org.hupo.psi.mi.rdf.BioPaxUriFixer.java Source code

Introduction

Here is the source code for org.hupo.psi.mi.rdf.BioPaxUriFixer.java

Source

/**
 * Copyright 2011 The European Bioinformatics Institute, and others.
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     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.hupo.psi.mi.rdf;

import org.apache.commons.lang.StringUtils;
import org.biopax.paxtools.io.jena.JenaIOHandler;
import org.biopax.paxtools.model.BioPAXLevel;
import org.biopax.paxtools.model.Model;
import org.biopax.paxtools.model.level3.SimplePhysicalEntity;
import org.biopax.paxtools.model.level3.Xref;
import org.biopax.validator.utils.Normalizer;

import java.io.*;
import java.util.HashMap;
import java.util.Map;
import java.util.Set;

/**
 * @author Bruno Aranda (baranda@ebi.ac.uk)
 * @version $Id$
 */
public class BioPaxUriFixer {

    private static final String NEW_LINE = System.getProperty("line.separator");
    private static final String IDENTIFIERS_ORG = "http://identifiers.org/";
    private BioPAXLevel biopaxLevel;

    public BioPaxUriFixer(BioPAXLevel biopaxLevel) {
        this.biopaxLevel = biopaxLevel;
    }

    public void fixBioPaxUris(Model model, Writer writer) throws IOException {
        model.getNameSpacePrefixMap().clear();

        Map<String, String> mappings = new HashMap<String, String>();
        mappings.put("psi-mi", "mi");
        mappings.put("rcsb pdb", "pdb");

        fixXrefs(model, mappings);

        Map<String, String> idMappings = calculateIdMapings(model);

        new Normalizer().normalize(model);

        OutputStream baos = new ByteArrayOutputStream();

        new JenaIOHandler(this.biopaxLevel).convertToOWL(model, baos);

        fixURIs(idMappings, new StringReader(baos.toString()), writer);

        // close OutputStream
        baos.close();
    }

    private void fixURIs(Map<String, String> idMappings, Reader reader, Writer writer) throws IOException {
        BufferedReader in = new BufferedReader(reader);
        String line;
        while ((line = in.readLine()) != null) {

            if (line.contains("Reference")) {
                for (Map.Entry<String, String> protMapEntry : idMappings.entrySet()) {
                    if (line.contains(protMapEntry.getKey())) {
                        line = line.replaceAll(protMapEntry.getKey(), protMapEntry.getValue());
                    }
                }
            }

            if (line.contains("urn:miriam:")) {
                String[] tokens = line.split("urn:miriam:");
                // hack : only take first word
                if (tokens[1].contains(" <")) {
                    int index = tokens[1].indexOf(" <");
                    String uriToFix = tokens[1].substring(0, index);
                    tokens[1] = StringUtils.replaceOnce(uriToFix, ":", "/") + tokens[1].substring(index);
                } else {
                    tokens[1] = StringUtils.replaceOnce(tokens[1], ":", "/");
                }

                line = StringUtils.join(tokens, IDENTIFIERS_ORG);
            }

            writer.write(line + NEW_LINE);
        }

        // close bufferReader
        in.close();
    }

    private Map<String, String> calculateIdMapings(Model model) {
        Map<String, String> idMappings = new HashMap<String, String>();

        final Set<SimplePhysicalEntity> proteins = model.getObjects(SimplePhysicalEntity.class);

        for (SimplePhysicalEntity protein : proteins) {
            final String protRefId = protein.getEntityReference().getRDFId();

            for (Xref xref : protein.getXref()) {
                if ("uniprotkb".equals(xref.getDb())) {
                    String newId = IDENTIFIERS_ORG + "uniprot/" + xref.getId();
                    idMappings.put(protRefId, newId);
                    break;
                } else if ("chebi".equals(xref.getDb())) {
                    String newId = IDENTIFIERS_ORG + xref.getDb() + "/" + xref.getId();
                    idMappings.put(protRefId, newId);
                    break;
                }
            }
        }
        return idMappings;
    }

    private void fixXrefs(Model model, Map<String, String> mappings) {
        final Set<Xref> xrefs = model.getObjects(Xref.class);

        for (Xref xref : xrefs) {
            if (mappings.containsKey(xref.getDb())) {
                xref.setDb(mappings.get(xref.getDb()));
            }
        }
    }

}