refactor: moved consent evaluation to new ConsentProcessor.kt

src/integrationTest/kotlin/dev/dnpm/etl/processor/input/MtbFileRestControllerTest.kt

@@ -23,9 +23,9 @@ import com.fasterxml.jackson.databind.ObjectMapper
 import de.ukw.ccc.bwhc.dto.*
 import dev.dnpm.etl.processor.anyValueClass
 import dev.dnpm.etl.processor.config.AppSecurityConfiguration
-import dev.dnpm.etl.processor.consent.ConsentCheckFileBased
+import dev.dnpm.etl.processor.consent.ConsentByMtbFile
 import dev.dnpm.etl.processor.consent.TtpConsentStatus
-import dev.dnpm.etl.processor.consent.ICheckConsent
+import dev.dnpm.etl.processor.consent.IGetConsent
 import dev.dnpm.etl.processor.security.TokenRepository
 import dev.dnpm.etl.processor.security.UserRoleRepository
 import dev.dnpm.etl.processor.services.RequestProcessor
@@ -55,7 +55,7 @@ import org.springframework.test.web.servlet.post
     classes = [
         MtbFileRestController::class,
         AppSecurityConfiguration::class,
-        ConsentCheckFileBased::class, ICheckConsent::class
+        ConsentByMtbFile::class, IGetConsent::class
     ]
 )
 @MockitoBean(types = [TokenRepository::class, RequestProcessor::class])

src/main/java/dev/dnpm/etl/processor/consent/ConsentByMtbFile.java

@@ -1,18 +1,15 @@
 package dev.dnpm.etl.processor.consent;
 
-import dev.pcvolkmer.mv64e.mtb.Mtb;
 import java.util.Date;
-import org.apache.commons.lang3.NotImplementedException;
 import org.hl7.fhir.r4.model.Bundle;
-import org.hl7.fhir.r4.model.Consent.ConsentProvisionType;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-public class ConsentCheckFileBased implements ICheckConsent {
+public class ConsentByMtbFile implements IGetConsent {
 
-    private static final Logger log = LoggerFactory.getLogger(ConsentCheckFileBased.class);
+    private static final Logger log = LoggerFactory.getLogger(ConsentByMtbFile.class);
 
-    public ConsentCheckFileBased() {
+    public ConsentByMtbFile() {
         log.info("ConsentCheckFileBased initialized...");
     }
 
@@ -23,12 +20,12 @@ public class ConsentCheckFileBased implements ICheckConsent {
 
     @Override
     public Bundle getBroadConsent(String personIdentifierValue, Date requestDate) {
-        return ICheckConsent.super.getBroadConsent(personIdentifierValue, requestDate);
+        return IGetConsent.super.getBroadConsent(personIdentifierValue, requestDate);
     }
 
     @Override
     public Bundle getGenomDeConsent(String personIdentifierValue, Date requestDate) {
-        return ICheckConsent.super.getGenomDeConsent(personIdentifierValue, requestDate);
+        return IGetConsent.super.getGenomDeConsent(personIdentifierValue, requestDate);
     }
 
     @Override
@@ -36,10 +33,4 @@ public class ConsentCheckFileBased implements ICheckConsent {
         ConsentDomain targetConsentDomain, Date requestDate) {
         return new Bundle();
     }
-
-    @Override
-    public ConsentProvisionType getProvisionTypeByPolicyCode(Bundle consentBundle,
-        Date requestDate, ConsentDomain consentDomain) {
-        return ConsentProvisionType.NULL;
-    }
 }

src/main/java/dev/dnpm/etl/processor/consent/GicsConsentService.java

@@ -2,27 +2,18 @@ package dev.dnpm.etl.processor.consent;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.parser.DataFormatException;
-import com.fasterxml.jackson.databind.ObjectMapper;
 import dev.dnpm.etl.processor.config.AppFhirConfig;
 import dev.dnpm.etl.processor.config.GIcsConfigProperties;
 import java.util.Date;
-import java.util.Optional;
-import org.apache.commons.lang3.NotImplementedException;
 import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.r4.model.BooleanType;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Coding;
-import org.hl7.fhir.r4.model.Consent;
-import org.hl7.fhir.r4.model.Consent.ConsentProvisionType;
-import org.hl7.fhir.r4.model.Consent.ConsentState;
-import org.hl7.fhir.r4.model.Consent.ProvisionComponent;
 import org.hl7.fhir.r4.model.DateType;
 import org.hl7.fhir.r4.model.Identifier;
 import org.hl7.fhir.r4.model.OperationOutcome;
 import org.hl7.fhir.r4.model.Parameters;
 import org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent;
-import org.hl7.fhir.r4.model.Period;
-import org.hl7.fhir.r4.model.ResourceType;
 import org.hl7.fhir.r4.model.StringType;
 import org.jetbrains.annotations.NotNull;
 import org.slf4j.Logger;
@@ -39,7 +30,7 @@ import org.springframework.web.client.RestTemplate;
 import org.springframework.web.util.UriComponentsBuilder;
 
 
-public class GicsConsentService implements ICheckConsent {
+public class GicsConsentService implements IGetConsent {
 
     private final Logger log = LoggerFactory.getLogger(GicsConsentService.class);
 
@@ -272,83 +263,4 @@ public class GicsConsentService implements ICheckConsent {
         return TtpConsentStatus.FAILED_TO_ASK;
     }
 
