feat: do not request research consent if reason missing is given (#298)

This is a first approach to make use of a reason missing given in MTB file at UKGM Marburg due to special handling of research consent.

Without these changes, the request will be canceled without any further processing.

2 files changed, 41 insertions, 10 deletions

diff --git a/src/main/kotlin/dev/dnpm/etl/processor/services/ConsentProcessor.kt b/src/main/kotlin/dev/dnpm/etl/processor/services/ConsentProcessor.kt
index a95420a..20a2ba3 100644
--- a/src/main/kotlin/dev/dnpm/etl/processor/services/ConsentProcessor.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/services/ConsentProcessor.kt
@@ -83,16 +83,6 @@ class ConsentProcessor(
     // 2.1 -> yes -> send mtb file
     // 2.2 -> no ->  warn/info no consent given
 
-    /*
-     * broad consent
-     */
-    val broadConsent =
-        consentService.getConsent(personIdentifierValue, requestDate, ConsentDomain.BROAD_CONSENT)
-    val broadConsentHasBeenAsked = broadConsent.entry.isNotEmpty()
-
-    // fast exit - if patient has not been asked, we can skip and exit
-    if (!broadConsentHasBeenAsked) return false
-
     // GenomDE_MV-Consent only if domain name available else fallback to file check
     val genomDeSequencingStatus = if (null != gIcsConfigProperties.genomDeConsentDomainName) {
         val genomeDeConsent =
@@ -111,6 +101,21 @@ class ConsentProcessor(
         true
     }
 
+    /*
+     * broad consent
+     */
+    if (null != mtbFile.metadata?.reasonResearchConsentMissing) {
+        // early return if there is a reason for missing broad consent
+        return false
+    }
+
+    val broadConsent =
+          consentService.getConsent(personIdentifierValue, requestDate, ConsentDomain.BROAD_CONSENT)
+    val broadConsentHasBeenAsked = broadConsent.entry.isNotEmpty()
+
+    // fast exit - if patient has not been asked, we can skip and exit
+    if (!broadConsentHasBeenAsked) return false
+
     embedBroadConsentResources(mtbFile, broadConsent)
 
     val broadConsentStatus =
diff --git a/src/test/kotlin/dev/dnpm/etl/processor/services/ConsentProcessorTest.kt b/src/test/kotlin/dev/dnpm/etl/processor/services/ConsentProcessorTest.kt
index a85d555..8899fc6 100644
--- a/src/test/kotlin/dev/dnpm/etl/processor/services/ConsentProcessorTest.kt
+++ b/src/test/kotlin/dev/dnpm/etl/processor/services/ConsentProcessorTest.kt
@@ -28,8 +28,10 @@ import dev.dnpm.etl.processor.consent.ConsentDomain
 import dev.dnpm.etl.processor.consent.GicsConsentService
 import dev.dnpm.etl.processor.consent.MtbFileConsentService
 import dev.pcvolkmer.mv64e.mtb.Mtb
+import dev.pcvolkmer.mv64e.mtb.MvhMetadata
 import dev.pcvolkmer.mv64e.mtb.MvhSubmissionType
 import dev.pcvolkmer.mv64e.mtb.Patient
+import dev.pcvolkmer.mv64e.mtb.ResearchConsentReasonMissing
 import org.assertj.core.api.Assertions.assertThat
 import org.hl7.fhir.r4.model.Bundle
 import org.hl7.fhir.r4.model.CodeableConcept
@@ -46,6 +48,8 @@ import org.mockito.junit.jupiter.MockitoExtension
 import org.mockito.kotlin.any
 import org.mockito.kotlin.doAnswer
 import org.mockito.kotlin.eq
+import org.mockito.kotlin.times
+import org.mockito.kotlin.verify
 import org.mockito.kotlin.whenever
 import org.springframework.core.io.ClassPathResource
 import tools.jackson.databind.json.JsonMapper
@@ -267,4 +271,26 @@ class ConsentProcessorTest {
       assertThat(inputMtb.metadata.type).isEqualTo(MvhSubmissionType.INITIAL)
     }
   }
+
+  @Test
+  fun doNotRequestBroadConsentIfReasonMissingIsGiven() {
+    doAnswer { Bundle() }
+        .whenever(gicsConsentService)
+        .getConsent(any(), any(), eq(ConsentDomain.MODELLVORHABEN_64E))
+
+    val inputMtb =
+        Mtb.builder()
+            .patient(Patient.builder().id("d611d429-5003-11f0-a144-661e92ac9503").build())
+            .metadata(MvhMetadata.builder().reasonResearchConsentMissing(ResearchConsentReasonMissing.OTHER_PATIENT_REASON).build())
+            .build()
+    val checkResult = consentProcessor.consentGatedCheckAndTryEmbedding(inputMtb)
+
+    verify(gicsConsentService, times(1))
+        .getConsent(any(), any(), eq(ConsentDomain.MODELLVORHABEN_64E))
+    verify(gicsConsentService, times(0))
+        .getConsent(any(), any(), eq(ConsentDomain.BROAD_CONSENT))
+
+    assertThat(checkResult).isFalse
+    assertThat(inputMtb.metadata.researchConsents).isEmpty()
+  }
 }