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; }