END_TEST
START_TEST (test_SBMLConvert_convertToL1_Species_Amount)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 4);
Model_t *m = SBMLDocument_createModel(d);
const char *sid = "C";
Compartment_t *c = Compartment_create(2, 4);
Species_t *s = Species_create(2, 4);
Compartment_setId ( c, sid );
Model_addCompartment( m, c );
Species_setCompartment ( s, sid );
Species_setInitialAmount( s, 2.34 );
Model_addSpecies ( m, s );
fail_unless( SBMLDocument_setLevelAndVersion(d, 1, 2) == 1, NULL );
fail_unless( Species_getInitialAmount(s) == 2.34, NULL );
SBMLDocument_free(d);
}
int
main (int argc, char *argv[])
{
SBMLDocument_t *d;
Model_t *m;
if (argc != 3)
{
printf("\n usage: drawMath <sbml filename> <output dot filename>\n\n");
return 1;
}
d = readSBML(argv[1]);
m = SBMLDocument_getModel(d);
SBMLDocument_printErrors(d, stdout);
if ((fout = fopen( argv[2], "w" )) == NULL )
{
printf( "The output file was not opened\n" );
}
else
{
printMath(m);
fclose(fout);
}
SBMLDocument_free(d);
return 0;
}
/** 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);
}
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_SBMLDocument_setModel)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 4);
Model_t *m1 = Model_create(2, 4);
Model_t *m2 = Model_create(2, 4);
Model_t *mout;
fail_unless(SBMLDocument_getModel(d) == NULL);
int i = SBMLDocument_setModel(d, m1);
fail_unless ( i == LIBSBML_OPERATION_SUCCESS );
mout = SBMLDocument_getModel(d);
fail_unless(mout != NULL);
fail_unless(mout != m1);
/* Reflexive case (pathological) */
i = SBMLDocument_setModel(d, SBMLDocument_getModel(d));
fail_unless ( i == LIBSBML_OPERATION_SUCCESS );
mout = SBMLDocument_getModel(d);
fail_unless(mout != NULL);
fail_unless(mout != m1);
i = SBMLDocument_setModel(d, m2);
fail_unless ( i == LIBSBML_OPERATION_SUCCESS );
mout = SBMLDocument_getModel(d);
fail_unless(mout != NULL);
fail_unless(mout != m2);
SBMLDocument_free(d);
/* m1 is freed by SBMLDocument_setModel(d, m2); */
}
END_TEST
START_TEST (test_SBMLDocument_free_NULL)
{
SBMLDocument_free(NULL);
}
END_TEST
START_TEST (test_SBMLDocument_setLevelAndVersion_UnitsError)
{
SBMLDocument_t *d = SBMLDocument_create();
SBMLDocument_setLevelAndVersionNonStrict(d, 2, 4);
Model_t *m1 = SBMLDocument_createModel(d);
Compartment_t *c = Model_createCompartment(m1);
Compartment_setId(c, "c");
Parameter_t *p = Model_createParameter(m1);
Parameter_setId(p, "p");
Parameter_setUnits(p, "mole");
Rule_t * r = Model_createAssignmentRule(m1);
Rule_setVariable(r, "c");
Rule_setFormula(r, "p*p");
fail_unless(SBMLDocument_setLevelAndVersionNonStrict(d,2,2) == 1);
fail_unless(SBMLDocument_setLevelAndVersionNonStrict(d,2,3) == 1);
fail_unless(SBMLDocument_setLevelAndVersionNonStrict(d,1,2) == 1);
fail_unless(SBMLDocument_setLevelAndVersionNonStrict(d,1,1) == 0);
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_SBMLDocument_setLevelAndVersion_Error)
{
SBMLDocument_t *d = SBMLDocument_create();
SBMLDocument_setLevelAndVersion(d, 2, 1);
Model_t *m1 = Model_create(2, 1);
/* add unitDefinition */
Unit_t * u = Unit_create(2, 1);
Unit_setKind(u, UnitKind_forName("mole"));
Unit_setOffset(u, 3.2);
UnitDefinition_t *ud =
UnitDefinition_create(2, 1);
UnitDefinition_setId(ud, "ud");
UnitDefinition_addUnit(ud, u);
Model_addUnitDefinition(m1, ud);
SBMLDocument_setModel(d, m1);
fail_unless(SBMLDocument_setLevelAndVersionStrict(d,2,2) == 0);
fail_unless(SBMLDocument_setLevelAndVersionStrict(d,2,3) == 0);
fail_unless(SBMLDocument_setLevelAndVersionStrict(d,1,2) == 0);
fail_unless(SBMLDocument_setLevelAndVersionStrict(d,1,1) == 0);
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);
}
int
main (int argc, char *argv[]){
int i, j;
char *model;
double time;
double printstep;
/* libSBML types */
SBMLDocument_t *d;
SBMLReader_t *sr;
Model_t *m;
/* SOSlib types */
SBMLResults_t *results;
timeCourse_t *tc;
cvodeSettings_t *set;
/* parsing command-line arguments */
if (argc < 4 ) {
fprintf(stderr,
"usage %s sbml-model-file simulation-time time-steps\n",
argv[0]);
exit(EXIT_FAILURE);
}
model = argv[1];
time = atof(argv[2]);
printstep = atoi(argv[3]);
/* parsing the SBML model with libSBML */
sr = SBMLReader_create();
d = SBMLReader_readSBML(sr, model);
SBMLReader_free(sr);
/* Setting SBML ODE Solver integration parameters */
set = CvodeSettings_create();
