/*
* 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 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 General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
/*
* InstanceQuery.java
* Copyright (C) 1999-2012 University of Waikato, Hamilton, New Zealand
*
*/
package weka.experiment;
import java.io.File;
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;
import weka.core.Attribute;
import weka.core.DenseInstance;
import weka.core.FastVector;
import weka.core.Instance;
import weka.core.Instances;
import weka.core.Option;
import weka.core.OptionHandler;
import weka.core.RevisionUtils;
import weka.core.SparseInstance;
import weka.core.Utils;
/**
* 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>
*
* <code><pre>
* jdbcDriver=jdbc.idbDriver
* jdbcURL=jdbc:idb=experiments.prp
* </pre></code><p>
*
* Command line use just outputs the instances to System.out. <p/>
*
<!-- options-start -->
* Valid options are: <p/>
*
* <pre> -Q <query>
* SQL query to execute.</pre>
*
* <pre> -S
* Return sparse rather than normal instances.</pre>
*
* <pre> -U <username>
* The username to use for connecting.</pre>
*
* <pre> -P <password>
* The password to use for connecting.</pre>
*
* <pre> -D
* Enables debug output.</pre>
*
<!-- options-end -->
*
* @author Len Trigg (trigg@cs.waikato.ac.nz)
* @version $Revision: 9183 $
*/
public class InstanceQuery
extends DatabaseUtils
implements OptionHandler, InstanceQueryAdapter {
/** for serialization */
static final long serialVersionUID = 718158370917782584L;
/** Determines whether sparse data is created */
protected boolean m_CreateSparseData = false;
/** Query to execute */
protected String m_Query = "SELECT * from ?";
/** the custom props file to use instead of default one. */
protected File m_CustomPropsFile = null;
/**
* Sets up the database drivers
*
* @throws Exception if an error occurs
*/
public InstanceQuery() throws Exception {
super();
}
/**
* 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.add(
new Option(
"\tThe custom properties file to use instead of default ones,\n"
+ "\tcontaining the database parameters.\n"
+ "\t(default: none)",
"custom-props", 1, "-custom-props <file>"));
result.addElement(
new Option("\tEnables debug output.",
"D", 0, "-D"));
return result.elements();
}
/**
* Parses a given list of options.
*
<!-- options-start -->
* Valid options are: <p/>
*
* <pre> -Q <query>
* SQL query to execute.</pre>
*
* <pre> -S
* Return sparse rather than normal instances.</pre>
*
* <pre> -U <username>
* The username to use for connecting.</pre>
*
* <pre> -P <password>
* The password to use for connecting.</pre>
*
* <pre> -D
* Enables debug output.</pre>
*
<!-- 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);
tmpStr = Utils.getOption("custom-props", options);
if (tmpStr.length() == 0)
setCustomPropsFile(null);
else
setCustomPropsFile(new File(tmpStr));
setDebug(Utils.getFlag('D',options));
}
/**
* 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.";
}
/**
* Set the query to execute against the database
* @param q the query to execute
*/
public void setQuery(String q) {
m_Query = q;
}
/**
* Get the query to execute against the database
* @return the query
*/
public String getQuery() {
return m_Query;
}
/**
* 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.";
}
/**
* 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 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 the custom properties file to use.
*
* @param value the custom props file to load database parameters from,
* use null or directory to disable custom properties.
* @see #initialize(File)
*/
public void setCustomPropsFile(File value) {
m_CustomPropsFile = value;
initialize(m_CustomPropsFile);
}
/**
* Returns the custom properties file in use, if any.
*
* @return the custom props file, null if none used
*/
public File getCustomPropsFile() {
return m_CustomPropsFile;
}
/**
* The tip text for this property.
*
* @return the tip text
*/
public String customPropsFileTipText(){
return "The custom properties that the user can use to override the default ones.";
}
/**
* 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 ((m_CustomPropsFile != null) && !m_CustomPropsFile.isDirectory()) {
options.add("-custom-props");
options.add(m_CustomPropsFile.toString());
}
if (getDebug())
options.add("-D");
return (String[]) options.toArray(new String[options.size()]);
}
/**
* 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);
}
public static Instances retrieveInstances(InstanceQueryAdapter adapter, ResultSet rs) throws Exception {
if (adapter.getDebug())
System.err.println("Getting metadata...");
ResultSetMetaData md = rs.getMetaData();
if (adapter.getDebug())
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 (adapter.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 (adapter.getDebug())
System.err.println("Creating instances...");
FastVector instances = new FastVector();
int rowCount = 0;
while(rs.next()) {
if (rowCount % 100 == 0) {
if (adapter.getDebug()) {
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 (adapter.translateDBColumnType(md.getColumnTypeName(i))) {
case STRING :
String str = rs.getString(i);
if (rs.wasNull()) {
vals[i - 1] = Utils.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] = Utils.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] = Utils.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] = Utils.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] = Utils.missingValue();
} else {
vals[i - 1] = (double)by;
}
break;
case SHORT:
short sh = rs.getShort(i);
if (rs.wasNull()) {
vals[i - 1] = Utils.missingValue();
} else {
vals[i - 1] = (double)sh;
}
break;
case INTEGER:
int in = rs.getInt(i);
if (rs.wasNull()) {
vals[i - 1] = Utils.missingValue();
} else {
vals[i - 1] = (double)in;
}
break;
case LONG:
long lo = rs.getLong(i);
if (rs.wasNull()) {
vals[i - 1] = Utils.missingValue();
} else {
vals[i - 1] = (double)lo;
}
break;
case FLOAT:
float fl = rs.getFloat(i);
if (rs.wasNull()) {
vals[i - 1] = Utils.missingValue();
} else {
vals[i - 1] = (double)fl;
}
break;
case DATE:
Date date = rs.getDate(i);
if (rs.wasNull()) {
vals[i - 1] = Utils.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] = Utils.missingValue();
} else {
// TODO: Do a value check here.
vals[i - 1] = (double) time.getTime();
}
break;
default:
vals[i - 1] = Utils.missingValue();
}
}
Instance newInst;
if (adapter.getSparseData()) {
newInst = new SparseInstance(1.0, vals);
} else {
newInst = new DenseInstance(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 (adapter.getDebug())
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 = adapter.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));
}
return result;
}
/**
* 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...");
Instances result = retrieveInstances(this, rs);
close(rs);
return result;
}
/**
* 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 {
InstanceQuery iq = new InstanceQuery();
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 the revision string.
*
* @return the revision
*/
public String getRevision() {
return RevisionUtils.extract("$Revision: 9183 $");
}
}