edu.udo.cs.yale.operator.io
Class DatabaseExampleSource

java.lang.Object
  edu.udo.cs.yale.operator.Operator
      edu.udo.cs.yale.operator.io.ResultSetExampleSource
          edu.udo.cs.yale.operator.io.DatabaseExampleSource

All Implemented Interfaces:

ConfigurationListener

public class DatabaseExampleSource
extends ResultSetExampleSource

This operator reads an ExampleSet from an SQL database. The SQL query can be passed to Yale via a parameter or, in case of long SQL statements, in a separate file. Please note that column names are often case sensitive. Databases may behave differently here.

The most convenient way of defining the necessary parameters is the configuration wizard. The most important parameters (database URL and user name) will be automatically determined by this wizard and it is also possible to define the special attributes like labels or ids.

Please note that this operator supports two basic working modes:

1. reading the data from the database and creating an example table in main memory
2. keeping the data in the database and directly working on the database table

The latter possibility will be turned on by the parameter "work_on_database". Please note that this working mode is still regarded as experimental and errors might occur. In order to ensure proper data changes the database working mode is only allowed on a single table which must be defined with the parameter "table_name". If you encounter during data updates (e.g. messages that the result set is not updatable) you have to define a primary key for your table.

If you are not directly working on the database the data will be read with an arbitrary SQL query statement (SELECT ... FROM ... WHERE ...) defined by "query" or "query_file". The memory mode is the recommended way of using this operator. This is especially important for following operators like learning schemes which would often load (most of) the data into main memory during the learning process.

Warning

As the java ResultSetMetaData interface does not provide information about the possible values of nominal attributes, the internal indices the nominal values are mapped to, will be dependent on the ordering they appear in the table. This may cause problems only when experiments are split up into training a experiment and an application or testing experiment. For learning schemes which are capable of handling nominal attributes, this is not a problem. If a learning scheme like a SVM is used with nominal data, Yale pretends that nominal attributes are numerical and uses indices for the nominal values as their numerical value. A SVM may perform well if there are only two possible values. If a test set is read in another experiment, the nominal values may be assigned different indices, and hence the SVM trained is useless. This is not a problem for label attributes, since the classes can be specified using the classes parameter and hence, all learning schemes intended to use with nominal data are safe to use.

Version:

$Id: DatabaseExampleSource.java,v 1.11 2006/03/27 13:22:00 ingomierswa Exp $

Author:

Simon Fischer, Ingo Mierswa, Timm Euler

To do:

Fix the above problem. This may not be possible effeciently since it is not supported by the Java ResultSet interface.

Field Summary

private DatabaseHandler

dbAccess

Constructor Summary

DatabaseExampleSource(OperatorDescription description)

Method Summary

IOObject[]	apply() Implement this method in subclasses.
private void	disconnect()
void	experimentFinished() Called at the end of the experiment.
private DatabaseHandler	getConnectedDatabaseHandler()
java.util.List<ParameterType>	getParameterTypes() Returns a list of ParameterTypes describing the parameters of this operator.
private java.lang.String	getQuery()
java.sql.ResultSet	getResultSet() This method reads the file whose name is given, extracts the database access information and the query from it and executes the query.
void	setNominalValues(java.util.List attributeList, java.sql.ResultSet resultSet, Attribute label) Since the ResultSet does not provide information about possible values of nominal attributes, subclasses must set these by implementing this method.
private void	setNominalValuesForLabel(Attribute label)

Methods inherited from class edu.udo.cs.yale.operator.io.ResultSetExampleSource

createExampleSet, getInputClasses, getOutputClasses

Methods inherited from class edu.udo.cs.yale.operator.Operator

addError, addValue, addWarning, apply, checkDeprecations, checkIO, checkProperties, clearErrorList, cloneOperator, createExperimentTree, createExperimentTree, createFromXML, createMarkedExperimentTree, delete, experimentStarts, getAddOnlyAdditionalOutput, getApplyCount, getDeliveredOutputClasses, getDeprecationInfo, getDesiredInputClasses, getErrorList, getExperiment, getInnerOperatorsXML, getInput, getInput, getInput, getInputDescription, getIOContainerForInApplyLoopBreakpoint, getName, getNumberOfSteps, getOperatorClassName, getOperatorDescription, getParameter, getParameterAsBoolean, getParameterAsColor, getParameterAsDouble, getParameterAsFile, getParameterAsInt, getParameterAsString, getParameterList, getParameters, getParameterType, getParent, getStartTime, getStatus, getUserDescription, getValue, getValues, getXML, hasBreakpoint, hasBreakpoint, hasInput, inApplyLoop, isEnabled, isParameterSet, logMessage, performAdditionalChecks, register, remove, rename, resume, setBreakpoint, setEnabled, setExperiment, setInput, setListParameter, setOperatorParameters, setParameter, setParameters, setParent, setUserDescription, toString, writeXML

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

dbAccess

private DatabaseHandler dbAccess

Constructor Detail

DatabaseExampleSource

public DatabaseExampleSource(OperatorDescription description)

Method Detail

setNominalValues

public void setNominalValues(java.util.List attributeList,
                             java.sql.ResultSet resultSet,
                             Attribute label)
                      throws UndefinedParameterError

Description copied from class: ResultSetExampleSource

Since the ResultSet does not provide information about possible values of nominal attributes, subclasses must set these by implementing this method.

Specified by:

setNominalValues in class ResultSetExampleSource

Parameters:

attributeList - List of Attribute

Throws:

UndefinedParameterError

setNominalValuesForLabel

private void setNominalValuesForLabel(Attribute label)
                               throws UndefinedParameterError

Throws:

UndefinedParameterError

apply

public IOObject[] apply()
                 throws OperatorException

Description copied from class: Operator

Implement this method in subclasses.

Overrides:

apply in class ResultSetExampleSource

Throws:

OperatorException

getQuery

private java.lang.String getQuery()
                           throws OperatorException

Throws:

OperatorException

getConnectedDatabaseHandler

private DatabaseHandler getConnectedDatabaseHandler()
                                             throws OperatorException,
                                                    java.sql.SQLException

Throws:

OperatorException

java.sql.SQLException

getResultSet

public java.sql.ResultSet getResultSet()
                                throws OperatorException

This method reads the file whose name is given, extracts the database access information and the query from it and executes the query. The query result is returned as a ResultSet.

Specified by:

getResultSet in class ResultSetExampleSource

Throws:

OperatorException

experimentFinished

public void experimentFinished()

Description copied from class: Operator

Called at the end of the experiment. The default implementation does nothing.

Overrides:

experimentFinished in class Operator

disconnect

private void disconnect()

getParameterTypes

public java.util.List<ParameterType> getParameterTypes()

Description copied from class: Operator

Returns a list of ParameterTypes describing the parameters of this operator. The default implementation returns an empty list if no input objects can be retained and special parameters for those input objects which can be prevented from being consumed.

Overrides:

getParameterTypes in class ResultSetExampleSource