From ce345f40b927ac1bcd1d159ec4383d768a678bbe Mon Sep 17 00:00:00 2001
From: Timm Fitschen <t.fitschen@indiscale.com>
Date: Wed, 16 Aug 2023 00:59:18 +0200
Subject: [PATCH] WIP: MAINT: refactor retrieve properties (move backend-logic
to backend)
---
.../java/org/caosdb/server/CaosDBServer.java | 1 -
.../server/accessControl/ACMPermissions.java | 3 -
.../caosdb/server/database/Replacement.java | 41 --------------
.../implementation/MySQL}/DatabaseUtils.java | 55 +++++--------------
.../MySQL/MySQLGetAllNames.java | 1 -
.../MySQL/MySQLInsertEntityProperties.java | 1 -
.../MySQL/MySQLInsertSparseEntity.java | 1 -
.../MySQL/MySQLRetrieveAll.java | 1 -
.../MySQL/MySQLRetrieveDatatypes.java | 5 +-
.../MySQL/MySQLRetrieveParents.java | 5 +-
.../MySQL/MySQLRetrievePasswordValidator.java | 2 +-
.../MySQL/MySQLRetrieveProperties.java | 20 ++-----
.../MySQL/MySQLRetrieveSparseEntity.java | 1 -
.../MySQL/MySQLRetrieveUser.java | 2 +-
.../MySQL/MySQLRetrieveVersionHistory.java | 1 -
.../MySQL/MySQLUpdateSparseEntity.java | 1 -
.../implementation/MySQL/Replacement.java | 53 ++++++++++++++++++
.../interfaces/RetrieveDatatypesImpl.java | 4 +-
.../interfaces/RetrieveParentsImpl.java | 4 +-
.../transaction/RetrieveDatatypes.java | 4 +-
.../backend/transaction/RetrieveParents.java | 27 ++++++---
.../transaction/RetrieveProperties.java | 2 +-
.../transaction/RetrieveSparseEntity.java | 7 ++-
.../server/database/proto/FlatProperty.java | 13 -----
.../server/database/proto/ProtoProperty.java | 6 --
.../caosdb/server/query/Backreference.java | 2 +-
.../org/caosdb/server/query/Conjunction.java | 2 +-
.../org/caosdb/server/query/Disjunction.java | 2 +-
.../org/caosdb/server/query/Negation.java | 2 +-
.../java/org/caosdb/server/query/POV.java | 2 +-
.../java/org/caosdb/server/query/Query.java | 2 +-
.../org/caosdb/server/query/SubProperty.java | 2 +-
.../server/utils/ResultSetIterator.java | 2 +-
.../implementation/MySQL}/InsertTest.java | 6 +-
34 files changed, 119 insertions(+), 164 deletions(-)
delete mode 100644 src/main/java/org/caosdb/server/database/Replacement.java
rename src/main/java/org/caosdb/server/database/{ => backend/implementation/MySQL}/DatabaseUtils.java (87%)
create mode 100644 src/main/java/org/caosdb/server/database/backend/implementation/MySQL/Replacement.java
rename src/test/java/org/caosdb/server/database/{ => backend/implementation/MySQL}/InsertTest.java (98%)
diff --git a/src/main/java/org/caosdb/server/CaosDBServer.java b/src/main/java/org/caosdb/server/CaosDBServer.java
index 05fb9485..deca9aae 100644
--- a/src/main/java/org/caosdb/server/CaosDBServer.java
+++ b/src/main/java/org/caosdb/server/CaosDBServer.java
@@ -223,7 +223,6 @@ public class CaosDBServer extends Application {
public boolean notifyObserver(String e, Observable sender) {
if (e.equals(ServerProperties.KEY_TIMEZONE)) {
- String[] availableIDs = TimeZone.getAvailableIDs();
TimeZone newZoneId =
TimeZone.getTimeZone(getServerProperty(ServerProperties.KEY_TIMEZONE));
TimeZone.setDefault(newZoneId);
diff --git a/src/main/java/org/caosdb/server/accessControl/ACMPermissions.java b/src/main/java/org/caosdb/server/accessControl/ACMPermissions.java
index 854fc07f..07503692 100644
--- a/src/main/java/org/caosdb/server/accessControl/ACMPermissions.java
+++ b/src/main/java/org/caosdb/server/accessControl/ACMPermissions.java
@@ -26,12 +26,9 @@ import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;
import java.util.Set;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
public class ACMPermissions implements Comparable<ACMPermissions> {
- private static Logger LOGGER = LoggerFactory.getLogger(ACMPermissions.class);
public static final String USER_PARAMETER = "?USER?";
public static final String REALM_PARAMETER = "?REALM?";
public static final String ROLE_PARAMETER = "?ROLE?";
diff --git a/src/main/java/org/caosdb/server/database/Replacement.java b/src/main/java/org/caosdb/server/database/Replacement.java
deleted file mode 100644
index 8606d51b..00000000
--- a/src/main/java/org/caosdb/server/database/Replacement.java
+++ /dev/null
