UserOntologyConfiguration.java

package org.obo.annotation.base;

import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.prefs.BackingStoreException;
import java.util.prefs.Preferences;

import org.apache.log4j.Logger;
import org.obo.app.util.PrefObj;

/**
 * An implementation of OntologyConfiguration which contains default ontology sources, and can also read and write a persistent 
 * list of ontology sources to the user's preferences.
 * @author Jim Balhoff
 */
public class UserOntologyConfiguration implements OntologyConfiguration {

	public static final String SOURCES_STORAGE_KEY = "sources";
	private static final List<OntologySource> defaultSources = new ArrayList<OntologySource>();
	static {
		try {
			defaultSources.add(new OntologySource("Phenoscape Anatomy", new URL("http://purl.obolibrary.org/obo/uberon/phenoscape-ext-simple.obo")));
			defaultSources.add(new OntologySource("Vertebrate Taxonomy", new URL("http://purl.obolibrary.org/obo/vto.obo")));
			defaultSources.add(new OntologySource("Museum Collections", new URL("http://svn.code.sf.net/p/phenoscape/code/trunk/vocab/fish_collection_abbreviation.obo")));
			defaultSources.add(new OntologySource("Phenotypic Qualities", new URL("http://purl.obolibrary.org/obo/pato.obo")));
			defaultSources.add(new OntologySource("Spatial Ontology", new URL("http://purl.obolibrary.org/obo/bspo.obo")));
			defaultSources.add(new OntologySource("Unit Ontology", new URL("http://unit-ontology.googlecode.com/svn/trunk/unit.obo")));
			defaultSources.add(new OntologySource("OBO Relations", new URL("http://purl.obolibrary.org/obo/ro.obo")));
			// need this?
			//defaultSources.add(new OntologySource("Gene Ontology", new URL("http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo")));
			defaultSources.add(new OntologySource("PATO Character slim", new URL("http://svn.code.sf.net/p/phenoscape/code/trunk/vocab/character_slims.obo")));
			defaultSources.add(new OntologySource("Phenex relations for post-composition", new URL("http://svn.code.sf.net/p/phenoscape/code/trunk/vocab/phenex_relations.obo")));
		} catch (MalformedURLException e) {
			log().error("One of the default URLs is malformed", e);
		}
	}

	public UserOntologyConfiguration() {
		//TODO create a constructor which accepts the default sources as a list instead of hardcoding above
		super();
		final List<OntologySource> storedSources = this.getStoredSources();
		if ((storedSources == null) || (storedSources.isEmpty())) {
			log().info("Storing default sources to preferences");
			this.storeSources(defaultSources);
		}
	}

	@Override
	public List<OntologySource> getSources() {
		return this.getStoredSources();
	}

	/**
	 * Retrieve the list of ontology sources from the user's preferences.
	 */
	@SuppressWarnings("unchecked")
	public List<OntologySource> getStoredSources() {
		try {
			if (this.getPrefsRoot().nodeExists(SOURCES_STORAGE_KEY)) {
				final Object data = PrefObj.getObject(this.getPrefsRoot(), SOURCES_STORAGE_KEY);
				if (data instanceof List<?>) {
					return (List<OntologySource>)data;
				} else {
					log().error("Data stored for ontology sources should be a list, but is not");
				}
			}
		} catch (IOException e) {
			log().error("Couldn't access ontology sources in preferences", e);
		} catch (BackingStoreException e) {
			log().error("Couldn't access ontology sources in preferences", e);
		} catch (ClassNotFoundException e) {
			log().error("Couldn't access ontology sources in preferences", e);
		}
		return null;
	}

	/**
	 * Store a given list of ontology sources to the user's preferences.
	 */
	public void storeSources(List<OntologySource> theSources) {
		//TODO would be nice to communicate these errors to the user
		try {
			PrefObj.putObject(this.getPrefsRoot(), SOURCES_STORAGE_KEY, theSources);
		} catch (IOException e) {
			log().error("Couldn't store ontology sources in preferences", e);
		} catch (BackingStoreException e) {
			log().error("Couldn't store ontology sources in preferences", e);
		} catch (ClassNotFoundException e) {
			log().error("Couldn't store ontology sources in preferences", e);
		}
	}

	public void clearStoredSources() {
		try {
			if (this.getPrefsRoot().nodeExists(SOURCES_STORAGE_KEY)) {
				log().debug("Clearing ontologies from configuration");
				PrefObj.putObject(this.getPrefsRoot(), SOURCES_STORAGE_KEY, Collections.EMPTY_LIST);
			}
		} catch (BackingStoreException e) {
			// TODO Auto-generated catch block
			log().error("Couldn't clear ontology sources from preferences", e);
		} catch (IOException e) {
			// TODO Auto-generated catch block
			e.printStackTrace();
		} catch (ClassNotFoundException e) {
			// TODO Auto-generated catch block
			e.printStackTrace();
		}
	}

	private Preferences getPrefsRoot() {
		return Preferences.userNodeForPackage(this.getClass()).node("ontologyConfig");
	}

	private static Logger log() {
		return Logger.getLogger(UserOntologyConfiguration.class);
	}


}