import org.jgrapht.alg.*
import org.jgrapht.experimental.dag.*
import org.jgrapht.*
import org.jgrapht.graph.*
import org.apache.lucene.analysis.*
import org.apache.lucene.analysis.standard.*
import org.apache.lucene.document.*
import org.apache.lucene.search.vectorhighlight.*
import org.apache.lucene.search.highlight.*
import org.apache.lucene.index.*
import org.apache.lucene.store.*
import org.apache.lucene.util.*
import org.apache.lucene.search.*
import org.apache.lucene.queryparser.classic.*
import com.aliasi.medline.*
import org.apache.lucene.analysis.fr.*
import edu.stanford.nlp.process.*
import edu.stanford.nlp.ling.*
import edu.stanford.nlp.trees.*
import edu.stanford.nlp.parser.lexparser.LexicalizedParser


LexicalizedParser lp = LexicalizedParser.loadModel("edu/stanford/nlp/models/lexparser/englishPCFG.ser.gz");
TreebankLanguagePack tlp = new PennTreebankLanguagePack();
GrammaticalStructureFactory gsf = tlp.grammaticalStructureFactory();

String indexPath = "lucene-index-english"
String ontologyIndexPath = "lucene-index-ontology"

def fout = new PrintWriter(new BufferedWriter(new FileWriter(args[0])))

Directory dir = FSDirectory.open(new File(indexPath)) // RAMDirectory()
Directory ontologyIndexDir = FSDirectory.open(new File(ontologyIndexPath)) // RAMDirectory()
Analyzer analyzer = new StandardAnalyzer(Version.LUCENE_47)

DirectoryReader reader = DirectoryReader.open(ontologyIndexDir)
IndexSearcher ontSearcher = new IndexSearcher(reader)

Map<String, Set<String>> frenchname2id = [:]
Map<String, Set<String>> name2id = [:].withDefault { new TreeSet() }
Map<String, String> id2name = [:]

new File("ont").eachFile { ontfile ->
  def id = ""
  def fname = ""
  ontfile.eachLine { line ->
    if (line.startsWith("id:")) {
      id = line.substring(3).trim()
    }
    if (line.startsWith("name:")) {
      def name = line.substring(5).trim()
      id2name[id] = name
      name2id[name].add(id)
   }
  }
}

reader = DirectoryReader.open(dir)
IndexSearcher searcher = new IndexSearcher(reader)
parser = new QueryParser(Version.LUCENE_47, "description", analyzer)
QueryBuilder builder = new QueryBuilder(analyzer)
BooleanQuery.setMaxClauseCount(2048)

name2id.each { name, ids ->
  ids.each { id ->
    name2id.each { name2, ids2 ->
      ids2.each { id2 ->
	if (id.startsWith("PO") && id2.startsWith("PATO")) {
	  Query query = new BooleanQuery()
	  //	  name2 = "stigmatic lobes"
	  Query q = builder.createPhraseQuery("description", name)
	  query.add(q, BooleanClause.Occur.MUST)
	  Query q1 = q
	  q = builder.createPhraseQuery("description", name2)
	  query.add(q, BooleanClause.Occur.MUST)
	  Query q2 = q
	  ScoreDoc[] hits = searcher.search(query, null, 1000, Sort.RELEVANCE, true, true).scoreDocs
	  hits.each { doc ->
	    def docId = doc.doc
	    Document hitDoc = searcher.doc(docId)
	    def sentence = hitDoc.get("description")
	    Highlighter highlighter = new Highlighter(new QueryScorer(q1))
	    Highlighter highlighter2 = new Highlighter(new QueryScorer(q2))
	    highlighter.getBestFragments(analyzer, "description", sentence, 50).each { frag1 ->
	      highlighter2.getBestFragments(analyzer, "description", sentence, 50).each { frag2 ->
		int index1 = frag1.indexOf("<B>")
		def eindex1 = frag1.indexOf("</B>")
		while (index1 >= 0) {
		  int index2 = frag2.indexOf("<B>")
		  def eindex2 = frag2.indexOf("</B>")
		  while (index2 >= 0) {
		    if (eindex1 < index2) {
		      def nf = frag1.substring(0, index1) + "<E>"+frag1.substring(index1+3, eindex1)+"</E>"+frag2.substring(eindex1-3,index2)+"<Q>"+frag2.substring(index2+3, eindex2)+"</Q>"+frag2.substring(eindex2+3)
		      def finalFragment = nf.replaceAll("<B>","").replaceAll("</B>","")
		      fout.println("$name\t$name2\t$finalFragment")
		    } else if (eindex2 < index1) {
		      def nf = frag2.substring(0, index2) + "<Q>"+frag2.substring(index2+3, eindex2)+"</Q>"+frag1.substring(eindex2-3,index1)+"<E>"+frag1.substring(index1+3, eindex1)+"</E>"+frag1.substring(eindex1+4)
		      def finalFragment = nf.replaceAll("<B>","").replaceAll("</B>","")
		      fout.println("$name\t$name2\t$finalFragment")
		    }
		    index2 = frag2.indexOf("<B>", eindex2+1);
		    eindex2 = frag2.indexOf("</B>", eindex2+1);
		  }
		  index1 = frag1.indexOf("<B>", eindex1+1);
		  eindex1 = frag1.indexOf("</B>", eindex1+1);
		}
	      }
	    }
	  }
	}
      }
    }
  }
}
fout.flush()
fout.close()