Merge branch 'f-fsm' into f-fsm-v0.2

CHANGELOG.md

@@ -13,6 +13,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   by setting the server property `EXT_ENTITY_STATE=ENABLED`. See
   [!62](https://gitlab.com/caosdb/caosdb-server/-/merge_requests/62) for more
   information.
+* New version history feature. The "H" container flag retrieves the full
+  version history during a transaction (e.g. during Retrievals) and constructs
+  a tree of successors and predecessors of the requested entity version.
 * New query functionality: `ANY VERSION OF` modifier. E.g. `FIND ANY VERSION OF
   RECORD WITH pname=val` returns all current and old versions of records where
   `pname=val`. For further information, examples and limitations see the wiki

conf/core/cache.ccf

@@ -28,8 +28,8 @@ jcs.region.BACKEND_JobRules.cacheattributes.MaxObjects=103
 jcs.region.BACKEND_SparseEntities
 jcs.region.BACKEND_SparseEntities.cacheattributes.MaxObjects=1002
 
-jcs.region.BACKEND_RetrieveFullVersionInfo
-jcs.region.BACKEND_RetrieveFullVersionInfo.cacheattributes.MaxObjects=1006
+jcs.region.BACKEND_RetrieveVersionHistory
+jcs.region.BACKEND_RetrieveVersionHistory.cacheattributes.MaxObjects=1006
 
 # PAM UserSource Caching: Cached Items expire after 60 seconds if they are not requested (idle) and after 600 seconds max.
 # PAM_UnixUserGroups

conf/core/server.conf

@@ -68,7 +68,7 @@ MYSQL_USER_NAME=caosdb
 # Password for the user
 MYSQL_USER_PASSWORD=caosdb
 # Schema of mysql procedures and tables which is required by this CaosDB instance
-MYSQL_SCHEMA_VERSION=v4.0.0-rc1
+MYSQL_SCHEMA_VERSION=v4.0.0-rc2
 
 
 # --------------------------------------------------

src/main/java/org/caosdb/server/database/BackendTransaction.java

@@ -59,7 +59,6 @@ import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveProp
 import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveQueryTemplateDefinition;
 import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveRole;
 import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveSparseEntity;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveTransactionHistory;
 import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveUser;
 import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveVersionHistory;
 import org.caosdb.server.database.backend.implementation.MySQL.MySQLRuleLoader;
@@ -116,7 +115,6 @@ import org.caosdb.server.database.backend.interfaces.RetrievePropertiesImpl;
 import org.caosdb.server.database.backend.interfaces.RetrieveQueryTemplateDefinitionImpl;
 import org.caosdb.server.database.backend.interfaces.RetrieveRoleImpl;
 import org.caosdb.server.database.backend.interfaces.RetrieveSparseEntityImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveTransactionHistoryImpl;
 import org.caosdb.server.database.backend.interfaces.RetrieveUserImpl;
 import org.caosdb.server.database.backend.interfaces.RetrieveVersionHistoryImpl;
 import org.caosdb.server.database.backend.interfaces.RuleLoaderImpl;
@@ -177,7 +175,6 @@ public abstract class BackendTransaction implements Undoable {
       setImpl(RetrieveAllImpl.class, MySQLRetrieveAll.class);
       setImpl(RegisterSubDomainImpl.class, MySQLRegisterSubDomain.class);
       setImpl(RetrieveDatatypesImpl.class, MySQLRetrieveDatatypes.class);
-      setImpl(RetrieveTransactionHistoryImpl.class, MySQLRetrieveTransactionHistory.class);
       setImpl(RetrieveUserImpl.class, MySQLRetrieveUser.class);
       setImpl(RetrieveParentsImpl.class, MySQLRetrieveParents.class);
       setImpl(GetFileRecordByPathImpl.class, MySQLGetFileRecordByPath.class);

src/main/java/org/caosdb/server/database/DatabaseUtils.java

@@ -216,10 +216,7 @@ public class DatabaseUtils {
     ret.fileSize = rs.getLong("FileSize");
     ret.fileHash = bytes2UTF8(rs.getBytes("FileHash"));
 
