// $Id: PsiToBiopax3Converter.java,v 1.2 2009/11/23 13:59:42 rodche Exp $
//------------------------------------------------------------------------------
/** Copyright (c) 2009 Memorial Sloan-Kettering Cancer Center.
 **
 ** 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
 ** Memorial Sloan-Kettering Cancer Center
 ** has no obligations to provide maintenance, support,
 ** updates, enhancements or modifications.  In no event shall
 ** Memorial Sloan-Kettering Cancer Center
 ** 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
 ** Memorial Sloan-Kettering Cancer Center
 ** has 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.
 **/
package org.biopax.paxtools.converter.psi;


import psidev.psi.mi.tab.PsimiTabException;
import psidev.psi.mi.tab.PsimiTabReader;
import psidev.psi.mi.tab.converter.tab2xml.Tab2Xml;
import psidev.psi.mi.tab.converter.tab2xml.XmlConversionException;
import psidev.psi.mi.tab.model.BinaryInteraction;
import psidev.psi.mi.xml.model.Entry;
import psidev.psi.mi.xml.model.EntrySet;
import psidev.psi.mi.xml.PsimiXmlReader;
import psidev.psi.mi.xml.PsimiXmlReaderException;

import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.util.Collection;

import org.biopax.paxtools.io.SimpleIOHandler;
import org.biopax.paxtools.model.BioPAXLevel;
import org.biopax.paxtools.model.Model;

/**
 * The PSIMI 2.5 to BioPAX Level3 converter. 
 *
 * @author Igor Rodchenkov (rodche)
 */
public class PsiToBiopax3Converter {

        private final String xmlBase; //common URI prefix

        /**
         * Constructor.
         * Will use the default empty string xml:base.
         *
         */
        public PsiToBiopax3Converter() {
                this.xmlBase = null;
        }

        /**
         * Constructor.
         * 
         * @param xmlBase xml:base to be used when generating non-canonical BioPAX objects' URIs
         */
        public PsiToBiopax3Converter(String xmlBase) {
                this.xmlBase = xmlBase;
        }

        
        /**
         * Converts the PSI-MI inputStream into BioPAX outputStream.
         * Streams will be closed by the converter.
         * 
         * Warning: for very large models (about 1-2Gb if serialized), and when ByteArrayOutputStream
         * is used, OutOfMemoryError might be thrown (increasing the "heap" RAM won't help; but using FileOutputStream will).
         *
         * @param inputStream PSI-MI
         * @param outputStream BioPAX
         * @param forceInteractionToComplex - always generate Complex instead of MolecularInteraction
         *
         * @throws IOException when an I/O error occur
         * @throws PsimiXmlReaderException when an error in the PSI-MI parser happens
         */
        public void convert(InputStream inputStream, OutputStream outputStream, 
                        boolean forceInteractionToComplex) throws IOException, PsimiXmlReaderException {

                // check args
                if (inputStream == null || outputStream == null) {
                        throw new IllegalArgumentException("convert(): " +
                                        "one or more null arguments.");
                }

                // unmarshall the data, close the stream
                PsimiXmlReader reader = new PsimiXmlReader();
                EntrySet entrySet = reader.read(inputStream);
                inputStream.close();
                
                // convert
                convert(entrySet, outputStream, forceInteractionToComplex);
        }

        
        /**
         * Converts the PSI-MITAB inputStream into BioPAX outputStream.
         * Streams will be closed by the converter.
         *
         * @param inputStream psi-mitab
         * @param outputStream biopax
         * @param forceInteractionToComplex - always generate Complex instead of MolecularInteraction
         *
         * @throws IOException when an I/O error occur
         * @throws PsimiTabException when there's a problem within the PSI-MITAB parser
         */
        public void convertTab(InputStream inputStream, OutputStream outputStream, 
                        boolean forceInteractionToComplex) throws IOException, PsimiTabException {

                // check args
                if (inputStream == null || outputStream == null) {
                        throw new IllegalArgumentException("convertTab(): " +
                                        "one or more null arguments.");
                }

                // unmarshall the data, close the stream
                PsimiTabReader reader = new PsimiTabReader();
                Collection<BinaryInteraction> interactions = reader.read(inputStream);
                Tab2Xml tab2Xml = new Tab2Xml();
                EntrySet entrySet;
                try {
                        entrySet = tab2Xml.convert(interactions);
                } catch (IllegalAccessException e) {
                        throw new RuntimeException(e);
                } catch (XmlConversionException e) {
                        throw new RuntimeException(e);
                }
                inputStream.close();
                
                // convert
                convert(entrySet, outputStream, forceInteractionToComplex);
        }       
        
        /**
         * Converts the PSI interactions from the EntrySet and places into BioPAX output stream.
         * Stream will be closed by the converter.
         *
         * @param entrySet PSI-MI entry set
         * @param outputStream output stream for writing the BioPAX RDF/XML result
         * @param forceInteractionToComplex true/false - whether to always generate Complex instead of MolecularInteraction
         */
        public void convert(EntrySet entrySet, OutputStream outputStream, 
                        boolean forceInteractionToComplex) {

                // check args
                if (entrySet == null || outputStream == null) {
                        throw new IllegalArgumentException("convert: one or more null arguments.");
                }
                if (entrySet.getLevel() != 2) {
                        throw new IllegalArgumentException("convert: only PSI-MI Level 2.5 is supported.");
                }

                //create a new empty BioPAX Model
                final Model model = BioPAXLevel.L3.getDefaultFactory().createModel();
                model.setXmlBase(xmlBase);
                
                // convert all psimi entries
                EntryMapper entryMapper = new EntryMapper(model, forceInteractionToComplex);
                for (Entry entry : entrySet.getEntries()) {
                        entryMapper.run(entry);
                }
                
                //try to release some RAM earlier
                entrySet.getEntries().clear();
                entrySet = null;
                
                // write BioPAX RDF/XML
                (new SimpleIOHandler()).convertToOWL(model, outputStream);
        }

        /**
         * @return the xml:base, a namespace for the converter-generated BioPAX objects' URIs.
         */
        public String getXmlBase() {
                return xmlBase;
        }
        
}