1# 2# @file convertSBML.R 3# @brief Converts SBML documents between levels 4# @author Frank Bergmann 5# 6# 7# <!-------------------------------------------------------------------------- 8# This sample program is distributed under a different license than the rest 9# of libSBML. This program uses the open-source MIT license, as follows: 10# 11# Copyright (c) 2013-2018 by the California Institute of Technology 12# (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK) 13# and the University of Heidelberg (Germany), with support from the National 14# Institutes of Health (USA) under grant R01GM070923. All rights reserved. 15# 16# Permission is hereby granted, free of charge, to any person obtaining a 17# copy of this software and associated documentation files (the "Software"), 18# to deal in the Software without restriction, including without limitation 19# the rights to use, copy, modify, merge, publish, distribute, sublicense, 20# and/or sell copies of the Software, and to permit persons to whom the 21# Software is furnished to do so, subject to the following conditions: 22# 23# The above copyright notice and this permission notice shall be included in 24# all copies or substantial portions of the Software. 25# 26# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 27# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 28# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL 29# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 30# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING 31# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 32# DEALINGS IN THE SOFTWARE. 33# 34# Neither the name of the California Institute of Technology (Caltech), nor 35# of the European Bioinformatics Institute (EMBL-EBI), nor of the University 36# of Heidelberg, nor the names of any contributors, may be used to endorse 37# or promote products derived from this software without specific prior 38# written permission. 39# ------------------------------------------------------------------------ --> 40# 41# 42# Usage: R --slave -f convertSBML.R --args <input-filename> <output-filename> 43# 44# 45 46library(libSBML) 47 48args <- commandArgs(trailingOnly = TRUE) 49 50latestLevel = SBMLDocument_getDefaultLevel(); 51latestVersion = SBMLDocument_getDefaultVersion(); 52 53if (length(args) != 2) { 54 stop( 55 paste( 56 "Usage: convertSBML <input-filename> <output-filename>\n", 57 "This program will attempt to convert a model either to\n", 58 "SBML Level ",latestLevel," Version ",latestVersion," (if the model is not already) or, if", 59 "the model is already expressed in Level ",latestLevel," Version ",latestVersion,", this\n", 60 "program will attempt to convert the model to Level 1 Version 2.\n", 61 sep = "") 62 ); 63} 64 65d = readSBML(args[1]); 66errors = SBMLErrorLog_getNumFailsWithSeverity( 67 SBMLDocument_getErrorLog(d), 68 enumToInteger("LIBSBML_SEV_ERROR", "_XMLErrorSeverity_t") 69 ); 70 71if (errors > 0) { 72 cat("Encountered the following SBML error(s):\n"); 73 SBMLDocument_printErrors(d); 74 stop("Conversion skipped. Please correct the problems above first.\n"); 75} else { 76 olevel = SBase_getLevel(d); 77 oversion = SBase_getVersion(d); 78 79 if (olevel < latestLevel || oversion < latestVersion) { 80 cat("Attempting to convert model to SBML Level ",latestLevel," Version ",latestVersion,".\n"); 81 success = SBMLDocument_setLevelAndVersion(d, latestLevel, latestVersion); 82 } else { 83 cat("Attempting to convert model to SBML Level 1 Version 2.\n"); 84 success = SBMLDocument_setLevelAndVersion(d, 1, 2); 85 } 86 87 errors = SBMLErrorLog_getNumFailsWithSeverity( 88 SBMLDocument_getErrorLog(d), 89 enumToInteger("LIBSBML_SEV_ERROR", "_XMLErrorSeverity_t") 90 ); 91 92 if (!success) { 93 cat("Unable to perform conversion due to the following:\n"); 94 SBMLDocument_printErrors(d); 95 96 cat("Conversion skipped. Either libSBML does not (yet) have\n"); 97 cat("ability to convert this model, or (automatic) conversion\n"); 98 cat("is not possible in this case.\n"); 99 } else if (errors > 0) { 100 cat("Information may have been lost in conversion; but a valid model "); 101 cat("was produced by the conversion.\nThe following information "); 102 cat("was provided:\n"); 103 SBMLDocument_printErrors(d); 104 writeSBML(d, args[2]); 105 } else { 106 cat("Conversion completed.\n"); 107 writeSBML(d, args[2]); 108 } 109} 110 111q(status=errors); 112