Fix adding id property duplicates

.github/workflows/gradle.yml

@@ -11,7 +11,6 @@ on:
   push:
     branches: [ main, development ]
   pull_request:
-    branches: [ main, development ]
   workflow_dispatch:
 
 env:

src/main/java/edu/kit/datamanager/ro_crate/RoCrate.java

@@ -10,13 +10,10 @@
 import edu.kit.datamanager.ro_crate.entities.AbstractEntity;
 import edu.kit.datamanager.ro_crate.entities.contextual.ContextualEntity;
 import edu.kit.datamanager.ro_crate.entities.contextual.JsonDescriptor;
-import edu.kit.datamanager.ro_crate.entities.contextual.OrganizationEntity;
 import edu.kit.datamanager.ro_crate.entities.data.DataEntity;
-import edu.kit.datamanager.ro_crate.entities.data.DataEntity.DataEntityBuilder;
-import edu.kit.datamanager.ro_crate.entities.data.FileEntity;
+
 import edu.kit.datamanager.ro_crate.entities.data.RootDataEntity;
 import edu.kit.datamanager.ro_crate.externalproviders.dataentities.ImportFromDataCite;
-import edu.kit.datamanager.ro_crate.externalproviders.organizationprovider.RorProvider;
 import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper;
 import edu.kit.datamanager.ro_crate.payload.CratePayload;
 import edu.kit.datamanager.ro_crate.payload.RoCratePayload;
@@ -26,12 +23,9 @@
 import edu.kit.datamanager.ro_crate.special.JsonUtilFunctions;
 import edu.kit.datamanager.ro_crate.validation.JsonSchemaValidation;
 import edu.kit.datamanager.ro_crate.validation.Validator;
-import edu.kit.datamanager.ro_crate.writer.FolderWriter;
-import edu.kit.datamanager.ro_crate.writer.RoCrateWriter;
 
 import java.io.File;
 import java.net.URI;
-import java.nio.file.Paths;
 import java.util.*;
 import java.util.stream.Collectors;
 import java.util.stream.StreamSupport;
@@ -354,6 +348,11 @@ public RoCrateBuilder addName(String name) {
             return this;
         }
 
+        public RoCrateBuilder addIdentifier(String identifier) {
+            this.rootDataEntity.addProperty("identifier", identifier.strip());
+            return this;
+        }
+
         public RoCrateBuilder addDescription(String description) {
             this.rootDataEntity.addProperty(PROPERTY_DESCRIPTION, description);
             return this;

src/main/java/edu/kit/datamanager/ro_crate/entities/AbstractEntity.java

@@ -239,33 +239,60 @@ private static boolean addProperty(ObjectNode whereToAdd, String key, JsonNode v
      * @param id the "id" of the property.
      */
     public void addIdProperty(String name, String id) {
-        JsonNode jsonNode = addToIdProperty(name, id, this.properties.get(name));
-        if (jsonNode != null) {
-            this.linkedTo.add(id);
-            this.properties.set(name, jsonNode);
-            this.notifyObservers();
-        }
+        mergeIdIntoValue(id, this.properties.get(name))
+                .ifPresent(newValue -> {
+                    this.linkedTo.add(id);
+                    this.properties.set(name, newValue);
+                    this.notifyObservers();
+                });
     }
 
-    private static JsonNode addToIdProperty(String name, String id, JsonNode property) {
-        ObjectMapper objectMapper = MyObjectMapper.getMapper();
-        if (name != null && id != null) {
-            if (property == null) {
-                return objectMapper.createObjectNode().put("@id", id);
-            } else {
-                if (property.isArray()) {
-                    ArrayNode ns = (ArrayNode) property;
-                    ns.add(objectMapper.createObjectNode().put("@id", id));
-                    return ns;
-                } else {
-                    ArrayNode newNodes = objectMapper.createArrayNode();
-                    newNodes.add(property);
-                    newNodes.add(objectMapper.createObjectNode().put("@id", id));
-                    return newNodes;
-                }
-            }
+    /**
+     * Merges the given id into the current value,
+     * using this representation: {"@id" : "id"}.
+     * <p>
+     * The current value can be null without errors.
+     * Only the id will be considered in this case.
+     * <p>
+     * If the id is null-ish, it will not be added, similar to a null-ish value.
+     * If the id is already present, nothing will be done.
+     * If it is not an array and the id is not present, an array will be applied.
+     *
+     * @param id the id to add.
+     * @param currentValue the current value of the property.
+     * @return The updated value of the property.
+     *               Empty if value does not change!
+     */
+    private static Optional<JsonNode> mergeIdIntoValue(String id, JsonNode currentValue) {
+        if (id == null || id.isBlank()) { return Optional.empty(); }
+
+        ObjectMapper jsonBuilder = MyObjectMapper.getMapper();
+        ObjectNode newIdObject = jsonBuilder.createObjectNode().put("@id", id);
+        if (currentValue == null || currentValue.isNull() || currentValue.isMissingNode()) {
+            return Optional.ofNullable(newIdObject);
+        }
+
+        boolean isIdAlready = currentValue.asText().equals(id);
+        boolean isIdObjectAlready = currentValue.path("@id").asText().equals(id);
+        boolean isArrayWithIdPresent = currentValue.valueStream()
+                .anyMatch(node -> node
+                        .path("@id")
+                        .asText()
+                        .equals(id));
+        if (isIdAlready || isIdObjectAlready || isArrayWithIdPresent) {
+            return Optional.empty();
+        }
+
+        if (currentValue.isArray() && currentValue instanceof ArrayNode currentValueAsArray) {
+            currentValueAsArray.add(newIdObject);
+            return Optional.of(currentValueAsArray);
+        } else {
+            // property is not an array, so we make it an array
+            ArrayNode newNodes = jsonBuilder.createArrayNode();
+            newNodes.add(currentValue);
+            newNodes.add(newIdObject);
+            return Optional.of(newNodes);
         }
-        return null;
     }
 
