API for creating interconnected FAIR-DOs (a FAIR-DO graph) in a single request

.gitignore

@@ -135,4 +135,8 @@ $RECYCLE.BIN/
 **/*.properties
 !/config/application-default.properties
 !/config/application-docker.properties
-##############
+##############
+
+test_prefix_data/
+config/*.bin
+config/*.pem

config/application-default.properties

@@ -131,14 +131,14 @@ spring.cloud.gateway.proxy.sensitive=content-length
 # the all properties with 'binding' define from where messages are received, e.g. the 
 # exchange aka. topic and the queue. The routingKeys are defining wich messages are 
 # routed to the aforementioned queue.
-repo.messaging.enabled: false
-repo.messaging.hostname: localhost
-repo.messaging.port: 5672
-repo.messaging.sender.exchange: record_events
-
+repo.messaging.enabled=false
+management.health.rabbit.enabled=false
+repo.messaging.hostname=localhost
+repo.messaging.port=5672
+repo.messaging.sender.exchange=record_events
 # The rate in milliseconds at which the repository itself will check for new messages.
 # E.g. if a resource has been created, the repository may has to perform additional
-# ingest steps. Therefor, special handlers can be added which will be executed at the
+# ingest steps. Therefore, special handlers can be added which will be executed at the
 # configured repo.schedule.rate if a new message has been received.
 repo.schedule.rate:1000
 
@@ -201,7 +201,7 @@ pit.validation.alwaysAllowAdditionalAttributes = true
 # where a DTR may not be available or an external validator is being
 # used.
 #
-# pit.validation.strategy = debug-none
+# pit.validation.strategy=none-debug
 ### DANGEROUS OPTIONS! Please read carefully! ########################################
 
 #######################################################

src/main/java/edu/kit/datamanager/pit/common/RecordValidationException.java

@@ -1,39 +1,54 @@
-package edu.kit.datamanager.pit.common;
+/*
+ * Copyright (c) 2024 Karlsruhe Institute of Technology.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
 
-import org.springframework.web.server.ResponseStatusException;
-import org.springframework.http.HttpStatus;
+package edu.kit.datamanager.pit.common;
 
 import edu.kit.datamanager.pit.domain.PIDRecord;
+import org.springframework.http.HttpStatus;
+import org.springframework.web.server.ResponseStatusException;
 
 /**
  * Indicates that a PID was given which could not be resolved to answer the
  * request properly.
  */
 public class RecordValidationException extends ResponseStatusException {
 
-	private static final String VALIDATION_OF_RECORD = "Validation of record ";
-	private static final long serialVersionUID = 1L;
-	private static final HttpStatus HTTP_STATUS = HttpStatus.BAD_REQUEST;
+    private static final String VALIDATION_OF_RECORD = "Validation of record ";
+    private static final long serialVersionUID = 1L;
+    private static final HttpStatus HTTP_STATUS = HttpStatus.BAD_REQUEST;
 
-	// For cases in which the PID record shold be appended to the error response.
-	private final transient PIDRecord pidRecord;
+    // For cases in which the PID record should be appended to the error response.
+    private final transient PIDRecord pidRecord;
 
-	public RecordValidationException(PIDRecord pidRecord) {
-		super(HTTP_STATUS, VALIDATION_OF_RECORD + pidRecord.getPid() + " failed.");
-		this.pidRecord = pidRecord;
-	}
+    public RecordValidationException(PIDRecord pidRecord) {
+        super(HTTP_STATUS, VALIDATION_OF_RECORD + pidRecord.getPid() + " failed.");
+        this.pidRecord = pidRecord;
+    }
 
-	public RecordValidationException(PIDRecord pidRecord, String reason) {
-		super(HTTP_STATUS, VALIDATION_OF_RECORD + pidRecord.getPid() + " failed. Reason: " + reason);
-		this.pidRecord = pidRecord;
-	}
+    public RecordValidationException(PIDRecord pidRecord, String reason) {
+      super(HTTP_STATUS, VALIDATION_OF_RECORD + pidRecord.getPid() + " failed. Reason: " + reason);
+      this.pidRecord = pidRecord;
+    }
 
