Java tutorial
package py.fpuna.lib; /* * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation; either version 2 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 General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. */ /* * InstanceQuery.java * Copyright (C) 1999 University of Waikato, Hamilton, New Zealand * */ import weka.core.*; import javax.sql.DataSource; import java.sql.ResultSet; import java.sql.ResultSetMetaData; import java.sql.Time; import java.util.Date; import java.util.Enumeration; import java.util.Hashtable; import java.util.Vector; /** * Convert the results of a database query into instances. The jdbc * driver and database to be used default to "jdbc.idbDriver" and * "jdbc:idb=experiments.prp". These may be changed by creating * a java properties file called DatabaseUtils.props in user.home or * the current directory. eg:<p> * <p/> * <code><pre> * jdbcDriver=jdbc.idbDriver * jdbcURL=jdbc:idb=experiments.prp * </pre></code><p> * <p/> * Command line use just outputs the instances to System.out. <p/> * <p/> * <!-- options-start --> * Valid options are: <p/> * <p/> * <pre> -Q <query> * SQL query to execute.</pre> * <p/> * <pre> -S * Return sparse rather than normal instances.</pre> * <p/> * <pre> -U <username> * The username to use for connecting.</pre> * <p/> * <pre> -P <password> * The password to use for connecting.</pre> * <p/> * <pre> -D * Enables debug output.</pre> * <p/> * <!-- options-end --> * * @author Len Trigg (trigg@cs.waikato.ac.nz) * @version $Revision: 9184 $ */ public class ExtendedInstanceQuery extends ExtendedDatabaseUtils implements OptionHandler { /** * for serialization */ static final long serialVersionUID = 718158370917782584L; /** * Determines whether sparse data is created */ boolean m_CreateSparseData = false; /** * Query to execute */ String m_Query = "SELECT * from ?"; /** * Sets up the database drivers using default Weka .prop file * * @throws Exception if an error occurs */ public ExtendedInstanceQuery() throws Exception { super(); } /** * Construct the the instance by defining the property file and an optional Datasource * * @param propertyFile .prop file used by Weka * @param dataSource datasource used to retreive connections, if is null a new connection is created using * the .prop file * Exception if an error occurs */ public ExtendedInstanceQuery(String propertyFile, DataSource dataSource) throws Exception { super(propertyFile, dataSource); } /** * Test the class from the command line. The instance * query should be specified with -Q sql_query * * @param args contains options for the instance query */ public static void main(String args[]) { try { ExtendedInstanceQuery iq = new ExtendedInstanceQuery(); String query = Utils.getOption('Q', args); if (query.length() == 0) { iq.setQuery("select * from Experiment_index"); } else { iq.setQuery(query); } iq.setOptions(args); try { Utils.checkForRemainingOptions(args); } catch (Exception e) { System.err.println("Options for weka.experiment.InstanceQuery:\n"); Enumeration en = iq.listOptions(); while (en.hasMoreElements()) { Option o = (Option) en.nextElement(); System.err.println(o.synopsis() + "\n" + o.description()); } System.exit(1); } Instances aha = iq.retrieveInstances(); iq.disconnectFromDatabase(); // query returned no result -> exit if (aha == null) return; // The dataset may be large, so to make things easier we'll // output an instance at a time (rather than having to convert // the entire dataset to one large string) System.out.println(new Instances(aha, 0)); for (int i = 0; i < aha.numInstances(); i++) { System.out.println(aha.instance(i)); } } catch (Exception e) { e.printStackTrace(); System.err.println(e.getMessage()); } } /** * Returns an enumeration describing the available options <p> * * @return an enumeration of all options */ public Enumeration listOptions() { Vector result = new Vector(); result.addElement(new Option("\tSQL query to execute.", "Q", 1, "-Q <query>")); result.addElement(new Option("\tReturn sparse rather than normal instances.", "S", 0, "-S")); result.addElement(new Option("\tThe username to use for connecting.", "U", 1, "-U <username>")); result.addElement(new Option("\tThe password to use for connecting.", "P", 1, "-P <password>")); result.addElement(new Option("\tEnables debug output.", "D", 0, "-D")); return result.elements(); } /** * Returns the tip text for this property * * @return tip text for this property suitable for * displaying in the explorer/experimenter gui */ public String queryTipText() { return "The SQL query to execute against the database."; } /** * Get the query to execute against the database * * @return the query */ public String getQuery() { return m_Query; } /** * Set the query to execute against the database * * @param q the query to execute */ public void setQuery(String q) { m_Query = q; } /** * Returns the tip text for this property * * @return tip text for this property suitable for * displaying in the explorer/experimenter gui */ public String sparseDataTipText() { return "Encode data as sparse instances."; } /** * Gets whether data is to be returned as a set of sparse instances * * @return true if data is to be encoded as sparse instances */ public boolean getSparseData() { return m_CreateSparseData; } /** * Sets whether data should be encoded as sparse instances * * @param s true if data should be encoded as a set of sparse instances */ public void setSparseData(boolean s) { m_CreateSparseData = s; } /** * Gets the current settings of InstanceQuery * * @return an array of strings suitable for passing to setOptions() */ public String[] getOptions() { Vector options = new Vector(); options.add("-Q"); options.add(getQuery()); if (getSparseData()) options.add("-S"); if (!getUsername().equals("")) { options.add("-U"); options.add(getUsername()); } if (!getPassword().equals("")) { options.add("-P"); options.add(getPassword()); } if (getDebug()) options.add("-D"); return (String[]) options.toArray(new String[options.size()]); } /** * Parses a given list of options. * <p/> * <!-- options-start --> * Valid options are: <p/> * <p/> * <pre> -Q <query> * SQL query to execute.</pre> * <p/> * <pre> -S * Return sparse rather than normal instances.</pre> * <p/> * <pre> -U <username> * The username to use for connecting.</pre> * <p/> * <pre> -P <password> * The password to use for connecting.</pre> * <p/> * <pre> -D * Enables debug output.</pre> * <p/> * <!-- options-end --> * * @param options the list of options as an array of strings * @throws Exception if an option is not supported */ public void setOptions(String[] options) throws Exception { String tmpStr; setSparseData(Utils.getFlag('S', options)); tmpStr = Utils.getOption('Q', options); if (tmpStr.length() != 0) setQuery(tmpStr); tmpStr = Utils.getOption('U', options); if (tmpStr.length() != 0) setUsername(tmpStr); tmpStr = Utils.getOption('P', options); if (tmpStr.length() != 0) setPassword(tmpStr); setDebug(Utils.getFlag('D', options)); } /** * Makes a database query using the query set through the -Q option * to convert a table into a set of instances * * @return the instances contained in the result of the query * @throws Exception if an error occurs */ public Instances retrieveInstances() throws Exception { return retrieveInstances(m_Query); } /** * Makes a database query to convert a table into a set of instances * * @param query the query to convert to instances * @return the instances contained in the result of the query, NULL if the * SQL query doesn't return a ResultSet, e.g., DELETE/INSERT/UPDATE * @throws Exception if an error occurs */ public Instances retrieveInstances(String query) throws Exception { if (m_Debug) System.err.println("Executing query: " + query); connectToDatabase(); if (execute(query) == false) { if (m_PreparedStatement.getUpdateCount() == -1) { throw new Exception("Query didn't produce results"); } else { if (m_Debug) System.err.println(m_PreparedStatement.getUpdateCount() + " rows affected."); close(); return null; } } ResultSet rs = getResultSet(); if (m_Debug) System.err.println("Getting metadata..."); ResultSetMetaData md = rs.getMetaData(); if (m_Debug) System.err.println("Completed getting metadata..."); // Determine structure of the instances int numAttributes = md.getColumnCount(); int[] attributeTypes = new int[numAttributes]; Hashtable[] nominalIndexes = new Hashtable[numAttributes]; FastVector[] nominalStrings = new FastVector[numAttributes]; for (int i = 1; i <= numAttributes; i++) { /* switch (md.getColumnType(i)) { case Types.CHAR: case Types.VARCHAR: case Types.LONGVARCHAR: case Types.BINARY: case Types.VARBINARY: case Types.LONGVARBINARY:*/ switch (translateDBColumnType(md.getColumnTypeName(i))) { case STRING: //System.err.println("String --> nominal"); attributeTypes[i - 1] = Attribute.NOMINAL; nominalIndexes[i - 1] = new Hashtable(); nominalStrings[i - 1] = new FastVector(); break; case TEXT: //System.err.println("Text --> string"); attributeTypes[i - 1] = Attribute.STRING; nominalIndexes[i - 1] = new Hashtable(); nominalStrings[i - 1] = new FastVector(); break; case BOOL: //System.err.println("boolean --> nominal"); attributeTypes[i - 1] = Attribute.NOMINAL; nominalIndexes[i - 1] = new Hashtable(); nominalIndexes[i - 1].put("false", new Double(0)); nominalIndexes[i - 1].put("true", new Double(1)); nominalStrings[i - 1] = new FastVector(); nominalStrings[i - 1].addElement("false"); nominalStrings[i - 1].addElement("true"); break; case DOUBLE: //System.err.println("BigDecimal --> numeric"); attributeTypes[i - 1] = Attribute.NUMERIC; break; case BYTE: //System.err.println("byte --> numeric"); attributeTypes[i - 1] = Attribute.NUMERIC; break; case SHORT: //System.err.println("short --> numeric"); attributeTypes[i - 1] = Attribute.NUMERIC; break; case INTEGER: //System.err.println("int --> numeric"); attributeTypes[i - 1] = Attribute.NUMERIC; break; case LONG: //System.err.println("long --> numeric"); attributeTypes[i - 1] = Attribute.NUMERIC; break; case FLOAT: //System.err.println("float --> numeric"); attributeTypes[i - 1] = Attribute.NUMERIC; break; case DATE: attributeTypes[i - 1] = Attribute.DATE; break; case TIME: attributeTypes[i - 1] = Attribute.DATE; break; default: //System.err.println("Unknown column type"); attributeTypes[i - 1] = Attribute.STRING; } } // For sqlite // cache column names because the last while(rs.next()) { iteration for // the tuples below will close the md object: Vector<String> columnNames = new Vector<String>(); for (int i = 0; i < numAttributes; i++) { columnNames.add(md.getColumnLabel(i + 1)); } // Step through the tuples if (m_Debug) System.err.println("Creating instances..."); FastVector instances = new FastVector(); int rowCount = 0; while (rs.next()) { if (rowCount % 100 == 0) { if (m_Debug) { System.err.print("read " + rowCount + " instances \r"); System.err.flush(); } } double[] vals = new double[numAttributes]; for (int i = 1; i <= numAttributes; i++) { /*switch (md.getColumnType(i)) { case Types.CHAR: case Types.VARCHAR: case Types.LONGVARCHAR: case Types.BINARY: case Types.VARBINARY: case Types.LONGVARBINARY:*/ switch (translateDBColumnType(md.getColumnTypeName(i))) { case STRING: String str = rs.getString(i); if (rs.wasNull()) { vals[i - 1] = Instance.missingValue(); } else { Double index = (Double) nominalIndexes[i - 1].get(str); if (index == null) { index = new Double(nominalStrings[i - 1].size()); nominalIndexes[i - 1].put(str, index); nominalStrings[i - 1].addElement(str); } vals[i - 1] = index.doubleValue(); } break; case TEXT: String txt = rs.getString(i); if (rs.wasNull()) { vals[i - 1] = Instance.missingValue(); } else { Double index = (Double) nominalIndexes[i - 1].get(txt); if (index == null) { // Need to add one because first value in // string attribute is dummy value. index = new Double(nominalStrings[i - 1].size()) + 1; nominalIndexes[i - 1].put(txt, index); nominalStrings[i - 1].addElement(txt); } vals[i - 1] = index.doubleValue(); } break; case BOOL: boolean boo = rs.getBoolean(i); if (rs.wasNull()) { vals[i - 1] = Instance.missingValue(); } else { vals[i - 1] = (boo ? 1.0 : 0.0); } break; case DOUBLE: // BigDecimal bd = rs.getBigDecimal(i, 4); double dd = rs.getDouble(i); // Use the column precision instead of 4? if (rs.wasNull()) { vals[i - 1] = Instance.missingValue(); } else { // newInst.setValue(i - 1, bd.doubleValue()); vals[i - 1] = dd; } break; case BYTE: byte by = rs.getByte(i); if (rs.wasNull()) { vals[i - 1] = Instance.missingValue(); } else { vals[i - 1] = (double) by; } break; case SHORT: short sh = rs.getShort(i); if (rs.wasNull()) { vals[i - 1] = Instance.missingValue(); } else { vals[i - 1] = (double) sh; } break; case INTEGER: int in = rs.getInt(i); if (rs.wasNull()) { vals[i - 1] = Instance.missingValue(); } else { vals[i - 1] = (double) in; } break; case LONG: long lo = rs.getLong(i); if (rs.wasNull()) { vals[i - 1] = Instance.missingValue(); } else { vals[i - 1] = (double) lo; } break; case FLOAT: float fl = rs.getFloat(i); if (rs.wasNull()) { vals[i - 1] = Instance.missingValue(); } else { vals[i - 1] = (double) fl; } break; case DATE: Date date = rs.getDate(i); if (rs.wasNull()) { vals[i - 1] = Instance.missingValue(); } else { // TODO: Do a value check here. vals[i - 1] = (double) date.getTime(); } break; case TIME: Time time = rs.getTime(i); if (rs.wasNull()) { vals[i - 1] = Instance.missingValue(); } else { // TODO: Do a value check here. vals[i - 1] = (double) time.getTime(); } break; default: vals[i - 1] = Instance.missingValue(); } } Instance newInst; if (m_CreateSparseData) { newInst = new SparseInstance(1.0, vals); } else { newInst = new Instance(1.0, vals); } instances.addElement(newInst); rowCount++; } //disconnectFromDatabase(); (perhaps other queries might be made) // Create the header and add the instances to the dataset if (m_Debug) System.err.println("Creating header..."); FastVector attribInfo = new FastVector(); for (int i = 0; i < numAttributes; i++) { /* Fix for databases that uppercase column names */ // String attribName = attributeCaseFix(md.getColumnName(i + 1)); String attribName = attributeCaseFix(columnNames.get(i)); switch (attributeTypes[i]) { case Attribute.NOMINAL: attribInfo.addElement(new Attribute(attribName, nominalStrings[i])); break; case Attribute.NUMERIC: attribInfo.addElement(new Attribute(attribName)); break; case Attribute.STRING: Attribute att = new Attribute(attribName, (FastVector) null); attribInfo.addElement(att); for (int n = 0; n < nominalStrings[i].size(); n++) { att.addStringValue((String) nominalStrings[i].elementAt(n)); } break; case Attribute.DATE: attribInfo.addElement(new Attribute(attribName, (String) null)); break; default: throw new Exception("Unknown attribute type"); } } Instances result = new Instances("QueryResult", attribInfo, instances.size()); for (int i = 0; i < instances.size(); i++) { result.add((Instance) instances.elementAt(i)); } close(rs); return result; } /** * Returns the revision string. * * @return the revision */ public String getRevision() { return RevisionUtils.extract("$Revision: 9184 $"); } }