#!/usr/bin/env ruby
#
## 
## \file    addingEvidenceCodes_2.py
## \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) 2013-2017 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
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## 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.
## ------------------------------------------------------------------------ -->
## 

require 'libSBML'

if ARGV.size != 2

  puts "usage: addingEvidenceCodes_2 <input-filename> <output-filename>"
  puts "       Adds controlled vocabulary term to a species"
  exit(2)
end

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);
end

n = d.getModel.getNumSpecies
if (n <= 0)
  print("Model has no species.\n Cannot add CV terms\n")
  exit(0);
end
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 (not s.isSetMetaId)
    s.setMetaId("metaid_0000052")
end
cv1 = LibSBML::CVTerm.new(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
blank_att = LibSBML::XMLAttributes.new

resource_att = LibSBML::XMLAttributes.new

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

statement_token = LibSBML::XMLToken.new(statement_triple, blank_att)

statement = LibSBML::XMLNode.new(statement_token)

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

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

subject_token = LibSBML::XMLToken.new(subject_triple, resource_att)

subject = LibSBML::XMLNode.new(subject_token)


#create the predicate node 
predicate_triple = LibSBML::XMLTriple.new("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")

predicate_token = LibSBML::XMLToken.new(predicate_triple, resource_att)

predicate = LibSBML::XMLNode.new(predicate_token)

#create the object node 
object_triple = LibSBML::XMLTriple.new("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")

object_token = LibSBML::XMLToken.new(object_triple, resource_att)

object_ = LibSBML::XMLNode.new(object_token)

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

bqbiol_token = LibSBML::XMLToken.new(bqbiol_triple, blank_att)

bqbiol = LibSBML::XMLNode.new(bqbiol_token)

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

bag_token = LibSBML::XMLToken.new(bag_triple, blank_att)

bag = LibSBML::XMLNode.new(bag_token)

# create each li node and add to the bag 
li_triple = LibSBML::XMLTriple.new("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")

li_token = LibSBML::XMLToken.new(li_triple, resource_att)
li_token.setEnd

li = LibSBML::XMLNode.new(li_token)

bag.addChild(li)

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

xmlns = LibSBML::XMLNamespaces.new
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")

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

rDF_token = LibSBML::XMLToken.new(rDF_triple, blank_att, xmlns)

annotation = LibSBML::XMLNode.new(rDF_token)

# add the staement node to the RDF node 
annotation.addChild(statement)

s.appendAnnotation(annotation)

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