/*
 File: BioDataServerRmi.java

 Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)

 The Cytoscape Consortium is:
 - Institute for Systems Biology
 - University of California San Diego
 - Memorial Sloan-Kettering Cancer Center
 - Institut Pasteur
 - Agilent Technologies

 This library is free software; you can redistribute it and/or modify it
 under the terms of the GNU Lesser General Public License as published
 by the Free Software Foundation; either version 2.1 of the License, or
 any later version.

 This library is distributed in the hope that it will be useful, but
 WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
 MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.  The software and
 documentation provided hereunder is on an "as is" basis, and the
 Institute for Systems Biology and the Whitehead Institute
 have no obligations to provide maintenance, support,
 updates, enhancements or modifications.  In no event shall the
 Institute for Systems Biology and the Whitehead Institute
 be liable to any party for direct, indirect, special,
 incidental or consequential damages, including lost profits, arising
 out of the use of this software and its documentation, even if the
 Institute for Systems Biology and the Whitehead Institute
 have been advised of the possibility of such damage.  See
 the GNU Lesser General Public License for more details.

 You should have received a copy of the GNU Lesser General Public License
 along with this library; if not, write to the Free Software Foundation,
 Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
 */

// BioDataServerRmi.java
package cytoscape.data.servers;

import cytoscape.data.annotation.Annotation;
import cytoscape.data.annotation.AnnotationDescription;

import cytoscape.data.synonyms.Thesaurus;
import cytoscape.logger.CyLogger;

import java.io.Serializable;

import java.rmi.Naming;
import java.rmi.RemoteException;
import java.rmi.server.UnicastRemoteObject;

import java.util.Date;
import java.util.HashMap;


/**
 * This is the actual class which implements BioDataServer Methods.
 *
 * @author kono
 *
 * 04/19/2006: Old code removed (to resolve naming issue.)
 */
public class BioDataServerRmi extends UnicastRemoteObject implements BioDataServerInterface,
                                                                     Serializable {
	/*
	 * gene (or other biological entity) annotations are specific to - a species
	 * (i.e., halobacterium, or yeast) - a curator (i.e., KEGG or GO) - a type
	 * (i.e., GO's biological process, or KEGG's metabolic pathway) these three
	 * attributes are contained in an 'AttributeDescription', instances of which
	 * are used as keys in the following HashMap
	 */
	protected HashMap annotations;
	protected HashMap thesauri;
	protected Date startTime;
	protected Date lastAccessTime;

	/**
	 * Creates a new BioDataServerRmi object.
	 *
	 * @throws RemoteException  DOCUMENT ME!
	 */
	public BioDataServerRmi() throws RemoteException {
		super();
		annotations = new HashMap();
		thesauri = new HashMap();

		startTime = new Date();
		lastAccessTime = new Date();
	}

	/**
	 * if the new annotation is to an already annotated species, curator and
	 * type, then simply add (with possible overwriting for identical
	 */
	public void addAnnotation(Annotation newAnnotation) {
		lastAccessTime = new Date();

		AnnotationDescription key = new AnnotationDescription(newAnnotation.getSpecies(),
		                                                      newAnnotation.getCurator(),
		                                                      newAnnotation.getType());

		if (annotations.containsKey(key)) {
			Annotation oldAnnotation = (Annotation) annotations.get(key);
			String[] newNames = newAnnotation.getNames();

			for (int i = 0; i < newNames.length; i++) {
				int[] classificationIDs = newAnnotation.getClassifications(newNames[i]);

				for (int c = 0; c < classificationIDs.length; c++)
					oldAnnotation.add(newNames[i], classificationIDs[c]);
			} // for i
		} else {
			annotations.put(key, newAnnotation);
		}
	} // addAnnotation (Annotation)

	/**
	 *  DOCUMENT ME!
	 */
	public void clear() {
		annotations = new HashMap();
		lastAccessTime = new Date();
	}

	/**
	 *  DOCUMENT ME!
	 *
	 * @return  DOCUMENT ME!
	 */
	public int getAnnotationCount() {
		lastAccessTime = new Date();

		return annotations.size();
	}

	/**
	 *  DOCUMENT ME!
	 *
	 * @return  DOCUMENT ME!
	 */
	public AnnotationDescription[] getAnnotationDescriptions() {
		lastAccessTime = new Date();

		AnnotationDescription[] result = (AnnotationDescription[]) annotations.keySet()
		                                                                      .toArray(new AnnotationDescription[0]);

		return result;
	} // getAnnotationDescriptions

	/**
	 *  DOCUMENT ME!
	 *
	 * @param species DOCUMENT ME!
	 * @param curator DOCUMENT ME!
	 * @param type DOCUMENT ME!
	 *
	 * @return  DOCUMENT ME!
	 */
	public Annotation getAnnotation(String species, String curator, String type) {
		lastAccessTime = new Date();

