END_TEST
START_TEST (test_L3_Species_hasRequiredAttributes )
{
Species_t *s = Species_create (3, 1);
fail_unless ( !Species_hasRequiredAttributes(s));
Species_setId(s, "id");
fail_unless ( !Species_hasRequiredAttributes(s));
Species_setCompartment(s, "cell");
fail_unless ( !Species_hasRequiredAttributes(s));
Species_setHasOnlySubstanceUnits(s, 0);
fail_unless ( !Species_hasRequiredAttributes(s));
Species_setBoundaryCondition(s, 0);
fail_unless ( !Species_hasRequiredAttributes(s));
Species_setConstant(s, 0);
fail_unless ( Species_hasRequiredAttributes(s));
Species_free(s);
}
END_TEST
/* since the setId function has been used as an
* alias for setName we cant require it to only
* be used on a L2 model
START_TEST (test_Species_setId1)
{
int i = Species_setId(C, "cell");
fail_unless( i == LIBSBML_UNEXPECTED_ATTRIBUTE );
fail_unless( !Species_isSetId(C) );
}
END_TEST
*/
START_TEST (test_Species_setId2)
{
Species_t *c =
Species_create(2, 2);
int i = Species_setId(c, "1cell");
fail_unless( i == LIBSBML_INVALID_ATTRIBUTE_VALUE );
fail_unless( !Species_isSetId(c) );
Species_free(c);
}
END_TEST
START_TEST (test_Species_setSpatialSizeUnits)
{
Species_t *s =
Species_create(2, 1);
const char *units = "volume";
Species_setSpatialSizeUnits(s, units);
fail_unless( !strcmp(Species_getSpatialSizeUnits(s), units) );
fail_unless( Species_isSetSpatialSizeUnits(s) );
if (Species_getSpatialSizeUnits(s) == units)
{
fail("Species_setSpatialSizeUnits(...) did not make a copy of string.");
}
/* Reflexive case (pathological) */
Species_setSpatialSizeUnits(s, Species_getSpatialSizeUnits(s));
fail_unless( !strcmp(Species_getSpatialSizeUnits(s), units) );
Species_setSpatialSizeUnits(s, NULL);
fail_unless( !Species_isSetSpatialSizeUnits(s) );
if (Species_getSpatialSizeUnits(s) != NULL)
{
fail("Species_setSpatialSizeUnits(S, NULL) did not clear string.");
}
Species_free(s);
}
END_TEST
START_TEST (test_Reaction_addProductBySpecies)
{
Species_t *s = Species_create(2, 4);
Species_setId(s, "s");
Reaction_addProductBySpecies(R, s, 2.0, "sr", 0);
fail_unless( Reaction_getNumReactants(R) == 0 );
fail_unless( Reaction_getNumProducts (R) == 1 );
fail_unless( Reaction_getNumModifiers(R) == 0 );
SpeciesReference_t *sr = Reaction_getProduct(R, 0);
fail_unless(!strcmp(SpeciesReference_getSpecies(sr), "s"));
fail_unless(util_isEqual(SpeciesReference_getStoichiometry(sr), 2.0) == 1);
fail_unless(!strcmp(SpeciesReference_getId(sr), "sr"));
fail_unless(SpeciesReference_getConstant(sr) == 0);
fail_unless(Reaction_addProductBySpecies(R, s, 1.0, "sr", 0) == LIBSBML_DUPLICATE_OBJECT_ID);
fail_unless( Reaction_getNumProducts (R) == 1 );
Species_free(s);
}
END_TEST
START_TEST (test_ListOf_append)
{
Model_t *m = Model_create(2, 4);
Model_createCompartment(m);
ListOf_t *loc = Model_getListOfCompartments(m);
fail_unless(ListOf_size(loc) == 1);
SBase_t *c = (SBase_t*)Compartment_create(2, 4);
int i = ListOf_append(loc, c);
fail_unless(i == LIBSBML_OPERATION_SUCCESS);
fail_unless(ListOf_size(loc) == 2);
SBase_t *sp = (SBase_t*)Species_create(2, 4);
i = ListOf_append(loc, sp);