@@ -1,41 +0,0 @@
-package org.caosdb.server.database;
-
-import org.caosdb.server.datatype.ReferenceValue;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.StatementStatus;
-import org.caosdb.server.entity.wrapper.Property;
-
-public class Replacement extends Property {
-
- public Property replacement;
- public EntityID replacementId;
-
- @Override
- public EntityID getId() {
- return replacementId;
- }
-
- public void setReplacementId(EntityID id) {
- replacementId.link(id);
- }
-
- public Replacement(Property p) {
- super(p);
- replacementId = new EntityID();
- replacement = new Property(new RetrieveEntity());
-
- replacement.setDomain(p.getDomainEntity());
- // replacement.setDatatypeOverride(p.isDatatypeOverride());
- // replacement.setDatatype(p.getDatatype());
- // replacement.setNameOverride(p.isNameOverride());
- // replacement.setName(p.getName());
- // replacement.setDescOverride(p.isDescOverride());
- // replacement.setDescription(p.getDescription());
-
- replacement.setId(replacementId);
- replacement.setStatementStatus(StatementStatus.REPLACEMENT);
- replacement.setValue(new ReferenceValue(p.getId()));
- replacement.setPIdx(0);
- }
-}
diff --git a/src/main/java/org/caosdb/server/database/DatabaseUtils.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseUtils.java
similarity index 87%
rename from src/main/java/org/caosdb/server/database/DatabaseUtils.java
rename to src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseUtils.java
index 6d72d965..0347028b 100644
--- a/src/main/java/org/caosdb/server/database/DatabaseUtils.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseUtils.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
@@ -17,10 +18,8 @@
*
* 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;
+package org.caosdb.server.database.backend.implementation.MySQL;
import com.google.common.base.Objects;
import java.sql.ResultSet;
@@ -46,7 +45,6 @@ import org.caosdb.server.entity.EntityInterface;
import org.caosdb.server.entity.Message;
import org.caosdb.server.entity.RetrieveEntity;
import org.caosdb.server.entity.StatementStatus;
-import org.caosdb.server.entity.wrapper.Parent;
import org.caosdb.server.entity.wrapper.Property;
public class DatabaseUtils {
@@ -154,13 +152,7 @@ public class DatabaseUtils {
}
}
- public static void parseFromSparseEntities(final EntityInterface e, final SparseEntity spe) {
- if (spe != null) {
- e.parseSparseEntity(spe);
- }
- }
-
- public static void parseOverrides(final List<FlatProperty> properties, final ResultSet rs)
+ public static void parseOverrides(final List<ProtoProperty> properties, final ResultSet rs)
throws SQLException {
while (rs.next()) {
final int property_id = rs.getInt("property_id");
@@ -187,15 +179,15 @@ public class DatabaseUtils {
}
}
- public static List<FlatProperty> parsePropertyResultset(final ResultSet rs) throws SQLException {
- final List<FlatProperty> ret = new LinkedList<>();
+ public static List<ProtoProperty> parsePropertyResultset(final ResultSet rs) throws SQLException {
+ final List<ProtoProperty> ret = new LinkedList<>();
while (rs.next()) {
- FlatProperty fp = new FlatProperty();
- fp.id = rs.getInt("PropertyID");
- fp.value = bytes2UTF8(rs.getBytes("PropertyValue"));
- fp.status = bytes2UTF8(rs.getBytes("PropertyStatus"));
- fp.idx = rs.getInt("PropertyIndex");
- ret.add(fp);
+ ProtoProperty pp = new ProtoProperty();
+ pp.id = rs.getInt("PropertyID");
+ pp.value = bytes2UTF8(rs.getBytes("PropertyValue"));
+ pp.status = bytes2UTF8(rs.getBytes("PropertyStatus"));
+ pp.idx = rs.getInt("PropertyIndex");
+ ret.add(pp);
}
return ret;
}
@@ -239,9 +231,9 @@ public class DatabaseUtils {
return ret;
}
- public static ArrayList<VerySparseEntity> parseParentResultSet(final ResultSet rs)
+ public static LinkedList<VerySparseEntity> parseParentResultSet(final ResultSet rs)
throws SQLException {
- final ArrayList<VerySparseEntity> ret = new ArrayList<VerySparseEntity>();
+ final LinkedList<VerySparseEntity> ret = new LinkedList<>();
while (rs.next()) {
final VerySparseEntity vsp = new VerySparseEntity();
