Hotfix/align with fdo

.github/workflows/.trivyignore

@@ -1,4 +1,9 @@
 # Date: Mar 5, 2024
 # Notes: Issue with libexpat, parsing large tokens can trigger a denial of service
 # Needs to be fixed in Docker Image.
-CVE-2023-52425
+CVE-2023-52425
+
+# Date: March 21, 2024
+# Issue: Vulnerability in spring-web
+# Solution: Spring boot needs to update its version of spring
+CVE-2024-22259

pom.xml

@@ -23,6 +23,7 @@
     <mockito-inline.version>5.2.0</mockito-inline.version>
     <testcontainers.version>1.19.5</testcontainers.version>
     <springdoc.version>2.3.0</springdoc.version>
+    <spring-security.version>6.2.3</spring-security.version> <!-- 21/03/24: CVE-2024-22257-->
     <sonar.organization>dissco</sonar.organization>
     <sonar.host.url>https://sonarcloud.io</sonar.host.url>
     <sonar.coverage.jacoco.xmlReportPaths>../app-it/target/site/jacoco-aggregate/jacoco.xml

src/main/java/eu/dissco/core/digitalspecimenprocessor/service/FdoRecordService.java

@@ -140,6 +140,15 @@ private void addOptionalAttributes(DigitalSpecimenWrapper specimen, ObjectNode a
     if (specimen.attributes().getOdsMarkedAsType() != null) {
       attributes.put(MARKED_AS_TYPE.getAttribute(), specimen.attributes().getOdsMarkedAsType());
     }
+    if (specimen.attributes().getIdentifiers() != null && !specimen.attributes().getIdentifiers().isEmpty()){
+      var idNodeArr = mapper.createArrayNode();
+      for (var id: specimen.attributes().getIdentifiers()){
+        idNodeArr.add(mapper.createObjectNode()
+            .put("identifierType", id.getIdentifierType())
+            .put("identifierValue", id.getIdentifierValue()));
+      }
+      attributes.set("otherSpecimenIds", idNodeArr);
+    }
   }
 
   public boolean handleNeedsUpdate(DigitalSpecimenWrapper currentDigitalSpecimenWrapper,

src/test/java/eu/dissco/core/digitalspecimenprocessor/service/FdoRecordServiceTest.java

@@ -10,6 +10,7 @@
 import static eu.dissco.core.digitalspecimenprocessor.utils.TestUtils.TYPE;
 import static eu.dissco.core.digitalspecimenprocessor.utils.TestUtils.generateSpecimenOriginalData;
 import static eu.dissco.core.digitalspecimenprocessor.utils.TestUtils.givenAttributes;
+import static eu.dissco.core.digitalspecimenprocessor.utils.TestUtils.givenAttributesPlusIdentifier;
 import static eu.dissco.core.digitalspecimenprocessor.utils.TestUtils.givenDigitalSpecimenEvent;
 import static eu.dissco.core.digitalspecimenprocessor.utils.TestUtils.givenDigitalSpecimenWrapper;
 import static eu.dissco.core.digitalspecimenprocessor.utils.TestUtils.givenDigitalSpecimenRecord;
@@ -202,6 +203,49 @@ void testGenRequestFull(boolean markedAsType) throws Exception {
     assertThat(response).isEqualTo(expected);
   }
 
+  @Test
+  void testGenRequestIdentifiers() throws Exception {
+    // Given
+    var markedAsType = false;
+    var specimen = new DigitalSpecimenWrapper(PHYSICAL_SPECIMEN_ID, TYPE,
+        givenAttributesPlusIdentifier(SPECIMEN_NAME, ORGANISATION_ID, markedAsType),
+        givenDigitalSpecimenAttributesFull(markedAsType));
+    var expectedJson = MAPPER.readTree(
+          """
+          {
+            "data": {
+              "type": "digitalSpecimen",
+              "attributes": {
+                "fdoProfile": "https://hdl.handle.net/21.T11148/d8de0819e144e4096645",
+                "digitalObjectType": "https://hdl.handle.net/21.T11148/894b1e6cad57e921764e",
+                "issuedForAgent": "https://ror.org/0566bfb96",
+                "primarySpecimenObjectId": "https://geocollections.info/specimen/23602",
+                "normalisedPrimarySpecimenObjectId":"https://geocollections.info/specimen/23602",
+                "primarySpecimenObjectIdType": "Global",
+                "specimenHost": "https://ror.org/0443cwa12",
+                "specimenHostName": "National Museum of Natural History",
+                "topicDiscipline": "Botany",
+                "referentName": "Biota",
+                "livingOrPreserved": "Preserved",
+                "markedAsType": false,
+                "otherSpecimenIds": [{
+                  "identifierType": "Specimen label",
+                  "identifierValue": "20.5000.1025/V1Z-176-LL4"
+                }]
+              }
+            }
+          }
+          """
+    );
+    var expected = new ArrayList<>(List.of(expectedJson));
+
+    // When
+    var response = builder.buildPostHandleRequest(List.of(specimen));
+
+    // Then
+    assertThat(response).isEqualTo(expected);
+  }
+
   @Test
   void testGenRequestFullTypeIsNull() throws Exception {
     // Given

src/test/java/eu/dissco/core/digitalspecimenprocessor/utils/TestUtils.java

@@ -16,6 +16,7 @@
 import eu.dissco.core.digitalspecimenprocessor.schema.DigitalSpecimen.OdsPhysicalSpecimenIdType;
 import eu.dissco.core.digitalspecimenprocessor.schema.DigitalSpecimen.OdsTopicDiscipline;
 import eu.dissco.core.digitalspecimenprocessor.schema.EntityRelationships;
+import eu.dissco.core.digitalspecimenprocessor.schema.Identifiers;
 import java.time.Instant;
 import java.util.HashMap;
 import java.util.List;
@@ -340,4 +341,9 @@ public static DigitalSpecimen givenAttributes(
         .withDctermsModified("2017-09-26T12:27:21.000+00:00");
   }
 
+  public static DigitalSpecimen givenAttributesPlusIdentifier(String specimenName, String organisation, Boolean markedAsType){
+    return givenAttributes(specimenName, organisation, markedAsType)
+        .withIdentifiers(List.of(new Identifiers("Specimen label", HANDLE, false, null, true)));
+  }
+
 }