Merge branch 'dev' into f-select-acl

CHANGELOG.md

@@ -5,6 +5,20 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unreleased]
+
+### Added
+
+### Changed
+
+### Deprecated
+
+### Removed
+
+### Fixed
+
+### Security
+
 ## [0.12.0] - 2023-10-25
 (Timm Fitschen)
 

RELEASE_GUIDELINES.md

@@ -40,11 +40,11 @@ guidelines of the CaosDB Project
   * `CHANGELOG.md`: Re-add the `[Unreleased]` section.
 
 11. Add a gitlab release in the respective repository:
-    https://gitlab.indiscale.com/caosdb/src/caosdb-server/-/releases
+    https://gitlab.com/linkahead/linkahead-server/-/releases
 
     Add a description, which can be a copy&paste from the CHANGELOG, possibly prepended by:
     ```md
 # Changelog
 
-[See full changelog](https://gitlab.indiscale.com/caosdb/src/caosdb-server/-/blob/${TAG}/CHANGELOG.md)
+[See full changelog](https://gitlab.com/linkahead/linkahead-server/-/blob/${TAG}/CHANGELOG.md)
     ```

conf/core/usersources.ini.template

@@ -46,11 +46,14 @@ class = org.caosdb.server.accessControl.Pam
 # scripts or the misc/pam_authentication/ldap_authentication.sh script here.
 ; pam_script = ./misc/pam_authentication/pam_authentication.sh
 default_status = ACTIVE
-# Only users which fulfill these criteria are accepted.
+# Only users which fulfill these criteria are accepted. The values are
+# user/group name(s) separated by whitespaces
 ;include.user = [uncomment and put your users here]
 ;include.group = [uncomment and put your groups here]
 ;exclude.user = [uncomment and put excluded users here]
 ;exclude.group = [uncomment and put excluded groups here]
 
 # It is typically necessary to add at least one admin
-;user.[uncomment a set a username here].roles = administration
+;user.[uncomment and set a username here].roles = administration
+# Several roles are separated by commas
+;user.[uncomment and set a username here].roles = role1, role2, role with spaces

pom.xml

@@ -25,7 +25,7 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.caosdb</groupId>
   <artifactId>caosdb-server</artifactId>
-  <version>0.12.0</version>
+  <version>0.13.0-SNAPSHOT</version>
   <packaging>jar</packaging>
   <name>CaosDB Server</name>
   <scm>

src/doc/conf.py

@@ -26,9 +26,9 @@ copyright = '2023, IndiScale GmbH'
 author = 'Daniel Hornung, Timm Fitschen'
 
 # The short X.Y version
-version = '0.12.0'
+version = '0.13.0'
 # The full version, including alpha/beta/rc tags
-release = '0.12.0'
+release = '0.13.0-dev'
 
 
 # -- General configuration ---------------------------------------------------

src/main/java/org/caosdb/server/CaosDBServer.java

@@ -73,7 +73,6 @@ import org.caosdb.server.resource.LogoutResource;
 import org.caosdb.server.resource.PermissionRulesResource;
 import org.caosdb.server.resource.RolesResource;
 import org.caosdb.server.resource.ScriptingResource;
-import org.caosdb.server.resource.ServerLogsResource;
 import org.caosdb.server.resource.ServerPropertiesResource;
 import org.caosdb.server.resource.SharedFileResource;
 import org.caosdb.server.resource.ThumbnailsResource;
@@ -746,12 +745,6 @@ public class CaosDBServer extends Application {
     protectedRouter.attach("/Role/{specifier}", RolesResource.class);
     protectedRouter.attach("/PermissionRules/{specifier}", PermissionRulesResource.class);
     protectedRouter.attach("/PermissionRules/{realm}/{specifier}", PermissionRulesResource.class);
-    protectedRouter
-        .attach("/ServerLogs/", ServerLogsResource.class)
-        .setMatchingMode(Template.MODE_STARTS_WITH);
-    protectedRouter
-        .attach("/ServerLogs", ServerLogsResource.class)
-        .setMatchingMode(Template.MODE_STARTS_WITH);
     protectedRouter.attach("/login?username={username}", AuthenticationResource.class);
     protectedRouter.attach("/logout", LogoutResource.class);
     protectedRouter.attach("/_server_properties", ServerPropertiesResource.class);