     /**
@@ -486,11 +513,11 @@ public T addProperty(String key, boolean value) {
          * @return the generic builder
          */
         public T addIdProperty(String name, String id) {
-            JsonNode jsonNode = AbstractEntity.addToIdProperty(name, id, this.properties.get(name));
-            if (jsonNode != null) {
-                this.properties.set(name, jsonNode);
-                this.relatedItems.add(id);
-            }
+            AbstractEntity.mergeIdIntoValue(id, this.properties.get(name))
+                    .ifPresent(newValue -> {
+                        this.properties.set(name, newValue);
+                        this.relatedItems.add(id);
+                    });
             return self();
         }
 

src/test/java/edu/kit/datamanager/ro_crate/HelpFunctions.java

@@ -34,15 +34,15 @@ public static void compareEntityWithFile(AbstractEntity entity, String string) t
 
     public static void compare(JsonNode node1, JsonNode node2, Boolean equals) {
         var comparator = new JsonComparator() {
-        public boolean compareValues(Object expected, Object actual) {
-
+            public boolean compareValues(Object expected, Object actual) {
                 return expected.equals(actual);
             }
 
             public boolean compareFields(String expected, String actual) {
                 return expected.equals(actual);
             }
         };
+
         if (equals) {
             JSONCompare.assertMatches(node1, node2, comparator);
         } else {

src/test/java/edu/kit/datamanager/ro_crate/examples/ExamplesOfSpecificationV1p1Test.java

@@ -18,13 +18,50 @@
  */
 public class ExamplesOfSpecificationV1p1Test {
 
+    /**
+     * From: <a href="https://www.researchobject.org/ro-crate/specification/1.1/root-data-entity.html#minimal-example-of-ro-crate">
+     *     Minimal Example
+     * </a>
+     * <p>
+     * This is equivalent to {@link #testMinimalCrateWithoutCrateBuilder()}, but using more convenient APIs.
+     */
+    @Test
+    void testMinimalCrateConvenient() {
+        // Example 1: Basic RO-Crate
+        RoCrate minimal = new RoCrate.RoCrateBuilder(
+                "Data files associated with the manuscript:Effects of facilitated family case conferencing for ...",
+                "Palliative care planning for nursing home residents with advanced dementia ...",
+                "2017",
+                "https://creativecommons.org/licenses/by-nc-sa/3.0/au/"
+        )
+                .setLicense( new ContextualEntity.ContextualEntityBuilder()
+                        .addType("CreativeWork")
+                        .setId("https://creativecommons.org/licenses/by-nc-sa/3.0/au/")
+                        .addProperty("description", "This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Australia License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/au/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.")
+                        .addProperty("identifier", "https://creativecommons.org/licenses/by-nc-sa/3.0/au/")
+                        .addProperty("name", "Attribution-NonCommercial-ShareAlike 3.0 Australia (CC BY-NC-SA 3.0 AU)")
+                        .build()
+                )
+                .addIdentifier("https://doi.org/10.4225/59/59672c09f4a4b")
+                .build();
+
+        // So you get something to see
+        prettyPrintJsonString(minimal.getJsonMetadata());
+        // Compare with the example from the specification
+        try {
+            HelpFunctions.compareCrateJsonToFileInResources(minimal, "/spec-v1.1-example-json-files/minimal.json");
+        } catch (IOException e) {
+            throw new AssertionFailedError("Missing resources file!", e);
+        }
+    }
+
     /**
      * From: <a href="https://www.researchobject.org/ro-crate/specification/1.1/root-data-entity.html#minimal-example-of-ro-crate">
      *     Minimal Example
      * </a>
      * <p>
      * In this example, the crate is created without the builder.
-     * For the following examples, more convenient methods are used.
+     * Otherwise, the example is the same as {@link #testMinimalCrateConvenient()}.
      */
     @Test
     void testMinimalCrateWithoutCrateBuilder() {