END_TEST
START_TEST (test_UnitDefinition_setId)
{
char *id = "mmls";
UnitDefinition_setId(UD, id);
fail_unless( !strcmp(UnitDefinition_getId(UD), id) );
fail_unless( UnitDefinition_isSetId(UD) );
if (UnitDefinition_getId(UD) == id)
{
fail("UnitDefinition_setId(...) did not make a copy of string.");
}
/* Reflexive case (pathological) */
UnitDefinition_setId(UD, UnitDefinition_getId(UD));
fail_unless( !strcmp(UnitDefinition_getId(UD), id) );
UnitDefinition_setId(UD, NULL);
fail_unless( !UnitDefinition_isSetId(UD) );
if (UnitDefinition_getId(UD) != NULL)
{
fail("UnitDefinition_setId(R, NULL) did not clear string.");
}
}
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_UnitDefinition_createWith)
//{
// UnitDefinition_t *ud = UnitDefinition_createWith("mmls", "");
//
//
// fail_unless( SBase_getTypeCode ((SBase_t *) ud) == SBML_UNIT_DEFINITION );
// fail_unless( SBase_getMetaId ((SBase_t *) ud) == NULL );
// fail_unless( SBase_getNotes ((SBase_t *) ud) == NULL );
// fail_unless( SBase_getAnnotation((SBase_t *) ud) == NULL );
//
// fail_unless( UnitDefinition_getName(ud) == NULL );
//
// fail_unless( !strcmp(UnitDefinition_getId(ud), "mmls") );
// fail_unless(UnitDefinition_isSetId(ud));
//
// fail_unless(UnitDefinition_getNumUnits(ud) == 0);
//
// UnitDefinition_free(ud);
//}
//END_TEST
START_TEST (test_UnitDefinition_createWithName)
{
UnitDefinition_t *ud = UnitDefinition_create(2, 4);
UnitDefinition_setName(ud, "mmol_per_liter_per_sec");
fail_unless( SBase_getTypeCode ((SBase_t *) ud) == SBML_UNIT_DEFINITION );
fail_unless( SBase_getMetaId ((SBase_t *) ud) == NULL );
fail_unless( SBase_getNotes ((SBase_t *) ud) == NULL );
fail_unless( SBase_getAnnotation((SBase_t *) ud) == NULL );
fail_unless( UnitDefinition_getId(ud) == NULL );
fail_unless( !strcmp(UnitDefinition_getName(ud), "mmol_per_liter_per_sec"),
NULL );
fail_unless(UnitDefinition_isSetName(ud));
fail_unless(UnitDefinition_getNumUnits(ud) == 0);
UnitDefinition_free(ud);
}
END_TEST
START_TEST (test_SBMLConvert_convertFromL3_modelUnits)
{
UnitDefinition_t *ud;
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(3, 1);
Model_t *m = SBMLDocument_createModel(d);
Model_setVolumeUnits(m, "litre");
fail_unless(Model_getNumUnitDefinitions(m) == 0);
fail_unless(SBMLDocument_setLevelAndVersionNonStrict(d, 1, 2) == 1);
m = SBMLDocument_getModel(d);
fail_unless(Model_getNumUnitDefinitions(m) == 1);
ud = Model_getUnitDefinition(m, 0);
fail_unless(!strcmp(UnitDefinition_getId(ud), "volume"));
fail_unless(UnitDefinition_getNumUnits(ud) == 1);
fail_unless(Unit_getKind(UnitDefinition_getUnit(ud, 0)) == UNIT_KIND_LITRE );
}
int
main (int argc, char* argv[])
{
unsigned int i,j,errors;
const char* filename;
SBMLDocument_t* document;
Model_t* m;
if (argc != 2)
{
printf("\nUsage: printNotes filename\n\n");
return 1;
}
filename = argv[1];
document = readSBML(filename);
errors = SBMLDocument_getNumErrors( document);
printf("\n%s\n\n", filename);
if(errors > 0)
{
SBMLDocument_printErrors(document, stderr);
SBMLDocument_free(document);
return errors;
}
/* Model */
m = SBMLDocument_getModel(document);
printNotes((SBase_t*)m, Model_getId(m));
for(i=0; i < Model_getNumReactions(m); i++)
{
Reaction_t* re = Model_getReaction( m, i);
printNotes((SBase_t*)re, Reaction_getId(re));
/* SpeciesReference (Reactant) */