-    /**
-     * @param consentBundle consent resource
-     * @param requestDate   date which must be within validation period of provision
-     * @return type of provision, will be {@link ConsentProvisionType#NULL} if none is found.
-     */
-    public ConsentProvisionType getProvisionTypeByPolicyCode(Bundle consentBundle,
-        Date requestDate, ConsentDomain consentDomain) {
-        String code;
-        String system;
-        if (ConsentDomain.BroadConsent == consentDomain) {
-            code = gIcsConfigProperties.getBroadConsentPolicyCode();
-            system = gIcsConfigProperties.getBroadConsentPolicySystem();
-        } else if (ConsentDomain.Modelvorhaben64e == consentDomain) {
-            code = gIcsConfigProperties.getGenomeDePolicyCode();
-            system = gIcsConfigProperties.getGenomeDePolicySystem();
-        } else {
-            throw new NotImplementedException("unknown consent domain " + consentDomain.name());
-        }
-
-        Optional<ConsentProvisionType> provisionTypeByPolicyCode = getProvisionTypeByPolicyCode(
-            consentBundle, code,
-            system, requestDate);
-        return provisionTypeByPolicyCode.orElse(ConsentProvisionType.NULL);
-    }
-
-    /**
-     * @param consentBundle            consent resource
-     * @param policyAndProvisionCode   policyRule and provision code value
-     * @param policyAndProvisionSystem policyRule and provision system value
-     * @param requestDate              date which must be within validation period of provision
-     * @return type of provision, will be {@link ConsentProvisionType#NULL} if none is found.
-     */
-    public Optional<ConsentProvisionType> getProvisionTypeByPolicyCode(Bundle consentBundle,
-        String policyAndProvisionCode, String policyAndProvisionSystem, Date requestDate) {
-        return consentBundle.getEntry().stream().filter(entry -> {
-            if (entry.getResource().getResourceType() != ResourceType.Consent) {
-                // no consent in bundle
-                return false;
-            }
-
-            Consent consent = (Consent) entry.getResource();
-
-            // consent ist active and its policy rule must fits search criteria
-            return consent.getStatus() == ConsentState.ACTIVE && checkCoding(
-                policyAndProvisionCode, policyAndProvisionSystem,
-                consent.getPolicyRule().getCodingFirstRep()) && isIsRequestDateInRange(requestDate,
-                consent.getProvision().getPeriod());
-
-        }).map(consentWithTargetPolicy -> {
-            ProvisionComponent provision = ((Consent) consentWithTargetPolicy.getResource()).getProvision();
-            var provisionComponentByCode = provision.getProvision().stream().filter(prov ->
-
-                checkCoding(policyAndProvisionCode, policyAndProvisionSystem,
-                    prov.getCodeFirstRep().getCodingFirstRep()) && isIsRequestDateInRange(
-                    requestDate, prov.getPeriod())
-
-            ).findFirst();
-
-            if (provisionComponentByCode.isPresent()) {
-                // actual provision we search for
-                return provisionComponentByCode.get().getType();
-            }
-            // no fitting nested provision found - fall back to wrapping provision with default value
-            return provision.getType();
-        }).findFirst().or(() -> Optional.of(ConsentProvisionType.NULL));
-    }
-
-    protected static boolean checkCoding(String researchAllowedPolicyOid,
-        String researchAllowedPolicySystem, Coding coding) {
-
-        return coding.getSystem().equals(researchAllowedPolicySystem) && coding.getCode()
-            .equals(researchAllowedPolicyOid);
-    }
-
-    protected static boolean isIsRequestDateInRange(Date requestdate, Period provPeriod) {
-        var isRequestDateAfterOrEqualStart = provPeriod.getStart().compareTo(requestdate);
-        var isRequestDateBeforeOrEqualEnd = provPeriod.getEnd().compareTo(requestdate);
-        return isRequestDateAfterOrEqualStart <= 0 && isRequestDateBeforeOrEqualEnd >= 0;
-    }
 }

src/main/java/dev/dnpm/etl/processor/consent/IGetConsent.java

@@ -2,9 +2,8 @@ package dev.dnpm.etl.processor.consent;
 
 import java.util.Date;
 import org.hl7.fhir.r4.model.Bundle;
-import org.hl7.fhir.r4.model.Consent.ConsentProvisionType;
 
-public interface ICheckConsent {
+public interface IGetConsent {
 
     /**
      * Get broad consent status for a patient identifier
@@ -50,12 +49,4 @@ public interface ICheckConsent {
     Bundle currentConsentForPersonAndTemplate(String personIdentifierValue,
         ConsentDomain targetConsentDomain, Date requestDate);
 
-    /**
-     * @param consentBundle consent resource
-     * @param requestDate   date which must be within validation period of provision
-     * @return type of provision, will be {@link ConsentProvisionType#NULL} if none is found.
-     */
-    ConsentProvisionType getProvisionTypeByPolicyCode(Bundle consentBundle, Date requestDate,
-        ConsentDomain consentDomain);
-
 }

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

@@ -20,8 +20,8 @@
 package dev.dnpm.etl.processor.config
 
 import com.fasterxml.jackson.databind.ObjectMapper
-import dev.dnpm.etl.processor.consent.ConsentCheckFileBased
+import dev.dnpm.etl.processor.consent.ConsentByMtbFile
-import dev.dnpm.etl.processor.consent.ICheckConsent
+import dev.dnpm.etl.processor.consent.IGetConsent
 import dev.dnpm.etl.processor.consent.GicsConsentService
 import dev.dnpm.etl.processor.monitoring.*
 import dev.dnpm.etl.processor.pseudonym.AnonymizingGenerator
@@ -212,7 +212,7 @@ class AppConfiguration {
     fun gicsConsentService(
         gIcsConfigProperties: GIcsConfigProperties,
         retryTemplate: RetryTemplate, restTemplate: RestTemplate, appFhirConfig: AppFhirConfig
-    ): ICheckConsent {
+    ): IGetConsent {
         return GicsConsentService(
             gIcsConfigProperties,
             retryTemplate,
@@ -227,7 +227,7 @@ class AppConfiguration {
         gIcsConfigProperties: GIcsConfigProperties,
         getObjectMapper: ObjectMapper,
         appFhirConfig: AppFhirConfig,
-        gicsConsentService: ICheckConsent
+        gicsConsentService: IGetConsent
     ): ConsentProcessor {
         return ConsentProcessor(
             gIcsConfigProperties,
@@ -253,8 +253,8 @@ class AppConfiguration {
 
     @Bean
     @ConditionalOnMissingBean
-    fun constService(): ICheckConsent {
+    fun iGetConsentService(): IGetConsent {
-        return ConsentCheckFileBased()
+        return ConsentByMtbFile()
     }
 }
 

