validateSBML.R

# 
# @file    validateSBML.R
# @brief   Validates an SBML file against the appropriate schema
# @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,
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# DEALINGS IN THE SOFTWARE.
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# 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
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# ------------------------------------------------------------------------ -->
# 
#
# Usage: R --slave -f validateSBML.R --args <full path to sbml file> 
#
#

library(libSBML)

args <- commandArgs(trailingOnly = TRUE)

if (length(args) != 1)
{
  stop("Usage: validateSBML filename\n")
}
filename <- args[1]
d <- readSBML(filename)

errors  <- SBMLDocument_getNumErrors(d) + SBMLDocument_checkConsistency(d)

size <- file.info(filename)[["size"]]

cat( "        filename: ", filename, "\n" )
cat( "       file size: ", size    , "\n" )
cat( "        error(s): ", errors  , "\n" )

if (errors > 0) SBMLDocument_printErrors(d)