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_parseModel_basic)
{
doc = parseModel(EXAMPLES_FILENAME("basic.xml"), 0, 1);
ck_assert(doc != NULL);
model = SBMLDocument_getModel(doc);
ck_assert(model != NULL);
ck_assert(Model_getNumFunctionDefinitions(model) == 0);
ck_assert(Model_getNumUnitDefinitions(model) == 0);
ck_assert(Model_getNumCompartmentTypes(model) == 0);
ck_assert(Model_getNumSpeciesTypes(model) == 0);
ck_assert(Model_getNumCompartments(model) == 1);
ck_assert(Model_getNumSpecies(model) == 2);
ck_assert(Model_getNumSpeciesWithBoundaryCondition(model) == 0);
ck_assert(Model_getNumParameters(model) == 1);
ck_assert(Model_getNumInitialAssignments(model) == 0);
ck_assert(Model_getNumRules(model) == 0);
ck_assert(Model_getNumConstraints(model) == 0);
ck_assert(Model_getNumReactions(model) == 2);
ck_assert(Model_getNumEvents(model) == 0);
CHECK_PARAMETER(model, 0, "k_1");
CHECK_REACTION(model, 0, "R1", "k_1 * S1");
CHECK_REACTION(model, 1, "R2", "k_2 * S2");
}
END_TEST
START_TEST(test_parseModel_repressilator)
{
doc = parseModel(EXAMPLES_FILENAME("repressilator.xml"), 0, 1);
ck_assert(doc != NULL);
model = SBMLDocument_getModel(doc);
ck_assert(model != NULL);
ck_assert(Model_getNumFunctionDefinitions(model) == 0);
ck_assert(Model_getNumUnitDefinitions(model) == 0);
ck_assert(Model_getNumCompartmentTypes(model) == 0);
ck_assert(Model_getNumSpeciesTypes(model) == 0);
ck_assert(Model_getNumCompartments(model) == 1);
ck_assert(Model_getNumSpecies(model) == 6);
ck_assert(Model_getNumSpeciesWithBoundaryCondition(model) == 0);
ck_assert(Model_getNumParameters(model) == 3);
ck_assert(Model_getNumInitialAssignments(model) == 0);
ck_assert(Model_getNumRules(model) == 6);
ck_assert(Model_getNumConstraints(model) == 0);
ck_assert(Model_getNumReactions(model) == 0);
ck_assert(Model_getNumEvents(model) == 0);
CHECK_PARAMETER(model, 0, "alpha");
CHECK_PARAMETER(model, 1, "beta");
CHECK_PARAMETER(model, 2, "rho");
CHECK_RULE(model, 0, "beta * (y1 - x1)");
CHECK_RULE(model, 1, "beta * (y2 - x2)");
CHECK_RULE(model, 2, "beta * (y3 - x3)");
CHECK_RULE(model, 3, "alpha * x1 / (1 + x1 + rho * x3) - y1");
CHECK_RULE(model, 4, "alpha * x2 / (1 + x2 + rho * x1) - y2");
CHECK_RULE(model, 5, "alpha * x3 / (1 + x3 + rho * x2) - y3");
}
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_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 );
}
END_TEST
START_TEST(test_parseModel_huang96)
{
doc = parseModel(EXAMPLES_FILENAME("huang96.xml"), 0, 1);
ck_assert(doc != NULL);
model = SBMLDocument_getModel(doc);
ck_assert(model != NULL);
ck_assert(Model_getNumFunctionDefinitions(model) == 0);
ck_assert(Model_getNumUnitDefinitions(model) == 0);
ck_assert(Model_getNumCompartmentTypes(model) == 0);
