chore: bump version

build.gradle.kts

@@ -7,22 +7,22 @@ plugins {
     war
     id("org.springframework.boot") version "3.5.5"
     id("io.spring.dependency-management") version "1.1.7"
-    kotlin("jvm") version "2.2.10"
-    kotlin("plugin.spring") version "2.2.10"
+    kotlin("jvm") version "1.9.25"
+    kotlin("plugin.spring") version "1.9.25"
     jacoco
 }
 
 group = "dev.dnpm"
-version = "0.12.0-SNAPSHOT"
+version = "0.11.1"
 
 var versions = mapOf(
     "mtb-dto" to "0.1.0-SNAPSHOT",
-    "hapi-fhir" to "8.4.0",
-    "mockito-kotlin" to "6.0.0",
-    "archunit" to "1.4.1",
+    "hapi-fhir" to "7.6.1",
+    "mockito-kotlin" to "5.4.0",
+    "archunit" to "1.3.0",
     // Webjars
     "webjars-locator" to "0.52",
-    "echarts" to "6.0.0",
+    "echarts" to "5.4.3",
     "htmx.org" to "1.9.12"
 )
 

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

@@ -39,8 +39,6 @@ public class GicsConsentService implements IConsentService {
     private final RestTemplate restTemplate;
     private final FhirContext fhirContext;
     private final GIcsConfigProperties gIcsConfigProperties;
-    private final String BROAD_CONSENT_PROFILE_URI = "https://www.medizininformatik-initiative.de/fhir/modul-consent/StructureDefinition/mii-pr-consent-einwilligung";
-    private final String BROAD_CONSENT_POLICY = "urn:oid:2.16.840.1.113883.3.1937.777.24.2.1791";
 
     public GicsConsentService(
         GIcsConfigProperties gIcsConfigProperties,
@@ -304,36 +302,6 @@ public class GicsConsentService implements IConsentService {
 
     @Override
     public Bundle getConsent(String patientId, Date requestDate, ConsentDomain consentDomain) {
-        Bundle gIcsResultBundle = currentConsentForPersonAndTemplate(patientId, consentDomain, requestDate);
-        if (ConsentDomain.BROAD_CONSENT == consentDomain) {
-            return convertGicsResultToMiiBroadConsent(gIcsResultBundle);
-        }
-        return gIcsResultBundle;
-    }
-
-    protected Bundle convertGicsResultToMiiBroadConsent(Bundle gIcsResultBundle) {
-        if (gIcsResultBundle == null
-                || gIcsResultBundle.getEntry().isEmpty()
-                || !(gIcsResultBundle.getEntry().getFirst().getResource() instanceof Consent))
-            return gIcsResultBundle;
-
-        Bundle.BundleEntryComponent bundleEntryComponent = gIcsResultBundle.getEntry().getFirst();
-
-        var consentAsOne = (Consent) bundleEntryComponent.getResource();
-        if (consentAsOne.getPolicy().stream().noneMatch(p -> p.getUri().equals(BROAD_CONSENT_POLICY))) {
-            consentAsOne.addPolicy(new Consent.ConsentPolicyComponent().setUri(BROAD_CONSENT_POLICY));
-        }
-
-        if (consentAsOne.getMeta().getProfile().stream().noneMatch(p -> p.getValue().equals(BROAD_CONSENT_PROFILE_URI))) {
-            consentAsOne.getMeta().addProfile(BROAD_CONSENT_PROFILE_URI);
-        }
-
-        consentAsOne.setPolicyRule(null);
-
-        gIcsResultBundle.getEntry().stream().skip(1).forEach(c -> consentAsOne.getProvision().addProvision(((Consent) c.getResource()).getProvision().getProvisionFirstRep()));
-
-        gIcsResultBundle.getEntry().clear();
-        gIcsResultBundle.addEntry(bundleEntryComponent);
-        return gIcsResultBundle;
+        return currentConsentForPersonAndTemplate(patientId, consentDomain, requestDate);
     }
 }

