au.csiro.snorocket.examples.Demo Maven / Gradle / Ivy

Go to download
/**
 * Copyright CSIRO Australian e-Health Research Centre (http://aehrc.com).
 * All rights reserved. Use is subject to license terms and conditions.
 */
package au.csiro.snorocket.examples;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import java.util.UUID;

import au.csiro.ontology.Factory;
import au.csiro.ontology.Node;
import au.csiro.ontology.Ontology;
import au.csiro.ontology.model.Axiom;
import au.csiro.ontology.model.Concept;
import au.csiro.snorocket.core.SnorocketReasoner;
import au.csiro.snorocket.core.util.Utils;

/**
 * Demo class for the final webinar. Shows how to load the base state for the
 * classifier and how to run an incremental classification.
 * 
 * @author Alejandro Metke
 *
 */
public class Demo {
    
    public Demo() {
        
    }
    
    public void start() {
        
        // 1. Load the base state
    	System.out.println("Loading base state from classifier_uuid.state");
        SnorocketReasoner reasoner = SnorocketReasoner.load(
                this.getClass().getResourceAsStream("/classifier_uuid.state"));
        
        // 2. Load SCT to UUID map
        System.out.println("Loading uuid description map");
//        Map sctToUuidMap = new HashMap();
        Map uuidToDescMap = new HashMap();
        BufferedReader reader = null;
        try {
            reader = new BufferedReader(new InputStreamReader(
                    this.getClass().getResourceAsStream("/nid_sctid_uuid_map.txt"), 
                    "UTF8"));
            String line = null;
            while ((line = reader.readLine()) != null) {
                String[] parts = line.split("[,]");
                String desc = null;
                if(parts.length < 4) {
                    desc = "";
                } else {
                	desc = parts[3];
                }
                if(parts[1].equals("NA")) continue;
//                sctToUuidMap.put(parts[1], parts[2]);
                uuidToDescMap.put(parts[2], desc);
            }      
        } catch (IOException e) {
            e.printStackTrace();
            return;
        } finally {
            if(reader != null) {
                try { reader.close(); } catch(Exception e) {}
            }
        }
        
        // 3. Add test axiom
        System.out.println("Adding test axiom");
        String newId = UUID.randomUUID().toString();
        uuidToDescMap.put(newId, "Special Appendicits");
        
        Concept specialAppendicitis = Factory.createNamedConcept(newId);
        String appendicitsUuid = "55450fab-6786-394d-89f9-a0fd44bd7e7e";
        Concept appendicitis = Factory.createNamedConcept(appendicitsUuid);
        Axiom a1 = Factory.createConceptInclusion(specialAppendicitis, appendicitis);
        Set axioms = new HashSet();
        axioms.add(a1);
        
        // 4. Classify incrementally
        System.out.println("Classifying incrementally");
        reasoner.loadAxioms(axioms);
        reasoner.classify();
        
        // 5. Retrieve taxonomy
        System.out.println("Retrieving taxonomy");
        Ontology ont = reasoner.getClassifiedOntology();
        
        // 6. Get node for new concept
        Node specialAppendicitisNode = ont.getNodeMap().get(appendicitsUuid);
        
        // 7. Print the new node
        Utils.printTaxonomy(
                specialAppendicitisNode.getParents().iterator().next(), 
                ont.getBottomNode(), 
                uuidToDescMap
        );
    }
    
    /**
     * @param args
     */
    public static void main(String[] args) {
        Demo d = new Demo();
        d.start();
    }

}