From e3aeee61de2e510173a4c4f190fe2339a0910260 Mon Sep 17 00:00:00 2001
From: Paul-Christian Volkmer
Date: Tue, 12 Mar 2024 13:13:31 +0100
Subject: feat: salted re-hash IDs within MTB file except patient ID

---
 .../etl/processor/pseudonym/PseudonymizeService.kt |   4 +
 .../dev/dnpm/etl/processor/pseudonym/extensions.kt | 172 ++++++++++++++++++++-
 .../etl/processor/services/RequestProcessor.kt     |   2 +
 3 files changed, 177 insertions(+), 1 deletion(-)

(limited to 'src/main')

diff --git a/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/PseudonymizeService.kt b/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/PseudonymizeService.kt
index ab8ce2f..d18cd2c 100644
--- a/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/PseudonymizeService.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/PseudonymizeService.kt
@@ -33,4 +33,8 @@ class PseudonymizeService(
         }
     }
 
+    fun prefix(): String {
+        return configProperties.prefix
+    }
+
 }
\ No newline at end of file
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 0bf4913..014570a 100644
--- a/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt
@@ -20,7 +20,14 @@
 package dev.dnpm.etl.processor.pseudonym
 
 import de.ukw.ccc.bwhc.dto.MtbFile
+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) {
     val patientPseudonym = pseudonymizeService.patientPseudonym(this.patient.id)
 