src/main/java/dev/dnpm/etl/processor/pseudonym/GpasPseudonymGenerator.java

@@ -23,6 +23,8 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.parser.IParser;
 import dev.dnpm.etl.processor.config.AppFhirConfig;
 import dev.dnpm.etl.processor.config.GPasConfigProperties;
+import java.net.URI;
+import java.net.URISyntaxException;
 import org.apache.commons.lang3.NotImplementedException;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.hc.core5.net.URIBuilder;
@@ -37,11 +39,9 @@ import org.springframework.http.*;
 import org.springframework.retry.support.RetryTemplate;
 import org.springframework.web.client.HttpClientErrorException.BadRequest;
 import org.springframework.web.client.HttpClientErrorException.Unauthorized;
+import org.springframework.web.client.RestClientException;
 import org.springframework.web.client.RestTemplate;
 
-import java.net.URI;
-import java.net.URISyntaxException;
-
 public class GpasPseudonymGenerator implements Generator {
 
     private final FhirContext r4Context;
@@ -52,10 +52,10 @@ public class GpasPseudonymGenerator implements Generator {
     private final RestTemplate restTemplate;
     private final @NotNull String genomDeTanDomain;
     private final @NotNull String pidPsnDomain;
-    protected static final String CREATE_OR_GET_PSN = "$pseudonymizeAllowCreate";
-    protected static final String CREATE_MULTI_DOMAIN_PSN = "$pseudonymize-secondary";
-    private static final String SINGLE_PSN_PART_NAME = "pseudonym";
-    private static final String MULTI_PSN_PART_NAME = "value";
+    protected final static String createOrGetPsn = "$pseudonymizeAllowCreate";
+    protected final static String createMultiDomainPsn = "$pseudonymize-secondary";
+    private final static String SINGLE_PSN_PART_NAME = "pseudonym";
+    private final static String MULTI_PSN_PART_NAME = "value";
 
     public GpasPseudonymGenerator(GPasConfigProperties gpasCfg, RetryTemplate retryTemplate,
         RestTemplate restTemplate, AppFhirConfig appFhirConfig) {
@@ -85,7 +85,7 @@ public class GpasPseudonymGenerator implements Generator {
         switch (domainType) {
             case SINGLE_PSN_DOMAIN -> {
                 final var requestBody = createSinglePsnRequestBody(id, pidPsnDomain);
-                final var responseEntity = getGpasPseudonym(requestBody, CREATE_OR_GET_PSN);
+                final var responseEntity = getGpasPseudonym(requestBody, createOrGetPsn);
                 final var gPasPseudonymResult = (Parameters) r4Context.newJsonParser()
                     .parseResource(responseEntity.getBody());
 
@@ -93,7 +93,7 @@ public class GpasPseudonymGenerator implements Generator {
             }
             case MULTI_PSN_DOMAIN -> {
                 final var requestBody = createMultiPsnRequestBody(id, genomDeTanDomain);
-                final var responseEntity = getGpasPseudonym(requestBody, CREATE_MULTI_DOMAIN_PSN);
+                final var responseEntity = getGpasPseudonym(requestBody, createMultiDomainPsn);
                 final var gPasPseudonymResult = (Parameters) r4Context.newJsonParser()
                     .parseResource(responseEntity.getBody());
 
@@ -150,22 +150,23 @@ public class GpasPseudonymGenerator implements Generator {
                 log.debug("API request succeeded. Response: {}", responseEntity.getStatusCode());
                 return responseEntity;
             }
-        } catch (BadRequest e) {
+        } catch (RestClientException rce) {
+            if (rce instanceof BadRequest) {
                 String msg = "gPas or request configuration is incorrect. Please check both."
-                + e.getMessage();
-            log.error(msg);
-            throw new PseudonymRequestFailed(msg, e);
-        } catch (Unauthorized e) {
-            var msg = "gPas access credentials are invalid  check your configuration. msg:  '%s"
-                .formatted(e.getMessage());
-            log.error(msg);
-            throw new PseudonymRequestFailed(msg, e);
+                    + rce.getMessage();
+                log.debug(
+                    msg);
+                throw new PseudonymRequestFailed(msg, rce);
             }
-        catch (Exception unexpected) {
+            if (rce instanceof Unauthorized) {
+                var msg = "gPas access credentials are invalid  check your configuration. msg:  '%s".formatted(
+                    rce.getMessage());
+                log.error(msg);
+                throw new PseudonymRequestFailed(msg, rce);
+            }
+        } catch (Exception unexpected) {
             throw new PseudonymRequestFailed(
-                "API request due unexpected error unsuccessful gPas unsuccessful.",
-                unexpected
-            );
+                "API request due unexpected error unsuccessful gPas unsuccessful.", unexpected);
         }
         throw new PseudonymRequestFailed(
             "API request due unexpected error unsuccessful gPas unsuccessful.");

