fix: handle null values in MtbFile

This should not occur but if, it should not result in NPE except for

* Patient
* Consent
* Episode

src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.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) 2024  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
@@ -31,31 +31,31 @@ import org.apache.commons.codec.digest.DigestUtils
 infix fun MtbFile.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
     val patientPseudonym = pseudonymizeService.patientPseudonym(this.patient.id)
 
-    this.episode.patient = patientPseudonym
+    this.episode?.patient = patientPseudonym
-    this.carePlans.forEach { it.patient = patientPseudonym }
+    this.carePlans?.forEach { it.patient = patientPseudonym }
     this.patient.id = patientPseudonym
-    this.claims.forEach { it.patient = patientPseudonym }
+    this.claims?.forEach { it.patient = patientPseudonym }
-    this.consent.patient = patientPseudonym
+    this.consent?.patient = patientPseudonym
-    this.claimResponses.forEach { it.patient = patientPseudonym }
+    this.claimResponses?.forEach { it.patient = patientPseudonym }
-    this.diagnoses.forEach { it.patient = patientPseudonym }
+    this.diagnoses?.forEach { it.patient = patientPseudonym }
-    this.ecogStatus.forEach { it.patient = patientPseudonym }
+    this.ecogStatus?.forEach { it.patient = patientPseudonym }
-    this.familyMemberDiagnoses.forEach { it.patient = patientPseudonym }
+    this.familyMemberDiagnoses?.forEach { it.patient = patientPseudonym }
-    this.geneticCounsellingRequests.forEach { it.patient = patientPseudonym }
+    this.geneticCounsellingRequests?.forEach { it.patient = patientPseudonym }
-    this.histologyReevaluationRequests.forEach { it.patient = patientPseudonym }
+    this.histologyReevaluationRequests?.forEach { it.patient = patientPseudonym }
-    this.histologyReports.forEach {
+    this.histologyReports?.forEach {
         it.patient = patientPseudonym
-        it.tumorMorphology.patient = patientPseudonym
+        it.tumorMorphology?.patient = patientPseudonym
     }
-    this.lastGuidelineTherapies.forEach { it.patient = patientPseudonym }
+    this.lastGuidelineTherapies?.forEach { it.patient = patientPseudonym }
-    this.molecularPathologyFindings.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.ngsReports?.forEach { it.patient = patientPseudonym }
-    this.previousGuidelineTherapies.forEach { it.patient = patientPseudonym }
+    this.previousGuidelineTherapies?.forEach { it.patient = patientPseudonym }
-    this.rebiopsyRequests.forEach { it.patient = patientPseudonym }
+    this.rebiopsyRequests?.forEach { it.patient = patientPseudonym }
-    this.recommendations.forEach { it.patient = patientPseudonym }
+    this.recommendations?.forEach { it.patient = patientPseudonym }
-    this.responses.forEach { it.patient = patientPseudonym }
+    this.responses?.forEach { it.patient = patientPseudonym }
-    this.studyInclusionRequests.forEach { it.patient = patientPseudonym }
+    this.studyInclusionRequests?.forEach { it.patient = patientPseudonym }
-    this.specimens.forEach { it.patient = patientPseudonym }
+    this.specimens?.forEach { it.patient = patientPseudonym }
 }
 
 /**

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

@@ -134,4 +134,65 @@ class ExtensionsTest {
            .isEqualTo("TESTDOMAIN44e20a53bbbf9f3ae39626d05df7014dcd77d6098")
     }
 
+    @Test
+    fun shouldNotThrowExceptionOnNullValues(@Mock pseudonymizeService: PseudonymizeService) {
+        doAnswer {
+            it.arguments[0]
+            "PSEUDO-ID"
+        }.whenever(pseudonymizeService).patientPseudonym(ArgumentMatchers.anyString())
+
+        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()
+    }
+
 }