/*
* Copyright 2015 Red Hat, Inc. and/or its affiliates.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.drools.beliefs.bayes.model;
import com.thoughtworks.xstream.XStream;
import com.thoughtworks.xstream.io.xml.DomDriver;
import org.drools.beliefs.bayes.BayesNetwork;
import org.drools.beliefs.bayes.BayesVariable;
import org.drools.beliefs.bayes.assembler.BayesNetworkAssemblerError;
import org.drools.beliefs.graph.Graph;
import org.drools.beliefs.graph.GraphNode;
import org.drools.beliefs.graph.impl.EdgeImpl;
import org.drools.compiler.compiler.ParserError;
import org.drools.core.io.internal.InternalResource;
import org.kie.api.io.Resource;
import org.kie.internal.builder.KnowledgeBuilderErrors;
import java.io.IOException;
import java.io.InputStream;
import java.net.URL;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
public class XmlBifParser {
public static Bif loadBif(Resource resource, KnowledgeBuilderErrors errors) {
InputStream is = null;
try {
is = resource.getInputStream();
} catch (IOException e) {
errors.add( new ParserError(resource, "Exception opening Stream:\n" + e.toString(), 0, 0) );
return null;
}
try {
String encoding = resource instanceof InternalResource ? ((InternalResource) resource).getEncoding() : null;
XStream xstream;
if (encoding != null) {
xstream = new XStream(new DomDriver(encoding));
} else {
xstream = new XStream();
}
initXStream(xstream);
Bif bif = (Bif) xstream.fromXML(is);
return bif;
} catch (Exception e) {
errors.add( new BayesNetworkAssemblerError(resource, "Unable to parse opening Stream:\n" + e.toString()) );
return null;
}
}
public static Bif loadBif(URL url) {
XStream xstream = new XStream();
initXStream( xstream );
Bif bif = (Bif) xstream.fromXML(url);
return bif;
}
private static void initXStream(XStream xstream) {
xstream.processAnnotations(Bif.class);
xstream.processAnnotations(Network.class);
xstream.processAnnotations(Probability.class);
xstream.processAnnotations(Definition.class);
}
public static BayesNetwork buildBayesNetwork(Bif bif) {
String name = bif.getNetwork().getName();
String packageName = "default";
List<String> props = bif.getNetwork().getProperties();
if (props != null ) {
for ( String prop : props ) {
prop = prop.trim();
if (prop.startsWith("package") ) {
packageName = prop.substring( prop.indexOf('=') + 1).trim();
}
}
}
BayesNetwork graph = new BayesNetwork(name, packageName);
Map<String, GraphNode<BayesVariable>> map = new HashMap<String, GraphNode<BayesVariable>>();
for (Definition def : bif.getNetwork().getDefinitions()) {
GraphNode<BayesVariable> node = graph.addNode();
BayesVariable var = buildVariable(def, bif.getNetwork(), node.getId());
node.setContent( var );
map.put( var.getName(), node );
}
for(Entry<String, GraphNode<BayesVariable>> entry : map.entrySet()) {
GraphNode<BayesVariable> node = entry.getValue();
BayesVariable var = node.getContent();
if ( var.getGiven() != null && var.getGiven().length > 0 ) {
for ( String given : var.getGiven() ) {
GraphNode<BayesVariable> givenNode = map.get( given );
EdgeImpl e = new EdgeImpl();
e.setOutGraphNode(givenNode);
e.setInGraphNode(node);
}
}
}
return graph;
}
private static BayesVariable buildVariable(Definition def, Network network, int id) {
List<String> outcomes = new ArrayList();
getOutcomesByVariable(network, def.getName(), outcomes);
List<String> given = (def.getGiven() == null) ? Collections.<String>emptyList() : def.getGiven();
return new BayesVariable<String>(def.getName(), id, outcomes.toArray( new String[ outcomes.size()] ),
getProbabilities(def.getProbabilities(), outcomes), given.toArray(new String[given.size()]) );
}
private static void getOutcomesByVariable(Network network, String nameDefinition, List<String> outcomes) {
for (Variable var : network.getVariables()) {
if (var.getName().equals(nameDefinition)) {
for (String outcome : var.getOutComes()) {
outcomes.add(outcome);
}
}
}
}
private static double[][] getProbabilities(String table,List<String> outcomes) {
table = table.trim();
String[] values = table.split(" ");
double probabilities[][] = new double[values.length/2][outcomes.size()];
int k = 0;
for(int i = 0, length = values.length/2; i < length; i++){
for(int j = 0; j < outcomes.size(); j++){
probabilities[i][j] = Double.valueOf(values[k++]);
}
}
return probabilities;
}
private static double[][] getPosition(String stringPosition, double[][] position) {
if (stringPosition != null) {
stringPosition = clearStringPostion(stringPosition);
int i = 0;
int j = 0;
for (String pos : stringPosition.split(",")) {
position[i][j] = Double.parseDouble(pos);
if (i < j) {
i += 1;
}
j += 1;
}
}
return null;
}
private static String clearStringPostion(String stringPosition){
stringPosition = stringPosition.replace("position", "");
stringPosition = stringPosition.replace("=", "");
stringPosition = stringPosition.replace("(", "");
stringPosition = stringPosition.replace(")", "");
stringPosition = stringPosition.trim();
return stringPosition;
}
// private void setIncomingNodes(BayesNetwork bayesNetwork){
// for(BayesVariable node : bayesNetwork.getNodos()){
// if(node.getGiven()!=null && !node.getGiven().isEmpty()){
// node.setIncomingNodes(this.getNodesByGiven(node.getGiven(), bayesNetwork.getNodos()));
// }
// }
// }
//
// private List<BayesVariable> getNodesByGiven(List<String> given, List<BayesVariable> nodes){
// List<BayesVariable> listIncoming = new ArrayList();
// for(String giv : given){
// for(BayesVariable node : nodes){
// if(node.getName().equals(giv)){
// listIncoming.add(node);
// break;
// }
// }
// }
// return listIncoming;
// }
}