diff options
Diffstat (limited to 'src/main/kotlin/dev/dnpm')
| -rw-r--r-- | src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt | 187 |
1 files changed, 175 insertions, 12 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 28a7d3c..01c781b 100644 --- a/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt +++ b/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt @@ -87,6 +87,8 @@ infix fun Mtb.pseudonymizeWith(pseudonymizeService: PseudonymizeService) { it.patient.id = patientPseudonym } + this.msiFindings?.forEach { it -> it.patient.id = patientPseudonym } + this.metadata?.researchConsents?.forEach { it -> val entry = it ?: return@forEach if (entry.contains("patient")) { @@ -115,14 +117,177 @@ infix fun Mtb.anonymizeContentWith(pseudonymizeService: PseudonymizeService) { } this.episodesOfCare?.forEach { - it?.apply { - id = id?.let { - anonymize(it) + it?.apply { id = id?.let(::anonymize) } + it.diagnoses?.forEach { it -> + it?.id = it.id?.let(::anonymize) + } + } + + this.carePlans?.onEach { carePlan -> + carePlan?.apply { + id = id?.let { anonymize(it) } + + diagnoses?.forEach { it -> it?.id = it.id?.let(::anonymize) } + geneticCounselingRecommendation?.apply { + id = geneticCounselingRecommendation.id?.let(::anonymize) + } + rebiopsyRequests?.forEach { it -> + it.id = it.id?.let(::anonymize) + it.tumorEntity?.id = it.tumorEntity?.id?.let(::anonymize) + } + histologyReevaluationRequests?.forEach { it -> + it.id = it?.id?.let(::anonymize) + it.specimen?.id = it.specimen?.id?.let(::anonymize) + } + + 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 -> + it?.reason?.id = it.reason?.id?.let(::anonymize) + } + + procedureRecommendations?.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) + + 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) + } + } } } } - // TODO all other properties + + this.responses?.forEach { it -> + + it?.id = it.id?.let(::anonymize) + it?.therapy?.id = it.therapy?.id?.let(::anonymize) + + } + + this.diagnoses?.forEach { it -> + + it.id = it?.id?.let(::anonymize) + it.histology?.forEach { it -> it.id = it?.id?.let(::anonymize) } + } + + this.ngsReports?.forEach { it -> + it.id = it?.id?.let(::anonymize) + it.results?.tumorCellContent?.id = it.results.tumorCellContent?.id?.let(::anonymize) + it.results?.tumorCellContent?.specimen?.id = + it.results?.tumorCellContent?.specimen?.id?.let(::anonymize) + it.results?.rnaFusions?.forEach { it -> + it?.id = it.id?.let(::anonymize) + } + it.results?.simpleVariants?.forEach { it -> + it?.id = it.id?.let(::anonymize) + it?.transcriptId?.value = it.transcriptId?.value?.let(::anonymize) + } + it.results?.tmb?.id = it.results?.tmb?.id?.let(::anonymize) + it.results?.tmb?.specimen?.id = it.results?.tmb?.specimen?.id?.let(::anonymize) + + it.results?.brcaness?.id = it.results?.brcaness?.id?.let(::anonymize) + it.results?.brcaness?.specimen?.id = it.results?.brcaness?.specimen?.id?.let(::anonymize) + it.results?.copyNumberVariants?.forEach { it -> it?.id = it.id?.let(::anonymize) } + it.results?.hrdScore?.id = it.results?.hrdScore?.id?.let(::anonymize) + it.results?.hrdScore?.specimen?.id = it.results?.hrdScore?.specimen?.id?.let(::anonymize) + it.results?.rnaSeqs?.forEach { it -> it?.id = it.id?.let(::anonymize) } + it.results?.dnaFusions?.forEach { it -> it?.id = it.id?.let(::anonymize) } + it.specimen?.id = it?.specimen?.id?.let(::anonymize) + + } + + this.histologyReports?.forEach { it -> + it.id = it?.id?.let(::anonymize) + it.results?.tumorCellContent?.id = it.results?.tumorCellContent?.id?.let(::anonymize) + it.results?.tumorCellContent?.specimen?.id = + it.results?.tumorCellContent?.specimen?.id?.let(::anonymize) + + it.results?.tumorMorphology?.id = it.results?.tumorMorphology?.id?.let(::anonymize) + it.results?.tumorMorphology?.specimen?.id = + it.results?.tumorMorphology?.specimen?.id?.let(::anonymize) + it.specimen?.id = it.specimen?.id?.let(::anonymize) + + } + this.claimResponses?.forEach { it -> + it.id = it?.id?.let(::anonymize) + it.claim?.id = it.claim?.id?.let(::anonymize) + } + this.claims?.forEach { it -> + + it.id = it?.id?.let(::anonymize) + it.recommendation?.id = it.recommendation?.id?.let(::anonymize) + + } + this.familyMemberHistories?.forEach { it -> it.id = it?.id?.let(::anonymize) } + this.guidelineProcedures?.forEach { it -> + it.id = it?.id?.let(::anonymize) + it.reason?.id = it.reason?.id?.let(::anonymize) + it.basedOn?.id = it.basedOn?.id?.let(::anonymize) + + } + + this.guidelineTherapies?.forEach { it -> + it.id = it?.id?.let(::anonymize) + it.reason?.id = it.reason?.id?.let(::anonymize) + it.basedOn?.id = it.basedOn?.id?.let(::anonymize) + } + 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) } + } + + this.msiFindings?.forEach { it -> + + it.id = it?.id?.let(::anonymize) + it.specimen?.id = it.specimen?.id?.let(::anonymize) + } + + this.performanceStatus?.forEach { it -> it.id = it?.id?.let(::anonymize) } + + this.priorDiagnosticReports?.forEach { it -> + + it.id = it?.id?.let(::anonymize) + it.specimen?.id = it.specimen?.id?.let(::anonymize) + } + + this.specimens?.forEach { it -> + + it.id = it?.id?.let(::anonymize) + it.diagnosis?.id = it.diagnosis?.id?.let(::anonymize) + + } + + this.systemicTherapies?.forEach { it -> + + it.history?.forEach { it -> + + it.id = it?.id?.let(::anonymize) + it.reason?.id = it.reason?.id?.let(::anonymize) + it.basedOn?.id = it.basedOn?.id?.let(::anonymize) + } + + } } fun Mtb.ensureMetaDataIsInitialized() { @@ -137,15 +302,13 @@ fun Mtb.ensureMetaDataIsInitialized() { if (this.metadata.modelProjectConsent == null) { this.metadata.modelProjectConsent = ModelProjectConsent() this.metadata.modelProjectConsent.provisions = mutableListOf() - } else - if (this.metadata.modelProjectConsent.provisions != null) { - // make sure list can be changed - this.metadata.modelProjectConsent.provisions = - this.metadata.modelProjectConsent.provisions.toMutableList() - } + } else if (this.metadata.modelProjectConsent.provisions != null) { + // make sure list can be changed + this.metadata.modelProjectConsent.provisions = + this.metadata.modelProjectConsent.provisions.toMutableList() + } } -infix fun Mtb.addGenomDeTan(pseudonymizeService: PseudonymizeService) -{ +infix fun Mtb.addGenomDeTan(pseudonymizeService: PseudonymizeService) { this.metadata.transferTan = pseudonymizeService.genomDeTan(PatientId(this.patient.id)) } |