ck_assert(Model_getNumSpeciesTypes(model) == 0);
ck_assert(Model_getNumCompartments(model) == 1);
ck_assert(Model_getNumSpecies(model) == 22);
ck_assert(Model_getNumSpeciesWithBoundaryCondition(model) == 0);
ck_assert(Model_getNumParameters(model) == 0);
ck_assert(Model_getNumInitialAssignments(model) == 0);
ck_assert(Model_getNumRules(model) == 0);
ck_assert(Model_getNumConstraints(model) == 0);
ck_assert(Model_getNumReactions(model) == 20);
ck_assert(Model_getNumEvents(model) == 0);
CHECK_REACTION(model, 0, "r1a", "a1 * E1 * KKK - d1 * E1_KKK");
CHECK_REACTION(model, 1, "r1b", "k2 * E1_KKK");
CHECK_REACTION(model, 2, "r2a", "a2 * E2 * P_KKK - d2 * E2_P_KKK");
CHECK_REACTION(model, 3, "r2b", "k2 * E2_P_KKK");
CHECK_REACTION(model, 4, "r3a", "a3 * KK * P_KKK - d3 * P_KKK_KK");
CHECK_REACTION(model, 5, "r3b", "k3 * P_KKK_KK");
CHECK_REACTION(model, 6, "r4a", "a4 * P_KK * KKPase - d4 * KKPase_P_KK");
CHECK_REACTION(model, 7, "r4b", "k4 * KKPase_P_KK");
CHECK_REACTION(model, 8, "r5a", "a5 * P_KK * P_KKK - d5 * P_KKK_P_KK");
CHECK_REACTION(model, 9, "r5b", "k5 * P_KKK_P_KK");
CHECK_REACTION(model, 10, "r6a", "a6 * PP_KK * KKPase - d6 * KKPase_PP_KK");
CHECK_REACTION(model, 11, "r6b", "k6 * KKPase_PP_KK");
CHECK_REACTION(model, 12, "r7a", "a7 * K * PP_KK - d7 * PP_KK_K");
CHECK_REACTION(model, 13, "r7b", "k7 * PP_KK_K");
CHECK_REACTION(model, 14, "r8a", "a8 * P_K * KPase - d8 * KPase_P_K");
CHECK_REACTION(model, 15, "r8b", "k8 * KPase_P_K");
CHECK_REACTION(model, 16, "r9a", "a9 * P_K * PP_KK - d9 * PP_KK_P_K");
CHECK_REACTION(model, 17, "r9b", "k9 * PP_KK_P_K");
CHECK_REACTION(model, 18, "r10a", "a10 * PP_K * KPase - d10 * KPase_PP_K");
CHECK_REACTION(model, 19, "r10b", "k10 * KPase_PP_K");
/* TODO */
}
END_TEST
START_TEST(test_parseModel_events_1_event_1_assignment_l2)
{
doc = parseModel(EXAMPLES_FILENAME("events-1-event-1-assignment-l2.xml"), 0, 1);
ck_assert(doc != NULL);
model = SBMLDocument_getModel(doc);
ck_assert(model != NULL);
ck_assert(Model_getNumFunctionDefinitions(model) == 0);
ck_assert(Model_getNumUnitDefinitions(model) == 0);
ck_assert(Model_getNumCompartmentTypes(model) == 0);
ck_assert(Model_getNumSpeciesTypes(model) == 0);
ck_assert(Model_getNumCompartments(model) == 1);
ck_assert(Model_getNumSpecies(model) == 2);
ck_assert(Model_getNumSpeciesWithBoundaryCondition(model) == 0);
ck_assert(Model_getNumParameters(model) == 0);
ck_assert(Model_getNumInitialAssignments(model) == 0);
ck_assert(Model_getNumRules(model) == 0);
ck_assert(Model_getNumConstraints(model) == 0);
ck_assert(Model_getNumReactions(model) == 1);
ck_assert(Model_getNumEvents(model) == 1);
CHECK_REACTION(model, 0, "R", "S1");
/* TODO */
}
int
main (int argc, char* argv[])
{
unsigned int i,j,errors;
const char* filename = argv[1];
SBMLDocument_t* document;
