diff --git a/CHANGELOG.md b/CHANGELOG.md
index 13a20975fb3cea4ebe6a120188e7999e5b59ee25..b70b2c179d9c340df77b3b42a103cbfd926b601f 100644
--- a/CHANGELOG.md
+++ b/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
diff --git a/conf/core/cache.ccf b/conf/core/cache.ccf
index b4e1f93596a6170ef04ec373dc7a8d70e51fedcc..ad73cb86d259a1de8ecd836f8e72de8aa254793e 100644
--- a/conf/core/cache.ccf
+++ b/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
diff --git a/conf/core/server.conf b/conf/core/server.conf
index 81ae7c2c43232024549c523636cfad090996d0fd..81b35a2a7498b0ad0f6feae7a20ce44dbe570865 100644
--- a/conf/core/server.conf
+++ b/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
# --------------------------------------------------
diff --git a/src/main/java/org/caosdb/server/database/BackendTransaction.java b/src/main/java/org/caosdb/server/database/BackendTransaction.java
index 20ec5b71a7ae6f4dd908dc38145df1c41f035e8e..5bf978343d72272309d4f4ab0f039770419c87b8 100644
--- a/src/main/java/org/caosdb/server/database/BackendTransaction.java
+++ b/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);
diff --git a/src/main/java/org/caosdb/server/database/DatabaseUtils.java b/src/main/java/org/caosdb/server/database/DatabaseUtils.java
index d5910eb9a93003106369f87f50bec1c0013a61bf..4f6a58a4fc50fa91170fad6139384bccb413fa81 100644
--- a/src/main/java/org/caosdb/server/database/DatabaseUtils.java
+++ b/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;
}
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertSparseEntity.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertSparseEntity.java
index 1f1f32c69a260d374ea930ba4e1be63e34cf9ca9..1b945acf566db938f12847f758636dbfddeac3d1 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertSparseEntity.java
+++ b/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.");
}
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveTransactionHistory.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveTransactionHistory.java
deleted file mode 100644
index 3273f49aa85776c4fd323ed4c027f4d1fcd3fbb0..0000000000000000000000000000000000000000
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveTransactionHistory.java
+++ /dev/null
@@ -1,75 +0,0 @@
-/*
- * ** 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);
- }
- }
-}
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveVersionHistory.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveVersionHistory.java
index a3c87ae6e97d3b26a99126b61d1d29db1ef6206a..7ecfbfb7ac70a4a5ec248eb0e2be2c590f0676aa 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveVersionHistory.java
+++ b/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);
}
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateSparseEntity.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateSparseEntity.java
index 18b59ef9121bd2f488efcb657a3bf158b6e14308..1c8039253b4c5e74a8054dfa937fec23c55440e8 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateSparseEntity.java
+++ b/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) {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveTransactionHistoryImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveTransactionHistoryImpl.java
deleted file mode 100644
index b02e4d9347e572941ab31e3a1a371470e1d8ee5c..0000000000000000000000000000000000000000
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveTransactionHistoryImpl.java
+++ /dev/null
@@ -1,32 +0,0 @@
-/*
- * ** 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;
-}
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/InsertSparseEntity.java b/src/main/java/org/caosdb/server/database/backend/transaction/InsertSparseEntity.java
index 1800168ebd2cd6ef4180e23046f95066597086e5..22720f836e5cbd4912f3aedccd25398e80a19324 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/InsertSparseEntity.java
+++ b/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);
}
}
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveTransactionHistory.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveTransactionHistory.java
deleted file mode 100644
index 632ce20cfe71d0e116bbe3987a60c45b11085eec..0000000000000000000000000000000000000000
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveTransactionHistory.java