for(j=0; j < Reaction_getNumReactants( re); j++)
{
SpeciesReference_t* rt = Reaction_getReactant(re, j);
if (SBase_isSetNotes((SBase_t*) rt)) printf(" ");
printNotes((SBase_t*)rt, SpeciesReference_getSpecies( rt ) );
}
/* SpeciesReference (Product) */
for(j=0; j < Reaction_getNumProducts( re ); j++)
{
SpeciesReference_t* rt = Reaction_getProduct( re, j);
if (SBase_isSetNotes((SBase_t*) rt)) printf(" ");
printNotes((SBase_t*)rt, SpeciesReference_getSpecies( rt ) );
}
/* ModifierSpeciesReference (Modifiers) */
for(j=0; j < Reaction_getNumModifiers( re ); j++)
{
SpeciesReference_t* md = Reaction_getModifier(re, j);
if (SBase_isSetNotes((SBase_t*) md)) printf(" ");
printNotes((SBase_t*)md, SpeciesReference_getSpecies( md ) );
}
/* KineticLaw */
if(Reaction_isSetKineticLaw( re ))
{
KineticLaw_t* kl = Reaction_getKineticLaw( re );
if (SBase_isSetNotes((SBase_t*) kl)) printf(" ");
printNotes((SBase_t*)kl, "");
/* Parameter */
for(j=0; j < KineticLaw_getNumParameters( kl ); j++)
{
Parameter_t* pa = KineticLaw_getParameter( kl, j);
if (SBase_isSetNotes((SBase_t*) pa)) printf(" ");
printNotes((SBase_t*)pa, Parameter_getId(pa));
}
}
}
/* Species */
for(i=0; i < Model_getNumSpecies(m); i++)
{
Species_t* sp = Model_getSpecies(m, i);
printNotes((SBase_t*)sp, Species_getId(sp));
}
/* Compartments */
for(i=0; i < Model_getNumCompartments( m ); i++)
{
Compartment_t* sp = Model_getCompartment(m, i);
printNotes((SBase_t*)sp, Compartment_getId(sp));
}
/* FunctionDefinition */
for(i=0; i < Model_getNumFunctionDefinitions(m); i++)
{
FunctionDefinition_t* sp = Model_getFunctionDefinition(m, i);
printNotes((SBase_t*)sp, FunctionDefinition_getId(sp));
}
/* UnitDefinition */
for(i=0; i < Model_getNumUnitDefinitions(m); i++)
{
UnitDefinition_t* sp = Model_getUnitDefinition( m, i);
printNotes((SBase_t*)sp, UnitDefinition_getId(sp));
}
/* Parameter */
for(i=0; i < Model_getNumParameters( m ); i++)
{
Parameter_t* sp = Model_getParameter( m, i);
printNotes((SBase_t*)sp, Parameter_getId(sp));
}
/* Rule */
for(i=0; i < Model_getNumReactions( m ); i++)
{
Rule_t* sp = Model_getRule(m, i);
printNotes((SBase_t*)sp, "");
}
/* InitialAssignment */
for(i=0; i < Model_getNumInitialAssignments(m); i++)
{
InitialAssignment_t* sp = Model_getInitialAssignment(m, i);
printNotes((SBase_t*)sp, "");
}
/* Event */
for(i=0; i < Model_getNumEvents(m); i++)
{
Event_t* sp = Model_getEvent(m, i);
printNotes((SBase_t*)sp, Event_getId(sp));
/* Trigger */
if(Event_isSetTrigger( sp ))
{
Trigger_t* tg = Event_getTrigger(sp);
if (SBase_isSetNotes( (SBase_t*) tg)) printf( " " );
printNotes((SBase_t*)tg, "");
}
/* Delay */
if(Event_isSetDelay(sp))
{
Delay_t* dl = Event_getDelay(sp);
if (SBase_isSetNotes( (SBase_t*) dl)) printf( " " );
printNotes((SBase_t*) dl, "");
}
/* EventAssignment */
for(j=0; j < Event_getNumEventAssignments(sp); j++)
{
EventAssignment_t* ea = Event_getEventAssignment(sp, j);
if (SBase_isSetNotes( (SBase_t*) ea)) printf( " " );
printNotes((SBase_t*)ea, "");
}
}
/* SpeciesType */
for(i=0; i < Model_getNumSpeciesTypes(m); i++)
{
SpeciesType_t* sp = Model_getSpeciesType(m, i);
printNotes((SBase_t*)sp, SpeciesType_getId(sp));
}
/* Constraints */
for(i=0; i < Model_getNumConstraints(m); i++)
{
Constraint_t* sp = Model_getConstraint(m, i);
printNotes((SBase_t*)sp, "");
}
SBMLDocument_free( document );
return errors;
}
