diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7bebc70ca8ade4d56695dca9e9c47379dcd90758..f0143f3d049d95f9f66034772e847d6ecdc34155 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -24,7 +24,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
[README.md](misc/move_files/README.md).
- LDAP server may now be given and may be different from LDAP domain. See
`misc/pam_authentication/ldap.conf`
-- #47 - Sub-properties can now be queried, such as in `SELECT window.width FROM house`.
+- #47 - Sub-properties can now be queried, such as in
+ `SELECT window.width FROM house`.
+- Added support for versioning, if it is enabled on the backend.
### Changed
diff --git a/conf/core/cache.ccf b/conf/core/cache.ccf
index 821e5d7862efb21e0aa13f8410886c6c14b10a7c..b4e1f93596a6170ef04ec373dc7a8d70e51fedcc 100644
--- a/conf/core/cache.ccf
+++ b/conf/core/cache.ccf
@@ -28,6 +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
# 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 d30d82b681a185a820783c6c2d8d81a62981eb64..3507886b0475341b06a8d676845e9280c67b991b 100644
--- a/conf/core/server.conf
+++ b/conf/core/server.conf
@@ -67,7 +67,7 @@ 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=v3.0.0-rc1
+MYSQL_SCHEMA_VERSION=v3.0.0-rc2
# --------------------------------------------------
@@ -181,3 +181,4 @@ CHECK_ENTITY_ACL_ROLES_MODE=MUST
# part of any Entity ACL.
GLOBAL_ENTITY_PERMISSIONS_FILE=./conf/core/global_entity_permissions.xml
+ENTITY_VERSIONING_ENABLED=true
diff --git a/pom.xml b/pom.xml
index 0594c0548331f0e834fc0bc10a61fec69ffa9a69..65174bd706023526d6aba948cf890dd2e73dc3bf 100644
--- a/pom.xml
+++ b/pom.xml
@@ -100,7 +100,7 @@
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
- <version>6.0.6</version>
+ <version>8.0.19</version>
</dependency>
<dependency>
<groupId>org.xerial</groupId>
@@ -150,7 +150,7 @@
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-jcs-core</artifactId>
- <version>2.1</version>
+ <version>2.2.1</version>
</dependency>
<dependency>
<groupId>org.kohsuke</groupId>
diff --git a/src/main/java/caosdb/datetime/UTCDateTime.java b/src/main/java/caosdb/datetime/UTCDateTime.java
index 215de67befe403aa6a202ed178244b3de898d23e..db66ef0ad08abf0d52a8f3b1b97c6a20cc613c8a 100644
--- a/src/main/java/caosdb/datetime/UTCDateTime.java
+++ b/src/main/java/caosdb/datetime/UTCDateTime.java
@@ -296,7 +296,7 @@ public class UTCDateTime implements Interval {
throw new NullPointerException("toString method!!!");
}
- public static UTCDateTime UTCSeconds(final Long utcseconds, final Integer nanosecond) {
+ public static UTCDateTime UTCSeconds(final Long utcseconds, final Integer nanoseconds) {
if (LEAP_SECONDS.isEmpty()) {
initLeapSeconds();
}
@@ -310,10 +310,10 @@ public class UTCDateTime implements Interval {
if (leapSeconds2 != leapSeconds && LEAP_SECONDS.contains(systemSeconds)) {
gc.add(Calendar.SECOND, -1);
return new UTCDateTime(
- systemSeconds, leapSeconds, nanosecond, new LeapSecondDateTimeStringStrategy(gc, 1));
+ systemSeconds, leapSeconds, nanoseconds, new LeapSecondDateTimeStringStrategy(gc, 1));
} else {
return new UTCDateTime(
- systemSeconds, leapSeconds, nanosecond, new GregorianCalendarDateTimeStringStrategy(gc));
+ systemSeconds, leapSeconds, nanoseconds, new GregorianCalendarDateTimeStringStrategy(gc));
}
}
diff --git a/src/main/java/caosdb/server/CaosDBServer.java b/src/main/java/caosdb/server/CaosDBServer.java
index 45da4eb0e655f011e06deede49eec2035745fac1..cdee262f08836071d19e5a75038f4291a917b1ff 100644
--- a/src/main/java/caosdb/server/CaosDBServer.java
+++ b/src/main/java/caosdb/server/CaosDBServer.java
@@ -64,7 +64,6 @@ import caosdb.server.transaction.ChecksumUpdater;
import caosdb.server.utils.FileUtils;
import caosdb.server.utils.Initialization;
import caosdb.server.utils.NullPrintStream;
-import caosdb.server.utils.Utils;
import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.IOException;
@@ -75,6 +74,7 @@ import java.util.ArrayList;
import java.util.Arrays;
import java.util.Properties;
import java.util.TimeZone;
+import java.util.UUID;
import java.util.logging.Handler;
import java.util.logging.Level;
import java.util.logging.LogRecord;
@@ -875,7 +875,7 @@ class CaosDBComponent extends Component {
public void handle(final Request request, final Response response) {
long t1 = System.currentTimeMillis();
// The server request ID is just a long random number
- request.getAttributes().put("SRID", Utils.getUID());
+ request.getAttributes().put("SRID", UUID.randomUUID().toString());
response.setServerInfo(CaosDBServer.getServerInfo());
super.handle(request, response);
log(request, response, t1);
diff --git a/src/main/java/caosdb/server/caching/JCSCacheHelper.java b/src/main/java/caosdb/server/caching/JCSCacheHelper.java
index 1ce455a949bcfb76a36815b3b14bcea89e676a4a..c471ed7ef860d902b56940da52a876a44fd97218 100644
--- a/src/main/java/caosdb/server/caching/JCSCacheHelper.java
+++ b/src/main/java/caosdb/server/caching/JCSCacheHelper.java
@@ -5,7 +5,7 @@
* 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)
+ * Copyright (C) 2019,2020 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
@@ -88,6 +88,9 @@ public class JCSCacheHelper implements CacheHelper {
}
logger.info("Configuring JCS Caching with {}", config);
}
+
+ // If the JCS config is updated/reset, it has to be shut down before.
+ JCS.shutdown();
JCS.setConfigProperties(config);
}
diff --git a/src/main/java/caosdb/server/database/BackendTransaction.java b/src/main/java/caosdb/server/database/BackendTransaction.java
index 14e65e86bd9fe05b074c731e27b601fa4ed51f68..55987005d2c8c76f432cb12065f45b598075ec9c 100644
--- a/src/main/java/caosdb/server/database/BackendTransaction.java
+++ b/src/main/java/caosdb/server/database/BackendTransaction.java
@@ -3,7 +3,9 @@
* 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
+ * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+ * Copyright (C) 2020 IndiScale GmbH
+ * 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
@@ -58,6 +60,7 @@ import caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveRole;
import caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveSparseEntity;
import caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveTransactionHistory;
import caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveUser;
+import caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveVersionHistory;
import caosdb.server.database.backend.implementation.MySQL.MySQLRuleLoader;
import caosdb.server.database.backend.implementation.MySQL.MySQLSetFileCheckedTimestampImpl;
import caosdb.server.database.backend.implementation.MySQL.MySQLSetPassword;
@@ -113,6 +116,7 @@ import caosdb.server.database.backend.interfaces.RetrieveRoleImpl;
import caosdb.server.database.backend.interfaces.RetrieveSparseEntityImpl;
import caosdb.server.database.backend.interfaces.RetrieveTransactionHistoryImpl;
import caosdb.server.database.backend.interfaces.RetrieveUserImpl;
+import caosdb.server.database.backend.interfaces.RetrieveVersionHistoryImpl;
import caosdb.server.database.backend.interfaces.RuleLoaderImpl;
import caosdb.server.database.backend.interfaces.SetFileCheckedTimestampImpl;
import caosdb.server.database.backend.interfaces.SetPasswordImpl;
@@ -204,6 +208,7 @@ public abstract class BackendTransaction implements Undoable {
setImpl(
RetrieveQueryTemplateDefinitionImpl.class, MySQLRetrieveQueryTemplateDefinition.class);
setImpl(InsertEntityDatatypeImpl.class, MySQLInsertEntityDatatype.class);
+ setImpl(RetrieveVersionHistoryImpl.class, MySQLRetrieveVersionHistory.class);
}
}
diff --git a/src/main/java/caosdb/server/database/CacheableBackendTransaction.java b/src/main/java/caosdb/server/database/CacheableBackendTransaction.java
index fc4c9659d9a8ea80393bebad945bd6badf9580c4..0131b740d81cbd41d1b9263c5f42029e1af4539c 100644
--- a/src/main/java/caosdb/server/database/CacheableBackendTransaction.java
+++ b/src/main/java/caosdb/server/database/CacheableBackendTransaction.java
@@ -4,8 +4,8 @@
*
* 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)
+ * Copyright (C) 2019,2020 IndiScale GmbH
+ * Copyright (C) 2019,2020 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
@@ -51,7 +51,7 @@ public abstract class CacheableBackendTransaction<K, V extends Serializable>
private final V execute(final K key) throws TransactionException {
// get from cache if possible...
if (cacheIsEnabled() && key != null) {
- final V cached = getCache().get(getKey());
+ final V cached = getCache().get(key);
if (cached != null) {
this.cached = true;
return cached;
@@ -64,7 +64,7 @@ public abstract class CacheableBackendTransaction<K, V extends Serializable>
if (notCached != null) {
if (cacheIsEnabled() && key != null) {
// now cache if possible
- getCache().put(getKey(), notCached);
+ getCache().put(key, notCached);
}
}
return notCached;
diff --git a/src/main/java/caosdb/server/database/DatabaseUtils.java b/src/main/java/caosdb/server/database/DatabaseUtils.java
index 84c38fa448b7d8a1035aa28ded7bbfcecc5a88b3..9edc0347abf8b63de0ce76ead06fb1f6883332e1 100644
--- a/src/main/java/caosdb/server/database/DatabaseUtils.java
+++ b/src/main/java/caosdb/server/database/DatabaseUtils.java
@@ -173,12 +173,7 @@ public class DatabaseUtils {
while (rs.next()) {
final FlatProperty fp = new FlatProperty();
fp.id = rs.getInt("PropertyID");
-
- final String v = bytes2UTF8(rs.getBytes("PropertyValue"));
- if (v != null) {
- fp.value = v;
- }
-
+ fp.value = bytes2UTF8(rs.getBytes("PropertyValue"));
fp.status = bytes2UTF8(rs.getBytes("PropertyStatus"));
fp.idx = rs.getInt("PropertyIndex");
ret.add(fp);
@@ -217,12 +212,14 @@ public class DatabaseUtils {
ret.datatype = bytes2UTF8(rs.getBytes("Datatype"));
ret.collection = bytes2UTF8(rs.getBytes("Collection"));
- final String path = bytes2UTF8(rs.getBytes("FilePath"));
- if (!rs.wasNull()) {
- ret.filePath = path;
- ret.fileSize = rs.getLong("FileSize");
- ret.fileHash = bytes2UTF8(rs.getBytes("FileHash"));
- }
+ ret.filePath = bytes2UTF8(rs.getBytes("FilePath"));
+ 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");
+
return ret;
}
diff --git a/src/main/java/caosdb/server/database/backend/implementation/MySQL/DatabaseConnectionPool.java b/src/main/java/caosdb/server/database/backend/implementation/MySQL/DatabaseConnectionPool.java
index 9700daf3a99b30e42baf8580f863998d7efe67a1..fc17dd1066cfa57660d44dbb6a521d3177e5fc72 100644
--- a/src/main/java/caosdb/server/database/backend/implementation/MySQL/DatabaseConnectionPool.java
+++ b/src/main/java/caosdb/server/database/backend/implementation/MySQL/DatabaseConnectionPool.java
@@ -85,8 +85,7 @@ class DatabaseConnectionPool {
+ CaosDBServer.getServerProperty(ServerProperties.KEY_MYSQL_PORT)
+ "/"
+ CaosDBServer.getServerProperty(ServerProperties.KEY_MYSQL_DATABASE_NAME)
- + "?noAccessToProcedureBodies=true&cacheCallableStmts=true&autoReconnect=true&useUnicode=true&characterEncoding=UTF-8&connectionCollation=utf8_unicode_ci&characterSetResults=utf8&serverTimezone=CET";
- // + "?profileSQL=true&characterSetResults=utf8";
+ + "?noAccessToProcedureBodies=true&autoReconnect=true&serverTimezone=UTC&characterEncoding=UTF-8";
final String user = CaosDBServer.getServerProperty(ServerProperties.KEY_MYSQL_USER_NAME);
final String pwd = CaosDBServer.getServerProperty(ServerProperties.KEY_MYSQL_USER_PASSWORD);
final ConnectionPool pool = new ConnectionPool("MySQL Pool", 2, 5, 0, 0, url, user, pwd);
diff --git a/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLHelper.java b/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLHelper.java
index 458823167423893b6defb166f013618be3a796d7..b443c54507e415ed4171fcf0ac99c3da762fb506 100644
--- a/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLHelper.java
+++ b/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLHelper.java
@@ -4,6 +4,8 @@
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+ * 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
@@ -22,15 +24,20 @@
*/
package caosdb.server.database.backend.implementation.MySQL;
+import caosdb.server.accessControl.Principal;
import caosdb.server.database.misc.DBHelper;
+import caosdb.server.transaction.ChecksumUpdater;
import caosdb.server.transaction.TransactionInterface;
import caosdb.server.transaction.WriteTransaction;
-import caosdb.server.utils.Info;
-import caosdb.server.utils.Initialization;
+import java.io.UnsupportedEncodingException;
+import java.sql.CallableStatement;
import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.SQLException;
+import java.sql.Statement;
import java.util.HashMap;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
/**
* Provides cached statements for a MySQL back-end.
@@ -41,23 +48,71 @@ public class MySQLHelper implements DBHelper {
private Connection connection = null;
+ private Logger logger = LoggerFactory.getLogger(getClass());
+
+ /**
+ * Initialize a transaction by calling the corresponding SQL procedure.
+ *
+ * <p>In the database, this adds a row to the transaction table with SRID, user and timestamp.