src/main/kotlin/dev/dnpm/etl/processor/monitoring/Request.kt

@@ -30,7 +30,6 @@ import org.springframework.data.relational.core.mapping.Table
 import org.springframework.data.repository.CrudRepository
 import org.springframework.data.repository.PagingAndSortingRepository
 import java.time.Instant
-import java.time.temporal.ChronoUnit
 import java.util.*
 
 @Table("request")
@@ -66,12 +65,6 @@ data class Request(
         processedAt: Instant
     ) :
             this(null, uuid, patientPseudonym, pid, fingerprint, type, status, processedAt)
-
-    fun isPendingUnknown(): Boolean {
-        return this.status == RequestStatus.UNKNOWN && this.processedAt.isBefore(
-            Instant.now().minus(10, ChronoUnit.MINUTES)
-        )
-    }
 }
 
 @JvmRecord
@@ -97,23 +90,19 @@ interface RequestRepository : CrudRepository<Request, Long>, PagingAndSortingRep
     @Query("SELECT count(*) AS count, status FROM request WHERE type = 'MTB_FILE' GROUP BY status ORDER BY status, count DESC;")
     fun countStates(): List<CountedState>
 
-    @Query(
-        "SELECT count(*) AS count, status FROM (" +
+    @Query("SELECT count(*) AS count, status FROM (" +
             "SELECT status, rank() OVER (PARTITION BY patient_pseudonym ORDER BY processed_at DESC) AS rank FROM request " +
             "WHERE type = 'MTB_FILE' AND status NOT IN ('DUPLICATION') " +
-                ") rank WHERE rank = 1 GROUP BY status ORDER BY status, count DESC;"
-    )
+            ") rank WHERE rank = 1 GROUP BY status ORDER BY status, count DESC;")
     fun findPatientUniqueStates(): List<CountedState>
 
     @Query("SELECT count(*) AS count, status FROM request WHERE type = 'DELETE' GROUP BY status ORDER BY status, count DESC;")
     fun countDeleteStates(): List<CountedState>
 
-    @Query(
-        "SELECT count(*) AS count, status FROM (" +
+    @Query("SELECT count(*) AS count, status FROM (" +
             "SELECT status, rank() OVER (PARTITION BY patient_pseudonym ORDER BY processed_at DESC) AS rank FROM request " +
             "WHERE type = 'DELETE'" +
-                ") rank WHERE rank = 1 GROUP BY status ORDER BY status, count DESC;"
-    )
+            ") rank WHERE rank = 1 GROUP BY status ORDER BY status, count DESC;")
     fun findPatientUniqueDeleteStates(): List<CountedState>
 
 }

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

@@ -137,7 +137,15 @@ class ConsentProcessor(
             }
 
             val provisionComponent: ProvisionComponent = provisions.first()
-            val provisionCode = getProvisionCode(provisionComponent)
+
+            var provisionCode: String? = null
+            if (provisionComponent.code != null && provisionComponent.code.isNotEmpty()) {
+                val codableConcept: CodeableConcept = provisionComponent.code.first()
+                if (codableConcept.coding != null && codableConcept.coding.isNotEmpty()) {
+                    provisionCode = codableConcept.coding.first().code
+                }
+            }
+
             if (provisionCode != null) {
                 try {
                     val modelProjectConsentPurpose =
@@ -169,17 +177,6 @@ class ConsentProcessor(
         }
     }
 