CvodeSettings_setTime(set, time, printstep);
CvodeSettings_setErrors(set, 1e-9, 1e-4, 1000);
/* calling the SBML ODE Solver which returns SBMLResults */
results = SBML_odeSolver(d, set);
if ( SolverError_getNum(FATAL_ERROR_TYPE) ) {
printf("Integration not sucessful!\n");
SolverError_dumpAndClearErrors();
return(EXIT_FAILURE);
}
/* now we have the results and can free the inputs */
CvodeSettings_free(set);
SBMLDocument_free(d);
/* print results */
printf("### RESULTS \n");
SBMLResults_dump(results);
SolverError_dumpAndClearErrors();
/* now we can also free the result structure */
SBMLResults_free(results);
return (EXIT_SUCCESS);
}
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_convertToL3_defaultUnits)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(1, 2);
Model_t *m = SBMLDocument_createModel(d);
const char *sid = "C";
Compartment_t *c = Model_createCompartment(m);
Compartment_setId ( c, sid );
Compartment_setSize ( c, 1.2 );
Compartment_setUnits( c, "volume");
fail_unless(Model_getNumUnitDefinitions(m) == 0);
fail_unless( SBMLDocument_setLevelAndVersion(d, 3, 1) == 1, NULL);
fail_unless(Model_getNumUnitDefinitions(m) == 2);
UnitDefinition_t *ud = Model_getUnitDefinition(m, 0);
fail_unless (ud != NULL);
fail_unless (!strcmp(UnitDefinition_getId( ud), "volume"));
fail_unless(UnitDefinition_getNumUnits(ud) == 1);
Unit_t * u = UnitDefinition_getUnit(ud, 0);
fail_unless(Unit_getKind(u) == UNIT_KIND_LITRE);
fail_unless(Unit_getExponent(u) == 1);
fail_unless(Unit_getMultiplier(u) == 1);
fail_unless(Unit_getScale(u) == 0);
ud = Model_getUnitDefinition(m, 1);
fail_unless (ud != NULL);
fail_unless (!strcmp(UnitDefinition_getId( ud), "time"));
fail_unless(UnitDefinition_getNumUnits(ud) == 1);
u = UnitDefinition_getUnit(ud, 0);
fail_unless(Unit_getKind(u) == UNIT_KIND_SECOND);
fail_unless(Unit_getExponent(u) == 1);
fail_unless(Unit_getMultiplier(u) == 1);
fail_unless(Unit_getScale(u) == 0);
fail_unless(!strcmp(Model_getTimeUnits(m), "time"));
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);
}
END_TEST
START_TEST (test_SBMLDocument_setModel2)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 2);
Model_t *m1 = Model_create(1, 2);
int i = SBMLDocument_setModel(d, m1);
fail_unless ( i == LIBSBML_LEVEL_MISMATCH);
fail_unless (SBMLDocument_getModel(d) == 0);
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_SBMLDocument_setModel3)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 2);
Model_t *m1 = Model_create(2, 2);
int i = SBMLDocument_setModel(d, m1);
fail_unless ( i == LIBSBML_OPERATION_SUCCESS);
fail_unless (SBMLDocument_getModel(d) != 0);
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;
#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;
}
END_TEST
START_TEST (test_SBMLDocument_setLevelAndVersion)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 2);
Model_t *m1 = Model_create(2, 2);
SBMLDocument_setModel(d, m1);
fail_unless(SBMLDocument_setLevelAndVersionNonStrict(d,2,3) == 1);
fail_unless(SBMLDocument_setLevelAndVersionNonStrict(d,2,1) == 1);
fail_unless(SBMLDocument_setLevelAndVersionNonStrict(d,1,2) == 1);
fail_unless(SBMLDocument_setLevelAndVersionNonStrict(d,1,1) == 0);
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_SBMLConvert_convertToL3_event)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 2);
Model_t *m = SBMLDocument_createModel(d);
Event_t *e = Model_createEvent(m);
Event_t *e1;
fail_unless( SBMLDocument_setLevelAndVersionNonStrict(d, 3, 1) == 1, NULL);
e1 = Model_getEvent(m, 0);
fail_unless(Event_hasRequiredAttributes(e1) == 1);
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);
}
END_TEST
START_TEST (test_SBMLConvert_convertToL1_Species_Concentration)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 1);
Model_t *m = SBMLDocument_createModel(d);
const char *sid = "C";
Compartment_t *c =
Compartment_create(2, 1);
Species_t *s =
Species_create(2, 1);
Compartment_setId ( c, sid );
Compartment_setSize ( c, 1.2 );
Model_addCompartment( m, c );
Species_setId ( s, "s" );
Species_setCompartment ( s, sid );
Species_setInitialConcentration( s, 2.34 );
Model_addSpecies ( m, s );
fail_unless( SBMLDocument_setLevelAndVersion(d, 1, 2) == 1, NULL);
/**
* These tests will fail under Cygwin because of a minimal
* setlocale() implementation (see setlocale manpage).
