pcvolkmer/etl-processor
1
0
Fork 0
mirror of https://github.com/pcvolkmer/etl-processor.git synced 2025-07-01 22:22:53 +00:00
Code Issues Releases Activity

Compare commits

base: pcvolkmer:v0.9.0
Branches Tags
pcvolkmer:master pcvolkmer:63-check-consent-status pcvolkmer:0.9.x
pcvolkmer:v0.10.0 pcvolkmer:v0.9.9 pcvolkmer:v0.9.8 pcvolkmer:v0.9.7 pcvolkmer:v0.9.6 pcvolkmer:v0.9.5 pcvolkmer:v0.9.4 pcvolkmer:v0.9.3 pcvolkmer:v0.9.2 pcvolkmer:v0.9.1 pcvolkmer:v0.9.0 pcvolkmer:v0.8.0 pcvolkmer:v0.7.0 pcvolkmer:v0.5.0 pcvolkmer:v0.4.0 pcvolkmer:v0.3.1 pcvolkmer:v0.3.0 pcvolkmer:v0.2.0 pcvolkmer:v0.1.2 pcvolkmer:v0.1.1 pcvolkmer:v0.1.0
..
compare: pcvolkmer:v0.9.2
Branches Tags
pcvolkmer:63-check-consent-status pcvolkmer:master pcvolkmer:0.9.x
pcvolkmer:v0.10.0 pcvolkmer:v0.9.9 pcvolkmer:v0.9.8 pcvolkmer:v0.9.7 pcvolkmer:v0.9.6 pcvolkmer:v0.9.5 pcvolkmer:v0.9.4 pcvolkmer:v0.9.3 pcvolkmer:v0.9.2 pcvolkmer:v0.9.1 pcvolkmer:v0.9.0 pcvolkmer:v0.8.0 pcvolkmer:v0.7.0 pcvolkmer:v0.5.0 pcvolkmer:v0.4.0 pcvolkmer:v0.3.1 pcvolkmer:v0.3.0 pcvolkmer:v0.2.0 pcvolkmer:v0.1.2 pcvolkmer:v0.1.1 pcvolkmer:v0.1.0

3 Commits
v0.9.0 ... v0.9.2

Author SHA1 Message Date
Paul-Christian Volkmer
a730ce2a53 fix: update spring security due to CVE-2024-22257 2024-03-19 16:40:32 +01:00
Paul-Christian Volkmer
12eb1feea6 fix: assign new value from scope function 2024-03-12 18:29:42 +01:00
Paul-Christian Volkmer
af714f7b64 fix: ignore possible null values in mtb files 2024-03-12 17:56:25 +01:00
2 changed files with 106 additions and 101 deletions
Expand all files Collapse all files

5
build.gradle.kts
View File

@ -11,7 +11,7 @@ plugins {
} }
group = "de.ukw.ccc" group = "de.ukw.ccc"
version = "0.9.0" version = "0.9.2"
var versions = mapOf( var versions = mapOf(
"bwhc-dto-java" to "0.2.0", "bwhc-dto-java" to "0.2.0",
@ -23,6 +23,9 @@ var versions = mapOf(
"htmx.org" to "1.9.10" "htmx.org" to "1.9.10"
) )
// Fixes and version overrides
ext["spring-security.version"] = "6.2.3"
java { java {
sourceCompatibility = JavaVersion.VERSION_21 sourceCompatibility = JavaVersion.VERSION_21
} }

