package org.biohackathon.SPARQLBuilder.OWL;

import java.util.ArrayList;
import java.util.HashMap;

import jp.riken.accc.db.rdf.crawler.dataStructure.sparql.JenaModelGenerator;
import jp.riken.accc.db.rdf.crawler.dataStructure.sparql.URICollection;

import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.Property;
import com.hp.hpl.jena.rdf.model.Resource;

//public class OWLQueryBuilderForCrawlerImpl implements OWLQueryBuilder {
public class AcquiredStructureAnalyzer implements RDFSchemaAnalyzer {

	private Model model = null;
	private String endpointURI = null;
	private String[] graphURIs = null;

	public String getEndpointURI(){
		return endpointURI;
	}

	public String[] getGraphURIs(){
		return graphURIs;
	}
	
	
	public static void main(String[] args) throws Exception{

		JenaModelGenerator jmGene = new JenaModelGenerator("c:\\temp\\biosamplesF11.ttl");
//		JenaModelGenerator jmGene = new JenaModelGenerator("c:\\temp\\reactomeF18s.ttl");
		AcquiredStructureAnalyzer impl 
			= new AcquiredStructureAnalyzer(jmGene.getEndpointURI(), jmGene.getGraphURIs(), jmGene.getModel());

		System.out.println("--------------------------");
		SClass[] scs = impl.getOWLClasses(null, null, null, true);
		System.out.println("list classes:---------------");
		for(SClass sc: scs){
			System.out.println(sc.toString());
		}
		System.out.println("--------------------------");
		
//		ClassLink[] cls = impl.getNextClass(null,"http://www.biopax.org/release/biopax-level3.owl#Protein",100,true );
//		for(ClassLink cl: cls){
//			System.out.println(cl.toString());
//		}
//		System.out.println("--------------------------");
		
	}
	
	
	public AcquiredStructureAnalyzer(String endpointURI, String[] graphURIs, Model model){
		this.model = model;
		this.endpointURI = endpointURI;
		this.graphURIs = graphURIs;
	}

	private String[] filterGraphURIs(String[] orgGraphURIs){
		// TODO
		return graphURIs;
	}

	
	public SClass[] listClasses(String[] graphURIs, boolean countInstances) throws Exception{
		return getOWLClasses(graphURIs, null, null, countInstances);
	}
		
		

	
	public SClass[] getOWLClasses(String[] graphURIs, String[] keywords, String language, boolean countInstances) throws Exception{
		String[] targetGraphURIs = filterGraphURIs(graphURIs);

		StringBuffer queryStr = new StringBuffer();
		queryStr.append("PREFIX owl: <http://www.w3.org/2002/07/owl#>\n");
		queryStr.append("PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\n");
		queryStr.append("PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n");
		queryStr.append("SELECT DISTINCT ?c ?pLabel ?entities\n");
//		if (targetGraphURIs != null) {
//			for (String graphURI : targetGraphURIs) {
//				queryStr.append("FROM <");
//				queryStr.append(graphURI);
//				queryStr.append(">\n");
//			}
//		}
		queryStr.append("WHERE{\n");
		queryStr.append(" ?cp <").append(URICollection.PROPERTY_VOID_CLASS).append("> ?c. \n");
		queryStr.append(" ?cp <");
		queryStr.append(URICollection.PROPERTY_VOID_ENTITIES);
		queryStr.append("> ?entities. \n");
		queryStr.append(" OPTIONAL{ ?c <");
		queryStr.append(URICollection.PROPERTY_RDFS_LABEL);
		queryStr.append("> ?pLabel. }\n");

		if (keywords != null && keywords.length != 0) {

			queryStr.append(" ?c rdfs:label ");
			queryStr.append("?keywords").append(".\n");
			queryStr.append("  filter((LANG(?keywords) = \'").append(language);
			queryStr.append("\') && \n (");

			for (int i = 0; i < keywords.length; i++) {
				if (i > 0)
					queryStr.append(" || \n ");

				queryStr.append("regex(str(").append("?keywords")
						.append("),\"");
				queryStr.append(keywords[i]);
				queryStr.append("\", \"i\" )");

			}
			queryStr.append("))\n");

		}
		queryStr.append("}");
		System.out.println(queryStr.toString());

		Query query = QueryFactory.create(queryStr.toString());