-	public RecordValidationException(PIDRecord pidRecord, String reason, Exception e) {
-		super(HTTP_STATUS, VALIDATION_OF_RECORD + pidRecord.getPid() + " failed. Reason: " + reason, e);
-		this.pidRecord = pidRecord;
-	}
+    public RecordValidationException(PIDRecord pidRecord, String reason, Exception e) {
+      super(HTTP_STATUS, VALIDATION_OF_RECORD + pidRecord.getPid() + " failed. Reason: " + reason, e);
+      this.pidRecord = pidRecord;
+    }
 
-	public PIDRecord getPidRecord() {
-		return pidRecord;
-	}
+    public PIDRecord getPidRecord() {
+        return pidRecord;
+    }
 }

src/main/java/edu/kit/datamanager/pit/domain/PIDRecord.java

@@ -1,17 +1,27 @@
+/*
+ * Copyright (c) 2025 Karlsruhe Institute of Technology.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
 package edu.kit.datamanager.pit.domain;
 
 import com.fasterxml.jackson.annotation.JsonIgnore;
-
 import edu.kit.datamanager.entities.EtagSupport;
 import edu.kit.datamanager.pit.pidsystem.impl.local.PidDatabaseObject;
 
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 import java.util.stream.Collectors;
-import java.util.Set;
 
 /**
  * The internal representation for a PID record, offering methods to manipulate
@@ -21,7 +31,7 @@
  * communication or representation for the outside. In contrast, this is the
  * internal representation offering methods for manipulation.
  */
-public class PIDRecord implements EtagSupport {
+public class PIDRecord implements EtagSupport, Cloneable {
 
     private String pid = "";
 
@@ -30,11 +40,12 @@ public class PIDRecord implements EtagSupport {
     /**
      * Creates an empty record without PID.
      */
-    public PIDRecord() {}
+    public PIDRecord() {
+    }
 
     /**
      * Creates a record with the same content as the given representation.
-     * 
+     *
      * @param dbo the given record representation.
      */
     public PIDRecord(PidDatabaseObject dbo) {
@@ -53,7 +64,7 @@ public PIDRecord(SimplePidRecord rec) {
 
     /**
      * Convenience setter / builder method.
-     * 
+     *
      * @param pid the pid to set in this object.
      * @return this object (builder method).
      */
@@ -74,6 +85,10 @@ public Map<String, List<PIDRecordEntry>> getEntries() {
         return entries;
     }
 
+    public void setEntries(Map<String, List<PIDRecordEntry>> entries) {
+        this.entries = entries;
+    }
+
     @JsonIgnore
     public Set<SimplePair> getSimpleEntries() {
         return this.entries
@@ -85,20 +100,16 @@ public Set<SimplePair> getSimpleEntries() {
                 .collect(Collectors.toSet());
     }
 
-    public void setEntries(Map<String, List<PIDRecordEntry>> entries) {
-        this.entries = entries;
-    }
-
     public void addEntry(String propertyIdentifier, String propertyValue) {
         this.addEntry(propertyIdentifier, "", propertyValue);
     }
 
     /**
      * Adds a new key-name-value triplet.
-     * 
+     *
      * @param propertyIdentifier the key/type PID.
-     * @param propertyName the human-readable name for the given key/type.
-     * @param propertyValue the value to this key/type.
+     * @param propertyName       the human-readable name for the given key/type.
+     * @param propertyValue      the value to this key/type.
      */
     public void addEntry(String propertyIdentifier, String propertyName, String propertyValue) {
         if (propertyIdentifier.isEmpty()) {
@@ -110,22 +121,22 @@ public void addEntry(String propertyIdentifier, String propertyName, String prop
         entry.setValue(propertyValue);
 
         this.entries
-            .computeIfAbsent(propertyIdentifier, key -> new ArrayList<>())
-            .add(entry);
+                .computeIfAbsent(propertyIdentifier, key -> new ArrayList<>())
+                .add(entry);
     }
 
