/**
 * \file    addingEvidenceCodes_2.cpp
 * \brief   adds evidence codes to a species in a model
 * \author  Sarah Keating
 *
 * <!--------------------------------------------------------------------------
 * This sample program is distributed under a different license than the rest
 * of libSBML.  This program uses the open-source MIT license, as follows:
 *
 * Copyright (c) 2013-2018 by the California Institute of Technology
 * (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
 * and the University of Heidelberg (Germany), with support from the National
 * Institutes of Health (USA) under grant R01GM070923.  All rights reserved.
 *
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the "Software"),
 * to deal in the Software without restriction, including without limitation
 * the rights to use, copy, modify, merge, publish, distribute, sublicense,
 * and/or sell copies of the Software, and to permit persons to whom the
 * Software is furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
 * THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 * DEALINGS IN THE SOFTWARE.
 *
 * Neither the name of the California Institute of Technology (Caltech), nor
 * of the European Bioinformatics Institute (EMBL-EBI), nor of the University
 * of Heidelberg, nor the names of any contributors, may be used to endorse
 * or promote products derived from this software without specific prior
 * written permission.
 * ------------------------------------------------------------------------ -->
 */

import org.sbml.libsbml.CVTerm;
import org.sbml.libsbml.SBMLDocument;
import org.sbml.libsbml.Species;
import org.sbml.libsbml.XMLAttributes;
import org.sbml.libsbml.XMLNamespaces;
import org.sbml.libsbml.XMLNode;
import org.sbml.libsbml.XMLToken;
import org.sbml.libsbml.XMLTriple;
import org.sbml.libsbml.libsbml;

public class addingEvidenceCodes_2 {
    public static void main(String[] args) {
        System.loadLibrary("sbmlj");

        if (args.length != 2) {
            System.out
                    .println("  usage: addingEvidenceCodes_2 <input-filename> <output-filename>");
            System.out
                    .println("  Adds controlled vocabulary term to a species");
            System.out.println();
            System.exit( 2);
        }

        SBMLDocument d = libsbml.readSBML(args[0]);
        long errors = d.getNumErrors();

        if (errors > 0) {
            System.out.println("Read Error(s):");
            d.printErrors();

            System.out.println("Correct the above and re-run.");
        } else {
            long n = d.getModel().getNumSpecies();

            if (n <= 0) {
                System.out
                        .println("Model has no species.\n Cannot add CV terms\n");
            } else {
                Species s = d.getModel().getSpecies(0);

                /*
                 * check that the species has a metaid no CVTerms will be added
                 * if there is no metaid to reference
                 */
                if (!s.isSetMetaId())
                    s.setMetaId("metaid_0000052");

                CVTerm cv1 = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER);
                cv1.setBiologicalQualifierType(libsbml.BQB_OCCURS_IN);
                cv1.addResource("urn:miriam:obo.go:GO%3A0005764");

                s.addCVTerm(cv1);

                // now create the additional annotation

                // <rdf:Statement>
                // <rdf:subject rdf:resource="#metaid_0000052"/>
                // <rdf:predicate
                // rdf:resource="http://biomodels.net/biology-qualifiers/occursIn"/>
                // <rdf:object rdf:resource="urn:miriam:obo.go:GO%3A0005764"/>
                // <bqbiol:isDescribedBy>
                // <rdf:Bag>
                // <rdf:li rdf:resource="urn:miriam:obo.eco:ECO%3A0000004"/>
                // <rdf:li rdf:resource="urn:miriam:pubmed:7017716"/>
                // </rdf:Bag>
                // </bqbiol:isDescribedBy>
                // </rdf:Statement>

                /* attributes */
                XMLAttributes blank_att = new XMLAttributes();

                XMLAttributes resource_att = new XMLAttributes();

                /* create the outer statement node */
                XMLTriple statement_triple = new XMLTriple("Statement",
                        "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");

                XMLToken statement_token = new XMLToken(statement_triple,
                        blank_att);

                XMLNode statement = new XMLNode(statement_token);

                /* create the subject node */
                XMLTriple subject_triple = new XMLTriple("subject",
                        "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");

                resource_att.clear();
                resource_att.add("rdf:resource", "#" + s.getMetaId());

                XMLToken subject_token = new XMLToken(subject_triple,
                        resource_att);

                XMLNode subject = new XMLNode(subject_token);

                /* create the predicate node */
                XMLTriple predicate_triple = new XMLTriple("predicate",
                        "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");

                resource_att.clear();
                resource_att.add("rdf:resource",
                        "http://biomodels.net/biology-qualifiers/occursIn");

                XMLToken predicate_token = new XMLToken(predicate_triple,
                        resource_att);

                XMLNode predicate = new XMLNode(predicate_token);

                /* create the object node */
                XMLTriple object_triple = new XMLTriple("object",
                        "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");

                resource_att.clear();
                resource_att.add("rdf:resource",
                        "urn:miriam:obo.go:GO%3A0005764");

                XMLToken object_token = new XMLToken(object_triple,
                        resource_att);

                XMLNode object_ = new XMLNode(object_token);

                /* create the bqbiol node */
                XMLTriple bqbiol_triple = new XMLTriple("isDescribedBy",
                        "http://biomodels.net/biology-qualifiers/", "bqbiol");

                XMLToken bqbiol_token = new XMLToken(bqbiol_triple, blank_att);

                XMLNode bqbiol = new XMLNode(bqbiol_token);

                /* create the bag node */
                XMLTriple bag_triple = new XMLTriple("Bag",
                        "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");

                XMLToken bag_token = new XMLToken(bag_triple, blank_att);

                XMLNode bag = new XMLNode(bag_token);

                /* create each li node and add to the bag */
                XMLTriple li_triple = new XMLTriple("li",
                        "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");

                resource_att.clear();
                resource_att.add("rdf:resource",
                        "urn:miriam:obo.eco:ECO%3A0000004");

                XMLToken li_token = new XMLToken(li_triple, resource_att);
                li_token.setEnd();

                XMLNode li = new XMLNode(li_token);

                bag.addChild(li);

                resource_att.clear();
                resource_att.add("rdf:resource", "urn:miriam:pubmed:7017716");
                li_token = new XMLToken(li_triple, resource_att);
                li_token.setEnd();
                li = new XMLNode(li_token);

                bag.addChild(li);

                /* add the bag to bqbiol */
                bqbiol.addChild(bag);

                /* add subject, predicate, object and bqbiol to statement */
                statement.addChild(subject);
                statement.addChild(predicate);
                statement.addChild(object_);
                statement.addChild(bqbiol);

                /*
                 * create a top-level RDF element this will ensure correct
                 * merging
                 */

                XMLNamespaces xmlns = new XMLNamespaces();
                xmlns.add("http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");
                xmlns.add("http://purl.org/dc/elements/1.1/", "dc");
                xmlns.add("http://purl.org/dc/terms/", "dcterms");
                xmlns.add("http://www.w3.org/2001/vcard-rdf/3.0#", "vCard");
                xmlns.add("http://biomodels.net/biology-qualifiers/", "bqbiol");
                xmlns.add("http://biomodels.net/model-qualifiers/", "bqmodel");

                XMLTriple RDF_triple = new XMLTriple("RDF",
                        "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");

                XMLToken RDF_token = new XMLToken(RDF_triple, blank_att, xmlns);

                XMLNode annotation = new XMLNode(RDF_token);

                /* add the staement node to the RDF node */
                annotation.addChild(statement);

                s.appendAnnotation(annotation);

                libsbml.writeSBML(d, args[1]);
            }
        }

        System.exit((int) errors);
    }
}