vsp.id = rs.getInt("ParentID");
@@ -254,25 +246,6 @@ public class DatabaseUtils {
return ret;
}
- public static <K extends EntityInterface> K parseEntityFromVerySparseEntity(
- final K entity, final VerySparseEntity vse) {
- entity.setId(new EntityID(vse.id));
- entity.setName(vse.name);
- entity.setRole(vse.role);
- entity.setDescription(vse.description);
- return entity;
- }
-
- public static void parseParentsFromVerySparseEntity(
- final EntityInterface entity, final List<VerySparseEntity> pars) {
- for (final VerySparseEntity vsp : pars) {
- final Parent p = new Parent(new RetrieveEntity(new EntityID(vsp.id)));
- p.setName(vsp.name);
- p.setDescription(vsp.description);
- entity.addParent(p);
- }
- }
-
public static ArrayList<Property> parseFromProtoProperties(
EntityInterface entity, List<ProtoProperty> protos) {
final ArrayList<Property> ret = new ArrayList<Property>();
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetAllNames.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetAllNames.java
index 09cae688..474048f1 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetAllNames.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetAllNames.java
@@ -5,7 +5,6 @@ import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.List;
-import org.caosdb.server.database.DatabaseUtils;
import org.caosdb.server.database.access.Access;
import org.caosdb.server.database.backend.interfaces.GetAllNamesImpl;
import org.caosdb.server.database.exceptions.TransactionException;
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 5c9ca6f9..f3977068 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
@@ -33,7 +33,6 @@ import java.util.Deque;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
-import org.caosdb.server.database.DatabaseUtils;
import org.caosdb.server.database.access.Access;
import org.caosdb.server.database.backend.interfaces.InsertEntityPropertiesImpl;
import org.caosdb.server.database.exceptions.IntegrityException;
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 1b945acf..27227926 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
@@ -26,7 +26,6 @@ import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLIntegrityConstraintViolationException;
import java.sql.Types;
-import org.caosdb.server.database.DatabaseUtils;
import org.caosdb.server.database.access.Access;
import org.caosdb.server.database.backend.interfaces.InsertSparseEntityImpl;
import org.caosdb.server.database.exceptions.IntegrityException;
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 f847bf63..9a2ea816 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
@@ -27,7 +27,6 @@ import java.sql.SQLException;
import java.util.LinkedList;
import java.util.List;
import org.apache.shiro.SecurityUtils;
-import org.caosdb.server.database.DatabaseUtils;
import org.caosdb.server.database.access.Access;
import org.caosdb.server.database.backend.interfaces.RetrieveAllImpl;
import org.caosdb.server.database.exceptions.TransactionException;
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveDatatypes.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveDatatypes.java
index e085f051..68524941 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveDatatypes.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveDatatypes.java
@@ -25,8 +25,7 @@ package org.caosdb.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
-import java.util.ArrayList;
-import org.caosdb.server.database.DatabaseUtils;
+import java.util.List;
import org.caosdb.server.database.access.Access;
import org.caosdb.server.database.backend.interfaces.RetrieveDatatypesImpl;
import org.caosdb.server.database.exceptions.TransactionException;
@@ -53,7 +52,7 @@ public class MySQLRetrieveDatatypes extends MySQLTransaction implements Retrieve
+ "FROM entities AS e WHERE e.role='DATATYPE'";
@Override
- public ArrayList<VerySparseEntity> execute() throws TransactionException {
+ public List<VerySparseEntity> execute() throws TransactionException {
try {
final PreparedStatement stmt = prepareStatement(STMT_GET_DATATYPE);
