diff --git a/CHANGELOG.md b/CHANGELOG.md
index be47de54cd33c917b8997eebaa55c31edfe71543..77982cc0837f905f10274f23f83bd53b6414bbb9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -17,9 +17,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Fixed ###
+* Inheritance of the unit is not working. (GRPC API)
+ [linkahead-server#264](https://gitlab.indiscale.com/caosdb/src/caosdb-server/-/issues/264)
+* Curly brackets in query lead to unexpected server error.
+ [linkahead-server#138](https://gitlab.com/linkahead/linkahead-server/-/issues/138)
* Wrong url returned by FileSystem resource behind proxy.
* `NullPointerException` in GRPC API converters when executing SELECT query on
NULL values.
+* Fix parsing of decimal numbers. Fixes https://gitlab.com/linkahead/linkahead-server/-/issues/239
## [0.10.0] - 2023-06-02 ##
(Florian Spreckelsen)
diff --git a/README_SETUP.md b/README_SETUP.md
index acb3a79ad256fbba6a0d0a69887bb7c7ba7b28b9..e3b6e3bc3e8a69c2ff1e162476819ec76b93dbe9 100644
--- a/README_SETUP.md
+++ b/README_SETUP.md
@@ -163,6 +163,9 @@ sources (if you called `make run` previously).
`$ make test`
+You can run single unit test with
+`mvn test -X -Dtest=TestCQL#testDecimalNumber`
+
## Setup Eclipse
diff --git a/conf/core/jobs.csv b/conf/core/jobs.csv
index 84795bee8657288473188cd9e7a6af81f6295221..3da052ff8529770646669c2f997d830dcb57d649 100644
--- a/conf/core/jobs.csv
+++ b/conf/core/jobs.csv
@@ -1,8 +1,8 @@
#
# This file is a part of the CaosDB Project.
#
-# Copyright (C) 2021 Timm Fitsche <t.fitschen@indiscale.com>
-# Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2021-2023 Timm Fitsche <t.fitschen@indiscale.com>
+# Copyright (C) 2021-2023 IndiScale GmbH <info@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 +22,7 @@
# DOMAIN_ID, ENTITY_ID, TRANSACTION, JOB, JOB_FAILURE_SEVERITY
# general rules
+0,0,INSERT,GenerateEntityId,ERROR
0,0,INSERT,CheckPropValid,ERROR
0,0,INSERT,CheckParValid,ERROR
0,0,INSERT,CheckParOblPropPresent,ERROR
@@ -30,8 +31,7 @@
0,0,UPDATE,CheckParValid,ERROR
0,0,UPDATE,CheckParOblPropPresent,ERROR
0,0,UPDATE,CheckValueParsable,ERROR
-0,0,DELETE,CheckReferenceDependencyExistent,ERROR
-0,0,DELETE,CheckChildDependencyExistent,ERROR
+0,0,DELETE,CheckDependenciesBeforeDeletion,ERROR
# role specific rules
diff --git a/conf/core/server.conf b/conf/core/server.conf
index 5df6c40ca04a9c6f22d03f61c937ab5fbeab565f..1e22c5c7a3aad2d0aa53b098eb4666e25e591f31 100644
--- a/conf/core/server.conf
+++ b/conf/core/server.conf
@@ -69,7 +69,7 @@ MYSQL_USER_NAME=caosdb
# Password for the user
MYSQL_USER_PASSWORD=random1234
# Schema of mysql procedures and tables which is required by this CaosDB instance
-MYSQL_SCHEMA_VERSION=v5.0
+MYSQL_SCHEMA_VERSION=v6.0.0-SNAPSHOT-EXTID
# --------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 05d1aa4b7d8e01b5cd3794b6fabbd01ea81a24ac..4fb8f7ac8f12b06c77f93906f29a950a2c6e083d 100644
--- a/pom.xml
+++ b/pom.xml
@@ -381,9 +381,9 @@
</executions>
</plugin>
<plugin>
- <groupId>com.coveo</groupId>
+ <groupId>com.spotify.fmt</groupId>
<artifactId>fmt-maven-plugin</artifactId>
- <version>2.5.1</version>
+ <version>2.21.1</version>
<configuration>
<skip>
<!-- Set skip to `true` to prevent auto-formatting while coding. -->
diff --git a/src/main/java/org/caosdb/datetime/FragmentDateTime.java b/src/main/java/org/caosdb/datetime/FragmentDateTime.java
index 38c16a988a0103a121767b99078c0ca41c6263d5..78ef7199970ac3aa52a53cae96744cd90fb23c20 100644
--- a/src/main/java/org/caosdb/datetime/FragmentDateTime.java
+++ b/src/main/java/org/caosdb/datetime/FragmentDateTime.java
@@ -21,7 +21,9 @@
* ** end header
*/
-/** @review Daniel Hornung 2022-03-04 */
+/**
+ * @review Daniel Hornung 2022-03-04
+ */
package org.caosdb.datetime;
import java.util.Objects;
diff --git a/src/main/java/org/caosdb/datetime/UTCDateTime.java b/src/main/java/org/caosdb/datetime/UTCDateTime.java
index 1dd86cc975d4b92066f2cf44fff51493ade5babe..a7719d5a3f30d862be0d7646796a4f2800149b06 100644
--- a/src/main/java/org/caosdb/datetime/UTCDateTime.java
+++ b/src/main/java/org/caosdb/datetime/UTCDateTime.java
@@ -21,7 +21,9 @@
* ** end header
*/
-/** @review Daniel Hornung 2022-03-04 */
+/**
+ * @review Daniel Hornung 2022-03-04
+ */
package org.caosdb.datetime;
import java.util.ArrayList;
diff --git a/src/main/java/org/caosdb/server/CaosDBServer.java b/src/main/java/org/caosdb/server/CaosDBServer.java
index 2a115c5cfa06ed0e3db85847c27fb4c8424eadaf..8c75cf51e9a85685c19c3de271f56b519b81add7 100644
--- a/src/main/java/org/caosdb/server/CaosDBServer.java
+++ b/src/main/java/org/caosdb/server/CaosDBServer.java
@@ -3,8 +3,8 @@
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- * Copyright (C) 2019-2021 IndiScale GmbH <info@indiscale.com>
- * Copyright (C) 2019-2021 Timm Fitschen <t.fitschen@indiscale.com>
+ * Copyright (C) 2019-2021,2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2019-2021,2023 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
@@ -129,6 +129,7 @@ public class CaosDBServer extends Application {
private static boolean NO_TLS = false;
public static final String REQUEST_TIME_LOGGER = "REQUEST_TIME_LOGGER";
public static final String REQUEST_ERRORS_LOGGER = "REQUEST_ERRORS_LOGGER";
+ private static boolean USE_CACHE = true;
private static Scheduler SCHEDULER;
public static String getServerProperty(final String key) {
@@ -153,6 +154,7 @@ public class CaosDBServer extends Application {
parseArguments(args);
initScheduler();
initServerProperties();
+ initCaching();
initTimeZone();
initOneTimeTokens();
initShiro();
@@ -198,6 +200,11 @@ public class CaosDBServer extends Application {
SERVER_PROPERTIES = ServerProperties.initServerProperties();
}
+ public static void initCaching() {
+ USE_CACHE =
+ !Boolean.parseBoolean(CaosDBServer.getServerProperty(ServerProperties.KEY_CACHE_DISABLE));
+ }
+
/**
* Precedence order:
*
@@ -664,7 +671,7 @@ public class CaosDBServer extends Application {
return 0;
}
return -1;
- };
+ }
@Override
public int match(final String formattedString) {
@@ -886,6 +893,10 @@ public class CaosDBServer extends Application {
throws SchedulerException {
SCHEDULER.scheduleJob(job, trigger);
}
+
+ public static boolean useCache() {
+ return USE_CACHE;
+ }
}
class CaosDBComponent extends Component {
diff --git a/src/main/java/org/caosdb/server/accessControl/Pam.java b/src/main/java/org/caosdb/server/accessControl/Pam.java
index 992665c1db3ef42d3770c71e89fa5444f43f9d95..76fde331dc97b51ed82083999e4d49b94176695d 100644
--- a/src/main/java/org/caosdb/server/accessControl/Pam.java
+++ b/src/main/java/org/caosdb/server/accessControl/Pam.java
@@ -145,7 +145,9 @@ public class Pam implements UserSource {
return this.map;
}
- /** @see {@link UserSource#resolveRolesForUsername(String)} */
+ /**
+ * @see {@link UserSource#resolveRolesForUsername(String)}
+ */
@Override
public Set<String> resolveRolesForUsername(final String username) {
final Set<String> resulting_roles = new HashSet<String>();
@@ -266,7 +268,9 @@ public class Pam implements UserSource {
return username != null && isIncorporated(username);
}
- /** @see {@link UserSource#isValid(String, String)}. */
+ /**
+ * @see {@link UserSource#isValid(String, String)}.
+ */
@Override
public boolean isValid(final String username, final String password) {
if (username != null && isIncorporated(username)) {
diff --git a/src/main/java/org/caosdb/server/caching/JCSCacheHelper.java b/src/main/java/org/caosdb/server/caching/JCSCacheHelper.java
index 1613b8be8194425ab14e5e68b9215a0ba92be8d3..f294e4bb029b7e03d2864ae832b3044685536404 100644
--- a/src/main/java/org/caosdb/server/caching/JCSCacheHelper.java
+++ b/src/main/java/org/caosdb/server/caching/JCSCacheHelper.java
@@ -62,8 +62,7 @@ public class JCSCacheHelper implements CacheHelper {
}
public static void init() {
- final boolean disabled =
- Boolean.parseBoolean(CaosDBServer.getServerProperty(ServerProperties.KEY_CACHE_DISABLE));
+ final boolean disabled = !CaosDBServer.useCache();
init(CaosDBServer.getServerProperty(ServerProperties.KEY_CACHE_CONF_LOC), disabled);
}
diff --git a/src/main/java/org/caosdb/server/database/BackendTransaction.java b/src/main/java/org/caosdb/server/database/BackendTransaction.java
index 05ea26c255ae5b2bd1e75df7f3fdc4d94fca5e5a..c014972ac52246e87a1d9e6f575a645125ab4c57 100644
--- a/src/main/java/org/caosdb/server/database/BackendTransaction.java
+++ b/src/main/java/org/caosdb/server/database/BackendTransaction.java
@@ -3,8 +3,8 @@
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- * Copyright (C) 2019-2021 IndiScale GmbH <info@indiscale.com>
- * Copyright (C) 2019-2021 Timm Fitschen <t.fitschen@indiscale.com>
+ * Copyright (C) 2019-2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2019-2023 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
@@ -29,7 +29,6 @@ import org.caosdb.server.database.backend.implementation.MySQL.MySQLDeleteRole;
import org.caosdb.server.database.backend.implementation.MySQL.MySQLDeleteSparseEntity;
import org.caosdb.server.database.backend.implementation.MySQL.MySQLDeleteUser;
import org.caosdb.server.database.backend.implementation.MySQL.MySQLGetAllNames;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLGetChildren;
import org.caosdb.server.database.backend.implementation.MySQL.MySQLGetDependentEntities;
import org.caosdb.server.database.backend.implementation.MySQL.MySQLGetFileRecordByPath;
import org.caosdb.server.database.backend.implementation.MySQL.MySQLGetIDByName;
@@ -49,6 +48,7 @@ import org.caosdb.server.database.backend.implementation.MySQL.MySQLListUsers;
import org.caosdb.server.database.backend.implementation.MySQL.MySQLLogUserVisit;
import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveAll;
import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveAllUncheckedFiles;
+import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveCurrentMaxId;
import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveDatatypes;
import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveEntityACL;
import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveLogRecord;
@@ -86,7 +86,6 @@ import org.caosdb.server.database.backend.interfaces.FileCheckSize;
import org.caosdb.server.database.backend.interfaces.FileExists;
import org.caosdb.server.database.backend.interfaces.FileWasModifiedAfter;
import org.caosdb.server.database.backend.interfaces.GetAllNamesImpl;
-import org.caosdb.server.database.backend.interfaces.GetChildrenImpl;
import org.caosdb.server.database.backend.interfaces.GetDependentEntitiesImpl;
import org.caosdb.server.database.backend.interfaces.GetFileIteratorImpl;
import org.caosdb.server.database.backend.interfaces.GetFileRecordByPathImpl;
@@ -107,6 +106,7 @@ import org.caosdb.server.database.backend.interfaces.ListUsersImpl;
import org.caosdb.server.database.backend.interfaces.LogUserVisitImpl;
import org.caosdb.server.database.backend.interfaces.RetrieveAllImpl;
import org.caosdb.server.database.backend.interfaces.RetrieveAllUncheckedFilesImpl;
+import org.caosdb.server.database.backend.interfaces.RetrieveCurrentMaxIdImpl;
import org.caosdb.server.database.backend.interfaces.RetrieveDatatypesImpl;
import org.caosdb.server.database.backend.interfaces.RetrieveEntityACLImpl;
import org.caosdb.server.database.backend.interfaces.RetrieveLogRecordImpl;
@@ -133,6 +133,18 @@ import org.caosdb.server.database.misc.TransactionBenchmark;
import org.caosdb.server.utils.UndoHandler;
import org.caosdb.server.utils.Undoable;
+/**
+ * Abstract class for backend transactions.
+ *
+ * <p>This class is the glue between the Transaction layer and the actual implementation of the
+ * communication with the back end.
+ *
+ * <p>This class also acts as a registry which stores which implementation is being used for which
+ * backend transaction interface.
+ *
+ * @see {@link Transaction}
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
public abstract class BackendTransaction implements Undoable {
private final UndoHandler undoHandler = new UndoHandler();
@@ -153,7 +165,7 @@ public abstract class BackendTransaction implements Undoable {
}
/**
- * Intialiaze the adapters to the database backend.
+ * Initialize the adapters to the database backend.
*
* <p>Currently this is hard-coded to the MySQL-Backend but the architecture of this class is
* designed to make it easy in the future to choose other implementations (i.e. other back-ends)
@@ -163,7 +175,6 @@ public abstract class BackendTransaction implements Undoable {
setImpl(GetAllNamesImpl.class, MySQLGetAllNames.class);
setImpl(DeleteEntityPropertiesImpl.class, MySQLDeleteEntityProperties.class);
setImpl(DeleteSparseEntityImpl.class, MySQLDeleteSparseEntity.class);
- setImpl(GetChildrenImpl.class, MySQLGetChildren.class);
setImpl(GetDependentEntitiesImpl.class, MySQLGetDependentEntities.class);
setImpl(GetIDByNameImpl.class, MySQLGetIDByName.class);
setImpl(GetInfoImpl.class, MySQLGetInfo.class);
@@ -213,6 +224,7 @@ public abstract class BackendTransaction implements Undoable {
setImpl(ListUsersImpl.class, MySQLListUsers.class);
setImpl(LogUserVisitImpl.class, MySQLLogUserVisit.class);
setImpl(RetrieveEntityACLImpl.class, MySQLRetrieveEntityACL.class);
+ setImpl(RetrieveCurrentMaxIdImpl.class, MySQLRetrieveCurrentMaxId.class);
}
}
diff --git a/src/main/java/org/caosdb/server/database/DatabaseAccessManager.java b/src/main/java/org/caosdb/server/database/DatabaseAccessManager.java
index f12c78e31bf28799b8c8ead1c9ff311a65bb01ef..478953cbbcd25693dca3df92a3ede6371b4f2212 100644
--- a/src/main/java/org/caosdb/server/database/DatabaseAccessManager.java
+++ b/src/main/java/org/caosdb/server/database/DatabaseAccessManager.java
@@ -60,6 +60,7 @@ class ReadAccessSemaphore extends Semaphore implements Releasable {
private AtomicInteger acquired = new AtomicInteger(0); // how many threads have read access
Semaphore writersBlock =
new Semaphore(1, true); // This semaphore is blocked as long as there are any
+
// unreleased read permits.
public ReadAccessSemaphore() {
diff --git a/src/main/java/org/caosdb/server/database/access/AbstractAccess.java b/src/main/java/org/caosdb/server/database/access/AbstractAccess.java
index 1d30bd3fee7187b9c44378e5b94c1c6d97287f00..574dabedd0db28ded611411ed8848f00be56a293 100644
--- a/src/main/java/org/caosdb/server/database/access/AbstractAccess.java
+++ b/src/main/java/org/caosdb/server/database/access/AbstractAccess.java
@@ -1,9 +1,10 @@
/*
- * ** 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) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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
@@ -17,8 +18,6 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.database.access;
@@ -26,11 +25,18 @@ import java.util.HashMap;
import org.caosdb.server.database.misc.DBHelper;
import org.caosdb.server.database.misc.RollBackHandler;
import org.caosdb.server.transaction.TransactionInterface;
+import org.caosdb.server.utils.UseCacheResourceDelegate;
-public abstract class AbstractAccess<T extends TransactionInterface> implements Access {
+/**
+ * Abstract implementation of an Access.
+ *
+ * @see {@link Access}
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
+public abstract class AbstractAccess<T extends TransactionInterface>
+ extends UseCacheResourceDelegate implements Access {
private HashMap<String, DBHelper> helpers = new HashMap<String, DBHelper>();
- private Boolean useCache = true;
private final T transaction;
private boolean released = false;
@@ -73,22 +79,6 @@ public abstract class AbstractAccess<T extends TransactionInterface> implements
}
}
- @Override
- public void setUseCache(final Boolean useCache) {
- this.useCache = useCache;
- }
- /**
- * Whether the transaction allows to use the query cache or other caches. This is controlled by
- * the "cache" flag.
- *
- * @see {@link NoCache}
- * @return true if caching is encouraged.
- */
- @Override
- public boolean useCache() {
- return this.useCache;
- }
-
@Override
public void commit() throws Exception {
synchronized (this.helpers) {
diff --git a/src/main/java/org/caosdb/server/database/access/Access.java b/src/main/java/org/caosdb/server/database/access/Access.java
index 228e8e004aea7454a287bccd898794c2bb4f1b9c..6b8a521cffd5f0d817f9a9b0a4ecce357fb82d76 100644
--- a/src/main/java/org/caosdb/server/database/access/Access.java
+++ b/src/main/java/org/caosdb/server/database/access/Access.java
@@ -1,9 +1,10 @@
/*
- * ** 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) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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
@@ -17,14 +18,29 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.database.access;
import org.caosdb.server.database.misc.DBHelper;
+import org.caosdb.server.utils.UseCacheResource;
-public interface Access {
+/**
+ * Access Interface.
+ *
+ * <p>The access object is part of a Transactions state and it is the glue between the Transaction
+ * and the actual backend implementation of those transactions. It represents different levels of
+ * access (RO, RW) and provides all the helper objects shared by all the single calls to the backend
+ * (package .../database/backend/implementation/...).
+ *
+ * <p>It is further used to commit or roll-back the owning transaction.
+ *
+ * <p>The DatabaseAccessManager issues the Access to a requesting Transaction.
+ *
+ * @see {@link Transaction}
+ * @see {@link DatabaseAccessManager}
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
+public interface Access extends UseCacheResource {
public abstract void setHelper(String name, DBHelper helper);
@@ -33,8 +49,4 @@ public interface Access {
public abstract void release();
public abstract void commit() throws Exception;
-
- public abstract void setUseCache(Boolean useCache);
-
- public boolean useCache();
}
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseConnectionPool.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseConnectionPool.java
index 997de3141db6fd49ac510fa61150a2d16e7d5416..8234d948eb3af1dd490e6ef1062de98504e3575d 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseConnectionPool.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseConnectionPool.java
@@ -23,7 +23,6 @@
package org.caosdb.server.database.backend.implementation.MySQL;
import com.google.common.base.Objects;
-import java.sql.CallableStatement;
import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
@@ -75,8 +74,12 @@ class DatabaseConnectionPool {
private static ConnectionPool instance = null;
private static synchronized ConnectionPool createConnectionPool()
- throws ClassNotFoundException, InstantiationException, IllegalAccessException, SQLException,
- ConnectionException, CaosDBException {
+ throws ClassNotFoundException,
+ InstantiationException,
+ IllegalAccessException,
+ SQLException,
+ ConnectionException,
+ CaosDBException {
final String url =
"jdbc:mysql://"
@@ -244,20 +247,6 @@ class DatabaseConnectionPool {
System.exit(1);
}
- // set auto_increment on table entities to the maximum entity_id of
- // table transaction_log;
- // Why? MYSQL seems to reset the
- // auto_increment value each time the MySQL server is being
- // restarted to the maximum of ids in the entities table. But if
- // some of the ids had been used yet, we don't want to use them
- // again.
- final CallableStatement prepareCall = con.prepareCall("call initAutoIncrement()");
- try {
- prepareCall.execute();
- } catch (final SQLException e) {
- logger.error("Could inititialize the autoincrement value for the entities table.", e);
- System.exit(1);
- }
} finally {
con.close();
}
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseUtils.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseUtils.java
index f7d364ae6376524ef892de3353d699547417717e..6528627d0e7080452827f8b70b87c34c78ac6c57 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseUtils.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseUtils.java
@@ -152,9 +152,10 @@ public class DatabaseUtils {
public static void parseOverrides(final List<ProtoProperty> properties, final ResultSet rs)
throws SQLException {
while (rs.next()) {
- final int property_id = rs.getInt("property_id");
+ String property_id = rs.getString("property_id");
+ if (rs.wasNull()) property_id = rs.getString("InternalPropertyID");
for (final FlatProperty p : properties) {
- if (p.id == property_id) {
+ if (p.id.equals(property_id)) {
final String name = bytes2UTF8(rs.getBytes("name_override"));
if (name != null) {
p.name = name;
@@ -180,7 +181,10 @@ public class DatabaseUtils {
final List<ProtoProperty> ret = new LinkedList<>();
while (rs.next()) {
ProtoProperty pp = new ProtoProperty();
- pp.id = rs.getInt("PropertyID");
+ pp.id = rs.getString("PropertyID");
+ if (rs.wasNull()) {
+ pp.id = rs.getString("InternalPropertyID");
+ }
pp.value = bytes2UTF8(rs.getBytes("PropertyValue"));
pp.status = bytes2UTF8(rs.getBytes("PropertyStatus"));
pp.idx = rs.getInt("PropertyIndex");
@@ -215,7 +219,7 @@ public class DatabaseUtils {
*/
public static SparseEntity parseEntityResultSet(final ResultSet rs) throws SQLException {
final SparseEntity ret = parseNameRoleACL(rs);
- ret.id = rs.getInt("EntityID");
+ ret.id = rs.getString("EntityID");
ret.description = bytes2UTF8(rs.getBytes("EntityDesc"));
ret.datatype = bytes2UTF8(rs.getBytes("Datatype"));
ret.collection = bytes2UTF8(rs.getBytes("Collection"));
@@ -233,7 +237,7 @@ public class DatabaseUtils {
final LinkedList<VerySparseEntity> ret = new LinkedList<>();
while (rs.next()) {
final VerySparseEntity vsp = new VerySparseEntity();
- vsp.id = rs.getInt("ParentID");
+ vsp.id = rs.getString("ParentID");
vsp.name = bytes2UTF8(rs.getBytes("ParentName"));
vsp.description = bytes2UTF8(rs.getBytes("ParentDescription"));
vsp.role = bytes2UTF8(rs.getBytes("ParentRole"));
@@ -247,7 +251,7 @@ public class DatabaseUtils {
EntityInterface entity, List<ProtoProperty> protos) {
final ArrayList<Property> ret = new ArrayList<Property>();
for (final ProtoProperty pp : protos) {
- if (pp.id.equals(entity.getId().toInteger())) {
+ if (pp.id.equals(entity.getId().toString())) {
if (pp.value != null) {
entity.setValue(new GenericValue(pp.value));
}
@@ -328,8 +332,7 @@ public class DatabaseUtils {
return ((Entry<Integer, String>) x).getKey() - ((Entry<Integer, String>) y).getKey();
});
pp.collValues =
- pp.collValues
- .stream()
+ pp.collValues.stream()
.map((x) -> (Object) ((Entry<Integer, String>) x).getValue())
.collect(Collectors.toList());
}
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteEntityProperties.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteEntityProperties.java
index f8cba7d4c9734c1e6e12b72498ceaa6c57ed1a17..747cf50d8390d943fce5ffbf596debe5659b8df9 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteEntityProperties.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteEntityProperties.java
@@ -1,9 +1,10 @@
/*
- * ** 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) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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
@@ -17,8 +18,6 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.database.backend.implementation.MySQL;
@@ -44,7 +43,7 @@ public class MySQLDeleteEntityProperties extends MySQLTransaction
try {
final PreparedStatement stmt = prepareStatement(STMT_DELETE_ENTITY_PROPERTIES);
- stmt.setInt(1, id.toInteger());
+ stmt.setString(1, id.toString());
stmt.execute();
} catch (final SQLIntegrityConstraintViolationException exc) {
throw new IntegrityException(exc);
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteSparseEntity.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteSparseEntity.java
index 7fe8ac303b53ec26dc947c1e4a84e648d7b6517d..a1ab389b6878c06c5fd965d0952d422f11134c0e 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteSparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteSparseEntity.java
@@ -1,9 +1,10 @@
/*
- * ** 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) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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
@@ -17,8 +18,6 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.database.backend.implementation.MySQL;
@@ -44,7 +43,7 @@ public class MySQLDeleteSparseEntity extends MySQLTransaction implements DeleteS
try {
final PreparedStatement stmt = prepareStatement(STMT_DELETE_SPARSE_ENTITY);
- stmt.setInt(1, id.toInteger());
+ stmt.setString(1, id.toString());
stmt.execute();
} catch (final SQLIntegrityConstraintViolationException exc) {
throw new IntegrityException(exc);
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetChildren.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetChildren.java
deleted file mode 100644
index 3c1cebf1e20a720a5f726e378bb22b1ad61c850a..0000000000000000000000000000000000000000
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetChildren.java
+++ /dev/null
@@ -1,67 +0,0 @@
-/*
- * ** header v3.0
- * This file is a part of the CaosDB Project.
- *
- * Copyright (C) 2018 Research Group Biomedical Physics,
- * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Affero General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Affero General Public License for more details.
- *
- * You should have received a copy of the GNU Affero General Public License
- * along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
- */
-package org.caosdb.server.database.backend.implementation.MySQL;
-
-import java.sql.PreparedStatement;
-import java.sql.ResultSet;
-import java.util.LinkedList;
-import java.util.List;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.GetChildrenImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
-
-public class MySQLGetChildren extends MySQLTransaction implements GetChildrenImpl {
-
- public MySQLGetChildren(final Access access) {
- super(access);
- }
-
- public static final String STMT_GET_CHILDREN =
- "Select child from isa_cache where parent=? and rpath=child";
-
- @Override
- public List<EntityID> execute(final EntityID entity) throws TransactionException {
- try {
- final PreparedStatement stmt = prepareStatement(STMT_GET_CHILDREN);
-
- stmt.setInt(1, entity.toInteger());
-
- ResultSet rs = null;
- try {
- rs = stmt.executeQuery();
- final List<EntityID> ret = new LinkedList<>();
- while (rs.next()) {
- ret.add(new EntityID(rs.getInt(1)));
- }
- return ret;
- } finally {
- if (rs != null && !rs.isClosed()) {
- rs.close();
- }
- }
- } catch (final Exception e) {
- throw new TransactionException(e);
- }
- }
-}
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetDependentEntities.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetDependentEntities.java
index 9384c8a04861a01f1e56236b0ab42433d87990f5..2af80f802ca19eca806856bb653788b50ae5ecf9 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetDependentEntities.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetDependentEntities.java
@@ -1,9 +1,10 @@
/*
- * ** 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) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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
@@ -17,8 +18,6 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.database.backend.implementation.MySQL;
@@ -31,6 +30,15 @@ import org.caosdb.server.database.backend.interfaces.GetDependentEntitiesImpl;
import org.caosdb.server.database.exceptions.TransactionException;
import org.caosdb.server.entity.EntityID;
+/**
+ * Get a list of ids of all entities which require the given entity to exists.
+ *
+ * <p>That is the list of all direct child entities (by is-a relation), referenced entities (i.e.
+ * the given entity is a property's value), all properties which have this entity as their data type
+ * and all implemented properties which use this entity as their abtract property.
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
public class MySQLGetDependentEntities extends MySQLTransaction
implements GetDependentEntitiesImpl {
@@ -45,13 +53,13 @@ public class MySQLGetDependentEntities extends MySQLTransaction
try {
final PreparedStatement stmt = prepareStatement(STMT_GET_DEPENDENT_ENTITIES);
- stmt.setInt(1, entity.toInteger());
+ stmt.setString(1, entity.toString());
final ResultSet rs = stmt.executeQuery();
try {
final List<EntityID> ret = new LinkedList<>();
while (rs.next()) {
- ret.add(new EntityID(rs.getInt(1)));
+ ret.add(new EntityID(rs.getString(1)));
}
return ret;
} finally {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetFileRecordByPath.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetFileRecordByPath.java
index 9b147d289b337f63dd359ce604719d9e00a149be..0dd10ec1bcdc97a095da661cb6cb2e2209da0955 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetFileRecordByPath.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetFileRecordByPath.java
@@ -1,9 +1,10 @@
/*
- * ** 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) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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
@@ -17,8 +18,6 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.database.backend.implementation.MySQL;
@@ -30,6 +29,11 @@ import org.caosdb.server.database.backend.interfaces.GetFileRecordByPathImpl;
import org.caosdb.server.database.exceptions.TransactionException;
import org.caosdb.server.database.proto.SparseEntity;
+/**
+ * Retrieve the entity id of a file with the given path (or null).
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
public class MySQLGetFileRecordByPath extends MySQLTransaction implements GetFileRecordByPathImpl {
public MySQLGetFileRecordByPath(final Access access) {
@@ -37,7 +41,7 @@ public class MySQLGetFileRecordByPath extends MySQLTransaction implements GetFil
}
public static final String STMT_GET_ID_BY_PATH =
- "SELECT file_id, size, hex(hash) AS file_hash, checked_timestamp FROM files WHERE path=?";
+ "SELECT (Select id from entity_ids WHERE internal_id = files.file_id) as entity_id, size, hex(hash) AS file_hash, checked_timestamp FROM files WHERE path=?";
@Override
public SparseEntity execute(final String path) throws TransactionException {
@@ -49,7 +53,7 @@ public class MySQLGetFileRecordByPath extends MySQLTransaction implements GetFil
try {
if (rs.next()) {
final SparseEntity ret = new SparseEntity();
- ret.id = rs.getInt("file_id");
+ ret.id = rs.getString("entity_id");
ret.fileHash = rs.getString("file_hash");
ret.fileSize = rs.getLong("size");
ret.fileChecked = rs.getLong("checked_timestamp");
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetIDByName.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetIDByName.java
index c2e28cd39929f71e874fb4a69c38261ed290b18a..5d3e3a7d707c0d7d451d0229426a959fc827e8ef 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetIDByName.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetIDByName.java
@@ -1,9 +1,10 @@
/*
- * ** 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) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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
@@ -17,13 +18,12 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
+import java.sql.Types;
import java.util.LinkedList;
import java.util.List;
import org.caosdb.server.database.access.Access;
@@ -31,6 +31,11 @@ import org.caosdb.server.database.backend.interfaces.GetIDByNameImpl;
import org.caosdb.server.database.exceptions.TransactionException;
import org.caosdb.server.entity.EntityID;
+/**
+ * Retrieve the entity id of an entity with the given name (or null).
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
public class MySQLGetIDByName extends MySQLTransaction implements GetIDByNameImpl {
public MySQLGetIDByName(final Access access) {
@@ -42,34 +47,29 @@ public class MySQLGetIDByName extends MySQLTransaction implements GetIDByNameImp
* Therefore {@link #STMT_AND_ROLE}, {@link #STMT_NOT_ROLE}, and {@link #STMT_LIMIT} can as
* additional conditions.
*/
- public static final String STMT_GET_ID_BY_NAME =
- "Select n.entity_id AS id "
- + "FROM name_data AS n JOIN entities AS e "
- + "ON (n.domain_id=0 AND n.property_id=20 AND e.id = n.entity_id)"
- + "WHERE n.value=?";
-
- public static final String STMT_AND_ROLE = " AND e.role=?";
- public static final String STMT_NOT_ROLE = " AND e.role!='ROLE'";
- public static final String STMT_LIMIT = " LIMIT ";
+ public static final String STMT_GET_ID_BY_NAME = "call getIdByName(?, ?, ?)";
@Override
public List<EntityID> execute(final String name, final String role, final String limit)
throws TransactionException {
try {
- final String stmtStr =
- STMT_GET_ID_BY_NAME
- + (role != null ? STMT_AND_ROLE : STMT_NOT_ROLE)
- + (limit != null ? STMT_LIMIT + limit : "");
- final PreparedStatement stmt = prepareStatement(stmtStr);
+ final PreparedStatement stmt = prepareStatement(STMT_GET_ID_BY_NAME);
stmt.setString(1, name);
if (role != null) {
stmt.setString(2, role);
+ } else {
+ stmt.setNull(2, Types.VARCHAR);
+ }
+ if (limit != null) {
+ stmt.setString(3, limit);
+ } else {
+ stmt.setNull(3, Types.VARCHAR);
}
try (ResultSet rs = stmt.executeQuery()) {
final List<EntityID> ret = new LinkedList<>();
while (rs.next()) {
- ret.add(new EntityID(rs.getInt("id")));
+ ret.add(new EntityID(rs.getString("id")));
}
return ret;
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetUpdateableChecksums.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetUpdateableChecksums.java
index 28c55032e0ae6b6c2fcfb779339a72b96c703ba0..81c0dfd6d489a104183e052aba6156372a96f8e9 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetUpdateableChecksums.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetUpdateableChecksums.java
@@ -1,9 +1,10 @@
/*
- * ** 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) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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
@@ -17,8 +18,6 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.database.backend.implementation.MySQL;
@@ -30,11 +29,17 @@ import org.caosdb.server.database.backend.interfaces.GetUpdateableChecksumsImpl;
import org.caosdb.server.database.exceptions.TransactionException;
import org.caosdb.server.entity.EntityID;
+/**
+ * Retrieve the entity ids of all files which have a checksum which should be updated (because the
+ * checksum is NULL, currently).
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
public class MySQLGetUpdateableChecksums extends MySQLTransaction
implements GetUpdateableChecksumsImpl {
private final String GET_UPDATEABLE_CHECKSUMS =
- "SELECT file_id FROM files WHERE hash IS NULL LIMIT 1";
+ "SELECT (SELECT id FROM entity_ids WHERE internal_id = files.file_id) AS entity_id FROM files WHERE hash IS NULL LIMIT 1";
public MySQLGetUpdateableChecksums(final Access access) {
super(access);
@@ -46,7 +51,7 @@ public class MySQLGetUpdateableChecksums extends MySQLTransaction
final PreparedStatement stmt = prepareStatement(this.GET_UPDATEABLE_CHECKSUMS);
final ResultSet rs = stmt.executeQuery();
if (rs.next()) {
- return new EntityID(rs.getInt(1));
+ return new EntityID(rs.getString(1));
} else {
return null;
}
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertEntityDatatype.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertEntityDatatype.java
index c4cb7cf98e5da51f98d71b4c5f6fc91e6961892e..4260ae03e76eec7fab1e33957a00dedc2ef77e17 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertEntityDatatype.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertEntityDatatype.java
@@ -1,3 +1,22 @@
+/*
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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 org.caosdb.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
@@ -8,6 +27,15 @@ import org.caosdb.server.database.exceptions.IntegrityException;
import org.caosdb.server.database.exceptions.TransactionException;
import org.caosdb.server.database.proto.SparseEntity;
+/**
+ * Insert an entity's (meaning: an abstract property's) data type.