-    ret.version = bytes2UTF8(rs.getBytes("Version"));
-    ret.versionSeconds = rs.getLong("VersionSeconds");
-    ret.versionNanos = rs.getInt("VersionNanos");
-
+    ret.versionId = bytes2UTF8(rs.getBytes("Version"));
     return ret;
   }
 

src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertSparseEntity.java

@@ -57,7 +57,7 @@ public class MySQLInsertSparseEntity extends MySQLTransaction implements InsertS
       try (final ResultSet rs = insertEntityStmt.executeQuery()) {
         if (rs.next()) {
           entity.id = rs.getInt("EntityID");
-          entity.version = DatabaseUtils.bytes2UTF8(rs.getBytes("Version"));
+          entity.versionId = DatabaseUtils.bytes2UTF8(rs.getBytes("Version"));
         } else {
           throw new TransactionException("Didn't get new EntityID back.");
         }

src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveTransactionHistory.java

-/*
- * ** header v3.0
- * This file is a part of the CaosDB Project.
- *
- * Copyright (C) 2018 Research Group Biomedical Physics,
- * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Affero General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU Affero General Public License for more details.
- *
- * You should have received a copy of the GNU Affero General Public License
- * along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
- */
-package org.caosdb.server.database.backend.implementation.MySQL;
-
-import static org.caosdb.server.database.DatabaseUtils.bytes2UTF8;
-
-import java.sql.PreparedStatement;
-import java.sql.ResultSet;
-import java.sql.SQLException;
-import java.util.ArrayList;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrieveTransactionHistoryImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoTransactionLogMessage;
-
-public class MySQLRetrieveTransactionHistory extends MySQLTransaction
-    implements RetrieveTransactionHistoryImpl {
-
-  public MySQLRetrieveTransactionHistory(final Access access) {
-    super(access);
-  }
-
-  public static final String STMT_RETRIEVE_HISTORY =
-      "SELECT transaction, realm, username, seconds, nanos FROM transaction_log WHERE entity_id=? ";
-
-  @Override
-  public ArrayList<ProtoTransactionLogMessage> execute(final Integer id)
-      throws TransactionException {
-    try {
-      final PreparedStatement stmt = prepareStatement(STMT_RETRIEVE_HISTORY);
-
-      final ArrayList<ProtoTransactionLogMessage> ret = new ArrayList<ProtoTransactionLogMessage>();
-      stmt.setInt(1, id);
-      final ResultSet rs = stmt.executeQuery();
-      try {
-        while (rs.next()) {
-          final String transaction = bytes2UTF8(rs.getBytes("transaction"));
-          final String realm = bytes2UTF8(rs.getBytes("realm"));
-          final String username = bytes2UTF8(rs.getBytes("username"));
-          final Integer seconds = rs.getInt("seconds");
-          final Integer nanos = rs.getInt("nanos");
-
-          ret.add(new ProtoTransactionLogMessage(transaction, realm, username, seconds, nanos));
-        }
-        return ret;
-      } finally {
-        rs.close();
-      }
-    } catch (final SQLException e) {
-      throw new TransactionException(e);
-    } catch (final ConnectionException e) {
-      throw new TransactionException(e);
-    }
-  }
-}

src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveVersionHistory.java

@@ -61,12 +61,16 @@ public class MySQLRetrieveVersionHistory extends MySQLTransaction
         String parentId = DatabaseUtils.bytes2UTF8(rs.getBytes("parent"));
         Long childSeconds = rs.getLong("child_seconds");
         Integer childNanos = rs.getInt("child_nanos");
+        String childUsername = DatabaseUtils.bytes2UTF8(rs.getBytes("child_username"));
+        String childRealm = DatabaseUtils.bytes2UTF8(rs.getBytes("child_realm"));
         VersionHistoryItem v = result.get(childId);
         if (v == null) {
           v = new VersionHistoryItem();
           v.id = childId;
           v.seconds = childSeconds;
           v.nanos = childNanos;
+          v.username = childUsername;
+          v.realm = childRealm;
           result.put(childId, v);
         }
 

src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateSparseEntity.java

@@ -80,7 +80,7 @@ public class MySQLUpdateSparseEntity extends MySQLTransaction implements UpdateS
       ResultSet rs = updateEntityStmt.executeQuery();
 
       if (rs.next()) {
-        spe.version = DatabaseUtils.bytes2UTF8(rs.getBytes("Version"));
+        spe.versionId = DatabaseUtils.bytes2UTF8(rs.getBytes("Version"));
       }
 
