DiSSCo · samleeflang · Nov 20, 2024 · Nov 19, 2024 · Nov 19, 2024 · Nov 19, 2024
diff --git a/src/main/java/eu/dissco/core/translator/terms/BaseDigitalObjectDirector.java b/src/main/java/eu/dissco/core/translator/terms/BaseDigitalObjectDirector.java
@@ -16,6 +16,7 @@
 import static eu.dissco.core.translator.schema.Agent.Type.SCHEMA_PERSON;
 import static eu.dissco.core.translator.terms.utils.AgentsUtils.addAgent;
 import static eu.dissco.core.translator.terms.utils.EntityRelationshipUtils.addEntityRelationship;
+import static eu.dissco.core.translator.terms.utils.IdentifierUtils.addIdentifier;
 
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
@@ -389,11 +390,7 @@ private List<eu.dissco.core.translator.schema.Identifier> assembleIdentifiers(Js
     var identifiers = new ArrayList<Identifier>();
     for (String identifierTerm : identifierTerms) {
       if (data.get(identifierTerm) != null) {
-        var identifier = new Identifier()
-            .withId(data.get(identifierTerm).asText())
-            .withType("ods:Identifier")
-            .withDctermsTitle(identifierTerm)
-            .withDctermsIdentifier(data.get(identifierTerm).asText());
+        var identifier = addIdentifier(data.get(identifierTerm).asText(), identifierTerm);
         identifiers.add(identifier);
       }
     }

diff --git a/src/main/java/eu/dissco/core/translator/terms/utils/AgentsUtils.java b/src/main/java/eu/dissco/core/translator/terms/utils/AgentsUtils.java
@@ -1,8 +1,12 @@
 package eu.dissco.core.translator.terms.utils;
 
+import static eu.dissco.core.translator.terms.utils.IdentifierUtils.addIdentifier;
+
 import eu.dissco.core.translator.domain.AgentRoleType;
 import eu.dissco.core.translator.schema.Agent;
 import eu.dissco.core.translator.schema.Agent.Type;
+import eu.dissco.core.translator.schema.Identifier.OdsIdentifierStatus;
+import eu.dissco.core.translator.schema.OdsHasRole;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
@@ -17,23 +21,28 @@ private AgentsUtils() {
 
   public static List<Agent> addAgent(List<Agent> currentAgents, String agentValue, String agentId,
       AgentRoleType role, Type type) {
+    return addAgent(currentAgents, agentValue, agentId, role, type, null);
+  }
+
+  public static List<Agent> addAgent(List<Agent> currentAgents, String agentValue, String agentId,
+      AgentRoleType role, Type type, OdsIdentifierStatus identifierStatus) {
     var agents = new ArrayList<Agent>();
     if (currentAgents != null) {
       agents.addAll(currentAgents);
     }
     if (agentValue != null || agentId != null) {
       if ((agentValue != null && (agentValue.contains("&") || agentValue.contains("|"))) || (
           agentId != null && (agentId.contains("&") || agentId.contains("|")))) {
-        handleMultipleAgents(agents, agentValue, agentId, role, type);
+        handleMultipleAgents(agents, agentValue, agentId, role, type, identifierStatus);
       } else {
-        constructAgent(agents, agentValue, agentId, role, type);
+        constructAgent(agents, agentValue, agentId, role, type, identifierStatus);
       }
     }
     return agents;
   }
 
   private static void constructAgent(List<Agent> agents, String agentValue, String agentId,
-      AgentRoleType role, Type type) {
+      AgentRoleType role, Type type, OdsIdentifierStatus identifierStatus) {
     String agentName = agentValue;
     if (agentValue != null && agentValue.contains("http") && agentId == null) {
       agentId = agentValue;
@@ -50,19 +59,17 @@ private static void constructAgent(List<Agent> agents, String agentValue, String
         .withSchemaName(agentName)
         .withSchemaIdentifier(agentId)
         .withOdsHasRoles(
-            List.of(new eu.dissco.core.translator.schema.OdsHasRole().withType("schema:Role")
+            List.of(new OdsHasRole().withType("schema:Role")
                 .withSchemaRoleName(role.getName())));
     if (agentId != null) {
-      agent.withOdsHasIdentifiers(List.of(
-          new eu.dissco.core.translator.schema.Identifier().withId(agentId)
-              .withType("ods:Identifier")
-              .withDctermsIdentifier(agentId)));
+      agent.withOdsHasIdentifiers(List.of(addIdentifier(agentId, null, identifierStatus)));
     }
     agents.add(agent);
   }
 
