END_TEST
START_TEST (test_SBMLConvertStrict_convertSBO)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 4);
Model_t * m = SBMLDocument_createModel(d);
/* create a compartment with SBO */
Compartment_t * c = Model_createCompartment(m);
Compartment_setId(c, "c");
SBase_setSBOTerm((SBase_t *) (c), 240);
fail_unless( SBMLDocument_setLevelAndVersionStrict(d, 2, 3) == 1 );
fail_unless( SBMLDocument_getLevel (d) == 2, NULL );
fail_unless( SBMLDocument_getVersion(d) == 3, NULL );
fail_unless( SBMLDocument_setLevelAndVersionStrict(d, 2, 2) == 1 );
fail_unless( SBMLDocument_getLevel (d) == 2, NULL );
fail_unless( SBMLDocument_getVersion(d) == 2, NULL );
/* check that sbo term has been removed */
Compartment_t *c1 = Model_getCompartment(SBMLDocument_getModel(d), 0);
fail_unless (SBase_getSBOTerm((SBase_t *) (c1)) == -1, NULL );
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_SBMLConvert_convertToL2v4_DuplicateAnnotations_model)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 1);
Model_t * m = SBMLDocument_createModel(d);
char * annotation = "<rdf/>\n<rdf/>";
int i = SBase_setAnnotationString((SBase_t *) (m), annotation);
fail_unless( SBMLDocument_getLevel (d) == 2, NULL );
fail_unless( SBMLDocument_getVersion(d) == 1, NULL );
fail_unless( XMLNode_getNumChildren(SBase_getAnnotation((SBase_t *) (m))) == 2);
fail_unless( SBMLDocument_setLevelAndVersion(d, 2, 4) == 1, NULL );
fail_unless( SBMLDocument_getLevel (d) == 2, NULL );
fail_unless( SBMLDocument_getVersion(d) == 4, NULL );
m = SBMLDocument_getModel(d);
fail_unless( XMLNode_getNumChildren(SBase_getAnnotation((SBase_t *) (m))) == 1);
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_SBMLConvertStrict_convertNonStrictSBO)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 4);
Model_t * m = SBMLDocument_createModel(d);
/* create a compartment with SBO */
Compartment_t * c = Model_createCompartment(m);
Compartment_setId(c, "c");
Compartment_setConstant(c, 0);
SBase_setSBOTerm((SBase_t *) (c), 64);
/* conversion to L2V3 and L2V2 should fail due to bad SBO
* but to L2V1 and L1 should pass as sbo terms not applicable
*/
fail_unless( SBMLDocument_setLevelAndVersionStrict(d, 2, 3) == 0 );
fail_unless( SBMLDocument_getLevel (d) == 2, NULL );
fail_unless( SBMLDocument_getVersion(d) == 4, NULL );
fail_unless( SBMLDocument_setLevelAndVersionStrict(d, 2, 2) == 0 );
fail_unless( SBMLDocument_getLevel (d) == 2, NULL );
fail_unless( SBMLDocument_getVersion(d) == 4, NULL );
fail_unless( SBMLDocument_setLevelAndVersionStrict(d, 2, 1) == 1 );
fail_unless( SBMLDocument_getLevel (d) == 2, NULL );
fail_unless( SBMLDocument_getVersion(d) == 1, NULL );
/* check that sbo term has been removed */
Compartment_t *c1 = Model_getCompartment(SBMLDocument_getModel(d), 0);
fail_unless (SBase_getSBOTerm((SBase_t *) (c1)) == -1, NULL );
fail_unless( SBMLDocument_setLevelAndVersionStrict(d, 1, 2) == 1 );
fail_unless( SBMLDocument_getLevel (d) == 1, NULL );
fail_unless( SBMLDocument_getVersion(d) == 2, NULL );
/* check that sbo term has been removed */
Compartment_t *c2 = Model_getCompartment(SBMLDocument_getModel(d), 0);
fail_unless (SBase_getSBOTerm((SBase_t *) (c2)) == -1, NULL );
SBMLDocument_free(d);
}
int
main (int argc, char *argv[])
{
const char *filename;
SBMLDocument_t *d;
Model_t *m;
unsigned int level, version;
if (argc != 2)
{
printf("Usage: printSBML filename\n");
return 2;
}
filename = argv[1];
d = readSBML(filename);
SBMLDocument_printErrors(d, stdout);
m = SBMLDocument_getModel(d);
level = SBMLDocument_getLevel (d);
version = SBMLDocument_getVersion(d);
printf("\n");
printf("File: %s (Level %u, version %u)\n", filename, level, version);
if (m == NULL)
{
printf("No model present.");
return 1;
}
printf(" ");
printf(" model id: %s\n", Model_isSetId(m) ? Model_getId(m) : "(empty)");
printf( "functionDefinitions: %d\n", Model_getNumFunctionDefinitions(m) );
printf( " unitDefinitions: %d\n", Model_getNumUnitDefinitions (m) );
printf( " compartmentTypes: %d\n", Model_getNumCompartmentTypes (m) );
printf( " specieTypes: %d\n", Model_getNumSpeciesTypes (m) );
printf( " compartments: %d\n", Model_getNumCompartments (m) );
