/**
 * 
 */
package oboannotator.ontology;

import java.io.IOException;
import java.net.URI;
import java.util.Set;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import oboannotator.util.AppConfig;
import oboannotator.util.Util;
import oboannotator.util.XmlEndec;

import org.semanticweb.owl.apibinding.OWLManager;
import org.semanticweb.owl.model.OWLAnnotation;
import org.semanticweb.owl.model.OWLClass;
import org.semanticweb.owl.model.OWLEntity;
import org.semanticweb.owl.model.OWLOntology;
import org.semanticweb.owl.model.OWLOntologyCreationException;
import org.semanticweb.owl.model.OWLOntologyManager;



/**
 * Author: Ahmed Abdeen Hamed<br>
 * Marine Biological Laboratory<br>
 * Biology of Aging Group<br>
 * Date: 11-Jan-2007<br><br>
 */
public class OBO_toLexiconConverter {
	public static final String ENVO_ONT_URI="http://www.berkeleybop.org/ontologies/obo-all/envo/envo.obo";
	public static final String GAZ_ONT_URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/environmental/gaz.obo";
	public static final String RESOURCES_OUTPUT_LOCATION="src/oboannotator/resources/dict/";
	public static final String ENVO_OBO_DICT="envo_dictionary.xml";
	public static final String GAZ_OBO_DICT="gaz_dictionary.xml";
	public static final String TEST_DICT="test_dicnary.xml";
	//public static final String DICTIONARY_EXTENSION=".xml";
	
	
	public static void compileDictionaryFromOwlURI(String ontologyURI, String dictionaryName, String outputDir, String addUpdateFlag){
    	//Pattern synonymPattern = Pattern.compile("\\\"([^\\\"]*)\\\"\\s([A-Z]*)\\s");	
        try {
            // A simple example of how to load and save an ontology
            // We first need to obtain a copy of an OWLOntologyManager, which, as the
            // name suggests, manages a set of ontologies.  An ontology is unique within
            // an ontology manager.  To load multiple copies of an ontology, multiple managers
            // would have to be used.
            OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
            // We load an ontology from a physical URI - in this case we'll load the pizza
            // ontology.
            URI physicalURI = URI.create(ontologyURI);
            // Now ask the manager to load the ontology
            OWLOntology ontology = manager.loadOntologyFromPhysicalURI(physicalURI);
            StringBuffer buffer = new StringBuffer("");
            StringBuffer tokenBuffer = new StringBuffer("");
            StringBuffer variantBuffer = new StringBuffer("");
            buffer.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"); 
            buffer.append("	<synonym>\n"); 
            boolean closeToken = false;
            for(OWLClass cls : ontology.getReferencedClasses()) {           	      
                //System.out.println("Class    : " + cls);
                //System.out.println("Class URI: " + cls.getURI());
                Set<OWLAnnotation> annotations = cls.getAnnotations(ontology);
                for (OWLAnnotation annotation: annotations){
        			//
                	String uriAnnotationName = OntoUtil.extractAnnotationNameFromURI(annotation.getAnnotationURI().toString());
            		if("label".equalsIgnoreCase(uriAnnotationName)){
            			
            			closeToken = true;
            			//tokenBuffer = new StringBuffer("");
            			tokenBuffer.append("		<token");
            			tokenBuffer.append(" canonical=\"");
            			String temp = OntoUtil.cleanupAnnotationFromCarretString(annotation.getAnnotationValue().toString());
            			temp = OntoUtil.extractTextFromQuotedText(temp);//temp.
            			tokenBuffer.append(XmlEndec.encodeXML(temp));
           			            			            			            			
            			tokenBuffer.append("[");
            			tokenBuffer.append(XmlEndec.encodeXML(cls.toString()));
            			
            			tokenBuffer.append("]");
            			tokenBuffer.append("\"> \n"); 
            			tokenBuffer.append("			<variant base=\"");
            			StringBuffer words = new StringBuffer("");
            			
            			String[] tokens = OntoUtil.tokenizeOwlTerm(temp);
            			for(String token: tokens){
            				words.append(XmlEndec.encodeXML(token + " "));            				
            			}
            			tokenBuffer.append(words.toString().trim());
            			tokenBuffer.append("\"/>\n");
            		}
            		if("comment".equalsIgnoreCase(uriAnnotationName)){            			            			
            			String temp = OntoUtil.cleanupAnnotationFromCarretString(annotation.getAnnotationValue().toString());
            			temp = OntoUtil.extractTextFromQuotedText(temp);
        				temp = OntoUtil.extractSynonymFromOwlComment(temp);
        				StringBuffer words = new StringBuffer("");
        				
        				
        				if(temp!=null){
	        				variantBuffer.append("			<variant base=\"");
	        				//System.out.println("Clean Synonyn Annotation Value:"+ temp);
	            			String[] tokens = OntoUtil.tokenizeOwlTerm(temp);
	            			for(String token: tokens){
	            				words.append(XmlEndec.encodeXML(token + " "));            				
	            			}            			            			
	        				variantBuffer.append(words.toString().trim());
	        				variantBuffer.append("\"/>\n");
        				}
            		}
            	}
                //System.out.println("--------------------------------------------");
            	buffer.append(tokenBuffer.toString());
            	buffer.append(variantBuffer.toString());
            	
            	
            	//buffer.append()
            	if(closeToken){
            		buffer.append("		</token>\n\n");
            	}
            	tokenBuffer = new StringBuffer("");
            	variantBuffer = new StringBuffer("");    
            	closeToken=false;

            }
        	buffer.append("	</synonym>\n\n");
        		
    	    try {
    	    	//writeStringToFile(String stringToBeWritten, String filePath, String fileName)
    	    	