   private static void handleMultipleAgents(
-      List<Agent> agents, String agentValue, String agentId, AgentRoleType role, Type type) {
+      List<Agent> agents, String agentValue, String agentId, AgentRoleType role, Type type,
+      OdsIdentifierStatus identifierStatus) {
     var ids = new String[0];
     var agentValues = new String[0];
     if (needsParsing(agentValue)) {
@@ -74,7 +81,7 @@ private static void handleMultipleAgents(
     }
     if (agentValues.length == ids.length) {
       for (int i = 0; i < agentValues.length; i++) {
-        constructAgent(agents, agentValues[i], ids[i], role, type);
+        constructAgent(agents, agentValues[i], ids[i], role, type, identifierStatus);
       }
     } else if (agentValues.length > ids.length) {
       if (ids.length != 0) {
@@ -83,7 +90,7 @@ private static void handleMultipleAgents(
             agentValue, agentId);
       }
       for (String agent : agentValues) {
-        constructAgent(agents, agent, null, role, type);
+        constructAgent(agents, agent, null, role, type, identifierStatus);
       }
     } else {
       if (agentValues.length != 0) {
@@ -92,7 +99,7 @@ private static void handleMultipleAgents(
             agentValue, agentId);
       }
       for (String idValue : ids) {
-        constructAgent(agents, null, idValue, role, type);
+        constructAgent(agents, null, idValue, role, type, identifierStatus);
       }
     }
   }

diff --git a/src/main/java/eu/dissco/core/translator/terms/utils/EntityRelationshipUtils.java b/src/main/java/eu/dissco/core/translator/terms/utils/EntityRelationshipUtils.java
@@ -2,6 +2,7 @@
 
 import static eu.dissco.core.translator.domain.AgentRoleType.DATA_TRANSLATOR;
 import static eu.dissco.core.translator.schema.Agent.Type.SCHEMA_SOFTWARE_APPLICATION;
+import static eu.dissco.core.translator.schema.Identifier.OdsIdentifierStatus.PREFERRED;
 import static eu.dissco.core.translator.terms.utils.AgentsUtils.addAgent;
 
 import eu.dissco.core.translator.domain.RelationshipType;
@@ -33,7 +34,7 @@ public static EntityRelationship addEntityRelationship(
         .withDwcRelationshipEstablishedDate(Date.from(Instant.now()));
     entityRelationship.setOdsHasAgents(
         addAgent(entityRelationship.getOdsHasAgents(), agentName, agentId, DATA_TRANSLATOR,
-            SCHEMA_SOFTWARE_APPLICATION));
+            SCHEMA_SOFTWARE_APPLICATION, PREFERRED));
     if (relatedResource.startsWith("http")) {
       try {
         entityRelationship.setOdsRelatedResourceURI(new URI(relatedResource));

