package de.lmu.ifi.dbs.elki.database; /* This file is part of ELKI: Environment for Developing KDD-Applications Supported by Index-Structures Copyright (C) 2015 Ludwig-Maximilians-Universität München Lehr- und Forschungseinheit für Datenbanksysteme ELKI Development Team 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 . */ import java.util.Collection; import de.lmu.ifi.dbs.elki.data.type.SimpleTypeInformation; import de.lmu.ifi.dbs.elki.database.datastore.DataStoreFactory; import de.lmu.ifi.dbs.elki.database.datastore.DataStoreUtil; import de.lmu.ifi.dbs.elki.database.datastore.WritableDataStore; import de.lmu.ifi.dbs.elki.database.ids.ArrayStaticDBIDs; import de.lmu.ifi.dbs.elki.database.ids.DBIDArrayIter; import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil; import de.lmu.ifi.dbs.elki.database.ids.DBIDs; import de.lmu.ifi.dbs.elki.database.relation.DBIDView; import de.lmu.ifi.dbs.elki.database.relation.MaterializedRelation; import de.lmu.ifi.dbs.elki.database.relation.Relation; import de.lmu.ifi.dbs.elki.datasource.DatabaseConnection; import de.lmu.ifi.dbs.elki.datasource.FileBasedDatabaseConnection; import de.lmu.ifi.dbs.elki.datasource.bundle.MultipleObjectsBundle; import de.lmu.ifi.dbs.elki.index.Index; import de.lmu.ifi.dbs.elki.index.IndexFactory; import de.lmu.ifi.dbs.elki.logging.Logging; import de.lmu.ifi.dbs.elki.logging.statistics.Duration; import de.lmu.ifi.dbs.elki.utilities.documentation.Description; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectListParameter; import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; /** * This database class uses array-based storage and thus does not allow for * dynamic insert, delete and update operations. However, array access is * expected to be faster and use less memory. * * @author Arthur Zimek * @author Erich Schubert * @since 0.2 * * @apiviz.landmark * @apiviz.composedOf ArrayStaticDBIDs * @apiviz.uses DatabaseConnection */ @Description("Database using an in-memory hashtable and at least providing linear scans.") public class StaticArrayDatabase extends AbstractDatabase { /** * Our logger */ private static final Logging LOG = Logging.getLogger(StaticArrayDatabase.class); /** * IDs of this database */ private ArrayStaticDBIDs ids; /** * The DBID representation we use */ private DBIDView idrep; /** * The data source we get the initial data from. */ protected DatabaseConnection databaseConnection; /** * Constructor. * * @param databaseConnection Database connection to get the initial data from. * @param indexFactories Indexes to add */ public StaticArrayDatabase(DatabaseConnection databaseConnection, Collection> indexFactories) { super(); this.databaseConnection = databaseConnection; this.ids = null; this.idrep = null; // Add indexes. if(indexFactories != null) { this.indexFactories.addAll(indexFactories); } } /** * Constructor with no indexes. */ public StaticArrayDatabase() { this(null, null); } /** * Initialize the database by getting the initial data from the database * connection. */ @Override public void initialize() { if(databaseConnection != null) { if(LOG.isDebugging()) { LOG.debugFine("Loading data from database connection."); } MultipleObjectsBundle bundle = databaseConnection.loadData(); // Run at most once. databaseConnection = null; // Find DBIDs for bundle { DBIDs bids = bundle.getDBIDs(); if(bids instanceof ArrayStaticDBIDs) { this.ids = (ArrayStaticDBIDs) bids; } else if(bids == null) { this.ids = DBIDUtil.generateStaticDBIDRange(bundle.dataLength()); } else { this.ids = (ArrayStaticDBIDs) DBIDUtil.makeUnmodifiable(bids); } } // Replace id representation (it would be nicer if we would not need // DBIDView at all) this.idrep = new DBIDView(this.ids); relations.add(this.idrep); getHierarchy().add(this, idrep); DBIDArrayIter it = this.ids.iter(); int numrel = bundle.metaLength(); for(int i = 0; i < numrel; i++) { SimpleTypeInformation meta = bundle.meta(i); @SuppressWarnings("unchecked") SimpleTypeInformation ometa = (SimpleTypeInformation) meta; WritableDataStore store = DataStoreUtil.makeStorage(ids, DataStoreFactory.HINT_DB, ometa.getRestrictionClass()); for(it.seek(0); it.valid(); it.advance()) { store.put(it, bundle.data(it.getOffset(), i)); } Relation relation = new MaterializedRelation<>(ometa, ids, null, store); relations.add(relation); getHierarchy().add(this, relation); // Try to add indexes where appropriate for(IndexFactory factory : indexFactories) { if(factory.getInputTypeRestriction().isAssignableFromType(ometa)) { @SuppressWarnings("unchecked") final IndexFactory ofact = (IndexFactory) factory; @SuppressWarnings("unchecked") final Relation orep = (Relation) relation; final Index index = ofact.instantiate(orep); Duration duration = LOG.isStatistics() ? LOG.newDuration(index.getClass().getName() + ".construction").begin() : null; index.initialize(); if(duration != null) { LOG.statistics(duration.end()); } getHierarchy().add(relation, index); } } } // fire insertion event eventManager.fireObjectsInserted(ids); } } @Override protected Logging getLogger() { return LOG; } /** * Parameterization class. * * @author Erich Schubert * * @apiviz.exclude */ public static class Parameterizer extends AbstractDatabase.Parameterizer { /** * Holds the database connection to get the initial data from. */ protected DatabaseConnection databaseConnection = null; /** * Indexes to add. */ private Collection> indexFactories; @Override protected void makeOptions(Parameterization config) { super.makeOptions(config); // Get database connection. final ObjectParameter dbcP = new ObjectParameter<>(DATABASE_CONNECTION_ID, DatabaseConnection.class, FileBasedDatabaseConnection.class); if(config.grab(dbcP)) { databaseConnection = dbcP.instantiateClass(config); } // Get indexes. final ObjectListParameter> indexFactoryP = new ObjectListParameter<>(INDEX_ID, IndexFactory.class, true); if(config.grab(indexFactoryP)) { indexFactories = indexFactoryP.instantiateClasses(config); } } @Override protected StaticArrayDatabase makeInstance() { return new StaticArrayDatabase(databaseConnection, indexFactories); } } }