     } catch (final SQLIntegrityConstraintViolationException e) {

src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveTransactionHistoryImpl.java

-/*
- * ** header v3.0
- * This file is a part of the CaosDB Project.
- *
- * Copyright (C) 2018 Research Group Biomedical Physics,
- * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Affero General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU Affero General Public License for more details.
- *
- * You should have received a copy of the GNU Affero General Public License
- * along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
- */
-package org.caosdb.server.database.backend.interfaces;
-
-import java.util.ArrayList;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoTransactionLogMessage;
-
-public interface RetrieveTransactionHistoryImpl extends BackendTransactionImpl {
-
-  public ArrayList<ProtoTransactionLogMessage> execute(Integer id) throws TransactionException;
-}

src/main/java/org/caosdb/server/database/backend/transaction/InsertSparseEntity.java

@@ -69,6 +69,7 @@ public class InsertSparseEntity extends BackendTransaction {
               public void cleanUp() {}
             });
     this.entity.setId(e.id);
-    this.entity.setVersion(new Version(e.version));
+    this.entity.setVersion(new Version(e.versionId));
+    this.entity.getVersion().setHead(true);
   }
 }

src/main/java/org/caosdb/server/database/backend/transaction/RetrieveTransactionHistory.java

-/*
- * ** header v3.0
- * This file is a part of the CaosDB Project.
- *
- * Copyright (C) 2018 Research Group Biomedical Physics,
- * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- * Copyright (C) 2019 IndiScale GmbH
- * Copyright (C) 2019 Timm Fitschen (t.fitschen@indiscale.com)
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Affero General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU Affero General Public License for more details.
- *
- * You should have received a copy of the GNU Affero General Public License
- * along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
- */
-package org.caosdb.server.database.backend.transaction;
-
-import java.util.ArrayList;
-import org.caosdb.datetime.UTCDateTime;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.RetrieveTransactionHistoryImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoTransactionLogMessage;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.utils.TransactionLogMessage;
-
-public class RetrieveTransactionHistory extends BackendTransaction {
-
-  private final EntityInterface entity;
-
-  public RetrieveTransactionHistory(final EntityInterface entity) {
-    this.entity = entity;
-  }
-
-  @Override
-  protected void execute() {
-    final RetrieveTransactionHistoryImpl t =
-        getImplementation(RetrieveTransactionHistoryImpl.class);
-    process(t.execute(entity.getId()));
-  }
-
-  private void process(final ArrayList<ProtoTransactionLogMessage> l) throws TransactionException {
-    for (final ProtoTransactionLogMessage t : l) {
-      final UTCDateTime dateTime = UTCDateTime.UTCSeconds(t.seconds, t.nanos);
-
-      this.entity.addTransactionLog(
-          new TransactionLogMessage(t.transaction, this.entity, t.username, dateTime));
-    }
-  }
-}

src/main/java/org/caosdb/server/database/backend/transaction/RetrieveVersionHistory.java

@@ -22,58 +22,43 @@
  */
 package org.caosdb.server.database.backend.transaction;
 
-import java.util.Collection;
 import java.util.HashMap;
-import org.caosdb.server.database.CacheableBackendTransaction;
-import org.caosdb.server.database.backend.interfaces.RetrieveVersionHistoryImpl;
+import org.caosdb.datetime.UTCDateTime;
 import org.caosdb.server.database.exceptions.TransactionException;
 import org.caosdb.server.database.proto.VersionHistoryItem;
 import org.caosdb.server.entity.EntityInterface;
+import org.caosdb.server.entity.Version;
 
-public abstract class RetrieveVersionHistory
-    extends CacheableBackendTransaction<Integer, HashMap<String, VersionHistoryItem>> {
-
-  // TODO
-  // private static final ICacheAccess<String, Version> cache =
-  // Cache.getCache("BACKEND_RetrieveVersionHistory");
-  private EntityInterface entity;
-  private HashMap<String, VersionHistoryItem> map;
-
-  public static void removeCached(Integer entityId) {
-    // TODO
-  }
+public class RetrieveVersionHistory extends VersionTransaction {
 
   public RetrieveVersionHistory(EntityInterface e) {
-    super(null); // TODO caching
-    this.entity = e;
-  }
-
-  @Override
-  public HashMap<String, VersionHistoryItem> executeNoCache() throws TransactionException {
-    RetrieveVersionHistoryImpl impl = getImplementation(RetrieveVersionHistoryImpl.class);
-    return impl.execute(getKey());
+    super(e);
   }
 
