feat: check consent for DNPM 2.1 requests (#126)

Co-authored-by: Jakub Lidke <jakub.lidke@uni-marburg.de>

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

@@ -73,8 +73,8 @@ data class GIcsConfigProperties(
      *
      */
     val uri: String?,
-    val username: String?,
-    val password: String?,
+    val username: String? = null,
+    val password: String? = null,
 
     /**
      * gICS specific system

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

@@ -20,9 +20,9 @@
 package dev.dnpm.etl.processor.config
 
 import com.fasterxml.jackson.databind.ObjectMapper
-import dev.dnpm.etl.processor.consent.ConsentByMtbFile
+import dev.dnpm.etl.processor.consent.MtbFileConsentService
 import dev.dnpm.etl.processor.consent.GicsConsentService
-import dev.dnpm.etl.processor.consent.IGetConsent
+import dev.dnpm.etl.processor.consent.IConsentService
 import dev.dnpm.etl.processor.monitoring.*
 import dev.dnpm.etl.processor.pseudonym.AnonymizingGenerator
 import dev.dnpm.etl.processor.pseudonym.Generator
@@ -218,7 +218,7 @@ class AppConfiguration {
         retryTemplate: RetryTemplate,
         restTemplate: RestTemplate,
         appFhirConfig: AppFhirConfig
-    ): IGetConsent {
+    ): IConsentService {
         return GicsConsentService(
             gIcsConfigProperties,
             retryTemplate,
@@ -234,7 +234,7 @@ class AppConfiguration {
         gIcsConfigProperties: GIcsConfigProperties,
         getObjectMapper: ObjectMapper,
         appFhirConfig: AppFhirConfig,
-        gicsConsentService: IGetConsent
+        gicsConsentService: IConsentService
     ): ConsentProcessor {
         return ConsentProcessor(
             configProperties,
@@ -261,8 +261,8 @@ class AppConfiguration {
 
     @Bean
     @ConditionalOnMissingBean
-    fun iGetConsentService(): IGetConsent {
-        return ConsentByMtbFile()
+    fun iGetConsentService(): IConsentService {
+        return MtbFileConsentService()
     }
 
 }
@@ -271,13 +271,9 @@ class GicsEnabledCondition :
     AnyNestedCondition(ConfigurationCondition.ConfigurationPhase.REGISTER_BEAN) {
 
     @ConditionalOnProperty(name = ["app.consent.service"], havingValue = "gics")
+    @ConditionalOnProperty(name = ["app.consent.gics.uri"])
     class OnGicsServiceSelected {
         // Just for Condition
     }
 
-    @ConditionalOnProperty(name = ["app.consent.gics.enabled"], havingValue = "true")
-    class OnGicsEnabled {
-        // Just for Condition
-    }
-
 }

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

@@ -20,6 +20,7 @@
 package dev.dnpm.etl.processor.config
 
 import com.fasterxml.jackson.databind.ObjectMapper
+import dev.dnpm.etl.processor.consent.ConsentEvaluator
 import dev.dnpm.etl.processor.input.KafkaInputListener
 import dev.dnpm.etl.processor.monitoring.ConnectionCheckResult
 import dev.dnpm.etl.processor.monitoring.ConnectionCheckService
@@ -100,9 +101,10 @@ class AppKafkaConfiguration {
     @ConditionalOnProperty(value = ["app.kafka.input-topic"])
     fun kafkaInputListener(
         requestProcessor: RequestProcessor,
-        objectMapper: ObjectMapper
+        objectMapper: ObjectMapper,
+        consentEvaluator: ConsentEvaluator
     ): KafkaInputListener {
-        return KafkaInputListener(requestProcessor, objectMapper)
+        return KafkaInputListener(requestProcessor, consentEvaluator, objectMapper)
     }
 
     @Bean
@@ -113,4 +115,4 @@ class AppKafkaConfiguration {
         return KafkaConnectionCheckService(consumerFactory.createConsumer(), connectionCheckUpdateProducer)
     }
 