+ *
+ * <p>This inserts the abstract property's data type as opposed to the (overridden data type which
+ * is being inserted/updated via InsertEntityPropertiesImpl.
+ *
+ * @see {@link InsertEntityPropertiesImpl}
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
public class MySQLInsertEntityDatatype extends MySQLTransaction
implements InsertEntityDatatypeImpl {
@@ -19,18 +47,13 @@ public class MySQLInsertEntityDatatype extends MySQLTransaction
* Inserts atomic data types of properties into the data_type table. Has two parameters, the
* property_id and the data type name.
*/
- public static final String STMT_INSERT_ENTITY_DATATYPE =
- "INSERT INTO data_type (domain_id, entity_id, property_id, datatype) "
- + "SELECT 0, 0, ?, "
- + "( SELECT entity_id FROM name_data WHERE domain_id = 0 AND property_id = 20 AND value = ? LIMIT 1);";
+ public static final String STMT_INSERT_ENTITY_DATATYPE = "call insertEntityDataType(?, ?)";
/**
* Inserts collection data types of properties into the data_type table. Has two parameters, the
* property_id and the type of collection (e.g. 'LIST').
*/
- public static final String STMT_INSERT_ENTITY_COLLECTION =
- "INSERT INTO collection_type (domain_id, entity_id, property_id, collection) "
- + "SELECT 0, 0, ?, ?;";
+ public static final String STMT_INSERT_ENTITY_COLLECTION = "call insertEntityCollection(?, ?)";
@Override
public void execute(final SparseEntity entity) {
@@ -38,7 +61,7 @@ public class MySQLInsertEntityDatatype extends MySQLTransaction
final PreparedStatement insertEntityDatatypeStmt =
prepareStatement(STMT_INSERT_ENTITY_DATATYPE);
- insertEntityDatatypeStmt.setInt(1, entity.id);
+ insertEntityDatatypeStmt.setString(1, entity.id);
insertEntityDatatypeStmt.setString(2, entity.datatype);
insertEntityDatatypeStmt.execute();
@@ -47,7 +70,7 @@ public class MySQLInsertEntityDatatype extends MySQLTransaction
final PreparedStatement insertEntityCollectionStmt =
prepareStatement(STMT_INSERT_ENTITY_COLLECTION);
- insertEntityCollectionStmt.setInt(1, entity.id);
+ insertEntityCollectionStmt.setString(1, entity.id);
insertEntityCollectionStmt.setString(2, entity.collection);
insertEntityCollectionStmt.execute();
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertEntityProperties.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertEntityProperties.java
index becb56a2397fffa323f005507463a586bdecc0cf..cef624dce3a022043a2f86e56acd6ca589d493d1 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertEntityProperties.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertEntityProperties.java
@@ -1,9 +1,10 @@
/*
- * ** 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) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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
@@ -17,8 +18,6 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.database.backend.implementation.MySQL;
@@ -48,6 +47,17 @@ import org.caosdb.server.entity.EntityID;
import org.caosdb.server.entity.EntityInterface;
import org.caosdb.server.entity.wrapper.Property;
+/**
+ * Insert the entity's properties.
+ *
+ * <p>This implementation transforms a deep tree of properties into a flat representation. This
+ * transformation is a MySQL-backend implementation detail and should not be leaked to the clients.
+ *
+ * <p>The reverse transformation happens in MySQLRetrieveProperties.
+ *
+ * @see {@link MySQLRetrieveProperties}
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
public class MySQLInsertEntityProperties extends MySQLTransaction
implements InsertEntityPropertiesImpl {
@@ -89,9 +99,9 @@ public class MySQLInsertEntityProperties extends MySQLTransaction
try {
final PreparedStatement stmt = prepareStatement(STMT_INSERT_ENTITY_PROPERTY);
- stmt.setInt(1, domain.toInteger());
- stmt.setInt(2, entity.toInteger());
- stmt.setInt(3, fp.id);
+ stmt.setString(1, domain.toString());
+ stmt.setString(2, entity.toString());
+ stmt.setString(3, fp.id);
stmt.setString(4, table.toString());
stmt.setString(5, fp.value);
@@ -124,7 +134,7 @@ public class MySQLInsertEntityProperties extends MySQLTransaction
final FlatProperty fp = new FlatProperty();
Table table = Table.null_data;
Long unit_sig = null;
- fp.id = property.getId().toInteger();
+ fp.id = property.getId().toString();
fp.idx = property.getPIdx();
fp.status = property.getStatementStatus().name();
@@ -140,7 +150,7 @@ public class MySQLInsertEntityProperties extends MySQLTransaction
fp.value = fp.id.toString();
// id is to be the replacement id (an internally used/private id)
- fp.id = ((ReferenceValue) property.getValue()).getId().toInteger();
+ fp.id = ((ReferenceValue) property.getValue()).getId().toString();
table = Table.reference_data;
} else {
@@ -215,7 +225,7 @@ public class MySQLInsertEntityProperties extends MySQLTransaction
}
}
- public static final String STMT_REGISTER_SUBDOMAIN = "call registerSubdomain(?)";
+ public static final String STMT_REGISTER_SUBDOMAIN = "call registerReplacementIds(?)";
public Deque<EntityID> registerReplacementId(final int domainCount)
throws SQLException, ConnectionException {
@@ -224,7 +234,7 @@ public class MySQLInsertEntityProperties extends MySQLTransaction
try (final ResultSet rs = stmt.executeQuery()) {
final Deque<EntityID> ret = new ArrayDeque<>();
while (rs.next()) {
- ret.add(new EntityID(rs.getInt(1)));
+ ret.add(new EntityID(rs.getString(1)));
}
return ret;
}
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertParents.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertParents.java
index 61a5e8c48cdc85098e1b0a2f5531c358d6c6058d..0e44c687b05d4184d81f05eeb8640a15b1e88662 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertParents.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertParents.java
@@ -40,8 +40,8 @@ public class MySQLInsertParents extends MySQLTransaction implements InsertParent
public void execute(final EntityID entity, final EntityID parent) throws TransactionException {
try {
final PreparedStatement stmt = prepareStatement(STMT_INSERT_ISA);
- stmt.setInt(1, entity.toInteger());
- stmt.setInt(2, parent.toInteger());
+ stmt.setString(1, entity.toString());
+ stmt.setString(2, parent.toString());
stmt.execute();
} catch (final Exception e) {
throw new TransactionException(e);
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertSparseEntity.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertSparseEntity.java
index 27227926156fc9b35ab75473e1efa2cce55f152e..fa70a1453b8dd2f2c761cf3e4e658cb77c5a445f 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertSparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertSparseEntity.java
@@ -1,9 +1,10 @@
/*
- * ** 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) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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
@@ -17,8 +18,6 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.database.backend.implementation.MySQL;
@@ -38,9 +37,8 @@ public class MySQLInsertSparseEntity extends MySQLTransaction implements InsertS
super(access);
}
- public static final String STMT_INSERT_SPARSE_ENTITY = "call insertEntity(?,?,?,?)";
- public static final String STMT_INSERT_FILE_PROPERTIES =
- "INSERT INTO files (file_id, hash, size, path) VALUES (?, unhex(?), ?, ?);";
+ public static final String STMT_INSERT_SPARSE_ENTITY = "call insertEntity(?,?,?,?,?)";
+ public static final String STMT_INSERT_FILE_PROPERTIES = "call setFileProperties(?,?,?,?)";
@Override
public void execute(final SparseEntity entity) {
@@ -48,29 +46,29 @@ public class MySQLInsertSparseEntity extends MySQLTransaction implements InsertS
final PreparedStatement insertEntityStmt = prepareStatement(STMT_INSERT_SPARSE_ENTITY);
final PreparedStatement insertFilePropsStmt = prepareStatement(STMT_INSERT_FILE_PROPERTIES);
- insertEntityStmt.setString(1, entity.name);
- insertEntityStmt.setString(2, entity.description);
- insertEntityStmt.setString(3, entity.role);
- insertEntityStmt.setString(4, entity.acl);
+ insertEntityStmt.setString(1, entity.id);
+ insertEntityStmt.setString(2, entity.name);
+ insertEntityStmt.setString(3, entity.description);
+ insertEntityStmt.setString(4, entity.role);
+ insertEntityStmt.setString(5, entity.acl);
try (final ResultSet rs = insertEntityStmt.executeQuery()) {
if (rs.next()) {
- entity.id = rs.getInt("EntityID");
entity.versionId = DatabaseUtils.bytes2UTF8(rs.getBytes("Version"));
} else {
- throw new TransactionException("Didn't get new EntityID back.");
+ throw new TransactionException("Didn't get the version id back.");
}
}
if (entity.filePath != null) {
- insertFilePropsStmt.setInt(1, entity.id);
+ insertFilePropsStmt.setString(1, entity.id);
+ insertFilePropsStmt.setString(2, entity.filePath);
+ insertFilePropsStmt.setLong(3, entity.fileSize);
if (entity.fileHash != null) {
- insertFilePropsStmt.setString(2, entity.fileHash);
+ insertFilePropsStmt.setString(4, entity.fileHash);
} else {
- insertFilePropsStmt.setNull(2, Types.VARCHAR);
+ insertFilePropsStmt.setNull(4, Types.VARCHAR);
}
- insertFilePropsStmt.setLong(3, entity.fileSize);
- insertFilePropsStmt.setString(4, entity.filePath);
insertFilePropsStmt.execute();
}
} catch (final SQLIntegrityConstraintViolationException exc) {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertTransactionHistory.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertTransactionHistory.java
index 0832790a0b56446570fbd7b9c3a4383390c443a7..155cb2d0b8c8db4948b4a2970785eecb636dcf9b 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertTransactionHistory.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertTransactionHistory.java
@@ -56,7 +56,7 @@ public class MySQLInsertTransactionHistory extends MySQLTransaction
logStmt.setString(3, user);
logStmt.setLong(4, seconds);
logStmt.setInt(5, nanos);
- logStmt.setInt(6, entity.toInteger());
+ logStmt.setString(6, entity.toString());
logStmt.execute();
} catch (final Exception e) {
throw new TransactionException(e);
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLIsSubType.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLIsSubType.java
index f6c2daf8d4a0bf4defcaa550cf715032d57cd9cd..0d469a79482069d1f19de3931433e90faf5c667a 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLIsSubType.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLIsSubType.java
@@ -43,8 +43,8 @@ public class MySQLIsSubType extends MySQLTransaction implements IsSubTypeImpl {
try {
final PreparedStatement isSubtypeStmt = prepareStatement(STMT_IS_SUBTYPE);
- isSubtypeStmt.setInt(1, child.toInteger());
- isSubtypeStmt.setInt(2, parent.toInteger());
+ isSubtypeStmt.setString(1, child.toString());
+ isSubtypeStmt.setString(2, parent.toString());
final ResultSet rs = isSubtypeStmt.executeQuery();
try {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLListUsers.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLListUsers.java
index 83ebffe679e6625da720fd2933a5d8defb7264c3..3b68c45d0ff60473ae837f3c9ebc17ae82e68c2d 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLListUsers.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLListUsers.java
@@ -53,8 +53,8 @@ public class MySQLListUsers extends MySQLTransaction implements ListUsersImpl {
user.name = rs.getString("name");
user.realm = rs.getString("realm");
user.email = rs.getString("email");
- user.entity = rs.getInt("entity");
- if (user.entity == 0) {
+ user.entity = rs.getString("entity");
+ if (user.entity.isBlank() || user.entity.equals("0")) {
user.entity = null;
}
user.status = UserStatus.valueOf(rs.getString("status"));
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLLogUserVisit.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLLogUserVisit.java
index 23050da87e324026be1eefa02690959d0a0590cc..d3b9167e13fb92df3b69e9418f9d3c0d61458233 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLLogUserVisit.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLLogUserVisit.java
@@ -36,6 +36,7 @@ public class MySQLLogUserVisit extends MySQLTransaction implements LogUserVisitI
public static final String LOG_USER_VISIT =
"SELECT status FROM user_info WHERE realm = ? AND name = ?";
+
// TODO Replace by "UPDATE user_info SET last_seen = ?";
/** Return true if this is not the first visit of this user. */
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAll.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAll.java
index 9a2ea81629853e3baf9de7757e1abe6c8f01fe28..55b8f194ea0be90b5a77fa0c50930c836c48b3f7 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAll.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAll.java
@@ -75,7 +75,7 @@ public class MySQLRetrieveAll extends MySQLTransaction implements RetrieveAllImp
final String acl = DatabaseUtils.bytes2UTF8(rs.getBytes("ACL"));
if (EntityACL.deserialize(acl)
.isPermitted(SecurityUtils.getSubject(), EntityPermission.RETRIEVE_ENTITY)) {
- ret.add(new EntityID(rs.getInt("ID")));
+ ret.add(new EntityID(rs.getString("ID")));
}
}
return ret;
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAllUncheckedFiles.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAllUncheckedFiles.java
index 09a4e7c2edabea49617224fdb9159116f2cd742b..cfbf2281b920382b30be10f2ff9e8a0ab16728ab 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAllUncheckedFiles.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAllUncheckedFiles.java
@@ -51,7 +51,7 @@ public class MySQLRetrieveAllUncheckedFiles extends MySQLTransaction
final ResultSet rs = stmt.executeQuery();
if (rs.next()) {
final SparseEntity first = new SparseEntity();
- first.id = rs.getInt("file_id");
+ first.id = rs.getString("file_id");
first.filePath = rs.getString("path");
first.fileHash = rs.getString("file_hash");
first.fileSize = rs.getLong("size");
@@ -71,7 +71,7 @@ public class MySQLRetrieveAllUncheckedFiles extends MySQLTransaction
try {
if (rs.next()) {
this.next = new SparseEntity();
- this.next.id = rs.getInt("file_id");
+ this.next.id = rs.getString("file_id");
this.next.filePath = rs.getString("path");
this.next.fileHash = rs.getString("file_hash");
this.next.fileSize = rs.getLong("size");
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveCurrentMaxId.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveCurrentMaxId.java
new file mode 100644
index 0000000000000000000000000000000000000000..9f56324f84cea47081f4f9901f10c772508309d4
--- /dev/null
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveCurrentMaxId.java
@@ -0,0 +1,61 @@
+/*
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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 org.caosdb.server.database.backend.implementation.MySQL;
+
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import org.caosdb.server.database.access.Access;
+import org.caosdb.server.database.backend.interfaces.RetrieveCurrentMaxIdImpl;
+import org.caosdb.server.database.exceptions.TransactionException;
+
+/**
+ * Implements {@link RetrieveCurrentMaxIdImpl} for a MySQL/MariaDB back-end.
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
+public class MySQLRetrieveCurrentMaxId extends MySQLTransaction
+ implements RetrieveCurrentMaxIdImpl {
+
+ public MySQLRetrieveCurrentMaxId(Access access) {
+ super(access);
+ }
+
+ public static final String STMT =
+ "SELECT max(CAST(entity_id AS UNSIGNED INT)) AS max_id FROM transaction_log WHERE transaction='Insert'";
+
+ @Override
+ public Integer execute() {
+ try {
+ try (PreparedStatement stmt = prepareStatement(STMT)) {
+
+ try (ResultSet rs = stmt.executeQuery()) {
+ if (rs.next()) {
+ return rs.getInt("max_id");
+ } else {
+ return 100;
+ }
+ }
+ }
+ } catch (SQLException | ConnectionException e) {
+ throw new TransactionException(e);
+ }
+ }
+}
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveEntityACL.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveEntityACL.java
index 5db8ed7597b1c0d357273848fb7c36febdcfed13..716b7ff65814d1464ccac39ef64af275996e096d 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveEntityACL.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveEntityACL.java
@@ -39,9 +39,9 @@ public class MySQLRetrieveEntityACL extends MySQLTransaction implements Retrieve
"SELECT a.acl FROM entities AS e LEFT JOIN entity_acl AS a ON (a.id = e.acl) WHERE e.id = ? LIMIT 1";
@Override
- public VerySparseEntity execute(Integer id) {
+ public VerySparseEntity execute(String id) {
try (PreparedStatement stmt = prepareStatement(STMT)) {
- stmt.setInt(1, id);
+ stmt.setString(1, id);
ResultSet rs = stmt.executeQuery();
if (rs.next()) {
VerySparseEntity result = new VerySparseEntity();
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveParents.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveParents.java
index 1e2a6621d2fb85a5a5260b1a607670e970f54701..6f48e755537b7cd891d0254c9f2255f537a1d10a 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveParents.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveParents.java
@@ -49,7 +49,7 @@ public class MySQLRetrieveParents extends MySQLTransaction implements RetrievePa
try {
final PreparedStatement prepareStatement = prepareStatement(stmtStr);
- prepareStatement.setInt(1, id.toInteger());
+ prepareStatement.setString(1, id.toString());
if (version == null) {
prepareStatement.setNull(2, Types.VARBINARY);
} else {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveProperties.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveProperties.java
index 100df4ce72ebae75d3022866b345bacc9752ad91..97fe4dc1b2453aac7e501db796da23ae25f2e317 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveProperties.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveProperties.java
@@ -1,9 +1,10 @@
/*
- * ** 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) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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
@@ -17,11 +18,10 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.database.backend.implementation.MySQL;
+import com.mysql.cj.jdbc.exceptions.MysqlDataTruncation;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
@@ -34,6 +34,16 @@ import org.caosdb.server.database.exceptions.TransactionException;
import org.caosdb.server.database.proto.ProtoProperty;
import org.caosdb.server.entity.EntityID;
+/**
+ * Retrieve the entity's properties.
+ *
+ * <p>This implemation transforms the flat structure of properties which is stored in the back end
+ * to a deep tree of properties (if applicable) which is the reverse transformation to that
+ * happening in MySQLInsertEntityProperties.
+ *
+ * @see {@link MySQLInsertEntityProperties}
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
public class MySQLRetrieveProperties extends MySQLTransaction implements RetrievePropertiesImpl {
public MySQLRetrieveProperties(final Access access) {
@@ -50,12 +60,12 @@ public class MySQLRetrieveProperties extends MySQLTransaction implements Retriev
final PreparedStatement prepareStatement = prepareStatement(stmtStr);
final List<ProtoProperty> propsStage1 =
- retrieveFlatPropertiesStage1(0, entity.toInteger(), version, prepareStatement);
+ retrieveFlatPropertiesStage1("0", entity.toString(), version, prepareStatement);
for (final ProtoProperty p : propsStage1) {
p.subProperties =
- retrieveFlatPropertiesStage1(entity.toInteger(), p.id, version, prepareStatement);
+ retrieveFlatPropertiesStage1(entity.toString(), p.id, version, prepareStatement);
}
return DatabaseUtils.transformToDeepPropertyTree(propsStage1, isHead);
} catch (final SQLException e) {
@@ -66,18 +76,11 @@ public class MySQLRetrieveProperties extends MySQLTransaction implements Retriev
}
private List<ProtoProperty> retrieveFlatPropertiesStage1(
- final Integer domain,
- final Integer entity,
- final String version,
- final PreparedStatement stmt)
+ final String domain, final String entity, final String version, final PreparedStatement stmt)
throws SQLException, ConnectionException {
- if (domain != null && domain >= 0) {
- stmt.setInt(1, domain);
- } else {
- stmt.setInt(1, 0);
- }
- stmt.setInt(2, entity);
+ stmt.setString(1, domain);
+ stmt.setString(2, entity);
if (version == null) {
stmt.setNull(3, Types.VARBINARY);
} else {
@@ -94,15 +97,19 @@ public class MySQLRetrieveProperties extends MySQLTransaction implements Retriev
final PreparedStatement retrieveOverrides = prepareStatement(stmtStr2);
- retrieveOverrides(domain, entity, version, retrieveOverrides, properties);
+ if (properties != null & !properties.isEmpty()) {
+ retrieveOverrides(domain, entity, version, retrieveOverrides, properties);
+ }
return properties;
+ } catch (MysqlDataTruncation e) {
+ throw e;
}
}
private void retrieveOverrides(
- final Integer domain,
- final Integer entity,
+ final String domain,
+ final String entity,
final String version,
final PreparedStatement retrieveOverrides,
final List<ProtoProperty> props)
@@ -110,8 +117,8 @@ public class MySQLRetrieveProperties extends MySQLTransaction implements Retriev
ResultSet rs = null;
try {
- retrieveOverrides.setInt(1, domain);
- retrieveOverrides.setInt(2, entity);
+ retrieveOverrides.setString(1, domain);
+ retrieveOverrides.setString(2, entity);
if (version == null) {
retrieveOverrides.setNull(3, Types.VARBINARY);
} else {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveQueryTemplateDefinition.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveQueryTemplateDefinition.java
index 1ab95ae7afc756742475ff2f3c79eddfd632aae9..5e96353af089d469faef2ef5c970fb4de725fab0 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveQueryTemplateDefinition.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveQueryTemplateDefinition.java
@@ -46,7 +46,7 @@ public class MySQLRetrieveQueryTemplateDefinition extends MySQLTransaction
try {
final PreparedStatement stmt = prepareStatement(STMT_RETRIEVE_QUERY_TEMPLATE_DEF);
- stmt.setInt(1, id.toInteger());
+ stmt.setString(1, id.toString());
if (version == null) {
stmt.setNull(2, Types.VARBINARY);
} else {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveSparseEntity.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveSparseEntity.java
index 48cd84b3869262ba7f1d8129fdde2335bed6cd8e..c4a9b6262a7506c38b8dff6215682014203da1c1 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveSparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveSparseEntity.java
@@ -51,7 +51,7 @@ public class MySQLRetrieveSparseEntity extends MySQLTransaction
try {
final PreparedStatement preparedStatement = prepareStatement(stmtStr);
- preparedStatement.setInt(1, id.toInteger());
+ preparedStatement.setString(1, id.toString());
if (version == null) {
preparedStatement.setNull(2, Types.VARBINARY);
} else {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveUser.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveUser.java
index 40f036f1d63753c0be9e6153f741db7d4f9d04ad..b149fae264549f88c21d996f854662401d744beb 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveUser.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveUser.java
@@ -66,7 +66,7 @@ public class MySQLRetrieveUser extends MySQLTransaction implements RetrieveUserI
if (rs.getString("entity") == null) {
ret.entity = null;
} else {
- ret.entity = rs.getInt("entity");
+ ret.entity = rs.getString("entity");
}
}
} finally {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveVersionHistory.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveVersionHistory.java
index 6c4c2629a5effee25128f478bef20f5558a027ba..9493b382ec61f11953f1ba045f5c914b7502f690 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveVersionHistory.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveVersionHistory.java
@@ -53,7 +53,7 @@ public class MySQLRetrieveVersionHistory extends MySQLTransaction
final HashMap<String, VersionHistoryItem> result = new HashMap<>();
try {
final PreparedStatement s = prepareStatement(VERSION_HISTORY_STMT);
- s.setInt(1, entityId.toInteger());
+ s.setString(1, entityId.toString());
final ResultSet rs = s.executeQuery();
while (rs.next()) {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetFileCheckedTimestampImpl.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetFileCheckedTimestampImpl.java
index 18d7d9b7f510f5cb24e1fe844ac4caac86ff4913..b08d05170dbc45168f597181389c18a1454ee103 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetFileCheckedTimestampImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetFileCheckedTimestampImpl.java
@@ -43,7 +43,7 @@ public class MySQLSetFileCheckedTimestampImpl extends MySQLTransaction
try {
final PreparedStatement stmt = getMySQLHelper().prepareStatement(STMT_SET_TS);
stmt.setLong(1, ts);
- stmt.setInt(2, id.toInteger());
+ stmt.setString(2, id.toString());
} catch (final SQLException e) {
throw new TransactionException(e);
} catch (final ConnectionException e) {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetFileChecksum.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetFileChecksum.java
index fb6d4188c835fbc895ed4d5e427bb1b2bbc0bb4c..79c7253103f1ed578c45102ee2bf1a920b2c6049 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetFileChecksum.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetFileChecksum.java
@@ -1,3 +1,22 @@
+/*
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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 org.caosdb.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
@@ -10,7 +29,7 @@ import org.caosdb.server.entity.EntityID;
/**
* Implements {@link SetFileChecksumImpl} for a MySQL/MariaDB back-end.
*
- * @author Timm Fitschen (t.fitschen@indiscale.com)
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
*/
public class MySQLSetFileChecksum extends MySQLTransaction implements SetFileChecksumImpl {
@@ -19,13 +38,13 @@ public class MySQLSetFileChecksum extends MySQLTransaction implements SetFileChe
}
public static final String STMT_SET_CHECKSUM =
- "UPDATE files SET hash = unhex(?) WHERE file_id = ?";
+ "UPDATE files SET hash = unhex(?) WHERE EXISTS (SELECT 1 FROM entity_ids AS eids WHERE eids.id = ? AND eids.internal_id = files.file_id)";
@Override
public void execute(final EntityID id, final String checksum) {
try {
final PreparedStatement stmt = prepareStatement(STMT_SET_CHECKSUM);
- stmt.setInt(2, id.toInteger());
+ stmt.setString(2, id.toString());
stmt.setString(1, checksum);
stmt.execute();
} catch (SQLException | ConnectionException e) {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetQueryTemplateDefinition.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetQueryTemplateDefinition.java
index f3ded949383c7d250d4ad58e6ae964aa9f96324c..70293edb974c2f12ba78caefc8474a768774e9d2 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetQueryTemplateDefinition.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetQueryTemplateDefinition.java
@@ -1,9 +1,10 @@
/*
- * ** 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) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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
@@ -17,8 +18,6 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.database.backend.implementation.MySQL;
@@ -29,6 +28,11 @@ import org.caosdb.server.database.backend.interfaces.SetQueryTemplateDefinitionI
import org.caosdb.server.database.exceptions.TransactionException;
import org.caosdb.server.entity.EntityID;
+/**
+ * Implements {@link SetQueryTemplateDefinitionImpl} for a MariaDB back-end.
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
public class MySQLSetQueryTemplateDefinition extends MySQLTransaction
implements SetQueryTemplateDefinitionImpl {
@@ -37,13 +41,13 @@ public class MySQLSetQueryTemplateDefinition extends MySQLTransaction
}
public static final String STMT_INSERT_QUERY_TEMPLATE_DEF =
- "INSERT INTO query_template_def (id, definition) VALUES (?,?) ON DUPLICATE KEY UPDATE definition=?;";
+ "INSERT INTO query_template_def (id, definition) VALUES ((SELECT internal_id FROM entity_ids WHERE entity_ids.id = ?),?) ON DUPLICATE KEY UPDATE definition=?;";
@Override
public void insert(final EntityID id, final String definition) {
try {
final PreparedStatement stmt = prepareStatement(STMT_INSERT_QUERY_TEMPLATE_DEF);
- stmt.setInt(1, id.toInteger());
+ stmt.setString(1, id.toString());
stmt.setString(2, definition);
stmt.setString(3, definition);
stmt.execute();
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateSparseEntity.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateSparseEntity.java
index b2d0fb9e3b7615e7e95243a2a7bde2fa99e98ca2..8d2af662f32d2f5a788d6470cf6cd526e15d0976 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateSparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateSparseEntity.java
@@ -47,7 +47,7 @@ public class MySQLUpdateSparseEntity extends MySQLTransaction implements UpdateS
try {
// file properties;
final PreparedStatement updateFilePropsStmt = prepareStatement(STMT_UPDATE_FILE_PROPS);
- updateFilePropsStmt.setInt(1, spe.id);
+ updateFilePropsStmt.setString(1, spe.id);
if (spe.filePath != null) {
updateFilePropsStmt.setString(2, spe.filePath);
updateFilePropsStmt.setLong(3, spe.fileSize);
@@ -65,7 +65,7 @@ public class MySQLUpdateSparseEntity extends MySQLTransaction implements UpdateS
// very sparse entity
final PreparedStatement updateEntityStmt = prepareStatement(STMT_UPDATE_ENTITY);
- updateEntityStmt.setInt(1, spe.id);
+ updateEntityStmt.setString(1, spe.id);
updateEntityStmt.setString(2, spe.name);
updateEntityStmt.setString(3, spe.description);
updateEntityStmt.setString(4, spe.role);
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateUser.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateUser.java
index bd368698956163a8473ead7507aac0ba2b83d552..43f71e386fcad42b4a3e39e14eeedf7cb924a535 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateUser.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateUser.java
@@ -49,7 +49,7 @@ public class MySQLUpdateUser extends MySQLTransaction implements UpdateUserImpl
stmt.setString(3, user.status.toString());
stmt.setString(4, user.email);
if (user.entity != null) {
- stmt.setInt(5, user.entity);
+ stmt.setString(5, user.entity);
} else {
stmt.setNull(5, Types.INTEGER);
}
@@ -57,7 +57,7 @@ public class MySQLUpdateUser extends MySQLTransaction implements UpdateUserImpl
stmt.setString(6, user.status.toString());
stmt.setString(7, user.email);
if (user.entity != null) {
- stmt.setInt(8, user.entity);
+ stmt.setString(8, user.entity);
} else {
stmt.setNull(8, Types.INTEGER);
}
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/Replacement.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/Replacement.java
index 61e431bab60b9973f6aa1f0b824ffc3e3b60744e..8ec47231d7d3644bc4c21a2b2125175a75f4bc97 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/Replacement.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/Replacement.java
@@ -28,6 +28,7 @@ import org.caosdb.server.entity.wrapper.Property;
enum ReplacementStatus implements StatementStatusInterface {
REPLACEMENT
}
+
/**
* A wrapper of {@link Property} objects used by the back-end implementation for the MySQL/MariaDB
* back-end.
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/GetChildrenImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveCurrentMaxIdImpl.java
similarity index 63%
rename from src/main/java/org/caosdb/server/database/backend/interfaces/GetChildrenImpl.java
rename to src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveCurrentMaxIdImpl.java
index 8b0211a0b56bec22e4823058dfa72c355e59d19d..ca711d52c3983b4f71bf41aa5ef63583430866a8 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/GetChildrenImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveCurrentMaxIdImpl.java
@@ -1,9 +1,8 @@
/*
- * ** 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) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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
@@ -17,16 +16,17 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.database.backend.interfaces;
-import java.util.List;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.caosdb.server.database.backend.transaction.RetrieveCurrentMaxId;
-public interface GetChildrenImpl extends BackendTransactionImpl {
+/**
+ * Interface for the backend implementation of {@link RetrieveCurrentMaxId}
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
+public interface RetrieveCurrentMaxIdImpl extends BackendTransactionImpl {
- public abstract List<EntityID> execute(EntityID entity) throws TransactionException;
+ public Integer execute();
}
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveEntityACLImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveEntityACLImpl.java
index 230d4d34103603d5499532a7dc1a941cf82068e7..cc61461996dc46ae5ea4a997bd0938587959cd24 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveEntityACLImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveEntityACLImpl.java
@@ -25,5 +25,5 @@ import org.caosdb.server.database.proto.VerySparseEntity;
public interface RetrieveEntityACLImpl extends BackendTransactionImpl {
- public VerySparseEntity execute(Integer id);
+ public VerySparseEntity execute(String id);
}
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/GetChildren.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveCurrentMaxId.java
similarity index 51%
rename from src/main/java/org/caosdb/server/database/backend/transaction/GetChildren.java
rename to src/main/java/org/caosdb/server/database/backend/transaction/RetrieveCurrentMaxId.java
index d0e2a809547ad2be4621ccab3f79d793dde70006..4dd76d30cd0cf1c63d5eb8ad48054093f064629f 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/GetChildren.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveCurrentMaxId.java
@@ -1,9 +1,8 @@
/*
- * ** 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) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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
@@ -17,33 +16,33 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.database.backend.transaction;
-import java.util.List;
import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.GetChildrenImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
-
-public class GetChildren extends BackendTransaction {
+import org.caosdb.server.database.backend.interfaces.RetrieveCurrentMaxIdImpl;
- private final EntityID entity;
- private List<EntityID> list;
+/**
+ * Retrieve the maximum currently known entity id.
+ *
+ * <p>This is used by the EntityIdRegistry for the legacy ids (i.e. integer ids) to generate
+ * sequential ids which have not been used yet.
+ *
+ * @see {@link EntityIdRegistry}
+ * @see {@link LegacyIds}
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
+public class RetrieveCurrentMaxId extends BackendTransaction {
- public GetChildren(final EntityID entity) {
- this.entity = entity;
- }
+ private Integer maxId;
@Override
- public void execute() throws TransactionException {
- final GetChildrenImpl t = getImplementation(GetChildrenImpl.class);
- this.list = t.execute(this.entity);
+ protected void execute() {
+ RetrieveCurrentMaxIdImpl t = getImplementation(RetrieveCurrentMaxIdImpl.class);
+ this.maxId = t.execute();
}
- public List<EntityID> getList() {
- return this.list;
+ public Integer getCurrentMaxId() {
+ return this.maxId;
}
}
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveEntityACLTransaction.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveEntityACLTransaction.java
index 8ef143b44e292e5b100ff30ca023e91c0adb190e..00f8c51026278d3c3660c798b5b0854aff5900eb 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveEntityACLTransaction.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveEntityACLTransaction.java
@@ -43,7 +43,7 @@ public class RetrieveEntityACLTransaction
@Override
public VerySparseEntity executeNoCache() throws TransactionException {
RetrieveEntityACLImpl t = getImplementation(RetrieveEntityACLImpl.class);
- return t.execute(getKey().toInteger());
+ return t.execute(getKey().toString());
}
@Override
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveFullEntityTransaction.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveFullEntityTransaction.java
index eee73735a07cc2e152e0099bf5d027d1413631b4..92f5aa841aed5f759d433076700a8b1ce13e26dc 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveFullEntityTransaction.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveFullEntityTransaction.java
@@ -160,6 +160,7 @@ public class RetrieveFullEntityTransaction extends BackendTransaction {
}
return false;
}
+
/**
* Return true iff the parents need to be retrieved.
*
diff --git a/src/main/java/org/caosdb/server/database/misc/TransactionBenchmark.java b/src/main/java/org/caosdb/server/database/misc/TransactionBenchmark.java
index 397a1f52201727d17b057dc92567893798b63cf5..6b14bd1d627a4dbe1b2ef131f76917586155a385 100644
--- a/src/main/java/org/caosdb/server/database/misc/TransactionBenchmark.java
+++ b/src/main/java/org/caosdb/server/database/misc/TransactionBenchmark.java
@@ -132,6 +132,7 @@ class RootBenchmark extends TransactionBenchmark implements ServerStat {
private static final long serialVersionUID = -95212746021180579L;
private transient boolean synced = false;
+
/**
* Fetch old data (from before last shutdown) and fill it into this instance.