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

@@ -37,7 +37,6 @@ import org.caosdb.server.database.backend.implementation.MySQL.MySQLGetUpdateabl
 import org.caosdb.server.database.backend.implementation.MySQL.MySQLInsertEntityDatatype;
 import org.caosdb.server.database.backend.implementation.MySQL.MySQLInsertEntityProperties;
 import org.caosdb.server.database.backend.implementation.MySQL.MySQLInsertLinCon;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLInsertLogRecord;
 import org.caosdb.server.database.backend.implementation.MySQL.MySQLInsertParents;
 import org.caosdb.server.database.backend.implementation.MySQL.MySQLInsertRole;
 import org.caosdb.server.database.backend.implementation.MySQL.MySQLInsertSparseEntity;
@@ -51,7 +50,6 @@ import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveAllU
 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;
 import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveParents;
 import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrievePasswordValidator;
 import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrievePermissionRules;
@@ -95,7 +93,6 @@ import org.caosdb.server.database.backend.interfaces.GetUpdateableChecksumsImpl;
 import org.caosdb.server.database.backend.interfaces.InsertEntityDatatypeImpl;
 import org.caosdb.server.database.backend.interfaces.InsertEntityPropertiesImpl;
 import org.caosdb.server.database.backend.interfaces.InsertLinConImpl;
-import org.caosdb.server.database.backend.interfaces.InsertLogRecordImpl;
 import org.caosdb.server.database.backend.interfaces.InsertParentsImpl;
 import org.caosdb.server.database.backend.interfaces.InsertRoleImpl;
 import org.caosdb.server.database.backend.interfaces.InsertSparseEntityImpl;
@@ -109,7 +106,6 @@ import org.caosdb.server.database.backend.interfaces.RetrieveAllUncheckedFilesIm
 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;
 import org.caosdb.server.database.backend.interfaces.RetrieveParentsImpl;
 import org.caosdb.server.database.backend.interfaces.RetrievePasswordValidatorImpl;
 import org.caosdb.server.database.backend.interfaces.RetrievePermissionRulesImpl;
@@ -213,8 +209,6 @@ public abstract class BackendTransaction implements Undoable {
       setImpl(SetPermissionRulesImpl.class, MySQLSetPermissionRules.class);
       setImpl(RetrievePermissionRulesImpl.class, MySQLRetrievePermissionRules.class);
       setImpl(UpdateUserRolesImpl.class, MySQLUpdateUserRoles.class);
-      setImpl(InsertLogRecordImpl.class, MySQLInsertLogRecord.class);
-      setImpl(RetrieveLogRecordImpl.class, MySQLRetrieveLogRecord.class);
       setImpl(SetQueryTemplateDefinitionImpl.class, MySQLSetQueryTemplateDefinition.class);
       setImpl(
           RetrieveQueryTemplateDefinitionImpl.class, MySQLRetrieveQueryTemplateDefinition.class);