+ */
+ public void initTransaction(Connection connection, WriteTransaction<?> transaction)
+ throws SQLException {
+ try (CallableStatement call = connection.prepareCall("CALL set_transaction(?,?,?,?,?)")) {
+
+ String username = ((Principal) transaction.getTransactor().getPrincipal()).getUsername();
+ String realm = ((Principal) transaction.getTransactor().getPrincipal()).getRealm();
+ long seconds = transaction.getTimestamp().getUTCSeconds();
+ int nanos = transaction.getTimestamp().getNanoseconds();
+ byte[] srid = transaction.getSRID().getBytes("UTF-8");
+
+ call.setBytes(1, srid);
+ call.setString(2, username);
+ call.setString(3, realm);
+ call.setLong(4, seconds);
+ call.setInt(5, nanos);
+ call.execute();
+
+ } catch (UnsupportedEncodingException e) {
+ e.printStackTrace();
+ System.exit(1);
+ }
+ }
+
+ public Connection initConnection(TransactionInterface transaction)
+ throws ConnectionException, SQLException {
+ Connection connection;
+ connection = DatabaseConnectionPool.getConnection();
+
+ if (transaction instanceof ChecksumUpdater) {
+ connection.setReadOnly(false);
+ connection.setAutoCommit(false);
+ } else if (transaction instanceof WriteTransaction) {
+ connection.setReadOnly(false);
+ connection.setAutoCommit(false);
+ initTransaction(connection, (WriteTransaction<?>) transaction);
+ } else {
+ connection.setReadOnly(false);
+ connection.setAutoCommit(true);
+ }
+
+ return connection;
+ }
+
public Connection getConnection() throws SQLException, ConnectionException {
if (this.connection == null) {
- this.connection = DatabaseConnectionPool.getConnection();
- if (this.transaction instanceof WriteTransaction) {
- this.connection.setReadOnly(false);
- this.connection.setAutoCommit(false);
- } else if (this.transaction instanceof Initialization || this.transaction instanceof Info) {
- this.connection.setReadOnly(false);
- this.connection.setAutoCommit(true);
- } else {
- this.connection.setReadOnly(false);
- this.connection.setAutoCommit(true);
- }
+ this.connection = initConnection(this.transaction);
}
return this.connection;
}
+ /**
+ * Prepare a statement from a string. Reuse prepared statements from the cache if available.
+ *
+ * @param statement
+ * @return
+ * @throws SQLException
+ * @throws ConnectionException
+ */
public PreparedStatement prepareStatement(final String statement)
throws SQLException, ConnectionException {
if (this.stmtCache.containsKey(statement)) {
@@ -81,6 +136,7 @@ public class MySQLHelper implements DBHelper {
private TransactionInterface transaction = null;
+ /** Make all changes permanent. */
@Override
public void commit() throws SQLException {
if (this.connection != null
@@ -90,13 +146,20 @@ public class MySQLHelper implements DBHelper {
}
}
+ /**
+ * Reset SRID variable, close all statements, roll back to last save point and close connection.
+ */
@Override
public void cleanUp() {
- // close all statements (if necessary), roll back to last save point (if
- // possible) and close connection (if necessary).
try {
if (this.connection != null && !this.connection.isClosed()) {
+ try (Statement s = connection.createStatement()) {
+ s.execute("SET @SRID = NULL");
+ } catch (SQLException e) {
+ logger.error("Exception while resetting the @SRID variable.", e);
+ }
+
// close all cached statements (if possible)
for (final PreparedStatement stmt : this.stmtCache.values()) {
try {
@@ -104,7 +167,7 @@ public class MySQLHelper implements DBHelper {
stmt.close();
}
} catch (final SQLException e) {
- e.printStackTrace();
+ logger.warn("Exception while closing a prepared statement.", e);
}
}
@@ -113,12 +176,12 @@ public class MySQLHelper implements DBHelper {
this.connection.rollback();
}
} catch (final SQLException r) {
- r.printStackTrace();
+ logger.warn("Exception during roll-back attempt.", r);
}
this.connection.close();
}
} catch (final SQLException e) {
- e.printStackTrace();
+ logger.warn("Exception during clean-up.", e);
}
// clear everything
diff --git a/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLInsertSparseEntity.java b/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLInsertSparseEntity.java
index 4ad9f5b6a3cc3e51c05bc83bbc9332807b79484d..97cfde68b1b9097152aca3ea68705e6cdfddfaad 100644
--- a/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLInsertSparseEntity.java
+++ b/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLInsertSparseEntity.java
@@ -22,6 +22,7 @@
*/
package caosdb.server.database.backend.implementation.MySQL;
+import caosdb.server.database.DatabaseUtils;
import caosdb.server.database.access.Access;
import caosdb.server.database.backend.interfaces.InsertSparseEntityImpl;
import caosdb.server.database.exceptions.IntegrityException;
@@ -56,6 +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"));
} else {
throw new TransactionException("Didn't get new EntityID back.");
}
diff --git a/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveParents.java b/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveParents.java
index c1c430cfee6e7a6b88391aa02df072e918f8d692..721ba566ed389732456342aab78691c171b33922 100644
--- a/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveParents.java
+++ b/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveParents.java
@@ -30,6 +30,7 @@ import caosdb.server.database.proto.VerySparseEntity;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
+import java.sql.Types;
import java.util.ArrayList;
public class MySQLRetrieveParents extends MySQLTransaction implements RetrieveParentsImpl {
@@ -38,16 +39,22 @@ public class MySQLRetrieveParents extends MySQLTransaction implements RetrievePa
super(access);
}
- private static final String stmtStr = "call retrieveEntityParents(?)";
+ private static final String stmtStr = "call retrieveEntityParents(?, ?)";
@Override
- public ArrayList<VerySparseEntity> execute(final Integer id) throws TransactionException {
+ public ArrayList<VerySparseEntity> execute(final Integer id, final String version)
+ throws TransactionException {
try {
ResultSet rs = null;
try {
final PreparedStatement prepareStatement = prepareStatement(stmtStr);
prepareStatement.setInt(1, id);
+ if (version == null) {
+ prepareStatement.setNull(2, Types.VARBINARY);
+ } else {
+ prepareStatement.setString(2, version);
+ }
rs = prepareStatement.executeQuery();
return DatabaseUtils.parseParentResultSet(rs);
} finally {
diff --git a/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveProperties.java b/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveProperties.java
index 8b9a547bac69cf221dbf7c204a93e95326bb484c..9b6704c4cb3e6395c5b8239a3aefc34bb818e937 100644
--- a/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveProperties.java
+++ b/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveProperties.java
@@ -31,6 +31,7 @@ import caosdb.server.database.proto.ProtoProperty;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
+import java.sql.Types;
import java.util.ArrayList;
import java.util.List;
@@ -40,15 +41,17 @@ public class MySQLRetrieveProperties extends MySQLTransaction implements Retriev
super(access);
}
- private static final String stmtStr = "call retrieveEntityProperties(?,?)";
- private static final String stmtStr2 = "call retrieveOverrides(?,?)";
+ private static final String stmtStr = "call retrieveEntityProperties(?,?,?)";
+ private static final String stmtStr2 = "call retrieveOverrides(?,?,?)";
@Override
- public ArrayList<ProtoProperty> execute(final Integer entity) throws TransactionException {
+ public ArrayList<ProtoProperty> execute(final Integer entity, final String version)
+ throws TransactionException {
try {
final PreparedStatement prepareStatement = prepareStatement(stmtStr);
- final List<FlatProperty> props = retrieveFlatPropertiesStage1(0, entity, prepareStatement);
+ final List<FlatProperty> props =
+ retrieveFlatPropertiesStage1(0, entity, version, prepareStatement);
final ArrayList<ProtoProperty> protos = new ArrayList<ProtoProperty>();
for (final FlatProperty p : props) {
@@ -56,7 +59,7 @@ public class MySQLRetrieveProperties extends MySQLTransaction implements Retriev
proto.property = p;
final List<FlatProperty> subProps =
- retrieveFlatPropertiesStage1(entity, p.id, prepareStatement);
+ retrieveFlatPropertiesStage1(entity, p.id, version, prepareStatement);
proto.subProperties = subProps;
@@ -71,7 +74,10 @@ public class MySQLRetrieveProperties extends MySQLTransaction implements Retriev
}
private List<FlatProperty> retrieveFlatPropertiesStage1(
- final Integer domain, final Integer entity, final PreparedStatement stmt)
+ final Integer domain,
+ final Integer entity,
+ final String version,
+ final PreparedStatement stmt)
throws SQLException, ConnectionException {
ResultSet rs = null;
try {
@@ -82,6 +88,12 @@ public class MySQLRetrieveProperties extends MySQLTransaction implements Retriev
}
stmt.setInt(2, entity);
+ if (version == null) {
+ stmt.setNull(3, Types.VARBINARY);
+ } else {
+ stmt.setString(3, version);
+ }
+
long t1 = System.currentTimeMillis();
rs = stmt.executeQuery();
long t2 = System.currentTimeMillis();
@@ -91,7 +103,7 @@ public class MySQLRetrieveProperties extends MySQLTransaction implements Retriev
final PreparedStatement stmt2 = prepareStatement(stmtStr2);
- retrieveOverrides(domain, entity, stmt2, props);
+ retrieveOverrides(domain, entity, version, stmt2, props);
return props;
} finally {
@@ -104,6 +116,7 @@ public class MySQLRetrieveProperties extends MySQLTransaction implements Retriev
private void retrieveOverrides(
final Integer domain,
final Integer entity,
+ final String version,
final PreparedStatement stmt2,
final List<FlatProperty> props)
throws SQLException {
@@ -112,6 +125,11 @@ public class MySQLRetrieveProperties extends MySQLTransaction implements Retriev
try {
stmt2.setInt(1, domain);
stmt2.setInt(2, entity);
+ if (version == null) {
+ stmt2.setNull(3, Types.VARBINARY);
+ } else {
+ stmt2.setString(3, version);
+ }
long t1 = System.currentTimeMillis();
rs = stmt2.executeQuery();
long t2 = System.currentTimeMillis();
diff --git a/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveQueryTemplateDefinition.java b/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveQueryTemplateDefinition.java
index 92f2cd5fe4c26d796112baec5d908b9431187ae7..c6d88ec9f8fca1651318456161ed2c0347a47f21 100644
--- a/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveQueryTemplateDefinition.java
+++ b/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveQueryTemplateDefinition.java
@@ -28,6 +28,7 @@ import caosdb.server.database.exceptions.TransactionException;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
+import java.sql.Types;
public class MySQLRetrieveQueryTemplateDefinition extends MySQLTransaction
implements RetrieveQueryTemplateDefinitionImpl {
@@ -37,14 +38,19 @@ public class MySQLRetrieveQueryTemplateDefinition extends MySQLTransaction
}
public static final String STMT_RETRIEVE_QUERY_TEMPLATE_DEF =
- "SELECT definition FROM query_template_def WHERE id=?";
+ "call retrieveQueryTemplateDef(?,?)";
@Override
- public String retrieve(final Integer id) {
+ public String retrieve(final Integer id, final String version) {
try {
final PreparedStatement stmt = prepareStatement(STMT_RETRIEVE_QUERY_TEMPLATE_DEF);
stmt.setInt(1, id);
+ if (version == null) {
+ stmt.setNull(2, Types.VARBINARY);
+ } else {
+ stmt.setString(2, version);
+ }
final ResultSet rs = stmt.executeQuery();
if (rs.next()) {
return rs.getString("definition");
diff --git a/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveSparseEntity.java b/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveSparseEntity.java
index 2aff2aaedda70672eb676597a2e3ba7a1db14352..097961974b0c599480e8186f170665838e7d046e 100644
--- a/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveSparseEntity.java
+++ b/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveSparseEntity.java
@@ -30,6 +30,7 @@ import caosdb.server.database.proto.SparseEntity;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
+import java.sql.Types;
/**
* Retrieve a single SparseEntity by id.
@@ -43,14 +44,19 @@ public class MySQLRetrieveSparseEntity extends MySQLTransaction
super(access);
}
- private static final String stmtStr = "call retrieveEntity(?)";
+ private static final String stmtStr = "call retrieveEntity(?,?)";
@Override
- public SparseEntity execute(final int id) throws TransactionException {
+ public SparseEntity execute(final int id, final String version) throws TransactionException {
try {
final PreparedStatement preparedStatement = prepareStatement(stmtStr);
preparedStatement.setInt(1, id);
+ if (version == null) {
+ preparedStatement.setNull(2, Types.VARBINARY);
+ } else {
+ preparedStatement.setString(2, version);
+ }
try (final ResultSet rs = preparedStatement.executeQuery()) {
if (rs.next()) {
return DatabaseUtils.parseEntityResultSet(rs);
diff --git a/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveVersionHistory.java b/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveVersionHistory.java
new file mode 100644
index 0000000000000000000000000000000000000000..22ac0c2e30c0f48fbc884f40593bac2dc45d7b7d
--- /dev/null
+++ b/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveVersionHistory.java
@@ -0,0 +1,85 @@
+/*
+ * ** 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 caosdb.server.database.backend.implementation.MySQL;
+
+import caosdb.server.database.DatabaseUtils;
+import caosdb.server.database.access.Access;
+import caosdb.server.database.backend.interfaces.RetrieveVersionHistoryImpl;
+import caosdb.server.database.exceptions.TransactionException;
+import caosdb.server.database.proto.VersionHistoryItem;
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.HashMap;
+import java.util.LinkedList;
+
+/**
+ * Transaction to retrieve all versions of an entity.