diff --git a/src/main/java/eu/dissco/core/translator/terms/utils/IdentifierUtils.java b/src/main/java/eu/dissco/core/translator/terms/utils/IdentifierUtils.java
@@ -0,0 +1,95 @@
+package eu.dissco.core.translator.terms.utils;
+
+import static eu.dissco.core.translator.schema.Identifier.DctermsType.*;
+import static eu.dissco.core.translator.schema.Identifier.OdsGupriLevel.GLOBALLY_UNIQUE_STABLE;
+import static eu.dissco.core.translator.schema.Identifier.OdsGupriLevel.GLOBALLY_UNIQUE_STABLE_PERSISTENT_RESOLVABLE;
+import static eu.dissco.core.translator.schema.Identifier.OdsGupriLevel.GLOBALLY_UNIQUE_STABLE_PERSISTENT_RESOLVABLE_FDO_COMPLIANT;
+import static java.util.regex.Pattern.compile;
+
+import eu.dissco.core.translator.schema.Identifier;
+import eu.dissco.core.translator.schema.Identifier.DctermsType;
+import eu.dissco.core.translator.schema.Identifier.OdsGupriLevel;
+import eu.dissco.core.translator.schema.Identifier.OdsIdentifierStatus;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.regex.Pattern;
+import lombok.extern.slf4j.Slf4j;
+import org.apache.commons.lang3.tuple.Triple;
+
+@Slf4j
+public class IdentifierUtils {
+
+  private static final Map<List<Pattern>, Triple<DctermsType, String, OdsGupriLevel>> PATTERN_MAP = patternMap();
+
+  private IdentifierUtils() {
+    // This is a Utility class
+  }
+
+  private static Map<List<Pattern>, Triple<DctermsType, String, OdsGupriLevel>> patternMap() {
+    var linkedMap = new LinkedHashMap<List<Pattern>, Triple<DctermsType, String, OdsGupriLevel>>();
+    linkedMap.put(List.of(compile("^https?://doi.org")),
+        Triple.of(DOI, "DOI", GLOBALLY_UNIQUE_STABLE_PERSISTENT_RESOLVABLE_FDO_COMPLIANT));
+    linkedMap.put(List.of(compile("^https?://hdl.handle.net")),
+        Triple.of(HANDLE, "Handle", GLOBALLY_UNIQUE_STABLE_PERSISTENT_RESOLVABLE_FDO_COMPLIANT));
+    linkedMap.put(List.of(compile("^https?://www.wikidata.org")),
+        Triple.of(URL, "Wikidata", GLOBALLY_UNIQUE_STABLE_PERSISTENT_RESOLVABLE));
+    linkedMap.put(List.of(compile("^https?://orcid.org")),
+        Triple.of(URL, "ORCID", GLOBALLY_UNIQUE_STABLE_PERSISTENT_RESOLVABLE));
+    linkedMap.put(List.of(compile("^https?://\\w+.\\w+/ark:/\\w+/\\w+")),
+        Triple.of(ARK, "ARK", GLOBALLY_UNIQUE_STABLE_PERSISTENT_RESOLVABLE));
+    linkedMap.put(List.of(compile("https?://purl.org")),
+        Triple.of(PURL, "PURL", GLOBALLY_UNIQUE_STABLE_PERSISTENT_RESOLVABLE));
+    linkedMap.put(List.of(compile("^https?")),
+        Triple.of(URL, "URL", GLOBALLY_UNIQUE_STABLE_PERSISTENT_RESOLVABLE));
+    linkedMap.put(List.of(compile(
+            "(uuid:)*[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}")),
+        Triple.of(UUID, "UUID", GLOBALLY_UNIQUE_STABLE));
+    return linkedMap;
+  }
+
+  public static Identifier addIdentifier(String identifierString) {
+    return addIdentifier(identifierString, null, null);
+  }
+
+  public static Identifier addIdentifier(String identifierString, String identifierName) {
+    return addIdentifier(identifierString, identifierName, null);
+  }
+
+  public static Identifier addIdentifier(String identifierString, String identifierName,
+      OdsIdentifierStatus identifierStatus) {
+    if (identifierString == null) {
+      return null;
+    }
+    var identifier = new Identifier()
+        .withId(identifierString)
+        .withType("ods:Identifier")
+        .withDctermsIdentifier(identifierString)
+        .withOdsIdentifierStatus(identifierStatus);
+    for (var entry : PATTERN_MAP.entrySet()) {
+      for (var prefix : entry.getKey()) {
+        if (prefix.matcher(identifierString).find()) {
+          identifier.setDctermsType(entry.getValue().getLeft());
+          identifier.setDctermsTitle(getDcTermsTitle(identifierName, entry.getValue().getMiddle()));
+          identifier.setOdsGupriLevel(entry.getValue().getRight());
+          return identifier;
+        }
+      }
+    }
+    log.debug(
+        "Unable to recognise the type of identifier: {}. Assuming locally unique identifier",
+        identifierString);
+    identifier.setDctermsType(DctermsType.LOCALLY_UNIQUE_IDENTIFIER);
+    identifier.setDctermsTitle(identifierName);
+    identifier.setOdsGupriLevel(OdsGupriLevel.LOCALLY_UNIQUE_STABLE);
+    return identifier;
+  }
+
+  private static String getDcTermsTitle(String identifierName, String defaultValue) {
+    if (identifierName != null) {
+      return identifierName;
+    } else {
+      return defaultValue;
+    }
+  }
+}
diff --git a/src/test/java/eu/dissco/core/translator/terms/utils/AgentUtilsTest.java b/src/test/java/eu/dissco/core/translator/terms/utils/AgentUtilsTest.java
@@ -72,8 +72,7 @@ private static Agent createAgent(String name, String id) {
                 .withSchemaRoleName(CREATOR.getName())));
     if (id != null) {
       agent.withOdsHasIdentifiers(
-          List.of(new eu.dissco.core.translator.schema.Identifier().withType("ods:Identifier")
-              .withId(id).withDctermsIdentifier(id)));
+          List.of(IdentifierUtils.addIdentifier(id)));
     }
     return agent;
   }