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

-/*
- * ** header v3.0
- * This file is a part of the CaosDB Project.
- *
- * Copyright (C) 2018 Research Group Biomedical Physics,
- * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Affero General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU Affero General Public License for more details.
- *
- * You should have received a copy of the GNU Affero General Public License
- * along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
- */
-package org.caosdb.server.database.backend.implementation.MySQL;
-
-import java.sql.PreparedStatement;
-import java.sql.SQLException;
-import java.util.List;
-import java.util.logging.LogRecord;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.InsertLogRecordImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-
-public class MySQLInsertLogRecord extends MySQLTransaction implements InsertLogRecordImpl {
-
-  public MySQLInsertLogRecord(final Access access) {
-    super(access);
-  }
-
-  public static final String STMT_INSERT_LOG_RECORD =
-      "INSERT INTO logging (level, logger, message, millis, logRecord) VALUES (?,?,?,?,?)";
-
-  @Override
-  public void insert(final List<LogRecord> toBeFlushed) throws TransactionException {
-    try {
-      final PreparedStatement prepInsert = prepareStatement(STMT_INSERT_LOG_RECORD);
-      for (final LogRecord record : toBeFlushed) {
-        prepInsert.setInt(1, record.getLevel().intValue());
-        prepInsert.setString(2, record.getLoggerName());
-        prepInsert.setString(3, record.getMessage());
-        prepInsert.setLong(4, record.getMillis());
-        prepInsert.setObject(5, record);
-        prepInsert.executeUpdate();
-      }
-    } catch (final SQLException e) {
-      throw new TransactionException(e);
-    } catch (final ConnectionException e) {
-      throw new TransactionException(e);
-    }
-  }
-}

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

-/*
- * ** header v3.0
- * This file is a part of the CaosDB Project.
- *
- * Copyright (C) 2018 Research Group Biomedical Physics,
- * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Affero General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU Affero General Public License for more details.
- *
- * You should have received a copy of the GNU Affero General Public License
- * along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
- */
-package org.caosdb.server.database.backend.implementation.MySQL;
-
-import java.io.ByteArrayInputStream;
-import java.io.IOException;
-import java.io.ObjectInputStream;
-import java.sql.PreparedStatement;
-import java.sql.ResultSet;
-import java.sql.SQLException;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.logging.Level;
-import java.util.logging.LogRecord;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrieveLogRecordImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-
-public class MySQLRetrieveLogRecord extends MySQLTransaction implements RetrieveLogRecordImpl {
-
-  public MySQLRetrieveLogRecord(final Access access) {
-    super(access);
-  }
-
-  public static final String STMT_RETRIEVE_LOG = "SELECT logRecord FROM logging";
-  public static final String WHERE = " WHERE ";
-  public static final String AND = " AND ";
-  public static final String LOGGER_COND = "logger LIKE ?";
-  public static final String MESSAGE_COND = "message LIKE ?";
-
-  public static final String LEVEL_COND(final Level level) {
-    return "level=" + level.intValue();
-  }
-
-  private static String getWhereClause(
-      final String logger, final Level level, final String message) {
-
-    if (logger != null || level != null || message != null) {
-      final StringBuilder sb = new StringBuilder();
-
-      if (logger != null) {
-        sb.append(LOGGER_COND);
-      }
-      if (level != null) {
-        if (sb.length() > 0) {
-          sb.append(AND);
-        }
-        sb.append(LEVEL_COND(level));
-      }
-      if (message != null) {
-        if (sb.length() > 0) {
-          sb.append(AND);
-        }
-        sb.append(MESSAGE_COND);
-      }
-      return WHERE + sb.toString();
-    }
-    return "";
-  }
-
-  @Override
-  public List<LogRecord> retrieve(final String logger, final Level level, final String message)
-      throws TransactionException {
-    final List<LogRecord> ret = new LinkedList<LogRecord>();
-
-    final String stmtStr = STMT_RETRIEVE_LOG + getWhereClause(logger, level, message);
-
-    try {
-      final PreparedStatement stmt = prepareStatement(stmtStr);
-      int index = 1;
-      if (logger != null) {
-        stmt.setString(index++, logger);
-      }
-      if (message != null) {
-        stmt.setString(index++, message);
-      }
-      ResultSet rs = null;
-      try {
-        rs = stmt.executeQuery();
-
-        while (rs.next()) {
-          final byte[] bytes = rs.getBytes("logRecord");
-
-          final ObjectInputStream s = new ObjectInputStream(new ByteArrayInputStream(bytes));
-          final Object o = s.readObject();
-          ret.add((LogRecord) o);
-        }
-      } finally {
-        if (rs != null && !rs.isClosed()) {
-          rs.close();
-        }
-      }
-    } catch (final ClassNotFoundException e) {
-      throw new TransactionException(e);
-    } catch (final IOException e) {
-      throw new TransactionException(e);
-    } catch (final SQLException e) {
-      throw new TransactionException(e);
-    } catch (final ConnectionException e) {
-      throw new TransactionException(e);
-    }
-
-    return ret;
-  }
-}