		QueryExecution qexec = null;
		ResultSet results = null;
		try {
//			long start = System.currentTimeMillis();
			qexec = QueryExecutionFactory.create(query, model);
			results = qexec.execSelect();
//			long end = System.currentTimeMillis();
//			System.out.println("EXEC TIME: " + (end - start));
		} catch (Exception ex) {
			ex.printStackTrace();
			throw ex;
		}

		HashMap<String, SClass> classMap = new HashMap<String, SClass>();
		for (; results.hasNext();) {
			QuerySolution sol = results.next();
			Resource res = sol.getResource("c");
			if (res != null && res.getURI() != null) {
				String uri = res.getURI();
				int numOfInstances = 0;
				if (countInstances) {
					numOfInstances = sol.getLiteral("entities").getInt();
				} //
				Literal labelLiteral = sol.getLiteral("pLabel");
				SClass sClass = null;
				if (classMap.containsKey(uri)) {
					sClass = classMap.get(uri);
				} else {
					sClass = new SClass(uri, null, numOfInstances);
					classMap.put(uri, sClass);
				}
				if (labelLiteral != null) {
					String label = labelLiteral.getString();
					String lang = labelLiteral.getLanguage();
					sClass.addLabel(new Label(label, lang));
				}
			}
		}
		qexec.close();
		return classMap.values().toArray(new SClass[0]);
	}

/*
	
	public Instance[] getInstances(String[] graphURIs, String keyword) throws Exception;
*/


	public ClassLink[] getNextClass(String[] graphURIs, String originClass, int limit, boolean countLinks) throws Exception{
		String[] targetGraphURIs = filterGraphURIs(graphURIs);

		StringBuffer queryStr = new StringBuffer();
		queryStr.append("PREFIX owl: <http://www.w3.org/2002/07/owl#>\n");
		queryStr.append("PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\n");
		queryStr.append("PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n");

		// SELECT
		queryStr.append("SELECT DISTINCT ?indPropCat ?c ?dat ?d ?p ?numLnkInsStart ?numLnkInsEnd ?numInsDom ?numInsRan ?numTriples\n");

//		if (targetGraphURIs != null) {
//			for (String graphURI : targetGraphURIs) {
//				queryStr.append("FROM <");
//				queryStr.append(graphURI);
//				queryStr.append(">\n");
//			}
//		}

		queryStr.append("WHERE{\n");
		queryStr.append(" ?cr <").append(URICollection.PROPERTY_RDF_TYPE).append("> <").append(URICollection.RESOURCE_SB_CLASS_RELATION).append(">. \n");
		queryStr.append(" ?propPart <").append(URICollection.PROPERTY_SB_CLASS_RELATION).append("> ?cr. \n");
		queryStr.append(" ?propPart <").append(URICollection.PROPERTY_VOID_PROPERTY).append("> ?p. \n");
		
		queryStr.append(" {");
		queryStr.append(" ?cr <").append(URICollection.PROPERTY_SB_SUBJECT_CLASS).append("> <" + originClass + ">. \n");
		queryStr.append(" ?cr <").append(URICollection.PROPERTY_SB_OBJECT_CLASS).append("> ?d. \n");
		queryStr.append(" ?cr <").append(URICollection.PROPERTY_VOID_DISTINCT_SUBJECTS).append("> ?numLnkInsStart. \n");
		queryStr.append(" ?cr <").append(URICollection.PROPERTY_VOID_DISTINCT_OBJECTS).append("> ?numLnkInsEnd. \n");
		queryStr.append(" ?cr <").append(URICollection.PROPERTY_VOID_TRIPLES).append("> ?numTriples. \n");
//		queryStr.append(" ?cr <http://sparqlbuilder.org/startClassLimitedQ> ?isStartClsLim. \n");
//		queryStr.append(" ?cr <http://sparqlbuilder.org/endClassLimitedQ> ?isEndClsLim. \n");
		queryStr.append("}\n");
		queryStr.append(" UNION\n");
		queryStr.append(" {");
		queryStr.append(" ?cr <").append(URICollection.PROPERTY_SB_SUBJECT_CLASS).append("> <" + originClass + ">. \n");
		queryStr.append(" ?cr <").append(URICollection.PROPERTY_SB_OBJECT_DATATYPE).append("> ?dat. \n");
		queryStr.append(" ?cr <").append(URICollection.PROPERTY_VOID_DISTINCT_SUBJECTS).append("> ?numLnkInsStart. \n");
		queryStr.append(" ?cr <").append(URICollection.PROPERTY_VOID_DISTINCT_OBJECTS).append("> ?numLnkInsEnd. \n");
		queryStr.append(" ?cr <").append(URICollection.PROPERTY_VOID_TRIPLES).append("> ?numTriples. \n");
//		queryStr.append(" ?cr <http://sparqlbuilder.org/startClassLimitedQ> ?isStartClsLim. \n");
//		queryStr.append(" ?cr <http://sparqlbuilder.org/endClassLimitedQ> ?isEndClsLim. \n");
		queryStr.append("}\n");
		queryStr.append(" UNION\n");
		queryStr.append(" {");
		queryStr.append(" ?cr <").append(URICollection.PROPERTY_SB_OBJECT_CLASS).append("> <" + originClass + ">. \n");
		queryStr.append(" ?cr <").append(URICollection.PROPERTY_SB_SUBJECT_CLASS).append("> ?c. \n");
		queryStr.append(" ?cr <").append(URICollection.PROPERTY_VOID_DISTINCT_SUBJECTS).append("> ?numLnkInsEnd. \n");
		queryStr.append(" ?cr <").append(URICollection.PROPERTY_VOID_DISTINCT_OBJECTS).append("> ?numLnkInsStart. \n");
		queryStr.append(" ?cr <").append(URICollection.PROPERTY_VOID_TRIPLES).append("> ?numTriples. \n");
//		queryStr.append(" ?cr <http://sparqlbuilder.org/startClassLimitedQ> ?isEndClsLim. \n");
//		queryStr.append(" ?cr <http://sparqlbuilder.org/endClassLimitedQ> ?isStartClsLim. \n");
		queryStr.append("}\n");
		