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 64ce7e90..1e2a6621 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
@@ -26,8 +26,7 @@ import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Types;
-import java.util.ArrayList;
-import org.caosdb.server.database.DatabaseUtils;
+import java.util.LinkedList;
import org.caosdb.server.database.access.Access;
import org.caosdb.server.database.backend.interfaces.RetrieveParentsImpl;
import org.caosdb.server.database.exceptions.TransactionException;
@@ -43,7 +42,7 @@ public class MySQLRetrieveParents extends MySQLTransaction implements RetrievePa
private static final String stmtStr = "call retrieveEntityParents(?, ?)";
@Override
- public ArrayList<VerySparseEntity> execute(final EntityID id, final String version)
+ public LinkedList<VerySparseEntity> execute(final EntityID id, final String version)
throws TransactionException {
try {
ResultSet rs = null;
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrievePasswordValidator.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrievePasswordValidator.java
index 1ff7dd7a..9fd7e0a8 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrievePasswordValidator.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrievePasswordValidator.java
@@ -22,7 +22,7 @@
*/
package org.caosdb.server.database.backend.implementation.MySQL;
-import static org.caosdb.server.database.DatabaseUtils.bytes2UTF8;
+import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.security.NoSuchAlgorithmException;
import java.sql.PreparedStatement;
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 c8843f9c..100df4ce 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
@@ -28,11 +28,9 @@ import java.sql.SQLException;
import java.sql.Types;
import java.util.LinkedList;
import java.util.List;
-import org.caosdb.server.database.DatabaseUtils;
import org.caosdb.server.database.access.Access;
import org.caosdb.server.database.backend.interfaces.RetrievePropertiesImpl;
import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.FlatProperty;
import org.caosdb.server.database.proto.ProtoProperty;
import org.caosdb.server.entity.EntityID;
@@ -92,32 +90,22 @@ public class MySQLRetrieveProperties extends MySQLTransaction implements Retriev
final long t2 = System.currentTimeMillis();
addMeasurement(this.getClass().getSimpleName() + ".retrieveFlatPropertiesStage1", t2 - t1);
- final List<FlatProperty> props = DatabaseUtils.parsePropertyResultset(rs);
+ final List<ProtoProperty> properties = DatabaseUtils.parsePropertyResultset(rs);
final PreparedStatement retrieveOverrides = prepareStatement(stmtStr2);
- retrieveOverrides(domain, entity, version, retrieveOverrides, props);
+ retrieveOverrides(domain, entity, version, retrieveOverrides, properties);
- return handleCollectionValues(props);
+ return properties;
}
}
- @Deprecated
- public List<ProtoProperty> handleCollectionValues(List<FlatProperty> props) throws SQLException {
-
- List<ProtoProperty> result = new LinkedList<>();
- for (FlatProperty fp : props) {
- result.add(new ProtoProperty(fp));
- }
- return result;
- }
-
private void retrieveOverrides(
final Integer domain,
final Integer entity,
final String version,
final PreparedStatement retrieveOverrides,
- final List<FlatProperty> props)
+ final List<ProtoProperty> props)
throws SQLException {
ResultSet rs = null;
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 ca3bd078..48cd84b3 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
@@ -26,7 +26,6 @@ import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Types;
-import org.caosdb.server.database.DatabaseUtils;
import org.caosdb.server.database.access.Access;
import org.caosdb.server.database.backend.interfaces.RetrieveSparseEntityImpl;
import org.caosdb.server.database.exceptions.TransactionException;
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 bde1878d..40f036f1 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
@@ -22,7 +22,7 @@
*/
package org.caosdb.server.database.backend.implementation.MySQL;
-import static org.caosdb.server.database.DatabaseUtils.bytes2UTF8;