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

@@ -23,7 +23,7 @@ import de.ukw.ccc.bwhc.dto.Consent
 import de.ukw.ccc.bwhc.dto.MtbFile
 import dev.dnpm.etl.processor.CustomMediaType
 import dev.dnpm.etl.processor.PatientId
-import dev.dnpm.etl.processor.consent.ICheckConsent
+import dev.dnpm.etl.processor.consent.IGetConsent
 import dev.dnpm.etl.processor.consent.TtpConsentStatus
 import dev.dnpm.etl.processor.services.RequestProcessor
 import dev.pcvolkmer.mv64e.mtb.Mtb
@@ -35,7 +35,7 @@ import org.springframework.web.bind.annotation.*
 @RestController
 @RequestMapping(path = ["mtbfile", "mtb"])
 class MtbFileRestController(
-    private val requestProcessor: RequestProcessor, private val iCheckConsent: ICheckConsent
+    private val requestProcessor: RequestProcessor, private val iGetConsent: IGetConsent
 ) {
 
     private val logger = LoggerFactory.getLogger(MtbFileRestController::class.java)
@@ -63,7 +63,7 @@ class MtbFileRestController(
     }
 
     private fun checkConsentStatus(mtbFile: MtbFile): Pair<TtpConsentStatus, Boolean> {
-        var ttpConsentStatus = iCheckConsent.getTtpBroadConsentStatus(mtbFile.patient.id)
+        var ttpConsentStatus = iGetConsent.getTtpBroadConsentStatus(mtbFile.patient.id)
 
         val isConsentOK =
             (ttpConsentStatus.equals(TtpConsentStatus.UNKNOWN_CHECK_FILE) && mtbFile.consent.status == Consent.Status.ACTIVE) ||

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

@@ -6,12 +6,14 @@ import com.fasterxml.jackson.core.type.TypeReference
 import com.fasterxml.jackson.databind.ObjectMapper
 import dev.dnpm.etl.processor.config.GIcsConfigProperties
 import dev.dnpm.etl.processor.consent.ConsentDomain
-import dev.dnpm.etl.processor.consent.ICheckConsent
+import dev.dnpm.etl.processor.consent.IGetConsent
 import dev.dnpm.etl.processor.pseudonym.ensureMetaDataIsInitialized
 import dev.pcvolkmer.mv64e.mtb.*
-import org.hl7.fhir.r4.model.Bundle
+import org.apache.commons.lang3.NotImplementedException
-import org.hl7.fhir.r4.model.CodeableConcept
+import org.hl7.fhir.r4.model.*
-import org.hl7.fhir.r4.model.Consent
+import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent
+import org.hl7.fhir.r4.model.Coding
+import org.hl7.fhir.r4.model.Consent.ConsentState
 import org.hl7.fhir.r4.model.Consent.ProvisionComponent
 import org.slf4j.Logger
 import org.slf4j.LoggerFactory
@@ -23,9 +25,10 @@ import java.util.*
 
 @Service
 class ConsentProcessor(
-    private val gIcsConfigProperties: GIcsConfigProperties, private val objectMapper: ObjectMapper,
+    private val gIcsConfigProperties: GIcsConfigProperties,
+    private val objectMapper: ObjectMapper,
     private val fhirContext: FhirContext,
-    private val consentService: ICheckConsent?
+    private val consentService: IGetConsent?
 ) {
     private var logger: Logger = LoggerFactory.getLogger("ConsentProcessor")
 
@@ -80,11 +83,11 @@ class ConsentProcessor(
 
         embedBroadConsentResources(mtbFile, broadConsent)
 
-        val broadConsentStatus = consentService.getProvisionTypeByPolicyCode(
+        val broadConsentStatus = getProvisionTypeByPolicyCode(
             broadConsent, requestDate, ConsentDomain.BroadConsent
         )
 
-        val genomDeSequencingStatus = consentService.getProvisionTypeByPolicyCode(
+        val genomDeSequencingStatus = getProvisionTypeByPolicyCode(
             genomeDeConsent, requestDate, ConsentDomain.Modelvorhaben64e
         )
 
@@ -92,27 +95,22 @@ class ConsentProcessor(
             // bc not asked
             return false
         }
-        if (Consent.ConsentProvisionType.PERMIT == broadConsentStatus ||
+        if (Consent.ConsentProvisionType.PERMIT == broadConsentStatus || Consent.ConsentProvisionType.PERMIT == genomDeSequencingStatus) return true
-            Consent.ConsentProvisionType.PERMIT == genomDeSequencingStatus
-        ) return true
 
         return false
     }
 
-    public fun embedBroadConsentResources(mtbFile: Mtb, broadConsent: Bundle) {
+    fun embedBroadConsentResources(mtbFile: Mtb, broadConsent: Bundle) {
         for (entry in broadConsent.getEntry()) {
             val resource = entry.getResource()
             if (resource is Consent) {
                 // since jackson convertValue does not work here,
                 // we need another step to back to string, before we convert to object map
-                val asJsonString =
+                val asJsonString = fhirContext.newJsonParser().encodeResourceToString(resource)
-                    fhirContext.newJsonParser().encodeResourceToString(resource)
                 try {
                     val mapOfJson: HashMap<String?, Any?>? =
                         objectMapper.readValue<HashMap<String?, Any?>?>(
-                            asJsonString,
+                            asJsonString, object : TypeReference<HashMap<String?, Any?>?>() {})
-                            object : TypeReference<HashMap<String?, Any?>?>() {
-                            })
                     mtbFile.metadata.researchConsents.add(mapOfJson)
                 } catch (e: JsonProcessingException) {
                     throw RuntimeException(e)
@@ -121,7 +119,7 @@ class ConsentProcessor(
         }
     }
 
