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_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_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);
}
END_TEST
START_TEST (test_SBMLConvert_convertFromL3)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(3, 1);
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_setConstant( c, 1);
Compartment_setSpatialDimensionsAsDouble(c, 3.4);
fail_unless(SBMLDocument_setLevelAndVersion(d, 1, 1) == 0);
fail_unless(SBMLDocument_setLevelAndVersion(d, 1, 2) == 0);
fail_unless(SBMLDocument_setLevelAndVersion(d, 2, 1) == 0);
fail_unless(SBMLDocument_setLevelAndVersion(d, 2, 2) == 0);
fail_unless(SBMLDocument_setLevelAndVersion(d, 2, 3) == 0);
fail_unless(SBMLDocument_setLevelAndVersion(d, 2, 4) == 0);
fail_unless(SBMLDocument_setLevelAndVersion(d, 3, 1) == 1);
}
END_TEST
START_TEST (test_SBMLConvert_invalidLevelVersion)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 1);
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(SBMLDocument_setLevelAndVersion(d, 1, 3) == 0);
fail_unless(SBMLDocument_setLevelAndVersion(d, 2, 5) == 0);
fail_unless(SBMLDocument_setLevelAndVersion(d, 3, 2) == 0);
fail_unless(SBMLDocument_setLevelAndVersion(d, 4, 1) == 0);
}
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_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_convertFromL3_conversionFactor)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(3, 1);
Model_t *m = SBMLDocument_createModel(d);
const char *sid = "P";
Model_setConversionFactor(m, sid);
Parameter_t *c = Model_createParameter(m);
Parameter_setId ( c, sid );
Parameter_setConstant( c, 1);
fail_unless(SBMLDocument_setLevelAndVersion(d, 1, 1) == 0);
fail_unless(SBMLDocument_setLevelAndVersion(d, 1, 2) == 0);
fail_unless(SBMLDocument_setLevelAndVersion(d, 2, 1) == 0);
fail_unless(SBMLDocument_setLevelAndVersion(d, 2, 2) == 0);
fail_unless(SBMLDocument_setLevelAndVersion(d, 2, 3) == 0);
fail_unless(SBMLDocument_setLevelAndVersion(d, 2, 4) == 0);
fail_unless(SBMLDocument_setLevelAndVersion(d, 3, 1) == 1);
}
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;
}