+import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
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 585be49a..6c4c2629 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
@@ -27,7 +27,6 @@ import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.HashMap;
import java.util.LinkedList;
-import org.caosdb.server.database.DatabaseUtils;
import org.caosdb.server.database.access.Access;
import org.caosdb.server.database.backend.interfaces.RetrieveVersionHistoryImpl;
import org.caosdb.server.database.exceptions.TransactionException;
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 1c803925..b2d0fb9e 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
@@ -27,7 +27,6 @@ import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.SQLIntegrityConstraintViolationException;
import java.sql.Types;
-import org.caosdb.server.database.DatabaseUtils;
import org.caosdb.server.database.access.Access;
import org.caosdb.server.database.backend.interfaces.UpdateSparseEntityImpl;
import org.caosdb.server.database.exceptions.IntegrityException;
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
new file mode 100644
index 00000000..66bf99c4
--- /dev/null
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/Replacement.java
@@ -0,0 +1,53 @@
+/*
+ * 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 org.caosdb.server.datatype.ReferenceValue;
+import org.caosdb.server.entity.EntityID;
+import org.caosdb.server.entity.RetrieveEntity;
+import org.caosdb.server.entity.StatementStatus;
+import org.caosdb.server.entity.wrapper.Property;
+
+public class Replacement extends Property {
+
+ public Property replacement;
+ public EntityID replacementId;
+
+ @Override
+ public EntityID getId() {
+ return replacementId;
+ }
+
+ public void setReplacementId(EntityID id) {
+ replacementId.link(id);
+ }
+
+ public Replacement(Property p) {
+ super(p);
+ replacementId = new EntityID();
+ replacement = new Property(new RetrieveEntity());
+
+ replacement.setDomain(p.getDomainEntity());
+ replacement.setId(replacementId);
+ replacement.setStatementStatus(StatementStatus.REPLACEMENT);
+ replacement.setValue(new ReferenceValue(p.getId()));
+ replacement.setPIdx(0);
+ }
+}
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveDatatypesImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveDatatypesImpl.java
index 91c68dc5..0886ff43 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveDatatypesImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveDatatypesImpl.java
@@ -22,11 +22,11 @@
*/
package org.caosdb.server.database.backend.interfaces;
-import java.util.ArrayList;
+import java.util.List;
import org.caosdb.server.database.exceptions.TransactionException;
import org.caosdb.server.database.proto.VerySparseEntity;
public interface RetrieveDatatypesImpl extends BackendTransactionImpl {
- public abstract ArrayList<VerySparseEntity> execute() throws TransactionException;
+ public abstract List<VerySparseEntity> execute() throws TransactionException;
}
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveParentsImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveParentsImpl.java
index 9bfddba1..9f7eba82 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveParentsImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveParentsImpl.java
@@ -22,13 +22,13 @@
*/
package org.caosdb.server.database.backend.interfaces;
-import java.util.ArrayList;
+import java.util.LinkedList;
import org.caosdb.server.database.exceptions.TransactionException;
import org.caosdb.server.database.proto.VerySparseEntity;
import org.caosdb.server.entity.EntityID;
public interface RetrieveParentsImpl extends BackendTransactionImpl {
- public ArrayList<VerySparseEntity> execute(EntityID id, String version)
+ public LinkedList<VerySparseEntity> execute(EntityID id, String version)
throws TransactionException;
}
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveDatatypes.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveDatatypes.java