+ *
+ * <p>Creates a mapping ID :: (VersionHistoryItem)
+ */
+public class MySQLRetrieveVersionHistory extends MySQLTransaction
+ implements RetrieveVersionHistoryImpl {
+
+ public static final String VERSION_HISTORY_STMT = "CALL get_version_history(?)";
+
+ public MySQLRetrieveVersionHistory(Access access) {
+ super(access);
+ }
+
+ @Override
+ public HashMap<String, VersionHistoryItem> execute(Integer entityId) {
+
+ HashMap<String, VersionHistoryItem> result = new HashMap<>();
+ try {
+ PreparedStatement s = prepareStatement(VERSION_HISTORY_STMT);
+ s.setInt(1, entityId);
+ ResultSet rs = s.executeQuery();
+
+ while (rs.next()) {
+ String childId = DatabaseUtils.bytes2UTF8(rs.getBytes("child"));
+ String parentId = DatabaseUtils.bytes2UTF8(rs.getBytes("parent"));
+ Long childSeconds = rs.getLong("child_seconds");
+ Integer childNanos = rs.getInt("child_nanos");
+ VersionHistoryItem v = result.get(childId);
+ if (v == null) {
+ v = new VersionHistoryItem();
+ v.id = childId;
+ v.seconds = childSeconds;
+ v.nanos = childNanos;
+ result.put(childId, v);
+ }
+
+ if (parentId != null) {
+ if (v.parents == null) {
+ v.parents = new LinkedList<>();
+ }
+ v.parents.add(parentId);
+ }
+ }
+ } catch (SQLException | ConnectionException e) {
+ throw new TransactionException(e);
+ }
+ return result;
+ }
+}
diff --git a/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateSparseEntity.java b/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateSparseEntity.java
index 4cc59f9d0f0a813bb92294f6fabb1cd51f43c151..73c589fade317586cc1b5bfb4b796578f9e819ba 100644
--- a/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateSparseEntity.java
+++ b/src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateSparseEntity.java
@@ -22,12 +22,14 @@
*/
package caosdb.server.database.backend.implementation.MySQL;
+import caosdb.server.database.DatabaseUtils;
import caosdb.server.database.access.Access;
import caosdb.server.database.backend.interfaces.UpdateSparseEntityImpl;
import caosdb.server.database.exceptions.IntegrityException;
import caosdb.server.database.exceptions.TransactionException;
import caosdb.server.database.proto.SparseEntity;
import java.sql.PreparedStatement;
+import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.SQLIntegrityConstraintViolationException;
import java.sql.Types;
@@ -39,15 +41,31 @@ public class MySQLUpdateSparseEntity extends MySQLTransaction implements UpdateS
}
public static final String STMT_UPDATE_ENTITY = "call updateEntity(?,?,?,?,?,?,?)";
- public static final String STMT_UPDATE_FILE_PROPS =
- "INSERT INTO files (hash, size, path, file_id) VALUES (unhex(?),?,?,?) ON DUPLICATE KEY UPDATE hash=unhex(?), size=?, path=?;";
+ public static final String STMT_UPDATE_FILE_PROPS = "call setFileProperties(?,?,?,?)";
@Override
public void execute(final SparseEntity spe) throws TransactionException {
try {
- final PreparedStatement updateEntityStmt = prepareStatement(STMT_UPDATE_ENTITY);
+ // file properties;
+ final PreparedStatement updateFilePropsStmt = prepareStatement(STMT_UPDATE_FILE_PROPS);
+ updateFilePropsStmt.setInt(1, spe.id);
+ if (spe.filePath != null) {
+ updateFilePropsStmt.setString(2, spe.filePath);
+ updateFilePropsStmt.setLong(3, spe.fileSize);
+ if (spe.fileHash != null) {
+ updateFilePropsStmt.setString(4, spe.fileHash);
+ } else {
+ updateFilePropsStmt.setNull(4, Types.VARCHAR);
+ }
+ } else {
+ updateFilePropsStmt.setNull(2, Types.VARCHAR);
+ updateFilePropsStmt.setNull(3, Types.BIGINT);
+ updateFilePropsStmt.setNull(4, Types.VARCHAR);
+ }
+ updateFilePropsStmt.execute();
// very sparse entity
+ final PreparedStatement updateEntityStmt = prepareStatement(STMT_UPDATE_ENTITY);
updateEntityStmt.setInt(1, spe.id);
updateEntityStmt.setString(2, spe.name);
updateEntityStmt.setString(3, spe.description);
@@ -59,28 +77,12 @@ public class MySQLUpdateSparseEntity extends MySQLTransaction implements UpdateS
}
updateEntityStmt.setString(6, spe.collection);
updateEntityStmt.setString(7, spe.acl);
- updateEntityStmt.execute();
+ ResultSet rs = updateEntityStmt.executeQuery();
- // file properties;
- if (spe.filePath != null) {
- final PreparedStatement updateFilePropsStmt = prepareStatement(STMT_UPDATE_FILE_PROPS);
- if (spe.fileHash != null) {
- updateFilePropsStmt.setString(1, spe.fileHash);
- updateFilePropsStmt.setString(5, spe.fileHash);
- } else {
- updateFilePropsStmt.setNull(1, Types.VARCHAR);
- updateFilePropsStmt.setNull(5, Types.VARCHAR);
- }
- updateFilePropsStmt.setLong(2, spe.fileSize);
- updateFilePropsStmt.setLong(6, spe.fileSize);
-
- updateFilePropsStmt.setString(3, spe.filePath);
- updateFilePropsStmt.setString(7, spe.filePath);
-
- updateFilePropsStmt.setInt(4, spe.id);
-
- updateFilePropsStmt.execute();
+ if (rs.next()) {
+ spe.version = DatabaseUtils.bytes2UTF8(rs.getBytes("Version"));
}
+
} catch (final SQLIntegrityConstraintViolationException e) {
throw new IntegrityException(e);
} catch (final SQLException e) {
diff --git a/src/main/java/caosdb/server/database/backend/interfaces/RetrieveParentsImpl.java b/src/main/java/caosdb/server/database/backend/interfaces/RetrieveParentsImpl.java
index 551ee962d8768aa90b9f5aaed313c050f0873079..9dfb8cf57c260c7fe154c25f095886ca6a3c2698 100644
--- a/src/main/java/caosdb/server/database/backend/interfaces/RetrieveParentsImpl.java
+++ b/src/main/java/caosdb/server/database/backend/interfaces/RetrieveParentsImpl.java
@@ -28,5 +28,6 @@ import java.util.ArrayList;
public interface RetrieveParentsImpl extends BackendTransactionImpl {
- public ArrayList<VerySparseEntity> execute(Integer id) throws TransactionException;
+ public ArrayList<VerySparseEntity> execute(Integer id, String version)
+ throws TransactionException;
}
diff --git a/src/main/java/caosdb/server/database/backend/interfaces/RetrievePropertiesImpl.java b/src/main/java/caosdb/server/database/backend/interfaces/RetrievePropertiesImpl.java
index 3c8449f7fc62581457091ea5ab0ccc5921b89a92..b9a15a526b857b9674432a96733c6f2fd8e5d4ea 100644
--- a/src/main/java/caosdb/server/database/backend/interfaces/RetrievePropertiesImpl.java
+++ b/src/main/java/caosdb/server/database/backend/interfaces/RetrievePropertiesImpl.java
@@ -28,5 +28,5 @@ import java.util.ArrayList;
public interface RetrievePropertiesImpl extends BackendTransactionImpl {
- public ArrayList<ProtoProperty> execute(Integer id) throws TransactionException;
+ public ArrayList<ProtoProperty> execute(Integer id, String version) throws TransactionException;
}
diff --git a/src/main/java/caosdb/server/database/backend/interfaces/RetrieveQueryTemplateDefinitionImpl.java b/src/main/java/caosdb/server/database/backend/interfaces/RetrieveQueryTemplateDefinitionImpl.java
index fee860ca2c0ee4341ae91a4a1736d518cd71a5e8..cda336044de4bd0d37a3d67da140c744f2699f32 100644
--- a/src/main/java/caosdb/server/database/backend/interfaces/RetrieveQueryTemplateDefinitionImpl.java
+++ b/src/main/java/caosdb/server/database/backend/interfaces/RetrieveQueryTemplateDefinitionImpl.java
@@ -24,5 +24,5 @@ package caosdb.server.database.backend.interfaces;
public interface RetrieveQueryTemplateDefinitionImpl extends BackendTransactionImpl {
- public String retrieve(final Integer id);
+ public String retrieve(Integer id, String version);
}
diff --git a/src/main/java/caosdb/server/database/backend/interfaces/RetrieveSparseEntityImpl.java b/src/main/java/caosdb/server/database/backend/interfaces/RetrieveSparseEntityImpl.java
index 82a534c03182d577e7b27eca9b2ff9def1c60677..5b6978f8f456bf978c3ca60ae0da479eaf54ed0a 100644
--- a/src/main/java/caosdb/server/database/backend/interfaces/RetrieveSparseEntityImpl.java
+++ b/src/main/java/caosdb/server/database/backend/interfaces/RetrieveSparseEntityImpl.java
@@ -27,5 +27,5 @@ import caosdb.server.database.proto.SparseEntity;
public interface RetrieveSparseEntityImpl extends BackendTransactionImpl {
- public SparseEntity execute(int id) throws TransactionException;
+ public SparseEntity execute(int id, String version) throws TransactionException;
}
diff --git a/src/main/java/caosdb/server/database/backend/interfaces/RetrieveVersionHistoryImpl.java b/src/main/java/caosdb/server/database/backend/interfaces/RetrieveVersionHistoryImpl.java
new file mode 100644
index 0000000000000000000000000000000000000000..118e783d816ce45d1a43738bf8959e4a94740d3c
--- /dev/null
+++ b/src/main/java/caosdb/server/database/backend/interfaces/RetrieveVersionHistoryImpl.java
@@ -0,0 +1,9 @@
+package caosdb.server.database.backend.interfaces;
+
+import caosdb.server.database.proto.VersionHistoryItem;
+import java.util.HashMap;
+
+public interface RetrieveVersionHistoryImpl extends BackendTransactionImpl {
+
+ public HashMap<String, VersionHistoryItem> execute(Integer entityId);
+}
diff --git a/src/main/java/caosdb/server/database/backend/transaction/DeleteEntityProperties.java b/src/main/java/caosdb/server/database/backend/transaction/DeleteEntityProperties.java
index 15ace2b9820398cb270a6a1e098e6f642b66ab9d..984ca5eb853e356814aafb69ebd9860bee4fe8a1 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/DeleteEntityProperties.java
+++ b/src/main/java/caosdb/server/database/backend/transaction/DeleteEntityProperties.java
@@ -40,8 +40,8 @@ public class DeleteEntityProperties extends BackendTransaction {
@Override
public void execute() {
- RetrieveProperties.removeCached(this.entity.getId());
- RetrieveParents.removeCached(this.entity.getId());
+ RetrieveProperties.removeCached(this.entity.getIdVersion());
+ RetrieveParents.removeCached(this.entity.getIdVersion());
final DeleteEntityPropertiesImpl ret = getImplementation(DeleteEntityPropertiesImpl.class);
diff --git a/src/main/java/caosdb/server/database/backend/transaction/DeleteSparseEntity.java b/src/main/java/caosdb/server/database/backend/transaction/DeleteSparseEntity.java
index 39deb1416c743f838bfc1b96c29fd845dbcef742..a2e4de6482d78053ab01c70ea3634c3f8af232a3 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/DeleteSparseEntity.java
+++ b/src/main/java/caosdb/server/database/backend/transaction/DeleteSparseEntity.java
@@ -42,7 +42,7 @@ public class DeleteSparseEntity extends BackendTransaction {
@Override
protected void execute() {
- RetrieveSparseEntity.removeCached(this.entity.getId());
+ RetrieveSparseEntity.removeCached(this.entity);
if (entity.hasFileProperties()) {
GetFileRecordByPath.removeCached(this.entity.getFileProperties().getPath());
}
diff --git a/src/main/java/caosdb/server/database/backend/transaction/InsertSparseEntity.java b/src/main/java/caosdb/server/database/backend/transaction/InsertSparseEntity.java
index f8711197064a88dd92c408f329d1a36df55c5ed2..c8e20895711e16c40c75c89c9776e8ad55851117 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/InsertSparseEntity.java
+++ b/src/main/java/caosdb/server/database/backend/transaction/InsertSparseEntity.java
@@ -30,6 +30,7 @@ import caosdb.server.database.exceptions.IntegrityException;
import caosdb.server.database.exceptions.TransactionException;
import caosdb.server.database.proto.SparseEntity;
import caosdb.server.entity.EntityInterface;
+import caosdb.server.entity.Version;
import caosdb.server.utils.Undoable;
public class InsertSparseEntity extends BackendTransaction {
@@ -68,5 +69,6 @@ public class InsertSparseEntity extends BackendTransaction {
public void cleanUp() {}
});
this.entity.setId(e.id);
+ this.entity.setVersion(new Version(e.version));
}
}
diff --git a/src/main/java/caosdb/server/database/backend/transaction/RetrieveFullEntity.java b/src/main/java/caosdb/server/database/backend/transaction/RetrieveFullEntity.java
index a1817767650175f604286a29ea82b5387a4dc2d6..ad0d39e94b56904def08a04a8a42a89627a7b4d6 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/RetrieveFullEntity.java
+++ b/src/main/java/caosdb/server/database/backend/transaction/RetrieveFullEntity.java
@@ -107,6 +107,7 @@ public class RetrieveFullEntity extends BackendTransaction {
}
execute(new RetrieveParents(e));
execute(new RetrieveProperties(e));
+ execute(new RetrieveVersionInfo(e));
// recursion! retrieveSubEntities calls retrieveFull sometimes, but with reduced selectors.
if (selections != null && !selections.isEmpty()) {
@@ -143,7 +144,7 @@ public class RetrieveFullEntity extends BackendTransaction {
RetrieveEntity ref = new RetrieveEntity(value.getId());
// recursion! (Only for the matching selections)
retrieveFullEntity(ref, getSubSelects(selections, propertyName));
- value.setEntity(ref);
+ value.setEntity(ref, true);
}
}
}
diff --git a/src/main/java/caosdb/server/database/backend/transaction/RetrieveParents.java b/src/main/java/caosdb/server/database/backend/transaction/RetrieveParents.java
index 5c1b0178f51496f83a4fac6a4ce3b2447abdccd5..d33d5e96d978fe86d6eb965113726eb79bb60d40 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/RetrieveParents.java
+++ b/src/main/java/caosdb/server/database/backend/transaction/RetrieveParents.java
@@ -34,10 +34,22 @@ import caosdb.server.entity.EntityInterface;
import java.util.ArrayList;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
+// TODO Problem with the caching.
+// When an old entity version has a parent which is deleted, the name is
+// still in the cached VerySparseEntity. This can be resolved by using a
+// similar strategy as in RetrieveProperties.java where the name etc. are
+// retrieved in a second step. Thus the deletion doesn't slip through
+// unnoticed.
+//
+// Changes are necessary in the backend-api, i.e. mysqlbackend and the
+// interfaces as well.
