Merge pull request #255 from kit-data-manager/development

Next Version (v2.1.0-rc2)

Author: Pfeil

.github/workflows/gradle.yml

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

README.md

@@ -38,7 +38,7 @@ repositories {
 }
 
 ext {
-    jacksonVersion  = '2.18.3'
+    jacksonVersion  = '2.19.0'
 }
 
 dependencies {
@@ -67,10 +67,15 @@ dependencies {
     implementation group: "com.networknt", name: "json-schema-validator", version: "1.5.6"
     implementation 'org.glassfish:jakarta.json:2.0.1'
     //JTE for template processing
-    implementation('gg.jte:jte:3.2.0')
+    implementation('gg.jte:jte:3.2.1')
     implementation("org.freemarker:freemarker:2.3.34")
 }
 
+// enable -Xlint:deprecation
+tasks.withType(JavaCompile).configureEach {
+    options.compilerArgs << "-Xlint:deprecation"
+}
+
 logging.captureStandardOutput LogLevel.INFO
 
 def signingTasks = tasks.withType(Sign)

build.gradle

@@ -1,6 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.13-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.14-bin.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME

gradle/wrapper/gradle-wrapper.jar

@@ -114,7 +114,7 @@ case "$( uname )" in                #(
   NONSTOP* )        nonstop=true ;;
 esac
 
-CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
+CLASSPATH="\\\"\\\""
 
 
 # Determine the Java command to use to start the JVM.
@@ -213,7 +213,7 @@ DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
 set -- \
         "-Dorg.gradle.appname=$APP_BASE_NAME" \
         -classpath "$CLASSPATH" \
-        org.gradle.wrapper.GradleWrapperMain \
+        -jar "$APP_HOME/gradle/wrapper/gradle-wrapper.jar" \
         "$@"
 
 # Stop when "xargs" is not available.

gradle/wrapper/gradle-wrapper.properties

@@ -70,11 +70,11 @@ goto fail
 :execute
 @rem Setup the command line
 
-set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
+set CLASSPATH=
 
 
 @rem Execute Gradle
-"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %*
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" -jar "%APP_HOME%\gradle\wrapper\gradle-wrapper.jar" %*
 
 :end
 @rem End local scope for the variables with windows NT shell

gradlew

@@ -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 +348,18 @@ public RoCrateBuilder addName(String name) {
             return this;
         }
 
+        /**
+         * Adds an "identifier" property to the root data entity.
+         * <p>
+         * This is useful e.g. to assign e.g. a DOI to this crate.
+         * @param identifier the identifier to add.
+         * @return this builder.
+         */
+        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;

gradlew.bat

@@ -113,9 +113,10 @@ public boolean checkEntity(AbstractEntity entity) {
     node.remove("@id");
     node.remove("@type");
 
-    Set<String> types = objectMapper.convertValue(entity.getProperties().get("@type"),
-        new TypeReference<>() {
-        });
+    Set<String> types = objectMapper.convertValue(
+            entity.getProperties().path("@type"),
+            new TypeReference<>() {}
+    );
     // check if the items in the array of types are present in the context
     for (String s : types) {
       // special cases:
@@ -174,15 +175,14 @@ public void addToContextFromUrl(String url) {
       }
     }
     if (jsonNode == null) {
-      CloseableHttpClient httpclient = HttpClients.createDefault();
       HttpGet httpGet = new HttpGet(url);
       CloseableHttpResponse response;
-      try {
+      try (CloseableHttpClient httpclient = HttpClients.createDefault()) {
         response = httpclient.execute(httpGet);
         jsonNode = objectMapper.readValue(response.getEntity().getContent(),
             JsonNode.class);
       } catch (IOException e) {
-        System.err.println(String.format("Cannot get context from url %s", url));
+        System.err.printf("Cannot get context from url %s%n", url);
         return;
       }
       if (url.equals(DEFAULT_CONTEXT)) {

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

@@ -239,33 +239,61 @@ 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();
-        }
+        if (id == null || id.isBlank()) { return; }
+        mergeIdIntoValue(id, this.properties.get(name))
+                .ifPresent(newValue -> {
+                    this.properties.set(name, newValue);
+                });
+        this.linkedTo.add(id);
+        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!
+     */
+    protected 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;
     }
 