*
@@ -286,7 +287,8 @@ public abstract class TransactionBenchmark implements Serializable {
protected TransactionBenchmark() {
stackTraceElements = Thread.currentThread().getStackTrace();
- };
+ }
+ ;
public Iterable<SubBenchmark> getSubBenchmarks() {
return this.subBenchmarks.values();
diff --git a/src/main/java/org/caosdb/server/database/proto/FlatProperty.java b/src/main/java/org/caosdb/server/database/proto/FlatProperty.java
index b92d3def38d26f0f5f6cd6a0455d472b8f4f3ccb..b2123ce206ce01acee3ef70b1c22151b94f59bd9 100644
--- a/src/main/java/org/caosdb/server/database/proto/FlatProperty.java
+++ b/src/main/java/org/caosdb/server/database/proto/FlatProperty.java
@@ -27,7 +27,7 @@ import java.io.Serializable;
public class FlatProperty implements Serializable {
private static final long serialVersionUID = 6039288034435124195L;
- public Integer id = null;
+ public String id = null;
public String value = null;
public String status = null;
public Integer idx = null;
diff --git a/src/main/java/org/caosdb/server/database/proto/ProtoUser.java b/src/main/java/org/caosdb/server/database/proto/ProtoUser.java
index 643f4250216c7829c8218113a8842ff139b313ec..8b2d97a85044881d61fa6ea795443ae13f3cabc2 100644
--- a/src/main/java/org/caosdb/server/database/proto/ProtoUser.java
+++ b/src/main/java/org/caosdb/server/database/proto/ProtoUser.java
@@ -36,7 +36,7 @@ public class ProtoUser implements Serializable {
public UserStatus status = null;
public String name = null;
public String email = null;
- public Integer entity = null;
+ public String entity = null;
public String realm = null;
public HashSet<String> roles = null;
}
diff --git a/src/main/java/org/caosdb/server/database/proto/VerySparseEntity.java b/src/main/java/org/caosdb/server/database/proto/VerySparseEntity.java
index 8f32bf52038a00275568688b016b830b19fba5f0..5ceca456abc58d945599cc978987eca783637f95 100644
--- a/src/main/java/org/caosdb/server/database/proto/VerySparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/proto/VerySparseEntity.java
@@ -35,7 +35,7 @@ public class VerySparseEntity implements Serializable {
private static final long serialVersionUID = 7370925076064714740L;
- public Integer id = null;
+ public String id = null;
public String name = null;
public String description = null;
public String role = null;
diff --git a/src/main/java/org/caosdb/server/datatype/AbstractEnumValue.java b/src/main/java/org/caosdb/server/datatype/AbstractEnumValue.java
index be88002543155771d2937e216c64d52931051c25..ffe630baa1e519df2044a487ea3ad0ffc4c4bd34 100644
--- a/src/main/java/org/caosdb/server/datatype/AbstractEnumValue.java
+++ b/src/main/java/org/caosdb/server/datatype/AbstractEnumValue.java
@@ -19,7 +19,9 @@
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-/** @review Daniel Hornung 2022-03-04 */
+/**
+ * @review Daniel Hornung 2022-03-04
+ */
package org.caosdb.server.datatype;
import com.google.common.base.Objects;
diff --git a/src/main/java/org/caosdb/server/datatype/CollectionValue.java b/src/main/java/org/caosdb/server/datatype/CollectionValue.java
index fc94f660490284e560a34d1c407e2d74c51f6358..9fb8c6b3012dd4e9a3fa263aab149a92ce1c7643 100644
--- a/src/main/java/org/caosdb/server/datatype/CollectionValue.java
+++ b/src/main/java/org/caosdb/server/datatype/CollectionValue.java
@@ -21,7 +21,9 @@
* ** end header
*/
-/** @review Daniel Hornung 2022-03-04 */
+/**
+ * @review Daniel Hornung 2022-03-04
+ */
package org.caosdb.server.datatype;
import java.util.ArrayList;
diff --git a/src/main/java/org/caosdb/server/datatype/ReferenceValue.java b/src/main/java/org/caosdb/server/datatype/ReferenceValue.java
index a24e2ddfda7faf333fd7d7f64420d4a6c7fdc290..e07b1b807c3226cb5bc074aeafd4d8c712ce2ec1 100644
--- a/src/main/java/org/caosdb/server/datatype/ReferenceValue.java
+++ b/src/main/java/org/caosdb/server/datatype/ReferenceValue.java
@@ -1,5 +1,4 @@
/*
- * ** header v3.0
* This file is a part of the CaosDB Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
@@ -20,11 +19,11 @@
*
* 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
*/
-/** @review Daniel Hornung 2022-03-04 */
+/**
+ * @review Daniel Hornung 2022-03-04
+ */
package org.caosdb.server.datatype;
import java.util.Objects;
@@ -41,7 +40,13 @@ import org.jdom2.Element;
* <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?
+ * <p>Ways to specify a reference value: {id}@{version} using either the version id (a hex'ed sha256
+ * string) or "HEAD", "HEAD~1", "HEAD~2" and so on. Note: "HEAD" always means the "HEAD"
+ * <i>after</i> the transaction. So, if you are changing the referenced entity in the same
+ * transaction and you want to reference the entity in the version before the change you need to use
+ * "HEAD~1" because that is the old version of the future.
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
*/
public class ReferenceValue implements SingleValue {
private EntityInterface entity = null;
@@ -66,7 +71,7 @@ public class ReferenceValue implements SingleValue {
throw ServerMessages.DATA_TYPE_DOES_NOT_ACCEPT_COLLECTION_VALUES;
} else {
try {
- return new ReferenceValue(Integer.parseInt(reference.toString()));
+ return new ReferenceValue(reference.toString());
} catch (final NumberFormatException e) {
return new ReferenceValue(reference.toString());
}
@@ -81,9 +86,9 @@ public class ReferenceValue implements SingleValue {
public static ReferenceValue parseIdVersion(final String str) {
final String[] split = str.split("@", 2);
if (split.length == 2) {
- return new ReferenceValue(Integer.parseInt(split[0]), split[1]);
+ return new ReferenceValue(split[0], split[1]);
} else {
- return new ReferenceValue(Integer.parseInt(str));
+ return new ReferenceValue(str);
}
}
@@ -150,14 +155,13 @@ public class ReferenceValue implements SingleValue {
/** If the reference is given by name, versioning is not possible (at the moment). */
public ReferenceValue(final String name) {
this.name = name;
+ this.id = new EntityID(name);
}
- public ReferenceValue(final int id, final String name) {
- this(new EntityID(id), name);
- }
-
- public ReferenceValue(final int id) {
- this(new EntityID(id));
+ public ReferenceValue(String name, String version) {
+ this.name = name;
+ this.id = new EntityID(name);
+ this.version = version;
}
public final EntityInterface getEntity() {
diff --git a/src/main/java/org/caosdb/server/entity/Entity.java b/src/main/java/org/caosdb/server/entity/Entity.java
index 614397c50526606176fc50b06e2f07e76cbfb9ff..b27eaa28e5111d783d1d8d3779f36a1938898173 100644
--- a/src/main/java/org/caosdb/server/entity/Entity.java
+++ b/src/main/java/org/caosdb/server/entity/Entity.java
@@ -1,11 +1,10 @@
/*
- * ** 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>
+ * Copyright (C) 2020 - 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020 - 2023 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
@@ -19,8 +18,6 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.entity;
@@ -62,6 +59,17 @@ import org.caosdb.server.utils.TransactionLogMessage;
import org.caosdb.unit.Unit;
import org.jdom2.Element;
+/**
+ * Abstract base class for all the important entity classes.
+ *
+ * <p>This is the central data class of the server. It represents Records, RecordTypes, Properties,
+ * and Files.
+ *
+ * <p>This class holds the messages and other transient information as well as the actual data that
+ * is being retrieved from or written to the back-end during a transaction.
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
public abstract class Entity extends AbstractObservable implements EntityInterface {
public static final String DATATYPE_CHANGED_EVENT = "DatatypeChangedEvent";
@@ -73,7 +81,7 @@ public abstract class Entity extends AbstractObservable implements EntityInterfa
private String name = null;
private String description = null;
private Value value = null;
- private final EntityID domain = new EntityID(0);
+ private final EntityID domain = new EntityID("0");
private final EntityID id = new EntityID();
private AbstractDatatype datatype = null;
private final ParentContainer parents = new ParentContainer(this);
@@ -349,7 +357,7 @@ public abstract class Entity extends AbstractObservable implements EntityInterfa
@Override
public SparseEntity getSparseEntity() {
final SparseEntity ret = new SparseEntity();
- ret.id = getId().toInteger();
+ ret.id = getId().toString();
ret.name = getName();
ret.description = getDescription();
ret.acl = getEntityACL().serialize();
@@ -646,13 +654,7 @@ public abstract class Entity extends AbstractObservable implements EntityInterfa
// Parse ID. Generate error if it isn't an integer.
if (element.getAttribute("id") != null && !element.getAttributeValue("id").equals("")) {
- try {
- setId(new EntityID(Integer.parseInt(element.getAttributeValue("id"))));
- } catch (final NumberFormatException e) {
- addInfo("Id was " + element.getAttributeValue("id") + ".");
- addError(ServerMessages.PARSING_FAILED);
- setEntityStatus(EntityStatus.UNQUALIFIED);
- }
+ this.setId(element.getAttributeValue("id"));
}
// Parse NAME.
@@ -727,6 +729,9 @@ public abstract class Entity extends AbstractObservable implements EntityInterfa
// record.
final Property property = new Property(new WritableEntity(pe, Role.Property));
+
+ // Ignore parents of properties
+ property.getParents().clear();
property.setPIdx(pidx++);
addProperty(property);
} else if (pe.getName().equalsIgnoreCase("Parent")) {
diff --git a/src/main/java/org/caosdb/server/entity/EntityID.java b/src/main/java/org/caosdb/server/entity/EntityID.java
index 6a2d2ca368088e54c2f3c77ae669c6feda07bb4e..9f61127db2969578300fbe2f12091c0f9f258d90 100644
--- a/src/main/java/org/caosdb/server/entity/EntityID.java
+++ b/src/main/java/org/caosdb/server/entity/EntityID.java
@@ -1,3 +1,22 @@
+/*
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2022 - 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2022 - 2023 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 org.caosdb.server.entity;
import java.io.Serializable;
@@ -11,39 +30,37 @@ import java.util.Objects;
* <p>It also allows to link entities together, e.g. an Entity's Property with the corresponding
* abstract Property, even when the abstract Property does not have a valid ID yet (during bulk
* inserts).
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
*/
public class EntityID implements Serializable {
- private static final long serialVersionUID = -9092133023135548179L;
+ private static final long serialVersionUID = -9062285447437546105L;
- public static final EntityID DEFAULT_DOMAIN = new EntityID(0);
- private Integer i = null;
+ public static final EntityID DEFAULT_DOMAIN = new EntityID("0");
+ private String id = null;
private EntityID link = null;
public EntityID() {}
- public EntityID(final Integer id) {
- this.i = id;
+ public EntityID(final String id) {
+ this.id = id;
}
- public void setId(final Integer i) {
- this.i = i;
- }
-
- public Integer toInteger() {
- if (this.link != null) {
- return this.link.toInteger();
- }
- return this.i;
+ public void setId(final String id) {
+ this.id = id;
}
@Override
public String toString() {
- return toInteger().toString();
+ if (this.link != null) {
+ return this.link.toString();
+ }
+ return this.id;
}
boolean hasId() {
- return this.i != null || this.link != null && this.link.hasId();
+ return this.id != null || this.link != null && this.link.hasId();
}
public void link(final EntityInterface entity) {
@@ -57,7 +74,7 @@ public class EntityID implements Serializable {
@Override
public boolean equals(final Object obj) {
if (obj instanceof EntityID) {
- return Objects.equals(((EntityID) obj).toInteger(), this.toInteger());
+ return Objects.equals(((EntityID) obj).toString(), this.toString());
}
return false;
}
@@ -65,16 +82,20 @@ public class EntityID implements Serializable {
@Override
public int hashCode() {
if (this.hasId()) {
- return toInteger();
+ return toString().hashCode();
}
return super.hashCode();
}
public boolean isTemporary() {
- return toInteger() < 0;
+ return toString().startsWith("-");
}
public static boolean isReserved(final EntityID id) {
- return id.toInteger() < 100;
+ try {
+ return id.hasId() && Integer.parseInt(id.toString()) < 100;
+ } catch (NumberFormatException e) {
+ return false;
+ }
}
}
diff --git a/src/main/java/org/caosdb/server/entity/EntityIdRegistry.java b/src/main/java/org/caosdb/server/entity/EntityIdRegistry.java
new file mode 100644
index 0000000000000000000000000000000000000000..e4e1158447decf9f98ece6f4de805919b404a5c5
--- /dev/null
+++ b/src/main/java/org/caosdb/server/entity/EntityIdRegistry.java
@@ -0,0 +1,80 @@
+/*
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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 org.caosdb.server.entity;
+
+import java.lang.reflect.Constructor;
+import java.lang.reflect.InvocationTargetException;
+import org.caosdb.server.database.exceptions.TransactionException;
+import org.caosdb.server.transaction.Transaction;
+
+/**
+ * An abstract layer for managing entity ids.
+ *
+ * <p>That is, checking whether something is a well-formed id, generating well-formed ids and more.
+ *
+ * <p>This class follows a Strategy Pattern. The actual implemenation can be found in one of the
+ * implementations of the {@link EntityIdRegistryStrategy} interface.
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
+public class EntityIdRegistry {
+
+ private EntityIdRegistryStrategy strategy;
+
+ public EntityIdRegistry(Transaction<?> t) {
+ // This is the place where we will inject the new string id behavior in the
+ // future:
+ //
+ // this("org.caosdb.server.entity.StringIds", t);
+ this("org.caosdb.server.entity.LegacyIds", t);
+ }
+
+ public EntityIdRegistry(EntityIdRegistryStrategy strategy) {
+ this.strategy = strategy;
+ }
+
+ /** Return a well-formed, new and unused entity id. */
+ public String generate() {
+ return this.strategy.generate();
+ }
+
+ public EntityIdRegistry(String strategy, Transaction<?> t) {
+ try {
+ @SuppressWarnings("unchecked")
+ Class<? extends EntityIdRegistry> clazz =
+ (Class<? extends EntityIdRegistry>) Class.forName(strategy);
+ Constructor<?> constructor = clazz.getConstructor(Transaction.class);
+ this.strategy = (EntityIdRegistryStrategy) constructor.newInstance(t);
+ } catch (ClassNotFoundException
+ | NoSuchMethodException
+ | SecurityException
+ | InstantiationException
+ | IllegalAccessException
+ | IllegalArgumentException
+ | InvocationTargetException e) {
+ throw new TransactionException(e);
+ }
+ }
+
+ /** Return true if the id is a well-formed id. */
+ public boolean matchIdPattern(String id) {
+ return this.strategy.matchIdPattern(id);
+ }
+}
diff --git a/src/main/java/org/caosdb/server/entity/EntityIdRegistryStrategy.java b/src/main/java/org/caosdb/server/entity/EntityIdRegistryStrategy.java
new file mode 100644
index 0000000000000000000000000000000000000000..e70f4f52d2e402e62d3442bfe4af91652247216b
--- /dev/null
+++ b/src/main/java/org/caosdb/server/entity/EntityIdRegistryStrategy.java
@@ -0,0 +1,44 @@
+/*
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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 org.caosdb.server.entity;
+
+import org.caosdb.server.transaction.Transaction;
+
+/**
+ * Strategy interface for {@link EntityIdRegistry}.
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
+public abstract class EntityIdRegistryStrategy {
+
+ private Transaction<?> transaction;
+
+ public EntityIdRegistryStrategy(Transaction<?> transaction) {
+ this.transaction = transaction;
+ }
+
+ public abstract String generate();
+
+ public Transaction<?> getTransaction() {
+ return transaction;
+ }
+
+ public abstract boolean matchIdPattern(String id);
+}
diff --git a/src/main/java/org/caosdb/server/entity/EntityInterface.java b/src/main/java/org/caosdb/server/entity/EntityInterface.java
index ba77b5c4ac8b5c833d2046dec506655531ff62cb..4a74920e7ac35d9d503de3802fbae10b2a7eaa3f 100644
--- a/src/main/java/org/caosdb/server/entity/EntityInterface.java
+++ b/src/main/java/org/caosdb/server/entity/EntityInterface.java
@@ -194,4 +194,8 @@ public interface EntityInterface
public abstract boolean isReferenceList();
public abstract SerializeFieldStrategy getSerializeFieldStrategy();
+
+ public default void setId(String id) {
+ getId().setId(id);
+ }
}
diff --git a/src/main/java/org/caosdb/server/entity/LegacyIds.java b/src/main/java/org/caosdb/server/entity/LegacyIds.java
new file mode 100644
index 0000000000000000000000000000000000000000..0454129397b90772a505ad5b791a823eabd3ea97
--- /dev/null
+++ b/src/main/java/org/caosdb/server/entity/LegacyIds.java
@@ -0,0 +1,76 @@
+/*
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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 org.caosdb.server.entity;
+
+import org.caosdb.server.database.backend.transaction.RetrieveCurrentMaxId;
+import org.caosdb.server.transaction.Transaction;
+
+/**
+ * Implementation of {@link EntityIdRegistryStrategy} which re-implements the legacy integer-based
+ * entity ids.
+ *
+ * <p>This implementation will generate sequences of entity ids and matches all strings which can be
+ * cast to integer as well-formed entity ids.
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
+public class LegacyIds extends EntityIdRegistryStrategy {
+
+ private boolean isInit;
+ private Integer currentMaxId;
+
+ public LegacyIds(Transaction<?> t) {
+ super(t);
+ this.isInit = false;
+ }
+
+ private void init() {
+ isInit = true;
+ initCurrentMaxId();
+ }
+
+ private void initCurrentMaxId() {
+ this.currentMaxId =
+ Math.max(
+ 101,
+ getTransaction()
+ .execute(new RetrieveCurrentMaxId(), getTransaction().getAccess())
+ .getCurrentMaxId());
+ }
+
+ @Override
+ public String generate() {
+ if (!isInit) {
+ init();
+ }
+ ++currentMaxId;
+ return Integer.toString(++currentMaxId);
+ }
+
+ @Override
+ public boolean matchIdPattern(String id) {
+ try {
+ Integer.parseInt(id);
+ return true;
+ } catch (NumberFormatException e) {
+ return false;
+ }
+ }
+}
diff --git a/src/main/java/org/caosdb/server/entity/MagicTypes.java b/src/main/java/org/caosdb/server/entity/MagicTypes.java
index 39556385235e6b72736bed8dff67a178cfe60aff..6e987af95c0188fa21a50f19d11a493d97bbe8d8 100644
--- a/src/main/java/org/caosdb/server/entity/MagicTypes.java
+++ b/src/main/java/org/caosdb/server/entity/MagicTypes.java
@@ -33,9 +33,9 @@ public enum MagicTypes {
NAME,
DESCRIPTION;
- private static final EntityID UNIT_ID = new EntityID(21);
- private static final EntityID DESCRIPTION_ID = new EntityID(24);
- private static final EntityID NAME_ID = new EntityID(20);
+ private static final EntityID UNIT_ID = new EntityID("21");
+ private static final EntityID DESCRIPTION_ID = new EntityID("24");
+ private static final EntityID NAME_ID = new EntityID("20");
public EntityID getId() {
switch (this) {
@@ -51,12 +51,12 @@ public enum MagicTypes {
}
public static MagicTypes getType(final EntityID id) {
- switch (id.toInteger()) {
- case 21:
+ switch (id.toString()) {
+ case "21":
return UNIT;
- case 20:
+ case "20":
return NAME;
- case 24:
+ case "24":
return DESCRIPTION;
default:
return null;
@@ -82,7 +82,7 @@ public enum MagicTypes {
final RetrieveContainer container =
new RetrieveContainer(null, System.currentTimeMillis(), null, null);
for (final MagicTypes mt : MagicTypes.values()) {
- container.add(mt.getId());
+ container.add(mt.getId(), null);
}
final Retrieve retrieve = new Retrieve(container);
retrieve.execute();
diff --git a/src/main/java/org/caosdb/server/entity/RetrieveEntity.java b/src/main/java/org/caosdb/server/entity/RetrieveEntity.java
index 2d1ca6f2175ca2377b7f1a73f847a48377cc4694..00a120fbf023024eae8acc5788a9260d020a956d 100644
--- a/src/main/java/org/caosdb/server/entity/RetrieveEntity.java
+++ b/src/main/java/org/caosdb/server/entity/RetrieveEntity.java
@@ -47,6 +47,11 @@ public class RetrieveEntity extends Entity {
this.setVersion(new Version(version));
}
+ public RetrieveEntity(final EntityID id, String name, final String version) {
+ this(id, version);
+ this.setName(name);
+ }
+
public RetrieveEntity(final String name, final String version) {
super(name);
this.setVersion(new Version(version));
diff --git a/src/main/java/org/caosdb/server/entity/Role.java b/src/main/java/org/caosdb/server/entity/Role.java
index f86158a99be307867c17f136a26e1097e6e7bc5f..a2a97f92546b2e63bac61ff059eeb6128d8bab6b 100644
--- a/src/main/java/org/caosdb/server/entity/Role.java
+++ b/src/main/java/org/caosdb/server/entity/Role.java
@@ -32,7 +32,6 @@ import org.caosdb.server.entity.xml.ToElementStrategy;
public enum Role {
RecordType,
Record,
- Domain,
File,
Property,
DataType,
diff --git a/src/main/java/org/caosdb/server/entity/StringIds.java b/src/main/java/org/caosdb/server/entity/StringIds.java
new file mode 100644
index 0000000000000000000000000000000000000000..e1f5cb04be995253cd16cdc0a809421122b3dc8e
--- /dev/null
+++ b/src/main/java/org/caosdb/server/entity/StringIds.java
@@ -0,0 +1,51 @@
+/*
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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 org.caosdb.server.entity;
+
+import java.util.UUID;
+import org.caosdb.server.transaction.Transaction;
+
+/**
+ * Example implementation for string ids based on UUID.
+ *
+ * @see {@link EntityIdRegistryStrategy}
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
+public class StringIds extends EntityIdRegistryStrategy {
+
+ public StringIds(Transaction<?> t) {
+ super(t);
+ }
+
+ @Override
+ public String generate() {
+ return UUID.randomUUID().toString();
+ }
+
+ @Override
+ public boolean matchIdPattern(String id) {
+ try {
+ UUID.fromString(id);
+ return true;
+ } catch (IllegalArgumentException e) {
+ return false;
+ }
+ }
+}
diff --git a/src/main/java/org/caosdb/server/entity/container/Container.java b/src/main/java/org/caosdb/server/entity/container/Container.java
index 1618fbed6a1594891ea3ddc615f48869227f2c92..fdbcbf0de68d77c3eef026ef68d559a69f2f0956 100644
--- a/src/main/java/org/caosdb/server/entity/container/Container.java
+++ b/src/main/java/org/caosdb/server/entity/container/Container.java
@@ -36,9 +36,11 @@ public class Container<T extends EntityInterface> extends ArrayList<T> {
* Return the entity with the matching id, if it can be found inside this Container, else null.
*/
public T getEntityById(final EntityID id) {
- for (final T e : this) {
- if (e.hasId() && e.getId().equals(id)) {
- return e;
+ if (id != null) {
+ for (final T e : this) {
+ if (e.hasId() && e.getId().equals(id)) {
+ return e;
+ }
}
}
return null;
diff --git a/src/main/java/org/caosdb/server/entity/container/EntityByIdContainer.java b/src/main/java/org/caosdb/server/entity/container/EntityByIdContainer.java
index a8c3e6a832848903884edda270e003a0c0dd6feb..1e756e3313fc4a816c096351527df7022a79f47b 100644
--- a/src/main/java/org/caosdb/server/entity/container/EntityByIdContainer.java
+++ b/src/main/java/org/caosdb/server/entity/container/EntityByIdContainer.java
@@ -37,7 +37,5 @@ public abstract class EntityByIdContainer extends TransactionContainer {
super(user, timestamp, srid, flags);
}
- public abstract void add(EntityID id);
-
public abstract void add(EntityID id, String version);
}
diff --git a/src/main/java/org/caosdb/server/entity/container/RetrieveContainer.java b/src/main/java/org/caosdb/server/entity/container/RetrieveContainer.java
index bc0da7c1de2bb876551d29ad7daffb50494f9720..99262f56d15d90ba86fb1a9cd8fd76b90c4dbf22 100644
--- a/src/main/java/org/caosdb/server/entity/container/RetrieveContainer.java
+++ b/src/main/java/org/caosdb/server/entity/container/RetrieveContainer.java
@@ -1,9 +1,10 @@
/*
- * ** 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) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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
@@ -17,8 +18,6 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.entity.container;
@@ -27,7 +26,24 @@ import org.apache.shiro.subject.Subject;
import org.caosdb.server.entity.EntityID;
import org.caosdb.server.entity.RetrieveEntity;
-public class RetrieveContainer extends EntityByIdContainer {
+/**
+ * A container of entities which are about to be retrieved.
+ *
+ * <p>A suitable name would also be `ReadOnlyEntitiesContainer` because entities in this container
+ * will only be retrieved, not changed, inserted or deleted.
+ *
+ * <p>Because all entities are expected to be existing, all entities can theoretically be identified
+ * via their (valid) entity id (plus version id, if applicable).
+ *
+ * <p>However, sometimes, entities are being retrieved via the name instead of the id. Then the id
+ * has to be resolved first. This happens during the init stage of the owning transaction.
+ *
+ * <p>The container also holds the flags of the current transaction (e.g. cache=false, ACL=true,
+ * ...).
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
+public class RetrieveContainer extends TransactionContainer {
private static final long serialVersionUID = 4816050921531043503L;
@@ -39,21 +55,11 @@ public class RetrieveContainer extends EntityByIdContainer {
super(user, timestamp, srid, flags);
}
- @Override
- public void add(final EntityID id) {
- add(new RetrieveEntity(id));
- }
-
- public void add(final String name) {
- add(new RetrieveEntity(name));
- }
-
- public void add(final String name, final String version) {
- add(new RetrieveEntity(name, version));
- }
-
- @Override
public void add(final EntityID id, final String version) {
add(new RetrieveEntity(id, version));
}
+
+ public void add(final EntityID id, final String name, final String version) {
+ add(new RetrieveEntity(id, name, version));
+ }
}
diff --git a/src/main/java/org/caosdb/server/entity/container/TransactionContainer.java b/src/main/java/org/caosdb/server/entity/container/TransactionContainer.java
index d396345508a028700db6fd8e973390fd634e54d9..049f54cd1ded0ece71c7082ddc960c4246ef0b28 100644
--- a/src/main/java/org/caosdb/server/entity/container/TransactionContainer.java
+++ b/src/main/java/org/caosdb/server/entity/container/TransactionContainer.java
@@ -1,9 +1,10 @@
/*
- * ** 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) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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
@@ -17,8 +18,6 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.entity.container;
@@ -38,6 +37,12 @@ import org.caosdb.server.query.Query;
import org.caosdb.server.utils.EntityStatus;
import org.jdom2.Element;
+/**
+ * Base class for transaction containers used by classes such as {@link RetrieveContainer} or {@link
+ * WritableContainer}.
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
public class TransactionContainer extends Container<EntityInterface>
implements ToElementable, JobTarget {
@@ -152,9 +157,11 @@ public class TransactionContainer extends Container<EntityInterface>
* @param name
*/
public EntityInterface getEntityByName(final String name) {
- for (final EntityInterface e : this) {
- if (e.hasName() && e.getName().equals(name)) {
- return e;
+ if (name != null) {
+ for (final EntityInterface e : this) {
+ if (e.hasName() && e.getName().equals(name)) {
+ return e;
+ }
}
}
return null;
diff --git a/src/main/java/org/caosdb/server/grpc/AccessControlManagementServiceImpl.java b/src/main/java/org/caosdb/server/grpc/AccessControlManagementServiceImpl.java
index 88429828f27ac843903cfcfc801847c35eedb607..00a433d72c0a00e8e8ef796777bfa016679cbfe6 100644
--- a/src/main/java/org/caosdb/server/grpc/AccessControlManagementServiceImpl.java
+++ b/src/main/java/org/caosdb/server/grpc/AccessControlManagementServiceImpl.java
@@ -129,8 +129,7 @@ public class AccessControlManagementServiceImpl extends AccessControlManagementS
result.setEmailSetting(EmailSetting.newBuilder().setEmail(user.email));
}
if (user.entity != null) {
- result.setEntitySetting(
- EntitySetting.newBuilder().setEntityId(Integer.toString(user.entity)));
+ result.setEntitySetting(EntitySetting.newBuilder().setEntityId(user.entity));
}
if (user.roles != null && !user.roles.isEmpty()) {
result.addAllRoles(user.roles);
diff --git a/src/main/java/org/caosdb/server/grpc/AuthInterceptor.java b/src/main/java/org/caosdb/server/grpc/AuthInterceptor.java
index ce8a62210d3c8e849397600fc112cd3103f15df4..49f2facefa845a6deeed5f07bf4fde364891fcb6 100644
--- a/src/main/java/org/caosdb/server/grpc/AuthInterceptor.java
+++ b/src/main/java/org/caosdb/server/grpc/AuthInterceptor.java
@@ -87,6 +87,7 @@ public class AuthInterceptor implements ServerInterceptor {
metadata.put(CookieSetter.SET_COOKIE, CookieSetter.EXPIRED_SESSION_COOKIE);
return metadata;
}
+
/**
* A no-op listener. This class is used for failed authentications. We couldn't return a null
* instead because the documentation of the {@link ServerInterceptor} explicitely forbids it.
@@ -281,7 +282,7 @@ final class CookieSetter<ReqT, RespT>
public void sendHeaders(Metadata headers) {
setSessionCookies(headers);
super.sendHeaders(headers);
- };
+ }
private void setSessionCookies(Metadata headers) {
// if authenticated as a normal user: generate and set session cookie.
diff --git a/src/main/java/org/caosdb/server/grpc/EntityTransactionServiceImpl.java b/src/main/java/org/caosdb/server/grpc/EntityTransactionServiceImpl.java
index 030b52544fec858ef3c62c531e9627baf5500551..3386676855dcaaae154a00700b83dc5e2852edff 100644
--- a/src/main/java/org/caosdb/server/grpc/EntityTransactionServiceImpl.java
+++ b/src/main/java/org/caosdb/server/grpc/EntityTransactionServiceImpl.java
@@ -1,8 +1,8 @@
/*
* This file is a part of the CaosDB Project.
*
- * Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
- * Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
+ * Copyright (C) 2021,2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2021,2023 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
@@ -18,7 +18,6 @@
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*
*/
-
package org.caosdb.server.grpc;
import io.grpc.stub.StreamObserver;
@@ -47,11 +46,11 @@ import org.caosdb.api.entity.v1.RetrieveResponse;
import org.caosdb.api.entity.v1.SelectQueryResult;
import org.caosdb.api.entity.v1.TransactionRequest;
import org.caosdb.api.entity.v1.TransactionRequest.WrappedRequestsCase;
-import org.caosdb.api.entity.v1.TransactionResponse;
import org.caosdb.api.entity.v1.UpdateRequest;
import org.caosdb.api.entity.v1.UpdateResponse;
import org.caosdb.server.CaosDBException;
import org.caosdb.server.entity.DeleteEntity;
+import org.caosdb.server.entity.EntityID;
import org.caosdb.server.entity.EntityInterface;
import org.caosdb.server.entity.FileProperties;
import org.caosdb.server.entity.InsertEntity;
@@ -68,6 +67,11 @@ import org.caosdb.server.transaction.UpdateACL;
import org.caosdb.server.transaction.WriteTransaction;
import org.caosdb.server.utils.ServerMessages;
+/**
+ * Main entry point for the entity transaction service of the servers GRPC API.
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBase {
// TODO(tf) let the clients define the time zone of the date time values which are being returned.
@@ -135,15 +139,11 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
} else { // or ID retrieves.
final String id = sub_request.getRetrieveRequest().getId();
if (!id.isBlank()) {
- try {
- final RetrieveEntity entity = new RetrieveEntity(grpcToCaosdb.getId(id));
- if (isFileDownload) {
- entity.setFlag("download_files", "true");
- }
- container.add(entity);
- } catch (final NumberFormatException e) {
- // We handle this after the retrieval
+ final RetrieveEntity entity = new RetrieveEntity(new EntityID(id));
+ if (isFileDownload) {
+ entity.setFlag("download_files", "true");
}
+ container.add(entity);
}
}
}
@@ -193,32 +193,9 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
}
}
- // Add those entities which have not been retrieved because they have a string id
- for (final TransactionRequest sub_request : request.getRequestsList()) {
- final String id = sub_request.getRetrieveRequest().getId();
- if (!id.isBlank()) {
- try {
- grpcToCaosdb.getId(id);
- } catch (final NumberFormatException e) {
- // ID wasn't an integer - the server doesn't support string ids yet, so that entity
- // cannot exist.
- builder.addResponses(
- TransactionResponse.newBuilder()
- .setRetrieveResponse(
- RetrieveResponse.newBuilder().setEntityResponse(entityDoesNotExist(id))));
- }
- }
- }
return builder.build();
}
- private EntityResponse entityDoesNotExist(final String id) {
- return EntityResponse.newBuilder()
- .addErrors(caosdbToGrpc.convert(ServerMessages.ENTITY_DOES_NOT_EXIST))
- .setEntity(Entity.newBuilder().setId(id))
- .build();
- }
-
private String getSRID() {
return UUID.randomUUID().toString();
}
@@ -295,29 +272,16 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
final UpdateRequest updateRequest = subRequest.getUpdateRequest();
final Entity updateEntity = updateRequest.getEntityRequest().getEntity();
- try {
- final UpdateEntity entity =
- new UpdateEntity(
- grpcToCaosdb.getId(updateEntity.getId()), // ID is not handled by grpc convert
- grpcToCaosdb.convert(updateEntity.getRole()));
- grpcToCaosdb.convert(updateEntity, entity);
- addFileUpload(container, entity, updateRequest.getEntityRequest());
- container.add(entity);
- } catch (final NumberFormatException e) {
- // ID wasn't an integer
- return failedWriteDueToStringId(requests);
- }
+ final UpdateEntity entity =
+ new UpdateEntity(
+ new EntityID(updateEntity.getId()), grpcToCaosdb.convert(updateEntity.getRole()));
+ grpcToCaosdb.convert(updateEntity, entity);
+ addFileUpload(container, entity, updateRequest.getEntityRequest());
+ container.add(entity);
break;
case DELETE_REQUEST:
final DeleteRequest deleteRequest = subRequest.getDeleteRequest();
- try {
- final DeleteEntity entity = new DeleteEntity(grpcToCaosdb.getId(deleteRequest.getId()));
- container.add(entity);
-
- } catch (final NumberFormatException e) {
- // ID wasn't an integer
- return failedWriteDueToStringId(requests);
- }
+ container.add(new DeleteEntity(new EntityID(deleteRequest.getId())));
break;
default:
throw new CaosDBException(
@@ -357,65 +321,6 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
return builder.build();
}
- /**
- * Handle a request which contains string id (which cannot be converted to integer ids) and return
- * a response which has the "ENTITY_DOES_NOT_EXIST" error for all entities with affected ids.
- *
- * <p>This does not attempt to execute a single request.
