132 fix consent check (#133)

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

@@ -92,6 +92,7 @@ class AppConfiguration {
         restTemplate: RestTemplate,
         appFhirConfig: AppFhirConfig
     ): Generator {
+        logger.info("Selected 'GpasPseudonym Generator'")
         return GpasPseudonymGenerator(configProperties, retryTemplate, restTemplate, appFhirConfig)
     }
 
@@ -102,6 +103,7 @@ class AppConfiguration {
     )
     @Bean
     fun buildinPseudonymGenerator(): Generator {
+        logger.info("Selected 'BUILDIN Pseudonym Generator'")
         return AnonymizingGenerator()
     }
 

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

@@ -222,60 +222,56 @@ class ConsentProcessor(
 
     /**
      * @param consentBundle            consent resource
-     * @param policyAndProvisionCode   policyRule and provision code value
+     * @param targetCode   policyRule and provision code value
-     * @param policyAndProvisionSystem policyRule and provision system value
+     * @param targetSystem 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,
+        consentBundle: Bundle, targetCode: String?, targetSystem: String?, requestDate: Date?
-        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(
+            val isConsentResource =
-                policyAndProvisionCode,
+                entry.resource.isResource && entry.resource.resourceType == ResourceType.Consent
-                policyAndProvisionSystem,
+            val consentIsActive = (entry.resource as Consent).status == ConsentState.ACTIVE
-                (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
 
+            isConsentResource && consentIsActive && checkCoding(
+                targetCode, targetSystem, (entry.resource as Consent).policyRule.coding
+            ) && isRequestDateInRange(requestDate, (entry.resource as Consent).provision.period)
+        }.map { entry: BundleEntryComponent ->
+            val consent = (entry.getResource() as Consent)
+            consent.provision.provision.filter { subProvision ->
+                isRequestDateInRange(requestDate, subProvision.period)
+                // search coding entries of current provision for code and system
+                subProvision.code.map { c -> c.coding }.flatten().firstOrNull { code ->
+                    targetCode.equals(code.code) && targetSystem.equals(code.system)
+                } != null
+            }.map { subProvision ->
+                subProvision
             }
-            return Consent.ConsentProvisionType.NULL
+        }.flatten()
-        }.firstOrNull()
 
-        if (entriesOfInterest == null) return Consent.ConsentProvisionType.NULL
+        if (!entriesOfInterest.isEmpty()) {
-        return entriesOfInterest
+            return entriesOfInterest.first().type
+        }
+        return Consent.ConsentProvisionType.NULL
     }
 
     fun checkCoding(
-        researchAllowedPolicyOid: String?, researchAllowedPolicySystem: String?, coding: Coding
+        researchAllowedPolicyOid: String?,
+        researchAllowedPolicySystem: String?,
+        policyRules: Collection<Coding>
     ): Boolean {
-        return coding.getSystem() == researchAllowedPolicySystem && (coding.getCode() == researchAllowedPolicyOid)
+        return policyRules.find { code ->
+            researchAllowedPolicySystem.equals(code.getSystem()) && (researchAllowedPolicyOid.equals(
+                code.getCode()
+            ))
+        } != null
     }
 
-    fun isIsRequestDateInRange(requestdate: Date?, provPeriod: Period): Boolean {
+    fun isRequestDateInRange(requestDate: Date?, provPeriod: Period): Boolean {
-        val isRequestDateAfterOrEqualStart = provPeriod.getStart().compareTo(requestdate)
+        val isRequestDateAfterOrEqualStart = provPeriod.getStart().compareTo(requestDate)
-        val isRequestDateBeforeOrEqualEnd = provPeriod.getEnd().compareTo(requestdate)
+        val isRequestDateBeforeOrEqualEnd = provPeriod.getEnd().compareTo(requestDate)
         return isRequestDateAfterOrEqualStart <= 0 && isRequestDateBeforeOrEqualEnd >= 0
     }
 

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

@@ -78,7 +78,7 @@ class ConsentProcessorTest {
         val checkResult = consentProcessor.consentGatedCheckAndTryEmbedding(inputMtb)
 
         assertThat(checkResult).isTrue
-        assertThat(inputMtb.metadata.researchConsents).hasSize(13)
+        assertThat(inputMtb.metadata.researchConsents).hasSize(26)
     }
 
     companion object {
@@ -93,13 +93,13 @@ class ConsentProcessorTest {
                 )
             )
             consent.provision.period.start =
-                Date.from(Instant.parse("2025-06-23T00:00:00.00Z"))
+                Date.from(Instant.parse("2025-08-15T00:00:00.00Z"))
             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.start = Date.from(Instant.parse("2025-08-15T00:00:00.00Z"))
             addProvision1.period.end = Date.from(Instant.parse("3000-01-01T00:00:00.00Z"))
             addProvision1.code.addLast(
                 CodeableConcept(
@@ -113,7 +113,7 @@ class ConsentProcessorTest {
 