+//
+// See also a failing test in caosdb-pyinttest:
+// tests/test_version.py::test_bug_cached_parent_name_in_old_version
public class RetrieveParents
- extends CacheableBackendTransaction<Integer, ArrayList<VerySparseEntity>> {
+ extends CacheableBackendTransaction<String, ArrayList<VerySparseEntity>> {
- private static final ICacheAccess<Integer, ArrayList<VerySparseEntity>> cache =
+ private static final ICacheAccess<String, ArrayList<VerySparseEntity>> cache =
Cache.getCache("BACKEND_EntityParents");
/**
@@ -45,9 +57,9 @@ public class RetrieveParents
*
* @param id
*/
- public static void removeCached(final Integer id) {
- if (id != null && cache != null) {
- cache.remove(id);
+ public static void removeCached(final String idVersion) {
+ if (idVersion != null && cache != null) {
+ cache.remove(idVersion);
}
}
@@ -61,18 +73,18 @@ public class RetrieveParents
@Override
public ArrayList<VerySparseEntity> executeNoCache() throws TransactionException {
final RetrieveParentsImpl t = getImplementation(RetrieveParentsImpl.class);
- final Integer key = getKey();
- return t.execute(key);
+ return t.execute(this.entity.getId(), this.entity.getVersion().getId());
}
@Override
protected void process(final ArrayList<VerySparseEntity> t) throws TransactionException {
this.entity.getParents().clear();
+
DatabaseUtils.parseParentsFromVerySparseEntity(this.entity, t);
}
@Override
- protected Integer getKey() {
- return this.entity.getId();
+ protected String getKey() {
+ return this.entity.getIdVersion();
}
}
diff --git a/src/main/java/caosdb/server/database/backend/transaction/RetrieveProperties.java b/src/main/java/caosdb/server/database/backend/transaction/RetrieveProperties.java
index 487feb56cf848e948fcacb8f33f49e4a0bc2267d..822f57fd49e54d7517578592acf09100924fe81b 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/RetrieveProperties.java
+++ b/src/main/java/caosdb/server/database/backend/transaction/RetrieveProperties.java
@@ -37,11 +37,11 @@ import java.util.ArrayList;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
public class RetrieveProperties
- extends CacheableBackendTransaction<Integer, ArrayList<ProtoProperty>> {
+ extends CacheableBackendTransaction<String, ArrayList<ProtoProperty>> {
private final EntityInterface entity;
public static final String CACHE_REGION = "BACKEND_EntityProperties";
- private static final ICacheAccess<Integer, ArrayList<ProtoProperty>> cache =
+ private static final ICacheAccess<String, ArrayList<ProtoProperty>> cache =
Cache.getCache(CACHE_REGION);
/**
@@ -49,9 +49,9 @@ public class RetrieveProperties
*
* @param id
*/
- protected static void removeCached(final Integer id) {
- if (id != null && cache != null) {
- cache.remove(id);
+ protected static void removeCached(final String idVersion) {
+ if (idVersion != null && cache != null) {
+ cache.remove(idVersion);
}
}
@@ -63,7 +63,7 @@ public class RetrieveProperties
@Override
public ArrayList<ProtoProperty> executeNoCache() throws TransactionException {
final RetrievePropertiesImpl t = getImplementation(RetrievePropertiesImpl.class);
- return t.execute(getKey());
+ return t.execute(this.entity.getId(), this.entity.getVersion().getId());
}
@Override
@@ -98,7 +98,7 @@ public class RetrieveProperties
}
@Override
- protected Integer getKey() {
- return this.entity.getId();
+ protected String getKey() {
+ return this.entity.getIdVersion();
}
}
diff --git a/src/main/java/caosdb/server/database/backend/transaction/RetrieveQueryTemplateDefinition.java b/src/main/java/caosdb/server/database/backend/transaction/RetrieveQueryTemplateDefinition.java
index 208c7439aa6cf9ff8f32abc8f5cd59ea9a3cba95..0c96c72cb0be41aaf368c22009526914994bc8ec 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/RetrieveQueryTemplateDefinition.java
+++ b/src/main/java/caosdb/server/database/backend/transaction/RetrieveQueryTemplateDefinition.java
@@ -39,6 +39,7 @@ public class RetrieveQueryTemplateDefinition extends BackendTransaction {
protected void execute() throws TransactionException {
final RetrieveQueryTemplateDefinitionImpl t =
getImplementation(RetrieveQueryTemplateDefinitionImpl.class);
- this.entity.setQueryTemplateDefinition(t.retrieve(this.entity.getId()));
+ this.entity.setQueryTemplateDefinition(
+ t.retrieve(this.entity.getId(), this.entity.getVersion().getId()));
}
}
diff --git a/src/main/java/caosdb/server/database/backend/transaction/RetrieveSparseEntity.java b/src/main/java/caosdb/server/database/backend/transaction/RetrieveSparseEntity.java
index a91b5021f1fa722a8e8831234fc8ebc2032ba115..7843f57957d392c4bbf65f01a60d559cff11c6c8 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/RetrieveSparseEntity.java
+++ b/src/main/java/caosdb/server/database/backend/transaction/RetrieveSparseEntity.java
@@ -3,9 +3,9 @@
* 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)
+ * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+ * Copyright (C) 2019,2020 IndiScale GmbH
+ * Copyright (C) 2019,2020 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
@@ -35,20 +35,21 @@ import caosdb.server.entity.EntityInterface;
import caosdb.server.utils.EntityStatus;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
-public class RetrieveSparseEntity extends CacheableBackendTransaction<Integer, SparseEntity> {
+public class RetrieveSparseEntity extends CacheableBackendTransaction<String, SparseEntity> {
private final EntityInterface entity;
- private static final ICacheAccess<Integer, SparseEntity> cache =
+ private static final ICacheAccess<String, SparseEntity> cache =
Cache.getCache("BACKEND_SparseEntities");
/**
- * To be called by {@link UpdateSparseEntity} and {@link DeleteEntity} on execution.
+ * To be called by {@link UpdateSparseEntity} and {@link DeleteSparseEntity} on execution.
*
- * @param id
+ * @param entity
*/
- public static void removeCached(final Integer id) {
- if (id != null && cache != null) {
- cache.remove(id);
+ public static void removeCached(final EntityInterface entity) {
+ if (entity != null && cache != null) {
+ cache.remove(entity.getId().toString());
+ cache.remove(entity.getIdVersion());
}
}
@@ -57,14 +58,15 @@ public class RetrieveSparseEntity extends CacheableBackendTransaction<Integer, S
this.entity = entity;
}
- public RetrieveSparseEntity(final int id) {
+ public RetrieveSparseEntity(final int id, final String version) {
this(new Entity(id));
+ this.entity.getVersion().setId(version);
}
@Override
public SparseEntity executeNoCache() throws TransactionException {
final RetrieveSparseEntityImpl t = getImplementation(RetrieveSparseEntityImpl.class);
- final SparseEntity ret = t.execute(getKey());
+ final SparseEntity ret = t.execute(getEntity().getId(), getEntity().getVersion().getId());
if (ret == null) {
this.entity.setEntityStatus(EntityStatus.NONEXISTENT);
}
@@ -78,8 +80,14 @@ public class RetrieveSparseEntity extends CacheableBackendTransaction<Integer, S
}
@Override
- protected Integer getKey() {
- return this.entity.getId();
+ protected String getKey() {
+ if ("HEAD".equalsIgnoreCase(entity.getVersion().getId())) {
+ return this.entity.getId().toString();
+ } else if (entity.hasVersion()
+ && entity.getVersion().getId().toUpperCase().startsWith("HEAD")) {
+ return null;
+ }
+ return this.entity.getIdVersion();
}
public EntityInterface getEntity() {
diff --git a/src/main/java/caosdb/server/database/backend/transaction/RetrieveVersionHistory.java b/src/main/java/caosdb/server/database/backend/transaction/RetrieveVersionHistory.java
new file mode 100644
index 0000000000000000000000000000000000000000..20be2f8fb60ce54877fdb2fd85d27a6944a71d86
--- /dev/null
+++ b/src/main/java/caosdb/server/database/backend/transaction/RetrieveVersionHistory.java
@@ -0,0 +1,79 @@
+/*
+ * ** 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 caosdb.server.database.backend.transaction;
+
+import caosdb.server.database.CacheableBackendTransaction;
+import caosdb.server.database.backend.interfaces.RetrieveVersionHistoryImpl;
+import caosdb.server.database.exceptions.TransactionException;
+import caosdb.server.database.proto.VersionHistoryItem;
+import caosdb.server.entity.EntityInterface;
+import java.util.Collection;
+import java.util.HashMap;
+
+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 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());
+ }
+
+ /** 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;
+ }
+
+ @Override
+ protected Integer getKey() {
+ return entity.getId();
+ }
+
+ public HashMap<String, VersionHistoryItem> getMap() {
+ return this.map;
+ }
+
+ public EntityInterface getEntity() {
+ return this.entity;
+ }
+
+ public Collection<VersionHistoryItem> getList() {
+ return this.map.values();
+ }
+}
diff --git a/src/main/java/caosdb/server/database/backend/transaction/RetrieveVersionInfo.java b/src/main/java/caosdb/server/database/backend/transaction/RetrieveVersionInfo.java
new file mode 100644
index 0000000000000000000000000000000000000000..1daab0504cafbd05e9e03dff78b2c230a0438ccd
--- /dev/null
+++ b/src/main/java/caosdb/server/database/backend/transaction/RetrieveVersionInfo.java
@@ -0,0 +1,84 @@
+/*
+ * ** 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 caosdb.server.database.backend.transaction;
+
+import caosdb.datetime.UTCDateTime;
+import caosdb.server.database.exceptions.TransactionException;
+import caosdb.server.database.proto.VersionHistoryItem;
+import caosdb.server.entity.EntityInterface;
+import caosdb.server.entity.Version;
+import java.util.HashMap;
+import java.util.LinkedList;
+
+public class RetrieveVersionInfo extends RetrieveVersionHistory {
+
+ public RetrieveVersionInfo(EntityInterface e) {
+ super(e);
+ }
+
+ @Override
+ protected void process(HashMap<String, VersionHistoryItem> map) throws TransactionException {
+ super.process(map); // Make the map available to the object.
+ if (!map.isEmpty()) 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;
+ }
+
+ /** 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;
+ }
+}
diff --git a/src/main/java/caosdb/server/database/backend/transaction/UpdateEntity.java b/src/main/java/caosdb/server/database/backend/transaction/UpdateEntity.java
index 6378e8bbbbd8aee87382d226df0691d004e641aa..a7c9ba43f32b1ef97a6a09544041b39a2cd5c71a 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/UpdateEntity.java
+++ b/src/main/java/caosdb/server/database/backend/transaction/UpdateEntity.java
@@ -53,6 +53,8 @@ public class UpdateEntity extends BackendTransaction {
execute(new InsertEntityValue(e));
execute(new InsertEntityProperties(e));
+
+ execute(new RetrieveVersionInfo(e));
}
}
}
diff --git a/src/main/java/caosdb/server/database/backend/transaction/UpdateSparseEntity.java b/src/main/java/caosdb/server/database/backend/transaction/UpdateSparseEntity.java
index c6a1c7683409e0c875484e14553e4aeac2757a71..309ff9cbde0131f4b90cc89301a2338a8b92971f 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/UpdateSparseEntity.java
+++ b/src/main/java/caosdb/server/database/backend/transaction/UpdateSparseEntity.java
@@ -29,6 +29,7 @@ import caosdb.server.database.backend.interfaces.UpdateSparseEntityImpl;
import caosdb.server.database.exceptions.TransactionException;
import caosdb.server.database.proto.SparseEntity;
import caosdb.server.entity.EntityInterface;
+import caosdb.server.entity.Version;
public class UpdateSparseEntity extends BackendTransaction {
@@ -40,7 +41,7 @@ public class UpdateSparseEntity extends BackendTransaction {
@Override
public void execute() throws TransactionException {
- RetrieveSparseEntity.removeCached(this.entity.getId());
+ RetrieveSparseEntity.removeCached(this.entity);
if (entity.hasFileProperties()) {
GetFileRecordByPath.removeCached(this.entity.getFileProperties().getPath());
}
@@ -50,5 +51,7 @@ public class UpdateSparseEntity extends BackendTransaction {
final SparseEntity spe = this.entity.getSparseEntity();
t.execute(spe);
+
+ this.entity.setVersion(new Version(spe.version));
}
}
diff --git a/src/main/java/caosdb/server/database/proto/SparseEntity.java b/src/main/java/caosdb/server/database/proto/SparseEntity.java
index 4f5dcc69ce5ed7c6afa636b97237b53abb56ab51..d70d4ae026eb72d8c782b763ae3fc21d03a73064 100644
--- a/src/main/java/caosdb/server/database/proto/SparseEntity.java
+++ b/src/main/java/caosdb/server/database/proto/SparseEntity.java
@@ -38,6 +38,9 @@ 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;
@Override
public String toString() {
@@ -51,6 +54,9 @@ public class SparseEntity extends VerySparseEntity {
.append(this.fileHash)
.append(this.filePath)
.append(this.fileSize)
+ .append(this.version)
+ .append(this.versionSeconds)
+ .append(this.versionNanos)
.toString();
}
}
diff --git a/src/main/java/caosdb/server/database/proto/VersionHistoryItem.java b/src/main/java/caosdb/server/database/proto/VersionHistoryItem.java
new file mode 100644
index 0000000000000000000000000000000000000000..e671950f39f40c0b93069d031f636ad964560508
--- /dev/null
+++ b/src/main/java/caosdb/server/database/proto/VersionHistoryItem.java
@@ -0,0 +1,13 @@
+package caosdb.server.database.proto;
+
+import java.io.Serializable;
+import java.util.LinkedList;
+
+public class VersionHistoryItem implements Serializable {
+
+ private static final long serialVersionUID = 7855704308135158698L;
+ public String id = null;
+ public LinkedList<String> parents = null;
+ public Long seconds = null;
+ public Integer nanos = null;
+}
diff --git a/src/main/java/caosdb/server/datatype/ReferenceDatatype2.java b/src/main/java/caosdb/server/datatype/ReferenceDatatype2.java
index ce92aa022cfe85573049eaaeed4e26653b400679..87c17079b0facdc193ea79dd6005598f7fe151b6 100644
--- a/src/main/java/caosdb/server/datatype/ReferenceDatatype2.java
+++ b/src/main/java/caosdb/server/datatype/ReferenceDatatype2.java
@@ -47,7 +47,7 @@ public class ReferenceDatatype2 extends ReferenceDatatype {
}
public void setEntity(final EntityInterface datatypeEntity) {
- this.refid.setEntity(datatypeEntity);
+ this.refid.setEntity(datatypeEntity, false);
}
@Override
diff --git a/src/main/java/caosdb/server/datatype/ReferenceValue.java b/src/main/java/caosdb/server/datatype/ReferenceValue.java
index 25fa0b381cb436236dd6e3676970cf7e54c17776..77f7aa8c56d97b8dc5abf914c0b6c88749683d69 100644
--- a/src/main/java/caosdb/server/datatype/ReferenceValue.java
+++ b/src/main/java/caosdb/server/datatype/ReferenceValue.java
@@ -3,7 +3,9 @@
* 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
+ * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+ * 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
@@ -26,27 +28,36 @@ import caosdb.server.datatype.AbstractDatatype.Table;
import caosdb.server.entity.EntityInterface;
import caosdb.server.entity.Message;
import caosdb.server.utils.ServerMessages;
+import java.util.Objects;
import org.jdom2.Element;
+/**
+ * A ReferenceValue represents the value of a reference property to another entity.
+ *
+ * <p>Differently from other properties, they may be versioned, i.e. they may reference to a
+ * specific version of an entity.
+ *
+ * <p>TODO: Ways to specify a reference value, what are the consequences of versioned references?