- *
- * @param request
- * @return
- */
- private MultiTransactionResponse failedWriteDueToStringId(final MultiTransactionRequest request) {
- final org.caosdb.api.entity.v1.MultiTransactionResponse.Builder builder =
- MultiTransactionResponse.newBuilder();
- for (final TransactionRequest subRequest : request.getRequestsList()) {
- final IdResponse.Builder idResponse = IdResponse.newBuilder();
- switch (subRequest.getWrappedRequestsCase()) {
- case INSERT_REQUEST:
- builder
- .addResponsesBuilder()
- .setInsertResponse(InsertResponse.newBuilder().setIdResponse(idResponse));
-
- break;
- case UPDATE_REQUEST:
- final UpdateRequest updateRequest = subRequest.getUpdateRequest();
- final Entity updateEntity = updateRequest.getEntityRequest().getEntity();
-
- idResponse.setId(updateEntity.getId());
- try {
- grpcToCaosdb.getId(updateEntity.getId());
- } catch (final NumberFormatException e) {
- // ID wasn't an integer
- idResponse.addErrors(caosdbToGrpc.convert(ServerMessages.ENTITY_DOES_NOT_EXIST));
- }
- builder
- .addResponsesBuilder()
- .setUpdateResponse(UpdateResponse.newBuilder().setIdResponse(idResponse));
- break;
- case DELETE_REQUEST:
- final DeleteRequest deleteRequest = subRequest.getDeleteRequest();
- idResponse.setId(deleteRequest.getId());
- try {
- grpcToCaosdb.getId(deleteRequest.getId());
- } catch (final NumberFormatException e) {
- // ID wasn't an integer
- idResponse.addErrors(caosdbToGrpc.convert(ServerMessages.ENTITY_DOES_NOT_EXIST));
- }
- builder
- .addResponsesBuilder()
- .setDeleteResponse(DeleteResponse.newBuilder().setIdResponse(idResponse));
- break;
- default:
- throw new CaosDBException(
- "Cannot process a "
- + subRequest.getWrappedRequestsCase().name()
- + " in a write request.");
- }
- }
- return builder.build();
- }
-
private void addFileUpload(
final WritableContainer container,
final EntityInterface entity,
diff --git a/src/main/java/org/caosdb/server/grpc/GRPCServer.java b/src/main/java/org/caosdb/server/grpc/GRPCServer.java
index 73356140b85fb09af93bdca034a69685ce8cd4eb..494ce94706eff75415264b175f58cdaf16a2a442 100644
--- a/src/main/java/org/caosdb/server/grpc/GRPCServer.java
+++ b/src/main/java/org/caosdb/server/grpc/GRPCServer.java
@@ -81,8 +81,11 @@ public class GRPCServer {
* @throws IOException
*/
private SslContext buildSslContext()
- throws NoSuchAlgorithmException, UnrecoverableKeyException, KeyStoreException,
- CertificateException, IOException {
+ throws NoSuchAlgorithmException,
+ UnrecoverableKeyException,
+ KeyStoreException,
+ CertificateException,
+ IOException {
final KeyManagerFactory kmf =
KeyManagerFactory.getInstance(KeyManagerFactory.getDefaultAlgorithm());
final char[] password =
@@ -112,7 +115,9 @@ public class GRPCServer {
return builder.build();
}
- /** @return A list of services which should be added to the gRPC end-point. */
+ /**
+ * @return A list of services which should be added to the gRPC end-point.
+ */
private List<ServerServiceDefinition> getEnabledServices() {
final List<ServerServiceDefinition> services = new LinkedList<>();
@@ -153,8 +158,11 @@ public class GRPCServer {
* @throws IOException
*/
private Server buildServer(final int port, final boolean tls)
- throws UnrecoverableKeyException, NoSuchAlgorithmException, KeyStoreException,
- CertificateException, IOException {
+ throws UnrecoverableKeyException,
+ NoSuchAlgorithmException,
+ KeyStoreException,
+ CertificateException,
+ IOException {
final NettyServerBuilder builder = NettyServerBuilder.forPort(port);
if (tls) {
@@ -182,8 +190,12 @@ public class GRPCServer {
* @throws UnrecoverableKeyException
*/
public static void startServer()
- throws IOException, InterruptedException, KeyStoreException, NoSuchAlgorithmException,
- CertificateException, UnrecoverableKeyException {
+ throws IOException,
+ InterruptedException,
+ KeyStoreException,
+ NoSuchAlgorithmException,
+ CertificateException,
+ UnrecoverableKeyException {
boolean started = false;
final String port_https_str = getServerProperty(ServerProperties.KEY_GRPC_SERVER_PORT_HTTPS);
diff --git a/src/main/java/org/caosdb/server/grpc/GrpcToCaosDBConverters.java b/src/main/java/org/caosdb/server/grpc/GrpcToCaosDBConverters.java
index 0430a795457152141473c2819997ebd1597028fd..587b89662456272d9a81aa910db3b1a962d67499 100644
--- a/src/main/java/org/caosdb/server/grpc/GrpcToCaosDBConverters.java
+++ b/src/main/java/org/caosdb/server/grpc/GrpcToCaosDBConverters.java
@@ -1,8 +1,8 @@
/*
* This file is a part of the CaosDB Project.
*
- * Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
- * Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
+ * Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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
@@ -16,9 +16,7 @@
*
* 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 org.caosdb.server.grpc;
import java.util.ArrayList;
@@ -64,12 +62,13 @@ import org.caosdb.server.permissions.EntityACLFactory;
import org.caosdb.server.utils.EntityStatus;
import org.caosdb.server.utils.ServerMessages;
+/**
+ * Utility class for converting GRPC's native objects into our own CaosDB objects.
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
public class GrpcToCaosDBConverters {
- public EntityID getId(final String id) {
- return new EntityID(Integer.parseInt(id));
- }
-
public Role convert(final EntityRole role) {
switch (role) {
case ENTITY_ROLE_FILE:
@@ -256,7 +255,7 @@ public class GrpcToCaosDBConverters {
final Property result = new Property(new RetrieveEntity());
try {
- result.setId(e.getId().isBlank() ? null : getId(e.getId()));
+ result.setId(e.getId().isBlank() ? null : new EntityID(e.getId()));
} catch (final NumberFormatException exc) {
result.addError(ServerMessages.ENTITY_DOES_NOT_EXIST);
}
@@ -314,7 +313,7 @@ public class GrpcToCaosDBConverters {
new org.caosdb.server.entity.wrapper.Parent(new RetrieveEntity());
try {
- result.setId(e.getId().isBlank() ? null : getId(e.getId()));
+ result.setId(e.getId().isBlank() ? null : new EntityID(e.getId()));
} catch (final NumberFormatException exc) {
result.addError(ServerMessages.ENTITY_DOES_NOT_EXIST);
}
@@ -336,7 +335,7 @@ public class GrpcToCaosDBConverters {
private EntityInterface convert(EntityACL acl) {
try {
- EntityID id = getId(acl.getId());
+ EntityID id = new EntityID(acl.getId());
UpdateEntity result = new UpdateEntity(id);
result.setEntityACL(convertAcl(acl));
return result;
diff --git a/src/main/java/org/caosdb/server/jobs/Job.java b/src/main/java/org/caosdb/server/jobs/Job.java
index 9da74edd0db86f6d81a8636020afcdaf3faa9e09..7bb94635ed21c14c80c92d315539dd4fab5416ab 100644
--- a/src/main/java/org/caosdb/server/jobs/Job.java
+++ b/src/main/java/org/caosdb/server/jobs/Job.java
@@ -3,8 +3,8 @@
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- * Copyright (C) 2020-2021 IndiScale GmbH <info@indiscale.com>
- * Copyright (C) 2020-2021 Timm Fitschen <t.fitschen@indiscale.com>
+ * Copyright (C) 2020-2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020-2023 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
@@ -22,10 +22,10 @@
package org.caosdb.server.jobs;
import java.lang.reflect.InvocationTargetException;
-import java.util.ArrayList;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
+import java.util.Map;
import java.util.Objects;
import java.util.Set;
import org.apache.shiro.subject.Subject;
@@ -33,9 +33,8 @@ import org.caosdb.server.CaosDBException;
import org.caosdb.server.database.BackendTransaction;
import org.caosdb.server.database.backend.transaction.GetIDByName;
import org.caosdb.server.database.backend.transaction.IsSubType;
-import org.caosdb.server.database.backend.transaction.RetrieveFullEntityTransaction;
-import org.caosdb.server.database.backend.transaction.RetrieveParents;
import org.caosdb.server.database.backend.transaction.RetrieveSparseEntity;
+import org.caosdb.server.database.exceptions.EntityDoesNotExistException;
import org.caosdb.server.database.exceptions.EntityWasNotUniqueException;
import org.caosdb.server.database.exceptions.TransactionException;
import org.caosdb.server.datatype.AbstractCollectionDatatype;
@@ -44,13 +43,12 @@ import org.caosdb.server.datatype.ReferenceDatatype2;
import org.caosdb.server.entity.EntityID;
import org.caosdb.server.entity.EntityInterface;
import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.container.ParentContainer;
+import org.caosdb.server.entity.Version;
import org.caosdb.server.entity.container.TransactionContainer;
import org.caosdb.server.entity.wrapper.Parent;
import org.caosdb.server.jobs.core.JobFailureSeverity;
import org.caosdb.server.transaction.Transaction;
import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
import org.reflections.Reflections;
/**
@@ -73,7 +71,7 @@ public abstract class Job {
public abstract JobTarget getTarget();
- protected <S, T> HashMap<S, T> getCache(final String name) {
+ protected <S, T> Map<S, T> getCache(final String name) {
return getTransaction().getCache(name);
}
@@ -89,7 +87,7 @@ public abstract class Job {
return getTransaction().getTransactor();
}
- public <K extends BackendTransaction> K execute(final K t) {
+ protected <K extends BackendTransaction> K execute(final K t) {
return getTransaction().execute(t, getTransaction().getAccess());
}
@@ -185,8 +183,8 @@ public abstract class Job {
if (targetParent.getId().equals(child.getId())) {
return true;
}
-
- } else if (targetParent.hasName()) {
+ }
+ if (targetParent.hasName()) {
if (targetParent.getName().equals(child.getName())) {
return true;
} else {
@@ -195,13 +193,7 @@ public abstract class Job {
}
// check direct parents of child
- ParentContainer directParents;
- if (child.hasParents()) {
- directParents = child.getParents();
- } else {
- directParents = resolve(child).getParents();
- }
- for (final Parent directParent : directParents) {
+ for (final Parent directParent : child.getParents()) {
EntityInterface resolvedDirectParent = null;
if (directParent.hasId() && targetParent.hasId()) {
if (directParent.getId().equals(targetParent.getId())) {
@@ -231,78 +223,73 @@ public abstract class Job {
}
protected final boolean isValidSubType(final EntityID child, final EntityID parent) {
- if (!"false".equals(getContainer().getFlags().get("cache"))) {
- final HashMap<String, Boolean> isSubTypeCache = getCache("isSubType");
- final String key = child + "->" + parent;
- final Boolean cached = isSubTypeCache.get(key);
- if (cached == null) {
- final Boolean toCache = isValidSubTypeNoCache(child, parent);
- isSubTypeCache.put(key, toCache);
- return toCache;
- } else {
- return cached;
- }
- } else {
- return isValidSubTypeNoCache(child, parent);
+ Boolean result = null;
+ final Map<String, Boolean> isSubTypeCache = getCache("isSubType");
+
+ final String key = child + "->" + parent;
+ result = isSubTypeCache.get(key);
+
+ if (result == null) {
+ result = isValidSubTypeNoCache(child, parent);
+ isSubTypeCache.put(key, result);
}
+
+ return result;
}
- protected final boolean isValidSubTypeNoCache(final EntityID child, final EntityID parent) {
+ private final boolean isValidSubTypeNoCache(final EntityID child, final EntityID parent) {
return Objects.equals(child, parent) || execute(new IsSubType(child, parent)).isSubType();
}
- protected final EntityInterface retrieveValidSparseEntityByName(final String name)
- throws Message {
- return retrieveValidSparseEntityById(retrieveValidIDByName(name), null);
+ private final EntityInterface retrieveValidLazyEntityByName(final String name, String version) {
+ EntityID id = null;
+
+ final Map<String, EntityID> cache = getCache("validEntityByName");
+ String key = name;
+ if (version != null && !version.equals("HEAD")) {
+ key += version;
+ }
+
+ id = cache.get(key);
+ if (id == null) {
+ id = retrieveValidIDByName(name, version);
+ cache.put(key, id);
+ }
+
+ return retrieveValidLazyEntityById(id, version);
}
- protected final EntityInterface retrieveValidSparseEntityById(
- final EntityID id, final String version) throws Message {
+ private final EntityInterface retrieveValidLazyEntityById(
+ final EntityID id, final String version) {
+ EntityInterface result = null;
- 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.
- final EntityInterface ret = getEntityById(id);
- if (ret != null) {
- return ret;
- }
- } else if (version.startsWith("HEAD~")) {
- final 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.
- final 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 Map<String, EntityInterface> cache = getCache("validEntityById");
+ String key = id.toString();
+ if (version != null && !version.equals("HEAD")) {
+ key += version;
}
- final EntityInterface ret =
- execute(new RetrieveSparseEntity(id, resulting_version)).getEntity();
- if (ret.getEntityStatus() == EntityStatus.NONEXISTENT) {
- throw ServerMessages.ENTITY_DOES_NOT_EXIST;
+ result = cache.get(key);
+ if (result == null) {
+ result = retrieveValidLazyEntityByIdNoCache(id, version);
+ cache.put(key, result);
}
- return ret;
- }
- protected final EntityInterface retrieveValidEntity(final EntityID id) {
- return execute(new RetrieveFullEntityTransaction(id)).getContainer().get(0);
+ return result;
}
- protected final EntityID retrieveValidIDByName(final String name) {
- return execute(new GetIDByName(name)).getId();
+ private final EntityInterface retrieveValidLazyEntityByIdNoCache(
+ final EntityID id, final String version) {
+
+ final EntityInterface ret = execute(new RetrieveSparseEntity(id, version)).getEntity();
+ if (ret.getEntityStatus() == EntityStatus.NONEXISTENT) {
+ throw new EntityDoesNotExistException();
+ }
+ return new LazyEntityResolver(ret, getTransaction());
}
- protected EntityInterface retrieveParentsOfValidEntity(final EntityInterface entity) {
- execute(new RetrieveParents(entity));
- return entity;
+ protected final EntityID retrieveValidIDByName(final String name, String version) {
+ return execute(new GetIDByName(name, version)).getId();
}
/**
@@ -334,7 +321,7 @@ public abstract class Job {
private static void scanJobClasspath() {
if (allClasses == null || loadAlways == null) {
allClasses = new HashMap<>();
- loadAlways = new ArrayList<>();
+ loadAlways = new LinkedList<>();
Reflections jobPackage = new Reflections("org.caosdb.server.jobs.core");
Set<Class<? extends Job>> allClassesSet = jobPackage.getSubTypesOf(Job.class);
allClassesSet.addAll(jobPackage.getSubTypesOf(FlagJob.class));
@@ -383,11 +370,11 @@ public abstract class Job {
final EntityInterface entity,
final Transaction<? extends TransactionContainer> transaction) {
if (dt == null) {
- return new ArrayList<Job>();
+ return new LinkedList<Job>();
}
if (dt instanceof ReferenceDatatype2) {
return jobConfig.getConfiguredJobs(
- EntityID.DEFAULT_DOMAIN, new EntityID(17), entity, transaction);
+ EntityID.DEFAULT_DOMAIN, new EntityID("17"), entity, transaction);
} else if (dt instanceof AbstractCollectionDatatype) {
final AbstractDatatype datatype = ((AbstractCollectionDatatype) dt).getDatatype();
return loadDataTypeSpecificJobs(datatype, entity, transaction);
@@ -401,18 +388,22 @@ public abstract class Job {
public List<Job> loadStandardJobs(
final EntityInterface entity, final Transaction<? extends TransactionContainer> transaction) {
- final ArrayList<Job> jobs = new ArrayList<>();
+ final List<Job> jobs = new LinkedList<>();
// load permanent jobs
- for (final Class<? extends Job> j : loadAlways) {
- if (EntityJob.class.isAssignableFrom(j)
- && j.getAnnotation(JobAnnotation.class).transaction().isInstance(transaction)) {
- jobs.add(getJob(j, JobFailureSeverity.ERROR, entity, transaction));
+ for (final Class<? extends Job> jobClass : loadAlways) {
+ if (EntityJob.class.isAssignableFrom(jobClass)
+ && jobClass.getAnnotation(JobAnnotation.class).transaction().isInstance(transaction)) {
+ Job j = getJob(jobClass, JobFailureSeverity.ERROR, entity, transaction);
+ if (j != null) {
+ jobs.add(j);
+ }
}
}
// load general rules
final List<Job> generalRules =
- jobConfig.getConfiguredJobs(EntityID.DEFAULT_DOMAIN, new EntityID(0), entity, transaction);
+ jobConfig.getConfiguredJobs(
+ EntityID.DEFAULT_DOMAIN, new EntityID("0"), entity, transaction);
if (generalRules != null) {
jobs.addAll(generalRules);
}
@@ -541,10 +532,6 @@ public abstract class Job {
+ "]";
}
- public void print() {
- System.out.println(toString());
- }
-
public TransactionStage getTransactionStage() {
return this.stage;
}
@@ -559,33 +546,80 @@ public abstract class Job {
*/
protected EntityInterface resolve(final EntityInterface entity)
throws EntityWasNotUniqueException {
- EntityInterface resolvedEntity = null;
- if (!entity.hasId() && entity.hasName()) {
- resolvedEntity = getEntityByName(entity.getName());
+ return resolve(entity.getId(), entity.getName(), entity.getVersion());
+ }
+
+ protected EntityInterface resolve(EntityID id) {
+ return resolve(id, null, (String) null);
+ }
+
+ protected EntityInterface resolve(EntityID id, String name, String versionId)
+ throws EntityDoesNotExistException, EntityWasNotUniqueException {
+ EntityInterface resolvedEntity = getEntityById(id);
+
+ String resulting_version = versionId;
+ if (versionId == null || versionId.equals("HEAD")) {
+ resulting_version = null;
+ versionId = null;
+ } else if (versionId.startsWith("HEAD~")) {
if (resolvedEntity == null) {
- final EntityID eid = retrieveValidIDByName(entity.getName());
- entity.setId(eid);
+ resolvedEntity = getEntityByName(name);
+ }
+ if (resolvedEntity != null && resolvedEntity.getEntityStatus() == EntityStatus.QUALIFIED) {
+ // if versionId 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.
+ final int offset = Integer.parseInt(versionId.substring(5)) - 1;
+ if (offset == 0) {
+ // special case HEAD~1
+ resulting_version = "HEAD";
+ } else {
+ resulting_version = new StringBuilder().append("HEAD~").append(offset).toString();
+ }
}
+ resolvedEntity = null;
+ } else {
+ // We want another version, throw away current result.
+ resolvedEntity = null;
}
- if (entity.hasId()) {
- // get entity from container
- resolvedEntity = getEntityById(entity.getId());
- if (resolvedEntity == null && !entity.getId().isTemporary()) {
- resolvedEntity = retrieveValidEntity(entity.getId());
+ if (resolvedEntity == null && id != null) {
+ try {
+ resolvedEntity = retrieveValidLazyEntityById(id, resulting_version);
+ } catch (EntityDoesNotExistException e) {
+ // ignore here, try to find by name.
}
}
+ // Last resort: find by name ...
+ if (resolvedEntity == null && versionId == null) {
+ // ... from current transaction's container
+ resolvedEntity = getEntityByName(name);
+ }
+
+ if (resolvedEntity == null && name != null) {
+ // ... from database
+ resolvedEntity = retrieveValidLazyEntityByName(name, resulting_version);
+ }
+
+ if (resolvedEntity == null) {
+ throw new EntityDoesNotExistException();
+ }
return resolvedEntity;
}
+ protected EntityInterface resolve(EntityID id, String name, Version version) {
+ String versionId = version != null ? version.getId() : null;
+ return resolve(id, name, versionId);
+ }
+
/**
* Return those matching jobs which are annotated with the "loadAlways" attribute.
*
* @return A list with the jobs.
*/
public static List<Job> loadPermanentContainerJobs(final Transaction<?> transaction) {
- final ArrayList<Job> jobs = new ArrayList<>();
+ final List<Job> jobs = new LinkedList<>();
// load permanent jobs: ContainerJob classes with the correct transaction
for (final Class<? extends Job> j : loadAlways) {
if (ContainerJob.class.isAssignableFrom(j)
@@ -595,4 +629,22 @@ public abstract class Job {
}
return jobs;
}
+
+ @Override
+ public boolean equals(Object obj) {
+ if (obj != null && obj instanceof Job) {
+ Job other = (Job) obj;
+ return other.getClass().equals(this.getClass())
+ && Objects.equals(other.getEntity(), this.getEntity())
+ && other.getFailureSeverity().equals(this.getFailureSeverity());
+ }
+ return false;
+ }
+
+ @Override
+ public int hashCode() {
+ return getClass().hashCode()
+ + (getEntity() == null ? 0 : getEntity().hashCode())
+ + getFailureSeverity().hashCode();
+ }
}
diff --git a/src/main/java/org/caosdb/server/jobs/JobConfig.java b/src/main/java/org/caosdb/server/jobs/JobConfig.java
index 40917b36714ee95ef491a266580068a06f51703a..b2bb0d4a1b13a98dd68893c9f0cad7bc8192edba 100644
--- a/src/main/java/org/caosdb/server/jobs/JobConfig.java
+++ b/src/main/java/org/caosdb/server/jobs/JobConfig.java
@@ -1,8 +1,8 @@
/*
* This file is a part of the CaosDB Project.
*
- * Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
- * Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
+ * Copyright (C) 2021,2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2021,2023 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
@@ -141,8 +141,8 @@ public class JobConfig {
"Could not parse the job rules. Lines of five comma-separated values expected");
}
try {
- final Integer domain = Integer.parseInt(row[0]);
- final Integer entity = Integer.parseInt(row[1]);
+ final String domain = row[0];
+ final String entity = row[1];
final String transaction = row[2];
final String job = row[3];
final JobFailureSeverity severity = JobFailureSeverity.valueOf(row[4]);
@@ -158,7 +158,7 @@ public class JobConfig {
}
/**
- * Factory method for the instanciation and configuration of jobs for a specific entity.
+ * Factory method for the instantiation and configuration of jobs for a specific entity.
*
* @param domain the domain of the rule
* @param entity the entity of the rule (this might be a particular datatype or a role, like
@@ -184,9 +184,13 @@ public class JobConfig {
final List<Job> result = new LinkedList<>();
jobRules.forEach(
config -> {
- result.add(
- Job.getJob(
- (String) config[0], (JobFailureSeverity) config[1], target, transaction));
+ Job j =
+ Job.getJob((String) config[0], (JobFailureSeverity) config[1], target, transaction);
+ if (j == null) {
+ throw new NullPointerException("Could not load job: " + config[0]);
+ } else {
+ result.add(j);
+ }
});
return result;
}
diff --git a/src/main/java/org/caosdb/server/jobs/LazyEntityResolver.java b/src/main/java/org/caosdb/server/jobs/LazyEntityResolver.java
new file mode 100644
index 0000000000000000000000000000000000000000..7088ce7d35903daf34a0e060241aa22d749988c0
--- /dev/null
+++ b/src/main/java/org/caosdb/server/jobs/LazyEntityResolver.java
@@ -0,0 +1,101 @@
+/*
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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 org.caosdb.server.jobs;
+
+import org.caosdb.server.database.backend.transaction.RetrieveParents;
+import org.caosdb.server.database.backend.transaction.RetrieveProperties;
+import org.caosdb.server.entity.EntityInterface;
+import org.caosdb.server.entity.container.ParentContainer;
+import org.caosdb.server.entity.container.PropertyContainer;
+import org.caosdb.server.entity.wrapper.EntityWrapper;
+import org.caosdb.server.transaction.Transaction;
+
+/**
+ * Implementation of {@link EntityInterface} which retrieves the parents and properties only when
+ * requested via getProperties and getParents.
+ *
+ * <p>This is particularly useful for jobs sharing the same entity object between jobs which need
+ * different parts of it while reducing the logic of checking whether the entity is "only" sparse,
+ * or has been retrieved fully and so on.
+ *
+ * <p>However, when the entities parents or properties are being retrieved after the transaction's
+ * access has been released, an {@link IllegalStateException} will be thrown.
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
+public class LazyEntityResolver extends EntityWrapper {
+
+ private Transaction<?> transaction;
+ private boolean propertiesResolved = false;
+ private boolean parentsResolved = false;
+
+ /**
+ * Constructor.
+ *
+ * <p>Initialize this with a sparse entity.
+ */
+ public LazyEntityResolver(EntityInterface entity, Transaction<?> transaction) {
+ super(entity);
+ this.transaction = transaction;
+ }
+
+ public void resolveParents() {
+ if (parentsResolved) return;
+ parentsResolved = true;
+ transaction.execute(new RetrieveParents(getWrapped()), transaction.getAccess());
+ }
+
+ private void resolveProperties() {
+ if (propertiesResolved) return;
+ propertiesResolved = true;
+ transaction.execute(new RetrieveProperties(getWrapped()), transaction.getAccess());
+ }
+
+ public void resolveAll() {
+ resolveParents();
+ resolveProperties();
+ // release the transaction for the garbage collector
+ this.transaction = null;
+ }
+
+ @Override
+ public ParentContainer getParents() {
+ resolveParents();
+ return super.getParents();
+ }
+
+ @Override
+ public boolean hasParents() {
+ resolveParents();
+ return super.hasParents();
+ }
+
+ @Override
+ public PropertyContainer getProperties() {
+ resolveProperties();
+ return super.getProperties();
+ }
+
+ @Override
+ public boolean hasProperties() {
+ resolveProperties();
+ return super.hasProperties();
+ }
+}
diff --git a/src/main/java/org/caosdb/server/jobs/Schedule.java b/src/main/java/org/caosdb/server/jobs/Schedule.java
index 57474da515418745ed0457962596dfce233bff48..1b7ac8f4b41118803e7d5a540be6a1a3ba57cfec 100644
--- a/src/main/java/org/caosdb/server/jobs/Schedule.java
+++ b/src/main/java/org/caosdb/server/jobs/Schedule.java
@@ -3,8 +3,8 @@
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- * Copyright (C) 2020-2021 IndiScale GmbH <info@indiscale.com>
- * Copyright (C) 2020-2021 Timm Fitschen <t.fitschen@indiscale.com>
+ * Copyright (C) 2020-2021,2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020-2021,2023 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
@@ -35,6 +35,8 @@ import org.caosdb.server.entity.EntityInterface;
* <p>The Schedule class orders jobs by {@link TransactionStage} and also assures that jobs are
* skipped when appropriate and to prevent that jobs run more than once (because sometimes they
* trigger each other).
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
*/
public class Schedule {
@@ -44,20 +46,26 @@ public class Schedule {
public List<ScheduledJob> addAll(final Collection<Job> jobs) {
final List<ScheduledJob> result = new ArrayList<ScheduledJob>(jobs.size());
for (final Job j : jobs) {
- result.add(add(j));
+ ScheduledJob scheduledJob = add(j);
+ if (scheduledJob != null) {
+ result.add(scheduledJob);
+ }
}
return result;
}
public ScheduledJob add(final Job j) {
- final ScheduledJob ret = new ScheduledJob(j);
- List<ScheduledJob> jobs = jobLists.get(ret.getTransactionStage().ordinal());
+ final ScheduledJob scheduled = new ScheduledJob(j);
+ List<ScheduledJob> jobs = jobLists.get(scheduled.getTransactionStage().ordinal());
if (jobs == null) {
jobs = new CopyOnWriteArrayList<ScheduledJob>();
- jobLists.put(ret.getTransactionStage().ordinal(), jobs);
+ jobLists.put(scheduled.getTransactionStage().ordinal(), jobs);
+ }
+ if (!jobs.contains(scheduled)) {
+ jobs.add(scheduled);
+ return scheduled;
}
- jobs.add(ret);
- return ret;
+ return null;
}
/** Run all Jobs from the specified {@link TransactionStage}. */
@@ -71,7 +79,7 @@ public class Schedule {
}
public void runJob(final ScheduledJob scheduledJob) {
- if (scheduledJob.skip()) {
+ if (scheduledJob == null || scheduledJob.skip()) {
return;
}
final ScheduledJob parent = this.running;
diff --git a/src/main/java/org/caosdb/server/jobs/ScheduledJob.java b/src/main/java/org/caosdb/server/jobs/ScheduledJob.java
index 2122b34de5f0b60db4c2b6d4c1c2358d3df02851..1754f19f5fdab5b32e19fcba7758481f0dba8948 100644
--- a/src/main/java/org/caosdb/server/jobs/ScheduledJob.java
+++ b/src/main/java/org/caosdb/server/jobs/ScheduledJob.java
@@ -1,8 +1,8 @@
/*
* 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>
+ * Copyright (C) 2020,2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020,2023 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
@@ -28,7 +28,7 @@ import org.caosdb.server.entity.Message;
* <p>It is mainly a means to have simplified interface for the Scheduler which also measures the
* execution time of the job "from outside".
*
- * @author Timm Fitschen (t.fitschen@indiscale.com)
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
*/
public class ScheduledJob {
@@ -102,4 +102,18 @@ public class ScheduledJob {
public Job getJob() {
return job;
}
+
+ @Override
+ public boolean equals(Object obj) {
+ if (obj instanceof ScheduledJob) {
+ ScheduledJob other = (ScheduledJob) obj;
+ return this.job.equals(other.job);
+ }
+ return false;
+ }
+
+ @Override
+ public int hashCode() {
+ return job.hashCode();
+ }
}
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckChildDependencyExistent.java b/src/main/java/org/caosdb/server/jobs/core/CheckChildDependencyExistent.java
deleted file mode 100644
index d60db5a3ea2f58caefe240894920318e01efc8a6..0000000000000000000000000000000000000000
--- a/src/main/java/org/caosdb/server/jobs/core/CheckChildDependencyExistent.java
+++ /dev/null
@@ -1,99 +0,0 @@
-/*
- * ** header v3.0
- * This file is a part of the CaosDB Project.
- *
- * Copyright (C) 2018 Research Group Biomedical Physics,
- * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Affero General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Affero General Public License for more details.
- *
- * You should have received a copy of the GNU Affero General Public License
- * along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
- */
-package org.caosdb.server.jobs.core;
-
-import java.util.List;
-import java.util.Objects;
-import org.caosdb.server.database.backend.transaction.GetChildren;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
-
-/**
- * Check whether any children of this entity do exist. There must not be any children left when an
- * entity is to be deleted. If all children are to be deleted, too, the test passes.
- *
- * @author tf
- */
-public class CheckChildDependencyExistent extends EntityJob {
-
- @Override
- public final void run() {
- if (getEntity().getDomain() == null
- || Objects.equals(getEntity().getDomain(), EntityID.DEFAULT_DOMAIN)) {
-
- final List<EntityID> children = execute(new GetChildren(getEntity().getId())).getList();
-
- // loop:
- for (final EntityID id : children) {
- final EntityInterface foreign = getEntityById(id);
- if (foreign == null) {
- // if the child is not in the container, the test fails.
- getEntity().addError(ServerMessages.REQUIRED_BY_PERSISTENT_ENTITY);
- getEntity().addInfo("Required by entity " + id + ".");
- getEntity().setEntityStatus(EntityStatus.UNQUALIFIED);
- }
-
- // // loop through all entities in the current container
- // for (final EntityInterface e : getContainer()) {
- //
- // // if e is a child
- // if (e.getId().equals(id)) {
- // if (e.getEntityStatus() == EntityStatus.UNQUALIFIED) {
- // getEntity().addError(ServerMessages.REQUIRED_BY_UNQUALIFIED);
- // getEntity().addInfo("Required by entity " + id + ".");
- // getEntity().setEntityStatus(EntityStatus.UNQUALIFIED);
- // } else {
- // // if the children are among the entities in the
- // // container which is to be deleted, the test passes
- // e.acceptObserver(new Observer() {
- // @Override
- // public boolean notifyObserver(final String evt,
- // final Observable o) {
- // if (evt == Entity.ENTITY_STATUS_CHANGED_EVENT && o == e) {
- // if (e.getEntityStatus() == EntityStatus.UNQUALIFIED) {
- // getEntity().addError(
- // ServerMessages.REQUIRED_BY_UNQUALIFIED);
- // getEntity().addInfo("Required by entity " + id + ".");
- // getEntity().setEntityStatus(EntityStatus.UNQUALIFIED);
- // return false;
- // }
- // }
- // return true;
- // }
- // });
- // }
- // continue loop;
- // }
- // }
-
- // // if the child is not in the container, the test fails.
- // getEntity().addError(ServerMessages.REQUIRED_BY_PERSISTENT_ENTITY);
- // getEntity().addInfo("Required by entity " + id + ".");
- // getEntity().setEntityStatus(EntityStatus.UNQUALIFIED);
- }
- }
- }
-}
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckDatatypePresent.java b/src/main/java/org/caosdb/server/jobs/core/CheckDatatypePresent.java
index 40e01d2636509774555f1514c75bb0bf16870539..b3a06ca09d7870da843a2f3ad295e019ab683c12 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckDatatypePresent.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckDatatypePresent.java
@@ -1,9 +1,10 @@
/*
- * ** 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) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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
@@ -17,8 +18,6 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.jobs.core;
@@ -41,10 +40,11 @@ import org.caosdb.server.utils.EntityStatus;
import org.caosdb.server.utils.ServerMessages;
/**
- * Check whether the entity has a data type. Assign the data type of the abstract property if
- * necessary
+ * Check whether the entity has a data type.
+ *
+ * <p>Assign the data type of the abstract property if necessary.
*
- * @author tf
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
*/
public final class CheckDatatypePresent extends EntityJob {
@@ -115,44 +115,15 @@ public final class CheckDatatypePresent extends EntityJob {
}
private void checkReference2(final ReferenceDatatype2 datatype) throws Message {
+ EntityInterface datatypeEntity = resolve(datatype.getId(), datatype.getName(), (String) null);
- if (datatype.getId() == null) {
- // try and get from container...
- final EntityInterface datatypeEntity = getEntityByName(datatype.getName());
-
- // if the container carried a corresponding entity
- if (datatypeEntity != null) {
- assertAllowedToUse(datatypeEntity);
-
- // ... we set it as the datatypevalue
- datatype.setEntity(datatypeEntity);
- } else {
-
- // else try and get from database.
- final EntityInterface validDatatypeEntity =
- retrieveValidSparseEntityByName(datatype.getName());
- assertAllowedToUse(validDatatypeEntity);
- datatype.setId(validDatatypeEntity.getId());
- }
- } else if (datatype.getId().isTemporary()) {
- final EntityInterface datatypeEntity = getEntityById(datatype.getId());
-
- // if the container carried a corresponding entity
- if (datatypeEntity != null) {
- assertAllowedToUse(datatypeEntity);
- // ... we set it as the datatype
- datatype.setEntity(datatypeEntity);
- } else {
-
- throw ServerMessages.UNKNOWN_DATATYPE;
- }
- } else {
-
- final EntityInterface validDatatypeEntity =
- retrieveValidSparseEntityById(datatype.getId(), null);
- assertAllowedToUse(validDatatypeEntity);
- datatype.setEntity(validDatatypeEntity);
+ if (datatypeEntity == null) {
+ throw ServerMessages.UNKNOWN_DATATYPE;
}
+
+ // do the actual checking
+ assertAllowedToUse(datatypeEntity);
+ datatype.setEntity(datatypeEntity);
}
private void assertAllowedToUse(final EntityInterface datatype) {
@@ -160,62 +131,39 @@ public final class CheckDatatypePresent extends EntityJob {
}
private void checkIfOverride() throws Message {
- if (getEntity().hasId() && !getEntity().getId().isTemporary()) {
- // get data type from database
- final EntityInterface foreign = retrieveValidSparseEntityById(getEntity().getId(), null);
-
- if (foreign.hasDatatype() && !foreign.getDatatype().equals(getEntity().getDatatype())) {
- // is override!