//		queryStr.append(" ?propPart <").append(URICollection.PROPERTY_RDF_TYPE).append("> <").append(URICollection.PROPERTY_VOID_PROPERTY_PARTITION).append(">. \n");
		queryStr.append(" ?propPart <").append(URICollection.PROPERTY_SB_PROPERTY_CATEGORY).append("> ?indPropCat. \n");

		queryStr.append(" ?propPart <").append(URICollection.PROPERTY_VOID_DISTINCT_SUBJECTS).append("> ?numInsDom. \n");
		queryStr.append(" ?propPart <").append(URICollection.PROPERTY_VOID_DISTINCT_OBJECTS).append("> ?numInsRan. \n");
	
		queryStr.append("}\n");
		
	
		if (limit > 0) {
			queryStr.append("limit ");
			queryStr.append(limit);
			queryStr.append("\n");
		}

//		System.out.println("getNextClasses SPARQL Query: ");
//		System.out.println(queryStr.toString());

		Query query = QueryFactory.create(queryStr.toString());
		QueryExecution qexec = null;
		ResultSet results = null;
		try {
			long start = System.currentTimeMillis();
			qexec = QueryExecutionFactory.create(query, model);
			results = qexec.execSelect();
			long end = System.currentTimeMillis();
			System.out.println("EXEC TIME: " + (end - start));
		} catch (Exception ex) {
			ex.printStackTrace();
			throw ex;
		}

		ArrayList<ClassLink> solCLs = new ArrayList<ClassLink>();
		for (; results.hasNext();) {
			QuerySolution sol = results.next();
			Resource pro = sol.getResource("p");
			String clsURI = null;
			String datURI = null;
			if (pro != null) {
				int indPropCat = 4;
				Literal indPropCatLit = sol.getLiteral("indPropCat");
				if( indPropCatLit != null ){
					indPropCat = indPropCatLit.getInt();
				}
				if( indPropCat < 4 ) {
				String proURI = pro.getURI();
				Resource ccls = sol.getResource("c");
				Resource dcls = sol.getResource("d");
				Resource dat = sol.getResource("dat");
				Direction direction = null;
				if(ccls != null && dcls == null ){
					// direction forward
					direction = Direction.reverse;
					clsURI = ccls.getURI();
				}else{
					if( ccls == null && dcls != null ){
						direction = Direction.forward;
						clsURI = dcls.getURI();
					}else{
						if( ccls == null && dat != null && dcls == null ){
							clsURI = null;
							direction = Direction.forward;
							datURI = dat.getURI();
						}
					}
				}
				
				
				int numTriples = 0;
				Literal numTriplesLit = sol.getLiteral("numTriples");
				if( numTriplesLit != null ){
					numTriples = numTriplesLit.getInt();
				}

