#!/usr/bin/python3
##
## \file    appendAnnotation.py
## \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) 2013-2018 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 sys
import os.path
from libsbml import *


def main(args):
    """usage: appendAnnotation <input-filename> <output-filename>
       Adds annotations
    """
    if len(args) != 3:
        print(main.__doc__)
        sys.exit(2)

    d = readSBML(args[1])
    errors = d.getNumErrors()

    if errors > 0:
        print("Read Error(s):")
        d.printErrors()

        print("Correct the above and re-run.")
    else:
        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:
            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);
            #
            #
            #

        writeSBML(d, args[2])
    return errors


if __name__ == '__main__':
    main(sys.argv)