#!/usr/bin/env perl
# -*-Perl-*-
## 
## \file    appendAnnotation.pl
## \brief   adds annotation strings to a model and a species
## \author  Akiya Jouraku
## 
## <!--------------------------------------------------------------------------
## 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) 2013-2017 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.
## ------------------------------------------------------------------------ -->
## 


use LibSBML;
no strict;

if ($#ARGV != 1){
  print "usage: appendAnnotation <input-filename> <output-filename>\n";
  print "       Adds annotatons\n";
  exit 2;
}

$d = LibSBML::readSBML($ARGV[0]);
$errors = $d->getNumErrors();

if (errors > 0) {
    print("Read Error(s):\n");
    $d->printErrors();  
    print("Correct the above and re-run.\n");
	exit $errors;
}
$model_history_annotation = '<annotation>
  <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
    <rdf:Description rdf:about="#">
      <dc:creator rdf:parseType="Resource">
        <rdf:Bag>
          <rdf:li rdf:parseType="Resource">
            <vCard:N rdf:parseType="Resource">
              <vCard:Family>Keating</vCard:Family>
              <vCard:Given>Sarah</vCard:Given>
            </vCard:N>
            <vCard:EMAIL>sbml-team@caltech.edu</vCard:EMAIL>
            <vCard:ORG>
              <vCard:Orgname>University of Hertfordshire</vCard:Orgname>
            </vCard:ORG>
          </rdf:li>
        </rdf:Bag>
      </dc:creator>
      <dcterms:created rdf:parseType="Resource">
        <dcterms:W3CDTF>1999-11-13T06:54:32Z</dcterms:W3CDTF>
      </dcterms:created>
      <dcterms:modified rdf:parseType="Resource">
        <dcterms:W3CDTF>2007-11-31T06:54:00-02:00</dcterms:W3CDTF>
      </dcterms:modified>
    </rdf:Description>
  </rdf:RDF>
</annotation>';

$d->getModel()->appendAnnotation($model_history_annotation);

# 
# The above code can be replaced by the following code.
# 
# 
# ModelHistory * h = ModelHistory();
# 
# ModelCreator *c = ModelCreator();
# c.setFamilyName("Keating");
# c.setGivenName("Sarah");
# c.setEmail("sbml-team@caltech.edu");
# c.setOrganisation("University of Hertfordshire");
# 
# h.addCreator(c);
# 
# Date * date = Date("1999-11-13T06:54:32");
# Date * date2 = Date("2007-11-31T06:54:00-02:00");
# 
# h.setCreatedDate(date);
# h.setModifiedDate(date2);
# 
# d.getModel().setModelHistory(h);
# 
# 
# 


$n = $d->getModel()->getNumSpecies();

if ($n <= 0) {
  print "No Species found, cannot attach annotation. Please load a model including species.\n";
  exit 0;
}

$s = $d->getModel()->getSpecies(0);

$cvterms_annotation = '<annotation>		  
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
  <rdf:Description rdf:about="#">
    <bqbiol:isVersionOf>
      <rdf:Bag>
        <rdf:li rdf:resource="http://www.geneontology.org/#GO:0005892"/>
        <rdf:li rdf:resource="http://www.ebi.ac.uk/interpro/#IPR002394"/>
      </rdf:Bag>
    </bqbiol:isVersionOf>
    <bqbiol:is>
      <rdf:Bag>
        <rdf:li rdf:resource="http://www.geneontology.org/#GO:0005895"/>
      </rdf:Bag>
    </bqbiol:is>
  </rdf:Description>
</rdf:RDF>
</annotation>';
  
  $s->appendAnnotation($cvterms_annotation);
}

# 
# The above code can be replaced by the following code.
# 
# 
# CVTerm *cv = CVTerm();
# cv.setQualifierType(BIOLOGICAL_QUALIFIER);
# cv.setBiologicalQualifierType(BQB_IS_VERSION_OF);
# cv.addResource("http://www.geneontology.org/#GO:0005892");
# 
# CVTerm *cv2 = CVTerm();
# cv2.setQualifierType(BIOLOGICAL_QUALIFIER);
# cv2.setBiologicalQualifierType(BQB_IS);
# cv2.addResource("http://www.geneontology.org/#GO:0005895");
# 
# CVTerm *cv1 = CVTerm();
# cv1.setQualifierType(BIOLOGICAL_QUALIFIER);
# cv1.setBiologicalQualifierType(BQB_IS_VERSION_OF);
# cv1.addResource("http://www.ebi.ac.uk/interpro/#IPR002394");
# 
# s.addCVTerm(cv);
# s.addCVTerm(cv2);
# s.addCVTerm(cv1);
# 
# 
# 

LibSBML::writeSBML($d, $ARGV[1]);
exit $errors;
 