printf( " species: %d\n", Model_getNumSpecies (m) );
printf( " parameters: %d\n", Model_getNumParameters (m) );
printf( " initialAssignments: %d\n", Model_getNumInitialAssignments (m) );
printf( " rules: %d\n", Model_getNumRules (m) );
printf( " constraints: %d\n", Model_getNumConstraints (m) );
printf( " reactions: %d\n", Model_getNumReactions (m) );
printf( " events: %d\n", Model_getNumEvents (m) );
printf( "\n" );
SBMLDocument_free(d);
return 0;
}
END_TEST
START_TEST (test_SBMLConvert_addModifiersToReaction)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(1, 2);
Model_t *m = SBMLDocument_createModel(d);
Reaction_t *r = Model_createReaction(m);
KineticLaw_t *kl = Reaction_createKineticLaw(r);
KineticLaw_setFormula(kl, "k1*S1*S2*S3*S4*S5");
SpeciesReference_t *ssr1;
SpeciesReference_t *ssr2;
Species_t *s1 = Model_createSpecies( m );
Species_setId( s1, "S1" );
Species_t *s2 = Model_createSpecies( m );
Species_setId( s2, "S2");
Species_t *s3 = Model_createSpecies( m );
Species_setId( s3, "S3");
Species_t *s4 = Model_createSpecies( m );
Species_setId( s4, "S4");
Species_t *s5 = Model_createSpecies( m );
Species_setId( s5, "S5");
SpeciesReference_t *sr1 = Reaction_createReactant( r );
SpeciesReference_t *sr2 = Reaction_createReactant( r );
SpeciesReference_t *sr3 = Reaction_createProduct ( r );
SpeciesReference_setSpecies(sr1, "S1");
SpeciesReference_setSpecies(sr2, "S2");
SpeciesReference_setSpecies(sr3, "S5");
fail_unless( Reaction_getNumModifiers(r) == 0, NULL );
fail_unless( SBMLDocument_setLevelAndVersionNonStrict(d, 2, 1) == 1, NULL );
fail_unless( SBMLDocument_getLevel (d) == 2, NULL );
fail_unless( SBMLDocument_getVersion(d) == 1, NULL );
fail_unless( Reaction_getNumModifiers(Model_getReaction(m, 0)) == 2, NULL );
ssr1 = (SpeciesReference_t *) Reaction_getModifier(Model_getReaction(m, 0), 0);
ssr2 = (SpeciesReference_t *) Reaction_getModifier(Model_getReaction(m, 0), 1);
fail_unless( !strcmp(SpeciesReference_getSpecies(ssr1), "S3"), NULL );
fail_unless( !strcmp(SpeciesReference_getSpecies(ssr2), "S4"), NULL );
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_SBMLConvert_convertToL1_SBMLDocument)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 1);
fail_unless( SBMLDocument_setLevelAndVersionNonStrict(d, 1, 2) == 1, NULL);
fail_unless( SBMLDocument_getLevel (d) == 1, NULL );
fail_unless( SBMLDocument_getVersion(d) == 2, NULL );
SBMLDocument_free(d);
}
BEGIN_C_DECLS
START_TEST (test_SBMLConvert_convertToL2_SBMLDocument)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(1, 2);
fail_unless( SBMLDocument_setLevelAndVersionNonStrict(d, 2, 1) == 1, NULL );
fail_unless( SBMLDocument_getLevel (d) == 2, NULL );
fail_unless( SBMLDocument_getVersion(d) == 1, NULL );
fail_unless( SBMLDocument_setLevelAndVersionNonStrict(d, 2, 2) == 1, NULL );
fail_unless( SBMLDocument_getLevel (d) == 2, NULL );
fail_unless( SBMLDocument_getVersion(d) == 2, NULL );
fail_unless( SBMLDocument_setLevelAndVersionNonStrict(d, 2, 3) == 1, NULL );
fail_unless( SBMLDocument_getLevel (d) == 2, NULL );
fail_unless( SBMLDocument_getVersion(d) == 3, NULL );
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_SBMLDocument_createWith)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(1, 2);
fail_unless( SBase_getTypeCode ((SBase_t *) d) == SBML_DOCUMENT );
fail_unless( SBase_getNotes ((SBase_t *) d) == NULL );
fail_unless( SBase_getAnnotation((SBase_t *) d) == NULL );
fail_unless( SBMLDocument_getLevel (d) == 1);
fail_unless( SBMLDocument_getVersion(d) == 2);
fail_unless( SBMLDocument_getNumErrors (d) == 0 );
SBMLDocument_free(d);
}
LIBSBML_CPP_NAMESPACE_USE
BEGIN_C_DECLS
START_TEST (test_SBMLDocument_create)
{
SBMLDocument_t *d = SBMLDocument_create();
fail_unless( SBase_getTypeCode ((SBase_t *) d) == SBML_DOCUMENT );
fail_unless( SBase_getNotes ((SBase_t *) d) == NULL );
fail_unless( SBase_getAnnotation((SBase_t *) d) == NULL );
fail_unless( SBMLDocument_getLevel (d) == 3);
fail_unless( SBMLDocument_getVersion(d) == 1);
fail_unless( SBMLDocument_getNumErrors (d) == 0 );
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_SBMLConvertStrict_convertToL1)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 4);
