor/pseudonym/ExtensionsTest.kt
+++ b/src/test/kotlin/dev/dnpm/etl/processor/pseudonym/ExtensionsTest.kt
@@ -112,7 +112,7 @@ class ExtensionsTest {
             }.whenever(pseudonymizeService).prefix()
 
             val mtbFile = Mtb().apply {
-                this.patient = dev.pcvolkmer.mv64e.mtb.Patient().apply {
+                this.patient = Patient().apply {
                     this.id = "PID"
                     this.birthDate = Date.from(Instant.now())
                     this.gender = GenderCoding().apply {
@@ -173,7 +173,7 @@ class ExtensionsTest {
                         Math.random().toLong().toString()
                     simpleVariant.fusionPartner5Prime?.transcriptId?.value =
                         Math.random().toLong().toString()
-                    simpleVariant.externalIds?.forEach { it ->
+                    simpleVariant.externalIds?.forEach {
                         it?.value = Math.random().toLong().toString()
                     }
                 }
@@ -197,4 +197,74 @@ class ExtensionsTest {
             }
         }
     }
+
+    @Test
+    fun shouldUseSameAnonymIdForDiagnosisAndDiagnosisReferences(@Mock pseudonymizeService: PseudonymizeService) {
+
+        doAnswer {
+            it.arguments[0]
+            "PSEUDO-ID"
+        }.whenever(pseudonymizeService).patientPseudonym(anyValueClass())
+
+        doAnswer {
+            "TESTDOMAIN"
+        }.whenever(pseudonymizeService).prefix()
+
+        val mtbFile = Mtb().apply {
+            this.patient = Patient().apply {
+                this.id = "PID"
+                this.birthDate = Date.from(Instant.now())
+                this.gender = GenderCoding().apply {
+                    this.code = GenderCodingCode.MALE
+                }
+            }
+            this.diagnoses = listOf(
+                MtbDiagnosis().apply {
+                    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"
+                    this.reason = Reference().apply {
+                        this.id = "Diagnosis-1"
+                    }
+                }
+            )
+            this.guidelineProcedures = listOf(
+                OncoProcedure().apply {
+                    this.id = "Onco-Procedure-1"
+                    this.reason = Reference().apply {
+                        this.id = "Diagnosis-1"
+                    }
+                }
+            )
+            this.specimens = listOf(
+                TumorSpecimen().apply {
+                    this.id = "Specimen-1"
+                    this.diagnosis = Reference().apply {
+                        this.id = "Diagnosis-1"
+                    }
+                }
+            )
+        }
+
+        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)
+    }
 }