     /**
      * Sets the name for a given key/type in all available pairs.
-     * 
+     *
      * @param propertyIdentifier the key/type.
-     * @param name the new name.
+     * @param name               the new name.
      */
     @JsonIgnore
     public void setPropertyName(String propertyIdentifier, String name) {
         List<PIDRecordEntry> propertyEntries = this.entries.get(propertyIdentifier);
         if (propertyEntries == null) {
             throw new IllegalArgumentException(
-                "Property identifier not listed in this record: " + propertyIdentifier);
+                    "Property identifier not listed in this record: " + propertyIdentifier);
         }
         for (PIDRecordEntry entry : propertyEntries) {
             entry.setName(name);
@@ -135,7 +146,7 @@ public void setPropertyName(String propertyIdentifier, String name) {
     /**
      * Check if there is a pair or triplet containing the given property (key/type)
      * is availeble in this record.
-     * 
+     *
      * @param propertyIdentifier the key/type to search for.
      * @return true, if the property/key/type is present.
      */
@@ -158,7 +169,7 @@ public void removeAllValuesOf(String attribute) {
 
     /**
      * Get all properties contained in this record.
-     * 
+     *
      * @return al contained properties.
      */
     @JsonIgnore
@@ -180,7 +191,7 @@ public String getPropertyValue(String propertyIdentifier) {
 
     /**
      * Get all values of a given property.
-     * 
+     *
      * @param propertyIdentifier the given property identifier.
      * @return all values of the given property.
      */
@@ -194,7 +205,7 @@ public String[] getPropertyValues(String propertyIdentifier) {
         for (PIDRecordEntry e : entry) {
             values.add(e.getValue());
         }
-        return values.toArray(new String[] {});
+        return values.toArray(new String[]{});
     }
 
     @Override
@@ -215,9 +226,15 @@ public int hashCode() {
      */
     @Override
     public boolean equals(Object obj) {
-        if (this == obj) {return true;}
-        if (obj == null) {return false;}
-        if (getClass() != obj.getClass()) {return false;}
+        if (this == obj) {
+            return true;
+        }
+        if (obj == null) {
+            return false;
+        }
+        if (getClass() != obj.getClass()) {
+            return false;
+        }
 
         PIDRecord other = (PIDRecord) obj;
         boolean isThisPidEmpty = pid == null || pid.isBlank();
@@ -240,13 +257,32 @@ public String toString() {
 
     /**
      * Calculates an etag for a record.
-     * 
+     *
      * @return an etag, which is independent of any order or duplicates in the
-     *         entries.
+     * entries.
      */
     @JsonIgnore
     @Override
     public String getEtag() {
         return Integer.toString(this.hashCode());
     }
+
+    @Override
+    public PIDRecord clone() {
+        try {
+            PIDRecord clone = (PIDRecord) super.clone();
+            clone.pid = this.pid;
+            clone.entries = new HashMap<>();
+            for (Map.Entry<String, List<PIDRecordEntry>> entry : this.entries.entrySet()) {
+                List<PIDRecordEntry> entryList = new ArrayList<>();
+                for (PIDRecordEntry e : entry.getValue()) {
+                    entryList.add(e.clone());
+                }
+                clone.entries.put(entry.getKey(), entryList);
+            }
+            return clone;
+        } catch (CloneNotSupportedException e) {
+            throw new AssertionError();
+        }
+    }
 }

src/main/java/edu/kit/datamanager/pit/domain/PIDRecordEntry.java

@@ -1,10 +1,39 @@
+/*
+ * Copyright (c) 2025 Karlsruhe Institute of Technology.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
 package edu.kit.datamanager.pit.domain;
 
 import lombok.Data;
 
 @Data
-public class PIDRecordEntry {
+public class PIDRecordEntry implements Cloneable {
     private String key;
     private String name;
     private String value;
+
+    @Override
+    public PIDRecordEntry clone() {
+        try {
+            PIDRecordEntry clone = (PIDRecordEntry) super.clone();
+            clone.setKey(this.key);
+            clone.setName(this.name);
+            clone.setValue(this.value);
+            return clone;
+        } catch (CloneNotSupportedException e) {
+            throw new AssertionError();
+        }
+    }
 }