+ */
public class ReferenceValue implements SingleValue {
private EntityInterface entity = null;
private String name = null;
private Integer id = null;
+ private String version = null;
+ private boolean versioned = false;
public static ReferenceValue parseReference(final Object reference) throws Message {
if (reference == null) {
return null;
}
if (reference instanceof EntityInterface) {
- return new ReferenceValue((EntityInterface) reference);
+ return new ReferenceValue(
+ (EntityInterface) reference, ((EntityInterface) reference).hasVersion());
} else if (reference instanceof ReferenceValue) {
return (ReferenceValue) reference;
} else if (reference instanceof GenericValue) {
- try {
- return new ReferenceValue(Integer.parseInt(((GenericValue) reference).toDatabaseString()));
- } catch (final NumberFormatException e) {
- return new ReferenceValue(((GenericValue) reference).toDatabaseString());
- }
+ String str = ((GenericValue) reference).toDatabaseString();
+ return parseFromString(str);
} else if (reference instanceof CollectionValue) {
throw ServerMessages.DATA_TYPE_DOES_NOT_ACCEPT_COLLECTION_VALUES;
} else {
@@ -58,24 +69,81 @@ public class ReferenceValue implements SingleValue {
}
}
+ /**
+ * Split a reference string into an entity part and a version part, if there is a version part.
+ *
+ * <p>If parsing the entity ID part to an integer fails, a NumberFormatException may be thrown.
+ */
+ public static ReferenceValue parseIdVersion(String str) {
+ String[] split = str.split("@", 2);
+ if (split.length == 2) {
+ return new ReferenceValue(Integer.parseInt(split[0]), split[1]);
+ } else {
+ return new ReferenceValue(Integer.parseInt(str));
+ }
+ }
+
+ /**
+ * Create a ReferenceValue from a string.
+ *
+ * <p>If the string looks like a valid "entityID@version" string, the result will have the
+ * corresponding entity and version parts.
+ */
+ public static ReferenceValue parseFromString(String str) {
+ try {
+ return parseIdVersion(str);
+ } catch (final NumberFormatException e) {
+ return new ReferenceValue(str);
+ }
+ }
+
+ /**
+ * Produce a nice but short string:
+ *
+ * <p>Case 1 "versioned" (reference to an entity without specifying that entity's version):
+ * Produces a string like "1234" or "Experiment". Note that referencing via name is never
+ * versioned.
+ *
+ * <p>Case 2 "unversioned" (reference to an entity with a specified version): Produces a string
+ * like "1234@ab987f".
+ */
@Override
public String toString() {
- if (this.entity != null) {
+ if (this.entity != null && versioned) { // Was specified as "versioned", with resolved entity
+ return this.entity.getIdVersion();
+ } else if (this.entity != null) { // resolved, but unversioned
return this.entity.getId().toString();
- } else if (this.id == null && this.name != null) {
+ } else if (this.id == null
+ && this.name != null) { // Only name is available, no id (and thus no resolved entity)
return this.name;
}
+ // Specification via id is the only remaining possibility
+ return getIdVersion(); // if version is null, returns ID only
+ }
+
+ public String getIdVersion() {
+ if (this.version != null) {
+ return new StringBuilder().append(this.id).append("@").append(this.version).toString();
+ }
return this.id.toString();
}
- public ReferenceValue(final EntityInterface entity) {
+ public ReferenceValue(final EntityInterface entity, boolean versioned) {
+ this.versioned = versioned;
this.entity = entity;
}
public ReferenceValue(final Integer id) {
+ this(id, null);
+ }
+
+ public ReferenceValue(final Integer id, final String version) {
this.id = id;
+ this.version = version;
+ this.versioned = version != null;
}
+ /** If the reference is given by name, versioning is not possible (at the moment). */
public ReferenceValue(final String name) {
this.name = name;
}
@@ -84,7 +152,8 @@ public class ReferenceValue implements SingleValue {
return this.entity;
}
- public final void setEntity(final EntityInterface entity) {
+ public final void setEntity(final EntityInterface entity, boolean versioned) {
+ this.versioned = versioned;
this.entity = entity;
}
@@ -102,6 +171,13 @@ public class ReferenceValue implements SingleValue {
return this.id;
}
+ public final String getVersion() {
+ if (this.entity != null && versioned && this.entity.hasVersion()) {
+ return this.entity.getVersion().getId();
+ }
+ return this.version;
+ }
+
public final void setId(final Integer id) {
this.id = id;
}
@@ -126,7 +202,8 @@ public class ReferenceValue implements SingleValue {
if (obj instanceof ReferenceValue) {
final ReferenceValue that = (ReferenceValue) obj;
if (that.getId() != null && getId() != null) {
- return that.getId().equals(getId());
+ return that.getId().equals(getId())
+ && Objects.deepEquals(that.getVersion(), this.getVersion());
} else if (that.getName() != null && getName() != null) {
return that.getName().equals(getName());
}
diff --git a/src/main/java/caosdb/server/entity/BaseEntity.java b/src/main/java/caosdb/server/entity/BaseEntity.java
deleted file mode 100644
index 62d4873b54c262eb75920f3f5c990e9988f07e50..0000000000000000000000000000000000000000
--- a/src/main/java/caosdb/server/entity/BaseEntity.java
+++ /dev/null
@@ -1,28 +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 caosdb.server.entity;
-
-class BaseEntity {
-
- EntityID id = null;
-}
diff --git a/src/main/java/caosdb/server/entity/DeleteEntity.java b/src/main/java/caosdb/server/entity/DeleteEntity.java
index 29b6a3a075b60e811cfb0e66d066278a47d2edcb..b27ab3a7745a9b4909dac642a9fccbaf035f52f7 100644
--- a/src/main/java/caosdb/server/entity/DeleteEntity.java
+++ b/src/main/java/caosdb/server/entity/DeleteEntity.java
@@ -3,7 +3,9 @@
* 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
+ * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+ * 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
@@ -27,4 +29,9 @@ public class DeleteEntity extends Entity {
public DeleteEntity(final int id) {
super(id);
}
+
+ public DeleteEntity(int id, String version) {
+ super(id);
+ setVersion(new Version(version));
+ }
}
diff --git a/src/main/java/caosdb/server/entity/Entity.java b/src/main/java/caosdb/server/entity/Entity.java
index 7fed351c51373e0cdb6aca9fe531c9699c2f9703..16f4f508e2d97a4c0f58c1775e95db9efbf4ffba 100644
--- a/src/main/java/caosdb/server/entity/Entity.java
+++ b/src/main/java/caosdb/server/entity/Entity.java
@@ -3,7 +3,9 @@
* 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
+ * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+ * 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
@@ -22,6 +24,7 @@
*/
package caosdb.server.entity;
+import caosdb.datetime.UTCDateTime;
import caosdb.server.CaosDBException;
import caosdb.server.database.proto.SparseEntity;
import caosdb.server.database.proto.VerySparseEntity;
@@ -800,7 +803,11 @@ public class Entity extends AbstractObservable implements EntityInterface {
final CollectionValue vals = new CollectionValue();
int pidx = 0;
for (final Element pe : element.getChildren()) {
- if (pe.getName().equalsIgnoreCase("EmptyString")) {
+ if (pe.getName().equalsIgnoreCase("Version")) {
+ // IGNORE: Once it becomes allowed for clients to set a version id, parsing
+ // the Version element would be done here. Until this is the case, the
+ // Version tag is ignored.
+ } else if (pe.getName().equalsIgnoreCase("EmptyString")) {
// special case: empty string which cannot be distinguished from null
// values otherwise.
setValue(new GenericValue(""));
@@ -1026,6 +1033,7 @@ public class Entity extends AbstractObservable implements EntityInterface {
}
private boolean datatypeOverride = false;
+ private Version version = new Version();
@Override
public EntityInterface setDatatypeOverride(final boolean b) {
@@ -1066,10 +1074,15 @@ public class Entity extends AbstractObservable implements EntityInterface {
}
@Override
- public EntityInterface parseSparseEntity(final SparseEntity spe) {
+ public final EntityInterface parseSparseEntity(final SparseEntity spe) {
setId(spe.id);
this.setRole(spe.role);
setEntityACL(spe.acl);
+ UTCDateTime versionDate = null;
+ if (spe.versionSeconds != null) {
+ versionDate = UTCDateTime.UTCSeconds(spe.versionSeconds, spe.versionNanos);
+ }
+ this.version = new Version(spe.version, versionDate);
if (!isNameOverride()) {
setName(spe.name);
@@ -1118,4 +1131,34 @@ public class Entity extends AbstractObservable implements EntityInterface {
public boolean skipJob() {
return false;
}
+
+ @Override
+ public Version getVersion() {
+ return this.version;
+ }
+
+ @Override
+ public boolean hasVersion() {
+ return this.version.getId() != null;
+ }
+
+ @Override
+ public void setVersion(Version version) {
+ this.version = version;
+ }
+
+ /** Return "id@version" if there is versioning information, else only "id". */
+ @Override
+ public String getIdVersion() {
+ if (!this.hasId()) {
+ return null;
+ } else if (this.hasVersion()) {
+ return new StringBuilder()
+ .append(getId())
+ .append("@")
+ .append(getVersion().getId())
+ .toString();
+ }
+ return getId().toString();
+ }
}
diff --git a/src/main/java/caosdb/server/entity/EntityID.java b/src/main/java/caosdb/server/entity/EntityID.java
deleted file mode 100644
index fbfb83c8028f5f2e0d8376c6dc480c19046c0d5b..0000000000000000000000000000000000000000
--- a/src/main/java/caosdb/server/entity/EntityID.java
+++ /dev/null
@@ -1,25 +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 caosdb.server.entity;
-
-public class EntityID {}
diff --git a/src/main/java/caosdb/server/entity/EntityInterface.java b/src/main/java/caosdb/server/entity/EntityInterface.java
index 20aa57a5b3f64ae5794d01235049c12740a0419b..4205111a58c30185d916c1d921acb7470d93f7a9 100644
--- a/src/main/java/caosdb/server/entity/EntityInterface.java
+++ b/src/main/java/caosdb/server/entity/EntityInterface.java
@@ -52,6 +52,8 @@ public interface EntityInterface
public abstract Integer getId();
+ public abstract String getIdVersion();
+
public abstract void setId(Integer id);
public abstract boolean hasId();
@@ -185,5 +187,11 @@ public interface EntityInterface
public abstract void setQueryTemplateDefinition(String query);
+ public abstract Version getVersion();
+
+ public abstract boolean hasVersion();
+
+ public abstract void setVersion(Version version);
+
public abstract void addToElement(Element element, SetFieldStrategy strategy);
}
diff --git a/src/main/java/caosdb/server/entity/NamedEntity.java b/src/main/java/caosdb/server/entity/NamedEntity.java
deleted file mode 100644
index 76ba79a317e146ca4b86793545f95d9e05e42480..0000000000000000000000000000000000000000
--- a/src/main/java/caosdb/server/entity/NamedEntity.java
+++ /dev/null
@@ -1,28 +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 caosdb.server.entity;
-
-class NamedEntity extends BaseEntity {
-
- String name = null;
-}
diff --git a/src/main/java/caosdb/server/entity/RetrieveEntity.java b/src/main/java/caosdb/server/entity/RetrieveEntity.java
index 5b54c2bcd4ce401bc469728f774ad68198ba0986..7035232b5a66df77518c8c1b586b7bcb43b7a22b 100644
--- a/src/main/java/caosdb/server/entity/RetrieveEntity.java
+++ b/src/main/java/caosdb/server/entity/RetrieveEntity.java
@@ -3,7 +3,9 @@
* 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
+ * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+ * 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
@@ -22,9 +24,6 @@
*/
package caosdb.server.entity;
-import caosdb.server.database.proto.SparseEntity;
-import caosdb.server.datatype.AbstractCollectionDatatype;
-
public class RetrieveEntity extends Entity {
public RetrieveEntity(final int id) {
@@ -35,38 +34,13 @@ public class RetrieveEntity extends Entity {
super(name);
}
- public RetrieveEntity parseSparseEntity(final SparseEntity spe) {
- setId(spe.id);
- this.setRole(spe.role);
- setEntityACL(spe.acl);
-
- if (!isNameOverride()) {
- setName(spe.name);
- }
- if (!isDescOverride()) {
- setDescription(spe.description);
- }
- if (!isDatatypeOverride()) {
- final String dt = spe.datatype;
- final String col = spe.collection;
-
- if (dt != null
- && !dt.equalsIgnoreCase("null")
- && (!hasDatatype() || !dt.equalsIgnoreCase(getDatatype().toString()))) {
- if (col != null && !col.equalsIgnoreCase("null")) {
- this.setDatatype(AbstractCollectionDatatype.collectionDatatypeFactory(col, dt));
- } else {
- this.setDatatype(dt);
- }
- }
- }
-
- if (spe.filePath != null) {
- setFileProperties(new FileProperties(spe.fileHash, spe.filePath, spe.fileSize));
- } else {
- setFileProperties(null);
- }
+ public RetrieveEntity(int id, String version) {
+ super(id);
+ this.setVersion(new Version(version));
+ }
- return this;
+ public RetrieveEntity(String name, String version) {
+ super(name);
+ this.setVersion(new Version(version));
}
}
diff --git a/src/main/java/caosdb/server/entity/ValidEntity.java b/src/main/java/caosdb/server/entity/ValidEntity.java
index 3e99d4ead10152f3ce434a91c8c3d3643cc61273..d2c8b519734f3732f6fc7c43047a99e59ccd71c4 100644
--- a/src/main/java/caosdb/server/entity/ValidEntity.java
+++ b/src/main/java/caosdb/server/entity/ValidEntity.java
@@ -22,47 +22,9 @@
*/
package caosdb.server.entity;
-import caosdb.server.database.proto.SparseEntity;
-import caosdb.server.datatype.AbstractCollectionDatatype;
-
public class ValidEntity extends Entity {
public ValidEntity(final int id) {
super(id);
}
-
- public ValidEntity parseSparseEntity(final SparseEntity spe) {
- setId(spe.id);
- this.setRole(spe.role);
- setEntityACL(spe.acl);
-
- if (!isNameOverride()) {
- setName(spe.name);
- }
- if (!isDescOverride()) {
- setDescription(spe.description);
- }
- if (!isDatatypeOverride()) {
- final String dt = spe.datatype;
- final String col = spe.collection;
-
- if (dt != null
- && !dt.equalsIgnoreCase("null")
- && (!hasDatatype() || !dt.equalsIgnoreCase(getDatatype().toString()))) {
- if (col != null && !col.equalsIgnoreCase("null")) {
- this.setDatatype(AbstractCollectionDatatype.collectionDatatypeFactory(col, dt));
- } else {
- this.setDatatype(dt);
- }
- }
- }
-
- if (spe.filePath != null) {
- setFileProperties(new FileProperties(spe.fileHash, spe.filePath, spe.fileSize));
- } else {
- setFileProperties(null);
- }
-
- return this;
- }
}
diff --git a/src/main/java/caosdb/server/entity/Version.java b/src/main/java/caosdb/server/entity/Version.java
new file mode 100644
index 0000000000000000000000000000000000000000..07c7387e8c419f962e1174504a28ceceda5c30e3
--- /dev/null
+++ b/src/main/java/caosdb/server/entity/Version.java
@@ -0,0 +1,84 @@
+/*
+ * 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/>.
