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");
}
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");
}
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_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 */
}