index b4a726da..1ca9f60e 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveDatatypes.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveDatatypes.java
@@ -22,7 +22,7 @@
*/
package org.caosdb.server.database.backend.transaction;
-import java.util.ArrayList;
+import java.util.List;
import org.caosdb.server.database.BackendTransaction;
import org.caosdb.server.database.backend.interfaces.RetrieveDatatypesImpl;
import org.caosdb.server.database.exceptions.TransactionException;
@@ -35,7 +35,7 @@ import org.caosdb.server.entity.container.Container;
public class RetrieveDatatypes extends BackendTransaction {
- private ArrayList<VerySparseEntity> list;
+ private List<VerySparseEntity> list;
@Override
public void execute() throws TransactionException {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveParents.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveParents.java
index b551430a..262ee271 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveParents.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveParents.java
@@ -24,15 +24,18 @@
*/
package org.caosdb.server.database.backend.transaction;
-import java.util.ArrayList;
+import java.util.LinkedList;
+import java.util.List;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
import org.caosdb.server.caching.Cache;
import org.caosdb.server.database.CacheableBackendTransaction;
-import org.caosdb.server.database.DatabaseUtils;
import org.caosdb.server.database.backend.interfaces.RetrieveParentsImpl;
import org.caosdb.server.database.exceptions.TransactionException;
import org.caosdb.server.database.proto.VerySparseEntity;
+import org.caosdb.server.entity.EntityID;
import org.caosdb.server.entity.EntityInterface;
+import org.caosdb.server.entity.RetrieveEntity;
+import org.caosdb.server.entity.wrapper.Parent;
// TODO Problem with the caching.
// When an old entity version has a parent which is deleted, the name is
@@ -47,9 +50,9 @@ import org.caosdb.server.entity.EntityInterface;
// See also a failing test in caosdb-pyinttest:
// tests/test_version.py::test_bug_cached_parent_name_in_old_version
public class RetrieveParents
- extends CacheableBackendTransaction<String, ArrayList<VerySparseEntity>> {
+ extends CacheableBackendTransaction<String, LinkedList<VerySparseEntity>> {
- private static final ICacheAccess<String, ArrayList<VerySparseEntity>> cache =
+ private static final ICacheAccess<String, LinkedList<VerySparseEntity>> cache =
Cache.getCache("BACKEND_EntityParents");
/**
@@ -71,16 +74,26 @@ public class RetrieveParents
}
@Override
- public ArrayList<VerySparseEntity> executeNoCache() throws TransactionException {
+ public LinkedList<VerySparseEntity> executeNoCache() throws TransactionException {
final RetrieveParentsImpl t = getImplementation(RetrieveParentsImpl.class);
return t.execute(this.entity.getId(), this.entity.getVersion().getId());
}
@Override
- protected void process(final ArrayList<VerySparseEntity> t) throws TransactionException {
+ protected void process(final LinkedList<VerySparseEntity> t) throws TransactionException {
this.entity.getParents().clear();
- DatabaseUtils.parseParentsFromVerySparseEntity(this.entity, t);
+ parseParentsFromVerySparseEntity(this.entity, t);
+ }
+
+ private void parseParentsFromVerySparseEntity(
+ final EntityInterface entity, final List<VerySparseEntity> pars) {
+ for (final VerySparseEntity vsp : pars) {
+ final Parent p = new Parent(new RetrieveEntity(new EntityID(vsp.id)));
+ p.setName(vsp.name);
+ p.setDescription(vsp.description);
+ entity.addParent(p);
+ }
}
@Override
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveProperties.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveProperties.java
index caa4b6cf..f9c11303 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveProperties.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveProperties.java
@@ -29,7 +29,7 @@ import java.util.List;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
import org.caosdb.server.caching.Cache;
import org.caosdb.server.database.CacheableBackendTransaction;
-import org.caosdb.server.database.DatabaseUtils;