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

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

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

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

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

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

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

-/*
- * ** header v3.0
- * This file is a part of the CaosDB Project.
- *
- * Copyright (C) 2018 Research Group Biomedical Physics,
- * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Affero General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU Affero General Public License for more details.
- *
- * You should have received a copy of the GNU Affero General Public License
- * along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
- */
-package org.caosdb.server.database.backend.transaction;
-
-import java.util.List;
-import java.util.logging.Level;
-import java.util.logging.LogRecord;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.RetrieveLogRecordImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-
-public class RetrieveLogRecord extends BackendTransaction {
-
-  private final Level level;
-  private final String logger;
-  private List<LogRecord> logRecords;
-  private final String message;
-
-  public RetrieveLogRecord(final String logger, final Level level, final String message) {
-    this.logger = logger;
-    this.level = level;
-    this.message = message;
-  }
-
-  @Override
-  protected void execute() throws TransactionException {
-    final RetrieveLogRecordImpl t = getImplementation(RetrieveLogRecordImpl.class);
-    this.logRecords = t.retrieve(this.logger, this.level, this.message);
-  }
-
-  public List<LogRecord> getLogRecords() {
-    return this.logRecords;
-  }
-}

src/main/java/org/caosdb/server/resource/ServerLogsResource.java

-/*
- * ** header v3.0
- * This file is a part of the CaosDB Project.
- *
- * Copyright (C) 2018 Research Group Biomedical Physics,
- * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Affero General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU Affero General Public License for more details.
- *
- * You should have received a copy of the GNU Affero General Public License
- * along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
- */
-package org.caosdb.server.resource;
-
-import java.io.IOException;
-import java.security.NoSuchAlgorithmException;
-import java.sql.SQLException;
-import java.util.List;
-import java.util.logging.Level;
-import java.util.logging.LogRecord;
-import java.util.logging.XMLFormatter;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.transaction.RetrieveLogRecordTransaction;
-import org.restlet.data.Form;
-import org.restlet.data.MediaType;
-import org.restlet.representation.Representation;
-import org.restlet.representation.StringRepresentation;
-
-public class ServerLogsResource extends AbstractCaosDBServerResource {
-
-  @Override
-  protected Representation httpGetInChildClass()
-      throws ConnectionException,
-          IOException,
-          SQLException,
-          CaosDBException,
-          NoSuchAlgorithmException,
-          Exception {
-
-    Level level = null;
-    String message = null;
-    final String logger =
-        getRequest().getResourceRef().getRemainingPart(true, false).replaceAll("/", ".");
-    final Form form = getRequest().getResourceRef().getQueryAsForm(true);
-    if (form != null) {
-      final String levelStr = form.getFirstValue("level");
-      if (levelStr != null) {
-        try {
-          level = Level.parse(levelStr);
-        } catch (final IllegalArgumentException e) {
-          level = Level.OFF;
-        }
-      }
-      message = form.getFirstValue("message");
-    }
-
-    final RetrieveLogRecordTransaction t = new RetrieveLogRecordTransaction(logger, level, message);
-    t.execute();
-
-    generateRootElement();
-    final List<LogRecord> logRecords = t.getLogRecords();
-
-    final XMLFormatter xmlFormatter = new XMLFormatter();
-    String ret = xmlFormatter.getHead(null);
-    for (final LogRecord r : logRecords) {
-      ret += xmlFormatter.format(r);
-    }
-    ret += xmlFormatter.getTail(null);
-
-    return new StringRepresentation(ret, MediaType.TEXT_XML);
-  }
-}