fail_unless(i == LIBSBML_INVALID_OBJECT);
fail_unless(ListOf_size(loc) == 2);
Model_free(m);
Species_free((Species_t*)sp);
}
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);
}
void
SpeciesTest_setup (void)
{
S = Species_create(2, 4);
if (S == NULL)
{
fail("Species_create() returned a NULL pointer.");
}
}
void
SpeciesTest1_setup (void)
{
C = Species_create(1, 2);
if (C == NULL)
{
fail("Species_create() returned a NULL pointer.");
}
}
END_TEST
START_TEST (test_L3_Species_initDefaults)
{
Species_t *s = Species_create(3,1);
fail_unless( Species_getId (s) == NULL );
fail_unless( Species_getName (s) == NULL );
fail_unless( Species_getCompartment (s) == NULL );
fail_unless( util_isNaN(Species_getInitialAmount (s)) );
fail_unless( util_isNaN(Species_getInitialConcentration (s)) );
fail_unless( Species_getSubstanceUnits (s) == NULL );
fail_unless( Species_getHasOnlySubstanceUnits(s) == 0 );
fail_unless( Species_getBoundaryCondition(s) == 0 );
fail_unless( Species_getConstant(s) == 0 );
fail_unless( Species_getConversionFactor (s) == NULL );
fail_unless( !Species_isSetId (s) );
fail_unless( !Species_isSetName (s) );
fail_unless( !Species_isSetCompartment (s) );
fail_unless( !Species_isSetInitialAmount (s) );
fail_unless( !Species_isSetInitialConcentration (s) );
fail_unless( !Species_isSetSubstanceUnits (s) );
fail_unless( !Species_isSetHasOnlySubstanceUnits(s) );
fail_unless( !Species_isSetBoundaryCondition(s) );
fail_unless( !Species_isSetConstant(s) );
fail_unless( !Species_isSetConversionFactor (s) );
Species_initDefaults(s);
fail_unless( Species_getId (s) == NULL );
fail_unless( Species_getName (s) == NULL );
fail_unless( Species_getCompartment (s) == NULL );
fail_unless( util_isNaN(Species_getInitialAmount (s)) );
fail_unless( util_isNaN(Species_getInitialConcentration (s)) );
fail_unless( !strcmp(Species_getSubstanceUnits (s),"mole" ));
fail_unless( Species_getHasOnlySubstanceUnits(s) == 0 );
fail_unless( Species_getBoundaryCondition(s) == 0 );
fail_unless( Species_getConstant(s) == 0 );
fail_unless( Species_getConversionFactor (s) == NULL );
fail_unless( !Species_isSetId (s) );
fail_unless( !Species_isSetName (s) );
fail_unless( !Species_isSetCompartment (s) );
fail_unless( !Species_isSetInitialAmount (s) );
fail_unless( !Species_isSetInitialConcentration (s) );
fail_unless( Species_isSetSubstanceUnits (s) );
fail_unless( Species_isSetHasOnlySubstanceUnits(s) );
fail_unless( Species_isSetBoundaryCondition(s) );
fail_unless( Species_isSetConstant(s) );
fail_unless( !Species_isSetConversionFactor (s) );
Species_free(s);
}
END_TEST
START_TEST (test_ListOf_clear)
{
ListOf_t *lo = (ListOf_t*) ListOf_create(2,4);
SBase_t *sp = (SBase_t*)Species_create(2, 4);
ListOf_append(lo, sp);
ListOf_append(lo, sp);
ListOf_append(lo, sp);
ListOf_append(lo, sp);
ListOf_append(lo, sp);
fail_unless( ListOf_size(lo) == 5 );
/* clear and delete */
ListOf_clear(lo, 1);
fail_unless( ListOf_size(lo) == 0 );
ListOf_append(lo, sp);
ListOf_append(lo, sp);
ListOf_append(lo, sp);
ListOf_append(lo, sp);
ListOf_appendAndOwn(lo, sp);