+++ /dev/null
@@ -1,59 +0,0 @@
-/*
- * ** 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));
- }
- }
-}
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveVersionHistory.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveVersionHistory.java
index 6077d6491fda93b96262b48783092578af37f4f8..a5079c4e033882c4b1068615551b5132e4ee0cba 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveVersionHistory.java
+++ b/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;
}
}
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveVersionInfo.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveVersionInfo.java
index 7d9fe5fd7ea42cf3d6aa29a127a7f82f7ec1764c..8d0e54c95d17d0eb83af541b9fee2fb605b17ec9 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveVersionInfo.java
+++ b/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;
}
}
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/UpdateEntity.java b/src/main/java/org/caosdb/server/database/backend/transaction/UpdateEntity.java
index 9c20cb1d2d112e8d64ce5be2cfa8a7f8da20fe10..2bf965575884f29640a80ec3d3ab284b7779c8f2 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/UpdateEntity.java
+++ b/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));
}
}
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/UpdateSparseEntity.java b/src/main/java/org/caosdb/server/database/backend/transaction/UpdateSparseEntity.java
index 2385ec843a3d499d1184b58eca06f8ae05cbe4f8..8548fb0477de9d8b52b18b8132af15295dbc9353 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/UpdateSparseEntity.java
+++ b/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));
}
}
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/VersionTransaction.java b/src/main/java/org/caosdb/server/database/backend/transaction/VersionTransaction.java
new file mode 100644
index 0000000000000000000000000000000000000000..8a98564050f5fb860402aff0f55f1dd9de417a39
--- /dev/null
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/VersionTransaction.java
@@ -0,0 +1,159 @@
+/*
+ * ** 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;
+ }
+}
diff --git a/src/main/java/org/caosdb/server/database/proto/ProtoTransactionLogMessage.java b/src/main/java/org/caosdb/server/database/proto/ProtoTransactionLogMessage.java
deleted file mode 100644
index dd5cdbebcda7dd2c5c7f9ca93be69972ecef0e2c..0000000000000000000000000000000000000000
--- a/src/main/java/org/caosdb/server/database/proto/ProtoTransactionLogMessage.java
+++ /dev/null
@@ -1,50 +0,0 @@
-/*
- * ** 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;
-}
diff --git a/src/main/java/org/caosdb/server/database/proto/SparseEntity.java b/src/main/java/org/caosdb/server/database/proto/SparseEntity.java
index 3d5a29c9c4a69670d49347864b7ed885e758192f..d2292c58825ac6807e24f3ad3d086b29dd8a6e7e 100644
--- a/src/main/java/org/caosdb/server/database/proto/SparseEntity.java
+++ b/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();
}
}
diff --git a/src/main/java/org/caosdb/server/database/proto/VersionHistoryItem.java b/src/main/java/org/caosdb/server/database/proto/VersionHistoryItem.java
index 26109760ecde53ea20405bd02095cd951818677d..4c0a60ce57cce03cfaa7a2c4d41af7039c463838 100644
--- a/src/main/java/org/caosdb/server/database/proto/VersionHistoryItem.java
+++ b/src/main/java/org/caosdb/server/database/proto/VersionHistoryItem.java
@@ -1,13 +1,27 @@
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;
+ }
}
diff --git a/src/main/java/org/caosdb/server/entity/Entity.java b/src/main/java/org/caosdb/server/entity/Entity.java
index 5522b9be33f2225412c0ba473d7c5c0eec2e4507..abbdaf3372a491e6b1b02bda12bbeff25f47de79 100644
--- a/src/main/java/org/caosdb/server/entity/Entity.java
+++ b/src/main/java/org/caosdb/server/entity/Entity.java
@@ -34,7 +34,6 @@ import org.apache.shiro.SecurityUtils;
import org.apache.shiro.authz.AuthorizationException;
import org.apache.shiro.authz.Permission;
import org.apache.shiro.subject.Subject;
-import org.caosdb.datetime.UTCDateTime;
import org.caosdb.server.CaosDBException;
import org.caosdb.server.accessControl.Principal;
import org.caosdb.server.database.proto.SparseEntity;
@@ -1055,11 +1054,9 @@ public class Entity extends AbstractObservable implements EntityInterface {