- getEntity().setDatatypeOverride(true);
- }
- } else {
- // get data type from container
- EntityInterface abstractProperty = null;
- if (getEntity().hasId()) {
- abstractProperty = getEntityById(getEntity().getId());
- } else if (getEntity().hasName()) {
- abstractProperty = getEntityByName(getEntity().getName());
- }
- if (abstractProperty != null && abstractProperty.hasDatatype()) {
- if (!getEntity().getDatatype().equals(abstractProperty.getDatatype())) {
- // is override!
- getEntity().setDatatypeOverride(true);
- }
- }
+ EntityInterface abstractProperty = resolve(getEntity());
+ if (abstractProperty != null
+ && abstractProperty.hasDatatype()
+ && !abstractProperty.getDatatype().equals(getEntity().getDatatype())) {
+ // is override!
+ getEntity().setDatatypeOverride(true);
}
}
+ /**
+ * If this is a record type property or a concrete property, assign the data type of the
+ * corresponding abstract property.
+ */
private void inheritDatatypeFromAbstractEntity() throws Message {
- // if this is a record type property or a concrete property, assign
- // the data type of the corresponding abstract property.
- if (getEntity().hasId() && !getEntity().getId().isTemporary()) {
- // get from data base
- final EntityInterface foreign = retrieveValidSparseEntityById(getEntity().getId(), null);
- inheritDatatypeFromForeignEntity(foreign);
- } else if (getEntity().hasId() && getEntity().getId().isTemporary()) {
- // get from container
- final EntityInterface foreign = getEntityById(getEntity().getId());
- inheritDatatypeFromForeignEntity(foreign);
- }
- }
-
- private void inheritDatatypeFromForeignEntity(final EntityInterface foreign) {
- if (foreign != null && foreign.hasDatatype()) {
- getEntity().setDatatype(foreign.getDatatype());
- } else if (foreign != null && foreign != getEntity() && foreign.getRole() == Role.RecordType) {
- getEntity().setDatatype(ReferenceDatatype2.datatypeFactory(foreign.getId()));
+ EntityInterface abstractProperty = resolve(getEntity());
+ if (abstractProperty != null && abstractProperty.hasDatatype()) {
+ getEntity().setDatatype(abstractProperty.getDatatype());
+ } else if (abstractProperty != null
+ && abstractProperty != getEntity()
+ && abstractProperty.getRole() == Role.RecordType) {
+ getEntity().setDatatype(ReferenceDatatype2.datatypeFactory(abstractProperty.getId()));
}
}
private void resolveId(final EntityInterface entity) {
if (!entity.hasId() && entity.hasName()) {
try {
- entity.setId(retrieveValidIDByName(entity.getName()));
- if (entity.getEntityStatus() != EntityStatus.UNQUALIFIED) {
- entity.setEntityStatus(EntityStatus.VALID);
+ EntityInterface resolved = resolve(entity);
+ if (resolved == null) {
+ entity.addError(ServerMessages.ENTITY_DOES_NOT_EXIST);
+ } else {
+ entity.setId(resolved.getId());
}
- } catch (final EntityDoesNotExistException exc) {
- entity.addError(ServerMessages.ENTITY_DOES_NOT_EXIST);
} catch (final EntityWasNotUniqueException exc) {
entity.addError(ServerMessages.ENTITY_NAME_DUPLICATES);
}
@@ -227,14 +175,12 @@ public final class CheckDatatypePresent extends EntityJob {
AbstractDatatype datatype = null;
for (final EntityInterface parent : getEntity().getParents()) {
- EntityInterface parentEntity = null;
- if (!parent.getId().isTemporary()) {
- parentEntity = retrieveValidSparseEntityById(parent.getId(), null);
- } else {
- parentEntity = getEntityById(parent.getId());
+ EntityInterface parentEntity = resolve(parent);
+ if (!parentEntity.hasDatatype() && parentEntity.getEntityStatus() == EntityStatus.QUALIFIED) {
runJobFromSchedule(parentEntity, CheckDatatypePresent.class);
}
- if (parentEntity.hasDatatype()) {
+ if (parentEntity.hasDatatype()
+ && parentEntity.getEntityStatus() != EntityStatus.UNQUALIFIED) {
if (datatype != null && !parentEntity.getDatatype().equals(datatype)) {
getEntity().addError(ServerMessages.DATATYPE_INHERITANCE_AMBIGUOUS);
return;
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckReferenceDependencyExistent.java b/src/main/java/org/caosdb/server/jobs/core/CheckDependenciesBeforeDeletion.java
similarity index 53%
rename from src/main/java/org/caosdb/server/jobs/core/CheckReferenceDependencyExistent.java
rename to src/main/java/org/caosdb/server/jobs/core/CheckDependenciesBeforeDeletion.java
index 2edbc5a270db93312c73b8c960c615a161e8907b..ecbbf4af7fb4a81605d61a3d251b88c4f1d0917a 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckReferenceDependencyExistent.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckDependenciesBeforeDeletion.java
@@ -1,9 +1,10 @@
/*
- * ** 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) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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
@@ -17,8 +18,6 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.jobs.core;
@@ -32,13 +31,13 @@ import org.caosdb.server.utils.EntityStatus;
import org.caosdb.server.utils.ServerMessages;
/**
- * Check whether an entity is referenced by other entities. In the event that someone wants to
- * delete this entity, this entity must not be referenced by any other entity which is not deleted
- * along with this entity.
+ * Check whether an entity is referenced by other entities, is being used as a data type by other
+ * entities or has direct children which are not to be deleted along with this entity and add an
+ * appropriate error if so.
*
- * @author tf
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
*/
-public class CheckReferenceDependencyExistent extends EntityJob {
+public class CheckDependenciesBeforeDeletion extends EntityJob {
@Override
public final void run() {
if (getEntity().getDomain() == null
@@ -59,42 +58,6 @@ public class CheckReferenceDependencyExistent extends EntityJob {
getEntity().addInfo("Required by entity " + id + ".");
getEntity().setEntityStatus(EntityStatus.UNQUALIFIED);
}
- // for (final EntityInterface e : getContainer()) {
- // if (e.getId().equals(id)) {
- // // entity is in the container.
- // if (e.getEntityStatus() == EntityStatus.UNQUALIFIED) {
- // getEntity().addError(ServerMessages.REQUIRED_BY_UNQUALIFIED);
- // getEntity().addInfo("Required by entity " + id + ".");
- // getEntity().setEntityStatus(EntityStatus.UNQUALIFIED);
- // } else {
- // e.acceptObserver(new Observer() {
- // @Override
- // public boolean notifyObserver(final String evt,
- // final Observable o) {
- // if (e == o && evt == Entity.ENTITY_STATUS_CHANGED_EVENT) {
- // if (e.getEntityStatus() == EntityStatus.UNQUALIFIED) {
- // getEntity().addError(
- // ServerMessages.REQUIRED_BY_UNQUALIFIED);
- // getEntity().addInfo("Required by entity " + id + ".");
- // getEntity().setEntityStatus(EntityStatus.UNQUALIFIED);
- // return false;
- // }
- // }
- // return true;
- // }
- // });
- // }
- //
- // continue loop;
- // }
- // }
-
- // // dependent entity is not in the container. That is, it will
- // // not be deleted. Therefore, this entity cannot be deleted
- // // either.
- // getEntity().addError(ServerMessages.REQUIRED_BY_PERSISTENT_ENTITY);
- // getEntity().addInfo("Required by entity " + id + ".");
- // getEntity().setEntityStatus(EntityStatus.UNQUALIFIED);
}
}
}
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckParOblPropPresent.java b/src/main/java/org/caosdb/server/jobs/core/CheckParOblPropPresent.java
index e6ba9da430e6218e5c40fba968c309ed94152bf6..eba79831468b1f6799507ca0866a64e594997caa 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckParOblPropPresent.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckParOblPropPresent.java
@@ -93,7 +93,7 @@ public class CheckParOblPropPresent extends EntityJob {
// loop over all properties of the entity
for (final EntityInterface entityProperty : getEntity().getProperties()) {
- if (isSubType(entityProperty, parentProperty)) {
+ if (isSubType(resolve(entityProperty), parentProperty)) {
// continue outer loop means that we
// found an entityProperty that
// implements the obligatory
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckParValid.java b/src/main/java/org/caosdb/server/jobs/core/CheckParValid.java
index 8895ae9adb4d12da2f7789a8798ca0fb9d183c05..fd235c21319d7b573db1cd42b23d9184aa7e56e6 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckParValid.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckParValid.java
@@ -1,9 +1,10 @@
/*
- * ** 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) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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
@@ -17,8 +18,6 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.jobs.core;
@@ -42,7 +41,7 @@ import org.caosdb.server.utils.ServerMessages;
/**
* Check whether all parents of an entity are valid/qualified.
*
- * @author tf
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
*/
@JobAnnotation(stage = TransactionStage.PRE_CHECK)
public class CheckParValid extends EntityJob {
@@ -60,73 +59,21 @@ public class CheckParValid extends EntityJob {
if (!parent.hasId() && !parent.hasName()) {
// The parent has neither an id nor a name.
// Therefore it cannot be identified.
-
- throw ServerMessages.ENTITY_HAS_NO_NAME_OR_ID;
- }
-
- if (parent.hasId()) {
- // check parent by id
- if (!parent.getId().isTemporary()) {
- // id isn't temporary, i.e., parent is already in the database and
- // can be retrieved by id
- final EntityInterface foreign = retrieveValidSparseEntityById(parent.getId(), null);
- // check permissions for this
- // parentforeign.acceptObserver(o)
- assertAllowedToUse(foreign);
- parent.setAffiliation(getAffiliation(getEntity().getRole(), foreign.getRole()));
- continue;
- } else {
- // id < 0 (parent is to be stored along with
- // this entity)
-
- // get entity with corresponding (negative) id
- // from container
- final EntityInterface foreign = getEntityById(parent.getId());
-
- // if the container carried a corresponding
- // entity
- if (foreign != null) {
- assertAllowedToUse(foreign);
-
- parent.setAffiliation(getAffiliation(getEntity().getRole(), foreign.getRole()));
-
- // ... we can set it as the parent
- parent.linkIdToEntity(foreign);
- continue;
- }
- }
+ parent.addError(ServerMessages.ENTITY_HAS_NO_NAME_OR_ID);
}
-
- // parent doesn't have an id.
- if (parent.hasName()) {
- if (getEntityByName(parent.getName()) != null) {
- // get the parent entity from the container by its
- // name
- final EntityInterface foreign = getEntityByName(parent.getName());
-
- assertAllowedToUse(foreign);
- parent.setAffiliation(getAffiliation(getEntity().getRole(), foreign.getRole()));
- parent.linkIdToEntity(foreign);
- continue;
- } else {
- // check parent by name (parent is expected to be
- // valid). This only works if the name is unique.
- final EntityInterface foreign = retrieveValidSparseEntityByName(parent.getName());
- assertAllowedToUse(foreign);
- parent.setAffiliation(getAffiliation(getEntity().getRole(), foreign.getRole()));
- parent.setId(foreign.getId());
- continue;
- }
+ try {
+ EntityInterface foreign = resolve(parent.getId(), parent.getName(), (String) null);
+ assertAllowedToUse(foreign);
+ parent.linkIdToEntity(foreign);
+ parent.setAffiliation(getAffiliation(getEntity().getRole(), foreign.getRole()));
+ } catch (EntityDoesNotExistException e) {
+ parent.addError(ServerMessages.ENTITY_DOES_NOT_EXIST);
}
-
- parent.addError(ServerMessages.ENTITY_DOES_NOT_EXIST);
} catch (final Message m) {
parent.addError(m);
} catch (AuthorizationException e) {
parent.addError(ServerMessages.AUTHORIZATION_ERROR);
parent.addInfo(e.getMessage());
- } catch (final EntityDoesNotExistException exc) {
- parent.addError(ServerMessages.ENTITY_DOES_NOT_EXIST);
} catch (final EntityWasNotUniqueException exc) {
parent.addError(ServerMessages.ENTITY_NAME_DUPLICATES);
}
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckPropValid.java b/src/main/java/org/caosdb/server/jobs/core/CheckPropValid.java
index 23a92340f5befbfbe7ded2fe95d3244b5ff78594..bfd2bc3019d1d4ae6204ebbe5b5975932603ed76 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckPropValid.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckPropValid.java
@@ -1,9 +1,10 @@
/*
- * ** 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) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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
@@ -17,8 +18,6 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.jobs.core;
@@ -41,7 +40,7 @@ import org.caosdb.server.utils.ServerMessages;
/**
* Check whether all properties of an entity are valid or qualified.
*
- * @author tf
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
*/
@JobAnnotation(stage = TransactionStage.PRE_CHECK)
public class CheckPropValid extends EntityJob {
@@ -54,75 +53,21 @@ public class CheckPropValid extends EntityJob {
if (property.getEntityStatus() == EntityStatus.QUALIFIED) {
// this property is to be tested.
- // does this property have an id at all?
- if (property.hasId()) {
- if (!property.getId().isTemporary()) {
-
- final EntityInterface abstractProperty =
- retrieveValidSparseEntityById(property.getId(), null);
-
- assertAllowedToUse(abstractProperty);
-
- deriveOverrideStatus(property, abstractProperty);
- continue;
- } else {
- // task here: find the corresponding abstract
- // property (or rarely any other entity) in this
- // container which has the same (negative) id.
-
- // fetch the abstractProperty from the container.
- final EntityInterface abstractProperty = getEntityById(property.getId());
-
- if (abstractProperty != null) {
- assertAllowedToUse(abstractProperty);
-
- // link the id of the property to the id of
- // the abstractProperty means. This has the
- // effect that the property will have a
- // valid id as soon as the abstractProperty
- // has been inserted.
- property.linkIdToEntity(abstractProperty);
- deriveOverrideStatus(property, abstractProperty);
- continue;
- } else if (!property.hasName()) {
- // an abstractProperty with this (negative) id
- // had not been found in this container.
- throw ENTITY_DOES_NOT_EXIST;
- }
- }
- }
-
- if (property.hasName()) {
-
- // try and get it from the container
- EntityInterface foreign = getEntityByName(property.getName());
- if (foreign != null) {
- assertAllowedToUse(foreign);
-
- // link the id of the property to the id of
- // the abstractProperty means. This has the
- // effect that the property will have a
- // valid id as soon as the abstractProperty
- // has been inserted.
- property.linkIdToEntity(foreign);
- deriveOverrideStatus(property, foreign);
- } else {
- foreign = retrieveValidSparseEntityByName(property.getName());
-
- assertAllowedToUse(foreign);
-
- property.setId(foreign.getId());
-
- deriveOverrideStatus(property, foreign);
- }
- }
-
if (!property.hasName() && !property.hasId()) {
// The property has neither an id nor a name.
// Thus it cannot be identified.
throw ServerMessages.ENTITY_HAS_NO_NAME_OR_ID;
}
+ EntityInterface abstractProperty =
+ resolve(property.getId(), property.getName(), (String) null);
+ if (abstractProperty == null) {
+ property.addError(ENTITY_DOES_NOT_EXIST);
+ continue;
+ }
+ assertAllowedToUse(abstractProperty);
+ deriveOverrideStatus(property, abstractProperty);
+ property.linkIdToEntity(abstractProperty);
}
} catch (final Message m) {
property.addError(m);
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckRefidIsaParRefid.java b/src/main/java/org/caosdb/server/jobs/core/CheckRefidIsaParRefid.java
index 0b8ba45b1cae19812641ed733be7aacc2fb78575..7b0a9977680c378db98dca4d3e7ee31dba06e840 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckRefidIsaParRefid.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckRefidIsaParRefid.java
@@ -1,9 +1,10 @@
/*
- * ** 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) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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
@@ -17,8 +18,6 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.jobs.core;
@@ -41,10 +40,11 @@ import org.caosdb.server.utils.Observer;
import org.caosdb.server.utils.ServerMessages;
/**
- * Check if the referenced entity is in the scope of the data type. E.g. if the data type is
- * 'Person' the referenced entity is to be a child of 'Person'.
+ * Check if the referenced entity is in the scope of the data type.
+ *
+ * <p>E.g. if the data type is 'Person' the referenced entity is to be a child of 'Person'.
*
- * @author tf
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
*/
public class CheckRefidIsaParRefid extends EntityJob implements Observer {
@@ -82,24 +82,8 @@ public class CheckRefidIsaParRefid extends EntityJob implements Observer {
for (final IndexedSingleValue v : vals) {
if (v != null && v.getWrapped() != null) {
final ReferenceValue rv = (ReferenceValue) v.getWrapped();
- if (rv.getEntity() != null
- && rv.getEntity().hasRole()
- && rv.getEntity().getRole() == Role.File) {
- } else if (rv.getId() != null
- && rv.getId().isTemporary()
- && getEntityById(rv.getId()) != null
- && getEntityById(rv.getId()).getRole() == Role.File) {
- } else if (rv.getId() == null
- && rv.getName() != null
- && getEntityByName(rv.getName()) != null
- && getEntityByName(rv.getName()).getRole() == Role.File) {
- } else if (rv.getId() != null
- && !rv.getId().isTemporary()
- && retrieveValidSparseEntityById(rv.getId(), rv.getVersion()).getRole()
- == Role.File) {
- } else if (rv.getName() != null
- && retrieveValidSparseEntityByName(rv.getName()).getRole() == Role.File) {
- } else {
+ EntityInterface referencedEntity = resolve(rv.getId(), rv.getName(), rv.getVersion());
+ if (referencedEntity.getRole() != Role.File) {
throw ServerMessages.REFERENCE_IS_NOT_ALLOWED_BY_DATATYPE;
}
}
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckRefidValid.java b/src/main/java/org/caosdb/server/jobs/core/CheckRefidValid.java
index 12b545b8e6fd608e20851d37f34e809acfcd1544..86e95542aaa0e6f373521149d9f7376f09d3972c 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckRefidValid.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckRefidValid.java
@@ -1,11 +1,10 @@
/*
- * ** 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) 2020-2021 IndiScale GmbH <info@indiscale.com>
- * Copyright (C) 2020-2021 Timm Fitschen <t.fitschen@indiscale.com>
+ * Copyright (C) 2020-2021,2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020-2021,2023 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
@@ -19,8 +18,6 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.jobs.core;
@@ -43,7 +40,7 @@ import org.caosdb.server.utils.ServerMessages;
/**
* Check whether a reference property is pointing to a valid entity.
*
- * @author tf
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
*/
public class CheckRefidValid extends EntityJob implements Observer {
@Override
@@ -83,61 +80,12 @@ public class CheckRefidValid extends EntityJob implements Observer {
}
private void checkRefValue(final ReferenceValue ref) throws Message {
- if (ref.getId() != null) {
- if (!ref.getId().isTemporary()) {
- final EntityInterface referencedValidEntity =
- retrieveValidSparseEntityById(ref.getId(), ref.getVersion());
- assertAllowedToUse(referencedValidEntity);
-
- // link the entity as versioned entity iff the reference specified a version
- ref.setEntity(referencedValidEntity, ref.getVersion() != null);
-
- } else {
-
- // is the referenced entity yet linked to this refid
- // property?
- if (ref.getEntity() == null) {
-
- // link the entity with the corresponding
- // negative id to this reference object
- final EntityInterface referencedEntity = getEntityById(ref.getId());
- if (referencedEntity != null) {
- assertAllowedToUse(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;
- }
- }
- ref.getEntity().acceptObserver(this);
- checkRefEntity(ref);
- }
- } else if (ref.getName() != null) {
- // is the referenced entity yet linked to this
- // refid property?
- if (ref.getEntity() == null) {
- // the entity is in this container?
- final EntityInterface referencedEntity = getEntityByName(ref.getName());
-
- if (referencedEntity != null) {
- assertAllowedToUse(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);
- }
- } else {
- final EntityInterface referencedValidEntity =
- retrieveValidSparseEntityByName(ref.getName());
- assertAllowedToUse(referencedValidEntity);
-
- // link the entity as versioned entity iff the reference specified a version
- ref.setEntity(referencedValidEntity, ref.getVersion() != null);
- }
- }
+ EntityInterface referencedEntity = resolve(ref.getId(), ref.getName(), ref.getVersion());
+ if (referencedEntity == null) {
+ throw ServerMessages.REFERENCED_ENTITY_DOES_NOT_EXIST;
}
+ assertAllowedToUse(referencedEntity);
+ ref.setEntity(referencedEntity, ref.getVersion() != null);
}
private void assertAllowedToUse(final EntityInterface referencedEntity) {
diff --git a/src/main/java/org/caosdb/server/jobs/core/EntityStateJob.java b/src/main/java/org/caosdb/server/jobs/core/EntityStateJob.java
index a4c50f8893935d7bbd6091b970b32a8811a08d93..01b0ecb2274a85635dee3fe88f041e50178936fe 100644
--- a/src/main/java/org/caosdb/server/jobs/core/EntityStateJob.java
+++ b/src/main/java/org/caosdb/server/jobs/core/EntityStateJob.java
@@ -1,8 +1,8 @@
/*
* 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>
+ * Copyright (C) 2020,2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020,2023 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
@@ -53,6 +53,7 @@ import org.caosdb.server.entity.container.TransactionContainer;
import org.caosdb.server.entity.wrapper.Property;
import org.caosdb.server.entity.xml.ToElementable;
import org.caosdb.server.jobs.EntityJob;
+import org.caosdb.server.jobs.LazyEntityResolver;
import org.caosdb.server.permissions.EntityACI;
import org.caosdb.server.permissions.EntityACL;
import org.caosdb.server.query.Query;
@@ -572,7 +573,7 @@ public abstract class EntityStateJob extends EntityJob {
final String key = "transition" + refid.toString();
EntityInterface transition = getCached(key);
if (transition == null) {
- transition = retrieveValidEntity(refid);
+ transition = resolve(refid);
putCache(key, transition);
}
result.add(new Transition(transition));
@@ -659,7 +660,7 @@ public abstract class EntityStateJob extends EntityJob {
private EntityInterface retrieveStateEntity(final String stateName) throws Message {
try {
- return retrieveValidEntity(retrieveValidIDByName(stateName));
+ return resolve(null, stateName, (String) null);
} catch (final EntityDoesNotExistException e) {
throw STATE_NOT_IN_STATE_MODEL;
}
@@ -667,7 +668,7 @@ public abstract class EntityStateJob extends EntityJob {
private EntityInterface retrieveStateModelEntity(final String stateModel) throws Message {
try {
- return retrieveValidEntity(retrieveValidIDByName(stateModel));
+ return resolve(null, stateModel, (String) null);
} catch (final EntityDoesNotExistException e) {
throw STATE_MODEL_NOT_FOUND;
}
@@ -676,7 +677,7 @@ public abstract class EntityStateJob extends EntityJob {
protected EntityInterface getStateRecordType() throws Message {
EntityInterface stateRecordType = getCached(STATE_RECORD_TYPE_NAME);
if (stateRecordType == null) {
- stateRecordType = retrieveValidSparseEntityByName(STATE_RECORD_TYPE_NAME);
+ stateRecordType = resolve(null, STATE_RECORD_TYPE_NAME, (String) null);
putCache(STATE_RECORD_TYPE_NAME, stateRecordType);
}
return stateRecordType;
@@ -797,7 +798,7 @@ public abstract class EntityStateJob extends EntityJob {
EntityInterface stateEntity = getCached(key);
if (stateEntity == null) {
- stateEntity = retrieveValidEntity(refid.getId());
+ stateEntity = resolve(refid.getId());
putCache(key, stateEntity);
}
@@ -834,7 +835,7 @@ public abstract class EntityStateJob extends EntityJob {
getUser(),
c);
query.execute(getTransaction().getAccess());
- result = retrieveValidEntity(c.get(0).getId());
+ result = resolve(c.get(0).getId());
putCache(key, result);
return result;
}
@@ -852,6 +853,11 @@ public abstract class EntityStateJob extends EntityJob {
if (value instanceof DeleteEntity) {
throw new RuntimeException("Delete entity in cache. This is an implementation error.");
}
+ if (value instanceof LazyEntityResolver) {
+ // resolve immediately, otherwise the access might be released when
+ // the object is being resolved.
+ ((LazyEntityResolver) value).resolveAll();
+ }
id_in_cache.add(value.getId());
cache.put(key, value);
}
diff --git a/src/main/java/org/caosdb/server/jobs/core/GenerateEntityId.java b/src/main/java/org/caosdb/server/jobs/core/GenerateEntityId.java
new file mode 100644
index 0000000000000000000000000000000000000000..e3b21d9bdf67ad7a1ebe23ea1b77816e72b12de3
--- /dev/null
+++ b/src/main/java/org/caosdb/server/jobs/core/GenerateEntityId.java
@@ -0,0 +1,50 @@
+/*
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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 org.caosdb.server.jobs.core;
+
+import org.caosdb.server.entity.EntityInterface;
+import org.caosdb.server.entity.InsertEntity;
+import org.caosdb.server.entity.Message;
+import org.caosdb.server.jobs.EntityJob;
+import org.caosdb.server.jobs.JobAnnotation;
+import org.caosdb.server.jobs.TransactionStage;
+import org.caosdb.server.transaction.WriteTransactionInterface;
+import org.caosdb.server.utils.EntityStatus;
+
+/**
+ * Generates entity ids for newly inserted entities.
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
+@JobAnnotation(stage = TransactionStage.PRE_TRANSACTION)
+public class GenerateEntityId extends EntityJob {
+
+ @Override
+ protected void run() throws Message {
+ EntityInterface entity = getEntity();
+ if (entity instanceof InsertEntity
+ && getTransaction() instanceof WriteTransactionInterface
+ && entity.getEntityStatus() == EntityStatus.QUALIFIED) {
+ String id = ((WriteTransactionInterface) getTransaction()).generateId();
+ entity.setId(id);
+ }
+ }
+}
diff --git a/src/main/java/org/caosdb/server/jobs/core/Inheritance.java b/src/main/java/org/caosdb/server/jobs/core/Inheritance.java
index a1bd800c7ca40b28d7b9ff27dd8f828ed112891f..70aea11281774230e90e586cad3e897426df8e83 100644
--- a/src/main/java/org/caosdb/server/jobs/core/Inheritance.java
+++ b/src/main/java/org/caosdb/server/jobs/core/Inheritance.java
@@ -1,11 +1,10 @@
/*
- * ** header v3.0
* This file is a part of the CaosDB Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- * Copyright (C) 2019-2021 IndiScale GmbH <info@indiscale.com>
- * Copyright (C) 2019-2021 Timm Fitschen <t.fitschen@indiscale.com>
+ * Copyright (C) 2019-2021,2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2019-2021,2023 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
@@ -19,20 +18,16 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.jobs.core;
import java.util.ArrayList;
import java.util.List;
import org.caosdb.api.entity.v1.MessageCode;
-import org.caosdb.server.database.backend.transaction.RetrieveFullEntityTransaction;
import org.caosdb.server.entity.EntityInterface;
import org.caosdb.server.entity.InsertEntity;
import org.caosdb.server.entity.Message;
import org.caosdb.server.entity.Message.MessageType;
-import org.caosdb.server.entity.RetrieveEntity;
import org.caosdb.server.entity.StatementStatus;
import org.caosdb.server.entity.UpdateEntity;
import org.caosdb.server.entity.wrapper.Property;
@@ -88,12 +83,7 @@ public class Inheritance extends EntityJob {
runJobFromSchedule(getEntity(), CheckParValid.class);
// try to get the parent entity from the current transaction container
- EntityInterface foreign = getEntityByName(parent.getName());
- if (foreign == null) {
- // was not in container -> retrieve from database.
- execute(new RetrieveFullEntityTransaction(parent));
- foreign = parent;
- }
+ EntityInterface foreign = resolve(parent);
collectInheritedProperties(transfer, foreign, inheritance);
} catch (final IllegalArgumentException e) {
@@ -136,26 +126,24 @@ public class Inheritance extends EntityJob {
break propertyLoop;
}
- EntityInterface validProperty = new RetrieveEntity(property.getId());
+ EntityInterface abstractProperty = null;
if (getEntity().hasParents()) {
outer:
for (EntityInterface par : getEntity().getParents()) {
- if (!par.hasProperties()) {
- par = resolve(par);
- }
+ par = resolve(par);
for (final EntityInterface prop : par.getProperties()) {
- if (validProperty.hasId() && validProperty.getId().equals(prop.getId())) {
- validProperty = prop;
+ if ((property.hasId() && property.getId().equals(prop.getId()))
+ || property.hasName() && property.getName().equals(prop.getName())) {
+ abstractProperty = prop;
break outer;
}
}
}
- } else {
- execute(new RetrieveFullEntityTransaction(validProperty));
}
- if (validProperty.getEntityStatus() == EntityStatus.VALID) {
- collectInheritedProperties(transfer, validProperty, inheritance);
+ if (abstractProperty == null) {
+ abstractProperty = resolve(property);
}
+ collectInheritedProperties(transfer, abstractProperty, inheritance);
} catch (final IllegalArgumentException e) {
property.addWarning(ILLEGAL_INHERITANCE_MODE);
break propertyLoop;
diff --git a/src/main/java/org/caosdb/server/jobs/core/NoCache.java b/src/main/java/org/caosdb/server/jobs/core/NoCache.java
index e408330ee2639d1c5d7dc5f145848e292daa9b3b..78b54f6c7ecf97669889097241a9ee5f595a9416 100644
--- a/src/main/java/org/caosdb/server/jobs/core/NoCache.java
+++ b/src/main/java/org/caosdb/server/jobs/core/NoCache.java
@@ -1,9 +1,10 @@
/*
- * ** 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) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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
@@ -17,8 +18,6 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.jobs.core;
@@ -26,6 +25,13 @@ import org.caosdb.server.jobs.FlagJob;
import org.caosdb.server.jobs.JobAnnotation;
import org.caosdb.server.jobs.TransactionStage;
+/**
+ * Turn off caching, just for the current transaction.
+ *
+ * <p>If the caching is disabled globally this has no effect.
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
@JobAnnotation(
flag = "cache",
defaultValue = "true",
@@ -37,6 +43,6 @@ public class NoCache extends FlagJob {
@Override
protected void job(final String value) {
- getTransaction().getAccess().setUseCache(Boolean.valueOf(value));
+ getTransaction().setUseCache(Boolean.valueOf(value));
}
}
diff --git a/src/main/java/org/caosdb/server/jobs/core/ProcessNameProperties.java b/src/main/java/org/caosdb/server/jobs/core/ProcessNameProperties.java
index 7196f04edc99cf1269603e820975a96703639965..ecac050455b385d2ecf27bb4ff5d39d46c941508 100644
--- a/src/main/java/org/caosdb/server/jobs/core/ProcessNameProperties.java
+++ b/src/main/java/org/caosdb/server/jobs/core/ProcessNameProperties.java
@@ -1,9 +1,10 @@
/*
- * ** 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) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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
@@ -17,17 +18,16 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.jobs.core;
import static org.caosdb.server.entity.MagicTypes.NAME;
-import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
+import java.util.LinkedList;
import java.util.Set;
+import org.caosdb.server.database.exceptions.EntityDoesNotExistException;
import org.caosdb.server.datatype.AbstractDatatype;
import org.caosdb.server.entity.EntityID;
import org.caosdb.server.entity.EntityInterface;
@@ -41,9 +41,13 @@ import org.caosdb.server.utils.EntityStatus;
import org.caosdb.server.utils.ServerMessages;
/**
- * To be called after CheckPropValid and Inheritance.
+ * Checks if a property is a subproperty of "name" and flags the entity accordingly.
+ *
+ * <p>This enables a different behavior in the search.
*
- * @author tf
+ * <p>To be called after CheckPropValid and Inheritance.
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
*/
@JobAnnotation(stage = TransactionStage.PRE_TRANSACTION)
public class ProcessNameProperties extends EntityJob {
@@ -133,21 +137,22 @@ public class ProcessNameProperties extends EntityJob {
}
private Collection<Object> getNearestValidParents(final Property prop) {
- if (prop.hasId() && !prop.getId().isTemporary()) {
- final ArrayList<Object> ret = new ArrayList<Object>();
- if (prop.hasParents()) {
- for (final Parent par : prop.getParents()) {
+ if (prop.hasParents()) {
+ final Collection<Object> ret = new LinkedList<Object>();
+ for (final Parent par : prop.getParents()) {
+ if (par.hasId()) {
ret.add(par.getId());
}
- } else {
- ret.add(prop.getId());
}
return ret;
} else if (prop.hasId()) {
- // property is new -> get valid parents of any depth
- final EntityInterface propertyEntity = getEntityById(prop.getId());
- if (propertyEntity != null) {
- return getNearestValidParents(propertyEntity);
+ try {
+ EntityInterface propertyEntity = resolve(prop.getId());
+ if (propertyEntity != null) {
+ return getNearestValidParents(propertyEntity);
+ }
+ } catch (EntityDoesNotExistException e) {
+ // return null
}
return null;
} else {
diff --git a/src/main/java/org/caosdb/server/jobs/core/ResolveNames.java b/src/main/java/org/caosdb/server/jobs/core/ResolveNames.java
index 5ab722c7176e89485e2bd40dfd515a77bc09e38b..e353375baaaa11c59d7e67c7e39c8cd5a8eb38ee 100644
--- a/src/main/java/org/caosdb/server/jobs/core/ResolveNames.java
+++ b/src/main/java/org/caosdb/server/jobs/core/ResolveNames.java
@@ -1,9 +1,10 @@
/*
- * ** 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) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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
@@ -17,14 +18,13 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.jobs.core;
import java.util.ArrayList;
import java.util.List;
import org.caosdb.server.database.backend.transaction.GetIDByName;
+import org.caosdb.server.database.backend.transaction.RetrieveSparseEntity;
import org.caosdb.server.database.exceptions.EntityDoesNotExistException;
import org.caosdb.server.entity.Entity;
import org.caosdb.server.entity.EntityID;
@@ -35,6 +35,18 @@ import org.caosdb.server.jobs.ContainerJob;
import org.caosdb.server.utils.EntityStatus;
import org.caosdb.server.utils.ServerMessages;
+/**
+ * Resolve the names to ids for all entities in the current retrieval.
+ *
+ * <p>If an entity has a name which looks like an id: Check whether that is an existing id first.
+ *
+ * <p>Otherwise, search via the name.
+ *
+ * <p>It there are multiple matching entities, add all of them to the current container. The clients
+ * may handle the ambiguity.
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
public class ResolveNames extends ContainerJob {
@Override
@@ -45,6 +57,20 @@ public class ResolveNames extends ContainerJob {
public void resolve(final TransactionContainer container) {
final ArrayList<Entity> add = new ArrayList<Entity>();
for (final EntityInterface e : container) {
+ if (!e.hasId() && e.hasName() && getTransaction().matchIdPattern(e.getName())) {
+ try {
+ EntityInterface valid =
+ execute(
+ new RetrieveSparseEntity(
+ new EntityID(e.getName()),
+ e.hasVersion() ? e.getVersion().getId() : null))
+ .getEntity();
+ e.setId(valid.getId());
+ } catch (final EntityDoesNotExistException exc) {
+ // Definitely not an existing id.
