de.sekmi.li2b2.services.impl.OntologyImpl Maven / Gradle / Ivy

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This project emulates the core components of an i2b2 server backend. Basic functionality of PM, CRC, ONT and WORK cells allows the official i2b2 webclient to connect ot this emulated server.

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package de.sekmi.li2b2.services.impl;

import java.io.InputStream;
import java.net.URL;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

import javax.xml.bind.JAXB;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlTransient;


import de.sekmi.li2b2.api.ont.Concept;
import de.sekmi.li2b2.api.ont.Ontology;

@XmlRootElement(name="ontology")
public class OntologyImpl implements Ontology {

	@XmlElement(name="concept")
	private List concepts;

	@XmlTransient
	private Map lookup;
	
	@Override
	public Iterable getCategories() {
		return concepts;
	}

	private void buildLookupTable()throws IllegalArgumentException{
		lookup = new HashMap<>();
		for( Concept category : getCategories() ){
			addDepthFirst(category);
		}
	}
	private void addDepthFirst(Concept concept)throws IllegalArgumentException{
		if( concept.hasNarrower() ){
			for( Concept child : concept.getNarrower() ){
				addDepthFirst(child);
			}
		}
		if( lookup.containsKey(concept.getKey()) ){
			throw new IllegalArgumentException("Duplicate concept key: "+concept.getKey());
		}
		lookup.put(concept.getKey(), concept);
	}
	@Override
	public Concept getConceptByKey(String key) {
		if( lookup == null ){
			buildLookupTable();
		}
		return lookup.get(key);
	}

	public static OntologyImpl parse(URL location){
		return JAXB.unmarshal(location, OntologyImpl.class);
	}
	public static OntologyImpl parse(InputStream xml){
		return JAXB.unmarshal(xml, OntologyImpl.class);
	}
}