Model_t* m;
if (argc != 3)
{
printf("\nUsage: unsetNotes <input-filename> <output-filename>\n");
return 1;
}
filename = argv[1];
document = readSBML(filename);
errors = SBMLDocument_getNumErrors(document);
if(errors > 0)
{
SBMLDocument_printErrors(document, stderr);
SBMLDocument_free(document);
return errors;
}
m = SBMLDocument_getModel( document );
SBase_unsetNotes((SBase_t*)m);
for(i=0; i < Model_getNumReactions(m); i++)
{
Reaction_t* re = Model_getReaction(m, i);
SBase_unsetNotes((SBase_t*)re);
for(j=0; j < Reaction_getNumReactants(re); j++)
{
SpeciesReference_t* rt = Reaction_getReactant(re,j);
SBase_unsetNotes((SBase_t*)rt);
}
for(j=0; j < Reaction_getNumProducts(re); j++)
{
SpeciesReference_t* rt = Reaction_getProduct(re,j);
SBase_unsetNotes((SBase_t*)rt);
}
for(j=0; j < Reaction_getNumModifiers(re); j++)
{
SpeciesReference_t* md = Reaction_getModifier(re,j);
SBase_unsetNotes((SBase_t*)md);
}
if(Reaction_isSetKineticLaw(re))
{
KineticLaw_t* kl = Reaction_getKineticLaw(re);
SBase_unsetNotes((SBase_t*)kl);
for(j=0; j < KineticLaw_getNumParameters(kl); j++)
{
Parameter_t* pa = KineticLaw_getParameter(kl, j);
SBase_unsetNotes((SBase_t*)pa);
}
}
}
for(i=0; i < Model_getNumSpecies(m); i++)
{
Species_t* sp = Model_getSpecies(m, i);
SBase_unsetNotes((SBase_t*)sp);
}
for(i=0; i < Model_getNumCompartments(m); i++)
{
Compartment_t* sp = Model_getCompartment(m,i);
SBase_unsetNotes((SBase_t*)sp);
}
for(i=0; i < Model_getNumFunctionDefinitions(m); i++)
{
FunctionDefinition_t* sp = Model_getFunctionDefinition(m,i);
SBase_unsetNotes((SBase_t*)sp);
}
for(i=0; i < Model_getNumUnitDefinitions(m); i++)
{
UnitDefinition_t* sp = Model_getUnitDefinition(m, i);
SBase_unsetNotes((SBase_t*)sp);
}
for(i=0; i < Model_getNumParameters(m); i++)
{
Parameter_t* sp = Model_getParameter(m, i);
SBase_unsetNotes((SBase_t*)sp);
}
for(i=0; i < Model_getNumRules(m); i++)
{
Rule_t* sp = Model_getRule(m, i);
SBase_unsetNotes((SBase_t*)sp);
}
for(i=0; i < Model_getNumInitialAssignments(m); i++)
{
InitialAssignment_t* sp = Model_getInitialAssignment(m, i);
SBase_unsetNotes((SBase_t*)sp);
}
for(i=0; i < Model_getNumEvents(m); i++)
{
Event_t* sp = Model_getEvent(m, i);
SBase_unsetNotes((SBase_t*)sp);
for(j=0; j < Event_getNumEventAssignments(sp); j++)
{
EventAssignment_t* ea = Event_getEventAssignment(sp, j);
SBase_unsetNotes((SBase_t*)ea);
}
}
for(i=0; i < Model_getNumSpeciesTypes(m); i++)
{
SpeciesType_t* sp = Model_getSpeciesType(m, i);
SBase_unsetNotes((SBase_t*)sp);
}
for(i=0; i < Model_getNumConstraints(m); i++)
{
Constraint_t* sp = Model_getConstraint(m, i);
SBase_unsetNotes((SBase_t*)sp);
}
writeSBML(document, argv[2]);
SBMLDocument_free(document);
return errors;
}
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;
}