+ }
+ }
+
if (e.hasName() && !e.hasId()) {
try {
final List<EntityID> c = execute(new GetIDByName(e.getName(), false)).getList();
diff --git a/src/main/java/org/caosdb/server/jobs/core/UniqueName.java b/src/main/java/org/caosdb/server/jobs/core/UniqueName.java
index 86e6c37e35ec91db647e14e30896abb6b884555b..079afdd9a922fa5758e5f4eb6bec80538338db21 100644
--- a/src/main/java/org/caosdb/server/jobs/core/UniqueName.java
+++ b/src/main/java/org/caosdb/server/jobs/core/UniqueName.java
@@ -40,7 +40,7 @@ public class UniqueName extends FlagJob {
// check against data base
try {
- final EntityID foreign = retrieveValidIDByName(entity.getName());
+ final EntityID foreign = retrieveValidIDByName(entity.getName(), null);
if (entity.hasId() && !foreign.equals(entity.getId())) {
throw new EntityWasNotUniqueException();
}
diff --git a/src/main/java/org/caosdb/server/query/CQLLexer.g4 b/src/main/java/org/caosdb/server/query/CQLLexer.g4
index be6dcfa99d2f9c48cba8a0f7fccb7f97b277e01d..f21caf26f0f19d0433b1cdef2d5975d472791e99 100644
--- a/src/main/java/org/caosdb/server/query/CQLLexer.g4
+++ b/src/main/java/org/caosdb/server/query/CQLLexer.g4
@@ -433,7 +433,7 @@ WHITE_SPACE_f:
/** */
WHITE_SPACE:
- [ \t\n\r]+
+ WHITE_SPACE_f
;
/** */
@@ -529,9 +529,9 @@ COLON:
/** Matches signed and unsigned numbers with decimal points, also numbers in scientific notation. */
DECIMAL_NUMBER:
- ((HYPHEN_f | PLUS ) WHITE_SPACE_f?)?
- ( NUM_f? DOT NUM_f WHITE_SPACE_f? E_NOTATION_f?
- | NUM_f WHITE_SPACE_f? E_NOTATION_f
+ ((HYPHEN_f | PLUS ) WHITE_SPACE_f?)?
+ ( NUM_f? DOT NUM_f (WHITE_SPACE_f? E_NOTATION_f)?
+ | NUM_f (WHITE_SPACE_f? E_NOTATION_f)?
)
;
diff --git a/src/main/java/org/caosdb/server/query/IDFilter.java b/src/main/java/org/caosdb/server/query/IDFilter.java
index ce01f5f242f914c6f6f812f0875332f7ca004c07..8011139796abff42c0e8109621c849d3e6328137 100644
--- a/src/main/java/org/caosdb/server/query/IDFilter.java
+++ b/src/main/java/org/caosdb/server/query/IDFilter.java
@@ -1,9 +1,10 @@
/*
- * ** 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) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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
@@ -17,8 +18,6 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.query;
@@ -32,24 +31,21 @@ import java.sql.SQLException;
import org.caosdb.server.query.Query.QueryException;
import org.jdom2.Element;
+/**
+ * Applies an ID filter to the query's current result set.
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
public class IDFilter implements EntityFilterInterface {
private final String operator;
private final String value;
private final String aggregate;
- private final Integer vInt;
public IDFilter(final String o, final String v, final String a) {
this.operator = o;
this.value = v;
this.aggregate = a;
- Integer i;
- try {
- i = Integer.valueOf(v);
- } catch (final NumberFormatException e) {
- i = null;
- }
- this.vInt = i;
}
@Override
@@ -79,7 +75,7 @@ public class IDFilter implements EntityFilterInterface {
if (getValue() == null) {
callIDFilter.setNull(4, INTEGER);
} else {
- callIDFilter.setInt(4, this.vInt);
+ callIDFilter.setString(4, this.getValue());
}
// aggregate
diff --git a/src/main/java/org/caosdb/server/query/POV.java b/src/main/java/org/caosdb/server/query/POV.java
index ebc35a16b1495accf8cd4a114dd688c2b2529c1b..6ee5f9d0122aa417c357e71ef6d6ea0516007215 100644
--- a/src/main/java/org/caosdb/server/query/POV.java
+++ b/src/main/java/org/caosdb/server/query/POV.java
@@ -1,9 +1,10 @@
/*
- * ** 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) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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
@@ -17,8 +18,6 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.query;
@@ -50,6 +49,11 @@ import org.jdom2.Element;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
+/**
+ * Applies a POV (Property-operator-value) filter to the query's current result set.
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
public class POV implements EntityFilterInterface {
public static final Pattern NUMBER_PATTERN =
Pattern.compile(
@@ -383,8 +387,8 @@ public class POV implements EntityFilterInterface {
query.getConnection().prepareCall("call initPOVRefidsTable(?,?)")) {
// stmt = this.connection.prepareCall("call initPOV(?,?,?,?,?)");
// initPOVRefidsTable(in vInt INT, in vText VARCHAR(255))
- if (this.vInt != null && this.vInt > 0) {
- stmt.setInt(1, this.vInt);
+ if (this.value != null) {
+ stmt.setString(1, this.value);
} else {
stmt.setNull(1, Types.INTEGER);
}
diff --git a/src/main/java/org/caosdb/server/query/Query.java b/src/main/java/org/caosdb/server/query/Query.java
index abaca4365e54c21ee2ba8cf8bf7727fe746c7277..53cd7bf04bccf03eab9422e591750849bfa48728 100644
--- a/src/main/java/org/caosdb/server/query/Query.java
+++ b/src/main/java/org/caosdb/server/query/Query.java
@@ -3,8 +3,8 @@
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- * Copyright (C) 2019-2021 IndiScale GmbH <info@indiscale.com>
- * Copyright (C) 2019-2021 Timm Fitschen <t.fitschen@indiscale.com>
+ * Copyright (C) 2019-2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2019-2023 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
@@ -73,7 +73,6 @@ import org.caosdb.server.query.CQLParser.CqContext;
import org.caosdb.server.query.CQLParsingErrorListener.ParsingError;
import org.caosdb.server.transaction.TransactionInterface;
import org.caosdb.server.transaction.WriteTransaction;
-import org.caosdb.server.utils.ResultSetIterator;
import org.jdom2.Element;
import org.slf4j.Logger;
@@ -218,22 +217,22 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
/** A data class for storing triplets of (Entity ID, version hash, ACL string) */
public static class IdVersionAclTriplet {
- public IdVersionAclTriplet(final Integer id, final String version, final String acl) {
+ public IdVersionAclTriplet(final String id, final String version, final String acl) {
this.id = id;
this.version = version;
this.acl = acl;
}
- public Integer id;
+ public String id;
public String version;
public String acl;
@Override
public String toString() {
if (version == null) {
- return Integer.toString(id);
+ return id;
}
- return Integer.toString(id) + "@" + version;
+ return id + "@" + version;
}
@Override
@@ -256,6 +255,14 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
public int hashCode() {
return toString().hashCode();
}
+
+ public boolean isInternal() {
+ try {
+ return Integer.parseInt(id) < 100;
+ } catch (NumberFormatException e) {
+ return false;
+ }
+ }
}
private final boolean filterEntitiesWithoutRetrievePermisions =
@@ -280,6 +287,7 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
private final ArrayList<ToElementable> messages = new ArrayList<>();
private Access access;
private boolean versioned = false;
+
/**
* This key-value cache stores lists of of (id, version hash, acl string) triplets. Those values
* are the result sets of queries. The keys are created such that they are different for different
@@ -294,8 +302,10 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
*/
private static ICacheAccess<String, Serializable> cache =
Cache.getCache("HIGH_LEVEL_QUERY_CACHE");
+
/** Cached=true means that the results of this query have actually been pulled from the cache. */
private boolean cached = false;
+
/**
* Cachable=false means that the results of this query cannot be used for the cache, because the
* query evaluation contains complex permission checking which could only be cached on a per-user
@@ -327,7 +337,8 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
this.container = container;
this.query = query;
this.user = user;
- };
+ }
+ ;
/**
* Fill the initially empty resultSet with all entities which match the name, or the id. Then
@@ -412,12 +423,19 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
final Map<EntityID, String> queryTemplates = getQueryTemplates(query, resultSet);
final PreparedStatement removeQTStmt =
- query.getConnection().prepareStatement("DELETE FROM `" + resultSet + "` WHERE id=?");
+ query
+ .getConnection()
+ .prepareStatement(
+ "DELETE FROM `"
+ + resultSet
+ + "` WHERE EXISTS (SELECT 1 FROM entity_ids AS eids WHERE eids.id=? AND eids.internal_id=`"
+ + resultSet
+ + "`.id)");
// Run thru all QTs found...
for (final Entry<EntityID, String> q : queryTemplates.entrySet()) {
// ... remove the QT from resultSet...
- removeQTStmt.setInt(1, q.getKey().toInteger());
+ removeQTStmt.setString(1, q.getKey().toString());
removeQTStmt.execute();
// ... check for RETRIEVE:ENTITY permission...
@@ -468,12 +486,12 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
query
.getConnection()
.prepareCall(
- "SELECT q.id, q.definition FROM query_template_def AS q INNER JOIN `"
+ "SELECT (SELECT eids.id FROM entity_ids AS eids WHERE eids.internal_id = q.id) as id, q.definition FROM query_template_def AS q INNER JOIN `"
+ resultSet
+ "` AS r ON (r.id=q.id);");
rs = stmt.executeQuery();
while (rs.next()) {
- ret.put(new EntityID(rs.getInt("id")), rs.getString("definition"));
+ ret.put(new EntityID(rs.getString("id")), rs.getString("definition"));
}
return ret;
} finally {
@@ -625,7 +643,7 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
if (this.entity != null) {
return sourceStrategy(initQuery(versioned));
} else if (this.role == Role.ENTITY && this.filter == null) {
- return "entities";
+ return "entity_ids";
} else {
return targetStrategy(initQuery(versioned));
}
@@ -644,29 +662,27 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
*/
private String generateSelectStatementForResultSet(
final String resultSetTableName, final boolean versioned) {
- // TODO remove the entities.role part when
- // https://gitlab.indiscale.com/caosdb/src/caosdb-server/-/issues/245 is resolved
- if (resultSetTableName.equals("entities")) {
+ if (resultSetTableName.equals("entity_ids")) {
final String baseStatement =
- "SELECT entities.id, entity_acl.acl FROM entities INNER JOIN entity_acl ON entity_acl.id=entities.acl WHERE entities.role!='DOMAIN'";
+ "SELECT entities.id AS internal_id, (SELECT id FROM entity_ids WHERE internal_id = entities.id) as id, entity_acl.acl FROM entities INNER JOIN entity_acl ON entity_acl.id=entities.acl";
if (!versioned) {
return baseStatement + ";";
}
// if versioned, the statement is surrounded with another SELECT and JOIN
return ("SELECT id, acl, version FROM ("
+ baseStatement
- + ") AS tmp JOIN entity_version ON entity_version.entity_id=tmp.id;");
+ + ") AS tmp JOIN entity_version ON entity_version.entity_id=tmp.internal_id;");
} else {
if (!versioned) {
- return (" SELECT tmp.id, entity_acl.acl FROM "
+ return (" SELECT (SELECT id FROM entity_ids WHERE internal_id = tmp.id) AS id, entity_acl.acl FROM "
+ " (SELECT results.id AS id, entities.acl AS acl_id FROM `"
+ resultSetTableName
- + "` AS results JOIN entities ON results.id=entities.id WHERE entities.role!='DOMAIN') AS tmp"
+ + "` AS results JOIN entities ON results.id=entities.id) AS tmp"
+ " JOIN entity_acl ON entity_acl.id=tmp.acl_id")
+ ";";
}
// if versioned, the statement is surrounded with another SELECT and JOIN
- return ("SELECT tmp2.id, acl, version FROM( SELECT tmp.id, entity_acl.acl, tmp._iversion AS _iversion FROM "
+ return ("SELECT (SELECT id FROM entity_ids WHERE internal_id = tmp2.id) AS id, acl, version FROM (SELECT tmp.id, entity_acl.acl, tmp._iversion AS _iversion FROM "
+ " (SELECT results.id AS id, entities.acl AS acl_id, results._iversion AS _iversion FROM `"
+ resultSetTableName
+ "` AS results JOIN entities ON results.id=entities.id) AS tmp"
@@ -692,10 +708,14 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
finishResultSet = finish.executeQuery();
final List<IdVersionAclTriplet> rs = new LinkedList<>();
while (finishResultSet.next()) {
+ final String id = finishResultSet.getString("id");
+ if (finishResultSet.wasNull()) {
+ continue;
+ }
final String version = versioned ? finishResultSet.getString("version") : null;
final String acl = finishResultSet.getString("acl");
- rs.add(new IdVersionAclTriplet(finishResultSet.getInt("id"), version, acl));
+ rs.add(new IdVersionAclTriplet(id, version, acl));
}
return rs;
} catch (final SQLException e) {
@@ -724,6 +744,7 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
this.resultSet = getCached(getCacheKey(false));
}
}
+
/** Store the content of `resultSet` member in the high level query cache. */
private void storeResultInCache() {
// Decide whether user specific cache needs to be used or not
@@ -735,6 +756,7 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
cacheItem(getCacheKey(false), this.resultSet);
}
}
+
/** Fill entities from `resultSet` into `container`. */
private void fillContainerWithResult() {
if (this.container != null && (this.type == Type.FIND || this.type == Type.SELECT)) {
@@ -786,6 +808,7 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
}
return this;
}
+
/** Remove all cached queries from the cache. */
public static void clearCache() {
cacheETag = UUID.randomUUID().toString();
@@ -798,7 +821,7 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
final List<IdVersionAclTriplet> filtered = new ArrayList<>();
for (final IdVersionAclTriplet triplet : resultSet) {
- if (triplet.id >= 100) {
+ if (!triplet.isInternal()) {
filtered.add(triplet);
}
}
@@ -908,11 +931,11 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
+ "left join entity_acl on entity_n_acl.acl=entity_acl.id;");
final ResultSet entitiesRS = stmt.executeQuery(query);
final ResultSetIterator entitiesWithACL = new ResultSetIterator(entitiesRS);
- final List<Integer> toBeDeleted = collectIdsWithoutPermission(entitiesWithACL);
+ final List<String> toBeDeleted = collectIdsWithoutPermission(entitiesWithACL);
try (final PreparedStatement pstmt =
this.getConnection().prepareStatement("DELETE FROM `" + tabname + "` WHERE id = ?")) {
- for (final Integer id : toBeDeleted) {
- pstmt.setInt(1, id);
+ for (final String id : toBeDeleted) {
+ pstmt.setString(1, id);
pstmt.execute();
}
}
@@ -931,8 +954,8 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
*/
private List<IdVersionAclTriplet> filterEntitiesWithoutRetrievePermission(
final List<IdVersionAclTriplet> resultSet) {
- final List<Integer> toBeDeleted = collectIdsWithoutPermission(resultSet.iterator());
- final List<IdVersionAclTriplet> filtered = new ArrayList<>();
+ final List<String> toBeDeleted = collectIdsWithoutPermission(resultSet.iterator());
+ final List<IdVersionAclTriplet> filtered = new LinkedList<>();
for (final IdVersionAclTriplet triplet : resultSet) {
if (-1 == toBeDeleted.indexOf(triplet.id)) {
filtered.add(triplet);
@@ -940,6 +963,7 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
}
return filtered;
}
+
/**
* Creates a list with IDs of those entities that do not have sufficient RETRIEVE permission
*
@@ -947,9 +971,9 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
* triplets.
* @return compiled list
*/
- private List<Integer> collectIdsWithoutPermission(Iterator<IdVersionAclTriplet> entityIterator) {
- final HashMap<String, Boolean> acl_cache = new HashMap<String, Boolean>();
- final List<Integer> toBeDeleted = new LinkedList<Integer>();
+ private List<String> collectIdsWithoutPermission(Iterator<IdVersionAclTriplet> entityIterator) {
+ final Map<String, Boolean> acl_cache = new HashMap<>();
+ final List<String> toBeDeleted = new LinkedList<>();
while (entityIterator.hasNext()) {
final long t1 = System.currentTimeMillis();
@@ -999,7 +1023,9 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
return this.access;
}
- /** @return the number of entities in the resultset. Might be updated by the filters. */
+ /**
+ * @return the number of entities in the resultset. Might be updated by the filters.
+ */
@Override
public int getTargetSetCount() {
return this.targetSetCount;
diff --git a/src/main/java/org/caosdb/server/utils/ResultSetIterator.java b/src/main/java/org/caosdb/server/query/ResultSetIterator.java
similarity index 95%
rename from src/main/java/org/caosdb/server/utils/ResultSetIterator.java
rename to src/main/java/org/caosdb/server/query/ResultSetIterator.java
index 71429f1a704299555ab1d86be0695e3104be828d..a26c1f41867e96722dd4ba6451344b689d0299e0 100644
--- a/src/main/java/org/caosdb/server/utils/ResultSetIterator.java
+++ b/src/main/java/org/caosdb/server/query/ResultSetIterator.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.utils;
+package org.caosdb.server.query;
import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
@@ -35,7 +35,8 @@ public class ResultSetIterator implements Iterator<IdVersionAclTriplet> {
this.cursorHasMoved = true;
}
return this.currentIsValid;
- };
+ }
+ ;
public IdVersionAclTriplet next() {
if (!this.cursorHasMoved) {
@@ -50,7 +51,7 @@ public class ResultSetIterator implements Iterator<IdVersionAclTriplet> {
throw new NoSuchElementException();
}
try {
- final Integer id = resultSet.getInt("id");
+ final String id = resultSet.getString("id");
final String acl_str = bytes2UTF8(resultSet.getBytes("ACL"));
return new IdVersionAclTriplet(id, "", acl_str);
} catch (SQLException e) {
diff --git a/src/main/java/org/caosdb/server/resource/AbstractCaosDBServerResource.java b/src/main/java/org/caosdb/server/resource/AbstractCaosDBServerResource.java
index 44ebfa22d08c975031f5bf5bfca325d6b706af24..de56fff3207cd554d23badcc63dbd8e5130e6e81 100644
--- a/src/main/java/org/caosdb/server/resource/AbstractCaosDBServerResource.java
+++ b/src/main/java/org/caosdb/server/resource/AbstractCaosDBServerResource.java
@@ -243,8 +243,12 @@ public abstract class AbstractCaosDBServerResource extends ServerResource {
}
protected abstract Representation httpGetInChildClass()
- throws ConnectionException, IOException, SQLException, CaosDBException,
- NoSuchAlgorithmException, Exception;
+ throws ConnectionException,
+ IOException,
+ SQLException,
+ CaosDBException,
+ NoSuchAlgorithmException,
+ Exception;
@Post
public Representation httpPost(final Representation entity) {
@@ -277,8 +281,12 @@ public abstract class AbstractCaosDBServerResource extends ServerResource {
}
protected Representation httpDeleteInChildClass()
- throws ConnectionException, SQLException, CaosDBException, IOException,
- NoSuchAlgorithmException, Exception {
+ throws ConnectionException,
+ SQLException,
+ CaosDBException,
+ IOException,
+ NoSuchAlgorithmException,
+ Exception {
getResponse().setStatus(Status.CLIENT_ERROR_METHOD_NOT_ALLOWED);
return null;
}
@@ -293,8 +301,14 @@ public abstract class AbstractCaosDBServerResource extends ServerResource {
}
protected Representation httpPostInChildClass(final Representation entity)
- throws ConnectionException, SQLException, CaosDBException, IOException,
- NoSuchAlgorithmException, xmlNotWellFormedException, JDOMException, Exception {
+ throws ConnectionException,
+ SQLException,
+ CaosDBException,
+ IOException,
+ NoSuchAlgorithmException,
+ xmlNotWellFormedException,
+ JDOMException,
+ Exception {
getResponse().setStatus(Status.CLIENT_ERROR_METHOD_NOT_ALLOWED);
return null;
}
diff --git a/src/main/java/org/caosdb/server/resource/AuthenticationResource.java b/src/main/java/org/caosdb/server/resource/AuthenticationResource.java
index ed60d7906b1cda003ed2a84f0e22200049d96c25..4f53ba12e958a33d694357372afba274fcfe4151 100644
--- a/src/main/java/org/caosdb/server/resource/AuthenticationResource.java
+++ b/src/main/java/org/caosdb/server/resource/AuthenticationResource.java
@@ -52,8 +52,12 @@ public class AuthenticationResource extends AbstractCaosDBServerResource {
/** Returns single "Login" element. XSLT will create a form. */
@Override
protected Representation httpGetInChildClass()
- throws ConnectionException, IOException, SQLException, CaosDBException,
- NoSuchAlgorithmException, Exception {
+ throws ConnectionException,
+ IOException,
+ SQLException,
+ CaosDBException,
+ NoSuchAlgorithmException,
+ Exception {
final Document doc = new Document();
final Element rootElem = generateRootElement();
doc.setRootElement(rootElem);
@@ -66,8 +70,12 @@ public class AuthenticationResource extends AbstractCaosDBServerResource {
@Override
protected Representation httpDeleteInChildClass()
- throws ConnectionException, SQLException, CaosDBException, IOException,
- NoSuchAlgorithmException, Exception {
+ throws ConnectionException,
+ SQLException,
+ CaosDBException,
+ IOException,
+ NoSuchAlgorithmException,
+ Exception {
final Subject user = SecurityUtils.getSubject();
if (user.isAuthenticated()) {
user.logout();
diff --git a/src/main/java/org/caosdb/server/resource/DefaultResource.java b/src/main/java/org/caosdb/server/resource/DefaultResource.java
index 488cd667c8832e4b90277e07144c65cbb7e4036d..39fbf47dcd4cde1d96642a0112b58c3285dec2c9 100644
--- a/src/main/java/org/caosdb/server/resource/DefaultResource.java
+++ b/src/main/java/org/caosdb/server/resource/DefaultResource.java
@@ -43,8 +43,12 @@ public class DefaultResource extends AbstractCaosDBServerResource {
@Override
protected Representation httpGetInChildClass()
- throws ConnectionException, IOException, SQLException, CaosDBException,
- NoSuchAlgorithmException, Exception {
+ throws ConnectionException,
+ IOException,
+ SQLException,
+ CaosDBException,
+ NoSuchAlgorithmException,
+ Exception {
final Document doc = new org.jdom2.Document();
final Element root = generateRootElement();
if (this.responseBody != null) {
diff --git a/src/main/java/org/caosdb/server/resource/LogoutResource.java b/src/main/java/org/caosdb/server/resource/LogoutResource.java
index 1659f751a4710fbf99fc473b586cc3b180c8a62c..f17bd0c65119bc21183a0d7165a62688e60f2d25 100644
--- a/src/main/java/org/caosdb/server/resource/LogoutResource.java
+++ b/src/main/java/org/caosdb/server/resource/LogoutResource.java
@@ -33,8 +33,12 @@ public class LogoutResource extends AuthenticationResource {
@Override
protected Representation httpGetInChildClass()
- throws ConnectionException, IOException, SQLException, CaosDBException,
- NoSuchAlgorithmException, Exception {
+ throws ConnectionException,
+ IOException,
+ SQLException,
+ CaosDBException,
+ NoSuchAlgorithmException,
+ Exception {
return super.httpDeleteInChildClass();
}
}
diff --git a/src/main/java/org/caosdb/server/resource/PermissionRulesResource.java b/src/main/java/org/caosdb/server/resource/PermissionRulesResource.java
index 8d2aa1720aaefcdbaccee18c6a1626a912319b6a..afdcb0d60f077ebcfc2dfcc0e99093289a6d621f 100644
--- a/src/main/java/org/caosdb/server/resource/PermissionRulesResource.java
+++ b/src/main/java/org/caosdb/server/resource/PermissionRulesResource.java
@@ -44,8 +44,12 @@ public class PermissionRulesResource extends AbstractCaosDBServerResource {
@Override
protected Representation httpGetInChildClass()
- throws ConnectionException, IOException, SQLException, CaosDBException,
- NoSuchAlgorithmException, Exception {
+ throws ConnectionException,
+ IOException,
+ SQLException,
+ CaosDBException,
+ NoSuchAlgorithmException,
+ Exception {
final String role = getRequestedItems()[0];
getUser().checkPermission(ACMPermissions.PERMISSION_RETRIEVE_ROLE_PERMISSIONS(role));
diff --git a/src/main/java/org/caosdb/server/resource/RolesResource.java b/src/main/java/org/caosdb/server/resource/RolesResource.java
index ad1544da3a326f1c16e0b01238985d10e93b0581..73dee43e1f6b49d2c73cf44fe80510bb704d4f0d 100644
--- a/src/main/java/org/caosdb/server/resource/RolesResource.java
+++ b/src/main/java/org/caosdb/server/resource/RolesResource.java
@@ -46,8 +46,12 @@ public class RolesResource extends AbstractCaosDBServerResource {
@Override
protected Representation httpGetInChildClass()
- throws ConnectionException, IOException, SQLException, CaosDBException,
- NoSuchAlgorithmException, Exception {
+ throws ConnectionException,
+ IOException,
+ SQLException,
+ CaosDBException,
+ NoSuchAlgorithmException,
+ Exception {
final Element root = generateRootElement();
final Document document = new Document();
@@ -74,8 +78,12 @@ public class RolesResource extends AbstractCaosDBServerResource {
@Override
protected Representation httpDeleteInChildClass()
- throws ConnectionException, SQLException, CaosDBException, IOException,
- NoSuchAlgorithmException, Exception {
+ throws ConnectionException,
+ SQLException,
+ CaosDBException,
+ IOException,
+ NoSuchAlgorithmException,
+ Exception {
if (getRequestedItems().length > 0) {
final String name = getRequestedItems()[0];
if (name != null) {
@@ -97,8 +105,14 @@ public class RolesResource extends AbstractCaosDBServerResource {
@Override
protected Representation httpPostInChildClass(final Representation entity)
- throws ConnectionException, SQLException, CaosDBException, IOException,
- NoSuchAlgorithmException, xmlNotWellFormedException, JDOMException, Exception {
+ throws ConnectionException,
+ SQLException,
+ CaosDBException,
+ IOException,
+ NoSuchAlgorithmException,
+ xmlNotWellFormedException,
+ JDOMException,
+ Exception {
String name = null;
String description = null;
diff --git a/src/main/java/org/caosdb/server/resource/ServerLogsResource.java b/src/main/java/org/caosdb/server/resource/ServerLogsResource.java
index f304f10062209d62855a0bff21e0c8cad54e1962..acc1833dc5158d23e72f06f15cf1ddd037185043 100644
--- a/src/main/java/org/caosdb/server/resource/ServerLogsResource.java
+++ b/src/main/java/org/caosdb/server/resource/ServerLogsResource.java
@@ -41,8 +41,12 @@ public class ServerLogsResource extends AbstractCaosDBServerResource {
@Override
protected Representation httpGetInChildClass()
- throws ConnectionException, IOException, SQLException, CaosDBException,
- NoSuchAlgorithmException, Exception {
+ throws ConnectionException,
+ IOException,
+ SQLException,
+ CaosDBException,
+ NoSuchAlgorithmException,
+ Exception {
Level level = null;
String message = null;
diff --git a/src/main/java/org/caosdb/server/resource/UserResource.java b/src/main/java/org/caosdb/server/resource/UserResource.java
index de07331e9637549285d71ca2fd910916cd13316a..ea8e8a264542474cccf74d20cf070342cb43d717 100644
--- a/src/main/java/org/caosdb/server/resource/UserResource.java
+++ b/src/main/java/org/caosdb/server/resource/UserResource.java
@@ -1,9 +1,10 @@
/*
- * ** 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) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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
@@ -17,8 +18,6 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.resource;
@@ -48,14 +47,18 @@ import org.restlet.representation.Representation;
/**
* This class handles requests for Users.
*
- * @author Timm Fitschen
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
*/
public class UserResource extends AbstractCaosDBServerResource {
@Override
protected Representation httpGetInChildClass()
- throws ConnectionException, IOException, SQLException, CaosDBException,
- NoSuchAlgorithmException, Exception {
+ throws ConnectionException,
+ IOException,
+ SQLException,
+ CaosDBException,
+ NoSuchAlgorithmException,
+ Exception {
final Document doc = new Document();
final Element rootElem = generateRootElement();
@@ -104,12 +107,12 @@ public class UserResource extends AbstractCaosDBServerResource {
form.getFirstValue("status") != null
? UserStatus.valueOf(form.getFirstValue("status").toUpperCase())
: null;
- Integer userEntity = null;
+ String userEntity = null;
if (form.getFirst("entity") != null) {
if (form.getFirstValue("entity").isEmpty()) {
- userEntity = 0;
+ userEntity = "";
} else {
- userEntity = Integer.parseInt(form.getFirstValue("entity"));
+ userEntity = form.getFirstValue("entity");
}
}
@@ -150,9 +153,9 @@ public class UserResource extends AbstractCaosDBServerResource {
"status",
CaosDBServer.getServerProperty(ServerProperties.KEY_NEW_USER_DEFAULT_ACTIVITY))
.toUpperCase());
- Integer userEntity = null;
+ String userEntity = null;
if (form.getFirst("entity") != null) {
- userEntity = Integer.parseInt(form.getFirstValue("entity"));
+ userEntity = form.getFirstValue("entity");
}
final InsertUserTransaction t =
@@ -177,8 +180,12 @@ public class UserResource extends AbstractCaosDBServerResource {
@Override
protected Representation httpDeleteInChildClass()
- throws ConnectionException, SQLException, CaosDBException, IOException,
- NoSuchAlgorithmException, Exception {
+ throws ConnectionException,
+ SQLException,
+ CaosDBException,
+ IOException,
+ NoSuchAlgorithmException,
+ Exception {
final Document doc = new Document();
final Element rootElem = generateRootElement();
diff --git a/src/main/java/org/caosdb/server/resource/UserRolesResource.java b/src/main/java/org/caosdb/server/resource/UserRolesResource.java
index 4eb7f6143038bb6e4b0c3fda4646e2730acfea04..72fc906a54b753166a4f5358dfda31ba0dff953e 100644
--- a/src/main/java/org/caosdb/server/resource/UserRolesResource.java
+++ b/src/main/java/org/caosdb/server/resource/UserRolesResource.java
@@ -45,8 +45,12 @@ public class UserRolesResource extends AbstractCaosDBServerResource {
@Override
protected Representation httpGetInChildClass()
- throws ConnectionException, IOException, SQLException, CaosDBException,
- NoSuchAlgorithmException, Exception {
+ throws ConnectionException,
+ IOException,
+ SQLException,
+ CaosDBException,
+ NoSuchAlgorithmException,
+ Exception {
final String user = getRequestedItems()[0];
final String realm =
(getRequestAttributes().get("realm") != null
diff --git a/src/main/java/org/caosdb/server/resource/transaction/EntityResource.java b/src/main/java/org/caosdb/server/resource/transaction/EntityResource.java
index 4cd7b2fcbd4ae9e9dd3d047555194172c4224d38..833043885ecb0843483417c97cc7569ae316e8ef 100644
--- a/src/main/java/org/caosdb/server/resource/transaction/EntityResource.java
+++ b/src/main/java/org/caosdb/server/resource/transaction/EntityResource.java
@@ -3,8 +3,8 @@
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- * Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
- * Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2021,2023 Timm Fitschen <t.fitschen@indiscale.com>
+ * Copyright (C) 2021,2023 IndiScale GmbH <info@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
@@ -53,11 +53,16 @@ import org.restlet.representation.Representation;
*
* <p>The GET requests (Retrieval) is handled in the superclass {@link RetrieveEntityResource}.
*
- * @author Timm Fitschen (t.fitschen@indiscale.com)
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
*/
public class EntityResource extends RetrieveEntityResource {
- /** Handle entity deletions (DELETE requests). */
+ /**
+ * Handle entity deletions (DELETE requests).
+ *
+ * <p>Note: The list of entity "specifier" is treated strictly as a list of entity ids. You cannot
+ * delete an entity by name.
+ */
@Override
protected final Representation httpDeleteInChildClass() throws Exception {
@@ -67,18 +72,14 @@ public class EntityResource extends RetrieveEntityResource {
for (final String item : getRequestedItems()) {
final String[] elem = item.split("@", 1);
- Integer id = null;
+ String id = null;
String version = null;
- try {
- id = Integer.parseInt(elem[0]);
- } catch (final NumberFormatException e) {
- // pass
- }
+ id = elem[0];
if (elem.length > 1) {
version = elem[1];
}
- if (id != null && id > 0) {
+ if (id != null) {
container.add(new DeleteEntity(new EntityID(id), version));
}
}
@@ -129,8 +130,12 @@ public class EntityResource extends RetrieveEntityResource {
* requests which also contain file blobs.
*/
private Element parseMultipartEntity(final WritableContainer container)
- throws FileUploadException, IOException, Message, xmlNotWellFormedException,
- NoSuchAlgorithmException, CaosDBException {
+ throws FileUploadException,
+ IOException,
+ Message,
+ xmlNotWellFormedException,
+ NoSuchAlgorithmException,
+ CaosDBException {
final DiskFileItemFactory factory = new DiskFileItemFactory();
factory.setSizeThreshold(1000240);
final RestletFileUpload upload = new RestletFileUpload(factory);
diff --git a/src/main/java/org/caosdb/server/resource/transaction/RetrieveEntityResource.java b/src/main/java/org/caosdb/server/resource/transaction/RetrieveEntityResource.java
index 6527376d71ba31718394f887b7335615d80db5c6..d5feea9a0fe815004230e697ff0fa38b74fc72b8 100644
--- a/src/main/java/org/caosdb/server/resource/transaction/RetrieveEntityResource.java
+++ b/src/main/java/org/caosdb/server/resource/transaction/RetrieveEntityResource.java
@@ -3,8 +3,8 @@
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- * Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
- * Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2021,2023 Timm Fitschen <t.fitschen@indiscale.com>
+ * Copyright (C) 2021,2023 IndiScale GmbH <info@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
@@ -26,8 +26,8 @@ import java.security.NoSuchAlgorithmException;
import java.sql.SQLException;
import org.caosdb.server.CaosDBException;
import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.entity.EntityID;
import org.caosdb.server.entity.container.RetrieveContainer;
+import org.caosdb.server.jobs.core.ResolveNames;
import org.caosdb.server.resource.AbstractCaosDBServerResource;
import org.caosdb.server.transaction.Retrieve;
import org.jdom2.Document;
@@ -38,44 +38,40 @@ import org.restlet.representation.Representation;
* Handles GET requests for different subclasses which all have in common that they retrieve
* Entities (plus other information in some cases).
*
- * @author Timm Fitschen (t.fitschen@indiscale.com)
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
*/
public abstract class RetrieveEntityResource extends AbstractCaosDBServerResource {
/**
- * Parse the segment which specifies the entities which are to be retrieved
+ * Parse the segment which specifies the entities which are to be retrieved.
*
- * @param container
+ * <p>The segments are being treated as names here. The {@link ResolveNames} job is responsible
+ * for detecting whether the name is actually an id.
