diff options
Diffstat (limited to 'src/main/kotlin/dev/dnpm')
| -rw-r--r-- | src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt | 469 |
1 files changed, 215 insertions, 254 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 179c69d..387119f 100644 --- a/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt +++ b/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt @@ -25,282 +25,243 @@ import dev.pcvolkmer.mv64e.mtb.Mtb import dev.pcvolkmer.mv64e.mtb.MvhMetadata import org.apache.commons.codec.digest.DigestUtils -/** Replaces patient ID with generated patient pseudonym - * - * @since 0.11.0 +/** + * Replaces patient ID with generated patient pseudonym * * @param pseudonymizeService The pseudonymizeService to be used * @return The MTB file containing patient pseudonymes + * @since 0.11.0 */ infix fun Mtb.pseudonymizeWith(pseudonymizeService: PseudonymizeService) { - val patientPseudonym = pseudonymizeService.patientPseudonym(PatientId(this.patient.id)).value - - 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 - } - 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.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 - } - this.ihcReports?.forEach { - 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.systemicTherapies?.forEach { - it.history?.forEach { - it.patient?.id = patientPseudonym - } - } - this.followUps?.forEach { - 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")) { - // here we expect only a patient reference any other data like display - // need to be removed, since may contain unsecure data - entry.remove("patient") - entry["patient"] = mapOf("reference" to "Patient/$patientPseudonym") - } + val patientPseudonym = pseudonymizeService.patientPseudonym(PatientId(this.patient.id)).value + + this.episodesOfCare?.filterNotNull()?.forEach { it.patient?.id = patientPseudonym } + this.carePlans?.filterNotNull()?.forEach { carePlan -> + carePlan.patient.id = patientPseudonym + carePlan.rebiopsyRequests?.filterNotNull()?.forEach { it.patient?.id = patientPseudonym } + carePlan.histologyReevaluationRequests?.filterNotNull()?.forEach { it.patient?.id = patientPseudonym } + carePlan.medicationRecommendations?.filterNotNull()?.forEach { it.patient?.id = patientPseudonym } + carePlan.studyEnrollmentRecommendations?.filterNotNull()?.forEach { it.patient?.id = patientPseudonym } + carePlan.procedureRecommendations?.filterNotNull()?.forEach { it.patient?.id = patientPseudonym } + carePlan.geneticCounselingRecommendation?.patient?.id = patientPseudonym + } + this.diagnoses?.filterNotNull()?.forEach { it.patient?.id = patientPseudonym } + this.guidelineTherapies?.filterNotNull()?.forEach { it.patient?.id = patientPseudonym } + this.guidelineProcedures?.filterNotNull()?.forEach { it.patient?.id = patientPseudonym } + this.patient.id = patientPseudonym + this.claims?.filterNotNull()?.forEach { it.patient?.id = patientPseudonym } + this.claimResponses?.filterNotNull()?.forEach { it.patient?.id = patientPseudonym } + this.familyMemberHistories?.filterNotNull()?.forEach { it.patient?.id = patientPseudonym } + this.histologyReports?.filterNotNull()?.forEach { + it.patient.id = patientPseudonym + it.results.tumorMorphology?.patient?.id = patientPseudonym + it.results.tumorCellContent?.patient?.id = patientPseudonym + } + this.ngsReports?.filterNotNull()?.forEach { ngsReport -> + ngsReport.patient?.id = patientPseudonym + ngsReport.results?.simpleVariants?.filterNotNull()?.forEach { it.patient?.id = patientPseudonym } + ngsReport.results?.copyNumberVariants?.filterNotNull()?.forEach { it.patient?.id = patientPseudonym } + ngsReport.results?.dnaFusions?.filterNotNull()?.forEach { it.patient?.id = patientPseudonym } + ngsReport.results?.rnaFusions?.filterNotNull()?.forEach { it.patient?.id = patientPseudonym } + ngsReport.results?.tumorCellContent?.patient?.id = patientPseudonym + ngsReport.results?.brcaness?.patient?.id = patientPseudonym + ngsReport.results?.tmb?.patient?.id = patientPseudonym + ngsReport.results?.hrdScore?.patient?.id = patientPseudonym + } + this.ihcReports?.filterNotNull()?.forEach { ihcReports -> + ihcReports.patient?.id = patientPseudonym + ihcReports.results?.msiMmr?.filterNotNull()?.forEach { it.patient?.id = patientPseudonym } + ihcReports.results?.proteinExpression?.filterNotNull()?.forEach { it.patient?.id = patientPseudonym } + } + this.responses?.filterNotNull()?.forEach { it.patient?.id = patientPseudonym } + this.specimens?.filterNotNull()?.forEach { it.patient?.id = patientPseudonym } + this.priorDiagnosticReports?.filterNotNull()?.forEach { it.patient?.id = patientPseudonym } + this.performanceStatus?.filterNotNull()?.forEach { it.patient?.id = patientPseudonym } + this.systemicTherapies?.filterNotNull()?.forEach { systemicTherapy -> systemicTherapy.history?.filterNotNull()?.forEach { it.patient?.id = patientPseudonym } } + this.followUps?.filterNotNull()?.forEach { it.patient?.id = patientPseudonym } + + this.msiFindings?.filterNotNull()?.forEach { it.patient?.id = patientPseudonym } + + this.metadata?.researchConsents?.filterNotNull()?.forEach { researchConsent -> + if (researchConsent.contains("patient")) { + // here we expect only a patient reference any other data like display + // need to be removed, since may contain unsecure data + researchConsent.remove("patient") + researchConsent["patient"] = mapOf("reference" to "Patient/$patientPseudonym") } + } } /** * Creates new hash of content IDs with given prefix except for patient IDs * - * @since 0.11.0 - * * @param pseudonymizeService The pseudonymizeService to be used * @return The MTB file containing rehashed content IDs + * @since 0.11.0 */ infix fun Mtb.anonymizeContentWith(pseudonymizeService: PseudonymizeService) { - val prefix = pseudonymizeService.prefix() - - fun anonymize(id: String): String { - val hash = DigestUtils.sha256Hex("$prefix-$id").substring(0, 41).lowercase() - return "$prefix$hash" + val prefix = pseudonymizeService.prefix() + + fun anonymize(id: String): String { + val hash = DigestUtils.sha256Hex("$prefix-$id").substring(0, 41).lowercase() + return "$prefix$hash" + } + + this.episodesOfCare?.filterNotNull()?.forEach { episodeOfCare -> + episodeOfCare.apply { id = id?.let(::anonymize) } + episodeOfCare.diagnoses?.filterNotNull()?.forEach { it.id = it.id?.let(::anonymize) } + } + + this.carePlans?.onEach { carePlan -> + carePlan?.apply { + this.id = id?.let { anonymize(it) } + + this.geneticCounselingRecommendation?.apply { this.id = this.id?.let(::anonymize) } + this.rebiopsyRequests?.filterNotNull()?.forEach { rebiopsyRequest -> + rebiopsyRequest.id = rebiopsyRequest.id?.let(::anonymize) + rebiopsyRequest.tumorEntity?.id = rebiopsyRequest.tumorEntity?.id?.let(::anonymize) + } + this.histologyReevaluationRequests?.filterNotNull()?.forEach { histologyReevaluationRequest -> + histologyReevaluationRequest.id = histologyReevaluationRequest.id?.let(::anonymize) + histologyReevaluationRequest.specimen?.id = histologyReevaluationRequest.specimen?.id?.let(::anonymize) + } + + this.medicationRecommendations?.filterNotNull()?.forEach { medicationRecommendations -> + medicationRecommendations.id = medicationRecommendations.id?.let(::anonymize) + medicationRecommendations.supportingVariants?.filterNotNull()?.forEach { it.variant?.id = it.variant?.id?.let(::anonymize) } + medicationRecommendations.reason?.id = medicationRecommendations.reason?.id?.let(::anonymize) + } + this.reason?.id = this.reason?.id?.let(::anonymize) + this.studyEnrollmentRecommendations?.filterNotNull()?.forEach { studyEnrollmentRecommendation -> + studyEnrollmentRecommendation.reason?.id = studyEnrollmentRecommendation.reason?.id?.let(::anonymize) + } + this.procedureRecommendations?.filterNotNull()?.forEach { procedureRecommendation -> + procedureRecommendation.id = procedureRecommendation.id?.let(::anonymize) + procedureRecommendation.supportingVariants?.filterNotNull()?.forEach { it.variant?.id = it.variant?.id?.let(::anonymize) } + procedureRecommendation.reason?.id = procedureRecommendation.reason?.id?.let(::anonymize) + } + this.studyEnrollmentRecommendations?.filterNotNull()?.forEach { studyEnrollmentRecommendation -> + studyEnrollmentRecommendation.id = studyEnrollmentRecommendation.id?.let(::anonymize) + studyEnrollmentRecommendation.supportingVariants.forEach { it.variant?.id = it?.variant?.id?.let(::anonymize) } + } } - - this.episodesOfCare?.forEach { - it?.apply { id = id?.let(::anonymize) } - it.diagnoses?.forEach { it -> - it?.id = it.id?.let(::anonymize) - } + } + + this.responses?.filterNotNull()?.forEach { response -> + response.id = response.id?.let(::anonymize) + response.therapy?.id = response.therapy?.id?.let(::anonymize) + } + + this.diagnoses?.filterNotNull()?.forEach { diagnose -> + diagnose.id = diagnose.id?.let(::anonymize) + diagnose.histology?.filterNotNull()?.forEach { it.id = it.id?.let(::anonymize) } + } + + this.ngsReports?.filterNotNull()?.forEach { ngsReport -> + ngsReport.id = ngsReport.id?.let(::anonymize) + ngsReport.results?.tumorCellContent?.id = ngsReport.results.tumorCellContent?.id?.let(::anonymize) + ngsReport.results?.tumorCellContent?.specimen?.id = + ngsReport.results?.tumorCellContent?.specimen?.id?.let(::anonymize) + ngsReport.results?.rnaFusions?.filterNotNull()?.forEach { it.id = it.id?.let(::anonymize) } + ngsReport.results?.simpleVariants?.filterNotNull()?.forEach { + it.id = it.id?.let(::anonymize) + it.transcriptId?.value = it.transcriptId?.value?.let(::anonymize) } - - this.carePlans?.onEach { carePlan -> - carePlan?.apply { - this.id = id?.let { anonymize(it) } - - this.geneticCounselingRecommendation?.apply { - this.id = this.id?.let(::anonymize) - } - this.rebiopsyRequests?.forEach { it -> - it.id = it.id?.let(::anonymize) - it.tumorEntity?.id = it.tumorEntity?.id?.let(::anonymize) - } - this.histologyReevaluationRequests?.forEach { it -> - it.id = it?.id?.let(::anonymize) - it.specimen?.id = it.specimen?.id?.let(::anonymize) - } - - 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) - } - this.reason?.id = this.reason?.id?.let(::anonymize) - this.studyEnrollmentRecommendations?.forEach { it -> - it?.reason?.id = it.reason?.id?.let(::anonymize) - } - this.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) - - } - this.studyEnrollmentRecommendations?.forEach { it -> - it.id = it?.id?.let(::anonymize) - it.supportingVariants.forEach { it -> - it.variant?.id = it?.variant?.id?.let(::anonymize) - } - } - } - } - - - 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) - } - + ngsReport.results?.tmb?.id = ngsReport.results?.tmb?.id?.let(::anonymize) + ngsReport.results?.tmb?.specimen?.id = ngsReport.results?.tmb?.specimen?.id?.let(::anonymize) + + ngsReport.results?.brcaness?.id = ngsReport.results?.brcaness?.id?.let(::anonymize) + ngsReport.results?.brcaness?.specimen?.id = ngsReport.results?.brcaness?.specimen?.id?.let(::anonymize) + ngsReport.results?.copyNumberVariants?.filterNotNull()?.forEach { it.id = it.id?.let(::anonymize) } + ngsReport.results?.hrdScore?.id = ngsReport.results?.hrdScore?.id?.let(::anonymize) + ngsReport.results?.hrdScore?.specimen?.id = ngsReport.results?.hrdScore?.specimen?.id?.let(::anonymize) + ngsReport.results?.rnaSeqs?.filterNotNull()?.forEach { it.id = it.id?.let(::anonymize) } + ngsReport.results?.dnaFusions?.filterNotNull()?.forEach { it.id = it.id?.let(::anonymize) } + ngsReport.specimen?.id = ngsReport.specimen?.id?.let(::anonymize) + } + + this.histologyReports?.filterNotNull()?.forEach { histologyReport -> + histologyReport.id = histologyReport.id?.let(::anonymize) + histologyReport.results?.tumorCellContent?.id = histologyReport.results?.tumorCellContent?.id?.let(::anonymize) + histologyReport.results?.tumorCellContent?.specimen?.id = + histologyReport.results?.tumorCellContent?.specimen?.id?.let(::anonymize) + + histologyReport.results?.tumorMorphology?.id = histologyReport.results?.tumorMorphology?.id?.let(::anonymize) + histologyReport.results?.tumorMorphology?.specimen?.id = + histologyReport.results?.tumorMorphology?.specimen?.id?.let(::anonymize) + histologyReport.specimen?.id = histologyReport.specimen?.id?.let(::anonymize) + } + this.claimResponses?.filterNotNull()?.forEach { claimResponse -> + claimResponse.id = claimResponse.id?.let(::anonymize) + claimResponse.claim?.id = claimResponse.claim?.id?.let(::anonymize) + } + this.claims?.filterNotNull()?.forEach { claim -> + claim.id = claim.id?.let(::anonymize) + claim.recommendation?.id = claim.recommendation?.id?.let(::anonymize) + } + this.familyMemberHistories?.filterNotNull()?.forEach { it.id = it.id?.let(::anonymize) } + this.guidelineProcedures?.filterNotNull()?.forEach { guidelineProcedure -> + guidelineProcedure.id = guidelineProcedure.id?.let(::anonymize) + guidelineProcedure.reason?.id = guidelineProcedure.reason?.id?.let(::anonymize) + guidelineProcedure.basedOn?.id = guidelineProcedure.basedOn?.id?.let(::anonymize) + } + + this.guidelineTherapies?.filterNotNull()?.forEach { guidelineTherapy -> + guidelineTherapy.id = guidelineTherapy.id?.let(::anonymize) + guidelineTherapy.reason?.id = guidelineTherapy.reason?.id?.let(::anonymize) + guidelineTherapy.basedOn?.id = guidelineTherapy.basedOn?.id?.let(::anonymize) + } + this.ihcReports?.filterNotNull()?.forEach { ihcReport -> + ihcReport.id = ihcReport.id?.let(::anonymize) + ihcReport.specimen?.id = ihcReport.specimen?.id?.let(::anonymize) + ihcReport.results?.proteinExpression?.filterNotNull()?.forEach { it.id = it.id.let(::anonymize) } + } + + this.msiFindings?.filterNotNull()?.forEach { msiFinding -> + msiFinding.id = msiFinding.id?.let(::anonymize) + msiFinding.specimen?.id = msiFinding.specimen?.id?.let(::anonymize) + } + + this.performanceStatus?.filterNotNull()?.forEach { it.id = it.id?.let(::anonymize) } + + this.priorDiagnosticReports?.filterNotNull()?.forEach { priorDiagnosticReport -> + priorDiagnosticReport.id = priorDiagnosticReport.id?.let(::anonymize) + priorDiagnosticReport.specimen?.id = priorDiagnosticReport.specimen?.id?.let(::anonymize) + } + + this.specimens?.filterNotNull()?.forEach { specimen -> + specimen.id = specimen.id?.let(::anonymize) + specimen.diagnosis?.id = specimen.diagnosis?.id?.let(::anonymize) + } + + this.systemicTherapies?.filterNotNull()?.forEach { systemicTherapy -> + systemicTherapy.history?.filterNotNull()?.forEach { history -> + history.id = history.id?.let(::anonymize) + history.reason?.id = history.reason?.id?.let(::anonymize) + history.basedOn?.id = history.basedOn?.id?.let(::anonymize) } + } } fun Mtb.ensureMetaDataIsInitialized() { - // init metadata if necessary - if (this.metadata == null) { - val mvhMetadata = MvhMetadata.builder().build() - this.metadata = mvhMetadata - } - if (this.metadata.researchConsents == null) { - this.metadata.researchConsents = mutableListOf() - } - 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() - } + // init metadata if necessary + if (this.metadata == null) { + val mvhMetadata = MvhMetadata.builder().build() + this.metadata = mvhMetadata + } + if (this.metadata.researchConsents == null) { + this.metadata.researchConsents = mutableListOf() + } + 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() + } } infix fun Mtb.addGenomDeTan(pseudonymizeService: PseudonymizeService) { - this.metadata?.transferTan = pseudonymizeService.genomDeTan(PatientId(this.patient.id)) + this.metadata?.transferTan = pseudonymizeService.genomDeTan(PatientId(this.patient.id)) } |