END_TEST
START_TEST(test_FbcExtension_read_and_validate_chemicals)
{
FbcPkgNamespaces *ns = new FbcPkgNamespaces();
SBMLDocument*doc = new SBMLDocument(ns);
doc->setPackageRequired("fbc", false);
Model* model = doc->createModel();
Compartment* comp = model->createCompartment();
comp->initDefaults();
comp->setId("comp");
comp->setSize(1);
Species *s = model->createSpecies();
s->initDefaults();
s->setId("s1");
s->setCompartment("comp");
s->setInitialAmount(1);
FbcSpeciesPlugin* splugin = static_cast<FbcSpeciesPlugin*>(s->getPlugin("fbc"));
fail_unless(splugin != NULL);
// valid
splugin->setChemicalFormula("H2O");
doc->checkInternalConsistency();
fail_unless(!doc->getErrorLog()->contains(FbcSpeciesFormulaMustBeString));
// valid
doc->getErrorLog()->clearLog();
splugin->setChemicalFormula("HO");
doc->checkInternalConsistency();
fail_unless(!doc->getErrorLog()->contains(FbcSpeciesFormulaMustBeString));
// valid
doc->getErrorLog()->clearLog();
splugin->setChemicalFormula("");
doc->checkInternalConsistency();
fail_unless(!doc->getErrorLog()->contains(FbcSpeciesFormulaMustBeString));
// invalid
doc->getErrorLog()->clearLog();
splugin->setChemicalFormula("hO");
doc->checkInternalConsistency();
fail_unless(doc->getErrorLog()->contains(FbcSpeciesFormulaMustBeString));
// invalid
doc->getErrorLog()->clearLog();
splugin->setChemicalFormula("h1O");
doc->checkInternalConsistency();
fail_unless(doc->getErrorLog()->contains(FbcSpeciesFormulaMustBeString));
// invalid
doc->getErrorLog()->clearLog();
splugin->setChemicalFormula("1hO");
doc->checkInternalConsistency();
fail_unless(doc->getErrorLog()->contains(FbcSpeciesFormulaMustBeString));
// invalid
doc->getErrorLog()->clearLog();
splugin->setChemicalFormula("hO");
doc->checkInternalConsistency();
fail_unless(doc->getErrorLog()->contains(FbcSpeciesFormulaMustBeString));
// invalid
doc->getErrorLog()->clearLog();
splugin->setChemicalFormula("_hO");
doc->checkInternalConsistency();
fail_unless(doc->getErrorLog()->contains(FbcSpeciesFormulaMustBeString));
// invalid
doc->getErrorLog()->clearLog();
splugin->setChemicalFormula("H 2 O");
doc->checkInternalConsistency();
fail_unless(doc->getErrorLog()->contains(FbcSpeciesFormulaMustBeString));
// invalid
doc->getErrorLog()->clearLog();
splugin->setChemicalFormula("H*_)(++2 O");
doc->checkInternalConsistency();
fail_unless(doc->getErrorLog()->contains(FbcSpeciesFormulaMustBeString));
delete doc;
}
END_TEST
START_TEST(test_FbcExtension_read_L3V1V1_with_wonky_chemicals)
{
const char* modelString = "<?xml version='1.0' encoding='UTF-8'?>"
"<sbml xmlns:html='http://www.w3.org/1999/xhtml' xmlns='http://www.sbml.org/sbml/level3/version1/core' xmlns:fbc='http://www.sbml.org/sbml/level3/version1/fbc/version1' level='3' version='1' fbc:required='false'>"
" <model metaid='xxx' id='yyy' timeUnits='dimensionless'>"
" <listOfCompartments>"
" <compartment id='Internal_Species' name='Internal_Species' spatialDimensions='3' size='1' constant='false'/>"
" <compartment id='External_Species' name='External_Species' spatialDimensions='3' size='1' constant='false'/>"
" </listOfCompartments>"
" <listOfSpecies>"
" <species metaid='meta_B1' id='B1' name='Protein component' compartment='Internal_Species' initialConcentration='0' hasOnlySubstanceUnits='false' boundaryCondition='false' constant='false' fbc:chemicalFormula='PROTEIN COMPONENT'>"