-  /** After this method call, the version map is available to the object. */
   @Override
   protected void process(HashMap<String, VersionHistoryItem> map) throws TransactionException {
-    this.map = map;
+    super.process(map);
+    if (!map.isEmpty()) getEntity().setVersion(getHistory());
   }
 
   @Override
-  protected Integer getKey() {
-    return entity.getId();
-  }
-
-  public HashMap<String, VersionHistoryItem> getMap() {
-    return this.map;
-  }
-
-  public EntityInterface getEntity() {
-    return this.entity;
+  protected Version getVersion(String id) {
+    Version v = new Version(id);
+    VersionHistoryItem i = getHistoryItems().get(v.getId());
+    if (i != null) {
+      v.setDate(UTCDateTime.UTCSeconds(i.seconds, i.nanos));
+      v.setUsername(i.username);
+      v.setRealm(i.realm);
+    }
+    return v;
   }
 
-  public Collection<VersionHistoryItem> getList() {
-    return this.map.values();
+  private Version getHistory() {
+    Version v = getVersion(getEntity().getVersion().getId());
+    v.setSuccessors(getSuccessors(v.getId(), true));
+    v.setPredecessors(getPredecessors(v.getId(), true));
+    v.setHead(v.getSuccessors().isEmpty());
+    v.setCompleteHistory(true);
+    return v;
   }
 }

src/main/java/org/caosdb/server/database/backend/transaction/RetrieveVersionInfo.java

@@ -23,14 +23,12 @@
 package org.caosdb.server.database.backend.transaction;
 
 import java.util.HashMap;
-import java.util.LinkedList;
-import org.caosdb.datetime.UTCDateTime;
 import org.caosdb.server.database.exceptions.TransactionException;
 import org.caosdb.server.database.proto.VersionHistoryItem;
 import org.caosdb.server.entity.EntityInterface;
 import org.caosdb.server.entity.Version;
 
-public class RetrieveVersionInfo extends RetrieveVersionHistory {
+public class RetrieveVersionInfo extends VersionTransaction {
 
   public RetrieveVersionInfo(EntityInterface e) {
     super(e);
@@ -39,46 +37,19 @@ public class RetrieveVersionInfo extends RetrieveVersionHistory {
   @Override
   protected void process(HashMap<String, VersionHistoryItem> map) throws TransactionException {
     super.process(map); // Make the map available to the object.
-    if (!map.isEmpty()) getVersion();
+    if (!map.isEmpty()) getEntity().setVersion(getVersion());
   }
 
-  public Version getVersion() {
-    Version v = getEntity().getVersion();
-    VersionHistoryItem i = getMap().get(v.getId());
-    if (i != null) v.setDate(UTCDateTime.UTCSeconds(i.seconds, i.nanos));
-
-    v.setPredecessors(getPredecessors(v.getId()));
-    v.setSuccessors(getSuccessors(v.getId()));
-    return v;
-  }
-
-  /** Return a list of direct children. */
-  private LinkedList<Version> getSuccessors(String id) {
-    LinkedList<Version> result = new LinkedList<>();
-
-    outer:
-    for (VersionHistoryItem i : getList()) {
-      if (i.parents != null)
-        for (String p : i.parents) {
-          if (id.equals(p)) {
-            Version successor = new Version(i.id, i.seconds, i.nanos);
-            result.add(successor);
-            continue outer;
-          }
-        }
-    }
-    return result;
+  @Override
+  protected Version getVersion(String id) {
+    return new Version(id);
   }
 
-  /** Return a list of direct parents. */
-  private LinkedList<Version> getPredecessors(String id) {
-    LinkedList<Version> result = new LinkedList<>();
-    if (getMap().containsKey(id) && getMap().get(id).parents != null)
-      for (String p : getMap().get(id).parents) {
-        VersionHistoryItem i = getMap().get(p);
-        Version predecessor = new Version(i.id, i.seconds, i.nanos);
-        result.add(predecessor);
-      }
-    return result;
+  public Version getVersion() {
+    Version v = getVersion(getEntity().getVersion().getId());
+    v.setPredecessors(getPredecessors(v.getId(), false));
+    v.setSuccessors(getSuccessors(v.getId(), false));
+    v.setHead(v.getSuccessors().isEmpty());
+    return v;
   }
 }

src/main/java/org/caosdb/server/database/backend/transaction/UpdateEntity.java

@@ -54,6 +54,7 @@ public class UpdateEntity extends BackendTransaction {
 
         execute(new InsertEntityProperties(e));
 
