119 add transaction (#124)

src/main/kotlin/dev/dnpm/etl/processor/config/AppConfigProperties.kt

@@ -48,7 +48,8 @@ data class PseudonymizeConfigProperties(
 @ConfigurationProperties(GPasConfigProperties.NAME)
 data class GPasConfigProperties(
     val uri: String?,
-    val target: String = "etl-processor",
+    val patientDomain: String = "etl-processor",
+    val genomDeTanDomain: String = "ccdn",
     val username: String?,
     val password: String?,
 ) {

src/main/kotlin/dev/dnpm/etl/processor/pseudonym/AnonymizingGenerator.kt

@@ -21,9 +21,12 @@ package dev.dnpm.etl.processor.pseudonym
 
 import org.apache.commons.codec.binary.Base32
 import org.apache.commons.codec.digest.DigestUtils
-
+import java.security.SecureRandom
 
 class AnonymizingGenerator : Generator {
+    companion object fun getSecureRandom() : SecureRandom {
+        return  SecureRandom()
+    }
 
     override fun generate(id: String): String {
         return Base32().encodeAsString(DigestUtils.sha256(id))
@@ -31,4 +34,14 @@ class AnonymizingGenerator : Generator {
             .lowercase()
     }
 
+    @OptIn(ExperimentalStdlibApi::class)
+    override fun generateGenomDeTan(id: String?): String {
+
+        val bytes = ByteArray(64 / 2)
+        getSecureRandom().nextBytes(bytes)
+
+        return bytes.joinToString("") { "%02x".format(it) }
+
+    }
+
 }

src/main/kotlin/dev/dnpm/etl/processor/pseudonym/PseudonymizeService.kt

@@ -35,6 +35,10 @@ class PseudonymizeService(
         }
     }
 
+    fun genomDeTan(patientId: PatientId): String {
+        return generator.generateGenomDeTan(patientId.value)
+    }
+
     fun prefix(): String {
         return configProperties.prefix
     }

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

@@ -349,3 +349,8 @@ fun Mtb.ensureMetaDataIsInitialized() {
                 this.metadata.modelProjectConsent.provisions.toMutableList()
         }
 }
+
+infix fun Mtb.addGenomDeTan(pseudonymizeService: PseudonymizeService)
+{
+    this.metadata.transferTan = pseudonymizeService.genomDeTan(PatientId(this.patient.id))
+}

src/main/kotlin/dev/dnpm/etl/processor/services/ConsentProcessor.kt

@@ -38,7 +38,7 @@ class ConsentProcessor(
     /**
      * In case an instance of {@link  ICheckConsent} is active, consent will be embedded and checked.
      *
-     * Logik:
+     * Logic:
      *  * <c>true</c> IF consent check is disabled.
      *  * <c>true</c> IF broad consent (BC) has been given.
      *  * <c>true</c> BC has been asked AND declined but genomDe consent has been consented.

src/main/kotlin/dev/dnpm/etl/processor/services/RequestProcessor.kt

@@ -30,8 +30,11 @@ import dev.dnpm.etl.processor.monitoring.RequestStatus
 import dev.dnpm.etl.processor.monitoring.RequestType
 import dev.dnpm.etl.processor.output.*
 import dev.dnpm.etl.processor.pseudonym.PseudonymizeService
+import dev.dnpm.etl.processor.pseudonym.addGenomDeTan
 import dev.dnpm.etl.processor.pseudonym.anonymizeContentWith
 import dev.dnpm.etl.processor.pseudonym.pseudonymizeWith
+import dev.pcvolkmer.mv64e.mtb.ConsentProvision
+import dev.pcvolkmer.mv64e.mtb.ModelProjectConsentPurpose
 import dev.pcvolkmer.mv64e.mtb.Mtb
 import org.apache.commons.codec.binary.Base32
 import org.apache.commons.codec.digest.DigestUtils
@@ -76,9 +79,12 @@ class RequestProcessor(
     fun processMtbFile(mtbFile: Mtb, requestId: RequestId) {
         val pid = PatientId(extractPatientIdentifier(mtbFile))
 
-        val isConsentOk = consentProcessor != null &&
-                consentProcessor.consentGatedCheckAndTryEmbedding(mtbFile) || consentProcessor == null
+        val isConsentOk =
+            consentProcessor != null && consentProcessor.consentGatedCheckAndTryEmbedding(mtbFile) || consentProcessor == null
         if (isConsentOk) {
+            if (isGenomDeConsented(mtbFile)) {
+                mtbFile addGenomDeTan pseudonymizeService
+            }
             mtbFile pseudonymizeWith pseudonymizeService
             mtbFile anonymizeContentWith pseudonymizeService
             val request = DnpmV2MtbFileRequest(requestId, transformationService.transform(mtbFile))
@@ -93,6 +99,13 @@ class RequestProcessor(
         }
     }
 
+    private fun isGenomDeConsented(mtbFile: Mtb): Boolean {
+        val isModelProjectConsented = mtbFile.metadata?.modelProjectConsent?.provisions?.any { p ->
+            p.purpose == ModelProjectConsentPurpose.SEQUENCING && p.type == ConsentProvision.PERMIT
+        } == true
+        return isModelProjectConsented
+    }
+
     private fun <T> saveAndSend(request: MtbFileRequest<T>, pid: PatientId) {
         requestService.save(
             Request(