-    private fun getProvisionCode(provisionComponent: ProvisionComponent): String? {
-        var provisionCode: String? = null
-        if (provisionComponent.code != null && provisionComponent.code.isNotEmpty()) {
-            val codableConcept: CodeableConcept = provisionComponent.code.first()
-            if (codableConcept.coding != null && codableConcept.coding.isNotEmpty()) {
-                provisionCode = codableConcept.coding.first().code
-            }
-        }
-        return provisionCode
-    }
-
     private fun setGenomDeSubmissionType(mtbFile: Mtb) {
         if (appConfigProperties.genomDeTestSubmission) {
             mtbFile.metadata.type = MvhSubmissionType.TEST
@@ -241,9 +238,9 @@ class ConsentProcessor(
             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().any { code ->
+                subProvision.code.map { c -> c.coding }.flatten().firstOrNull { code ->
                     targetCode.equals(code.code) && targetSystem.equals(code.system)
-                }
+                } != null
             }.map { subProvision ->
                 subProvision
             }
@@ -260,11 +257,11 @@ class ConsentProcessor(
         researchAllowedPolicySystem: String?,
         policyRules: Collection<Coding>
     ): Boolean {
-        return policyRules.any { code ->
+        return policyRules.find { code ->
             researchAllowedPolicySystem.equals(code.getSystem()) && (researchAllowedPolicyOid.equals(
                 code.getCode()
             ))
-        }
+        } != null
     }
 
     fun isRequestDateInRange(requestDate: Date?, provPeriod: Period): Boolean {

src/main/resources/templates/index.html

@@ -52,8 +52,7 @@
                         <td th:if="${request.status.value.contains('success')}" class="bg-green"><small>[[ ${request.status} ]]</small></td>
                         <td th:if="${request.status.value.contains('warning')}" class="bg-yellow"><small>[[ ${request.status} ]]</small></td>
                         <td th:if="${request.status.value.contains('error')}" class="bg-red"><small>[[ ${request.status} ]]</small></td>
-                        <td th:if="${request.status.value == 'unknown' and not request.isPendingUnknown()}" class="bg-gray"><small>[[ ${request.status} ]]</small></td>
-                        <td th:if="${request.status.value == 'unknown' and request.isPendingUnknown()}" class="bg-yellow"><small>⏰ [[ ${request.status} ]] ⏰</small></td>
+                        <td th:if="${request.status.value == 'unknown'}" class="bg-gray"><small>[[ ${request.status} ]]</small></td>
                         <td th:if="${request.status.value == 'duplication'}" class="bg-gray"><small>[[ ${request.status} ]]</small></td>
                         <td th:if="${request.status.value == 'no-consent'}" class="bg-blue"><small>[[ ${request.status} ]]</small></td>
                         <td th:style="${request.type.value == 'delete'} ? 'color: red;'"><small>[[ ${request.type} ]]</small></td>

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

@@ -24,7 +24,6 @@ import java.time.Instant;
 import java.util.Date;
 
 import static org.assertj.core.api.Assertions.assertThat;
-import static org.assertj.core.api.Assertions.fail;
 import static org.springframework.test.web.client.match.MockRestRequestMatchers.requestTo;
 import static org.springframework.test.web.client.response.MockRestResponseCreators.withServerError;
 import static org.springframework.test.web.client.response.MockRestResponseCreators.withSuccess;
@@ -178,8 +177,5 @@ class GicsConsentServiceTest {
             );
     }
 
-    @Test
-    public void convertGicsResultToMiiBroadConsent() {
-        fail("todo: implement Test gicsConsentService.convertGicsResultToMiiBroadConsent");
-    }
+
 }

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

@@ -80,7 +80,7 @@ class ConsentProcessorTest {
         val checkResult = consentProcessor.consentGatedCheckAndTryEmbedding(inputMtb)
 
         assertThat(checkResult).isTrue
-        assertThat(inputMtb.metadata.researchConsents).isNotEmpty
+        assertThat(inputMtb.metadata.researchConsents).hasSize(26)
     }
 
     companion object {