/* $RCSfile$
* $Author: rajarshi $
* $Date: 2007-10-22 02:38:43 +0200 (Mon, 22 Oct 2007) $
* $Revision: 9172 $
*
* Copyright (C) 2003-2007 The Chemistry Development Kit (CDK) project
*
* Contact: cdk-devel@lists.sourceforge.net
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
* All we ask is that proper credit is given for our work, which includes
* - but is not limited to - adding the above copyright notice to the beginning
* of your source code files, and to any copyright notice that you may distribute
* with programs based on this work.
*
* 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 Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
*
*/
package org.openscience.cdk.dict;
import java.io.IOException;
import java.io.Reader;
import java.util.ArrayList;
import java.util.List;
import nu.xom.Attribute;
import nu.xom.Builder;
import nu.xom.Document;
import nu.xom.Element;
import nu.xom.Elements;
import nu.xom.ParsingException;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
/**
* Dictionary with entries build from an OWL React.
*
* @author Miguel Rojas <miguelrojasch@users.sf.net>
* @cdk.created 2008-01-01
* @cdk.keyword dictionary
* @cdk.module dict
*
* @cdk.depends xom-1.0.jar
*/
public class OWLReact extends Dictionary {
private static String rdfNS = "http://www.w3.org/1999/02/22-rdf-syntax-ns#";
private static String rdfsNS = "http://www.w3.org/2000/01/rdf-schema#";
/**
* Constructor of the OWLReact object.
*/
public OWLReact() {
super();
}
/**
*
* @param reader The Reader
* @return The Dictionary
*/
public static Dictionary unmarshal(Reader reader) {
ILoggingTool logger =
LoggingToolFactory.createLoggingTool(OWLReact.class);
Dictionary dict = new OWLReact();
try {
Builder parser = new Builder();
Document doc = parser.build(reader);
Element root = doc.getRootElement();
logger.debug("Found root element: ", root.getQualifiedName());
// Extract ownNS from root element
// final String ownNS = root.getBaseURI();
final String ownNS = root.getBaseURI();
dict.setNS(ownNS);
logger.debug("Found ontology namespace: ", ownNS);
// process the defined facts
Elements entries = root.getChildElements();
logger.info("Found #elements in OWL dict:", entries.size());
for (int i=0; i<entries.size(); i++) {
Element entry = entries.get(i);
if (entry.getNamespaceURI().equals(ownNS)) {
EntryReact dbEntry = unmarshal(entry, ownNS);
dict.addEntry(dbEntry);
logger.debug("Added entry: ", dbEntry);
} else {
logger.debug("Found a non-fact: ", entry.getQualifiedName());
}
}
} catch (ParsingException ex) {
logger.error("Dictionary is not well-formed: ", ex.getMessage());
logger.debug("Error at line " + ex.getLineNumber(),
", column " + ex.getColumnNumber());
dict = null;
} catch (IOException ex) {
logger.error("Due to an IOException, the parser could not check:",
ex.getMessage()
);
logger.debug(ex);
dict = null;
}
return dict;
}
public static EntryReact unmarshal(Element entry, String ownNS) {
ILoggingTool logger =
LoggingToolFactory.createLoggingTool(OWLReact.class);
// create a new entry by ID
Attribute id = entry.getAttribute("ID", rdfNS);
logger.debug("ID: ", id);
EntryReact dbEntry = new EntryReact(id.getValue());
// set additional, optional data
Element label = entry.getFirstChildElement("label", rdfsNS);
logger.debug("label: ", label);
if (label != null) dbEntry.setLabel(label.getValue());
dbEntry.setClassName(entry.getQualifiedName());
logger.debug("class name: ", dbEntry.getClassName());
Element definition = entry.getFirstChildElement("definition", ownNS);
if (definition != null) {
dbEntry.setDefinition(definition.getValue());
logger.debug("definition name: ", definition.getValue());
}
Element description = entry.getFirstChildElement("description", ownNS);
if (description != null) {
dbEntry.setDescription(description.getValue());
logger.debug("description name: ", description.getValue());
}
Elements representations = entry.getChildElements("representation", ownNS);
if (representations != null)
for(int i = 0 ; i< representations.size(); i++){
// String idRepr = representations.get(i).getAttributeValue("id");
String contentRepr = representations.get(i).getAttributeValue("content");
dbEntry.setRepresentation(contentRepr);
}
Elements params = entry.getChildElements("parameters", ownNS);
if (params != null)
for(int i = 0 ; i< params.size(); i++){
String typeParam = params.get(i).getAttributeValue("dataType");
typeParam = typeParam.substring(typeParam.indexOf(":")+1, typeParam.length());
String nameParam = params.get(i).getAttributeValue("resource");
String value = params.get(i).getValue();
dbEntry.setParameters(nameParam,typeParam,value);
}
Elements paramsList = entry.getChildElements("parameterList", ownNS);
if (paramsList != null)
for(int i = 0 ; i< paramsList.size(); i++){
Elements params2 = paramsList.get(i).getChildElements("parameter2", ownNS);
if (params2 != null)
for(int j = 0 ; j< params2.size(); j++){
String paramClass = params2.get(i).getAttribute(0).getValue();
paramClass = paramClass.substring(paramClass.indexOf("#")+1);
logger.debug("parameter class: ", paramClass);
String needsToSet = "";
String value = "";
String dataType = "";
Elements paramSubt1 = params2.get(i).getChildElements("isSetParameter", ownNS);
if (paramSubt1 != null)
for(int k = 0 ; k< 1; k++)
needsToSet = paramSubt1.get(k).getValue();
Elements paramSubt2 = params2.get(i).getChildElements("value", ownNS);
if (paramSubt1 != null)
for(int k = 0 ; k< 1; k++){
value = paramSubt2.get(k).getValue();
dataType = paramSubt2.get(k).getAttributeValue("dataType");
dataType = dataType.substring(dataType.indexOf(":")+1, dataType.length());
}
List<String> pp = new ArrayList<String>();
pp.add(paramClass);
pp.add(needsToSet);
pp.add(dataType);
pp.add(value);
dbEntry.addParameter(pp);
}
}
Elements mechanismDependence = entry.getChildElements("mechanismDependence", ownNS);
String mechanism = "";
if (mechanismDependence != null)
for(int i = 0 ; i< mechanismDependence.size(); i++){
mechanism = mechanismDependence.get(i).getAttribute(0).getValue();
mechanism = mechanism.substring(mechanism.indexOf("#")+1);
logger.debug("mechanism name: ", mechanism);
}
dbEntry.setMechanism(mechanism);
// System.out.println("mechan: "+mechan);
Elements exampleReact = entry.getChildElements("example-Reactions", ownNS);
if (exampleReact != null)
for(int i = 0 ; i< exampleReact.size(); i++){
Elements reaction = exampleReact.get(i).getChildElements("reaction", ownNS);
if (reaction != null)
for(int j = 0 ; j< reaction.size(); j++){
dbEntry.addExampleReaction(reaction.get(0).toXML());
}
}
return dbEntry;
}
}