1#
2# @file    stripPackage.R
3# @brief   Strips the given package from the given SBML file.
4# @author  Frank Bergmann
5#
6# <!--------------------------------------------------------------------------
7# This sample program is distributed under a different license than the rest
8# of libSBML.  This program uses the open-source MIT license, as follows:
9#
10# Copyright (c) 2013-2018 by the California Institute of Technology
11# (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
12# and the University of Heidelberg (Germany), with support from the National
13# Institutes of Health (USA) under grant R01GM070923.  All rights reserved.
14#
15# Permission is hereby granted, free of charge, to any person obtaining a
16# copy of this software and associated documentation files (the "Software"),
17# to deal in the Software without restriction, including without limitation
18# the rights to use, copy, modify, merge, publish, distribute, sublicense,
19# and/or sell copies of the Software, and to permit persons to whom the
20# Software is furnished to do so, subject to the following conditions:
21#
22# The above copyright notice and this permission notice shall be included in
23# all copies or substantial portions of the Software.
24#
25# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
26# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
27# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
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30# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
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34# of the European Bioinformatics Institute (EMBL-EBI), nor of the University
35# of Heidelberg, nor the names of any contributors, may be used to endorse
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38# ------------------------------------------------------------------------ -->
39#
40#
41# Usage: R --slave -f stripPackage.R --args <full path to input file> <package-to-strip> <full path to output file>
42#
43#
44
45library(libSBML)
46
47args <- commandArgs(trailingOnly = TRUE)
48
49if (length(args) != 3)
50{
51  stop("Usage: stripPackage input-filename package-to-strip output-filename\n");
52}
53
54doc = readSBML(args[1]);
55
56if (SBMLDocument_getNumErrors(doc) > 0) {
57  SBMLDocument_printErrors(doc);
58} else {
59  props = ConversionProperties();
60  ConversionProperties_addOption(props, "stripPackage", TRUE, "Strip SBML Level 3 package constructs from the model");
61  ConversionProperties_addOption(props, "package", args[2], "Name of the SBML Level 3 package to be stripped");
62  if (SBMLDocument_convert(doc, props) != 0) {
63	stop("Error: conversion failed...\n");
64  }
65  writeSBML(doc, args[3]);
66}
67
68