             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.start = Date.from(Instant.parse("2025-08-15T00:00:00.00Z"))
             addProvision2.period.end = Date.from(Instant.parse("3000-01-01T00:00:00.00Z"))
             addProvision2.code.addLast(
                 CodeableConcept(
@@ -130,13 +130,14 @@ class ConsentProcessorTest {
 
     @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:2.16.840.1.113883.3.1937.777.24.5.3,2025-08-15T00:00:00+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:2.16.840.1.113883.3.1937.777.24.5.3,2025-08-15T00:00:00+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:2.16.840.1.113883.3.1937.777.24.5.3,2055-08-15T00:00:00+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:2.16.840.1.113883.3.1937.777.24.5.3,2021-08-15T00:00:00+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,urn:oid:2.16.840.1.113883.3.1937.777.24.5.3,2060-08-15T00:00:00+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:2.16.840.1.113883.3.1937.777.24.5.3,2025-08-15T00:00:00+02:00,DENY,provision is denied",
-        "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"
+        "unknownCode,urn:oid:2.16.840.1.113883.3.1937.777.24.5.3,2025-08-15T00:00:00+02:00,NULL,code does not exist - therefore expect NULL",
+        "2.16.840.1.113883.3.1937.777.24.5.3.8,XXXX,2025-08-15T00:00:00+02:00,NULL,system not found - therefore expect NULL",
     )
     fun getProvisionTypeByPolicyCode(
         code: String?, system: String?, timeStamp: String, expected: String?,
@@ -155,6 +156,27 @@ class ConsentProcessorTest {
             .isEqualTo(Consent.ConsentProvisionType.valueOf(expected!!))
     }
 
+    @Test
+    fun getProvisionTypeOnEmptyConsent(
+    ) {
+        val emptyResources = Bundle().addEntry(Bundle.BundleEntryComponent().setResource(Consent()))
+
+        val requestDate = Date.from(OffsetDateTime.parse("2025-08-15T00:00:00+02:00").toInstant())
+
+        val result: Consent.ConsentProvisionType =
+            consentProcessor.getProvisionTypeByPolicyCode(
+                emptyResources,
+                "anyCode",
+                "anySystem",
+                requestDate
+            )
+        assertThat(result).isNotNull()
+
+
+        assertThat(result).`as`("empty consent resource - expect NULL")
+            .isEqualTo(Consent.ConsentProvisionType.NULL)
+    }
+
     fun getDummyBroadConsentBundle(): Bundle {
         val bundle: InputStream?
         try {

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

@@ -97,18 +97,18 @@ class TransformationServiceTest {
 
         assertThat(mvhMetadata).isNotNull
         mvhMetadata.modelProjectConsent =
-            ModelProjectConsent.builder().date(Date.from(Instant.parse("2025-06-23T00:00:00.00Z")))
+            ModelProjectConsent.builder().date(Date.from(Instant.parse("2025-08-15T00:00:00.00Z")))
                 .version("1").provisions(
                     listOf(
                         Provision.builder().type(ConsentProvision.PERMIT)
                             .purpose(ModelProjectConsentPurpose.SEQUENCING)
-                            .date(Date.from(Instant.parse("2025-06-23T00:00:00.00Z"))).build(),
+                            .date(Date.from(Instant.parse("2025-08-15T00:00:00.00Z"))).build(),
                         Provision.builder().type(ConsentProvision.PERMIT)
                             .purpose(ModelProjectConsentPurpose.REIDENTIFICATION)
-                            .date(Date.from(Instant.parse("2025-06-23T00:00:00.00Z"))).build(),
+                            .date(Date.from(Instant.parse("2025-08-15T00:00:00.00Z"))).build(),
                         Provision.builder().type(ConsentProvision.DENY)
                             .purpose(ModelProjectConsentPurpose.CASE_IDENTIFICATION)
-                            .date(Date.from(Instant.parse("2025-06-23T00:00:00.00Z"))).build()
+                            .date(Date.from(Instant.parse("2025-08-15T00:00:00.00Z"))).build()
                     )
                 ).build()
         val consent = ConsentProcessorTest.getDummyGenomDeConsent()