org.genemania.completion.lucene.GeneCompletionProvider.java Source code

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Here is the source code for org.genemania.completion.lucene.GeneCompletionProvider.java

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/**
 * This file is part of GeneMANIA.
 * Copyright (C) 2010 University of Toronto.
 *
 * This library 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.
 *
 * This library 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 library; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 */

package org.genemania.completion.lucene;

import java.io.IOException;
import java.util.Collections;
import java.util.HashSet;
import java.util.Set;

import org.apache.lucene.analysis.Analyzer;
import org.apache.lucene.analysis.TokenStream;
import org.apache.lucene.analysis.tokenattributes.TermAttribute;
import org.apache.lucene.document.Document;
import org.apache.lucene.index.IndexReader;
import org.apache.lucene.index.Term;
import org.apache.lucene.queryParser.ParseException;
import org.apache.lucene.search.PhraseQuery;
import org.apache.lucene.search.Query;
import org.genemania.domain.Gene;
import org.genemania.mediator.lucene.AbstractCollector;
import org.genemania.mediator.lucene.LuceneGeneMediator;

@Deprecated
public class GeneCompletionProvider extends LuceneCompletionProvider {

    // __[constructors]________________________________________________________
    // Spring IOC support  
    private GeneCompletionProvider() {
        this(null, null);
    }

    public GeneCompletionProvider(IndexReader reader, Analyzer analyzer) {
        super(reader, GeneIndexBuilder.GENE_FIELD, analyzer);
    }

    // __[public interface]____________________________________________________
    public Set<String> getSynonyms(String symbol) {
        try {
            Query query = parser.parse(String.format("\"%s\"", symbol));
            final Long[] node = new Long[] { -1L };
            searcher.search(query, new AbstractCollector() {
                @Override
                public void handleHit(int id) {
                    try {
                        Document document = searcher.doc(id);
                        node[0] = Long.parseLong(document.get(GeneIndexBuilder.NODE_ID_FIELD));
                    } catch (IOException e) {
                        log(e);
                    }
                }
            });
            if (node[0] == -1L) {
                return Collections.emptySet();
            }
            return getSynonyms(node[0]);
        } catch (ParseException e) {
            log(e);
        } catch (IOException e) {
            log(e);
        }
        return Collections.emptySet();
    }

    public Set<String> getSynonyms(Long nodeId) {
        try {
            Query query = parser.parse(String.format("%s:%d", GeneIndexBuilder.NODE_ID_FIELD, nodeId));
            final Set<String> synonyms = new HashSet<String>();
            searcher.search(query, new AbstractCollector() {
                @Override
                public void handleHit(int id) {
                    try {
                        Document document = searcher.doc(id);
                        synonyms.add(document.get(GeneIndexBuilder.GENE_FIELD));
                    } catch (IOException e) {
                        log(e);
                    }
                }
            });
            return synonyms;
        } catch (ParseException e) {
            log(e);
        } catch (IOException e) {
            log(e);
        }
        return Collections.emptySet();
    }

    public Long getNodeId(String symbol) {
        try {
            TokenStream tokens = analyze(symbol);
            PhraseQuery query = new PhraseQuery();
            tokens.reset();
            while (tokens.incrementToken()) {
                TermAttribute term = tokens.getAttribute(TermAttribute.class);
                query.add(new Term(GeneIndexBuilder.GENE_FIELD, term.term()));
            }
            tokens.end();
            tokens.close();

            final Set<Long> nodes = new HashSet<Long>();
            searcher.search(query, new AbstractCollector() {
                @Override
                public void handleHit(int id) {
                    try {
                        Document document = searcher.doc(id);
                        nodes.add(Long.parseLong(document.get(GeneIndexBuilder.NODE_ID_FIELD)));
                    } catch (IOException e) {
                        log(e);
                    }
                }
            });
            if (nodes.size() > 0) {
                return nodes.iterator().next();
            }
        } catch (IOException e) {
            log(e);
        }
        return null;
    }

    // throws an NPE - needs to be revisited
    public Gene getGene(String symbol) {
        Analyzer analyzer = parser.getAnalyzer();
        LuceneGeneMediator mediator = new LuceneGeneMediator(searcher, analyzer);
        return mediator.getGeneForSymbol(null, symbol);
    }

}