Merge pull request #60 from CCC-MF/issue_44

feat: salted re-hash IDs within MTB file except patient ID

6 files changed, 254 insertions, 5 deletions

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))
 
diff --git a/src/test/kotlin/dev/dnpm/etl/processor/pseudonym/ExtensionsTest.kt b/src/test/kotlin/dev/dnpm/etl/processor/pseudonym/ExtensionsTest.kt
index ac6ac07..c980635 100644
--- a/src/test/kotlin/dev/dnpm/etl/processor/pseudonym/ExtensionsTest.kt
+++ b/src/test/kotlin/dev/dnpm/etl/processor/pseudonym/ExtensionsTest.kt
@@ -20,9 +20,10 @@
 package dev.dnpm.etl.processor.pseudonym
 
 import com.fasterxml.jackson.databind.ObjectMapper
-import de.ukw.ccc.bwhc.dto.MtbFile
+import de.ukw.ccc.bwhc.dto.*
 import org.assertj.core.api.Assertions.assertThat
 import org.junit.jupiter.api.Test
+import org.junit.jupiter.api.assertThrows
 import org.junit.jupiter.api.extension.ExtendWith
 import org.mockito.ArgumentMatchers
 import org.mockito.Mock
@@ -61,4 +62,76 @@ class ExtensionsTest {
         assertThat(mtbFile.serialized()).doesNotContain(CLEAN_PATIENT_ID)
     }
 