-    public fun addGenomeDbProvisions(mtbFile: Mtb, consentGnomeDe: Bundle) {
+    fun addGenomeDbProvisions(mtbFile: Mtb, consentGnomeDe: Bundle) {
         for (entry in consentGnomeDe.getEntry()) {
             val resource = entry.getResource()
             if (resource !is Consent) {
@@ -157,8 +155,7 @@ class ConsentProcessor(
                     val provision = Provision.builder()
                         .type(ConsentProvision.valueOf(provisionComponent.getType().name))
                         .date(provisionComponent.getPeriod().getStart())
-                        .purpose(modelProjectConsentPurpose)
+                        .purpose(modelProjectConsentPurpose).build()
-                        .build()
 
                     mtbFile.metadata.modelProjectConsent.provisions.add(provision)
                 } catch (ioe: IOException) {
@@ -183,4 +180,89 @@ class ConsentProcessor(
         mtbFile.metadata.type = MvhSubmissionType.INITIAL
     }
 
+    /**
+     * @param consentBundle consent resource
+     * @param requestDate   date which must be within validation period of provision
+     * @return type of provision, will be [org.hl7.fhir.r4.model.Consent.ConsentProvisionType.NULL] if none is found.
+     */
+    fun getProvisionTypeByPolicyCode(
+        consentBundle: Bundle, requestDate: Date?, consentDomain: ConsentDomain
+    ): Consent.ConsentProvisionType {
+        val code: String?
+        val system: String?
+        if (ConsentDomain.BroadConsent == consentDomain) {
+            code = gIcsConfigProperties.broadConsentPolicyCode
+            system = gIcsConfigProperties.broadConsentPolicySystem
+        } else if (ConsentDomain.Modelvorhaben64e == consentDomain) {
+            code = gIcsConfigProperties.genomeDePolicyCode
+            system = gIcsConfigProperties.genomeDePolicySystem
+        } else {
+            throw NotImplementedException("unknown consent domain " + consentDomain.name)
+        }
+
+        val provisionTypeByPolicyCode = getProvisionTypeByPolicyCode(
+            consentBundle, code, system, requestDate
+        )
+        return provisionTypeByPolicyCode
+    }
+
+    /**
+     * @param consentBundle            consent resource
+     * @param policyAndProvisionCode   policyRule and provision code value
+     * @param policyAndProvisionSystem policyRule and provision system value
+     * @param requestDate              date which must be within validation period of provision
+     * @return type of provision, will be [org.hl7.fhir.r4.model.Consent.ConsentProvisionType.NULL] if none is found.
+     */
+    fun getProvisionTypeByPolicyCode(
+        consentBundle: Bundle,
+        policyAndProvisionCode: String?,
+        policyAndProvisionSystem: String?,
+        requestDate: Date?
+    ): Consent.ConsentProvisionType {
+        val entriesOfInterest = consentBundle.entry.filter { entry ->
+            entry.resource.isResource && entry.resource.resourceType == ResourceType.Consent && (entry.resource as Consent).status == ConsentState.ACTIVE && checkCoding(
+                policyAndProvisionCode,
+                policyAndProvisionSystem,
+                (entry.resource as Consent).policyRule.codingFirstRep
+            ) && isIsRequestDateInRange(
+                requestDate, (entry.resource as Consent).provision.period
+            )
+        }.map { consentWithTargetPolicy: BundleEntryComponent ->
+            val provision = (consentWithTargetPolicy.getResource() as Consent).getProvision()
+            val provisionComponentByCode =
+                provision.getProvision().stream().filter { prov: ProvisionComponent? ->
+                    checkCoding(
+                        policyAndProvisionCode,
+                        policyAndProvisionSystem,
+                        prov!!.getCodeFirstRep().getCodingFirstRep()
+                    ) && isIsRequestDateInRange(
+                        requestDate, prov.getPeriod()
+                    )
+                }.findFirst()
+            if (provisionComponentByCode.isPresent) {
+                // actual provision we search for
+                return@map provisionComponentByCode.get().getType()
+            } else {
+                if (provision.type != null) return provision.type
+
+            }
+            return Consent.ConsentProvisionType.NULL
+        }.firstOrNull()
+
+        if (entriesOfInterest == null) return Consent.ConsentProvisionType.NULL
+        return entriesOfInterest
+    }
+
+    fun checkCoding(
+        researchAllowedPolicyOid: String?, researchAllowedPolicySystem: String?, coding: Coding
+    ): Boolean {
+        return coding.getSystem() == researchAllowedPolicySystem && (coding.getCode() == researchAllowedPolicyOid)
+    }
+
+    fun isIsRequestDateInRange(requestdate: Date?, provPeriod: Period): Boolean {
+        val isRequestDateAfterOrEqualStart = provPeriod.getStart().compareTo(requestdate)
+        val isRequestDateBeforeOrEqualEnd = provPeriod.getEnd().compareTo(requestdate)
+        return isRequestDateAfterOrEqualStart <= 0 && isRequestDateBeforeOrEqualEnd >= 0
+    }
+
 }

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

@@ -23,8 +23,6 @@ import com.fasterxml.jackson.databind.ObjectMapper
 import de.ukw.ccc.bwhc.dto.MtbFile
 import dev.dnpm.etl.processor.*
 import dev.dnpm.etl.processor.config.AppConfigProperties
-import dev.dnpm.etl.processor.consent.ConsentDomain
-import dev.dnpm.etl.processor.consent.ICheckConsent
 import dev.dnpm.etl.processor.consent.TtpConsentStatus
 import dev.dnpm.etl.processor.monitoring.Report
 import dev.dnpm.etl.processor.monitoring.Request
@@ -33,19 +31,15 @@ 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.anonymizeContentWith
-import dev.dnpm.etl.processor.pseudonym.ensureMetaDataIsInitialized
 import dev.dnpm.etl.processor.pseudonym.pseudonymizeWith
 import dev.pcvolkmer.mv64e.mtb.Mtb
-import dev.pcvolkmer.mv64e.mtb.MvhSubmissionType
 import org.apache.commons.codec.binary.Base32
 import org.apache.commons.codec.digest.DigestUtils
-import org.hl7.fhir.r4.model.Consent
 import org.slf4j.Logger
 import org.slf4j.LoggerFactory
 import org.springframework.context.ApplicationEventPublisher
 import org.springframework.stereotype.Service
 import java.lang.RuntimeException
-import java.time.Clock
 import java.time.Instant
 import java.util.*
 
