diff options
Diffstat (limited to 'src/main')
| -rw-r--r-- | src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt | 101 |
1 files changed, 95 insertions, 6 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 bf645f6..111494b 100644 --- a/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt +++ b/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt @@ -21,12 +21,12 @@ package dev.dnpm.etl.processor.pseudonym import de.ukw.ccc.bwhc.dto.MtbFile import dev.dnpm.etl.processor.PatientId +import dev.pcvolkmer.mv64e.mtb.Mtb import org.apache.commons.codec.digest.DigestUtils /** Replaces patient ID with generated patient pseudonym * * @param pseudonymizeService The pseudonymizeService to be used - * * @return The MTB file containing patient pseudonymes */ infix fun MtbFile.pseudonymizeWith(pseudonymizeService: PseudonymizeService) { @@ -49,7 +49,11 @@ infix fun MtbFile.pseudonymizeWith(pseudonymizeService: PseudonymizeService) { } this.lastGuidelineTherapies?.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.previousGuidelineTherapies?.forEach { it.patient = patientPseudonym } this.rebiopsyRequests?.forEach { it.patient = patientPseudonym } @@ -63,7 +67,6 @@ infix fun MtbFile.pseudonymizeWith(pseudonymizeService: PseudonymizeService) { * Creates new hash of content IDs with given prefix except for patient IDs * * @param pseudonymizeService The pseudonymizeService to be used - * * @return The MTB file containing rehashed content IDs */ infix fun MtbFile.anonymizeContentWith(pseudonymizeService: PseudonymizeService) { @@ -120,8 +123,8 @@ infix fun MtbFile.anonymizeContentWith(pseudonymizeService: PseudonymizeService) id = id?.let { anonymize(it) } } } - this.geneticCounsellingRequests?.onEach { geneticCounsellingRequest -> - geneticCounsellingRequest?.apply { + this.geneticCounsellingRequests?.onEach { geneticCounsellingRequest -> + geneticCounsellingRequest?.apply { id = id?.let { anonymize(it) } } } @@ -223,4 +226,90 @@ infix fun MtbFile.anonymizeContentWith(pseudonymizeService: PseudonymizeService) id = id?.let { anonymize(it) } } } -}
\ No newline at end of file +} + +/** Replaces patient ID with generated patient pseudonym + * + * @since 0.11.0 + * + * @param pseudonymizeService The pseudonymizeService to be used + * @return The MTB file containing patient pseudonymes + */ +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.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 + } + } +} + +/** + * 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 + */ +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" + } + + this.episodesOfCare?.forEach { + it?.apply { + id = id?.let { + anonymize(it) + } + } + } + + // TODO all other properties +} |