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#
# \file addingEvidenceCodes_1.R
# \brief adds controlled vocabulary terms to a reaction in a model
# \author Frank Bergmann
#
# <!--------------------------------------------------------------------------
# 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.
# ------------------------------------------------------------------------ -->
#
#
#
# Usage: R --slave -f addingEvidenceCodes_1.R --args <input-filename> <output-filename>
#
#
library(libSBML)
args <- commandArgs(trailingOnly = TRUE)
if (length(args) != 2) {
stop(
" usage: addingEvidenceCodes_1 <input-filename> <output-filename>\n Adds controlled vocabulary term to a reaction\n"
);
}
d = readSBML(args[1]);
errors = SBMLDocument_getNumErrors(d);
if (errors > 0) {
cat("Read Error(s):\n");
SBMLDocument_printErrors(d);
cat("Correct the above and re-run.\n");
} else {
m = SBMLDocument_getModel(d);
n = Model_getNumReactions(m);
if (n <= 0) {
cat( "Model has no reactions.\n Cannot add CV terms\n");
} else {
r = Model_getReaction(m, 0);
# check that the reaction has a metaid
# no CVTerms will be added if there is no metaid to reference
#
if (SBase_isSetMetaId(r) == FALSE)
SBase_setMetaId(r, "metaid_0000052");
cv1 = CVTerm("BIOLOGICAL_QUALIFIER");
CVTerm_setBiologicalQualifierType(cv1, "BQB_IS_DESCRIBED_BY");
CVTerm_addResource(cv1, "urn:miriam:obo.eco:ECO%3A0000183");
SBase_addCVTerm(r, cv1);
cv2 = CVTerm("BIOLOGICAL_QUALIFIER");
CVTerm_setBiologicalQualifierType(cv2, "BQB_IS");
CVTerm_addResource(cv2, "urn:miriam:kegg.reaction:R00756");
CVTerm_addResource(cv2, "urn:miriam:reactome:REACT_736");
SBase_addCVTerm(r, cv2);
writeSBML(d, args[2]);
}
}
q(status=errors);
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