+import org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils;
import org.caosdb.server.database.backend.interfaces.RetrievePropertiesImpl;
import org.caosdb.server.database.exceptions.TransactionException;
import org.caosdb.server.database.proto.ProtoProperty;
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveSparseEntity.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveSparseEntity.java
index aabd490b..f1ba8354 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveSparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveSparseEntity.java
@@ -27,7 +27,6 @@ package org.caosdb.server.database.backend.transaction;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
import org.caosdb.server.caching.Cache;
import org.caosdb.server.database.CacheableBackendTransaction;
-import org.caosdb.server.database.DatabaseUtils;
import org.caosdb.server.database.backend.interfaces.RetrieveSparseEntityImpl;
import org.caosdb.server.database.exceptions.TransactionException;
import org.caosdb.server.database.proto.SparseEntity;
@@ -81,8 +80,10 @@ public class RetrieveSparseEntity extends CacheableBackendTransaction<String, Sp
@Override
protected void process(final SparseEntity t) throws TransactionException {
- DatabaseUtils.parseFromSparseEntities(this.entity, t);
- this.entity.setEntityStatus(EntityStatus.VALID);
+ if (t != null) {
+ this.entity.parseSparseEntity(t);
+ this.entity.setEntityStatus(EntityStatus.VALID);
+ }
}
@Override
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 b4f0f62a..b92d3def 100644
--- a/src/main/java/org/caosdb/server/database/proto/FlatProperty.java
+++ b/src/main/java/org/caosdb/server/database/proto/FlatProperty.java
@@ -26,19 +26,6 @@ import java.io.Serializable;
public class FlatProperty implements Serializable {
- public FlatProperty() {}
-
- public FlatProperty(FlatProperty fp) {
- id = fp.id;
- value = fp.value;
- status = fp.status;
- idx = fp.idx;
- name = fp.name;
- desc = fp.desc;
- type = fp.type;
- collection = fp.collection;
- }
-
private static final long serialVersionUID = 6039288034435124195L;
public Integer id = null;
public String value = null;
diff --git a/src/main/java/org/caosdb/server/database/proto/ProtoProperty.java b/src/main/java/org/caosdb/server/database/proto/ProtoProperty.java
index c6cdbd54..7a11cd4d 100644
--- a/src/main/java/org/caosdb/server/database/proto/ProtoProperty.java
+++ b/src/main/java/org/caosdb/server/database/proto/ProtoProperty.java
@@ -28,12 +28,6 @@ import java.util.List;
public class ProtoProperty extends FlatProperty implements Serializable {
private static final long serialVersionUID = 7731301985162924975L;
- public ProtoProperty(FlatProperty fp) {
- super(fp);
- }
-
- public ProtoProperty() {}
-
public List<ProtoProperty> subProperties = null;
public List<Object> collValues = null;
}
diff --git a/src/main/java/org/caosdb/server/query/Backreference.java b/src/main/java/org/caosdb/server/query/Backreference.java
index 7d551fd4..b801ffaf 100644
--- a/src/main/java/org/caosdb/server/query/Backreference.java
+++ b/src/main/java/org/caosdb/server/query/Backreference.java
@@ -23,7 +23,7 @@
package org.caosdb.server.query;
import static java.sql.Types.VARCHAR;
-import static org.caosdb.server.database.DatabaseUtils.bytes2UTF8;
+import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.sql.CallableStatement;
import java.sql.Connection;
diff --git a/src/main/java/org/caosdb/server/query/Conjunction.java b/src/main/java/org/caosdb/server/query/Conjunction.java
index 03b33124..59dfd57b 100644
--- a/src/main/java/org/caosdb/server/query/Conjunction.java
+++ b/src/main/java/org/caosdb/server/query/Conjunction.java
@@ -22,7 +22,7 @@
*/
package org.caosdb.server.query;
-import static org.caosdb.server.database.DatabaseUtils.bytes2UTF8;
+import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.sql.CallableStatement;
import java.sql.Connection;
diff --git a/src/main/java/org/caosdb/server/query/Disjunction.java b/src/main/java/org/caosdb/server/query/Disjunction.java
index edd2e6da..925ef859 100644
--- a/src/main/java/org/caosdb/server/query/Disjunction.java