@@ -46,8 +53,171 @@ infix fun MtbFile.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
     this.previousGuidelineTherapies.forEach { it.patient = patientPseudonym }
     this.rebiopsyRequests.forEach { it.patient = patientPseudonym }
     this.recommendations.forEach { it.patient = patientPseudonym }
-    this.recommendations.forEach { it.patient = patientPseudonym }
     this.responses.forEach { it.patient = patientPseudonym }
     this.studyInclusionRequests.forEach { it.patient = patientPseudonym }
     this.specimens.forEach { it.patient = patientPseudonym }
+}
+
+/**
+ * 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) {
+    val prefix = pseudonymizeService.prefix()
+
+    fun anonymize(id: String): String {
+        val hash = DigestUtils.sha256Hex("$prefix-$id").substring(0, 41).lowercase()
+        return "$prefix$hash"
+    }
+
+    this.episode.apply {
+        id = anonymize(id)
+    }
+    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 ->
+        claim.apply {
+            id = anonymize(id)
+            therapy = anonymize(therapy)
+        }
+    }
+    this.claimResponses.onEach { claimResponse ->
+        claimResponse.apply {
+            id = anonymize(id)
+            claim = anonymize(claim)
+        }
+    }
+    this.consent.apply {
+        id = anonymize(id)
+    }
+    this.diagnoses.onEach { diagnosis ->
+        diagnosis.apply {
+            id = anonymize(id)
+            histologyResults = histologyResults.map { anonymize(it) }
+        }
+    }
+    this.ecogStatus.onEach { ecogStatus ->
+        ecogStatus.apply {
+            id = anonymize(id)
+        }
+    }
+    this.familyMemberDiagnoses.onEach { familyMemberDiagnosis ->
+        familyMemberDiagnosis.apply {
+            id = anonymize(id)
+        }
+    }
+    this.geneticCounsellingRequests.onEach { geneticCounsellingRequest -> 
+        geneticCounsellingRequest.apply { 
+            id = anonymize(id)
+        }
+    }
+    this.histologyReevaluationRequests.onEach { histologyReevaluationRequest ->
+        histologyReevaluationRequest.apply {
+            id = anonymize(id)
+            specimen = anonymize(specimen)
+        }
+    }
+    this.histologyReports.onEach { histologyReport ->
+        histologyReport.apply {
+            id = anonymize(id)
+            specimen = anonymize(specimen)
+            tumorMorphology.apply {
+                id = anonymize(id)
+                specimen = anonymize(specimen)
+            }
+            tumorCellContent.apply {
+                id = anonymize(id)
+                specimen = anonymize(specimen)
+            }
+        }
+    }
+    this.lastGuidelineTherapies.onEach { lastGuidelineTherapy ->
+        lastGuidelineTherapy.apply {
+            id = anonymize(id)
+            diagnosis = anonymize(diagnosis)
+        }
+    }
+    this.molecularPathologyFindings.onEach { molecularPathologyFinding ->
+        molecularPathologyFinding.apply {
+            id = anonymize(id)
+            specimen = anonymize(specimen)
+        }
+    }
+    this.molecularTherapies.onEach { molecularTherapy ->
+        molecularTherapy.apply {
+            history.onEach { history ->
+                history.apply {
+                    id = anonymize(id)
+                    basedOn = anonymize(basedOn)
+                }
+            }
+        }
+    }
+    this.ngsReports.onEach { ngsReport ->
+        ngsReport.apply {
+            id = anonymize(id)
+            specimen = anonymize(specimen)
+            tumorCellContent.apply {
+                id = anonymize(id)
+                specimen = anonymize(specimen)
+            }
+            simpleVariants.onEach { simpleVariant ->
+                simpleVariant.apply {
+                    id = anonymize(id)
+                }
+            }
+        }
+    }
+    this.previousGuidelineTherapies.onEach { previousGuidelineTherapy ->
+        previousGuidelineTherapy.apply {
+            id = anonymize(id)
+            diagnosis = anonymize(diagnosis)
+            this.medication.forEach { medication ->
+                medication.apply {
+                    id = anonymize(id)
+                }
+            }
+        }
+    }
+    this.rebiopsyRequests.onEach { rebiopsyRequest ->
+        rebiopsyRequest.apply {
+            id = anonymize(id)
+            specimen = anonymize(specimen)
+        }
+    }
+    this.recommendations.onEach { recommendation ->
+        recommendation.apply {
+            id = anonymize(id)
+            diagnosis = anonymize(diagnosis)
+            ngsReport = anonymize(ngsReport)
+        }
+    }
+    this.responses.onEach { response ->
+        response.apply {
+            id = anonymize(id)
+            therapy = anonymize(therapy)
+        }
+    }
+    this.studyInclusionRequests.onEach { studyInclusionRequest ->
+        studyInclusionRequest.apply {
+            id = anonymize(id)
+            reason = anonymize(reason)
+        }
+    }
+    this.specimens.onEach { specimen ->
+        specimen.apply {
+            id = anonymize(id)
+        }
+    }
 }
\ No newline at end of file
diff --git a/src/main/kotlin/dev/dnpm/etl/processor/services/RequestProcessor.kt b/src/main/kotlin/dev/dnpm/etl/processor/services/RequestProcessor.kt
index 66ff291..bdf07cb 100644
--- a/src/main/kotlin/dev/dnpm/etl/processor/services/RequestProcessor.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/services/RequestProcessor.kt
@@ -28,6 +28,7 @@ import dev.dnpm.etl.processor.monitoring.RequestStatus
 import dev.dnpm.etl.processor.monitoring.RequestType
 import dev.dnpm.etl.processor.output.MtbFileSender
 import dev.dnpm.etl.processor.pseudonym.PseudonymizeService
+import dev.dnpm.etl.processor.pseudonym.anonymizeContentWith
 import dev.dnpm.etl.processor.pseudonym.pseudonymizeWith
 import org.apache.commons.codec.binary.Base32
 import org.apache.commons.codec.digest.DigestUtils
@@ -55,6 +56,7 @@ class RequestProcessor(
         val pid = mtbFile.patient.id
 
         mtbFile pseudonymizeWith pseudonymizeService
+        mtbFile anonymizeContentWith pseudonymizeService
 
         val request = MtbFileSender.MtbFileRequest(requestId, transformationService.transform(mtbFile))
 
-- 
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