edu.pitt.dbmi.deep.phe.i2b2.I2b2OntologyBuilder.java Source code

Introduction

Here is the source code for edu.pitt.dbmi.deep.phe.i2b2.I2b2OntologyBuilder.java

Source

package edu.pitt.dbmi.deep.phe.i2b2;

/*
 * To change this license header, choose License Headers in Project Properties.
 * To change this template file, choose Tools | Templates
 * and open the template in the editor.
 */

import java.io.File;
import java.io.IOException;
import java.sql.SQLException;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.Queue;
import java.util.TreeSet;

import org.apache.commons.io.FileUtils;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.io.StringDocumentSource;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLClass;
import org.semanticweb.owlapi.model.OWLDataFactory;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.reasoner.Node;
import org.semanticweb.owlapi.reasoner.NodeSet;
import org.semanticweb.owlapi.reasoner.OWLReasoner;
import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
import org.semanticweb.owlapi.reasoner.structural.StructuralReasonerFactory;

/**
 *
 * @author kjm84
 */
public class I2b2OntologyBuilder {

    public static final String CONST_TOP_LEVEL_ENTRY = "http://slidetutor.upmc.edu/deepPhe/BreastCancer.owl#Breast_Cancer_TNM_Finding_v7";

    private String ontologyPath;

    final TreeSet<PartialPath> partialPaths = new TreeSet<PartialPath>();
    final HashMap<String, PartialPath> partialPathMap = new HashMap<String, PartialPath>();

    public void execute() throws OWLOntologyCreationException, IOException, ClassNotFoundException, SQLException {
        partialPaths.addAll(extractOntologyPartialPaths());
        displayPaths(partialPaths);
        for (PartialPath partialPath : partialPaths) {
            partialPathMap.put(partialPath.getBaseCode(), partialPath);
        }
    }

    private TreeSet<PartialPath> extractOntologyPartialPaths() throws OWLOntologyCreationException, IOException {

        final TreeSet<PartialPath> partialPaths = new TreeSet<PartialPath>();

        OWLOntologyManager m = OWLManager.createOWLOntologyManager();
        // OWLOntology o = m.loadOntologyFromOntologyDocument(pizza_iri);
        OWLOntology o = loadDeepPheOntology(m);
        OWLReasonerFactory reasonerFactory;
        reasonerFactory = new StructuralReasonerFactory();
        OWLReasoner reasoner = reasonerFactory.createReasoner(o);
        OWLDataFactory fac = m.getOWLDataFactory();
        OWLClass elementConcept = fac.getOWLClass(IRI.create(CONST_TOP_LEVEL_ENTRY));

        final Queue<PartialPath> partialPathQueue = new LinkedList<PartialPath>();
        NodeSet<OWLClass> subClses = reasoner.getSubClasses(elementConcept, true);
        for (Node<OWLClass> subCls : subClses) {
            PartialPath path = new PartialPath();
            path.setReasoner(reasoner);
            path.setCls(subCls.getRepresentativeElement());
            path.setLevel(1);
            partialPathQueue.add(path);
        }

        while (true) {
            PartialPath path;
            path = partialPathQueue.poll();
            if (path == null) {
                break;
            } else {
                partialPathQueue.addAll(path.expand());
            }
            partialPaths.add(path);
        }

        PartialPath topLevel = new PartialPath();
        topLevel.setPath("\\DEEPPHE");
        topLevel.setLevel(0);
        topLevel.setLeaf(false);
        partialPaths.add(topLevel);

        return partialPaths;
    }

    private OWLOntology loadDeepPheOntology(OWLOntologyManager manager)
            throws IOException, OWLOntologyCreationException {
        File f = new File(ontologyPath);
        String fText = FileUtils.readFileToString(f, "UTF-8");
        OWLOntology o = manager.loadOntologyFromOntologyDocument(new StringDocumentSource(fText));
        return o;
    }

    private void displayPaths(TreeSet<PartialPath> paths) {
        /*paths.stream().forEach((path) -> {
           System.out.println(path);
        });*/
        for (PartialPath p : paths) {
            System.out.println(p);
        }
    }

    public void setOntologyPath(String ontologyPath) {
        this.ontologyPath = ontologyPath;

    }

    public HashMap<String, PartialPath> getPartialPathMap() {
        return partialPathMap;
    }

}