@@ -83,7 +77,7 @@ class RequestProcessor(
         val pid = PatientId(extractPatientIdentifier(mtbFile))
 
         val isConsentOk = consentProcessor != null &&
-                consentProcessor.consentGatedCheckAndTryEmbedding(mtbFile) || consentProcessor == null;
+                consentProcessor.consentGatedCheckAndTryEmbedding(mtbFile) || consentProcessor == null
         if (isConsentOk) {
             mtbFile pseudonymizeWith pseudonymizeService
             mtbFile anonymizeContentWith pseudonymizeService
@@ -190,7 +184,7 @@ class RequestProcessor(
                 )
             )
 
-        } catch (e: Exception) {
+        } catch (_: Exception) {
             requestService.save(
                 Request(
                     uuid = requestId,

src/test/java/dev/dnpm/etl/processor/consent/GicsConsentServiceTest.java

@@ -3,20 +3,13 @@ package dev.dnpm.etl.processor.consent;
 import static org.assertj.core.api.Assertions.assertThat;
 import static org.springframework.test.web.client.match.MockRestRequestMatchers.requestTo;
 import static org.springframework.test.web.client.response.MockRestResponseCreators.withSuccess;
-
-import ca.uhn.fhir.context.FhirContext;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import dev.dnpm.etl.processor.config.AppConfiguration;
 import dev.dnpm.etl.processor.config.AppFhirConfig;
 import dev.dnpm.etl.processor.config.GIcsConfigProperties;
-import java.io.IOException;
-import java.io.InputStream;
 import java.time.Instant;
-import java.time.OffsetDateTime;
 import java.util.Date;
 import org.hl7.fhir.r4.model.BooleanType;
-import org.hl7.fhir.r4.model.Bundle;
-import org.hl7.fhir.r4.model.Consent.ConsentProvisionType;
 import org.hl7.fhir.r4.model.Identifier;
 import org.hl7.fhir.r4.model.OperationOutcome;
 import org.hl7.fhir.r4.model.OperationOutcome.IssueSeverity;
@@ -27,17 +20,13 @@ import org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent;
 import org.hl7.fhir.r4.model.StringType;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
-import org.junit.jupiter.params.ParameterizedTest;
-import org.junit.jupiter.params.provider.CsvSource;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.test.autoconfigure.web.client.RestClientTest;
-import org.springframework.core.io.ClassPathResource;
 import org.springframework.http.MediaType;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.TestPropertySource;
 import org.springframework.test.web.client.MockRestServiceServer;
 
-
 @ContextConfiguration(classes = {AppConfiguration.class, ObjectMapper.class})
 @TestPropertySource(properties = {"app.consent.gics.enabled=true",
     "app.consent.gics.uri=http://localhost:8090/ttp-fhir/fhir/gics"})
@@ -63,7 +52,6 @@ public class GicsConsentServiceTest {
     @BeforeEach
     public void setUp() {
         mockRestServiceServer = MockRestServiceServer.createServer(appConfiguration.restTemplate());
-
     }
 
     @Test
@@ -72,12 +60,10 @@ public class GicsConsentServiceTest {
             new ParametersParameterComponent().setName("consented")
                 .setValue(new BooleanType().setValue(true)));
 
-        mockRestServiceServer.expect(
+        mockRestServiceServer.expect(requestTo(
-            requestTo("http://localhost:8090/ttp-fhir/fhir/gics"
+                "http://localhost:8090/ttp-fhir/fhir/gics" + GicsConsentService.IS_CONSENTED_ENDPOINT))
-                + GicsConsentService.IS_CONSENTED_ENDPOINT)).andRespond(
+            .andRespond(withSuccess(appFhirConfig.fhirContext().newJsonParser()
-            withSuccess(appFhirConfig.fhirContext().newJsonParser()
+                .encodeResourceToString(responseConsented), MediaType.APPLICATION_JSON));
-                    .encodeResourceToString(responseConsented),
-                MediaType.APPLICATION_JSON));
 
         var consentStatus = gicsConsentService.getTtpBroadConsentStatus("123456");
         assertThat(consentStatus).isEqualTo(TtpConsentStatus.BROAD_CONSENT_GIVEN);
@@ -89,11 +75,10 @@ public class GicsConsentServiceTest {
             new ParametersParameterComponent().setName("consented")
                 .setValue(new BooleanType().setValue(false)));
 
-        mockRestServiceServer.expect(
+        mockRestServiceServer.expect(requestTo(
-            requestTo("http://localhost:8090/ttp-fhir/fhir/gics"
+                "http://localhost:8090/ttp-fhir/fhir/gics" + GicsConsentService.IS_CONSENTED_ENDPOINT))
-                + GicsConsentService.IS_CONSENTED_ENDPOINT)).andRespond(
+            .andRespond(withSuccess(
-            withSuccess(appFhirConfig.fhirContext().newJsonParser()
+                appFhirConfig.fhirContext().newJsonParser().encodeResourceToString(responseRevoced),
-                    .encodeResourceToString(responseRevoced),
                 MediaType.APPLICATION_JSON));
 
         var consentStatus = gicsConsentService.getTtpBroadConsentStatus("123456");
@@ -104,15 +89,13 @@ public class GicsConsentServiceTest {
     @Test
     void gicsParameterInvalid() {
         final OperationOutcome responseErrorOutcome = new OperationOutcome().addIssue(
-            new OperationOutcomeIssueComponent().setSeverity(
+            new OperationOutcomeIssueComponent().setSeverity(IssueSeverity.ERROR)
-                    IssueSeverity.ERROR).setCode(IssueType.PROCESSING)
+                .setCode(IssueType.PROCESSING).setDiagnostics("Invalid policy parameter..."));
-                .setDiagnostics("Invalid policy parameter..."));
 
         mockRestServiceServer.expect(
             requestTo(GICS_BASE_URI + GicsConsentService.IS_CONSENTED_ENDPOINT)).andRespond(
             withSuccess(appFhirConfig.fhirContext().newJsonParser()
-                    .encodeResourceToString(responseErrorOutcome),
+                .encodeResourceToString(responseErrorOutcome), MediaType.APPLICATION_JSON));
-                MediaType.APPLICATION_JSON));
 
         var consentStatus = gicsConsentService.getTtpBroadConsentStatus("123456");
         assertThat(consentStatus).isEqualTo(TtpConsentStatus.FAILED_TO_ASK);
@@ -122,51 +105,19 @@ public class GicsConsentServiceTest {
     void buildRequestParameterCurrentPolicyStatesForPersonTest() {
 