+    @Test
+    fun shouldNotContainAnyUuidAfterRehashingOfIds(@Mock pseudonymizeService: PseudonymizeService) {
+        doAnswer {
+            it.arguments[0]
+            "PSEUDO-ID"
+        }.whenever(pseudonymizeService).patientPseudonym(ArgumentMatchers.anyString())
+
+        doAnswer {
+            "TESTDOMAIN"
+        }.whenever(pseudonymizeService).prefix()
+
+        val mtbFile = fakeMtbFile()
+
+        mtbFile.pseudonymizeWith(pseudonymizeService)
+        mtbFile.anonymizeContentWith(pseudonymizeService)
+
+        val pattern = "\"[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}\"".toRegex().toPattern()
+        val matcher = pattern.matcher(mtbFile.serialized())
+
+        assertThrows<IllegalStateException> {
+            matcher.find()
+            matcher.group()
+        }.also {
+            assertThat(it.message).isEqualTo("No match found")
+        }
+
+    }
+
+    @Test
+    fun shouldRehashIdsWithPrefix(@Mock pseudonymizeService: PseudonymizeService) {
+        doAnswer {
+            it.arguments[0]
+            "PSEUDO-ID"
+        }.whenever(pseudonymizeService).patientPseudonym(ArgumentMatchers.anyString())
+
+        doAnswer {
+            "TESTDOMAIN"
+        }.whenever(pseudonymizeService).prefix()
+
+        val mtbFile = MtbFile.builder()
+            .withPatient(
+                Patient.builder()
+                    .withId("1")
+                    .withBirthDate("2000-08-08")
+                    .withGender(Patient.Gender.MALE)
+                    .build()
+            )
+            .withConsent(
+                Consent.builder()
+                    .withId("1")
+                    .withStatus(Consent.Status.ACTIVE)
+                    .withPatient("123")
+                    .build()
+            )
+            .withEpisode(
+                Episode.builder()
+                    .withId("1")
+                    .withPatient("1")
+                    .withPeriod(PeriodStart("2023-08-08"))
+                    .build()
+            )
+            .build()
+
+        mtbFile.pseudonymizeWith(pseudonymizeService)
+        mtbFile.anonymizeContentWith(pseudonymizeService)
+
+
+       assertThat(mtbFile.episode.id)
+           // TESTDOMAIN<sha256(TESTDOMAIN-1)[0-41]>
+           .isEqualTo("TESTDOMAIN44e20a53bbbf9f3ae39626d05df7014dcd77d6098")
+    }
+
 }
\ No newline at end of file
diff --git a/src/test/kotlin/dev/dnpm/etl/processor/services/RequestProcessorTest.kt b/src/test/kotlin/dev/dnpm/etl/processor/services/RequestProcessorTest.kt
index 722ab7a..611c0ff 100644
--- a/src/test/kotlin/dev/dnpm/etl/processor/services/RequestProcessorTest.kt
+++ b/src/test/kotlin/dev/dnpm/etl/processor/services/RequestProcessorTest.kt
@@ -92,7 +92,7 @@ class RequestProcessorTest {
                 uuid = UUID.randomUUID().toString(),
                 patientId = "TEST_12345678901",
                 pid = "P1",
-                fingerprint = "xrysxpozhbs2lnrjgf3yq4fzj33kxr7xr5c2cbuskmelfdmckl3a",
+                fingerprint = "zdlzv5s5ydmd4ktw2v5piohegc4jcyrm6j66bq6tv2uxuerndmga",
                 type = RequestType.MTB_FILE,
                 status = RequestStatus.SUCCESS,
                 processedAt = Instant.parse("2023-08-08T02:00:00Z")
@@ -151,7 +151,7 @@ class RequestProcessorTest {
                 uuid = UUID.randomUUID().toString(),
                 patientId = "TEST_12345678901",
                 pid = "P1",
-                fingerprint = "xrysxpozhbs2lnrjgf3yq4fzj33kxr7xr5c2cbuskmelfdmckl3a",
+                fingerprint = "zdlzv5s5ydmd4ktw2v5piohegc4jcyrm6j66bq6tv2uxuerndmga",
                 type = RequestType.MTB_FILE,
                 status = RequestStatus.SUCCESS,
                 processedAt = Instant.parse("2023-08-08T02:00:00Z")
diff --git a/src/test/resources/fake_MTBFile.json b/src/test/resources/fake_MTBFile.json
index 600eb39..3f4e8a3 100644
--- a/src/test/resources/fake_MTBFile.json
+++ b/src/test/resources/fake_MTBFile.json
@@ -1 +1 @@
-{"patient":{"id":"5dad2f0b-49c6-47d8-a952-7b9e9e0f7549","gender":"female","birthDate":"1971-03","insurance":"Barmer"},"consent":{"id":"b93e4717-7b0e-4ca5-a5d6-cf8d0f7b14cf","patient":"5dad2f0b-49c6-47d8-a952-7b9e9e0f7549","status":"active"},"episode":{"id":"8ddb893f-0d55-412f-a257-9bc8bb054549","patient":"5dad2f0b-49c6-47d8-a952-7b9e9e0f7549","period":{"start":"2021-12-29"}},"diagnoses":[{"id":"ed1f151c-0707-4bbf-bb02-9654310ac1f8","patient":"5dad2f0b-49c6-47d8-a952-7b9e9e0f7549","recordedOn":"2023-12-14","icd10":{"code":"C16.0","display":"Bösartige Neubildung: Kardia","version":"2023","system":"ICD-10-GM"},"whoGrade":{"code":"III","system":"WHO-Grading-CNS-Tumors"},"histologyResults":["385926d9-51f2-4a3a-96b6-57c5effefd84"],"statusHistory":[{"status":"local","date":"2023-12-14"},{"status":"unknown","date":"2023-12-14"}],"guidelineTreatmentStatus":"no-guidelines-available"}],"familyMemberDiagnoses":[{"id":"c434f063-76d9-4a7f-8ff2-34cd55fc56b2","patient":"5dad2f0b-49c6-47d8-a952-7b9e9e0f7549","relationship":{"code":"EXT","system":"http://terminology.hl7.org/ValueSet/v3-FamilyMember"}},{"id":"b07a73a8-70ed-48f8-a745-e82e7a5907a8","patient":"5dad2f0b-49c6-47d8-a952-7b9e9e0f7549","relationship":{"code":"EXT","system":"http://terminology.hl7.org/ValueSet/v3-FamilyMember"}}],"previousGuidelineTherapies":[{"id":"6435d684-18e3-45ad-b063-cdc303f61aa2","patient":"5dad2f0b-49c6-47d8-a952-7b9e9e0f7549","diagnosis":"ed1f151c-0707-4bbf-bb02-9654310ac1f8","therapyLine":4,"medication":[{"code":"L01XC18","system":"ATC","display":"Pembrolizumab","version":"2020"},{"code":"L01XE21","system":"ATC","display":"Regorafenib","version":"2020"},{"code":"L01XC17","system":"ATC","display":"Nivolumab","version":"2020"}]},{"id":"e35731db-7447-4c4b-896a-0e90f1e68c67","patient":"5dad2f0b-49c6-47d8-a952-7b9e9e0f7549","diagnosis":"ed1f151c-0707-4bbf-bb02-9654310ac1f8","therapyLine":4,"medication":[{"code":"L01XX46","system":"ATC","display":"Olaparib","version":"2020"},{"code":"L01XX32","system":"ATC","display":"Bortezomib","version":"2020"},{"code":"L01XE02","system":"ATC","display":"Gefitinib","version":"2020"}]},{"id":"d8a46cf9-cdc9-4f0d-b106-5aa57e08c4d0","patient":"5dad2f0b-49c6-47d8-a952-7b9e9e0f7549","diagnosis":"ed1f151c-0707-4bbf-bb02-9654310ac1f8","therapyLine":1,"medication":[{"code":"L01XC28","system":"ATC","display":"Durvalumab","version":"2020"},{"code":"L01XC06","system":"ATC","display":"Cetuximab","version":"2020"},{"code":"L01XE47","system":"ATC","display":"Dacomitinib","version":"2020"}]}],"lastGuidelineTherapies":[{"id":"9152b20d-ac04-406c-b18b-5b6f7f4d1911","patient":"5dad2f0b-49c6-47d8-a952-7b9e9e0f7549","diagnosis":"ed1f151c-0707-4bbf-bb02-9654310ac1f8","therapyLine":1,"period":{"start":"2023-12-14","end":"2024-01-04"},"medication":[{"code":"L01DB01","system":"ATC","display":"Doxorubicin","version":"2020"}],"reasonStopped":{"code":"toxicity","system":"MTB-CDS:GuidelineTherapy-StopReason"}}],"ecogStatus":[{"id":"51589dd2-f48d-4c41-8740-292b88d63b30","patient":"5dad2f0b-49c6-47d8-a952-7b9e9e0f7549","effectiveDate":"2023-12-14","value":{"code":"2","system":"ECOG-Performance-Status"}},{"id":"30caf153-a30a-4a1c-9056-fd4eae2a55da","patient":"5dad2f0b-49c6-47d8-a952-7b9e9e0f7549","effectiveDate":"2023-12-14","value":{"code":"4","system":"ECOG-Performance-Status"}}],"specimens":[{"id":"40043ae5-d4cb-48e4-85c6-b34266b7693f","patient":"5dad2f0b-49c6-47d8-a952-7b9e9e0f7549","icd10":{"code":"C16.0","display":"Bösartige Neubildung: Kardia","version":"2023","system":"ICD-10-GM"},"type":"liquid-biopsy","collection":{"date":"2023-12-14","localization":"unknown","method":"liquid-biopsy"}}],"molecularPathologyFindings":[{"id":"c7622342-3297-489e-850a-26aaf1225b36","patient":"5dad2f0b-49c6-47d8-a952-7b9e9e0f7549","specimen":"40043ae5-d4cb-48e4-85c6-b34266b7693f","performingInstitute":"12244cd7-c9dd-474e-881f-b8ab5c689b85","issuedOn":"2023-12-14","note":"MolecularPathologyFinding notes..."}],"histologyReports":[{"id":"385926d9-51f2-4a3a-96b6-57c5effefd84","patient":"5dad2f0b-49c6-47d8-a952-7b9e9e0f7549","specimen":"40043ae5-d4cb-48e4-85c6-b34266b7693f","issuedOn":"2023-12-14","tumorMorphology":{"id":"592b13c7-9507-4f31-a544-5cff90e35581","patient":"5dad2f0b-49c6-47d8-a952-7b9e9e0f7549","specimen":"40043ae5-d4cb-48e4-85c6-b34266b7693f","value":{"code":"8851/3","display":"Gut differenziertes Liposarkom","version":"Zweite Revision","system":"ICD-O-3-M"},"note":"Histology finding notes..."},"tumorCellContent":{"id":"f6af339c-415c-4682-b700-499e392b4558","specimen":"40043ae5-d4cb-48e4-85c6-b34266b7693f","method":"histologic","value":0.38164}}],"ngsReports":[{"id":"223e3e6e-d99b-415e-83c0-18bcfc5729ca","patient":"5dad2f0b-49c6-47d8-a952-7b9e9e0f7549","specimen":"40043ae5-d4cb-48e4-85c6-b34266b7693f","issueDate":"2023-12-14","sequencingType":"WGS","metadata":[{"kitType":"Agilent ExomV6","kitManufacturer":"Agilent","sequencer":"Sequencer-XYZ","referenceGenome":"HG19","pipeline":"dummy/uri/to/pipeline"}],"tumorCellContent":{"id":"e865f20a-1307-4ca3-b2ef-3a863b8afde0","specimen":"40043ae5-d4cb-48e4-85c6-b34266b7693f","method":"bioinformatic","value":0.74991},"brcaness":0.39,"msi":0.35,"tmb":594349.91,"simpleVariants":[{"id":"SNV_599c38d4-af9f-416c-ad38-eb2fee8159e1","chromosome":"chr6","gene":{"ensemblId":"ENSG00000242908","hgncId":"HGNC:50301","symbol":"AADACL2-AS1","name":"AADACL2 antisense RNA 1"},"startEnd":{"start":6736035388467870105},"refAllele":"A","altAllele":"G","dnaChange":{"code":"A>G","system":"HGVS.c"},"aminoAcidChange":{"code":"Amino acid change code...","system":"HGVS.p"},"readDepth":19,"allelicFrequency":0.75,"cosmicId":"f106c745-dbaa-453f-8dca-2f584bc1e6cb","dbSNPId":"c3f51fb2-31f3-4b27-bbcc-aac52736986f","interpretation":{"code":"Probably Inactivating","system":"ClinVAR"}},{"id":"SNV_963a3ea1-a1d5-4a52-b8d4-2e969be74b7b","chromosome":"chr2","gene":{"ensemblId":"ENSG00000141338","hgncId":"HGNC:38","symbol":"ABCA8","name":"ATP binding cassette subfamily A member 8"},"startEnd":{"start":1672464855319477743},"refAllele":"T","altAllele":"C","dnaChange":{"code":"T>C","system":"HGVS.c"},"aminoAcidChange":{"code":"Amino acid change 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