-}
+}

src/main/kotlin/dev/dnpm/etl/processor/consent/ConsentEvaluator.kt

@@ -0,0 +1,66 @@
+/*
+ * This file is part of ETL-Processor
+ *
+ * Copyright (c) 2025  Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as published
+ * by the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program.  If not, see <https://www.gnu.org/licenses/>.
+ */
+
+package dev.dnpm.etl.processor.consent
+
+import dev.pcvolkmer.mv64e.mtb.ConsentProvision
+import dev.pcvolkmer.mv64e.mtb.ModelProjectConsentPurpose
+import dev.pcvolkmer.mv64e.mtb.Mtb
+import org.springframework.stereotype.Service
+
+/**
+ * Evaluates consent using provided consent service and file based consent information
+ */
+@Service
+class ConsentEvaluator(
+    private val consentService: IConsentService
+) {
+    fun check(mtbFile: Mtb): ConsentEvaluation {
+        val ttpConsentStatus = consentService.getTtpBroadConsentStatus(mtbFile.patient.id)
+        val consentGiven = ttpConsentStatus == TtpConsentStatus.BROAD_CONSENT_GIVEN
+                || ttpConsentStatus == TtpConsentStatus.GENOM_DE_CONSENT_SEQUENCING_PERMIT
+                // Aktuell nur Modellvorhaben Consent im File
+                || ttpConsentStatus == TtpConsentStatus.UNKNOWN_CHECK_FILE && mtbFile.metadata?.modelProjectConsent?.provisions?.any {
+                    it.purpose == ModelProjectConsentPurpose.SEQUENCING
+                            && it.type == ConsentProvision.PERMIT
+                } == true
+
+        return ConsentEvaluation(ttpConsentStatus, consentGiven)
+    }
+}
+
+data class ConsentEvaluation(private val ttpConsentStatus: TtpConsentStatus, private val consentGiven: Boolean) {
+    /**
+     * Checks if any required consent is present
+     */
+    fun hasConsent(): Boolean {
+        return consentGiven
+    }
+
+    /**
+     * Returns the consent status
+     */
+    fun getStatus(): TtpConsentStatus {
+        if (ttpConsentStatus == TtpConsentStatus.UNKNOWN_CHECK_FILE) {
+            // in case ttp check is disabled - we propagate rejected status anyway
+            return TtpConsentStatus.BROAD_CONSENT_MISSING_OR_REJECTED
+        }
+        return ttpConsentStatus
+    }
+}

src/main/kotlin/dev/dnpm/etl/processor/input/KafkaInputListener.kt

@@ -23,9 +23,9 @@ import com.fasterxml.jackson.databind.ObjectMapper
 import dev.dnpm.etl.processor.CustomMediaType
 import dev.dnpm.etl.processor.PatientId
 import dev.dnpm.etl.processor.RequestId
+import dev.dnpm.etl.processor.consent.ConsentEvaluator
 import dev.dnpm.etl.processor.consent.TtpConsentStatus
 import dev.dnpm.etl.processor.services.RequestProcessor
-import dev.pcvolkmer.mv64e.mtb.ConsentProvision
 import dev.pcvolkmer.mv64e.mtb.Mtb
 import org.apache.kafka.clients.consumer.ConsumerRecord
 import org.slf4j.LoggerFactory
@@ -34,6 +34,7 @@ import org.springframework.kafka.listener.MessageListener
 
 class KafkaInputListener(
     private val requestProcessor: RequestProcessor,
+    private val consentEvaluator: ConsentEvaluator,
     private val objectMapper: ObjectMapper
 ) : MessageListener<String, String> {
     private val logger = LoggerFactory.getLogger(KafkaInputListener::class.java)
@@ -70,8 +71,7 @@ class KafkaInputListener(
             RequestId("")
         }
 
-        // TODO: Use MV Consent for now - needs to be replaced with proper consent evaluation
-        if (mtbFile.metadata.modelProjectConsent.provisions.filter { it.type == ConsentProvision.PERMIT }.isNotEmpty()) {
+        if (consentEvaluator.check(mtbFile).hasConsent()) {
             logger.debug("Accepted MTB File for processing")
             if (requestId.isBlank()) {
                 requestProcessor.processMtbFile(mtbFile)

src/main/kotlin/dev/dnpm/etl/processor/input/MtbFileRestController.kt

@@ -21,7 +21,7 @@ package dev.dnpm.etl.processor.input
 
 import dev.dnpm.etl.processor.CustomMediaType
 import dev.dnpm.etl.processor.PatientId
-import dev.dnpm.etl.processor.consent.IGetConsent
+import dev.dnpm.etl.processor.consent.ConsentEvaluator
 import dev.dnpm.etl.processor.consent.TtpConsentStatus
 import dev.dnpm.etl.processor.services.RequestProcessor
 import dev.pcvolkmer.mv64e.mtb.Mtb
@@ -34,9 +34,8 @@ import org.springframework.web.bind.annotation.*
 @RequestMapping(path = ["mtbfile", "mtb"])
 class MtbFileRestController(
     private val requestProcessor: RequestProcessor,
-    private val iGetConsent: IGetConsent
+    private val consentEvaluator: ConsentEvaluator
 ) {
-
     private val logger = LoggerFactory.getLogger(MtbFileRestController::class.java)
 