         String pid = "12345678";
-        var result = GicsConsentService.buildRequestParameterCurrentPolicyStatesForPerson(gIcsConfigProperties,
+        var result = GicsConsentService.buildRequestParameterCurrentPolicyStatesForPerson(
-            pid, Date.from(Instant.now()),gIcsConfigProperties.getGenomDeConsentDomainName());
+            gIcsConfigProperties, pid, Date.from(Instant.now()),
+            gIcsConfigProperties.getGenomDeConsentDomainName());
 
-        assertThat(result.getParameter().size()).as("should contain 3 parameter resources").isEqualTo(3);
+        assertThat(result.getParameter().size()).as("should contain 3 parameter resources")
+            .isEqualTo(3);
 
-        assertThat(((StringType)result.getParameter("domain").getValue()).getValue()).isEqualTo(gIcsConfigProperties.getGenomDeConsentDomainName());
+        assertThat(((StringType) result.getParameter("domain").getValue()).getValue()).isEqualTo(
-        assertThat(((Identifier)result.getParameter("personIdentifier").getValue()).getValue()).isEqualTo(pid);
+            gIcsConfigProperties.getGenomDeConsentDomainName());
+        assertThat(
+            ((Identifier) result.getParameter("personIdentifier").getValue()).getValue()).isEqualTo(
+            pid);
     }
 
 
-    @ParameterizedTest
-    @CsvSource({
-        "2.16.840.1.113883.3.1937.777.24.5.3.8,urn:oid:2.16.840.1.113883.3.1937.777.24.5.3,2025-07-23T00:00:00+02:00,PERMIT,expect permit",
-        "2.16.840.1.113883.3.1937.777.24.5.3.8,urn:oid:2.16.840.1.113883.3.1937.777.24.5.3,2025-06-23T00:00:00+02:00,PERMIT,expect permit date is exactly on start",
-        "2.16.840.1.113883.3.1937.777.24.5.3.8,urn:oid:2.16.840.1.113883.3.1937.777.24.5.3,2055-06-23T00:00:00+02:00,PERMIT,expect permit date is exactly on end",
-        "2.16.840.1.113883.3.1937.777.24.5.3.8,urn:oid:2.16.840.1.113883.3.1937.777.24.5.3,2021-06-23T00:00:00+02:00,NULL,date is before start",
-        "2.16.840.1.113883.3.1937.777.24.5.3.8,urn:oid:2.16.840.1.113883.3.1937.777.24.5.3,2060-06-23T00:00:00+02:00,NULL,date is after end",
-        "2.16.840.1.113883.3.1937.777.24.5.3.8,XXXX,2025-07-23T00:00:00+02:00,NULL,system not found - therefore expect NULL",
-        "2.16.840.1.113883.3.1937.777.24.5.3.27,urn:oid:2.16.840.1.113883.3.1937.777.24.5.3,2025-07-23T00:00:00+02:00,DENY,provision is denied"})
-    void getProvisionTypeByPolicyCode(String code, String system, String timeStamp, String expected,
-        String desc) {
-
-        var testData = getDummyBroadConsent();
-
-        Date requestDate = Date.from(OffsetDateTime.parse(timeStamp).toInstant());
-
-        var result = gicsConsentService.getProvisionTypeByPolicyCode(testData, code, system, requestDate);
-        assertThat(result).isNotNull();
-        assertThat(result).isNotEmpty();
-
-        assertThat(result.get()).as(desc).isEqualTo(ConsentProvisionType.valueOf(expected));
-    }
-
-    private Bundle getDummyBroadConsent() {
-
-        InputStream bundle;
-        try {
-            bundle = new ClassPathResource(
-                "fake_broadConsent_gics_response_permit.json").getInputStream();
-        } catch (IOException e) {
-            throw new RuntimeException(e);
-        }
-
-        return FhirContext.forR4().newJsonParser().parseResource(Bundle.class, bundle);
-
-    }
-
 }

src/test/kotlin/dev/dnpm/etl/processor/input/MtbFileRestControllerTest.kt

@@ -23,7 +23,7 @@ import com.fasterxml.jackson.databind.ObjectMapper
 import de.ukw.ccc.bwhc.dto.*
 import de.ukw.ccc.bwhc.dto.Consent.Status
 import dev.dnpm.etl.processor.CustomMediaType
-import dev.dnpm.etl.processor.consent.ConsentCheckFileBased
+import dev.dnpm.etl.processor.consent.ConsentByMtbFile
 import dev.dnpm.etl.processor.consent.GicsConsentService
 import dev.dnpm.etl.processor.consent.TtpConsentStatus
 import dev.dnpm.etl.processor.services.RequestProcessor
@@ -68,7 +68,7 @@ class MtbFileRestControllerTest {
         ) {
             this.requestProcessor = requestProcessor
             val controller = MtbFileRestController(requestProcessor,
-                ConsentCheckFileBased()
+                ConsentByMtbFile()
             )
             this.mockMvc = MockMvcBuilders.standaloneSetup(controller).build()
         }
@@ -220,7 +220,7 @@ class MtbFileRestControllerTest {
         ) {
             this.requestProcessor = requestProcessor
             val controller = MtbFileRestController(requestProcessor,
-                ConsentCheckFileBased()
+                ConsentByMtbFile()
             )
             this.mockMvc = MockMvcBuilders.standaloneSetup(controller).build()
         }

src/test/kotlin/dev/dnpm/etl/processor/pseudonym/ExtensionsTest.kt

@@ -26,7 +26,7 @@ import de.ukw.ccc.bwhc.dto.Patient
 import dev.dnpm.etl.processor.config.GIcsConfigProperties
 import dev.dnpm.etl.processor.config.JacksonConfig
 import dev.dnpm.etl.processor.services.ConsentProcessor
-import dev.dnpm.etl.processor.services.TransformationServiceTest
+import dev.dnpm.etl.processor.services.ConsentProcessorTest
 import dev.pcvolkmer.mv64e.mtb.*
 import org.assertj.core.api.Assertions.assertThat
 import org.hl7.fhir.r4.model.Bundle
@@ -252,7 +252,7 @@ class ExtensionsTest {
 
