/** C.0: Loads, validates and parses an SBML file,
also converts SBML level 1 to level 2 files,
return NULL if errors were encountered during libSBML
validation and consistency check, stores libSBML warngings
*/
SBMLDocument_t *
parseModel(char *file, int printMessage, int validate, char *schemaPath,
char *schema11FileName,
char *schema12FileName,
char *schema21FileName)
{
unsigned int i, errors ;
SBMLDocument_t *d;
SBMLDocument_t *d2;
SBMLReader_t *sr;
if ( validate ) {
if ( printMessage ) {
fprintf(stderr, "Validating SBML.\n");
fprintf(stderr, "This can take a while for SBML level 2.\n");
}
sr = newSBMLReader(schemaPath,
schema11FileName,
schema12FileName,
schema21FileName);
}
else {
sr = SBMLReader_create();
}
d = SBMLReader_readSBML(sr, file);
SBMLReader_free(sr);
errors = 0;
if ( validate ) {
errors = SBMLDocument_getNumFatals(d) + SBMLDocument_getNumErrors(d);
}
if (SBMLDocument_getNumFatals(d) + SBMLDocument_getNumErrors(d) == 0)
SBMLDocument_checkConsistency(d);
/* AMF 9th Dec 2005 added back because inconsistent models can cause the
solver to crash despite the consistancy check causing memory leaks - talk to Ben B! */
/* check for warnings and errors */
for (i =0 ; i != SBMLDocument_getNumWarnings(d); i++)
storeSBMLError(WARNING_ERROR_TYPE, SBMLDocument_getWarning(d, i));
for (i =0 ; i != SBMLDocument_getNumErrors(d); i++)
storeSBMLError(ERROR_ERROR_TYPE, SBMLDocument_getError(d, i));
for (i =0 ; i != SBMLDocument_getNumFatals(d); i++)
storeSBMLError(FATAL_ERROR_TYPE, SBMLDocument_getFatal(d, i));
RETURN_ON_ERRORS_WITH(NULL);
/* convert level 1 models to level 2 */
if ( SBMLDocument_getLevel(d) == 1 ) {
d2 = convertModel(d);
SBMLDocument_free(d);
if ( printMessage )
fprintf(stderr, "SBML converted from level 1 to level 2.\n");
return (d2);
}
return (d);
}
int
main (int argc, char *argv[])
{
const char *filename;
#ifdef __BORLANDC__
unsigned long start, stop;
#else
unsigned long long start, stop;
#endif
unsigned long size;
unsigned int errors = 0;
SBMLDocument_t *d;
if (argc != 2)
{
printf("Usage: validateSBML filename\n");
return 2;
}
filename = argv[1];
start = getCurrentMillis();
d = readSBML(filename);
stop = getCurrentMillis();
errors = SBMLDocument_getNumErrors(d);
errors += SBMLDocument_checkConsistency(d);
size = getFileSize(filename);
printf( "\n" );
printf( " filename: %s\n" , filename );
printf( " file size: %lu\n", size );
printf( " read time (ms): %llu\n", stop - start );
printf( " error(s): %u\n" , errors );
if (errors > 0) SBMLDocument_printErrors(d, stdout);
printf("\n");
SBMLDocument_free(d);
return errors;
}