     @GetMapping
@@ -46,8 +45,15 @@ class MtbFileRestController(
 
     @PostMapping(consumes = [MediaType.APPLICATION_JSON_VALUE, CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE])
     fun mtbFile(@RequestBody mtbFile: Mtb): ResponseEntity<Unit> {
-        logger.debug("Accepted MTB File (DNPM V2) for processing")
-        requestProcessor.processMtbFile(mtbFile)
+        val consentEvaluation = consentEvaluator.check(mtbFile)
+        if (consentEvaluation.hasConsent()) {
+            logger.debug("Accepted MTB File (DNPM V2) for processing")
+            requestProcessor.processMtbFile(mtbFile)
+        } else {
+            logger.debug("Accepted MTB File (DNPM V2) and process deletion")
+            val patientId = PatientId(mtbFile.patient.id)
+            requestProcessor.processDeletion(patientId, consentEvaluation.getStatus())
+        }
         return ResponseEntity.accepted().build()
     }
 

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

@@ -6,9 +6,9 @@ import com.fasterxml.jackson.core.type.TypeReference
 import com.fasterxml.jackson.databind.ObjectMapper
 import dev.dnpm.etl.processor.config.AppConfigProperties
 import dev.dnpm.etl.processor.config.GIcsConfigProperties
-import dev.dnpm.etl.processor.consent.ConsentByMtbFile
+import dev.dnpm.etl.processor.consent.MtbFileConsentService
 import dev.dnpm.etl.processor.consent.ConsentDomain
-import dev.dnpm.etl.processor.consent.IGetConsent
+import dev.dnpm.etl.processor.consent.IConsentService
 import dev.dnpm.etl.processor.pseudonym.ensureMetaDataIsInitialized
 import dev.pcvolkmer.mv64e.mtb.*
 import org.apache.commons.lang3.NotImplementedException
@@ -31,7 +31,7 @@ class ConsentProcessor(
     private val gIcsConfigProperties: GIcsConfigProperties,
     private val objectMapper: ObjectMapper,
     private val fhirContext: FhirContext,
-    private val consentService: IGetConsent
+    private val consentService: IConsentService
 ) {
     private var logger: Logger = LoggerFactory.getLogger("ConsentProcessor")
 
@@ -49,7 +49,7 @@ class ConsentProcessor(
      *
      */
     fun consentGatedCheckAndTryEmbedding(mtbFile: Mtb): Boolean {
-        if (consentService is ConsentByMtbFile) {
+        if (consentService is MtbFileConsentService) {
             // consent check is disabled
             return true
         }
@@ -70,7 +70,7 @@ class ConsentProcessor(
          * broad consent
          */
         val broadConsent = consentService.getConsent(
-            personIdentifierValue, requestDate, ConsentDomain.BroadConsent
+            personIdentifierValue, requestDate, ConsentDomain.BROAD_CONSENT
         )
         val broadConsentHasBeenAsked = !broadConsent.entry.isEmpty()
 
@@ -78,7 +78,7 @@ class ConsentProcessor(
         if (!broadConsentHasBeenAsked) return false
 
         val genomeDeConsent = consentService.getConsent(
-            personIdentifierValue, requestDate, ConsentDomain.Modelvorhaben64e
+            personIdentifierValue, requestDate, ConsentDomain.MODELLVORHABEN_64E
         )
 
         addGenomeDbProvisions(mtbFile, genomeDeConsent)
@@ -88,11 +88,11 @@ class ConsentProcessor(
         embedBroadConsentResources(mtbFile, broadConsent)
 
         val broadConsentStatus = getProvisionTypeByPolicyCode(
-            broadConsent, requestDate, ConsentDomain.BroadConsent
+            broadConsent, requestDate, ConsentDomain.BROAD_CONSENT
         )
 
         val genomDeSequencingStatus = getProvisionTypeByPolicyCode(
-            genomeDeConsent, requestDate, ConsentDomain.Modelvorhaben64e
+            genomeDeConsent, requestDate, ConsentDomain.MODELLVORHABEN_64E
         )
 
         if (Consent.ConsentProvisionType.NULL == broadConsentStatus) {
@@ -204,10 +204,10 @@ class ConsentProcessor(
     ): Consent.ConsentProvisionType {
         val code: String?
         val system: String?
-        if (ConsentDomain.BroadConsent == consentDomain) {
+        if (ConsentDomain.BROAD_CONSENT == consentDomain) {
             code = gIcsConfigProperties.broadConsentPolicyCode
             system = gIcsConfigProperties.broadConsentPolicySystem
-        } else if (ConsentDomain.Modelvorhaben64e == consentDomain) {
+        } else if (ConsentDomain.MODELLVORHABEN_64E == consentDomain) {
             code = gIcsConfigProperties.genomeDePolicyCode
             system = gIcsConfigProperties.genomeDePolicySystem
         } else {
@@ -279,4 +279,4 @@ class ConsentProcessor(
         return isRequestDateAfterOrEqualStart <= 0 && isRequestDateBeforeOrEqualEnd >= 0
     }
 
-}
+}