+ */
+
+package caosdb.server.entity;
+
+import caosdb.datetime.UTCDateTime;
+import java.util.LinkedList;
+
+/**
+ * Plain old java object (POJO) for an entity's version.
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
+public class Version {
+
+ private String id = null;
+ private LinkedList<Version> predecessors = null;
+ private LinkedList<Version> successors = null;
+ private UTCDateTime date = null;
+
+ public Version(String id, long seconds, int nanos) {
+ this(id, UTCDateTime.UTCSeconds(seconds, nanos));
+ }
+
+ public Version(String id, UTCDateTime date) {
+ this.id = id;
+ this.date = date;
+ }
+
+ public Version(String id) {
+ this(id, null);
+ }
+
+ public Version() {}
+
+ public UTCDateTime getDate() {
+ return date;
+ }
+
+ public void setDate(UTCDateTime date) {
+ this.date = date;
+ }
+
+ public String getId() {
+ return id;
+ }
+
+ public void setId(String id) {
+ this.id = id;
+ }
+
+ public LinkedList<Version> getSuccessors() {
+ return successors;
+ }
+
+ public void setSuccessors(LinkedList<Version> successors) {
+ this.successors = successors;
+ }
+
+ public LinkedList<Version> getPredecessors() {
+ return predecessors;
+ }
+
+ public void setPredecessors(LinkedList<Version> predecessors) {
+ this.predecessors = predecessors;
+ }
+}
diff --git a/src/main/java/caosdb/server/entity/container/DeleteContainer.java b/src/main/java/caosdb/server/entity/container/DeleteContainer.java
index c219ee5e4399caeee857006f995748435d023963..c3d57bc656a7c9609dd8fb6ca4d031e0e82f63fa 100644
--- a/src/main/java/caosdb/server/entity/container/DeleteContainer.java
+++ b/src/main/java/caosdb/server/entity/container/DeleteContainer.java
@@ -42,4 +42,9 @@ public class DeleteContainer extends EntityByIdContainer {
public void add(final int id) {
add(new DeleteEntity(id));
}
+
+ @Override
+ public void add(int id, String version) {
+ add(new DeleteEntity(id, version));
+ }
}
diff --git a/src/main/java/caosdb/server/entity/container/EntityByIdContainer.java b/src/main/java/caosdb/server/entity/container/EntityByIdContainer.java
index 1bfda2024c4ff11375ad619d64946e1036c714b0..29a0978b8acdc809b75c52de643ee131cd62b129 100644
--- a/src/main/java/caosdb/server/entity/container/EntityByIdContainer.java
+++ b/src/main/java/caosdb/server/entity/container/EntityByIdContainer.java
@@ -37,4 +37,6 @@ public abstract class EntityByIdContainer extends TransactionContainer {
}
public abstract void add(int id);
+
+ public abstract void add(int id, String version);
}
diff --git a/src/main/java/caosdb/server/entity/container/RetrieveContainer.java b/src/main/java/caosdb/server/entity/container/RetrieveContainer.java
index 9b4f7364d4ecdc63da1be8f1ead292545801a078..5b205bc27f38e3d1a04b2ed3c5a7e874af229489 100644
--- a/src/main/java/caosdb/server/entity/container/RetrieveContainer.java
+++ b/src/main/java/caosdb/server/entity/container/RetrieveContainer.java
@@ -46,4 +46,13 @@ public class RetrieveContainer extends EntityByIdContainer {
public void add(final String name) {
add(new RetrieveEntity(name));
}
+
+ public void add(final String name, String version) {
+ add(new RetrieveEntity(name, version));
+ }
+
+ @Override
+ public void add(int id, String version) {
+ add(new RetrieveEntity(id, version));
+ }
}
diff --git a/src/main/java/caosdb/server/entity/wrapper/EntityWrapper.java b/src/main/java/caosdb/server/entity/wrapper/EntityWrapper.java
index 056f342c6b09b8f07130e6c89013777809c567b8..f8d563de1776d155b2f66b913de454c7e5b952fd 100644
--- a/src/main/java/caosdb/server/entity/wrapper/EntityWrapper.java
+++ b/src/main/java/caosdb/server/entity/wrapper/EntityWrapper.java
@@ -33,6 +33,7 @@ import caosdb.server.entity.FileProperties;
import caosdb.server.entity.Message;
import caosdb.server.entity.Role;
import caosdb.server.entity.StatementStatus;
+import caosdb.server.entity.Version;
import caosdb.server.entity.container.ParentContainer;
import caosdb.server.entity.container.PropertyContainer;
import caosdb.server.entity.xml.SetFieldStrategy;
@@ -555,6 +556,26 @@ public class EntityWrapper implements EntityInterface {
return this.entity.hasPermission(subject, permission);
}
+ @Override
+ public Version getVersion() {
+ return this.entity.getVersion();
+ }
+
+ @Override
+ public boolean hasVersion() {
+ return this.entity.hasVersion();
+ }
+
+ @Override
+ public void setVersion(Version version) {
+ this.entity.setVersion(version);
+ }
+
+ @Override
+ public String getIdVersion() {
+ return this.entity.getIdVersion();
+ }
+
@Override
public void addToElement(Element element, SetFieldStrategy strategy) {
this.entity.addToElement(element, strategy);
diff --git a/src/main/java/caosdb/server/entity/wrapper/Parent.java b/src/main/java/caosdb/server/entity/wrapper/Parent.java
index c36ffa9c2c1a16062add2eb912ca01132af9872c..f3686b5b802e004e55d572e58076e5e08bb5988d 100644
--- a/src/main/java/caosdb/server/entity/wrapper/Parent.java
+++ b/src/main/java/caosdb/server/entity/wrapper/Parent.java
@@ -57,4 +57,10 @@ public class Parent extends EntityWrapper {
public Affiliation getAffiliation() {
return this.affiliation;
}
+
+ @Override
+ public boolean hasVersion() {
+ // parents are not versioned (yet).
+ return false;
+ }
}
diff --git a/src/main/java/caosdb/server/entity/wrapper/Property.java b/src/main/java/caosdb/server/entity/wrapper/Property.java
index f6bb840a75d9216ee3fd56f3d2bf95f701280492..1d1cd2a8ae11489479b9e9191365843182d136ca 100644
--- a/src/main/java/caosdb/server/entity/wrapper/Property.java
+++ b/src/main/java/caosdb/server/entity/wrapper/Property.java
@@ -134,4 +134,10 @@ public class Property extends EntityWrapper {
public EntityInterface getDomainEntity() {
return this.domain;
}
+
+ @Override
+ public boolean hasVersion() {
+ // properties are not versioned (yet).
+ return false;
+ }
}
diff --git a/src/main/java/caosdb/server/entity/xml/EntityToElementStrategy.java b/src/main/java/caosdb/server/entity/xml/EntityToElementStrategy.java
index ae69b94024eac0fdd9667233b507545e2b0f09af..6cfe8fa9f3628cc0670ccb3e6f30a263a0bc5cf3 100644
--- a/src/main/java/caosdb/server/entity/xml/EntityToElementStrategy.java
+++ b/src/main/java/caosdb/server/entity/xml/EntityToElementStrategy.java
@@ -87,6 +87,10 @@ public class EntityToElementStrategy implements ToElementStrategy {
if (setFieldStrategy.isToBeSet("id") && entity.hasId()) {
element.setAttribute("id", Integer.toString(entity.getId()));
}
+ if (setFieldStrategy.isToBeSet("version") && entity.hasVersion()) {
+ Element v = new VersionXMLSerializer().toElement(entity.getVersion());
+ element.addContent(v);
+ }
if (setFieldStrategy.isToBeSet("cuid") && entity.hasCuid()) {
element.setAttribute("cuid", entity.getCuid());
}
diff --git a/src/main/java/caosdb/server/entity/xml/SetFieldStrategy.java b/src/main/java/caosdb/server/entity/xml/SetFieldStrategy.java
index 3e7e735e6d863721a7591b8a2fc18f6fc9dfa15c..7a4a29a16cc545ca5316c7b086a8b1ec46cfcfc3 100644
--- a/src/main/java/caosdb/server/entity/xml/SetFieldStrategy.java
+++ b/src/main/java/caosdb/server/entity/xml/SetFieldStrategy.java
@@ -112,10 +112,10 @@ public class SetFieldStrategy {
* are actually used, e.g ["a.b.c.d1", "a.b.c.d2"].
*/
return new SetFieldStrategy() {
- // Always-true-strategy
+ // Return true for everything except version fields.
@Override
public boolean isToBeSet(String field) {
- return true;
+ return field == null || !field.equalsIgnoreCase("version");
}
};
}
diff --git a/src/main/java/caosdb/server/entity/xml/VersionXMLSerializer.java b/src/main/java/caosdb/server/entity/xml/VersionXMLSerializer.java
new file mode 100644
index 0000000000000000000000000000000000000000..badd1a95f2a2338bde43a1de23774097ab2c45ed
--- /dev/null
+++ b/src/main/java/caosdb/server/entity/xml/VersionXMLSerializer.java
@@ -0,0 +1,57 @@
+/*
+ * 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/>.
+ */
+
+package caosdb.server.entity.xml;
+
+import caosdb.server.entity.Version;
+import java.util.TimeZone;
+import org.jdom2.Element;
+
+/**
+ * Creates a JDOM Element for a Version instance.
+ *
+ * @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()));
+ }
+ 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);
+ }
+ }
+ 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);
+ }
+ }
+ return result;
+ }
+}
diff --git a/src/main/java/caosdb/server/jobs/Job.java b/src/main/java/caosdb/server/jobs/Job.java
index 110809e77ae0d40076642d953c15b0d9566eddd6..ff214b977dfd870a9aa56b3e8efa4f12967b2083 100644
--- a/src/main/java/caosdb/server/jobs/Job.java
+++ b/src/main/java/caosdb/server/jobs/Job.java
@@ -3,7 +3,9 @@
* 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
+ * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+ * 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
@@ -171,11 +173,39 @@ public abstract class Job extends AbstractObservable implements Observer {
protected final EntityInterface retrieveValidSparseEntityByName(final String name)
throws Message {
- return retrieveValidSparseEntityById(retrieveValidIDByName(name));
+ return retrieveValidSparseEntityById(retrieveValidIDByName(name), null);
}
- protected final EntityInterface retrieveValidSparseEntityById(final Integer id) throws Message {
- final EntityInterface ret = execute(new RetrieveSparseEntity(id)).getEntity();
+ protected final EntityInterface retrieveValidSparseEntityById(
+ final Integer id, final String version) throws Message {
+
+ String resulting_version = version;
+ if (version == null || version.equals("HEAD")) {
+ // the targeted entity version is the entity after the transaction or the
+ // entity without a specific version. Thus we have to fetch the entity
+ // from the container if possible.
+ EntityInterface ret = getEntityById(id);
+ if (ret != null) {
+ return ret;
+ }
+ } else if (version.startsWith("HEAD~")) {
+ EntityInterface entById = getEntityById(id);
+ if (entById != null && entById.getEntityStatus() != EntityStatus.VALID) {
+ // if version is HEAD~{OFFSET} with {OFFSET} > 0 and the targeted entity is is to be
+ // updated, the actual offset has to be reduced by 1. HEAD always denotes the entity@HEAD
+ // *after* the successful transaction, so that it is consistent with subsequent retrieves.
+ int offset = Integer.parseInt(version.substring(5)) - 1;
+ if (offset == 0) {
+ // special case HEAD~1
+ resulting_version = "HEAD";
+ } else {
+ resulting_version = new StringBuilder().append("HEAD~").append(offset).toString();
+ }
+ }
+ }
+
+ final EntityInterface ret =
+ execute(new RetrieveSparseEntity(id, resulting_version)).getEntity();
if (ret.getEntityStatus() == EntityStatus.NONEXISTENT) {
throw ServerMessages.ENTITY_DOES_NOT_EXIST;
}
diff --git a/src/main/java/caosdb/server/jobs/core/CheckDatatypePresent.java b/src/main/java/caosdb/server/jobs/core/CheckDatatypePresent.java
index 69d36f42fa2f457b05dcc394659b5c088976bff4..faf481dba5ac16836b4495d6112fc25c887a6f1f 100644
--- a/src/main/java/caosdb/server/jobs/core/CheckDatatypePresent.java
+++ b/src/main/java/caosdb/server/jobs/core/CheckDatatypePresent.java
@@ -138,7 +138,8 @@ public final class CheckDatatypePresent extends EntityJob {
}
} else {
- final EntityInterface validDatatypeEntity = retrieveValidSparseEntityById(datatype.getId());
+ final EntityInterface validDatatypeEntity =
+ retrieveValidSparseEntityById(datatype.getId(), null);
assertAllowedToUse(validDatatypeEntity);
datatype.setEntity(validDatatypeEntity);
}
@@ -151,7 +152,7 @@ public final class CheckDatatypePresent extends EntityJob {
private void checkIfOverride() throws Message {
if (getEntity().hasId() && getEntity().getId() > 0) {
// get data type from database
- final EntityInterface foreign = retrieveValidSparseEntityById(getEntity().getId());
+ final EntityInterface foreign = retrieveValidSparseEntityById(getEntity().getId(), null);
if (foreign.hasDatatype() && !foreign.getDatatype().equals(getEntity().getDatatype())) {
// is override!