" <notes>"
" <html:p>chemFormula: Protein component</html:p>"
" </notes>"
" <annotation>"
" <listOfKeyValueData xmlns='http://pysces.sourceforge.net/KeyValueData'>"
" <data id='chemFormula' type='string' value='Protein component'/>"
" </listOfKeyValueData>"
" </annotation>"
" </species>"
" <species metaid='meta_B2' id='B2' name='DNA component' compartment='Internal_Species' initialConcentration='0' hasOnlySubstanceUnits='false' boundaryCondition='false' constant='false' fbc:chemicalFormula='DNA COMPONENT'>"
" <notes>"
" <html:p>chemFormula: DNA component</html:p>"
" </notes>"
" <annotation>"
" <listOfKeyValueData xmlns='http://pysces.sourceforge.net/KeyValueData'>"
" <data id='chemFormula' type='string' value='DNA component'/>"
" </listOfKeyValueData>"
" </annotation>"
" </species>"
" </listOfSpecies>"
" <listOfReactions>"
" <reaction metaid='meta_R00192' id='R00192' name='R106' reversible='false' fast='false'>"
" <notes>"
" <html:p>EC Number: 3.3.1.1</html:p>"
" <html:p>GENE ASSOCIATION: sll1234</html:p>"
" </notes>"
" <annotation>"
" <listOfKeyValueData xmlns='http://pysces.sourceforge.net/KeyValueData'>"
" <data id='EC_Number' type='string' value='3.3.1.1'/>"
" <data id='GENE_ASSOCIATION' type='string' value='sll1234'/>"
" </listOfKeyValueData>"
" </annotation>"
" <listOfReactants>"
" <speciesReference species='B1' stoichiometry='1' constant='true'/>"
" </listOfReactants>"
" <listOfProducts>"
" <speciesReference species='B2' stoichiometry='1' constant='true'/>"
" </listOfProducts>"
" </reaction>"
" </listOfReactions>"
" <fbc:listOfFluxBounds>"
" <fbc:fluxBound fbc:reaction='R00192' fbc:operation='greaterEqual' fbc:value='0'/>"
" <fbc:fluxBound fbc:reaction='R00192' fbc:operation='lessEqual' fbc:value='999999'/> "
" </fbc:listOfFluxBounds>"
" <fbc:listOfObjectives fbc:activeObjective='obj'>"
" <fbc:objective fbc:id='obj' fbc:type='maximize'>"
" <fbc:listOfFluxObjectives>"
" <fbc:fluxObjective fbc:reaction='R00192' fbc:coefficient='1'/>"
" </fbc:listOfFluxObjectives>"
" </fbc:objective>"
" </fbc:listOfObjectives>"
" </model>"
"</sbml>";
SBMLDocument* doc = readSBMLFromString(modelString);
doc->checkConsistency();
fail_unless(doc->getErrorLog()->contains(FbcSpeciesFormulaMustBeString));
//convert to cobra just to test
ConversionProperties prop;
prop.addOption("convert fbc to cobra", true);
fail_unless(doc->convert(prop) == LIBSBML_OPERATION_SUCCESS);
// add species with notes
Species* testSpecies = doc->getModel()->createSpecies();
testSpecies->initDefaults();
testSpecies->setId("testSpecies");
testSpecies->setNotes(
"<body xmlns='http://www.w3.org/1999/xhtml'>"
" <p>FORMULA: Fe2S2X</p> "
" <p>CHARGE: -1</p> "
"</body> "
);
// convert it back
prop.addOption("convert cobra", true);
fail_unless(doc->convert(prop) == LIBSBML_OPERATION_SUCCESS);
// check the formula
Species* tested = doc->getModel()->getSpecies("testSpecies");
fail_unless(tested != NULL);
FbcSpeciesPlugin* fbcSpeciesPlugin = dynamic_cast<FbcSpeciesPlugin*>(tested->getPlugin("fbc"));
fail_unless(fbcSpeciesPlugin != NULL);
fail_unless(fbcSpeciesPlugin->getCharge() == -1);
fail_unless(fbcSpeciesPlugin->getChemicalFormula() == "Fe2S2X");
}