    	    	//System.out.println("PRINT PLEASE: " + outputDir + dictionaryName);
    	    	if(addUpdateFlag.equals(AppConfig.ADD_NEW_DICTION)){
    	    		Util.writeStringToFile(buffer.toString(), outputDir, dictionaryName+AppConfig.XML_EXTENSION);
    	    	}
    	    	else if(addUpdateFlag.equals(AppConfig.UPDATE_DICTION)){
    	    		//System.out.println("OBO_toLexiconConvertor class : " + dictionaryName);
    	    		Util.writeStringToFile(buffer.toString(), outputDir, dictionaryName);
    	    	}
    	    } 
    	    catch (IOException e) {
    	    	e.printStackTrace();
    	    }
        }
        catch (OWLOntologyCreationException e) {
            System.out.println("The ontology could not be created: " + e.getMessage());
        }			
	}
	
	
	
	public static void compileDictionaryFromOboUri(String ontologyURI, String dictionaryName, String outputDir, String addUpdateFlag){
    	Pattern synonymPattern = Pattern.compile("\\\"([^\\\"]*)\\\"\\s([A-Z]*)\\s");	
        try {
            // A simple example of how to load and save an ontology
            // We first need to obtain a copy of an OWLOntologyManager, which, as the
            // name suggests, manages a set of ontologies.  An ontology is unique within
            // an ontology manager.  To load multiple copies of an ontology, multiple managers
            // would have to be used.
            OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
            // We load an ontology from a physical URI - in this case we'll load the pizza
            // ontology.
            URI physicalURI = URI.create(ontologyURI);
            // Now ask the manager to load the ontology
            OWLOntology ontology = manager.loadOntologyFromPhysicalURI(physicalURI);
            StringBuffer buffer = new StringBuffer("");
            StringBuffer tokenBuffer = new StringBuffer("");
            StringBuffer variantBuffer = new StringBuffer("");
            buffer.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"); 
            buffer.append("	<synonym>\n"); 
            for(OWLEntity entity: ontology.getReferencedEntities()){           	            	
            	for(OWLAnnotation annot: entity.getAnnotations(ontology)){
            		if("label".equalsIgnoreCase(annot.getAnnotationURI().getFragment())){
            			//tokenBuffer = new StringBuffer("");
            			tokenBuffer.append("		<token");
            			tokenBuffer.append(" canonical=\"");
            			tokenBuffer.append(XmlEndec.encodeXML(annot.getAnnotationValue().toString()));
            			
            			
            			//System.out.println("Annotation Value: "+ annot.getAnnotationValue());
            			
            			
            			tokenBuffer.append("[");
            			tokenBuffer.append(XmlEndec.encodeXML(entity.getURI().getFragment()));
            			//System.out.println("Fragement Value: "+ entity.getURI().getFragment());
            			
            			tokenBuffer.append("]");
            			tokenBuffer.append("\"> \n"); 
            			tokenBuffer.append("			<variant base=\"");
            			tokenBuffer.append(XmlEndec.encodeXML(annot.getAnnotationValue().toString()));
            			tokenBuffer.append("\"/>\n");
            		}
            		if("synonym".equalsIgnoreCase(annot.getAnnotationURI().getFragment())){            			            			
            			Matcher synonymMatcher = synonymPattern.matcher(annot.getAnnotationValue().toString());            			            	
            			
            		    while (synonymMatcher.find()) {
            		    	//if ("RELATED".equalsIgnoreCase(synonymMatcher.group(2).toString())){
            		    	if ("RELATED".equalsIgnoreCase(synonymMatcher.group(1).toString())){            		    		            		    		
            		    		variantBuffer.append("			<variant base=\"");
            		    		variantBuffer.append(XmlEndec.encodeXML(synonymMatcher.group(1).toString()));            		    		
            		    		//System.out.println("Group two: "+ synonymMatcher.group(2).toString());  
            		    		variantBuffer.append("\"/>\n");            		    		
            		    	}else{
            		    		variantBuffer.append("			<variant base=\"");
            		    		variantBuffer.append(XmlEndec.encodeXML(synonymMatcher.group(1).toString()));
            		    		//System.out.println("Group one: "+ synonymMatcher.group(1).toString());
            		    		variantBuffer.append("\"/>\n");  
            		    	}
            		     }
            		}
            	}
            	buffer.append(tokenBuffer.toString());
            	buffer.append(variantBuffer.toString());
            	buffer.append("		</token>\n\n");
            	tokenBuffer = new StringBuffer("");
            	variantBuffer = new StringBuffer("");
            }
        	buffer.append("	</synonym>\n\n");
        		
    	    try {
    	    	//writeStringToFile(String stringToBeWritten, String filePath, String fileName)
    	    	
    	    	//System.out.println("PRINT PLEASE: " + outputDir + dictionaryName);
    	    	if(addUpdateFlag.equals(AppConfig.ADD_NEW_DICTION)){
    	    		Util.writeStringToFile(buffer.toString(), outputDir, dictionaryName+AppConfig.XML_EXTENSION);
    	    	}else if(addUpdateFlag.equals(AppConfig.UPDATE_DICTION)){
    	    		Util.writeStringToFile(buffer.toString(), outputDir, dictionaryName);
    	    	}
    	    } 
    	    catch (IOException e) {
    	    	e.printStackTrace();
    	    }
        }
        catch (OWLOntologyCreationException e) {
            System.out.println("The ontology could not be created: " + e.getMessage());
        }		
	}
	
    public static void main(String[] args) {
    	
    	OBO_toLexiconConverter.compileDictionaryFromOwlURI("https://msi-workgroups.svn.sourceforge.net/svnroot/msi-workgroups/ontology/NMR.owl", "nmrOWL", "/Users/ahmedabdeenhamed/Test/", AppConfig.ADD_NEW_DICTION);
    	
    }
}