     /**
@@ -369,6 +397,11 @@ protected String getId() {
         /**
          * Setting the id property of the entity, if the given value is not
          * null. If the id is not encoded, the encoding will be done.
+         * <p>
+         * <b>NOTE: IDs are not just names!</b> The ID may have effects
+         * on parts of your crate! For example: If the entity represents a
+         * file which will be copied into the crate, writers must use the
+         * ID as filename.
          *
          * @param id the String representing the id.
          * @return the generic builder.
@@ -486,11 +519,11 @@ 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();
         }
 
@@ -526,20 +559,62 @@ public T addIdFromCollectionOfEntities(String name, Collection<AbstractEntity> e
         }
 
         /**
-         * This sets everything from a json object to the property. Can be
-         * useful when the entity is already available somewhere.
+         * Deprecated. Equivalent to {@link #setAllIfValid(ObjectNode)}.
          *
          * @param properties the Json representing all the properties.
-         * @return the generic builder.
+         * @return the generic builder, either including all given properties
+         *          * or unchanged.
+         *
+         * @deprecated To enforce the user know what this method does,
+         *   we want the user to use one of the more explicitly named
+         *   methods {@link #setAllIfValid(ObjectNode)} or
+         *   {@link #setAllIfValid(ObjectNode)}.
+         * @see #setAllIfValid(ObjectNode)
          */
+        @Deprecated(since = "2.1.0", forRemoval = true)
         public T setAll(ObjectNode properties) {
+            return setAllIfValid(properties);
+        }
+
+        /**
+         * This sets everything from a json object to the property,
+         * <b>if the result is valid</b>. Otherwise, it will do <b>nothing</b>.
+         * <p>
+         * Valid means here that the json object needs to be flat as specified
+         * in the RO-Crate specification. In principle, this means that
+         * primitives and objects referencing an ID are allowed,
+         * as well as arrays of these.
+         *
+         * @param properties the Json representing all the properties.
+         * @return the generic builder, either including all given properties
+         * or unchanged.
+         */
+        public T setAllIfValid(ObjectNode properties) {
             if (AbstractEntity.entityValidation.entityValidation(properties)) {
                 this.properties = properties;
                 this.relatedItems.addAll(JsonUtilFunctions.getIdPropertiesFromJsonNode(properties));
             }
             return self();
         }
 
+        /**
+         * This sets everything from a json object to the property. Can be
+         * useful when the entity is already available somewhere.
+         * <p>
+         * Errors on validation are printed, but everything will be added.
+         * For more about validation, see {@link #setAllIfValid(ObjectNode)}.
+         *
+         * @param properties the Json representing all the properties.
+         * @return the generic builder with all properties added.
+         */
+        public T setAllUnsafe(ObjectNode properties) {
+            // This will currently only print errors.
+            AbstractEntity.entityValidation.entityValidation(properties);
+            this.properties = properties;
+            this.relatedItems.addAll(JsonUtilFunctions.getIdPropertiesFromJsonNode(properties));
+            return self();
+        }
+
         public abstract T self();
 
         public abstract AbstractEntity build();

src/main/java/edu/kit/datamanager/ro_crate/context/RoCrateMetadataContext.java

@@ -13,8 +13,8 @@
 
 public class JsonDescriptor extends ContextualEntity {
 
-    private static final String CONFORMS_TO = "conformsTo";
-    protected static final String ID = "ro-crate-metadata.json";
+    protected static final String CONFORMS_TO = "conformsTo";
+    public static final String ID = "ro-crate-metadata.json";
 
     /**
      * Returns a JsonDescriptor with the conformsTo value set to the latest stable
@@ -39,7 +39,7 @@ private JsonDescriptor(ContextualEntityBuilder builder) {
 
     /**
      * Builder for the JsonDescriptor.
-     * 
+     * <p>
      * Defaults to the latest stable crate version and no other conformsTo values.
      */
     public static final class Builder {