@@ -179,7 +180,7 @@ public final class CheckDatatypePresent extends EntityJob {
// the data type of the corresponding abstract property.
if (getEntity().hasId() && getEntity().getId() > 0) {
// get from data base
- final EntityInterface foreign = retrieveValidSparseEntityById(getEntity().getId());
+ final EntityInterface foreign = retrieveValidSparseEntityById(getEntity().getId(), null);
inheritDatatypeFromForeignEntity(foreign);
} else if (getEntity().hasId() && getEntity().getId() < 0) {
// get from container
@@ -218,7 +219,7 @@ public final class CheckDatatypePresent extends EntityJob {
for (final EntityInterface parent : getEntity().getParents()) {
EntityInterface parentEntity = null;
if (parent.getId() > 0) {
- parentEntity = retrieveValidSparseEntityById(parent.getId());
+ parentEntity = retrieveValidSparseEntityById(parent.getId(), null);
} else {
parentEntity = getEntityById(parent.getId());
runJobFromSchedule(parentEntity, CheckDatatypePresent.class);
diff --git a/src/main/java/caosdb/server/jobs/core/CheckParValid.java b/src/main/java/caosdb/server/jobs/core/CheckParValid.java
index 005053a4a7d59c6c9f1a05171085701c606970b5..560558dce6e494fa4857fefadfa7d22ef79ee5aa 100644
--- a/src/main/java/caosdb/server/jobs/core/CheckParValid.java
+++ b/src/main/java/caosdb/server/jobs/core/CheckParValid.java
@@ -65,7 +65,7 @@ public class CheckParValid extends EntityJob {
if (parent.getId() >= 0) {
// id >= 0 (parent is yet in the database)
// retrieve parent by id
- final EntityInterface foreign = retrieveValidSparseEntityById(parent.getId());
+ final EntityInterface foreign = retrieveValidSparseEntityById(parent.getId(), null);
// check permissions for this
// parentforeign.acceptObserver(o)
assertAllowedToUse(foreign);
diff --git a/src/main/java/caosdb/server/jobs/core/CheckPropValid.java b/src/main/java/caosdb/server/jobs/core/CheckPropValid.java
index 6a7cbb51556dd0b9c634da4c8a56d20204fc9f50..5e199e848984a4d042c3a755d83a8d57ba91987f 100644
--- a/src/main/java/caosdb/server/jobs/core/CheckPropValid.java
+++ b/src/main/java/caosdb/server/jobs/core/CheckPropValid.java
@@ -55,7 +55,7 @@ public class CheckPropValid extends EntityJob {
if (property.getId() >= 0) {
final EntityInterface abstractProperty =
- retrieveValidSparseEntityById(property.getId());
+ retrieveValidSparseEntityById(property.getId(), null);
assertAllowedToUse(abstractProperty);
diff --git a/src/main/java/caosdb/server/jobs/core/CheckRefidIsaParRefid.java b/src/main/java/caosdb/server/jobs/core/CheckRefidIsaParRefid.java
index fa2b21ccaea7ba3c8bd2b733f8420c213e4f03f7..04a1ac8c5bf6aa42bf2dcec803e6bc1b68a3a7f0 100644
--- a/src/main/java/caosdb/server/jobs/core/CheckRefidIsaParRefid.java
+++ b/src/main/java/caosdb/server/jobs/core/CheckRefidIsaParRefid.java
@@ -94,7 +94,8 @@ public class CheckRefidIsaParRefid extends EntityJob {
&& getEntityByName(rv.getName()).getRole() == Role.File) {
} else if (rv.getId() != null
&& rv.getId() > 0
- && retrieveValidSparseEntityById(rv.getId()).getRole() == Role.File) {
+ && retrieveValidSparseEntityById(rv.getId(), rv.getVersion()).getRole()
+ == Role.File) {
} else if (rv.getName() != null
&& retrieveValidSparseEntityByName(rv.getName()).getRole() == Role.File) {
} else {
diff --git a/src/main/java/caosdb/server/jobs/core/CheckRefidValid.java b/src/main/java/caosdb/server/jobs/core/CheckRefidValid.java
index 14d98962f48c300ae77fe0811922bf3b1d7eb4ae..36591070cd64558114bb56e22860b95f42fc6463 100644
--- a/src/main/java/caosdb/server/jobs/core/CheckRefidValid.java
+++ b/src/main/java/caosdb/server/jobs/core/CheckRefidValid.java
@@ -3,7 +3,9 @@
* 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
+ * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+ * 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
@@ -85,9 +87,12 @@ public class CheckRefidValid extends EntityJob {
private void checkRefValue(final ReferenceValue ref) throws Message {
if (ref.getId() != null) {
if (ref.getId() >= 0) {
- final EntityInterface referencedValidEntity = retrieveValidSparseEntityById(ref.getId());
+ final EntityInterface referencedValidEntity =
+ retrieveValidSparseEntityById(ref.getId(), ref.getVersion());
assertAllowedToUse(referencedValidEntity);
- ref.setEntity(referencedValidEntity);
+
+ // link the entity as versioned entity iff the reference specified a version
+ ref.setEntity(referencedValidEntity, ref.getVersion() != null);
} else {
@@ -100,7 +105,9 @@ public class CheckRefidValid extends EntityJob {
final EntityInterface referencedEntity = getEntityById(ref.getId());
if (referencedEntity != null) {
assertAllowedToUse(referencedEntity);
- ref.setEntity(referencedEntity);
+
+ // link the entity as versioned entity iff the reference specified a version
+ ref.setEntity(referencedEntity, ref.getVersion() != null);
} else {
throw ServerMessages.REFERENCED_ENTITY_DOES_NOT_EXIST;
}
@@ -117,7 +124,9 @@ public class CheckRefidValid extends EntityJob {
if (referencedEntity != null) {
assertAllowedToUse(referencedEntity);
- ref.setEntity(referencedEntity);
+
+ // link the entity as versioned entity iff the reference specified a version
+ ref.setEntity(referencedEntity, ref.getVersion() != null);
if (checkRefEntity(ref)) {
ref.getEntity().acceptObserver(this);
}
@@ -125,7 +134,9 @@ public class CheckRefidValid extends EntityJob {
final EntityInterface referencedValidEntity =
retrieveValidSparseEntityByName(ref.getName());
assertAllowedToUse(referencedValidEntity);
- ref.setEntity(referencedValidEntity);
+
+ // link the entity as versioned entity iff the reference specified a version
+ ref.setEntity(referencedValidEntity, ref.getVersion() != null);
}
}
}
diff --git a/src/main/java/caosdb/server/jobs/core/RemoveDuplicates.java b/src/main/java/caosdb/server/jobs/core/RemoveDuplicates.java
index a104c124293cf07ecc3b871c4bc6b31470ec2a15..a09f66533cb3bc3c7cc01b2d6931bc120f87f7a7 100644
--- a/src/main/java/caosdb/server/jobs/core/RemoveDuplicates.java
+++ b/src/main/java/caosdb/server/jobs/core/RemoveDuplicates.java
@@ -30,17 +30,20 @@ public class RemoveDuplicates extends ContainerJob {
@Override
protected void run() {
- final HashSet<EntityInterface> rm = new HashSet<EntityInterface>();
+ // collect duplicates
+ final HashSet<EntityInterface> duplicates = new HashSet<EntityInterface>();
for (final EntityInterface e : getContainer()) {
- if (e.hasId() && !rm.contains(e)) {
+ if (e.hasId() && !duplicates.contains(e)) {
for (final EntityInterface e2 : getContainer()) {
- if (e2 != e && e.getId().equals(e2.getId())) {
- rm.add(e2);
+ if (e2 != e && e.getIdVersion().equals(e2.getIdVersion())) {
+ // this is a duplicate of another entity in this container
+ duplicates.add(e2);
}
}
}
}
- for (final EntityInterface e : rm) {
+ // remove duplicates.
+ for (final EntityInterface e : duplicates) {
getContainer().remove(e);
}
}
diff --git a/src/main/java/caosdb/server/query/Query.java b/src/main/java/caosdb/server/query/Query.java
index 4eeaafc03a8f94b0df845aff40a923d1f52dc60a..a2d6e48767f5835bd9bf40ce65717bf9e8363f98 100644
--- a/src/main/java/caosdb/server/query/Query.java
+++ b/src/main/java/caosdb/server/query/Query.java
@@ -301,7 +301,7 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
// ... check for RETRIEVE:ENTITY permission...
final EntityInterface e =
- execute(new RetrieveSparseEntity(q.getKey()), query.getAccess()).getEntity();
+ execute(new RetrieveSparseEntity(q.getKey(), null), query.getAccess()).getEntity();
final EntityACL entityACL = e.getEntityACL();
if (!entityACL.isPermitted(query.getUser(), EntityPermission.RETRIEVE_ENTITY)) {
// ... and ignore if not.
@@ -555,7 +555,7 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
while (rs.next()) {
final long t1 = System.currentTimeMillis();
final Integer id = rs.getInt("id");
- if (!execute(new RetrieveSparseEntity(id), query.getAccess())
+ if (!execute(new RetrieveSparseEntity(id, null), query.getAccess())
.getEntity()
.getEntityACL()
.isPermitted(query.getUser(), EntityPermission.RETRIEVE_ENTITY)) {
@@ -588,7 +588,7 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
while (iterator.hasNext()) {
final long t1 = System.currentTimeMillis();
final Integer id = iterator.next();
- if (!execute(new RetrieveSparseEntity(id), getAccess())
+ if (!execute(new RetrieveSparseEntity(id, null), getAccess())
.getEntity()
.getEntityACL()
.isPermitted(getUser(), EntityPermission.RETRIEVE_ENTITY)) {
diff --git a/src/main/java/caosdb/server/resource/AbstractCaosDBServerResource.java b/src/main/java/caosdb/server/resource/AbstractCaosDBServerResource.java
index d7897450b2caaa7a70f20ead02ed1bb0c67e192d..97488a6ba2a7984d66bb94332b4d7df0f9478cfb 100644
--- a/src/main/java/caosdb/server/resource/AbstractCaosDBServerResource.java
+++ b/src/main/java/caosdb/server/resource/AbstractCaosDBServerResource.java
@@ -4,7 +4,8 @@
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- * Copyright (C) 2019 IndiScale GmbH
+ * Copyright (C) 2019,2020 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
@@ -23,7 +24,6 @@
*/
package caosdb.server.resource;
-import static caosdb.server.utils.Utils.isNonNullInteger;
import static java.net.URLDecoder.decode;
import caosdb.server.CaosDBException;
@@ -38,7 +38,6 @@ import java.io.InputStream;
import java.io.UnsupportedEncodingException;
import java.security.NoSuchAlgorithmException;
import java.sql.SQLException;
-import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.LinkedList;
@@ -77,9 +76,7 @@ public abstract class AbstractCaosDBServerResource extends ServerResource {
private static final XMLParser xmlparser = new XMLParser();
protected String sRID = null; // Server side request ID
private String cRID = null; // Client side request ID
- private String[] requestedItems = null;
- private ArrayList<Integer> requestedIDs = new ArrayList<Integer>();
- private ArrayList<String> requestedNames = new ArrayList<String>();
+ private String[] requestedItems = {};
private WebinterfaceUtils utils;
/** Return the {@link WebinterfaceUtils} instance for this resource. */
@@ -141,21 +138,6 @@ public abstract class AbstractCaosDBServerResource extends ServerResource {
}
this.requestedItems = specifier.split("&");
- for (final String requestedItem : this.requestedItems) {
- if (isNonNullInteger(requestedItem)) {
- final int id = Integer.parseInt(requestedItem);
- if (id > 0) {
- getRequestedIDs().add(id);
- }
- } else if (requestedItem.equalsIgnoreCase("all")) {
- getRequestedNames().clear();
- getRequestedIDs().clear();
- getRequestedNames().add("all");
- break;
- } else {
- getRequestedNames().add(requestedItem);
- }
- }
}
// flags
@@ -427,16 +409,8 @@ public abstract class AbstractCaosDBServerResource extends ServerResource {
}
}
- public ArrayList<Integer> getRequestedIDs() {
- return this.requestedIDs;
- }
-
- public ArrayList<String> getRequestedNames() {
- return this.requestedNames;
- }
-
- public void setRequestedNames(final ArrayList<String> requestedNames) {
- this.requestedNames = requestedNames;
+ public String[] getRequestedItems() {
+ return this.requestedItems;
}
public HashMap<String, String> getFlags() {
diff --git a/src/main/java/caosdb/server/resource/PermissionRulesResource.java b/src/main/java/caosdb/server/resource/PermissionRulesResource.java
index 1610ba372def0b758b76d15d6d839b825a9d96c6..dba1797a03287c503e5898c7e9a7dde6c389630c 100644
--- a/src/main/java/caosdb/server/resource/PermissionRulesResource.java
+++ b/src/main/java/caosdb/server/resource/PermissionRulesResource.java
@@ -46,7 +46,7 @@ public class PermissionRulesResource extends AbstractCaosDBServerResource {
protected Representation httpGetInChildClass()
throws ConnectionException, IOException, SQLException, CaosDBException,
NoSuchAlgorithmException, Exception {
- final String role = getRequestedNames().get(0);
+ final String role = getRequestedItems()[0];
getUser().checkPermission(ACMPermissions.PERMISSION_RETRIEVE_ROLE_PERMISSIONS(role));
@@ -73,7 +73,7 @@ public class PermissionRulesResource extends AbstractCaosDBServerResource {
public Representation httpPutInChildClass(final Representation entity) throws Exception {
final Element root = parseEntity(entity).getRootElement();
- final String role = getRequestedNames().get(0);
+ final String role = getRequestedItems()[0];
final HashSet<PermissionRule> rules = new HashSet<PermissionRule>();
for (final Element e : root.getChildren()) {
diff --git a/src/main/java/caosdb/server/resource/RolesResource.java b/src/main/java/caosdb/server/resource/RolesResource.java
index ef9b30f5b831454fac392317e2c57833657c62d6..0f1b01e3230cf3e73f1c20949f38e180bd8f7e3b 100644
--- a/src/main/java/caosdb/server/resource/RolesResource.java
+++ b/src/main/java/caosdb/server/resource/RolesResource.java
@@ -52,8 +52,8 @@ public class RolesResource extends AbstractCaosDBServerResource {
final Element root = generateRootElement();
final Document document = new Document();
- if (!getRequestedNames().isEmpty()) {
- final String name = getRequestedNames().get(0);
+ if (getRequestedItems().length > 0) {
+ final String name = getRequestedItems()[0];
if (name != null) {
getUser().checkPermission(ACMPermissions.PERMISSION_RETRIEVE_ROLE_DESCRIPTION(name));
final RetrieveRoleTransaction t = new RetrieveRoleTransaction(name);
@@ -78,8 +78,8 @@ public class RolesResource extends AbstractCaosDBServerResource {
protected Representation httpDeleteInChildClass()
throws ConnectionException, SQLException, CaosDBException, IOException,
NoSuchAlgorithmException, Exception {
- if (!getRequestedNames().isEmpty()) {
- final String name = getRequestedNames().get(0);
+ if (getRequestedItems().length > 0) {
+ final String name = getRequestedItems()[0];
if (name != null) {
final DeleteRoleTransaction t = new DeleteRoleTransaction(name);
try {
@@ -133,26 +133,28 @@ public class RolesResource extends AbstractCaosDBServerResource {
protected Representation httpPutInChildClass(final Representation entity)
throws ConnectionException, JDOMException, Exception, xmlNotWellFormedException {
- final String name = getRequestedNames().get(0);
- String description = null;