diff --git a/src/test/java/eu/dissco/core/translator/terms/utils/EntityRelationshipUtilsTest.java b/src/test/java/eu/dissco/core/translator/terms/utils/EntityRelationshipUtilsTest.java
@@ -4,7 +4,7 @@
 import static eu.dissco.core.translator.domain.RelationshipType.HAS_FDO_TYPE;
 import static eu.dissco.core.translator.domain.RelationshipType.HAS_ORGANISATION_ID;
 import static eu.dissco.core.translator.schema.Agent.Type.SCHEMA_SOFTWARE_APPLICATION;
-import static eu.dissco.core.translator.terms.utils.AgentsUtils.addAgent;
+import static eu.dissco.core.translator.schema.Identifier.OdsIdentifierStatus.PREFERRED;
 import static org.assertj.core.api.Assertions.assertThat;
 
 import eu.dissco.core.translator.domain.RelationshipType;
@@ -74,8 +74,8 @@ private EntityRelationship createEntityRelationship(RelationshipType relationshi
         .withDwcRelatedResourceID(relatedResource)
         .withOdsRelatedResourceURI(relatedResourceURI)
         .withDwcRelationshipEstablishedDate(Date.from(Instant.now()))
-        .withOdsHasAgents(addAgent(List.of(), APP_NAME, APP_PID,
-            DATA_TRANSLATOR, SCHEMA_SOFTWARE_APPLICATION));
+        .withOdsHasAgents(AgentsUtils.addAgent(List.of(), APP_NAME, APP_PID,
+            DATA_TRANSLATOR, SCHEMA_SOFTWARE_APPLICATION, PREFERRED));
 