 
             val bundle = Bundle()
-            val dummyConsent = TransformationServiceTest.getDummyConsent()
+            val dummyConsent = ConsentProcessorTest.getDummyGenomDeConsent()
             dummyConsent.patient.reference = "Patient/$CLEAN_PATIENT_ID"
             bundle.addEntry().resource = dummyConsent
 

src/test/kotlin/dev/dnpm/etl/processor/services/ConsentProcessorTest.kt

@@ -0,0 +1,160 @@
+package dev.dnpm.etl.processor.services
+
+import ca.uhn.fhir.context.FhirContext
+import com.fasterxml.jackson.databind.ObjectMapper
+import dev.dnpm.etl.processor.config.GIcsConfigProperties
+import dev.dnpm.etl.processor.config.JacksonConfig
+import dev.dnpm.etl.processor.consent.GicsConsentService
+import dev.pcvolkmer.mv64e.mtb.*
+import org.assertj.core.api.Assertions.assertThat
+import org.hl7.fhir.r4.model.Bundle
+import org.hl7.fhir.r4.model.CodeableConcept
+import org.hl7.fhir.r4.model.Coding
+import org.hl7.fhir.r4.model.Consent
+import org.junit.jupiter.api.BeforeEach
+import org.junit.jupiter.api.Test
+import org.junit.jupiter.api.extension.ExtendWith
+import org.junit.jupiter.params.ParameterizedTest
+import org.junit.jupiter.params.provider.CsvSource
+import org.mockito.Mock
+import org.mockito.junit.jupiter.MockitoExtension
+import org.mockito.kotlin.any
+import org.mockito.kotlin.doAnswer
+import org.mockito.kotlin.whenever
+import org.springframework.core.io.ClassPathResource
+import java.io.IOException
+import java.io.InputStream
+import java.time.Instant
+import java.time.OffsetDateTime
+import java.util.*
+
+@ExtendWith(MockitoExtension::class)
+class ConsentProcessorTest {
+
+    private lateinit var gicsConsentService: GicsConsentService
+    private lateinit var objectMapper: ObjectMapper
+    private lateinit var gIcsConfigProperties: GIcsConfigProperties
+    private lateinit var fhirContext: FhirContext
+    private lateinit var consentProcessor: ConsentProcessor
+
+    @BeforeEach
+    fun setups(
+        @Mock gicsConsentService: GicsConsentService,
+    ) {
+
+        this.gIcsConfigProperties = GIcsConfigProperties(null, null, null, true)
+        val jacksonConfig = JacksonConfig()
+        this.objectMapper = jacksonConfig.objectMapper()
+        this.fhirContext = JacksonConfig.fhirContext()
+        this.gicsConsentService = gicsConsentService
+
+        this.consentProcessor =
+            ConsentProcessor(gIcsConfigProperties, objectMapper, fhirContext, gicsConsentService)
+    }
+
+    @Test
+    fun consentOk() {
+        assertThat(consentProcessor.toString()).isNotNull
+        // prep gICS response
+        doAnswer { getDummyBroadConsentBundle() }.whenever(gicsConsentService)
+            .getBroadConsent(any(), any())
+        doAnswer { Bundle() }.whenever(gicsConsentService)
+            .getGenomDeConsent(any(), any())
+
+        val inputMtb = Mtb.builder()
+            .patient(Patient.builder().id("d611d429-5003-11f0-a144-661e92ac9503").build()).build()
+        val checkResult = consentProcessor.consentGatedCheckAndTryEmbedding(inputMtb)
+
+        assertThat(checkResult).isTrue
+        assertThat(inputMtb.metadata.researchConsents).hasSize(13)
+    }
+
+    companion object {
+        fun getDummyGenomDeConsent(): Consent {
+            val consent = Consent()
+            consent.id = "consent 1 id"
+            consent.patient.reference = "Patient/1234-pat1"
+
+            consent.provision.setType(
+                Consent.ConsentProvisionType.fromCode(
+                    "deny"
+                )
+            )
+            consent.provision.period.start =
+                Date.from(Instant.parse("2025-06-23T00:00:00.00Z"))
+            consent.provision.period.end =
+                Date.from(Instant.parse("3000-01-01T00:00:00.00Z"))
+
+            val addProvision1 = consent.provision.addProvision()
+            addProvision1.setType(Consent.ConsentProvisionType.fromCode("permit"))
+            addProvision1.period.start = Date.from(Instant.parse("2025-06-23T00:00:00.00Z"))
+            addProvision1.period.end = Date.from(Instant.parse("3000-01-01T00:00:00.00Z"))
+            addProvision1.code.addLast(
+                CodeableConcept(
+                    Coding(
+                        "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
+                        "Teilnahme",
+                        "Teilnahme am Modellvorhaben und Einwilligung zur Genomsequenzierung"
+                    )
+                )
+            )
+
+            val addProvision2 = consent.provision.addProvision()
+            addProvision2.setType(Consent.ConsentProvisionType.fromCode("deny"))
+            addProvision2.period.start = Date.from(Instant.parse("2025-06-23T00:00:00.00Z"))
+            addProvision2.period.end = Date.from(Instant.parse("3000-01-01T00:00:00.00Z"))
+            addProvision2.code.addLast(
+                CodeableConcept(
+                    Coding(
+                        "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
+                        "Rekontaktierung",
+                        "Re-Identifizierung meiner Daten über die Vertrauensstelle beim Robert Koch-Institut und in die erneute Kontaktaufnahme durch meine behandelnde Ärztin oder meinen behandelnden Arzt"
+                    )
+                )
+            )
+            return consent
+        }
+    }
+
+    @ParameterizedTest
+    @CsvSource(
+        "2.16.840.1.113883.3.1937.777.24.5.3.8,urn:oid:2.16.840.1.113883.3.1937.777.24.5.3,2025-07-23T00:00:00+02:00,PERMIT,expect permit",
+        "2.16.840.1.113883.3.1937.777.24.5.3.8,urn:oid:2.16.840.1.113883.3.1937.777.24.5.3,2025-06-23T00:00:00+02:00,PERMIT,expect permit date is exactly on start",
+        "2.16.840.1.113883.3.1937.777.24.5.3.8,urn:oid:2.16.840.1.113883.3.1937.777.24.5.3,2055-06-23T00:00:00+02:00,PERMIT,expect permit date is exactly on end",
+        "2.16.840.1.113883.3.1937.777.24.5.3.8,urn:oid:2.16.840.1.113883.3.1937.777.24.5.3,2021-06-23T00:00:00+02:00,NULL,date is before start",
+        "2.16.840.1.113883.3.1937.777.24.5.3.8,urn:oid:2.16.840.1.113883.3.1937.777.24.5.3,2060-06-23T00:00:00+02:00,NULL,date is after end",
+        "2.16.840.1.113883.3.1937.777.24.5.3.8,XXXX,2025-07-23T00:00:00+02:00,NULL,system not found - therefore expect NULL",
+        "2.16.840.1.113883.3.1937.777.24.5.3.27,urn:oid:2.16.840.1.113883.3.1937.777.24.5.3,2025-07-23T00:00:00+02:00,DENY,provision is denied"
+    )
+    fun getProvisionTypeByPolicyCode(
+        code: String?, system: String?, timeStamp: String, expected: String?,
+        desc: String?
+    ) {
+        val testData = getDummyBroadConsentBundle()
+
+        val requestDate = Date.from(OffsetDateTime.parse(timeStamp).toInstant())
+
+        val result: Consent.ConsentProvisionType =
+            consentProcessor.getProvisionTypeByPolicyCode(testData, code, system, requestDate)
+        assertThat(result).isNotNull()
+
+
+        assertThat(result).`as`(desc)
+            .isEqualTo(Consent.ConsentProvisionType.valueOf(expected!!))
+    }
+
+    fun getDummyBroadConsentBundle(): Bundle {
+        val bundle: InputStream?
+        try {
+            bundle = ClassPathResource(
+                "fake_broadConsent_gics_response_permit.json"
+            ).getInputStream()
+        } catch (e: IOException) {
+            throw RuntimeException(e)
+        }
+
+        return FhirContext.forR4().newJsonParser()
+            .parseResource<Bundle>(Bundle::class.java, bundle)
+    }
+
+}

