uk.ac.bbk.dcs.automed.pathgen
Class PathwayGenerator

java.lang.Object
  uk.ac.bbk.dcs.automed.pathgen.PathwayGenerator

public class PathwayGenerator
extends java.lang.Object

This class reads an input XML file that describe two types of transformations:

- AutoMed transformations
- Other transformations, such as lowerCase, which converts the input data into lowercase.

The format of the file is the following:

<dbName&ft;
<transformation type="am.rename"&ft; <oldName&ft;PCDATA</oldName&ft; <newName&ft;PCDATA</newName&ft; </transformation&ft; <transformation type="lowerCase"&ft; </transformation&ft; </dbName&ft;

Author:

Lucas Zamboulis

Field Summary

private javax.xml.parsers.DocumentBuilder	builder
protected java.util.logging.Logger	logger
protected PathwayGeneratorBAV	ptBAV
protected PathwayGeneratorCleansing	ptCleansing
protected PathwayGeneratorMatch	ptMatch
protected Schema	s
protected static java.lang.String	TRANSFORMATION_BAV
protected static java.lang.String	TRANSFORMATION_CLEANSING
protected static java.lang.String	TRANSFORMATION_MATCH
protected org.w3c.dom.Document	xmlFile

Constructor Summary

PathwayGenerator()

Method Summary

static org.w3c.dom.Document	addMatchItem(org.w3c.dom.Document d, java.lang.String model, java.util.List sourceConstructs, java.util.List sourceQueries, java.util.List targetConstructs, java.util.List targetQueries)
protected Schema	applyTransformation(Schema s, org.w3c.dom.Element transformation, boolean justChecking)
private static org.w3c.dom.Element	createConstructElement(org.w3c.dom.Document d, java.lang.String constructString, java.lang.String constructName, java.lang.String query)
static org.w3c.dom.Document	createMatchesDoc(java.lang.String schemaName, java.lang.String conformedSchemaName)
void	listPathway()
Schema	perform(org.w3c.dom.Document d)
Schema	perform(java.lang.String url)
private Schema	processTransformations(Schema s, boolean justChecking) Reads through the XML file and issues the necessary transformations.

Methods inherited from class java.lang.Object

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

Field Detail

s

protected Schema s

builder

private javax.xml.parsers.DocumentBuilder builder

xmlFile

protected org.w3c.dom.Document xmlFile

logger

protected java.util.logging.Logger logger

TRANSFORMATION_BAV

protected static final java.lang.String TRANSFORMATION_BAV

See Also:

Constant Field Values

TRANSFORMATION_MATCH

protected static final java.lang.String TRANSFORMATION_MATCH

See Also:

Constant Field Values

TRANSFORMATION_CLEANSING

protected static final java.lang.String TRANSFORMATION_CLEANSING

See Also:

Constant Field Values

ptBAV

protected PathwayGeneratorBAV ptBAV

ptMatch

protected PathwayGeneratorMatch ptMatch

ptCleansing

protected PathwayGeneratorCleansing ptCleansing

Constructor Detail

PathwayGenerator

public PathwayGenerator()

Method Detail

listPathway

public void listPathway()

perform

public Schema perform(java.lang.String url)
               throws NotFoundException,
                      org.xml.sax.SAXException,
                      java.io.IOException

Throws:

NotFoundException

org.xml.sax.SAXException

java.io.IOException

perform

public Schema perform(org.w3c.dom.Document d)
               throws java.lang.Exception

Throws:

java.lang.Exception

processTransformations

private Schema processTransformations(Schema s,
                                      boolean justChecking)
                               throws java.lang.Exception

Reads through the XML file and issues the necessary transformations.

Throws:

java.lang.Exception

applyTransformation

protected Schema applyTransformation(Schema s,
                                     org.w3c.dom.Element transformation,
                                     boolean justChecking)
                              throws java.lang.Exception

Throws:

java.lang.Exception

createMatchesDoc

public static org.w3c.dom.Document createMatchesDoc(java.lang.String schemaName,
                                                    java.lang.String conformedSchemaName)

addMatchItem

public static org.w3c.dom.Document addMatchItem(org.w3c.dom.Document d,
                                                java.lang.String model,
                                                java.util.List sourceConstructs,
                                                java.util.List sourceQueries,
                                                java.util.List targetConstructs,
                                                java.util.List targetQueries)

createConstructElement

private static org.w3c.dom.Element createConstructElement(org.w3c.dom.Document d,
                                                          java.lang.String constructString,
                                                          java.lang.String constructName,
                                                          java.lang.String query)