/* create model with metaid */
Model_t * m = SBMLDocument_createModel(d);
SBase_setMetaId((SBase_t *) (m), "_m");
/* create a compartment with sbo*/
Compartment_t * c = Model_createCompartment(m);
Compartment_setId(c, "c");
SBase_setSBOTerm((SBase_t *) (c), 240);
/* create a species with hasOnlySubstanceUnits = true*/
Species_t *s = Model_createSpecies(m);
Species_setId(s, "s");
Species_setCompartment(s, "c");
Species_setHasOnlySubstanceUnits(s, 1);
fail_unless( SBMLDocument_setLevelAndVersionStrict(d, 1, 2) == 1 );
fail_unless( SBMLDocument_getLevel (d) == 1, NULL );
fail_unless( SBMLDocument_getVersion(d) == 2, NULL );
///* check that attributes that are no longer valid have been removed */
Model_t * m1 = SBMLDocument_getModel(d);
fail_unless (SBase_getMetaId((SBase_t *) (m1)) == NULL);
Compartment_t *c1 = Model_getCompartment(m1, 0);
fail_unless (SBase_getSBOTerm((SBase_t *) (c1)) == -1, NULL );
Species_t *s1 = Model_getSpecies(m1, 0);
fail_unless (Species_getHasOnlySubstanceUnits(s1) == 0);
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_SBMLConvertStrict_convertL1ParamRule)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(1, 2);
Model_t * m = SBMLDocument_createModel(d);
/* create a compartment */
Compartment_t * c = Model_createCompartment(m);
Compartment_setId(c, "c");
/* create a parameter */
Parameter_t * p = Model_createParameter(m);
Parameter_setId(p, "p");
Parameter_t * p1 = Model_createParameter(m);
Parameter_setId(p1, "p1");
/* create a math element */
ASTNode_t *math = SBML_parseFormula("p");
/* create an assignment rule */
Rule_t *ar = Model_createAssignmentRule(m);
Rule_setVariable(ar, "p1");
Rule_setMath(ar, math);
Rule_setUnits(ar, "mole");
fail_unless( SBMLDocument_setLevelAndVersionStrict(d, 2, 1) == 1 );
fail_unless( SBMLDocument_getLevel (d) == 2, NULL );
fail_unless( SBMLDocument_getVersion(d) == 1, NULL );
Rule_t * r1 = Model_getRule(SBMLDocument_getModel(d), 0);
fail_unless (Rule_getUnits(r1) == NULL );
SBMLDocument_free(d);
}
int
main (int argc, char *argv[])
{
unsigned int latestLevel = SBMLDocument_getDefaultLevel();
unsigned int latestVersion = SBMLDocument_getDefaultVersion();
unsigned int errors;
SBMLDocument_t *d;
if (argc != 3)
{
printf("Usage: convertSBML input-filename output-filename\n");
printf("This program will attempt to convert a model either to\n");
printf("SBML Level %d Version %d (if the model is not already) or, if",
latestLevel, latestVersion);
printf("the model is already expressed in Level %d Version %d, this\n",
latestLevel, latestVersion);
printf("program will attempt to convert the model to Level 1 Version 2.\n");
return 1;
}
d = readSBML(argv[1]);
errors = SBMLDocument_getNumErrors(d);
if (errors > 0)
{
printf("Encountered the following SBML error(s):\n");
SBMLDocument_printErrors(d, stdout);
printf("Conversion skipped. Please correct the problems above first.\n");
return errors;
}
else
{
unsigned int olevel = SBMLDocument_getLevel(d);
unsigned int oversion = SBMLDocument_getVersion(d);
int success;
if (olevel < latestLevel || oversion < latestVersion)
{
printf("Attempting to convert model to SBML Level %d Version %d.\n",
latestLevel, latestVersion);
success = SBMLDocument_setLevelAndVersion(d, latestLevel, latestVersion);
}
else
{
printf("Attempting to convert model to SBML Level 1 Version 2.\n");
success = SBMLDocument_setLevelAndVersion(d, 1, 2);
}
errors = SBMLDocument_getNumErrors(d);
if (!success)
{
printf("Unable to perform conversion due to the following:\n");
SBMLDocument_printErrors(d, stdout);
printf("Conversion skipped. Either libSBML does not (yet) have\n");
printf("ability to convert this model, or (automatic) conversion\n");
printf("is not possible in this case.\n");
}
else if (errors > 0)
{
printf("Information may have been lost in conversion; but a valid model ");
printf("was produced by the conversion.\nThe following information ");
printf("was provided:\n");
SBMLDocument_printErrors(d, stdout);
writeSBML(d, argv[2]);
}
else
{
printf("Conversion completed.\n");
writeSBML(d, argv[2]);
}
}
SBMLDocument_free(d);
return errors;
}