+++ b/src/main/java/org/caosdb/server/query/Disjunction.java
@@ -22,7 +22,7 @@
*/
package org.caosdb.server.query;
-import static org.caosdb.server.database.DatabaseUtils.bytes2UTF8;
+import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.sql.CallableStatement;
import java.sql.Connection;
diff --git a/src/main/java/org/caosdb/server/query/Negation.java b/src/main/java/org/caosdb/server/query/Negation.java
index cfdfd05e..431124df 100644
--- a/src/main/java/org/caosdb/server/query/Negation.java
+++ b/src/main/java/org/caosdb/server/query/Negation.java
@@ -22,7 +22,7 @@
*/
package org.caosdb.server.query;
-import static org.caosdb.server.database.DatabaseUtils.bytes2UTF8;
+import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.sql.CallableStatement;
import java.sql.Connection;
diff --git a/src/main/java/org/caosdb/server/query/POV.java b/src/main/java/org/caosdb/server/query/POV.java
index 0de160cd..ebc35a16 100644
--- a/src/main/java/org/caosdb/server/query/POV.java
+++ b/src/main/java/org/caosdb/server/query/POV.java
@@ -25,7 +25,7 @@ package org.caosdb.server.query;
import static java.sql.Types.DOUBLE;
import static java.sql.Types.INTEGER;
import static java.sql.Types.VARCHAR;
-import static org.caosdb.server.database.DatabaseUtils.bytes2UTF8;
+import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import de.timmfitschen.easyunits.parser.ParserException;
import java.sql.CallableStatement;
diff --git a/src/main/java/org/caosdb/server/query/Query.java b/src/main/java/org/caosdb/server/query/Query.java
index c4a45863..abaca436 100644
--- a/src/main/java/org/caosdb/server/query/Query.java
+++ b/src/main/java/org/caosdb/server/query/Query.java
@@ -21,7 +21,7 @@
*/
package org.caosdb.server.query;
-import static org.caosdb.server.database.DatabaseUtils.bytes2UTF8;
+import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.io.Serializable;
import java.sql.CallableStatement;
diff --git a/src/main/java/org/caosdb/server/query/SubProperty.java b/src/main/java/org/caosdb/server/query/SubProperty.java
index 8ff167ea..d5ce9234 100644
--- a/src/main/java/org/caosdb/server/query/SubProperty.java
+++ b/src/main/java/org/caosdb/server/query/SubProperty.java
@@ -23,7 +23,7 @@
package org.caosdb.server.query;
import static java.sql.Types.VARCHAR;
-import static org.caosdb.server.database.DatabaseUtils.bytes2UTF8;
+import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.sql.CallableStatement;
import java.sql.Connection;
diff --git a/src/main/java/org/caosdb/server/utils/ResultSetIterator.java b/src/main/java/org/caosdb/server/utils/ResultSetIterator.java
index 0912d278..71429f1a 100644
--- a/src/main/java/org/caosdb/server/utils/ResultSetIterator.java
+++ b/src/main/java/org/caosdb/server/utils/ResultSetIterator.java
@@ -1,6 +1,6 @@
package org.caosdb.server.utils;
-import static org.caosdb.server.database.DatabaseUtils.bytes2UTF8;
+import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.sql.ResultSet;
import java.sql.SQLException;
diff --git a/src/test/java/org/caosdb/server/database/InsertTest.java b/src/test/java/org/caosdb/server/database/backend/implementation/MySQL/InsertTest.java
similarity index 98%
rename from src/test/java/org/caosdb/server/database/InsertTest.java
rename to src/test/java/org/caosdb/server/database/backend/implementation/MySQL/InsertTest.java
index 0484e623..03bd185c 100644
--- a/src/test/java/org/caosdb/server/database/InsertTest.java
+++ b/src/test/java/org/caosdb/server/database/backend/implementation/MySQL/InsertTest.java
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database;
+package org.caosdb.server.database.backend.implementation.MySQL;
-import static org.caosdb.server.database.DatabaseUtils.deriveStage1Inserts;
-import static org.caosdb.server.database.DatabaseUtils.deriveStage2Inserts;
+import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.deriveStage1Inserts;
+import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.deriveStage2Inserts;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue;
--
GitLab