*/
protected void handleRetrieveContainer(final RetrieveContainer container) {
for (final String item : getRequestedItems()) {
final String[] elem = item.split("@", 2);
- Integer id = null;
- String name = null;
+ String id = null;
String version = null;
- try {
- id = Integer.parseInt(elem[0]);
- } catch (final NumberFormatException e) {
- name = elem[0];
- }
+ id = elem[0];
if (elem.length > 1) {
version = elem[1];
}
- if (id != null) {
- container.add(new EntityID(id), version);
- } else {
- container.add(name);
- }
+ container.add(null, id, version);
}
}
/** Handle the GET request. */
@Override
protected final Representation httpGetInChildClass()
- throws ConnectionException, IOException, SQLException, CaosDBException,
- NoSuchAlgorithmException, Exception {
+ throws ConnectionException,
+ IOException,
+ SQLException,
+ CaosDBException,
+ NoSuchAlgorithmException,
+ Exception {
final RetrieveContainer entityContainer =
new RetrieveContainer(getUser(), getTimestamp(), getSRID(), getFlags());
diff --git a/src/main/java/org/caosdb/server/scripting/ServerSideScriptingCaller.java b/src/main/java/org/caosdb/server/scripting/ServerSideScriptingCaller.java
index edb6b39a4e92466e5a3e5a489669d366bbe8ce37..9a710e25fad549e5d4c14bb623378a2e6aaff806 100644
--- a/src/main/java/org/caosdb/server/scripting/ServerSideScriptingCaller.java
+++ b/src/main/java/org/caosdb/server/scripting/ServerSideScriptingCaller.java
@@ -253,7 +253,9 @@ public class ServerSideScriptingCaller {
if (pwd.exists()) FileUtils.forceDelete(pwd);
}
- /** @fixme Should be injected into environment instead. Will be changed in v0.4 of SSS-API */
+ /**
+ * @fixme Should be injected into environment instead. Will be changed in v0.4 of SSS-API
+ */
String[] injectAuthToken(String[] commandLine) {
String[] newCommandLine = new String[commandLine.length + 1];
newCommandLine[0] = commandLine[0];
diff --git a/src/main/java/org/caosdb/server/transaction/EntityTransactionInterface.java b/src/main/java/org/caosdb/server/transaction/EntityTransactionInterface.java
new file mode 100644
index 0000000000000000000000000000000000000000..9d96c4e7499728ca11c348ac1875d94ece100a72
--- /dev/null
+++ b/src/main/java/org/caosdb/server/transaction/EntityTransactionInterface.java
@@ -0,0 +1,37 @@
+/*
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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 org.caosdb.server.transaction;
+
+import org.caosdb.server.entity.EntityID;
+
+/**
+ * This interface is implemented by all transactions of entities (as opposed to transaction which
+ * only concern users or other kinds of transactions).
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
+public interface EntityTransactionInterface extends TransactionInterface {
+
+ public boolean matchIdPattern(String id);
+
+ public default boolean matchIdPattern(EntityID id) {
+ return id != null && matchIdPattern(id.toString());
+ }
+}
diff --git a/src/main/java/org/caosdb/server/transaction/InsertUserTransaction.java b/src/main/java/org/caosdb/server/transaction/InsertUserTransaction.java
index f3f4c7f5fd583ff0ff16d4fd1ce583394258f35b..3174dabf4e3d6a581f27aaf59cb8ffd866401bf5 100644
--- a/src/main/java/org/caosdb/server/transaction/InsertUserTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/InsertUserTransaction.java
@@ -50,7 +50,7 @@ public class InsertUserTransaction extends AccessControlTransaction {
final String password,
final String email,
final UserStatus status,
- final Integer entity) {
+ final String entity) {
this(new ProtoUser(), password);
this.user.realm = UserSources.getInternalRealm().getName();
this.user.name = username;
diff --git a/src/main/java/org/caosdb/server/transaction/ListRolesTransaction.java b/src/main/java/org/caosdb/server/transaction/ListRolesTransaction.java
index ed3cd3cc5a154e82946e76f9934ee8608fe6980c..f0b0db78eeff6c04ca466dbd6f65f8350fbab783 100644
--- a/src/main/java/org/caosdb/server/transaction/ListRolesTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/ListRolesTransaction.java
@@ -39,9 +39,7 @@ public class ListRolesTransaction extends AccessControlTransaction {
protected void transaction() throws Exception {
Subject currentUser = SecurityUtils.getSubject();
roles =
- execute(new ListRoles(), getAccess())
- .getRoles()
- .stream()
+ execute(new ListRoles(), getAccess()).getRoles().stream()
.filter(
role ->
currentUser.isPermitted(
diff --git a/src/main/java/org/caosdb/server/transaction/ListUsersTransaction.java b/src/main/java/org/caosdb/server/transaction/ListUsersTransaction.java
index 2ade4e8595f159d1fc6996c1e04913f4195ecd97..fe9b9c172d2c6b4361790d30590650ae0233a2ad 100644
--- a/src/main/java/org/caosdb/server/transaction/ListUsersTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/ListUsersTransaction.java
@@ -37,9 +37,7 @@ public class ListUsersTransaction extends AccessControlTransaction {
protected void transaction() throws Exception {
Subject currentUser = SecurityUtils.getSubject();
users =
- execute(new ListUsers(), getAccess())
- .getUsers()
- .stream()
+ execute(new ListUsers(), getAccess()).getUsers().stream()
.filter(
user ->
currentUser.isPermitted(
diff --git a/src/main/java/org/caosdb/server/transaction/RetrieveACL.java b/src/main/java/org/caosdb/server/transaction/RetrieveACL.java
index ac0a2896451a43ca10985bd38787ad4f847a05cc..b5a4a489c60269dbae906bba1942f8e9525eb710 100644
--- a/src/main/java/org/caosdb/server/transaction/RetrieveACL.java
+++ b/src/main/java/org/caosdb/server/transaction/RetrieveACL.java
@@ -40,7 +40,7 @@ public class RetrieveACL extends Transaction<TransactionContainer> {
new TransactionContainer(
SecurityUtils.getSubject(), System.currentTimeMillis(), UUID.randomUUID().toString()));
for (String strId : idList) {
- getContainer().add(new RetrieveEntity(new EntityID(Integer.parseInt(strId))));
+ getContainer().add(new RetrieveEntity(new EntityID(strId)));
}
}
diff --git a/src/main/java/org/caosdb/server/transaction/RetrieveUserTransaction.java b/src/main/java/org/caosdb/server/transaction/RetrieveUserTransaction.java
index eb24fb24db4f1b6a50a279cfcd9e158003a70948..72a1d61929e692e551a53013ac1aabb1a4f28f5a 100644
--- a/src/main/java/org/caosdb/server/transaction/RetrieveUserTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/RetrieveUserTransaction.java
@@ -77,7 +77,7 @@ public class RetrieveUserTransaction extends AccessControlTransaction {
ret.setAttribute("email", user.email);
}
if (user.entity != null) {
- ret.setAttribute("entity", Integer.toString(user.entity));
+ ret.setAttribute("entity", user.entity);
}
if (user.status != null) {
ret.setAttribute("status", user.status.toString());
diff --git a/src/main/java/org/caosdb/server/transaction/Transaction.java b/src/main/java/org/caosdb/server/transaction/Transaction.java
index 5fc06f5ec82066d3515cbf524e64beb001ba0fcd..69dde0ea3602a650e52dadcdbc0107ff7cf12ded 100644
--- a/src/main/java/org/caosdb/server/transaction/Transaction.java
+++ b/src/main/java/org/caosdb/server/transaction/Transaction.java
@@ -3,8 +3,8 @@
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- * Copyright (C) 2019-2021 IndiScale GmbH <info@indiscale.com>
- * Copyright (C) 2019-2021 Timm Fitschen <t.fitschen@indiscale.com>
+ * Copyright (C) 2019-2021,2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2019-2021,2023 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
@@ -21,8 +21,12 @@
*/
package org.caosdb.server.transaction;
+import java.util.Collection;
+import java.util.Collections;
import java.util.HashMap;
import java.util.List;
+import java.util.Map;
+import java.util.Set;
import org.apache.shiro.subject.Subject;
import org.caosdb.datetime.UTCDateTime;
import org.caosdb.server.accessControl.Principal;
@@ -31,6 +35,7 @@ import org.caosdb.server.database.access.Access;
import org.caosdb.server.database.backend.transaction.InsertTransactionHistory;
import org.caosdb.server.database.exceptions.TransactionException;
import org.caosdb.server.database.misc.TransactionBenchmark;
+import org.caosdb.server.entity.EntityIdRegistry;
import org.caosdb.server.entity.EntityInterface;
import org.caosdb.server.entity.Message;
import org.caosdb.server.entity.container.TransactionContainer;
@@ -47,9 +52,89 @@ import org.caosdb.server.permissions.EntityACL;
import org.caosdb.server.utils.AbstractObservable;
import org.caosdb.server.utils.Info;
import org.caosdb.server.utils.Observer;
+import org.caosdb.server.utils.UseCacheResource;
+import org.caosdb.server.utils.UseCacheResourceDelegate;
+/**
+ * The NoOpCache is used when the caching is diabled (globally or for the current transaction.
+ *
+ * <p>It results in much simpler code when the callers do not need to check whether the caching is
+ * active all the time.
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
+@SuppressWarnings("rawtypes")
+class NoOpCache implements Map {
+
+ @Override
+ public int size() {
+ // TODO Auto-generated method stub
+ return 0;
+ }
+
+ @Override
+ public boolean isEmpty() {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public boolean containsKey(Object key) {
+ return false;
+ }
+
+ @Override
+ public boolean containsValue(Object value) {
+ return false;
+ }
+
+ @Override
+ public Object get(Object key) {
+ return null;
+ }
+
+ @Override
+ public Object put(Object key, Object value) {
+ return null;
+ }
+
+ @Override
+ public Object remove(Object key) {
+ return null;
+ }
+
+ @Override
+ public void putAll(Map m) {}
+
+ @Override
+ public void clear() {}
+
+ @Override
+ public Set keySet() {
+ return Collections.EMPTY_SET;
+ }
+
+ @Override
+ public Collection values() {
+ return Collections.EMPTY_LIST;
+ }
+
+ @Override
+ public Set entrySet() {
+ return Collections.EMPTY_SET;
+ }
+}
+
+/**
+ * Abstract base implementation for all EntityTransactions (Transaction involving entities).
+ *
+ * <p>Handles caching, benchmark timing, the access to the back end, generates and checks entity
+ * ids, holds the state of the transaction and triggers the scheduler to run the jobs.
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
public abstract class Transaction<C extends TransactionContainer> extends AbstractObservable
- implements TransactionInterface {
+ implements EntityTransactionInterface, UseCacheResource {
@Override
public TransactionBenchmark getTransactionBenchmark() {
@@ -59,6 +144,8 @@ public abstract class Transaction<C extends TransactionContainer> extends Abstra
private static final DatabaseAccessManager monitor = DatabaseAccessManager.getInstance();
public static final String CLEAN_UP = "TransactionCleanUp";
+
+ protected EntityIdRegistry idRegistry = null;
private final C container;
private Access access = null;
private final Schedule schedule = new Schedule();
@@ -270,61 +357,104 @@ public abstract class Transaction<C extends TransactionContainer> extends Abstra
}
}
- /** @see {@link #execute()} */
+ /**
+ * @see {@link #execute()}
+ */
protected void rollBack() {
this.schedule.runJobs(TransactionStage.ROLL_BACK);
}
- /** @see {@link #execute()} */
+ /**
+ * @see {@link #execute()}
+ */
protected abstract void init() throws Exception;
- /** @see {@link #execute()} */
+ /**
+ * @see {@link #execute()}
+ */
protected abstract void preCheck() throws InterruptedException, Exception;
- /** @see {@link #execute()} */
+ /**
+ * @see {@link #execute()}
+ */
protected final void check() {
this.schedule.runJobs(TransactionStage.CHECK);
}
- /** @see {@link #execute()} */
+ /**
+ * @see {@link #execute()}
+ */
protected abstract void postCheck();
- /** @see {@link #execute()} */
+ /**
+ * @see {@link #execute()}
+ */
protected abstract void preTransaction() throws InterruptedException;
- /** @see {@link #execute()} */
+ /**
+ * @see {@link #execute()}
+ */
protected abstract void transaction() throws Exception;
- /** @see {@link #execute()} */
+ /**
+ * @see {@link #execute()}
+ */
protected abstract void postTransaction() throws Exception;
- /** @see {@link #execute()} */
+ /**
+ * @see {@link #execute()}
+ */
protected abstract void cleanUp();
- /** @see {@link #execute()} */
+ /**
+ * @see {@link #execute()}
+ */
protected void commit() throws Exception {}
- public boolean useCache() {
- return getContainer().getFlags() != null
- && !getContainer().getFlags().containsKey("disableCache");
- }
-
public final Access getAccess() {
return this.access;
}
protected void setAccess(final Access a) {
this.access = a;
+ if (access != null) {
+ this.access.setUseCacheResourceDelegate(useCacheResourceDelegate);
+ }
}
@SuppressWarnings("unchecked")
- public <S, T> HashMap<S, T> getCache(final String name) {
+ public <S, T> Map<S, T> getCache(final String name) {
+ if (!useCache()) {
+ return NO_OP_CACHE;
+ }
if (!this.caches.containsKey(name)) {
this.caches.put(name, new HashMap<S, T>());
}
return this.caches.get(name);
}
+ private static final NoOpCache NO_OP_CACHE = new NoOpCache();
+
@SuppressWarnings("rawtypes")
- private final HashMap<String, HashMap> caches = new HashMap<>();
+ private final Map<String, Map> caches = new HashMap<>();
+
+ private final UseCacheResource useCacheResourceDelegate = new UseCacheResourceDelegate();
+
+ @Override
+ public UseCacheResource getUseCacheResourceDelegate() {
+ return this.useCacheResourceDelegate.getUseCacheResourceDelegate();
+ }
+
+ @Override
+ public void setUseCacheResourceDelegate(UseCacheResource delegate) {
+ this.useCacheResourceDelegate.setUseCacheResourceDelegate(delegate);
+ }
+
+ @Override
+ public boolean matchIdPattern(String id) {
+ if (this.idRegistry == null) {
+ this.idRegistry = new EntityIdRegistry(this);
+ }
+ return idRegistry.matchIdPattern(id);
+ }
}
diff --git a/src/main/java/org/caosdb/server/transaction/UpdateACL.java b/src/main/java/org/caosdb/server/transaction/UpdateACL.java
index 84c73080550d8899f4f1a5156bebb2a44c39df6a..289b5d53a14c642b4ac85bd9c02dd5c69484fa91 100644
--- a/src/main/java/org/caosdb/server/transaction/UpdateACL.java
+++ b/src/main/java/org/caosdb/server/transaction/UpdateACL.java
@@ -143,4 +143,10 @@ public class UpdateACL extends Transaction<TransactionContainer>
public String getSRID() {
return getContainer().getRequestId();
}
+
+ @Override
+ public String generateId() {
+ throw new UnsupportedOperationException(
+ "This is not implemented on purpose. This exception indicates a usage error of this UpdateACL class.");
+ }
}
diff --git a/src/main/java/org/caosdb/server/transaction/UpdateUserTransaction.java b/src/main/java/org/caosdb/server/transaction/UpdateUserTransaction.java
index 6808968f20574242cfdaa9b87793d7a4ad4b6914..7730d82b2fc2fb7ff3d34430ea3d1b60ffb9c16e 100644
--- a/src/main/java/org/caosdb/server/transaction/UpdateUserTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/UpdateUserTransaction.java
@@ -63,7 +63,7 @@ public class UpdateUserTransaction extends AccessControlTransaction {
final String username,
final UserStatus status,
final String email,
- final Integer entity,
+ final String entity,
final String password) {
this.user = new ProtoUser();
this.user.realm =
@@ -177,7 +177,7 @@ public class UpdateUserTransaction extends AccessControlTransaction {
ACMPermissions.PERMISSION_UPDATE_USER_ENTITY(this.user.realm, this.user.name));
isToBeUpdated = true;
- if (this.user.entity.equals(0)) {
+ if (this.user.entity.isEmpty()) {
// this means that the entity is to be reset.
this.user.entity = null;
} else {
diff --git a/src/main/java/org/caosdb/server/transaction/WriteTransaction.java b/src/main/java/org/caosdb/server/transaction/WriteTransaction.java
index 47b7a53c71ddebb7c1b062c2c8599cf44eabe039..b780d3d68f20cb6973c902cbe92fbd4fd46d51c1 100644
--- a/src/main/java/org/caosdb/server/transaction/WriteTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/WriteTransaction.java
@@ -3,8 +3,8 @@
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- * Copyright (C) 2019-2022 IndiScale GmbH <info@indiscale.com>
- * Copyright (C) 2019-2022 Timm Fitschen <t.fitschen@indiscale.com>
+ * Copyright (C) 2019-2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2019-2023 Timm Fitschen <t.fitschen@indiscale.com>
* Copyright (C) 2022 Daniel Hornung <d.hornung@indiscale.com>
*
* This program is free software: you can redistribute it and/or modify
@@ -40,6 +40,7 @@ import org.caosdb.server.database.backend.transaction.UpdateEntityTransaction;
import org.caosdb.server.database.misc.RollBackHandler;
import org.caosdb.server.entity.DeleteEntity;
import org.caosdb.server.entity.EntityID;
+import org.caosdb.server.entity.EntityIdRegistry;
import org.caosdb.server.entity.EntityInterface;
import org.caosdb.server.entity.FileProperties;
import org.caosdb.server.entity.InsertEntity;
@@ -593,4 +594,13 @@ public class WriteTransaction extends Transaction<WritableContainer>
public String getSRID() {
return getContainer().getRequestId();
}
+
+ @Override
+ public String generateId() {
+ if (this.idRegistry == null) {
+ this.idRegistry = new EntityIdRegistry(this);
+ }
+
+ return this.idRegistry.generate();
+ }
}
diff --git a/src/main/java/org/caosdb/server/transaction/WriteTransactionInterface.java b/src/main/java/org/caosdb/server/transaction/WriteTransactionInterface.java
index 4e2938e18d061cbd1a7575baa59322356731859a..c39d2c14a7dc625b1aa8bf0529feaeec2c4ca8b3 100644
--- a/src/main/java/org/caosdb/server/transaction/WriteTransactionInterface.java
+++ b/src/main/java/org/caosdb/server/transaction/WriteTransactionInterface.java
@@ -10,4 +10,6 @@ public interface WriteTransactionInterface extends TransactionInterface {
public Subject getTransactor();
public String getSRID();
+
+ public String generateId();
}
diff --git a/src/main/java/org/caosdb/server/utils/AbstractObservable.java b/src/main/java/org/caosdb/server/utils/AbstractObservable.java
index abc7f0a0ae1cdcbeff613c2778637de97a507c57..1bb4fc472a90c05d656f0d4250299801b73f07a2 100644
--- a/src/main/java/org/caosdb/server/utils/AbstractObservable.java
+++ b/src/main/java/org/caosdb/server/utils/AbstractObservable.java
@@ -37,7 +37,9 @@ public abstract class AbstractObservable implements Observable {
return this.observers.add(o);
}
- /** @param e A String denoting the notification event. */
+ /**
+ * @param e A String denoting the notification event.
+ */
@Override
public void notifyObservers(final String e) {
if (this.observers != null) {
diff --git a/src/main/java/org/caosdb/server/utils/UseCacheResource.java b/src/main/java/org/caosdb/server/utils/UseCacheResource.java
new file mode 100644
index 0000000000000000000000000000000000000000..89057f51c59f0f99a3eed3346ec18ab29ada74c0
--- /dev/null
+++ b/src/main/java/org/caosdb/server/utils/UseCacheResource.java
@@ -0,0 +1,41 @@
+/*
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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 org.caosdb.server.utils;
+
+/**
+ * Interface which indicates that a class can turn on and off the caching of the current transaction
+ * and inform the caller about the state of the transactions's caching.
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
+public interface UseCacheResource {
+
+ public default boolean useCache() {
+ return getUseCacheResourceDelegate().useCache();
+ }
+
+ public default void setUseCache(boolean useCache) {
+ getUseCacheResourceDelegate().setUseCache(useCache);
+ }
+
+ public void setUseCacheResourceDelegate(UseCacheResource delegate);
+
+ public UseCacheResource getUseCacheResourceDelegate();
+}
diff --git a/src/main/java/org/caosdb/server/utils/UseCacheResourceDelegate.java b/src/main/java/org/caosdb/server/utils/UseCacheResourceDelegate.java
new file mode 100644
index 0000000000000000000000000000000000000000..c537f0a813fe149b7338909f0dc95e8f3728dec1
--- /dev/null
+++ b/src/main/java/org/caosdb/server/utils/UseCacheResourceDelegate.java
@@ -0,0 +1,70 @@
+/*
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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 org.caosdb.server.utils;
+
+import org.caosdb.server.CaosDBServer;
+
+/**
+ * Basic implementation of the {@link UseCacheResource} interface.
+ *
+ * <p>This implementation uses a Delegator Pattern to link different UseCacheResources together.
+ * This is uses to delegate the responsibility to the transaction as the final Object of the
+ * delegation.
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
+public class UseCacheResourceDelegate implements UseCacheResource {
+ private boolean useCache = CaosDBServer.useCache();
+ private UseCacheResource delegate = null;
+
+ @Override
+ public void setUseCache(boolean useCache) {
+ if (this.delegate != null) {
+ this.delegate.setUseCache(useCache);
+ } else {
+ this.useCache = useCache;
+ }
+ }
+
+ @Override
+ public boolean useCache() {
+ if (delegate != null) {
+ return delegate.useCache();
+ }
+ return CaosDBServer.useCache() && useCache;
+ }
+
+ @Override
+ public void setUseCacheResourceDelegate(UseCacheResource delegate) {
+ if (delegate == this) {
+ this.delegate = null;
+ } else {
+ this.delegate = delegate;
+ }
+ }
+
+ @Override
+ public UseCacheResource getUseCacheResourceDelegate() {
+ if (this.delegate != null) {
+ return this.delegate;
+ }
+ return this;
+ }
+}
diff --git a/src/test/java/org/caosdb/server/caching/TestCaching.java b/src/test/java/org/caosdb/server/caching/TestCaching.java
index 1aba2ff6f16cea7a1f62e84e50e2cc9797114e27..8ff05660afde6e67d65e94011b662f09bdda9294 100644
--- a/src/test/java/org/caosdb/server/caching/TestCaching.java
+++ b/src/test/java/org/caosdb/server/caching/TestCaching.java
@@ -1,3 +1,22 @@
+/*
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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 org.caosdb.server.caching;
import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -17,6 +36,7 @@ public class TestCaching {
@BeforeAll
public static void init() throws IOException {
CaosDBServer.initServerProperties();
+ CaosDBServer.initCaching();
JCSCacheHelper.init();
}
diff --git a/src/test/java/org/caosdb/server/caching/TestNoCaching.java b/src/test/java/org/caosdb/server/caching/TestNoCaching.java
index 4fc73adf89f9355d1ff6addcd0f71fd9eda4e653..7eeeee71a909a106ad93b8c440ad895e366cca5f 100644
--- a/src/test/java/org/caosdb/server/caching/TestNoCaching.java
+++ b/src/test/java/org/caosdb/server/caching/TestNoCaching.java
@@ -1,3 +1,22 @@
+/*
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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 org.caosdb.server.caching;
import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -17,6 +36,7 @@ public class TestNoCaching {
public static void init() throws IOException {
CaosDBServer.initServerProperties();
CaosDBServer.setProperty(ServerProperties.KEY_CACHE_DISABLE, "TRUE");
+ CaosDBServer.initCaching();
JCSCacheHelper.init();
}
diff --git a/src/test/java/org/caosdb/server/database/backend/implementation/MySQL/InsertTest.java b/src/test/java/org/caosdb/server/database/backend/implementation/MySQL/InsertTest.java
index 03bd185c8884822f89f8ff323a1c32125b66f88b..feee1360bf7fa0ae865422b31d8a2ad2bcf64ebe 100644
--- a/src/test/java/org/caosdb/server/database/backend/implementation/MySQL/InsertTest.java
+++ b/src/test/java/org/caosdb/server/database/backend/implementation/MySQL/InsertTest.java
@@ -1,9 +1,10 @@
/*
- * ** 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) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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
@@ -17,8 +18,6 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.database.backend.implementation.MySQL;
@@ -50,7 +49,7 @@ public class InsertTest {
private Deque<EntityID> registerReplacementIds(int count) {
Deque<EntityID> replacementIds = new ArrayDeque<>();
for (int i = 1; i < count + 1; i++) {
- replacementIds.add(new EntityID(-i));
+ replacementIds.add(new EntityID(Integer.toString(-i)));
}
return replacementIds;
}
@@ -63,70 +62,70 @@ public class InsertTest {
@Test
public void testTransformation1() throws Exception {
final Entity r = new InsertEntity("Test", Role.Record);
- final Property p1 = new Property(new RetrieveEntity(new EntityID(1)));
+ final Property p1 = new Property(new RetrieveEntity(new EntityID("1")));
p1.setRole("Property");
p1.setValue(new GenericValue("V1"));
p1.setDatatype("TEXT");
p1.setStatementStatus(StatementStatus.FIX);
r.addProperty(p1);
- final Property p2 = new Property(new RetrieveEntity(new EntityID(2)));
+ final Property p2 = new Property(new RetrieveEntity(new EntityID("2")));
p2.setRole("Property");
p2.setValue(new GenericValue("V2"));
p2.setDatatype("TEXT");
p2.setStatementStatus(StatementStatus.RECOMMENDED);
r.addProperty(p2);
- final Property p3 = new Property(new RetrieveEntity(new EntityID(3)));
+ final Property p3 = new Property(new RetrieveEntity(new EntityID("3")));
p3.setRole("Property");
p3.setValue(new GenericValue("V3"));
p3.setDatatype("TEXT");
p3.setStatementStatus(StatementStatus.OBLIGATORY);
p2.addProperty(p3);
- final Property p4 = new Property(new RetrieveEntity(new EntityID(4)));
+ final Property p4 = new Property(new RetrieveEntity(new EntityID("4")));
p4.setRole("Property");
p4.setValue(new GenericValue("V4"));
p4.setDatatype("TEXT");
p4.setStatementStatus(StatementStatus.OBLIGATORY);
r.addProperty(p4);
- final Property p5 = new Property(new RetrieveEntity(new EntityID(5)));
+ final Property p5 = new Property(new RetrieveEntity(new EntityID("5")));
p5.setRole("Property");
p5.setValue(new GenericValue("V5"));
p5.setDatatype("TEXT");
p5.setStatementStatus(StatementStatus.OBLIGATORY);
p4.addProperty(p5);
- final Property p6 = new Property(new RetrieveEntity(new EntityID(6)));
+ final Property p6 = new Property(new RetrieveEntity(new EntityID("6")));
p6.setRole("Property");
p6.setValue(new GenericValue("V6"));
p6.setDatatype("TEXT");
p6.setStatementStatus(StatementStatus.OBLIGATORY);
p5.addProperty(p6);
- final Property p7 = new Property(new RetrieveEntity(new EntityID(7)));
+ final Property p7 = new Property(new RetrieveEntity(new EntityID("7")));
p7.setRole("Property");
p7.setValue(new GenericValue("V7"));
p7.setDatatype("TEXT");
p7.setStatementStatus(StatementStatus.OBLIGATORY);
r.addProperty(p7);
- final Property p8 = new Property(new RetrieveEntity(new EntityID(8)));
+ final Property p8 = new Property(new RetrieveEntity(new EntityID("8")));
p8.setRole("Property");
p8.setValue(new GenericValue("V8"));
p8.setDatatype("TEXT");
p8.setStatementStatus(StatementStatus.OBLIGATORY);
p7.addProperty(p8);
- final Property p9 = new Property(new RetrieveEntity(new EntityID(9)));
+ final Property p9 = new Property(new RetrieveEntity(new EntityID("9")));
p9.setRole("Property");
p9.setValue(new GenericValue("V9"));
p9.setDatatype("TEXT");
p9.setStatementStatus(StatementStatus.OBLIGATORY);
p8.addProperty(p9);
- final Property p10 = new Property(new RetrieveEntity(new EntityID(10)));
+ final Property p10 = new Property(new RetrieveEntity(new EntityID("10")));
p10.setRole("Property");
p10.setValue(new GenericValue("V10"));
p10.setDatatype("TEXT");
@@ -143,57 +142,57 @@ public class InsertTest {
assertEquals(7, stage1Inserts.size());
assertFalse(stage1Inserts.get(0) instanceof Replacement);
- assertEquals(1, stage1Inserts.get(0).getId().toInteger());
+ assertEquals("1", stage1Inserts.get(0).getId().toString());
assertEquals("V1", ((SingleValue) stage1Inserts.get(0).getValue()).toDatabaseString());
assertFalse(stage1Inserts.get(1) instanceof Replacement);
- assertEquals(2, stage1Inserts.get(1).getId().toInteger());
+ assertEquals("2", stage1Inserts.get(1).getId().toString());
assertEquals("V2", ((SingleValue) stage1Inserts.get(1).getValue()).toDatabaseString());
assertFalse(stage1Inserts.get(2) instanceof Replacement);
- assertEquals(4, stage1Inserts.get(2).getId().toInteger());
+ assertEquals("4", stage1Inserts.get(2).getId().toString());
assertEquals("V4", ((SingleValue) stage1Inserts.get(2).getValue()).toDatabaseString());
assertTrue(stage1Inserts.get(3) instanceof Replacement);
- assertEquals(-1, stage1Inserts.get(3).getId().toInteger());
+ assertEquals("-1", stage1Inserts.get(3).getId().toString());
assertEquals("V5", ((SingleValue) stage1Inserts.get(3).getValue()).toDatabaseString());
assertFalse(stage1Inserts.get(4) instanceof Replacement);
- assertEquals(7, stage1Inserts.get(4).getId().toInteger());
+ assertEquals("7", stage1Inserts.get(4).getId().toString());
assertEquals("V7", ((SingleValue) stage1Inserts.get(4).getValue()).toDatabaseString());
assertTrue(stage1Inserts.get(5) instanceof Replacement);
- assertEquals(-2, stage1Inserts.get(5).getId().toInteger());
+ assertEquals("-2", stage1Inserts.get(5).getId().toString());
assertEquals("V8", ((SingleValue) stage1Inserts.get(5).getValue()).toDatabaseString());
assertTrue(stage1Inserts.get(6) instanceof Replacement);
- assertEquals(-3, stage1Inserts.get(6).getId().toInteger());
+ assertEquals("-3", stage1Inserts.get(6).getId().toString());
assertEquals("V9", ((SingleValue) stage1Inserts.get(6).getValue()).toDatabaseString());
assertEquals(6, stage2Inserts.size());
- assertEquals(new EntityID(3), stage2Inserts.get(0).getId());
+ assertEquals(new EntityID("3"), stage2Inserts.get(0).getId());
assertEquals("V3", ((SingleValue) stage2Inserts.get(0).getValue()).toDatabaseString());
- assertEquals(new EntityID(2), stage2Inserts.get(0).getDomain());
+ assertEquals(new EntityID("2"), stage2Inserts.get(0).getDomain());
- assertEquals(new EntityID(5), stage2Inserts.get(1).getId());
+ assertEquals(new EntityID("5"), stage2Inserts.get(1).getId());
assertEquals("V5", ((SingleValue) stage2Inserts.get(1).getValue()).toDatabaseString());
- assertEquals(new EntityID(4), stage2Inserts.get(1).getDomain());
+ assertEquals(new EntityID("4"), stage2Inserts.get(1).getDomain());
- assertEquals(new EntityID(6), stage2Inserts.get(2).getId());
+ assertEquals(new EntityID("6"), stage2Inserts.get(2).getId());
assertEquals("V6", ((SingleValue) stage2Inserts.get(2).getValue()).toDatabaseString());
- assertEquals(new EntityID(-1), stage2Inserts.get(2).getDomain());
+ assertEquals(new EntityID("-1"), stage2Inserts.get(2).getDomain());
- assertEquals(new EntityID(8), stage2Inserts.get(3).getId());
+ assertEquals(new EntityID("8"), stage2Inserts.get(3).getId());
assertEquals("V8", ((SingleValue) stage2Inserts.get(3).getValue()).toDatabaseString());
- assertEquals(new EntityID(7), stage2Inserts.get(3).getDomain());
+ assertEquals(new EntityID("7"), stage2Inserts.get(3).getDomain());
- assertEquals(new EntityID(9), stage2Inserts.get(4).getId());
+ assertEquals(new EntityID("9"), stage2Inserts.get(4).getId());
assertEquals("V9", ((SingleValue) stage2Inserts.get(4).getValue()).toDatabaseString());
- assertEquals(new EntityID(-2), stage2Inserts.get(4).getDomain());
+ assertEquals(new EntityID("-2"), stage2Inserts.get(4).getDomain());
- assertEquals(new EntityID(10), stage2Inserts.get(5).getId());
+ assertEquals(new EntityID("10"), stage2Inserts.get(5).getId());
assertEquals("V10", ((SingleValue) stage2Inserts.get(5).getValue()).toDatabaseString());
- assertEquals(new EntityID(-3), stage2Inserts.get(5).getDomain());
+ assertEquals(new EntityID("-3"), stage2Inserts.get(5).getDomain());
}
/**
@@ -205,21 +204,21 @@ public class InsertTest {
@Test
public void testTransformation2() throws Exception {
final Entity r = new InsertEntity("Test", Role.Record);
- final Property p1 = new Property(new RetrieveEntity(new EntityID(1)));
+ final Property p1 = new Property(new RetrieveEntity(new EntityID("1")));
p1.setRole("Property");
p1.setValue(new GenericValue("V1-1"));
p1.setDatatype("TEXT");
p1.setStatementStatus(StatementStatus.FIX);
r.addProperty(p1);
- final Property p2 = new Property(new RetrieveEntity(new EntityID(1)));
+ final Property p2 = new Property(new RetrieveEntity(new EntityID("1")));
p2.setRole("Property");
p2.setValue(new GenericValue("V1-2"));
p2.setDatatype("TEXT");
p2.setStatementStatus(StatementStatus.FIX);
r.addProperty(p2);
- final Property subp = new Property(new RetrieveEntity(new EntityID(2)));
+ final Property subp = new Property(new RetrieveEntity(new EntityID("2")));
subp.setRole("Property");
subp.setValue(new GenericValue("V2"));
subp.setDatatype("TEXT");
@@ -235,21 +234,21 @@ public class InsertTest {
assertEquals(3, stage1Inserts.size());
assertFalse(stage1Inserts.get(0) instanceof Replacement);
- assertEquals(new EntityID(1), stage1Inserts.get(0).getId());
+ assertEquals(new EntityID("1"), stage1Inserts.get(0).getId());
assertEquals("V1-1", ((SingleValue) stage1Inserts.get(0).getValue()).toDatabaseString());
assertTrue(stage1Inserts.get(1) instanceof Replacement);
assertEquals("V1-2", ((SingleValue) stage1Inserts.get(1).getValue()).toDatabaseString());
- assertEquals(new EntityID(-1), stage1Inserts.get(1).getId());
+ assertEquals(new EntityID("-1"), stage1Inserts.get(1).getId());
assertFalse(stage1Inserts.get(2) instanceof Replacement);
- assertEquals(new EntityID(-1), stage1Inserts.get(2).getId());
+ assertEquals(new EntityID("-1"), stage1Inserts.get(2).getId());
assertEquals("1", ((SingleValue) stage1Inserts.get(2).getValue()).toDatabaseString());
assertEquals(1, stage2Inserts.size());
assertFalse(stage2Inserts.get(0) instanceof Replacement);
- assertEquals(new EntityID(2), stage2Inserts.get(0).getId());
+ assertEquals(new EntityID("2"), stage2Inserts.get(0).getId());
assertEquals("V2", ((SingleValue) stage2Inserts.get(0).getValue()).toDatabaseString());
}
@@ -262,25 +261,25 @@ public class InsertTest {
@Test
public void testTransformation3() throws Exception {
final Entity r = new InsertEntity("Test", Role.Record);
- final Property p1 = new Property(new RetrieveEntity(new EntityID(1)));
+ final Property p1 = new Property(new RetrieveEntity(new EntityID("1")));
p1.setRole("Property");
p1.setDatatype("TEXT");
p1.setStatementStatus(StatementStatus.FIX);
r.addProperty(p1);
- final Property p2 = new Property(new RetrieveEntity(new EntityID(1)));
+ final Property p2 = new Property(new RetrieveEntity(new EntityID("1")));
p2.setRole("Property");
p2.setDatatype("TEXT");
p2.setStatementStatus(StatementStatus.FIX);
r.addProperty(p2);
- final Property p3 = new Property(new RetrieveEntity(new EntityID(1)));
+ final Property p3 = new Property(new RetrieveEntity(new EntityID("1")));
p3.setRole("Property");
p3.setDatatype("TEXT");
p3.setStatementStatus(StatementStatus.FIX);
r.addProperty(p3);
- final Property sub1 = new Property(new RetrieveEntity(new EntityID(2)));
+ final Property sub1 = new Property(new RetrieveEntity(new EntityID("2")));
sub1.setRole("Property");
sub1.setDatatype("TEXT");
sub1.setValue(new GenericValue("V1"));
@@ -295,25 +294,25 @@ public class InsertTest {
assertEquals(4, stage1Inserts.size());
assertTrue(stage1Inserts.get(0) instanceof Replacement);
- assertEquals(new EntityID(-1), stage1Inserts.get(0).getId());
+ assertEquals(new EntityID("-1"), stage1Inserts.get(0).getId());
assertEquals(null, stage1Inserts.get(0).getValue());
assertFalse(stage1Inserts.get(1) instanceof Replacement);
- assertEquals(new EntityID(-1), stage1Inserts.get(1).getId());
- assertEquals(1, ((ReferenceValue) stage1Inserts.get(1).getValue()).getId().toInteger());
+ assertEquals(new EntityID("-1"), stage1Inserts.get(1).getId());
+ assertEquals("1", ((ReferenceValue) stage1Inserts.get(1).getValue()).getId().toString());
assertFalse(stage1Inserts.get(2) instanceof Replacement);
- assertEquals(new EntityID(1), stage1Inserts.get(2).getId());
+ assertEquals(new EntityID("1"), stage1Inserts.get(2).getId());
assertEquals(null, stage1Inserts.get(2).getValue());
assertFalse(stage1Inserts.get(3) instanceof Replacement);
- assertEquals(new EntityID(1), stage1Inserts.get(3).getId());
+ assertEquals(new EntityID("1"), stage1Inserts.get(3).getId());
assertEquals(null, stage1Inserts.get(3).getValue());
assertEquals(1, stage2Inserts.size());
- assertEquals(new EntityID(2), stage2Inserts.get(0).getId());
+ assertEquals(new EntityID("2"), stage2Inserts.get(0).getId());
assertEquals("V1", ((SingleValue) stage2Inserts.get(0).getValue()).toDatabaseString());
- assertEquals(new EntityID(-1), stage2Inserts.get(0).getDomain());
+ assertEquals(new EntityID("-1"), stage2Inserts.get(0).getDomain());
}
/**
@@ -325,14 +324,14 @@ public class InsertTest {
public void testTransformation4() throws Exception {
final Entity r = new InsertEntity("Test", Role.Record);
- final Property p1 = new Property(new RetrieveEntity(new EntityID(1)));
+ final Property p1 = new Property(new RetrieveEntity(new EntityID("1")));
p1.setRole("Property");
p1.setDatatype("TEXT");
p1.setValue(new GenericValue("V1"));
p1.setStatementStatus(StatementStatus.FIX);
r.addProperty(p1);
- final Property p2 = new Property(new RetrieveEntity(new EntityID(2)));
+ final Property p2 = new Property(new RetrieveEntity(new EntityID("2")));
p2.setRole("Property");
p2.setDatatype("LIST<TEXT>");
p2.setStatementStatus(StatementStatus.FIX);
@@ -343,7 +342,7 @@ public class InsertTest {
p2.setValue(vals);
r.addProperty(p2);
- final Property p3 = new Property(new RetrieveEntity(new EntityID(3)));
+ final Property p3 = new Property(new RetrieveEntity(new EntityID("3")));
p3.setRole("Property");
p3.setDatatype("TEXT");
p3.setValue(new GenericValue("V3"));
@@ -359,19 +358,19 @@ public class InsertTest {
assertEquals(4, stage1Inserts.size());
assertFalse(stage1Inserts.get(0) instanceof Replacement);
- assertEquals(new EntityID(1), stage1Inserts.get(0).getId());
+ assertEquals(new EntityID("1"), stage1Inserts.get(0).getId());
assertEquals("V1", ((SingleValue) stage1Inserts.get(0).getValue()).toDatabaseString());
assertTrue(stage1Inserts.get(1) instanceof Replacement);
- assertEquals(new EntityID(-1), stage1Inserts.get(1).getId());
+ assertEquals(new EntityID("-1"), stage1Inserts.get(1).getId());
assertTrue(stage1Inserts.get(1).getValue() instanceof CollectionValue);
assertFalse(stage1Inserts.get(2) instanceof Replacement);
- assertEquals(new EntityID(-1), stage1Inserts.get(2).getId());
- assertEquals(2, ((ReferenceValue) stage1Inserts.get(2).getValue()).getId().toInteger());
+ assertEquals(new EntityID("-1"), stage1Inserts.get(2).getId());
+ assertEquals("2", ((ReferenceValue) stage1Inserts.get(2).getValue()).getId().toString());
assertFalse(stage1Inserts.get(3) instanceof Replacement);
- assertEquals(new EntityID(3), stage1Inserts.get(3).getId());
+ assertEquals(new EntityID("3"), stage1Inserts.get(3).getId());
assertEquals("V3", ((SingleValue) stage1Inserts.get(3).getValue()).toDatabaseString());
assertEquals(0, stage2Inserts.size());
@@ -381,7 +380,7 @@ public class InsertTest {
@Test
public void testTransformation5() {
final Entity r = new InsertEntity("Test", Role.RecordType);
- final Property p1 = new Property(new RetrieveEntity(new EntityID(1)));
+ final Property p1 = new Property(new RetrieveEntity(new EntityID("1")));
p1.setRole("Property");
p1.setDatatype("TEXT");
p1.setDescription("desc1");
@@ -391,7 +390,7 @@ public class InsertTest {
p1.setStatementStatus(StatementStatus.RECOMMENDED);
r.addProperty(p1);
- final Property p2 = new Property(new RetrieveEntity(new EntityID(2)));
+ final Property p2 = new Property(new RetrieveEntity(new EntityID("2")));
p2.setRole("Property");
p2.setDatatype("TEXT");
p2.setDescription("desc2");
@@ -401,7 +400,7 @@ public class InsertTest {
p2.setStatementStatus(StatementStatus.RECOMMENDED);
r.addProperty(p2);
- final Property p21 = new Property(new RetrieveEntity(new EntityID(1)));
+ final Property p21 = new Property(new RetrieveEntity(new EntityID("1")));
p21.setRole("Property");
p21.setDatatype("TEXT");
p21.setDescription("desc21");
@@ -411,7 +410,7 @@ public class InsertTest {
p21.setStatementStatus(StatementStatus.FIX);
p2.addProperty(p21);
- final Property p22 = new Property(new RetrieveEntity(new EntityID(2)));
+ final Property p22 = new Property(new RetrieveEntity(new EntityID("2")));
p22.setRole("Property");
p22.setDatatype("TEXT");
p22.setDescription("desc22");
@@ -421,7 +420,7 @@ public class InsertTest {
p22.setStatementStatus(StatementStatus.FIX);
p2.addProperty(p22);
- final Property p3 = new Property(new RetrieveEntity(new EntityID(3)));
+ final Property p3 = new Property(new RetrieveEntity(new EntityID("3")));
p3.setRole("Property");
p3.setDatatype("TEXT");
p3.setDescription("desc3");
@@ -431,7 +430,7 @@ public class InsertTest {
p3.setStatementStatus(StatementStatus.RECOMMENDED);
r.addProperty(p3);
- final Property p31 = new Property(new RetrieveEntity(new EntityID(1)));
+ final Property p31 = new Property(new RetrieveEntity(new EntityID("1")));
p31.setRole("Property");
p31.setDatatype("TEXT");
p31.setDescription("desc31");
@@ -441,7 +440,7 @@ public class InsertTest {
p31.setStatementStatus(StatementStatus.FIX);
p3.addProperty(p31);
- final Property p32 = new Property(new RetrieveEntity(new EntityID(2)));
+ final Property p32 = new Property(new RetrieveEntity(new EntityID("2")));
p32.setRole("Property");
p32.setDatatype("TEXT");
p32.setDescription("desc32");
@@ -451,7 +450,7 @@ public class InsertTest {
p32.setStatementStatus(StatementStatus.FIX);
p3.addProperty(p32);
- final Property p321 = new Property(new RetrieveEntity(new EntityID(1)));
+ final Property p321 = new Property(new RetrieveEntity(new EntityID("1")));
p321.setRole("Property");
p321.setDatatype("TEXT");
p321.setDescription("desc321");
@@ -461,7 +460,7 @@ public class InsertTest {
p321.setStatementStatus(StatementStatus.FIX);
p32.addProperty(p321);
- final Property p322 = new Property(new RetrieveEntity(new EntityID(2)));
+ final Property p322 = new Property(new RetrieveEntity(new EntityID("2")));
p322.setRole("Property");
p322.setDatatype("TEXT");
p322.setDescription("desc322");
@@ -471,7 +470,7 @@ public class InsertTest {
p322.setStatementStatus(StatementStatus.FIX);
p32.addProperty(p322);
- final Property p323 = new Property(new RetrieveEntity(new EntityID(3)));
+ final Property p323 = new Property(new RetrieveEntity(new EntityID("3")));
p323.setRole("Property");
p323.setDatatype("TEXT");
p323.setDescription("desc323");
@@ -481,7 +480,7 @@ public class InsertTest {
p323.setStatementStatus(StatementStatus.FIX);
p32.addProperty(p323);
- final Property p33 = new Property(new RetrieveEntity(new EntityID(3)));
+ final Property p33 = new Property(new RetrieveEntity(new EntityID("3")));
p33.setRole("Property");
p33.setDatatype("TEXT");
p33.setDescription("desc33");
diff --git a/src/test/java/org/caosdb/server/database/backend/transaction/RetrieveFullEntityTest.java b/src/test/java/org/caosdb/server/database/backend/transaction/RetrieveFullEntityTest.java
index 72c84d1f7b262a854a257c8ae764d4e3da9b8e80..cfd8fcc9ba39cdf68dbf43be77de30f81c4fbec9 100644
--- a/src/test/java/org/caosdb/server/database/backend/transaction/RetrieveFullEntityTest.java
+++ b/src/test/java/org/caosdb/server/database/backend/transaction/RetrieveFullEntityTest.java
@@ -1,9 +1,8 @@
/*
- * ** header v3.0
* This file is a part of the CaosDB Project.