fail_unless( ListOf_size(lo) == 5 );
/* delete each item */
SBase_t *elem;
elem = ListOf_get(lo, 0);
Species_free((Species_t*) elem);
elem = ListOf_get(lo, 1);
Species_free((Species_t*) elem);
elem = ListOf_get(lo, 2);
Species_free((Species_t*) elem);
elem = ListOf_get(lo, 3);
Species_free((Species_t*) elem);
elem = ListOf_get(lo, 4);
Species_free((Species_t*) elem);
/* clear only */
ListOf_clear(lo, 0);
fail_unless( ListOf_size(lo) == 0 );
ListOf_free(lo);
}
END_TEST
START_TEST (test_Species_setSpatialSizeUnits2)
{
Species_t *c =
Species_create(2, 2);
int i = Species_setSpatialSizeUnits(c, "1cell");
fail_unless( i == LIBSBML_INVALID_ATTRIBUTE_VALUE );
fail_unless( !Species_isSetSpatialSizeUnits(c) );
Species_free(c);
}
END_TEST
START_TEST (test_Species_setConstant2)
{
Species_t *c =
Species_create(2, 2);
int i = Species_setConstant(c, 1);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( Species_getConstant(c) == 1 );
Species_free(c);
}
END_TEST
START_TEST (test_Species_setSpatialSizeUnits4)
{
Species_t *c =
Species_create(2, 2);
int i = Species_setSpatialSizeUnits(c, NULL);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( !Species_isSetSpatialSizeUnits(c) );
Species_free(c);
}
END_TEST
START_TEST (test_Species_setCharge2)
{
Species_t *c =
Species_create(2, 2);
int i = Species_setCharge(c, 4);
fail_unless( i == LIBSBML_UNEXPECTED_ATTRIBUTE );
fail_unless( !Species_isSetCharge(c));
Species_free(c);
}
END_TEST
START_TEST (test_Species_setCharge3)
{
Species_t *c =
Species_create(2, 1);
int i = Species_unsetCharge(c);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( !Species_isSetCharge(c));
Species_free(c);
}
END_TEST
START_TEST (test_Species_setId3)
{
Species_t *c =
Species_create(2, 2);
int i = Species_setId(c, "cell");
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( Species_isSetId(c) );
fail_unless( !strcmp(Species_getId(c), "cell" ));
Species_free(c);
}
END_TEST
START_TEST (test_Species_setSpatialSizeUnits3)
{
Species_t *c =
Species_create(2, 2);
int i = Species_setSpatialSizeUnits(c, "mole");
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( !strcmp(Species_getSpatialSizeUnits(c), "mole") );
fail_unless( Species_isSetSpatialSizeUnits(c) );
Species_free(c);
}
END_TEST
START_TEST (test_ListOf_remove)
{
ListOf_t *lo = (ListOf_t*) ListOf_create(2,4);
SBase_t *sp = (SBase_t*)Species_create(2, 4);
fail_unless( ListOf_size(lo) == 0 );
ListOf_append(lo, sp);
ListOf_append(lo, sp);
ListOf_append(lo, sp);
ListOf_append(lo, sp);
ListOf_append(lo, sp);
fail_unless( ListOf_size(lo) == 5 );
SBase_t *elem;
elem = ListOf_remove(lo, 0);
Species_free((Species_t*) elem);
elem = ListOf_remove(lo, 0);
Species_free((Species_t*) elem);
elem = ListOf_remove(lo, 0);
Species_free((Species_t*) elem);
elem = ListOf_remove(lo, 0);
Species_free((Species_t*) elem);
elem = ListOf_remove(lo, 0);
Species_free((Species_t*) elem);
fail_unless( ListOf_size(lo) == 0 );
ListOf_append(lo, sp);
ListOf_append(lo, sp);
ListOf_append(lo, sp);
ListOf_append(lo, sp);
ListOf_appendAndOwn(lo, sp);
fail_unless( ListOf_size(lo) == 5 );
