fix: serialize fhir consent resources to string, object map

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

@@ -1,5 +1,9 @@
 package dev.dnpm.etl.processor.consent;
 
+import ca.uhn.fhir.context.FhirContext;
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import dev.dnpm.etl.processor.config.GIcsConfigProperties;
 import dev.pcvolkmer.mv64e.mtb.ConsentProvision;
 import dev.pcvolkmer.mv64e.mtb.ModelProjectConsentPurpose;
@@ -8,7 +12,6 @@ import dev.pcvolkmer.mv64e.mtb.Provision;
 import java.io.IOException;
 import java.util.HashMap;
 import java.util.List;
-import java.util.Map;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.CodeableConcept;
 import org.hl7.fhir.r4.model.Consent;
@@ -20,24 +23,38 @@ import org.slf4j.LoggerFactory;
 public abstract class BaseConsentService implements ICheckConsent {
 
     protected final GIcsConfigProperties gIcsConfigProperties;
-    protected Logger logger = LoggerFactory.getLogger(BaseConsentService.class);
 
-    public BaseConsentService(GIcsConfigProperties gIcsConfigProperties) {
+    private final ObjectMapper objectMapper;
+    protected Logger logger = LoggerFactory.getLogger(BaseConsentService.class);
+    static FhirContext fhirCtx = FhirContext.forR4();
+
+    public BaseConsentService(GIcsConfigProperties gIcsConfigProperties,
+        ObjectMapper objectMapper) {
         this.gIcsConfigProperties = gIcsConfigProperties;
+        this.objectMapper = objectMapper;
     }
 
     public void embedBroadConsentResources(Mtb mtbFile, Bundle broadConsent) {
+
         for (Bundle.BundleEntryComponent entry : broadConsent.getEntry()) {
             Resource resource = entry.getResource();
             if (resource instanceof Consent) {
-                Map<String, Object> consentMap = new HashMap<>();
+                // since jackson convertValue does not work here,
-                consentMap.put(resource.getIdElement().getIdPart(), resource);
+                // we need another step to back to string, before we convert to object map
-                mtbFile.getMetadata().getResearchConsents().add(consentMap);
+                var asJsonString = fhirCtx.newJsonParser().encodeResourceToString(resource);
+                try {
+                    var mapOfJson = objectMapper.readValue(asJsonString,
+                        new TypeReference<HashMap<String, Object>>() {
+                        });
+                    mtbFile.getMetadata().getResearchConsents().add(mapOfJson);
+                } catch (JsonProcessingException e) {
+                    throw new RuntimeException(e);
+                }
             }
         }
     }
 
-     public void addGenomeDbProvisions(Mtb mtbFile, Bundle consentGnomeDe) {
+    public void addGenomeDbProvisions(Mtb mtbFile, Bundle consentGnomeDe) {
         for (Bundle.BundleEntryComponent entry : consentGnomeDe.getEntry()) {
             Resource resource = entry.getResource();
             if (!(resource instanceof Consent consentFhirResource)) {
@@ -67,7 +84,8 @@ public abstract class BaseConsentService implements ICheckConsent {
 
                     if (ModelProjectConsentPurpose.SEQUENCING.equals(modelProjectConsentPurpose)) {
                         // CONVENTION: wrapping date is date of SEQUENCING consent
-                        mtbFile.getMetadata().getModelProjectConsent().setDate(consentFhirResource.getDateTime());
+                        mtbFile.getMetadata().getModelProjectConsent()
+                            .setDate(consentFhirResource.getDateTime());
                     }
 
                     Provision provision = Provision.builder()
@@ -79,12 +97,15 @@ public abstract class BaseConsentService implements ICheckConsent {
                     mtbFile.getMetadata().getModelProjectConsent().getProvisions().add(provision);
 
                 } catch (IOException ioe) {
-                    logger.error("Provision code '" + provisionCode + "' is unknown and cannot be mapped.", ioe.toString());
+                    logger.error(
+                        "Provision code '" + provisionCode + "' is unknown and cannot be mapped.",
+                        ioe.toString());
                 }
             }
 
             if (!mtbFile.getMetadata().getModelProjectConsent().getProvisions().isEmpty()) {
-                mtbFile.getMetadata().getModelProjectConsent().setVersion(gIcsConfigProperties.getGenomeDeConsentVersion());
+                mtbFile.getMetadata().getModelProjectConsent()
+                    .setVersion(gIcsConfigProperties.getGenomeDeConsentVersion());
             }
         }
     }