*
- * Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
- * Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020,2023 Timm Fitschen <t.fitschen@indiscale.com>
+ * Copyright (C) 2020,2023 IndiScale GmbH <info@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
@@ -17,8 +16,6 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.database.backend.transaction;
@@ -43,32 +40,33 @@ public class RetrieveFullEntityTest {
@Test
public void testRetrieveSubEntities() {
final RetrieveFullEntityTransaction r =
- new RetrieveFullEntityTransaction(new EntityID(0)) {
+ new RetrieveFullEntityTransaction(new EntityID("0")) {
/** Mock-up */
@Override
public void retrieveFullEntity(
final EntityInterface e, final List<Selection> selections) {
// The id of the referenced window
- assertEquals(new EntityID(1234), e.getId());
+ assertEquals(new EntityID("1234"), e.getId());
// The level of selectors has been reduced by 1
assertEquals("description", selections.get(0).getSelector());
e.setDescription("A heart-shaped window.");
- };
+ }
+ ;
};
- final Property window = new Property(new RetrieveEntity(new EntityID(2345)));
+ final Property window = new Property(new RetrieveEntity(new EntityID("2345")));
window.setName("Window");
window.setDatatype("Window");
- window.setValue(new ReferenceValue(1234));
+ window.setValue(new ReferenceValue("1234"));
- final Entity house = new RetrieveEntity(new EntityID(3456));
+ final Entity house = new RetrieveEntity(new EntityID("3456"));
house.addProperty(window);
final ReferenceValue value =
- (ReferenceValue) house.getProperties().getEntityById(new EntityID(2345)).getValue();
- assertEquals(new EntityID(1234), value.getId());
+ (ReferenceValue) house.getProperties().getEntityById(new EntityID("2345")).getValue();
+ assertEquals(new EntityID("1234"), value.getId());
assertNull(value.getEntity());
final List<Selection> selections = new ArrayList<>();
@@ -76,7 +74,7 @@ public class RetrieveFullEntityTest {
r.retrieveSubEntities(house, selections);
- assertEquals(new EntityID(1234), value.getId());
+ assertEquals(new EntityID("1234"), value.getId());
assertNotNull(value.getEntity());
assertEquals("A heart-shaped window.", value.getEntity().getDescription());
}
diff --git a/src/test/java/org/caosdb/server/entity/container/PropertyContainerTest.java b/src/test/java/org/caosdb/server/entity/container/PropertyContainerTest.java
index a8ccdbdc9f7a9522020332e01cba96a1667d70b6..f8fb0217adb0cc35cbc51d90b96f76d5f7b3592e 100644
--- a/src/test/java/org/caosdb/server/entity/container/PropertyContainerTest.java
+++ b/src/test/java/org/caosdb/server/entity/container/PropertyContainerTest.java
@@ -1,9 +1,8 @@
/*
- * ** header v3.0
* This file is a part of the CaosDB Project.
*
- * Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
- * Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020,2023 Timm Fitschen <t.fitschen@indiscale.com>
+ * Copyright (C) 2020,2023 IndiScale GmbH <info@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
@@ -17,8 +16,6 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.entity.container;
@@ -48,7 +45,7 @@ public class PropertyContainerTest {
@BeforeAll
public static void setup() {
- window = new RetrieveEntity(new EntityID(1234));
+ window = new RetrieveEntity(new EntityID("1234"));
windowHeight = new Property(new RetrieveEntity("window.height", Role.Property));
window.addProperty(windowHeight);
windowHeight.setValue(new GenericValue("windowHeight"));
@@ -59,7 +56,7 @@ public class PropertyContainerTest {
houseHeight = new Property(new RetrieveEntity("height", Role.Property));
houseHeight.setValue(new GenericValue("houseHeight"));
house.addProperty(houseHeight);
- windowProperty = new Property(new RetrieveEntity(new EntityID(2345)));
+ windowProperty = new Property(new RetrieveEntity(new EntityID("2345")));
windowProperty.setName("window");
windowProperty.setValue(new ReferenceValue(window.getId()));
house.addProperty(windowProperty);
diff --git a/src/test/java/org/caosdb/server/entity/xml/PropertyToElementStrategyTest.java b/src/test/java/org/caosdb/server/entity/xml/PropertyToElementStrategyTest.java
index a2c9676b9759fc55fb0d1e089808ab50d016288e..bab174c88ed595ec4b79b1cf47b1cf2dbb0cbc95 100644
--- a/src/test/java/org/caosdb/server/entity/xml/PropertyToElementStrategyTest.java
+++ b/src/test/java/org/caosdb/server/entity/xml/PropertyToElementStrategyTest.java
@@ -1,9 +1,8 @@
/*
- * ** header v3.0
* This file is a part of the CaosDB Project.
*
- * Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
- * Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020,2023 Timm Fitschen <t.fitschen@indiscale.com>
+ * Copyright (C) 2020,2023 IndiScale GmbH <info@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
@@ -17,8 +16,6 @@
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
*/
package org.caosdb.server.entity.xml;
@@ -66,7 +63,7 @@ public class PropertyToElementStrategyTest {
@BeforeEach
public void setup() {
- window = new RetrieveEntity(new EntityID(1234), Role.Record);
+ window = new RetrieveEntity(new EntityID("1234"), Role.Record);
windowHeight = new Property(new RetrieveEntity("height", Role.Property));
window.addProperty(windowHeight);
windowHeight.setValue(new GenericValue("windowHeight"));
@@ -77,7 +74,7 @@ public class PropertyToElementStrategyTest {
houseHeight = new Property(new RetrieveEntity("height", Role.Property));
houseHeight.setValue(new GenericValue("houseHeight"));
house.addProperty(houseHeight);
- windowProperty = new Property(new RetrieveEntity(new EntityID(2345)));
+ windowProperty = new Property(new RetrieveEntity(new EntityID("2345")));
windowProperty.setName("window");
windowProperty.setDatatype("window");
windowProperty.setValue(new ReferenceValue(window.getId()));
diff --git a/src/test/java/org/caosdb/server/grpc/CaosDBToGrpcConvertersTest.java b/src/test/java/org/caosdb/server/grpc/CaosDBToGrpcConvertersTest.java
index d46c187324b76e179ef8d562cd5a150ab7968a45..ad85d3d4c00727134440d0f4eaa1a424fb550372 100644
--- a/src/test/java/org/caosdb/server/grpc/CaosDBToGrpcConvertersTest.java
+++ b/src/test/java/org/caosdb/server/grpc/CaosDBToGrpcConvertersTest.java
@@ -1,3 +1,22 @@
+/*
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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 org.caosdb.server.grpc;
import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -74,7 +93,7 @@ public class CaosDBToGrpcConvertersTest {
RetrieveEntity entity = new RetrieveEntity();
// must be printed
- entity.setId(new EntityID(1234));
+ entity.setId(new EntityID("1234"));
entity.addInfo("info");
entity.addWarning(new Message("warning"));
entity.addError(new Message("error"));
@@ -136,7 +155,7 @@ public class CaosDBToGrpcConvertersTest {
RetrieveEntity person1 = new RetrieveEntity();
person1.addProperty(fullName1);
- ReferenceValue val1 = new ReferenceValue(new EntityID(1234));
+ ReferenceValue val1 = new ReferenceValue(new EntityID("1234"));
val1.setEntity(person1, false);
col.add(val1);
@@ -147,7 +166,7 @@ public class CaosDBToGrpcConvertersTest {
RetrieveEntity person2 = new RetrieveEntity();
person2.addProperty(fullName2);
- ReferenceValue val2 = new ReferenceValue(new EntityID(1234));
+ ReferenceValue val2 = new ReferenceValue(new EntityID("1234"));
val2.setEntity(person2, false);
col.add(val2);
p.setValue(col);
diff --git a/src/test/java/org/caosdb/server/jobs/JobConfigTest.java b/src/test/java/org/caosdb/server/jobs/JobConfigTest.java
index e176c2111189fb52ca9946e10ae5ec705549b6c8..c097d0a76ec5444881e9dd58bb735015b9fe8db1 100644
--- a/src/test/java/org/caosdb/server/jobs/JobConfigTest.java
+++ b/src/test/java/org/caosdb/server/jobs/JobConfigTest.java
@@ -1,3 +1,22 @@
+/*
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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 org.caosdb.server.jobs;
import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -26,7 +45,7 @@ public class JobConfigTest {
final JobConfig jobConfig = JobConfig.getInstance();
assertEquals("Retrieve", jobConfig.getTransactionType(new RetrieveEntity("test")));
assertEquals("Insert", jobConfig.getTransactionType(new InsertEntity("test", Role.Record)));
- assertEquals("Delete", jobConfig.getTransactionType(new DeleteEntity(new EntityID(1234))));
+ assertEquals("Delete", jobConfig.getTransactionType(new DeleteEntity(new EntityID("1234"))));
assertEquals("Update", jobConfig.getTransactionType(new UpdateEntity(new Element("Record"))));
}
}
diff --git a/src/test/java/org/caosdb/server/query/TestCQL.java b/src/test/java/org/caosdb/server/query/TestCQL.java
index 8d7a7e8fb219f286d6cdaffc4b28240a7b2897d5..61a87b7f5764a8da26bc7bb6ccd8f06a320302f1 100644
--- a/src/test/java/org/caosdb/server/query/TestCQL.java
+++ b/src/test/java/org/caosdb/server/query/TestCQL.java
@@ -36,6 +36,7 @@ import java.util.regex.Matcher;
import org.antlr.v4.runtime.CharStreams;
import org.antlr.v4.runtime.CommonTokenStream;
import org.antlr.v4.runtime.Token;
+import org.antlr.v4.runtime.Vocabulary;
import org.antlr.v4.runtime.tree.ParseTree;
import org.caosdb.server.CaosDBServer;
import org.caosdb.server.database.access.Access;
@@ -3546,7 +3547,10 @@ public class TestCQL {
*/
@Test
public void TestTicket147i()
- throws InterruptedException, SQLException, ConnectionException, QueryException,
+ throws InterruptedException,
+ SQLException,
+ ConnectionException,
+ QueryException,
TransactionException {
CQLLexer lexer;
lexer = new CQLLexer(CharStreams.fromString(this.ticket147i));
@@ -6754,6 +6758,7 @@ public class TestCQL {
// must not throw ParsingException
new Query(this.queryIssue134).parse();
}
+
/**
* Space before special character unit
*
@@ -7103,4 +7108,32 @@ public class TestCQL {
assertTrue(conj.getFilters().get(0) instanceof POV);
assertTrue(conj.getFilters().get(1) instanceof POV);
}
+
+ @Test
+ public void testDecimalNumber() {
+ // This should always be DEC, WHITESPACE, AND repeat
+ final String text =
+ "1.2123e+3 AND 1.21234E+3 AND 1.21234E-3 AND 1.21234E3 AND 16.0 AND 1.2 AND -1.2 AND +1.2 AND 1.2 AND - 1.2 AND + 1.2 AND 2e-323 AND 2E-323 AND 2E- 323 AND 2 e -323 AND + 1.2123e+323";
+ CQLLexer lexer = new CQLLexer(CharStreams.fromString(text));
+ final CommonTokenStream tokens = new CommonTokenStream(lexer);
+ Vocabulary vocab = lexer.getVocabulary();
+
+ final CQLParser parser = new CQLParser(tokens);
+ final CqContext sfq = parser.cq();
+ int no = 0;
+ for (final Token t : tokens.getTokens()) {
+ if (no % 3 == 0) {
+ assertEquals(vocab.getSymbolicName(t.getType()), "DECIMAL_NUMBER");
+ }
+ if (no % 3 == 1) {
+ if (vocab.getSymbolicName(t.getType()) != "EOF") {
+ assertEquals(vocab.getSymbolicName(t.getType()), "WHITE_SPACE");
+ }
+ }
+ if (no % 3 == 2) {
+ assertEquals(vocab.getSymbolicName(t.getType()), "AND");
+ }
+ no = no + 1;
+ }
+ }
}
diff --git a/src/test/java/org/caosdb/server/resource/TestAbstractCaosDBServerResource.java b/src/test/java/org/caosdb/server/resource/TestAbstractCaosDBServerResource.java
index ca4fbb0954f469055c2da3d0bf00b03cdc9dd563..4da4ba5cb4959787f5aaf1bf12e47140fdf4ee00 100644
--- a/src/test/java/org/caosdb/server/resource/TestAbstractCaosDBServerResource.java
+++ b/src/test/java/org/caosdb/server/resource/TestAbstractCaosDBServerResource.java
@@ -95,8 +95,12 @@ public class TestAbstractCaosDBServerResource {
@Override
protected Representation httpGetInChildClass()
- throws ConnectionException, IOException, SQLException, CaosDBException,
- NoSuchAlgorithmException, Exception {
+ throws ConnectionException,
+ IOException,
+ SQLException,
+ CaosDBException,
+ NoSuchAlgorithmException,
+ Exception {
// TODO Auto-generated method stub
return null;
}
diff --git a/src/test/java/org/caosdb/server/resource/TestScriptingResource.java b/src/test/java/org/caosdb/server/resource/TestScriptingResource.java
index 31d4a384c4a2a7e12b48c99073119cb7a38e3acc..3ce449ae2eea5ab5b4487ee4c14c22692423c8aa 100644
--- a/src/test/java/org/caosdb/server/resource/TestScriptingResource.java
+++ b/src/test/java/org/caosdb/server/resource/TestScriptingResource.java
@@ -178,12 +178,12 @@ public class TestScriptingResource {
return 0;
}
return -1;
- };
+ }
@Override
public Element generateRootElement(ServerSideScriptingCaller caller) {
return new Element("OK");
- };
+ }
@Override
public Object generateAuthToken(String purpose) {
diff --git a/src/test/java/org/caosdb/server/transaction/RetrieveTest.java b/src/test/java/org/caosdb/server/transaction/RetrieveTest.java
index a3ac40e1bf1e0fe6489a74f45d6c253b903b4478..95a019d46d9325759a3ad032ec285e98c9e51210 100644
--- a/src/test/java/org/caosdb/server/transaction/RetrieveTest.java
+++ b/src/test/java/org/caosdb/server/transaction/RetrieveTest.java
@@ -1,3 +1,22 @@
+/*
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 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 org.caosdb.server.transaction;
import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -62,7 +81,7 @@ public class RetrieveTest {
public void testMissingRetrievePermission() {
Subject subject = SecurityUtils.getSubject();
subject.login(AnonymousAuthenticationToken.getInstance());
- EntityInterface entity = new RetrieveEntity(new EntityID(1234));
+ EntityInterface entity = new RetrieveEntity(new EntityID("1234"));
EntityACLFactory fac = new EntityACLFactory();
fac.deny(AnonymousAuthenticationToken.PRINCIPAL, "RETRIEVE:ENTITY");
entity.setEntityACL(fac.create());
diff --git a/src/test/java/org/caosdb/server/transaction/UpdateTest.java b/src/test/java/org/caosdb/server/transaction/UpdateTest.java
index a0891a3eb34e1759100c78916d0fb250de149ef8..9a138106f4313f06ac2457728e3b5bd218470fa5 100644
--- a/src/test/java/org/caosdb/server/transaction/UpdateTest.java
+++ b/src/test/java/org/caosdb/server/transaction/UpdateTest.java
@@ -3,8 +3,9 @@
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- * Copyright (C) 2022 Indiscale GmbH <info@indiscale.com>
+ * Copyright (C) 2022,2023 Indiscale GmbH <info@indiscale.com>
* Copyright (C) 2022 Daniel Hornung <d.hornung@indiscale.com>
+ * Copyright (C) 2023 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
@@ -75,11 +76,11 @@ public class UpdateTest {
@Test
public void testDeriveUpdate_SameProperty()
throws NoSuchAlgorithmException, IOException, CaosDBException {
- final Entity newEntity = new RetrieveEntity(new EntityID(1234));
- final Property newProperty = new Property(new RetrieveEntity(new EntityID(1)));
+ final Entity newEntity = new RetrieveEntity(new EntityID("1234"));
+ final Property newProperty = new Property(new RetrieveEntity(new EntityID("1")));
newEntity.addProperty(newProperty);
- final Property oldProperty = new Property(new RetrieveEntity(new EntityID(1)));
- final Entity oldEntity = new RetrieveEntity(new EntityID(1234));
+ final Property oldProperty = new Property(new RetrieveEntity(new EntityID("1")));
+ final Entity oldEntity = new RetrieveEntity(new EntityID("1234"));
oldEntity.addProperty(oldProperty);
new WriteTransaction(null).deriveUpdate(newEntity, oldEntity);
@@ -89,13 +90,13 @@ public class UpdateTest {
@Test
public void testDeriveUpdate_AnotherProperty()
throws NoSuchAlgorithmException, IOException, CaosDBException {
- final Entity newEntity = new RetrieveEntity(new EntityID(1234));
- final Property newProperty = new Property(new RetrieveEntity(new EntityID(1)));
- final Property newProperty2 = new Property(new RetrieveEntity(new EntityID(2)));
+ final Entity newEntity = new RetrieveEntity(new EntityID("1234"));
+ final Property newProperty = new Property(new RetrieveEntity(new EntityID("1")));
+ final Property newProperty2 = new Property(new RetrieveEntity(new EntityID("2")));
newEntity.addProperty(newProperty);
newEntity.addProperty(newProperty2);
- final Property oldProperty = new Property(new RetrieveEntity(new EntityID(1)));
- final Entity oldEntity = new RetrieveEntity(new EntityID(1234));
+ final Property oldProperty = new Property(new RetrieveEntity(new EntityID("1")));
+ final Entity oldEntity = new RetrieveEntity(new EntityID("1234"));
oldEntity.addProperty(oldProperty);
new WriteTransaction(null).deriveUpdate(newEntity, oldEntity);
@@ -107,15 +108,15 @@ public class UpdateTest {
@Test
public void testDeriveUpdate_SameUnit()
throws NoSuchAlgorithmException, IOException, CaosDBException {
- final EntityInterface magicUnit = new RetrieveEntity(new EntityID(1234));
+ final EntityInterface magicUnit = new RetrieveEntity(new EntityID("1234"));
magicUnit.setName("Unit");
- magicUnit.setId(new EntityID(24));
+ magicUnit.setId(new EntityID("24"));
magicUnit.setDatatype("TEXT");
- final Entity newEntity = new RetrieveEntity(new EntityID(1234));
- final Property newProperty = new Property(new RetrieveEntity(new EntityID(1)));
+ final Entity newEntity = new RetrieveEntity(new EntityID("1234"));
+ final Property newProperty = new Property(new RetrieveEntity(new EntityID("1")));
- final Property newUnit = new Property(new RetrieveEntity(new EntityID(5)));
+ final Property newUnit = new Property(new RetrieveEntity(new EntityID("5")));
newUnit.setName(magicUnit.getName());
newUnit.setId(magicUnit.getId());
newUnit.setDatatype(magicUnit.getDatatype());
@@ -126,10 +127,10 @@ public class UpdateTest {
newEntity.addProperty(newProperty);
- final Entity oldEntity = new RetrieveEntity(new EntityID(1234));
- final Property oldProperty = new Property(new RetrieveEntity(new EntityID(1)));
+ final Entity oldEntity = new RetrieveEntity(new EntityID("1234"));
+ final Property oldProperty = new Property(new RetrieveEntity(new EntityID("1")));
- final Property oldUnit = new Property(new RetrieveEntity(new EntityID(5)));
+ final Property oldUnit = new Property(new RetrieveEntity(new EntityID("5")));
oldUnit.setName(magicUnit.getName());
oldUnit.setId(magicUnit.getId());
oldUnit.setDatatype(magicUnit.getDatatype());
@@ -149,15 +150,15 @@ public class UpdateTest {
@Test
public void testDeriveUpdate_DifferentUnit()
throws NoSuchAlgorithmException, IOException, CaosDBException {
- final EntityInterface magicUnit = new RetrieveEntity(new EntityID(1234));
+ final EntityInterface magicUnit = new RetrieveEntity(new EntityID("1234"));
magicUnit.setName("Unit");
- magicUnit.setId(new EntityID(24));
+ magicUnit.setId(new EntityID("24"));
magicUnit.setDatatype("TEXT");
- final Entity newEntity = new RetrieveEntity(new EntityID(1234));
- final Property newProperty = new Property(new RetrieveEntity(new EntityID(1)));
+ final Entity newEntity = new RetrieveEntity(new EntityID("1234"));
+ final Property newProperty = new Property(new RetrieveEntity(new EntityID("1")));
- final Property newUnit = new Property(new RetrieveEntity(new EntityID(5)));
+ final Property newUnit = new Property(new RetrieveEntity(new EntityID("5")));
newUnit.setName(magicUnit.getName());
newUnit.setId(magicUnit.getId());
newUnit.setDatatype(magicUnit.getDatatype());
@@ -168,10 +169,10 @@ public class UpdateTest {
newEntity.addProperty(newProperty);
- final Entity oldEntity = new RetrieveEntity(new EntityID(1234));
- final Property oldProperty = new Property(new RetrieveEntity(new EntityID(1)));
+ final Entity oldEntity = new RetrieveEntity(new EntityID("1234"));
+ final Property oldProperty = new Property(new RetrieveEntity(new EntityID("1")));
- final Property oldUnit = new Property(new RetrieveEntity(new EntityID(5)));
+ final Property oldUnit = new Property(new RetrieveEntity(new EntityID("5")));
oldUnit.setName(magicUnit.getName());
oldUnit.setId(magicUnit.getId());
oldUnit.setDatatype(magicUnit.getDatatype());
@@ -192,10 +193,10 @@ public class UpdateTest {
throws NoSuchAlgorithmException, CaosDBException, IOException {
final Entity newEntity = new UpdateEntity();
- final Property newProperty = new Property(new UpdateEntity(new EntityID(1)));
+ final Property newProperty = new Property(new UpdateEntity(new EntityID("1")));
newProperty.setDatatype("List<Person>");
CollectionValue newValue = new CollectionValue();
- newValue.add(new ReferenceValue(1234));
+ newValue.add(new ReferenceValue("1234"));
newValue.add(null);
newValue.add(new GenericValue(2345));
newValue.add(new GenericValue(3465));
@@ -206,14 +207,14 @@ public class UpdateTest {
// old entity represents the stored entity.
final Entity oldEntity = new UpdateEntity();
- final Property oldProperty = new Property(new UpdateEntity(new EntityID(1)));
+ final Property oldProperty = new Property(new UpdateEntity(new EntityID("1")));
oldProperty.setDatatype("List<Person>");
CollectionValue oldValue = new CollectionValue();
// Values are shuffled but have the correct index
oldValue.add(1, null);
oldValue.add(3, new GenericValue(3465));
- oldValue.add(2, new ReferenceValue(2345));
- oldValue.add(0, new ReferenceValue(1234));
+ oldValue.add(2, new ReferenceValue("2345"));
+ oldValue.add(0, new ReferenceValue("1234"));
oldProperty.setValue(oldValue);
oldEntity.addProperty(oldProperty);
@@ -245,8 +246,8 @@ public class UpdateTest {
// Values are shuffled but have the correct index
oldValue2.add(0, null);
oldValue2.add(1, new GenericValue(3465));
- oldValue2.add(2, new ReferenceValue(2345));
- oldValue2.add(3, new ReferenceValue(1234));
+ oldValue2.add(2, new ReferenceValue("2345"));
+ oldValue2.add(3, new ReferenceValue("1234"));
oldValue2.add(4, null);
oldProperty.setValue(oldValue2);
@@ -266,8 +267,8 @@ public class UpdateTest {
public void testDeriveUpdate_UpdateList()
throws NoSuchAlgorithmException, CaosDBException, IOException {
// @review Florian Spreckelsen 2022-03-15
- final Property oldProperty = new Property(new UpdateEntity(new EntityID(1)));
- final Property newProperty = new Property(new UpdateEntity(new EntityID(1)));
+ final Property oldProperty = new Property(new UpdateEntity(new EntityID("1")));
+ final Property newProperty = new Property(new UpdateEntity(new EntityID("1")));
oldProperty.setDatatype("List<Person>");
newProperty.setDatatype("List<Person>");
final Entity oldEntity = new UpdateEntity();
diff --git a/src/test/java/org/caosdb/server/utils/FileUtilsTest.java b/src/test/java/org/caosdb/server/utils/FileUtilsTest.java
index e05a3c7f6f082f2432137737c5937e67ff75d4ef..36851c4eacc7d78c4fcfd033f16c53f5e086b49b 100644
--- a/src/test/java/org/caosdb/server/utils/FileUtilsTest.java
+++ b/src/test/java/org/caosdb/server/utils/FileUtilsTest.java
@@ -573,7 +573,10 @@ public class FileUtilsTest {
@Test
public void testFileSystemConsistencyCheck()
- throws NoSuchAlgorithmException, IOException, TransactionException, InterruptedException,
+ throws NoSuchAlgorithmException,
+ IOException,
+ TransactionException,
+ InterruptedException,
Message {
final String rootPath = "./testFileSystemConsistencyCheck/";
final File root = new File(rootPath);