				int numLnkInsStart = 0;
				Literal numInsStartLit = sol.getLiteral("numLnkInsStart");
				if( numInsStartLit != null ){
					numLnkInsStart = numInsStartLit.getInt();
				}
				int numLnkInsEnd = 0;
				Literal numInsEndLit = sol.getLiteral("numLnkInsEnd");
				if( numInsEndLit != null ){
					numLnkInsEnd = numInsEndLit.getInt();
				}

				int numInsDom = 0;
				Literal numInsDomLit = sol.getLiteral("numInsDom");
				if( numInsDomLit != null ){
					numInsDom = numInsDomLit.getInt();
				}
				int numInsRan = 0;
				Literal numInsRanLit = sol.getLiteral("numInsRan");
				if( numInsRanLit != null ){
					numInsRan = numInsRanLit.getInt();
				}

				boolean isStartClsLim = false;
				Literal isStartClsLimLit = sol.getLiteral("isStartClsLim");
				if( isStartClsLimLit != null ){
					isStartClsLim = isStartClsLimLit.getBoolean();
				}
				boolean isEndClsLim = false;
				Literal isEndClsLimLit = sol.getLiteral("isEndClsLim");
				if( isEndClsLimLit != null ){
					isEndClsLim = isEndClsLimLit.getBoolean();
				}
				
				ClassLink cl = new ClassLink(proURI, clsURI, datURI, direction,
						numTriples, numInsDom, numInsRan,  numLnkInsStart, numLnkInsEnd, isStartClsLim, isEndClsLim);
				solCLs.add(cl);

				}
			}
		}
		qexec.close();	
		return solCLs.toArray(new ClassLink[0]);
	}

	
	
	/*

	public ClassLink[] getNextClassViaInstanceLink(String[] graphURIs, String originClass, int limit) throws Exception;

	public Path[] getPaths(String startClass, String endClass, int mode, boolean countLinks) throws Exception;

	public String createSPARQL(Path path) throws Exception;

 InstanceLink[] getNextInstancesViaInstanceLink(String[] graphURIs, String originInstance,
			int limit) throws Exception;
*/

	public LabelMap[] getLabels(String[] graphURIs, String[] resourceURIs,
			String language) throws Exception {
		if (resourceURIs == null || resourceURIs.length == 0) {
			return new LabelMap[0];
		}
		StringBuffer queryStr = new StringBuffer();
		queryStr.append("PREFIX owl: <http://www.w3.org/2002/07/owl#>\n");
		queryStr.append("PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\n");
		queryStr.append("PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n");
		queryStr.append("SELECT DISTINCT ?res ?label \n");
		if (graphURIs != null) {
			for (String graphURI : graphURIs) {
				queryStr.append("FROM <");
				queryStr.append(graphURI);
				queryStr.append(">\n");
			}
		}
		queryStr.append("WHERE{\n");
		queryStr.append("  ?res rdfs:label ?label.\n");
		queryStr.append("  FILTER(?res IN (");
		boolean f = false;
		for (String resourceURI : resourceURIs) {
			if (f) {
				queryStr.append(", ");
			}
			f = true;
			queryStr.append("<");
			queryStr.append(resourceURI);
			queryStr.append(">");
		}
		queryStr.append("))\n");
		queryStr.append("}");

//		System.out.println(queryStr.toString());

		Query query = QueryFactory.create(queryStr.toString());
		QueryExecution qexec = QueryExecutionFactory.create(query, model);
		
		ResultSet results = qexec.execSelect();
		HashMap<String, LabelMap> lMap = new HashMap<String, LabelMap>();
		for (; results.hasNext();) {
			QuerySolution sol = results.next();
			String uri = sol.getResource("res").getURI();
			Literal literal = sol.getLiteral("label");
			if (literal != null) {
				String label = literal.getString();
				String lang = literal.getLanguage();
				if (language != null && language.equals(lang)) {
					Label lbl = new Label(label, lang);
					if (lMap.containsKey(uri)) {
						LabelMap lm = lMap.get(uri);
						lm.addLabel(lbl);
					} else {
						LabelMap lm = new LabelMap(uri, new Label[] { lbl });
						lMap.put(uri, lm);
					}
				}
			}
		}
		return lMap.values().toArray(new LabelMap[0]);
	}

/*
 	public ClassLink[] countLinks(String[] graphURIs, String startClassURI, ClassLink[] classLinks) throws Exception;
	public SClass[] countInstances(String[] graphURIs, SClass[] classes) throws Exception;
	
*/

}