		AnnotationDescription description = new AnnotationDescription(species, curator, type);

		return getAnnotation(description);
	} // getAnnotations

	/**
	 *  DOCUMENT ME!
	 *
	 * @param description DOCUMENT ME!
	 *
	 * @return  DOCUMENT ME!
	 */
	public Annotation getAnnotation(AnnotationDescription description) {
		lastAccessTime = new Date();

		return (Annotation) annotations.get(description);
	} // getAnnotations

	/**
	 *  DOCUMENT ME!
	 *
	 * @param species DOCUMENT ME!
	 * @param curator DOCUMENT ME!
	 * @param type DOCUMENT ME!
	 * @param entity DOCUMENT ME!
	 *
	 * @return  DOCUMENT ME!
	 */
	public int[] getClassifications(String species, String curator, String type, String entity) {
		lastAccessTime = new Date();

		AnnotationDescription description = new AnnotationDescription(species, curator, type);

		return (getClassifications(description, entity));
	} // getClassifications

	/**
	 *  DOCUMENT ME!
	 *
	 * @param description DOCUMENT ME!
	 * @param entity DOCUMENT ME!
	 *
	 * @return  DOCUMENT ME!
	 */
	public int[] getClassifications(AnnotationDescription description, String entity) {
		lastAccessTime = new Date();

		Annotation annotation = (Annotation) annotations.get(description);

		return annotation.getClassifications(entity);
	} // getClassifications

	/**
	 *  DOCUMENT ME!
	 *
	 * @param description DOCUMENT ME!
	 * @param entity DOCUMENT ME!
	 *
	 * @return  DOCUMENT ME!
	 */
	public String[][] getAllAnnotations(AnnotationDescription description, String entity) {
		lastAccessTime = new Date();

		Annotation annotation = (Annotation) annotations.get(description);

		return annotation.getAllHierarchyPathsAsNames(entity);
	}

	/**
	 *  DOCUMENT ME!
	 *
	 * @return  DOCUMENT ME!
	 */
	public String describe() {
		StringBuffer sb = new StringBuffer();
		Annotation[] tmp = (Annotation[]) annotations.values().toArray(new Annotation[0]);

		for (int i = 0; i < tmp.length; i++) {
			sb.append(tmp[i]);
			sb.append("\n");
		}

		Thesaurus[] tmp2 = (Thesaurus[]) thesauri.values().toArray(new Thesaurus[0]);

		for (int i = 0; i < tmp2.length; i++) {
			sb.append(tmp2[i]);
			sb.append("\n");
		}

		sb.append("\n");
		sb.append("    started: " + startTime);
		sb.append("\n");

		sb.append("last access: " + lastAccessTime);
		sb.append("\n");

		return sb.toString();
	} // describe

	/**
	 *  DOCUMENT ME!
	 *
	 * @param species DOCUMENT ME!
	 * @param thesaurus DOCUMENT ME!
	 */
	public void addThesaurus(String species, Thesaurus thesaurus) {
		thesauri.put(species, thesaurus);
	}

	/**
	 *  DOCUMENT ME!
	 *
	 * @param species DOCUMENT ME!
	 * @param commonName DOCUMENT ME!
	 *
	 * @return  DOCUMENT ME!
	 */
	public String getCanonicalName(String species, String commonName) {
		if (thesauri.containsKey(species)) {
			Thesaurus t = (Thesaurus) thesauri.get(species);

			if (t != null) {
				String result = t.getNodeLabel(commonName);

				if (result != null)
					return result;
			} // if thesaurus exists
		} // if key

		return commonName;
	} // getCanonicalName

	/**
	 *  DOCUMENT ME!
	 *
	 * @param species DOCUMENT ME!
	 * @param commonName DOCUMENT ME!
	 *
	 * @return  DOCUMENT ME!
	 */
	public String[] getAllCommonNames(String species, String commonName) {
		if (thesauri.containsKey(species)) {
			Thesaurus t = (Thesaurus) thesauri.get(species);

			if (t != null) {
				String[] result = t.getAllCommonNames(commonName);

				if (result != null)
					return result;
			} // if thesaurus exists
		} // if key

		String[] result = new String[1];
		result[0] = commonName;

		return result;
	}

	/**
	 *  DOCUMENT ME!
	 *
	 * @param species DOCUMENT ME!
	 * @param canonicalName DOCUMENT ME!
	 *
	 * @return  DOCUMENT ME!
	 */
	public String getCommonName(String species, String canonicalName) {
		if (thesauri.containsKey(species)) {
			Thesaurus t = (Thesaurus) thesauri.get(species);

			if (t != null) {
				String result = t.getCommonName(canonicalName);

				if (result != null)
					return result;
			} // if thesaurus exists
		} // if key

		return canonicalName;
	}

	/**
	 *  DOCUMENT ME!
	 *
	 * @param args DOCUMENT ME!
	 */
	public static void main(String[] args) {
		if (args.length != 1) {
			System.out.println("usage:  BioDataServerRmi <server name>");
			System.exit(1);
		}

		String name = args[0];

		try {
			BioDataServerRmi rmiServer = new BioDataServerRmi();
			Naming.rebind(name, rmiServer);
			System.out.println("BioDataServer bound as '" + name + "'");
		} catch (Exception e) {
			System.out.println("BioDataServer exception: " + e.getMessage());
			e.printStackTrace();
		}
	} // main
} // class BioDataServerRmi