   }
 }
diff --git a/src/test/java/eu/dissco/core/translator/terms/utils/IdentifierUtilsTest.java b/src/test/java/eu/dissco/core/translator/terms/utils/IdentifierUtilsTest.java
@@ -0,0 +1,84 @@
+package eu.dissco.core.translator.terms.utils;
+
+import static eu.dissco.core.translator.schema.Identifier.DctermsType.ARK;
+import static eu.dissco.core.translator.schema.Identifier.DctermsType.HANDLE;
+import static eu.dissco.core.translator.schema.Identifier.DctermsType.LOCALLY_UNIQUE_IDENTIFIER;
+import static eu.dissco.core.translator.schema.Identifier.DctermsType.PURL;
+import static eu.dissco.core.translator.schema.Identifier.DctermsType.URL;
+import static eu.dissco.core.translator.schema.Identifier.DctermsType.UUID;
+import static eu.dissco.core.translator.schema.Identifier.OdsGupriLevel.GLOBALLY_UNIQUE_STABLE;
+import static eu.dissco.core.translator.schema.Identifier.OdsGupriLevel.GLOBALLY_UNIQUE_STABLE_PERSISTENT_RESOLVABLE;
+import static eu.dissco.core.translator.schema.Identifier.OdsGupriLevel.GLOBALLY_UNIQUE_STABLE_PERSISTENT_RESOLVABLE_FDO_COMPLIANT;
+import static eu.dissco.core.translator.schema.Identifier.OdsGupriLevel.LOCALLY_UNIQUE_STABLE;
+import static eu.dissco.core.translator.schema.Identifier.OdsIdentifierStatus.PREFERRED;
+import static eu.dissco.core.translator.terms.utils.IdentifierUtils.addIdentifier;
+import static org.assertj.core.api.Assertions.assertThat;
+
+import eu.dissco.core.translator.schema.Identifier;
+import eu.dissco.core.translator.schema.Identifier.DctermsType;
+import eu.dissco.core.translator.schema.Identifier.OdsGupriLevel;
+import eu.dissco.core.translator.schema.Identifier.OdsIdentifierStatus;
+import java.util.stream.Stream;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.Arguments;
+import org.junit.jupiter.params.provider.MethodSource;
+import org.mockito.junit.jupiter.MockitoExtension;
+
+@ExtendWith(MockitoExtension.class)
+class IdentifierUtilsTest {
+
+
+  public static Stream<Arguments> identifierProvider() {
+    return Stream.of(
+        Arguments.of("https://www.wikidata.org/wiki/Q66581882", null, null,
+            createIdentifier("https://www.wikidata.org/wiki/Q66581882", URL, "Wikidata",
+                GLOBALLY_UNIQUE_STABLE_PERSISTENT_RESOLVABLE, null)),
+        Arguments.of("https://hdl.handle.net/XXX-XXX-XXX", null, PREFERRED,
+            createIdentifier("https://hdl.handle.net/XXX-XXX-XXX", HANDLE, "Handle",
+                GLOBALLY_UNIQUE_STABLE_PERSISTENT_RESOLVABLE_FDO_COMPLIANT, PREFERRED)),
+        Arguments.of("88e320d5-c47a-4288-b265-fa3c93c57440", "dwc:catalogueNumber", null,
+            createIdentifier("88e320d5-c47a-4288-b265-fa3c93c57440", UUID, "dwc:catalogueNumber",
+                GLOBALLY_UNIQUE_STABLE, null)),
+        Arguments.of("urn:uuid:541fd754-17e8-43c8-ba4e-b413a1bf3a2f", "dwca:ID", null,
+            createIdentifier("urn:uuid:541fd754-17e8-43c8-ba4e-b413a1bf3a2f", UUID, "dwca:ID",
+                GLOBALLY_UNIQUE_STABLE, null)),
+        Arguments.of("https://geocollections.info/specimen/126758", "abcd:unitGUID", null,
+            createIdentifier("https://geocollections.info/specimen/126758", URL, "abcd:unitGUID",
+                GLOBALLY_UNIQUE_STABLE_PERSISTENT_RESOLVABLE, null)),
+        Arguments.of("http://n2t.net/ark:/65665/3173bef93-f5c6-4534-bd31-42289606938b", "dwc:catalogueNumber", null,
+            createIdentifier("http://n2t.net/ark:/65665/3173bef93-f5c6-4534-bd31-42289606938b", ARK, "dwc:catalogueNumber",
+                GLOBALLY_UNIQUE_STABLE_PERSISTENT_RESOLVABLE, null)),
+        Arguments.of("http://purl.org/dc/terms/accessRights", null, null,
+            createIdentifier("http://purl.org/dc/terms/accessRights", PURL, "PURL",
+                GLOBALLY_UNIQUE_STABLE_PERSISTENT_RESOLVABLE, null)),
+        Arguments.of("AVES-071259", "dwc:occurrenceID", null,
+            createIdentifier("AVES-071259", LOCALLY_UNIQUE_IDENTIFIER, "dwc:occurrenceID",
+                LOCALLY_UNIQUE_STABLE, null)),
+        Arguments.of(null, null, null, null)
+    );
+  }
+
+  private static Identifier createIdentifier(String id, DctermsType type, String title,
+      OdsGupriLevel gupriLevel, OdsIdentifierStatus status) {
+    return new Identifier()
+        .withId(id)
+        .withType("ods:Identifier")
+        .withDctermsIdentifier(id)
+        .withDctermsTitle(title)
+        .withDctermsType(type)
+        .withOdsGupriLevel(gupriLevel)
+        .withOdsIdentifierStatus(status);
+  }
+
+  @ParameterizedTest
+  @MethodSource("identifierProvider")
+  void testAddIdentifier(String identifier, String identifierName, OdsIdentifierStatus status,
+      Identifier expected) {
+    // When
+    var result = addIdentifier(identifier, identifierName, status);
+
+    // Then
+    assertThat(result).isEqualTo(expected);
+  }
+}