+        VersionTransaction.removeCached(e.getId());
         execute(new RetrieveVersionInfo(e));
       }
     }

src/main/java/org/caosdb/server/database/backend/transaction/UpdateSparseEntity.java

@@ -52,6 +52,6 @@ public class UpdateSparseEntity extends BackendTransaction {
 
     t.execute(spe);
 
-    this.entity.setVersion(new Version(spe.version));
+    this.entity.setVersion(new Version(spe.versionId));
   }
 }

src/main/java/org/caosdb/server/database/backend/transaction/VersionTransaction.java

+/*
+ * ** header v3.0
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program. If not, see <https://www.gnu.org/licenses/>.
+ *
+ * ** end header
+ */
+package org.caosdb.server.database.backend.transaction;
+
+import java.util.HashMap;
+import java.util.LinkedList;
+import java.util.List;
+import org.apache.commons.jcs.access.behavior.ICacheAccess;
+import org.caosdb.server.caching.Cache;
+import org.caosdb.server.database.CacheableBackendTransaction;
+import org.caosdb.server.database.backend.interfaces.RetrieveVersionHistoryImpl;
+import org.caosdb.server.database.exceptions.TransactionException;
+import org.caosdb.server.database.proto.VersionHistoryItem;
+import org.caosdb.server.entity.EntityInterface;
+import org.caosdb.server.entity.Version;
+
+/**
+ * Abstract base class which retrieves and caches the full, but flag version history. The
+ * implementations then use the flat version history to construct either single version information
+ * items (see {@link RetrieveVersionInfo}) or the complete history as a tree (see {@link
+ * RetrieveVersionHistory})
+ *
+ * @author Timm Fitschen (t.fitschen@indiscale.com)
+ */
+public abstract class VersionTransaction
+    extends CacheableBackendTransaction<Integer, HashMap<String, VersionHistoryItem>> {
+
+  private static final ICacheAccess<Integer, HashMap<String, VersionHistoryItem>> cache =
+      Cache.getCache("BACKEND_RetrieveVersionHistory");
+  private EntityInterface entity;
+
+  /** A map of all history items which belong to this entity. The keys are the version ids. */
+  private HashMap<String, VersionHistoryItem> historyItems;
+
+  /**
+   * Invalidate a cache item. This should be called upon update of entities.
+   *
+   * @param entityId
+   */
+  public static void removeCached(Integer entityId) {
+    cache.remove(entityId);
+  }
+
+  public VersionTransaction(EntityInterface e) {
+    super(cache);
+    this.entity = e;
+  }
+
+  @Override
+  public HashMap<String, VersionHistoryItem> executeNoCache() throws TransactionException {
+    RetrieveVersionHistoryImpl impl = getImplementation(RetrieveVersionHistoryImpl.class);
+    return impl.execute(getKey());
+  }
+
+  /** After this method call, the version map is available to the object. */
+  @Override
+  protected void process(HashMap<String, VersionHistoryItem> historyItems)
+      throws TransactionException {
+    this.historyItems = historyItems;
+  }
+
+  @Override
+  protected Integer getKey() {
+    return entity.getId();
+  }
+
+  public HashMap<String, VersionHistoryItem> getHistoryItems() {
+    return this.historyItems;
+  }
+
+  public EntityInterface getEntity() {
+    return this.entity;
+  }
+
+  /**
+   * Return a list of direct predecessors. The predecessors are constructed by {@link
+   * #getVersion(String)}.
+   *
+   * <p>If transitive is true, this function is called recursively on the predecessors as well,
+   * resulting in a list of trees of predecessors, with the direct predecessors at the root(s).
+   *
+   * @param versionId
+   * @param transitive
+   * @return A list of predecessors.
+   */
+  protected List<Version> getPredecessors(String versionId, boolean transitive) {
+    LinkedList<Version> result = new LinkedList<>();
+    if (getHistoryItems().containsKey(versionId)
+        && getHistoryItems().get(versionId).parents != null)
+      for (String p : getHistoryItems().get(versionId).parents) {
+        Version predecessor = getVersion(p);
+        if (transitive) {
+          predecessor.setPredecessors(getPredecessors(p, transitive));
+        }
+        result.add(predecessor);
+      }
+    return result;
+  }
+
+  /**
+   * To be implemented by the base class. The idea is, that the base class decides which information
+   * is being included into the Version instance.
+   *
+   * @param versionId - the id of the version
+   * @return
+   */
+  protected abstract Version getVersion(String versionId);
+
+  /**
+   * Return a list of direct successors. The successors are constructed by {@link
+   * #getVersion(String)}.
+   *
+   * <p>If transitive is true, this function is called recursively on the successors as well,
+   * resulting in a list of trees of successors, with the direct successors at the root(s).
+   *
+   * @param versionId
+   * @param transitive
+   * @return A list of successors.
+   */
+  protected List<Version> getSuccessors(String versionId, boolean transitive) {
+    LinkedList<Version> result = new LinkedList<>();
+
+    outer:
+    for (VersionHistoryItem i : getHistoryItems().values()) {
+      if (i.parents != null)
+        for (String p : i.parents) {
+          if (versionId.equals(p)) {
+            Version successor = getVersion(i.id);
+            result.add(successor);
+            if (transitive) {
+              successor.setSuccessors(getSuccessors(i.id, transitive));
+            }
+            continue outer;
+          }
+        }
+    }
+    return result;
+  }
+}