+ if (getRequestedItems().length > 0) {
+ final String name = getRequestedItems()[0];
+ String description = null;
- final Form f = new Form(entity);
- if (!f.isEmpty()) {
- description = f.getFirstValue("role_description");
- }
+ final Form f = new Form(entity);
+ if (!f.isEmpty()) {
+ description = f.getFirstValue("role_description");
+ }
- if (name != null && description != null) {
- final Role role = new Role();
- role.name = name;
- role.description = description;
- final UpdateRoleTransaction t = new UpdateRoleTransaction(role);
- try {
- t.execute();
- } catch (final Message m) {
- if (m == ServerMessages.ROLE_DOES_NOT_EXIST) {
- return error(m, Status.CLIENT_ERROR_NOT_FOUND);
- } else {
- throw m;
+ if (name != null && description != null) {
+ final Role role = new Role();
+ role.name = name;
+ role.description = description;
+ final UpdateRoleTransaction t = new UpdateRoleTransaction(role);
+ try {
+ t.execute();
+ } catch (final Message m) {
+ if (m == ServerMessages.ROLE_DOES_NOT_EXIST) {
+ return error(m, Status.CLIENT_ERROR_NOT_FOUND);
+ } else {
+ throw m;
+ }
}
}
}
diff --git a/src/main/java/caosdb/server/resource/UserResource.java b/src/main/java/caosdb/server/resource/UserResource.java
index b77ff8a49035d2be930a3f957e743ed2f0dae067..7dc9111ee332421fd27d1c32632cc458cbf6c800 100644
--- a/src/main/java/caosdb/server/resource/UserResource.java
+++ b/src/main/java/caosdb/server/resource/UserResource.java
@@ -60,9 +60,9 @@ public class UserResource extends AbstractCaosDBServerResource {
final Document doc = new Document();
final Element rootElem = generateRootElement();
- if (!getRequestedNames().isEmpty()) {
+ if (getRequestedItems().length > 0) {
try {
- final String username = getRequestedNames().get(0);
+ final String username = getRequestedItems()[0];
final String realm =
(getRequestAttributes().containsKey("realm")
? (String) getRequestAttributes().get("realm")
@@ -92,7 +92,7 @@ public class UserResource extends AbstractCaosDBServerResource {
try {
final Form form = new Form(entity);
- final String username = getRequestedNames().get(0);
+ final String username = getRequestedItems()[0];
final String realm =
(getRequestAttributes().containsKey("realm")
? (String) getRequestAttributes().get("realm")
@@ -187,7 +187,8 @@ public class UserResource extends AbstractCaosDBServerResource {
final Document doc = new Document();
final Element rootElem = generateRootElement();
- final DeleteUserTransaction t = new DeleteUserTransaction(getRequestedNames().get(0));
+ final String username = getRequestedItems()[0];
+ final DeleteUserTransaction t = new DeleteUserTransaction(username);
try {
t.execute();
} catch (final Message m) {
diff --git a/src/main/java/caosdb/server/resource/UserRolesResource.java b/src/main/java/caosdb/server/resource/UserRolesResource.java
index 27e147157675982f036b88981b1dce221abae754..46d51ca4d60bec89b584cefc362e54ab37063503 100644
--- a/src/main/java/caosdb/server/resource/UserRolesResource.java
+++ b/src/main/java/caosdb/server/resource/UserRolesResource.java
@@ -47,7 +47,7 @@ public class UserRolesResource extends AbstractCaosDBServerResource {
protected Representation httpGetInChildClass()
throws ConnectionException, IOException, SQLException, CaosDBException,
NoSuchAlgorithmException, Exception {
- final String user = getRequestedNames().get(0);
+ final String user = getRequestedItems()[0];
final String realm =
(getRequestAttributes().get("realm") != null
? (String) getRequestAttributes().get("realm")
@@ -73,7 +73,7 @@ public class UserRolesResource extends AbstractCaosDBServerResource {
@Override
protected Representation httpPutInChildClass(final Representation entity)
throws ConnectionException, JDOMException, Exception, xmlNotWellFormedException {
- final String user = getRequestedNames().get(0);
+ final String user = getRequestedItems()[0];
final String realm =
(getRequestAttributes().get("realm") != null
? (String) getRequestAttributes().get("realm")
diff --git a/src/main/java/caosdb/server/resource/transaction/EntityResource.java b/src/main/java/caosdb/server/resource/transaction/EntityResource.java
index dc25bcff3418b3f46f90e965a6b80cdf3111c07f..70e7bdf73adbf5e950fe0a51e119a8dbbe2e054f 100644
--- a/src/main/java/caosdb/server/resource/transaction/EntityResource.java
+++ b/src/main/java/caosdb/server/resource/transaction/EntityResource.java
@@ -30,8 +30,8 @@ import caosdb.server.entity.container.RetrieveContainer;
import caosdb.server.entity.container.UpdateContainer;
import caosdb.server.resource.AbstractCaosDBServerResource;
import caosdb.server.resource.transaction.handlers.FileUploadHandler;
-import caosdb.server.resource.transaction.handlers.IDHandler;
import caosdb.server.resource.transaction.handlers.RequestHandler;
+import caosdb.server.resource.transaction.handlers.SimpleDeleteRequestHandler;
import caosdb.server.resource.transaction.handlers.SimpleGetRequestHandler;
import caosdb.server.resource.transaction.handlers.SimpleWriteHandler;
import caosdb.server.transaction.Delete;
@@ -72,7 +72,7 @@ public class EntityResource extends AbstractCaosDBServerResource {
}
protected RequestHandler<DeleteContainer> getDeleteRequestHandler() {
- return new IDHandler<DeleteContainer>();
+ return new SimpleDeleteRequestHandler();
}
protected RequestHandler<InsertContainer> getPostRequestHandler() {
diff --git a/src/main/java/caosdb/server/resource/transaction/handlers/IDHandler.java b/src/main/java/caosdb/server/resource/transaction/handlers/IDHandler.java
deleted file mode 100644
index e641ed416c86075d23a37d70ad791c26a820a966..0000000000000000000000000000000000000000
--- a/src/main/java/caosdb/server/resource/transaction/handlers/IDHandler.java
+++ /dev/null
@@ -1,36 +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 caosdb.server.resource.transaction.handlers;
-
-import caosdb.server.entity.container.EntityByIdContainer;
-import caosdb.server.resource.transaction.EntityResource;
-
-public class IDHandler<T extends EntityByIdContainer> extends RequestHandler<T> {
-
- @Override
- public void handle(final EntityResource t, final T container) throws Exception {
- for (final int id : t.getRequestedIDs()) {
- container.add(id);
- }
- }
-}
diff --git a/src/main/java/caosdb/server/resource/transaction/handlers/SimpleDeleteRequestHandler.java b/src/main/java/caosdb/server/resource/transaction/handlers/SimpleDeleteRequestHandler.java
new file mode 100644
index 0000000000000000000000000000000000000000..7fb416451bd8f053df5231eb1002db0c03544f99
--- /dev/null
+++ b/src/main/java/caosdb/server/resource/transaction/handlers/SimpleDeleteRequestHandler.java
@@ -0,0 +1,55 @@
+/*
+ * ** 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) 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 caosdb.server.resource.transaction.handlers;
+
+import caosdb.server.entity.container.DeleteContainer;
+import caosdb.server.resource.transaction.EntityResource;
+
+public class SimpleDeleteRequestHandler extends RequestHandler<DeleteContainer> {
+
+ @Override
+ public void handle(final EntityResource t, final DeleteContainer container) throws Exception {
+ // TODO a lot of code duplication, see SimpleGetRequestHandle#handle.
+ // However, this is about to be changed again when string ids are
+ // introduced, anyways. So we just leave it.
+ for (final String item : t.getRequestedItems()) {
+ String[] elem = item.split("@", 1);
+ Integer id = null;
+ String version = null;
+ try {
+ id = Integer.parseInt(elem[0]);
+ } catch (NumberFormatException e) {
+ // pass
+ }
+ if (elem.length > 1) {
+ version = elem[1];
+ }
+
+ if (id != null) {
+ container.add(id, version);
+ }
+ }
+ }
+}
diff --git a/src/main/java/caosdb/server/resource/transaction/handlers/SimpleGetRequestHandler.java b/src/main/java/caosdb/server/resource/transaction/handlers/SimpleGetRequestHandler.java
index 8fbb9d25cb33d2d0a75ce8405a164c1e8c9ce0fd..18c89d46966a3e22b1a9066b84dcf2d05efd122c 100644
--- a/src/main/java/caosdb/server/resource/transaction/handlers/SimpleGetRequestHandler.java
+++ b/src/main/java/caosdb/server/resource/transaction/handlers/SimpleGetRequestHandler.java
@@ -25,13 +25,29 @@ package caosdb.server.resource.transaction.handlers;
import caosdb.server.entity.container.RetrieveContainer;
import caosdb.server.resource.transaction.EntityResource;
-public class SimpleGetRequestHandler extends IDHandler<RetrieveContainer> {
+public class SimpleGetRequestHandler extends RequestHandler<RetrieveContainer> {
@Override
public void handle(final EntityResource t, final RetrieveContainer container) throws Exception {
- super.handle(t, container);
- for (final String name : t.getRequestedNames()) {
- container.add(name);
+ for (final String item : t.getRequestedItems()) {
+ String[] elem = item.split("@", 2);
+ Integer id = null;
+ String name = null;
+ String version = null;
+ try {
+ id = Integer.parseInt(elem[0]);
+ } catch (NumberFormatException e) {
+ name = elem[0];
+ }
+ if (elem.length > 1) {
+ version = elem[1];
+ }
+
+ if (id != null) {
+ container.add(id, version);
+ } else {
+ container.add(name);
+ }
}
}
}
diff --git a/src/main/java/caosdb/server/scripting/ServerSideScriptingCaller.java b/src/main/java/caosdb/server/scripting/ServerSideScriptingCaller.java
index fa51d5ff49c9693d2216fd5dc168873f850e6e25..faeb96e02738395647abb75fca3eaafe18040ad3 100644
--- a/src/main/java/caosdb/server/scripting/ServerSideScriptingCaller.java
+++ b/src/main/java/caosdb/server/scripting/ServerSideScriptingCaller.java
@@ -166,8 +166,11 @@ public class ServerSideScriptingCaller {
if (f.getPath() == null || f.getPath().isEmpty()) {
throw new CaosDBException("The path must not be null or empty!");
}
- caosdb.server.utils.FileUtils.createSymlink(
- getUploadFilesDir().toPath().resolve(f.getPath()).toFile(), f.getFile());
+ File link = getUploadFilesDir().toPath().resolve(f.getPath()).toFile();
+ if (!link.getParentFile().exists()) {
+ link.getParentFile().mkdirs();
+ }
+ caosdb.server.utils.FileUtils.createSymlink(link, f.getFile());
}
}
diff --git a/src/main/java/caosdb/server/transaction/ChecksumUpdater.java b/src/main/java/caosdb/server/transaction/ChecksumUpdater.java
index 30313478c263a131658005daa39da3b495c85eb2..29603fc5833837dfef4a16e8886cdca995c41b94 100644
--- a/src/main/java/caosdb/server/transaction/ChecksumUpdater.java
+++ b/src/main/java/caosdb/server/transaction/ChecksumUpdater.java
@@ -141,7 +141,7 @@ public class ChecksumUpdater extends WriteTransaction<TransactionContainer> impl
instance.running = false;
return null;
}
- return execute(new RetrieveSparseEntity(id), weakAccess).getEntity();
+ return execute(new RetrieveSparseEntity(id, null), weakAccess).getEntity();
}
} catch (final Exception e) {
e.printStackTrace();
diff --git a/src/main/java/caosdb/server/transaction/Insert.java b/src/main/java/caosdb/server/transaction/Insert.java
index 627ada52655c5e7802e98172d1c32f8280a95fb4..c1d53f3051eb65efd9d658179e514e13863c313b 100644
--- a/src/main/java/caosdb/server/transaction/Insert.java
+++ b/src/main/java/caosdb/server/transaction/Insert.java
@@ -26,6 +26,7 @@ import caosdb.server.database.access.Access;
import caosdb.server.database.backend.transaction.InsertEntity;
import caosdb.server.entity.EntityInterface;
import caosdb.server.entity.FileProperties;
+import caosdb.server.entity.Version;
import caosdb.server.entity.container.InsertContainer;
import caosdb.server.entity.container.TransactionContainer;
import caosdb.server.permissions.EntityACL;
@@ -103,6 +104,10 @@ 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()));
+ }
}
}
diff --git a/src/main/java/caosdb/server/transaction/WriteTransaction.java b/src/main/java/caosdb/server/transaction/WriteTransaction.java
index e67ae0600bc573efbdf67b9b341299fe1fe3ca00..ec37d19d6f5a4663c0af0adda186c282215a302b 100644
--- a/src/main/java/caosdb/server/transaction/WriteTransaction.java
+++ b/src/main/java/caosdb/server/transaction/WriteTransaction.java
@@ -64,4 +64,8 @@ public abstract class WriteTransaction<C extends TransactionContainer> extends T
}
}
}
+
+ public String getSRID() {
+ return getContainer().getRequestId();
+ }
}
diff --git a/src/main/java/caosdb/server/utils/Utils.java b/src/main/java/caosdb/server/utils/Utils.java
index 085be51d0929ce76d10ed5e4e8c32696e0b48476..752d828d0e89e790aa7d42e1358b91d3fb5f3c1b 100644
--- a/src/main/java/caosdb/server/utils/Utils.java
+++ b/src/main/java/caosdb/server/utils/Utils.java
@@ -47,24 +47,6 @@ public class Utils {
/** Secure random number generator, for secret random numbers. */
private static final SecureRandom srand = new SecureRandom();
- /**
- * Check whether obj is non-null and can be parsed to an integer.
- *
- * @param obj The object to check.
- * @return true if obj is not null and obj.toString() can be parsed as an integer
- */
- public static boolean isNonNullInteger(final Object obj) {
- if (obj == null) {
- return false;
- }
- try {
- Integer.parseInt(obj.toString());
- } catch (final NumberFormatException e) {
- return false;
- }
- return true;
- }
-
/**
* Regular expression pattern that checks a mail for RFC822 compliance.
*
diff --git a/src/test/java/caosdb/server/entity/xml/PropertyToElementStrategyTest.java b/src/test/java/caosdb/server/entity/xml/PropertyToElementStrategyTest.java
index 7e0feec8915283170b2964420d3ef1f6a42c0031..0d60ebd70feebe2e8e8810f296908e8b3a74100e 100644
--- a/src/test/java/caosdb/server/entity/xml/PropertyToElementStrategyTest.java
+++ b/src/test/java/caosdb/server/entity/xml/PropertyToElementStrategyTest.java
@@ -89,7 +89,7 @@ public class PropertyToElementStrategyTest {
PropertyToElementStrategy strategy = new PropertyToElementStrategy();
SetFieldStrategy setFieldStrategy = new SetFieldStrategy().addSelection(parse("height"));
EntityInterface property = windowProperty;
- ((ReferenceValue) property.getValue()).setEntity(window);
+ ((ReferenceValue) property.getValue()).setEntity(window, true);
Element element = strategy.toElement(property, setFieldStrategy);
assertEquals("Property", element.getName());
assertEquals("2345", element.getAttributeValue("id"));