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

@@ -2,6 +2,7 @@ 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;
@@ -51,8 +52,8 @@ public class GicsConsentService extends BaseConsentService   {
     private String url;
 
     public GicsConsentService(GIcsConfigProperties gIcsConfigProperties,
-        RetryTemplate retryTemplate, RestTemplate restTemplate, AppFhirConfig appFhirConfig) {
+        RetryTemplate retryTemplate, RestTemplate restTemplate, AppFhirConfig appFhirConfig, ObjectMapper objectMapper) {
-        super(gIcsConfigProperties);
+        super(gIcsConfigProperties,objectMapper);
 
         this.retryTemplate = retryTemplate;
         this.restTemplate = restTemplate;

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

@@ -184,12 +184,13 @@ class AppConfiguration {
     @Bean
     @ConditionalOnProperty(name = ["app.consent.gics.enabled"], havingValue = "true")
     fun gicsConsentService( gIcsConfigProperties: GIcsConfigProperties,
-                           retryTemplate: RetryTemplate,  restTemplate: RestTemplate,  appFhirConfig: AppFhirConfig): ICheckConsent {
+                           retryTemplate: RetryTemplate,  restTemplate: RestTemplate,  appFhirConfig: AppFhirConfig, getObjectMapper: ObjectMapper): ICheckConsent {
         return GicsConsentService(
             gIcsConfigProperties,
             retryTemplate,
             restTemplate,
-            appFhirConfig
+            appFhirConfig,
+            getObjectMapper
         )
     }
 

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

@@ -25,7 +25,6 @@ import dev.pcvolkmer.mv64e.mtb.ModelProjectConsent
 import dev.pcvolkmer.mv64e.mtb.Mtb
 import dev.pcvolkmer.mv64e.mtb.MvhMetadata
 import org.apache.commons.codec.digest.DigestUtils
-import org.hl7.fhir.r4.model.Consent
 
 /** Replaces patient ID with generated patient pseudonym
  *
@@ -295,11 +294,12 @@ infix fun Mtb.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
 
     this.metadata?.researchConsents?.forEach { it ->
         val entry = it ?: return@forEach
-        val key = entry.keys.first()
+        if (entry.contains("patient")) {
-        val consent = entry[key] as? Consent ?: return@forEach
+            // here we expect only a patient reference any other data like display
-            val patRef= "Patient/$patientPseudonym"
+            // need to be removed, since may contain unsecure data
-            consent.patient?.setReference(patRef)
+            entry.remove("patient")
-            consent.patient?.display = null
+            entry["patient"] = mapOf("reference" to "Patient/$patientPseudonym")
+        }
     }
 }
 

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

@@ -36,6 +36,7 @@ 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
@@ -122,6 +123,10 @@ class RequestProcessor(
         )
 
         consentService.addGenomeDbProvisions(mtbFile, genomeDeConsent)
+
+        // fixme: currently we do not have information about submission type
+        if (!genomeDeConsent.entry.isEmpty()) mtbFile.metadata.type = MvhSubmissionType.INITIAL
+
         consentService.embedBroadConsentResources(mtbFile, broadConsent)
 
         val broadConsentStatus = consentService.getProvisionTypeByPolicyCode(

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

@@ -251,7 +251,8 @@ class ExtensionsTest {
         private fun addConsentData(mtbFile: Mtb) {
             val gIcsConfigProperties = GIcsConfigProperties("", "", "", true)
 
-            val baseConsentService = object : BaseConsentService(gIcsConfigProperties) {
+            val baseConsentService = object : BaseConsentService(gIcsConfigProperties,
+                JacksonConfig().objectMapper()) {
                 override fun getTtpBroadConsentStatus(personIdentifierValue: String?): TtpConsentStatus? {
                     throw NotImplementedError("dummy")
                 }