*/
#ifndef CYGWIN
fail_unless( Species_getInitialAmount(Model_getSpecies(m, 0)) == 2.808, NULL );
#endif
Species_t * s1 = Model_getSpecies(m, 0);
fail_unless (s1 != NULL);
fail_unless (!strcmp(Species_getCompartment(s1), "C"));
fail_unless(Compartment_getSize(Model_getCompartmentById(m, "C")) == 1.2);
fail_unless(Species_getInitialConcentration(s1) == 2.34);
fail_unless(Species_isSetInitialConcentration(s1) == 1);
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_SBMLConvert_convertToL3_reaction)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 2);
Model_t *m = SBMLDocument_createModel(d);
const char *sid = "C";
Reaction_t *r = Model_createReaction(m);
Reaction_setId ( r, sid );
fail_unless( SBMLDocument_setLevelAndVersionNonStrict(d, 3, 1) == 1, NULL);
Reaction_t *r1 = Model_getReaction(m, 0);
fail_unless(Reaction_hasRequiredAttributes(r1) == 1);
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_SBMLConvert_convertToL3_stoichiometryMath)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 1);
Model_t *m = SBMLDocument_createModel(d);
Compartment_t *c = Model_createCompartment(m);
Compartment_setId ( c, "c" );
Species_t *s = Model_createSpecies(m);
Species_setId(s, "s");
Species_setCompartment(s, "c");
Reaction_t * r = Model_createReaction(m);
SpeciesReference_t *sr = Reaction_createReactant(r);
SpeciesReference_setSpecies(sr, "s");
StoichiometryMath_t *sm = SpeciesReference_createStoichiometryMath(sr);
ASTNode_t * ast = SBML_parseFormula("c*2");
StoichiometryMath_setMath(sm, ast);
fail_unless(Model_getNumRules(m) == 0);
fail_unless(SpeciesReference_isSetId(sr) == 0);
fail_unless( SBMLDocument_setLevelAndVersionNonStrict(d, 3, 1) == 1);
m = SBMLDocument_getModel(d);
r = Model_getReaction(m, 0);
sr = Reaction_getReactant(r, 0);
fail_unless(Model_getNumRules(m) == 1);
fail_unless(SpeciesReference_isSetId(sr) == 1);
Rule_t *rule = Model_getRule(m, 0);
fail_unless( strcmp(SpeciesReference_getId(sr), Rule_getVariable(rule)) == 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_SBMLConvert_convertToL3_trigger)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 2);
Model_t *m = SBMLDocument_createModel(d);
Event_t *e = Model_createEvent(m);
Trigger_t *t = Event_createTrigger(e);
Trigger_t *t1;
fail_unless( SBMLDocument_setLevelAndVersionNonStrict(d, 3, 1) == 1, NULL);
t1 = Event_getTrigger(Model_getEvent(m, 0));
fail_unless(Trigger_hasRequiredAttributes(t1) == 1);
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_SBMLConvert_convertToL3_unit)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 2);
Model_t *m = SBMLDocument_createModel(d);
const char *sid = "C";
UnitDefinition_t *ud = Model_createUnitDefinition(m);
UnitDefinition_setId ( ud, sid );
Unit_t *u = UnitDefinition_createUnit(ud);
Unit_setKind(u, UNIT_KIND_MOLE);
fail_unless( SBMLDocument_setLevelAndVersionNonStrict(d, 3, 1) == 1, NULL);
Unit_t *u1 = UnitDefinition_getUnit(Model_getUnitDefinition(m, 0), 0);
fail_unless(Unit_hasRequiredAttributes(u1) == 1);
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_SBMLConvert_convertToL3_parameter)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 2);
Model_t *m = SBMLDocument_createModel(d);
const char *sid = "C";
Parameter_t *p = Model_createParameter(m);
Parameter_t *p1;
Parameter_setId ( p, sid );
fail_unless( SBMLDocument_setLevelAndVersionNonStrict(d, 3, 1) == 1, NULL);
p1 = Model_getParameter(m, 0);
fail_unless(Parameter_hasRequiredAttributes(p1) == 1);
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_SBMLConvert_convertToL3_product)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 2);
Model_t *m = SBMLDocument_createModel(d);
Reaction_t *r = Model_createReaction(m);
SpeciesReference_t *sr = Reaction_createProduct(r);
SpeciesReference_t *sr1;
SpeciesReference_setSpecies ( sr, "s" );
fail_unless( SBMLDocument_setLevelAndVersionNonStrict(d, 3, 1) == 1, NULL);
sr1 = Reaction_getProduct(Model_getReaction(m, 0), 0);
fail_unless(SpeciesReference_hasRequiredAttributes(sr1) == 1);
SBMLDocument_free(d);
}
