fix: usage and serialisation of null values (#174)

2 files changed, 36 insertions, 34 deletions

diff --git a/src/main/kotlin/dev/dnpm/etl/processor/config/JacksonConfig.kt b/src/main/kotlin/dev/dnpm/etl/processor/config/JacksonConfig.kt
index fb03d66..2ba81b5 100644
--- a/src/main/kotlin/dev/dnpm/etl/processor/config/JacksonConfig.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/config/JacksonConfig.kt
@@ -1,6 +1,7 @@
 package dev.dnpm.etl.processor.config
 
 import ca.uhn.fhir.context.FhirContext
+import com.fasterxml.jackson.annotation.JsonInclude
 import org.springframework.context.annotation.Bean
 import org.springframework.context.annotation.Configuration
 import com.fasterxml.jackson.databind.ObjectMapper
@@ -24,4 +25,5 @@ class JacksonConfig {
         .disable(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS).registerModule(
             JavaTimeModule()
         )
+        .setSerializationInclusion(JsonInclude.Include.NON_NULL)
 }
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 01c781b..21d49c2 100644
--- a/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt
@@ -35,56 +35,56 @@ import org.apache.commons.codec.digest.DigestUtils
 infix fun Mtb.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
     val patientPseudonym = pseudonymizeService.patientPseudonym(PatientId(this.patient.id)).value
 
-    this.episodesOfCare?.forEach { it.patient.id = patientPseudonym }
+    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
+        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.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.familyMemberHistories?.forEach { it.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.familyMemberHistories?.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
+        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 }
+        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.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
+            it.patient?.id = patientPseudonym
         }
     }
     this.followUps?.forEach {
-        it.patient.id = patientPseudonym
+        it.patient?.id = patientPseudonym
     }
 
     this.msiFindings?.forEach { it -> it.patient.id = patientPseudonym }
@@ -254,7 +254,7 @@ infix fun Mtb.anonymizeContentWith(pseudonymizeService: PseudonymizeService) {
     this.ihcReports?.forEach { it ->
         it.id = it?.id?.let(::anonymize)
         it.specimen?.id = it.specimen?.id?.let(::anonymize)
-        it.results.proteinExpression.forEach { it -> it?.id = it.id.let(::anonymize) }
+        it.results?.proteinExpression?.forEach { it -> it?.id = it.id.let(::anonymize) }
     }
 
     this.msiFindings?.forEach { it ->
@@ -310,5 +310,5 @@ fun Mtb.ensureMetaDataIsInitialized() {
 }
 
 infix fun Mtb.addGenomDeTan(pseudonymizeService: PseudonymizeService) {
-    this.metadata.transferTan = pseudonymizeService.genomDeTan(PatientId(this.patient.id))
+    this.metadata?.transferTan = pseudonymizeService.genomDeTan(PatientId(this.patient.id))
 }