src/test/kotlin/dev/dnpm/etl/processor/services/TransformationServiceTest.kt

@@ -34,8 +34,6 @@ import dev.pcvolkmer.mv64e.mtb.Mtb
 import dev.pcvolkmer.mv64e.mtb.MvhMetadata
 import dev.pcvolkmer.mv64e.mtb.Provision
 import org.hl7.fhir.instance.model.api.IBaseResource
-import org.hl7.fhir.r4.model.CodeableConcept
-import org.hl7.fhir.r4.model.Coding
 import java.time.Instant
 import java.util.Date
 
@@ -145,7 +143,7 @@ class TransformationServiceTest {
                             .date(Date.from(Instant.parse("2025-06-23T00:00:00.00Z"))).build()
                     )
                 ).build()
-        val consent = getDummyConsent()
+        val consent = ConsentProcessorTest.getDummyGenomDeConsent()
 
         mvhMetadata.researchConsents = mutableListOf()
         mvhMetadata.researchConsents.add(mapOf(consent.id to consent as IBaseResource))
@@ -157,51 +155,5 @@ class TransformationServiceTest {
 
     }
 
-    companion object {
-        fun getDummyConsent(): org.hl7.fhir.r4.model.Consent {
-            val modelVorhabenConsent = org.hl7.fhir.r4.model.Consent()
-            modelVorhabenConsent.id = "consent 1 id"
-            modelVorhabenConsent.patient.reference = "Patient/1234-pat1"
 
-            modelVorhabenConsent.provision.setType(
-                org.hl7.fhir.r4.model.Consent.ConsentProvisionType.fromCode(
-                    "deny"
-                )
-            )
-            modelVorhabenConsent.provision.period.start =
-                Date.from(Instant.parse("2025-06-23T00:00:00.00Z"))
-            modelVorhabenConsent.provision.period.end =
-                Date.from(Instant.parse("3000-01-01T00:00:00.00Z"))
-
-
-            val addProvision1 = modelVorhabenConsent.provision.addProvision()
-            addProvision1.setType(org.hl7.fhir.r4.model.Consent.ConsentProvisionType.fromCode("permit"))
-            addProvision1.period.start = Date.from(Instant.parse("2025-06-23T00:00:00.00Z"))
-            addProvision1.period.end = Date.from(Instant.parse("3000-01-01T00:00:00.00Z"))
-            addProvision1.code.addLast(
-                CodeableConcept(
-                    Coding(
-                        "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
-                        "Teilnahme",
-                        "Teilnahme am Modellvorhaben und Einwilligung zur Genomsequenzierung"
-                    )
-                )
-            )
-
-            val addProvision2 = modelVorhabenConsent.provision.addProvision()
-            addProvision2.setType(org.hl7.fhir.r4.model.Consent.ConsentProvisionType.fromCode("deny"))
-            addProvision2.period.start = Date.from(Instant.parse("2025-06-23T00:00:00.00Z"))
-            addProvision2.period.end = Date.from(Instant.parse("3000-01-01T00:00:00.00Z"))
-            addProvision2.code.addLast(
-                CodeableConcept(
-                    Coding(
-                        "https://ths-greifswald.de/fhir/CodeSystem/gics/Policy/GenomDE_MV",
-                        "Rekontaktierung",
-                        "Re-Identifizierung meiner Daten über die Vertrauensstelle beim Robert Koch-Institut und in die erneute Kontaktaufnahme durch meine behandelnde Ärztin oder meinen behandelnden Arzt"
-                    )
-                )
-            )
-            return modelVorhabenConsent
-        }
-    }
 }