src/main/java/org/caosdb/server/transaction/InsertLogRecordTransaction.java

-/*
- * ** header v3.0
- * This file is a part of the CaosDB Project.
- *
- * Copyright (C) 2018 Research Group Biomedical Physics,
- * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Affero General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU Affero General Public License for more details.
- *
- * You should have received a copy of the GNU Affero General Public License
- * along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
- */
-package org.caosdb.server.transaction;
-
-import java.util.List;
-import java.util.logging.LogRecord;
-import org.caosdb.datetime.UTCDateTime;
-import org.caosdb.server.database.DatabaseAccessManager;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.transaction.InsertLogRecord;
-
-public class InsertLogRecordTransaction implements TransactionInterface {
-
-  private final List<LogRecord> toBeFlushed;
-  private UTCDateTime timestamp;
-
-  public InsertLogRecordTransaction(final List<LogRecord> toBeFlushed) {
-    this.timestamp = UTCDateTime.SystemMillisToUTCDateTime(System.currentTimeMillis());
-    this.toBeFlushed = toBeFlushed;
-  }
-
-  @Override
-  public void execute() throws Exception {
-    final Access access = DatabaseAccessManager.getInstance().acquireReadAccess(this);
-    try {
-      execute(new InsertLogRecord(this.toBeFlushed), access);
-    } finally {
-      access.release();
-    }
-  }
-
-  @Override
-  public UTCDateTime getTimestamp() {
-    return timestamp;
-  }
-}

src/main/java/org/caosdb/server/transaction/RetrieveLogRecordTransaction.java

-/*
- * ** header v3.0
- * This file is a part of the CaosDB Project.
- *
- * Copyright (C) 2018 Research Group Biomedical Physics,
- * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Affero General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU Affero General Public License for more details.
- *
- * You should have received a copy of the GNU Affero General Public License
- * along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
- */
-package org.caosdb.server.transaction;
-
-import java.util.List;
-import java.util.logging.Level;
-import java.util.logging.LogRecord;
-import org.apache.shiro.SecurityUtils;
-import org.caosdb.datetime.UTCDateTime;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.database.DatabaseAccessManager;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.transaction.RetrieveLogRecord;
-
-public class RetrieveLogRecordTransaction implements TransactionInterface {
-
-  private List<LogRecord> logRecords;
-  private final String logger;
-  private final Level level;
-  private final String message;
-  private UTCDateTime timestamp;
-
-  public RetrieveLogRecordTransaction(
-      final String logger, final Level level, final String message) {
-    this.level = level;
-    this.timestamp = UTCDateTime.SystemMillisToUTCDateTime(System.currentTimeMillis());
-    if (message != null && message.isEmpty()) {
-      this.message = null;
-    } else if (message != null) {
-      this.message = message.replaceAll("\\*", "%");
-    } else {
-      this.message = null;
-    }
-    if (logger != null && logger.isEmpty()) {
-      this.logger = null;
-    } else if (logger != null) {
-      this.logger = logger.replaceAll("\\*", "%");
-    } else {
-      this.logger = logger;
-    }
-  }
-
-  @Override
-  public void execute() throws Exception {
-    SecurityUtils.getSubject().checkPermission(ACMPermissions.PERMISSION_RETRIEVE_SERVERLOGS);
-    final Access access = DatabaseAccessManager.getInstance().acquireReadAccess(this);
-    try {
-      this.logRecords =
-          execute(new RetrieveLogRecord(this.logger, this.level, this.message), access)
-              .getLogRecords();
-    } finally {
-      access.release();
-    }
-  }
-
-  public List<LogRecord> getLogRecords() {
-    return this.logRecords;
-  }
-
-  @Override
-  public UTCDateTime getTimestamp() {
-    return timestamp;
-  }
-}