ListOf_free(lo);
}
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_Species_setName2)
{
Species_t *c =
Species_create(2, 2);
int i = Species_setName(c, "1cell");
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( Species_isSetName(c) );
i = Species_unsetName(c);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( !Species_isSetName(c) );
Species_free(c);
}
END_TEST
START_TEST (test_Species_setSpeciesType2)
{
Species_t *c =
Species_create(2, 2);
int i = Species_setSpeciesType(c, "1cell");
fail_unless( i == LIBSBML_INVALID_ATTRIBUTE_VALUE );
fail_unless( !Species_isSetSpeciesType(c) );
i = Species_unsetSpeciesType(c);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( !Species_isSetSpeciesType(c) );
Species_free(c);
}
END_TEST
START_TEST (test_Species_setHasOnlySubstanceUnits2)
{
Species_t *c =
Species_create(2, 2);
int i = Species_setHasOnlySubstanceUnits(c, 0);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( Species_getHasOnlySubstanceUnits(c) == 0 );
i = Species_setHasOnlySubstanceUnits(c, 1);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( Species_getHasOnlySubstanceUnits(c) == 1 );
Species_free(c);
}
END_TEST
START_TEST (test_Species_setInitialAmount2)
{
Species_t *c =
Species_create(2, 2);
int i = Species_setInitialAmount(c, 4);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( Species_getInitialAmount(c) == 4.0 );
fail_unless( Species_isSetInitialAmount(c));
i = Species_unsetInitialAmount(c);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( !Species_isSetInitialAmount(c));
Species_free(c);
}
END_TEST
START_TEST (test_Reaction_addModifierBySpecies)
{
Species_t *s = Species_create(2, 4);
Species_setId(s, "s");
Reaction_addModifierBySpecies(R, s, "sr");
fail_unless( Reaction_getNumReactants(R) == 0 );
fail_unless( Reaction_getNumProducts (R) == 0 );
fail_unless( Reaction_getNumModifiers(R) == 1 );
SpeciesReference_t *sr = Reaction_getModifier(R, 0);
fail_unless(!strcmp(SpeciesReference_getSpecies(sr), "s"));
fail_unless(!strcmp(SpeciesReference_getId(sr), "sr"));
fail_unless(Reaction_addModifierBySpecies(R, s, "sr") == LIBSBML_DUPLICATE_OBJECT_ID);
fail_unless( Reaction_getNumModifiers (R) == 1 );
Species_free(s);
}
static Species_t *
rsbml_build_doc_species(SEXP r_species)
{
Species_t * species;
species = Species_create();
rsbml_build_doc_s_base((SBase_t *)species, r_species);
SET_ATTR(Species, species, Id, id, STRING);
SET_ATTR(Species, species, Name, name, STRING);
SET_ATTR(Species, species, InitialConcentration, initialConcentration, REAL);
SET_ATTR(Species, species, InitialAmount, initialAmount, REAL);
SET_ATTR(Species, species, SubstanceUnits, substanceUnits, STRING);
SET_ATTR(Species, species, SpatialSizeUnits, spatialSizeUnits, STRING);
SET_ATTR(Species, species, Units, units, STRING);
SET_ATTR(Species, species, HasOnlySubstanceUnits, hasOnlySubstanceUnits, LOGICAL);
SET_ATTR(Species, species, BoundaryCondition, boundaryCondition, LOGICAL);
SET_ATTR(Species, species, Charge, charge, INTEGER);
SET_ATTR(Species, species, Constant, constant, LOGICAL);
return species;
}