202
src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt
View File

@ -73,151 +73,153 @@ infix fun MtbFile.anonymizeContentWith(pseudonymizeService: PseudonymizeService)
return "$prefix$hash" return "$prefix$hash"
} }
this.episode.apply { this.episode?.apply {
id = anonymize(id) id = id?.let {
} anonymize(it)
this.carePlans.onEach { carePlan ->
carePlan.apply {
id = anonymize(id)
diagnosis = anonymize(diagnosis)
geneticCounsellingRequest = anonymize(geneticCounsellingRequest)
rebiopsyRequests = rebiopsyRequests.map { anonymize(it) }
recommendations = recommendations.map { anonymize(it) }
studyInclusionRequests = studyInclusionRequests.map { anonymize(it) }
} }
} }
this.claims.onEach { claim -> this.carePlans?.onEach { carePlan ->
claim.apply { carePlan?.apply {
id = anonymize(id) id = id?.let { anonymize(it) }
therapy = anonymize(therapy) diagnosis = diagnosis?.let { anonymize(it) }
geneticCounsellingRequest = geneticCounsellingRequest?.let { anonymize(it) }
rebiopsyRequests = rebiopsyRequests.map { it?.let { anonymize(it) } }
recommendations = recommendations.map { it?.let { anonymize(it) } }
studyInclusionRequests = studyInclusionRequests.map { it?.let { anonymize(it) } }
} }
} }
this.claimResponses.onEach { claimResponse -> this.claims?.onEach { claim ->
claimResponse.apply { claim?.apply {
id = anonymize(id) id = id?.let { anonymize(it) }
claim = anonymize(claim) therapy = therapy?.let { anonymize(it) }
} }
} }
this.consent.apply { this.claimResponses?.onEach { claimResponse ->
id = anonymize(id) claimResponse?.apply {
} id = id?.let { anonymize(it) }
this.diagnoses.onEach { diagnosis -> claim = claim?.let { anonymize(it) }
diagnosis.apply {
id = anonymize(id)
histologyResults = histologyResults.map { anonymize(it) }
} }
} }
this.ecogStatus.onEach { ecogStatus -> this.consent?.apply {
ecogStatus.apply { id = id?.let { anonymize(it) }
id = anonymize(id) }
this.diagnoses?.onEach { diagnosis ->
diagnosis?.apply {
id = id?.let { anonymize(it) }
histologyResults = histologyResults?.map { it?.let { anonymize(it) } }
} }
} }
this.familyMemberDiagnoses.onEach { familyMemberDiagnosis -> this.ecogStatus?.onEach { ecogStatus ->
familyMemberDiagnosis.apply { ecogStatus?.apply {
id = anonymize(id) id = id?.let { anonymize(it) }
} }
} }
this.geneticCounsellingRequests.onEach { geneticCounsellingRequest -> this.familyMemberDiagnoses?.onEach { familyMemberDiagnosis ->
geneticCounsellingRequest.apply { familyMemberDiagnosis?.apply {
id = anonymize(id) id = id?.let { anonymize(it) }
} }
} }
this.histologyReevaluationRequests.onEach { histologyReevaluationRequest -> this.geneticCounsellingRequests?.onEach { geneticCounsellingRequest ->
histologyReevaluationRequest.apply { geneticCounsellingRequest?.apply {
id = anonymize(id) id = id?.let { anonymize(it) }
specimen = anonymize(specimen)
} }
} }
this.histologyReports.onEach { histologyReport -> this.histologyReevaluationRequests?.onEach { histologyReevaluationRequest ->
histologyReport.apply { histologyReevaluationRequest?.apply {
id = anonymize(id) id = id?.let { anonymize(it) }
specimen = anonymize(specimen) specimen = specimen?.let { anonymize(it) }
tumorMorphology.apply { }
id = anonymize(id) }
specimen = anonymize(specimen) this.histologyReports?.onEach { histologyReport ->
histologyReport?.apply {
id = id?.let { anonymize(it) }
specimen = specimen?.let { anonymize(it) }
tumorMorphology?.apply {
id = id?.let { anonymize(it) }
specimen = specimen?.let { anonymize(it) }
} }
tumorCellContent.apply { tumorCellContent?.apply {
id = anonymize(id) id = id?.let { anonymize(it) }
