DOC: add CHANGELOG, remove unused classes

CHANGELOG.md

@@ -9,6 +9,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+* Related to #146, a new flag for entities and complete transactions:
+  `force-missing-obligatory=[ignore|warn|error]`. The flag overrides the
+  default behavior of the server (throwing an error when an obligatory property
+  is missing). `ignore` just discards the consistency check, `warn` only issues
+  a warning when obligatory properties are missing and `error` throws an error
+  in that case. The flag can be set for the complete transaction and each
+  single entity, while the entity flag takes precedence.
 * New EntityState plug-in. The plug-in disabled by default and can be enabled
   by setting the server property `EXT_ENTITY_STATE=ENABLED`. See
   [!62](https://gitlab.com/caosdb/caosdb-server/-/merge_requests/62) for more
@@ -31,6 +38,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+* #146 - Default behavior for missing obligatory properties
 * #131 - CQL Parsing error when white space characters before some units.
 * #134 - CQL Parsing error when multiple white space characters after `FROM`.
 * #130 - Error during `FIND ENTITY` when

src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRuleLoader.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 static org.caosdb.server.database.DatabaseUtils.bytes2UTF8;
-//
-// import java.sql.PreparedStatement;
-// import java.sql.ResultSet;
-// import java.sql.SQLException;
-// import java.util.ArrayList;
-// import org.caosdb.server.database.access.Access;
-// import org.caosdb.server.database.backend.interfaces.RuleLoaderImpl;
-// import org.caosdb.server.database.exceptions.TransactionException;
-// import org.caosdb.server.database.proto.Rule;
-// import org.caosdb.server.jobs.core.Mode;
-//
-// public class MySQLRuleLoader extends MySQLTransaction implements RuleLoaderImpl {
-//
-//  public MySQLRuleLoader(final Access access) {
-//    super(access);
-//  }
-//
-//  public static final String STMT_GET_RULES =
-//      "SELECT rules.transaction, rules.criterion, rules.modus from rules where rules.domain_id=?
-// AND rules.entity_id=? AND rules.transaction=?";
-//
-//  @Override
-//  public ArrayList<Rule> executeNoCache(
-//      final Integer domain, final Integer entity, final String transaction)
-//      throws TransactionException {
-//    try {
-//      final PreparedStatement stmt = prepareStatement(STMT_GET_RULES);
-//
-//      stmt.setInt(1, domain);
-//      stmt.setInt(2, entity);
-//      stmt.setString(3, transaction);
-//      stmt.execute();
-//
-//      final ResultSet rs = stmt.executeQuery();
-//      try {
-//        final ArrayList<Rule> ret = new ArrayList<Rule>();
-//        while (rs.next()) {
-//          final Rule r = new Rule();
-//          r.mode = Mode.valueOf(bytes2UTF8(rs.getBytes("modus")));
-//          r.job = bytes2UTF8(rs.getBytes("criterion"));
-//          r.domain = domain;
-//          r.entity = entity;
-//          r.transaction = transaction;
-//          ret.add(r);
-//        }
-//        return ret;
-//      } finally {
-//        rs.close();
-//      }
-//    } catch (final SQLException e) {
-//      throw new TransactionException(e);
-//    } catch (final ConnectionException e) {
-//      throw new TransactionException(e);
-//    }
-//  }
-// }

src/main/java/org/caosdb/server/database/backend/interfaces/RuleLoaderImpl.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.ArrayList;
-// import org.caosdb.server.database.exceptions.TransactionException;
-// import org.caosdb.server.database.proto.Rule;
-//
-// public interface RuleLoaderImpl extends BackendTransactionImpl {
-//
-//  public ArrayList<Rule> executeNoCache(Integer domain, Integer entity, String transaction)
-//      throws TransactionException;
-// }

src/main/java/org/caosdb/server/database/backend/transaction/RuleLoader.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
-// * Copyright (C) 2019 IndiScale GmbH
-// * Copyright (C) 2019 Timm Fitschen (t.fitschen@indiscale.com)
-// *
-// * This program is free software: you can redistribute it and/or modify
-// * it under the terms of the GNU Affero General Public License as
-// * published by the Free Software Foundation, either version 3 of the
-// * License, or (at your option) any later version.
-// *
-// * This program is distributed in the hope that it will be useful,
-// * but WITHOUT ANY WARRANTY; without even the implied warranty of
-// * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-// * GNU Affero General Public License for more details.
-// *
-// * You should have received a copy of the GNU Affero General Public License
-// * along with this program. If not, see <https://www.gnu.org/licenses/>.
-// *
-// * ** end header
-// */
-// package org.caosdb.server.database.backend.transaction;
-//
-// import java.util.ArrayList;
-// import org.apache.commons.jcs.access.behavior.ICacheAccess;
-// import org.caosdb.server.caching.Cache;
-// import org.caosdb.server.database.CacheableBackendTransaction;
-// import org.caosdb.server.database.backend.interfaces.RuleLoaderImpl;
-// import org.caosdb.server.database.exceptions.TransactionException;
-// import org.caosdb.server.database.proto.Rule;
-// import org.caosdb.server.entity.EntityInterface;
-// import org.caosdb.server.entity.container.TransactionContainer;
-// import org.caosdb.server.entity.wrapper.Property;
-// import org.caosdb.server.jobs.Job;
-// import org.caosdb.server.transaction.Transaction;
-//
-/// **
-// * Load transaction rules (e.g. "Referenced entities must always exist") and their configuration
-// * from the back-end.
-// *
-// * @author Timm Fitschen (t.fitschen@indiscale.com)
-// */
-// public class RuleLoader extends CacheableBackendTransaction<String, ArrayList<Rule>> {
-//
-//  private static final ICacheAccess<String, ArrayList<Rule>> cache =
-//      Cache.getCache("BACKEND_JobRules");
-//  private final Transaction<? extends TransactionContainer> transaction;
-//  private final EntityInterface e;
-//  private final Integer entity;
-//  private final Integer domain;
-//  private ArrayList<Job> jobs;
-//  private String transactionType;
-//
-//  public RuleLoader(
-//      final Integer domain,
-//      final Integer entity,
-//      final EntityInterface e,
-//      final Transaction<? extends TransactionContainer> transaction) {
-//    super(cache);
-//    this.domain = domain;
-//    this.entity = entity;
-//    this.e = e;
-//    if (e instanceof Property) {
-//      this.transactionType = getTransactionType(((Property) e).getDomainEntity());
-//    } else {
-//      this.transactionType = getTransactionType(e);
-//    }
-//    this.transaction = transaction;
-//  }
-//
-//  @Override
-//  protected String getKey() {
-//    return "<" + this.domain + "," + this.entity + "," + this.transactionType + ">";
-//  }
-//
-//  public ArrayList<Job> getJobs() {
-//    return this.jobs;
-//  }
-//
-//  @Override
-//  public ArrayList<Rule> executeNoCache() throws TransactionException {
-//    final RuleLoaderImpl t = getImplementation(RuleLoaderImpl.class);
-//    return t.executeNoCache(this.domain, this.entity, this.transactionType);
-//  }
-//
-//  @Override
-//  protected void process(final ArrayList<Rule> t) throws TransactionException {
-//    this.jobs = new ArrayList<Job>();
-//    for (final Rule r : t) {
-//      this.jobs.add(Job.getJob(r.job, r.mode, this.e, this.transaction));
-//    }
-//  }
-// }