src/main/java/org/caosdb/server/database/proto/ProtoTransactionLogMessage.java

-/*
- * ** header v3.0
- * This file is a part of the CaosDB Project.
- *
- * Copyright (C) 2018 Research Group Biomedical Physics,
- * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Affero General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU Affero General Public License for more details.
- *
- * You should have received a copy of the GNU Affero General Public License
- * along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
- */
-package org.caosdb.server.database.proto;
-
-import java.io.Serializable;
-
-public class ProtoTransactionLogMessage implements Serializable {
-
-  public ProtoTransactionLogMessage(
-      final String transaction,
-      final String realm,
-      final String username,
-      final long seconds,
-      final int nanos) {
-    this.transaction = transaction;
-    this.realm = realm;
-    this.username = username;
-    this.seconds = seconds;
-    this.nanos = nanos;
-  }
-
-  public ProtoTransactionLogMessage() {}
-
-  private static final long serialVersionUID = -5856887517281480754L;
-  public String transaction = null;
-  public String realm;
-  public String username = null;
-  public Long seconds = null;
-  public Integer nanos = null;
-}

src/main/java/org/caosdb/server/database/proto/SparseEntity.java

@@ -38,9 +38,7 @@ public class SparseEntity extends VerySparseEntity {
   public String filePath = null;
   public Long fileSize = null;
   public Long fileChecked = null;
-  public String version = null;
-  public Long versionSeconds = null;
-  public Integer versionNanos = null;
+  public String versionId = null;
 
   @Override
   public String toString() {
@@ -54,9 +52,7 @@ public class SparseEntity extends VerySparseEntity {
         .append(this.fileHash)
         .append(this.filePath)
         .append(this.fileSize)
-        .append(this.version)
-        .append(this.versionSeconds)
-        .append(this.versionNanos)
+        .append(this.versionId)
         .toString();
   }
 }

src/main/java/org/caosdb/server/database/proto/VersionHistoryItem.java

 package org.caosdb.server.database.proto;
 
 import java.io.Serializable;
-import java.util.LinkedList;
+import java.util.List;
 
+/**
+ * This class is a flat, data-only representation of a single item of version information. This
+ * class is an intermediate representation which abstracts away the data base results and comes in a
+ * form which is easily cacheable.
+ *
+ * @author Timm Fitschen (t.fitschen@indiscale.com)
+ */
 public class VersionHistoryItem implements Serializable {
 
-  private static final long serialVersionUID = 6319362462701459355L;
+  private static final long serialVersionUID = 428030617967255942L;
   public String id = null;
-  public LinkedList<String> parents = null;
+  public List<String> parents = null;
   public Long seconds = null;
   public Integer nanos = null;
+  public String username = null;
+  public String realm = null;
+
+  @Override
+  public String toString() {
+    return id;
+  }
 }