specimen = anonymize(specimen) specimen = specimen?.let { anonymize(it) }
} }
} }
} }
this.lastGuidelineTherapies.onEach { lastGuidelineTherapy -> this.lastGuidelineTherapies?.onEach { lastGuidelineTherapy ->
lastGuidelineTherapy.apply { lastGuidelineTherapy?.apply {
id = anonymize(id) id = id?.let { anonymize(it) }
diagnosis = anonymize(diagnosis) diagnosis = diagnosis?.let { anonymize(it) }
} }
} }
this.molecularPathologyFindings.onEach { molecularPathologyFinding -> this.molecularPathologyFindings?.onEach { molecularPathologyFinding ->
molecularPathologyFinding.apply { molecularPathologyFinding?.apply {
id = anonymize(id) id = id?.let { anonymize(it) }
specimen = anonymize(specimen) specimen = specimen?.let { anonymize(it) }
} }
} }
this.molecularTherapies.onEach { molecularTherapy -> this.molecularTherapies?.onEach { molecularTherapy ->
molecularTherapy.apply { molecularTherapy?.apply {
history.onEach { history -> history?.onEach { history ->
history.apply { history?.apply {
id = anonymize(id) id = id?.let { anonymize(it) }
basedOn = anonymize(basedOn) basedOn = basedOn?.let { anonymize(it) }
} }
} }
} }
} }
this.ngsReports.onEach { ngsReport -> this.ngsReports?.onEach { ngsReport ->
ngsReport.apply { ngsReport?.apply {
id = anonymize(id) id = id?.let { anonymize(it) }
specimen = anonymize(specimen) specimen = specimen?.let { anonymize(it) }
tumorCellContent.apply { tumorCellContent?.apply {
id = anonymize(id) id = id?.let { anonymize(it) }
specimen = anonymize(specimen) specimen = specimen?.let { anonymize(it) }
} }
simpleVariants.onEach { simpleVariant -> simpleVariants?.onEach { simpleVariant ->
simpleVariant.apply { simpleVariant?.apply {
id = anonymize(id) id = id?.let { anonymize(it) }
} }
} }
} }
} }
this.previousGuidelineTherapies.onEach { previousGuidelineTherapy -> this.previousGuidelineTherapies?.onEach { previousGuidelineTherapy ->
previousGuidelineTherapy.apply { previousGuidelineTherapy?.apply {
id = anonymize(id) id = id?.let { anonymize(it) }
diagnosis = anonymize(diagnosis) diagnosis = diagnosis?.let { anonymize(it) }
this.medication.forEach { medication -> medication.forEach { medication ->
medication.apply { medication?.apply {
id = anonymize(id) id = id?.let { anonymize(it) }
} }
} }
} }
} }
this.rebiopsyRequests.onEach { rebiopsyRequest -> this.rebiopsyRequests?.onEach { rebiopsyRequest ->
rebiopsyRequest.apply { rebiopsyRequest?.apply {
id = anonymize(id) id = id?.let { anonymize(it) }
specimen = anonymize(specimen) specimen = specimen?.let { anonymize(it) }
} }
} }
this.recommendations.onEach { recommendation -> this.recommendations?.onEach { recommendation ->
recommendation.apply { recommendation?.apply {
id = anonymize(id) id = id?.let { anonymize(it) }
diagnosis = anonymize(diagnosis) diagnosis = diagnosis?.let { anonymize(it) }
ngsReport = anonymize(ngsReport) ngsReport = ngsReport?.let { anonymize(it) }
} }
} }
this.responses.onEach { response -> this.responses?.onEach { response ->
response.apply { response?.apply {
id = anonymize(id) id = id?.let { anonymize(it) }
therapy = anonymize(therapy) therapy = therapy?.let { anonymize(it) }
} }
} }
this.studyInclusionRequests.onEach { studyInclusionRequest -> this.studyInclusionRequests?.onEach { studyInclusionRequest ->
studyInclusionRequest.apply { studyInclusionRequest?.apply {
id = anonymize(id) id = id?.let { anonymize(it) }
reason = anonymize(reason) reason = reason?.let { anonymize(it) }
} }
} }
this.specimens.onEach { specimen -> this.specimens?.onEach { specimen ->
specimen.apply { specimen?.apply {
id = anonymize(id) id = id?.let { anonymize(it) }
} }
} }
} }