setId(spe.id);
this.setRole(spe.role);
setEntityACL(spe.acl);
- UTCDateTime versionDate = null;
- if (spe.versionSeconds != null) {
- versionDate = UTCDateTime.UTCSeconds(spe.versionSeconds, spe.versionNanos);
+ if (spe.versionId != null) {
+ this.version = new Version(spe.versionId);
}
- this.version = new Version(spe.version, versionDate);
if (!isNameOverride()) {
setName(spe.name);
diff --git a/src/main/java/org/caosdb/server/entity/Version.java b/src/main/java/org/caosdb/server/entity/Version.java
index 3f9e148583686887fab39038aa427bccf1c69b25..5529c7c5f5e8c83d95ad5afae7c1ae786806df89 100644
--- a/src/main/java/org/caosdb/server/entity/Version.java
+++ b/src/main/java/org/caosdb/server/entity/Version.java
@@ -20,7 +20,7 @@
package org.caosdb.server.entity;
-import java.util.LinkedList;
+import java.util.List;
import org.caosdb.datetime.UTCDateTime;
/**
@@ -31,25 +31,35 @@ import org.caosdb.datetime.UTCDateTime;
public class Version {
private String id = null;
- private LinkedList<Version> predecessors = null;
- private LinkedList<Version> successors = null;
+ private String username = null;
+ private String realm = null;
+ private List<Version> predecessors = null;
+ private List<Version> successors = null;
private UTCDateTime date = null;
+ private boolean isHead = false;
+ private boolean isCompleteHistory = false;
public Version(String id, long seconds, int nanos) {
- this(id, UTCDateTime.UTCSeconds(seconds, nanos));
+ this(id, UTCDateTime.UTCSeconds(seconds, nanos), null, null);
}
- public Version(String id, UTCDateTime date) {
+ public Version(String id, UTCDateTime date, String username, String realm) {
this.id = id;
this.date = date;
+ this.username = username;
+ this.realm = realm;
}
public Version(String id) {
- this(id, null);
+ this(id, null, null, null);
}
public Version() {}
+ public Version(String id, UTCDateTime timestamp) {
+ this(id, timestamp, null, null);
+ }
+
public UTCDateTime getDate() {
return date;
}
@@ -66,19 +76,55 @@ public class Version {
this.id = id;
}
- public LinkedList<Version> getSuccessors() {
+ public List<Version> getSuccessors() {
return successors;
}
- public void setSuccessors(LinkedList<Version> successors) {
+ public void setSuccessors(List<Version> successors) {
this.successors = successors;
}
- public LinkedList<Version> getPredecessors() {
+ public List<Version> getPredecessors() {
return predecessors;
}
- public void setPredecessors(LinkedList<Version> predecessors) {
+ public void setPredecessors(List<Version> predecessors) {
this.predecessors = predecessors;
}
+
+ public String getRealm() {
+ return realm;
+ }
+
+ public void setRealm(String realm) {
+ this.realm = realm;
+ }
+
+ public String getUsername() {
+ return username;
+ }
+
+ public void setUsername(String username) {
+ this.username = username;
+ }
+
+ public void setDate(Long timestamp) {
+ this.date = UTCDateTime.SystemMillisToUTCDateTime(timestamp);
+ }
+
+ public boolean isHead() {
+ return isHead;
+ }
+
+ public void setHead(boolean isHead) {
+ this.isHead = isHead;
+ }
+
+ public boolean isCompleteHistory() {
+ return isCompleteHistory;
+ }
+
+ public void setCompleteHistory(boolean isCompleteHistory) {
+ this.isCompleteHistory = isCompleteHistory;
+ }
}
diff --git a/src/main/java/org/caosdb/server/entity/xml/VersionXMLSerializer.java b/src/main/java/org/caosdb/server/entity/xml/VersionXMLSerializer.java
index 65ec9880dfef43a4e460bba692ece6c9f87faa7e..40d19a5f3a0ef6d9448ed8567840e610be712391 100644
--- a/src/main/java/org/caosdb/server/entity/xml/VersionXMLSerializer.java
+++ b/src/main/java/org/caosdb/server/entity/xml/VersionXMLSerializer.java
@@ -30,28 +30,43 @@ import org.jdom2.Element;
* @author Timm Fitschen <t.fitschen@indiscale.com>
*/
class VersionXMLSerializer {
+
public Element toElement(Version version) {
- Element result = new Element("Version");
- result.setAttribute("id", version.getId());
- if (version.getDate() != null) {
- result.setAttribute("date", version.getDate().toDateTimeString(TimeZone.getDefault()));
- }
+ return toElement(version, "Version");
+ }
+
+ private Element toElement(Version version, String tag) {
+ Element element = new Element(tag);
+ setAttributes(version, element);
if (version.getPredecessors() != null) {
for (Version p : version.getPredecessors()) {
- Element predecessor = new Element("Predecessor");
- predecessor.setAttribute("id", p.getId());
- predecessor.setAttribute("date", p.getDate().toDateTimeString(TimeZone.getDefault()));
- result.addContent(predecessor);
+ element.addContent(toElement(p, "Predecessor"));
}
}
if (version.getSuccessors() != null) {
for (Version s : version.getSuccessors()) {
- Element successor = new Element("Successor");
- successor.setAttribute("id", s.getId());
- successor.setAttribute("date", s.getDate().toDateTimeString(TimeZone.getDefault()));
- result.addContent(successor);
+ element.addContent(toElement(s, "Successor"));
}
}
- return result;
+ return element;
+ }
+
+ private void setAttributes(Version version, Element element) {
+ element.setAttribute("id", version.getId());
+ if (version.getUsername() != null) {
+ element.setAttribute("username", version.getUsername());
+ }
+ if (version.getRealm() != null) {
+ element.setAttribute("realm", version.getRealm());
+ }
+ if (version.getDate() != null) {
+ element.setAttribute("date", version.getDate().toDateTimeString(TimeZone.getDefault()));
+ }
+ if (version.isHead()) {
+ element.setAttribute("head", "true");
+ }
+ if (version.isCompleteHistory()) {
+ element.setAttribute("completeHistory", "true");
+ }
}
}
diff --git a/src/main/java/org/caosdb/server/jobs/core/History.java b/src/main/java/org/caosdb/server/jobs/core/History.java
index a7c58979f49b2a7abdc313924dc8fb6b86bbffd4..5594b5afdb841436dbdd63f96b8e2c44faef51c6 100644
--- a/src/main/java/org/caosdb/server/jobs/core/History.java
+++ b/src/main/java/org/caosdb/server/jobs/core/History.java
@@ -23,7 +23,7 @@
package org.caosdb.server.jobs.core;
import org.apache.shiro.authz.AuthorizationException;
-import org.caosdb.server.database.backend.transaction.RetrieveTransactionHistory;
+import org.caosdb.server.database.backend.transaction.RetrieveVersionHistory;
import org.caosdb.server.entity.EntityInterface;
import org.caosdb.server.jobs.FlagJob;
import org.caosdb.server.jobs.JobAnnotation;
@@ -32,6 +32,11 @@ import org.caosdb.server.permissions.EntityPermission;
import org.caosdb.server.utils.EntityStatus;
import org.caosdb.server.utils.ServerMessages;
+/**
+ * Retrieves the complete version history of each entity and appends it to the entity.
+ *
+ * @author Timm Fitschen (t.fitschen@indiscale.com)
+ */
@JobAnnotation(time = JobExecutionTime.POST_TRANSACTION, flag = "H")
public class History extends FlagJob {
@@ -42,7 +47,7 @@ public class History extends FlagJob {
if (entity.getId() != null && entity.getId() > 0) {
try {
entity.checkPermission(EntityPermission.RETRIEVE_HISTORY);
- final RetrieveTransactionHistory t = new RetrieveTransactionHistory(entity);
+ final RetrieveVersionHistory t = new RetrieveVersionHistory(entity);
execute(t);
} catch (final AuthorizationException e) {
entity.setEntityStatus(EntityStatus.UNQUALIFIED);
diff --git a/src/main/java/org/caosdb/server/transaction/Insert.java b/src/main/java/org/caosdb/server/transaction/Insert.java
index f60fc1286ae909eb7fd999aa3af1f8379dd331ff..d37f7ce516f36252466555ea18fe249f2730fea1 100644
--- a/src/main/java/org/caosdb/server/transaction/Insert.java
+++ b/src/main/java/org/caosdb/server/transaction/Insert.java
@@ -27,7 +27,6 @@ import org.caosdb.server.database.access.Access;
import org.caosdb.server.database.backend.transaction.InsertEntity;
import org.caosdb.server.entity.EntityInterface;
import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.entity.Version;
import org.caosdb.server.entity.container.InsertContainer;
import org.caosdb.server.entity.container.TransactionContainer;
import org.caosdb.server.permissions.EntityACL;
@@ -104,10 +103,6 @@ public class Insert extends WriteTransaction<InsertContainer> {
public void insert(final TransactionContainer container, final Access access) throws Exception {
if (container.getStatus().ordinal() >= EntityStatus.QUALIFIED.ordinal()) {
execute(new InsertEntity(container), access);
- for (EntityInterface e : container) {
- // TODO move to InsertEntity transaction
- e.setVersion(new Version(e.getVersion().getId(), this.getTimestamp()));
- }
}
}