Examples with VCUnitSystem cbit.vcell.units.VCUnitSystem used on opensource projects

Example 6 with VCUnitSystem

use of cbit.vcell.units.VCUnitSystem in project vcell by virtualcell.

the class SBMLUnitTranslatorTest method testSBMLtoVCell.

@Test
public void testSBMLtoVCell() throws XMLStreamException, IOException, SbmlException {
    File[] sbmlFiles = getBiomodelsCuratedSBMLFiles();
    // };
    for (File sbmlFile : sbmlFiles) {
        if (sbmlFile.getName().equals("BIOMD0000000539.xml")) {
            System.err.println("skipping this model, seems like a bug in jsbml  RenderParser.processEndDocument() ... line 403 ... wrong constant for extension name");
            continue;
        }
        SBMLDocument doc = SBMLReader.read(sbmlFile);
        BioModel bioModel = new BioModel(null);
        VCUnitSystem unitSystem = bioModel.getModel().getUnitSystem();
        Model sbmlModel = doc.getModel();
        ListOf<UnitDefinition> listOfUnitDefinitions = sbmlModel.getListOfUnitDefinitions();
        for (UnitDefinition sbmlUnitDef : listOfUnitDefinitions) {
            VCUnitDefinition vcUnit = SBMLUnitTranslator.getVCUnitDefinition(sbmlUnitDef, unitSystem);
            UnitDefinition new_sbmlUnitDef = SBMLUnitTranslator.getSBMLUnitDefinition(vcUnit, 3, 1, unitSystem);
            VCUnitDefinition new_vcUnit = SBMLUnitTranslator.getVCUnitDefinition(new_sbmlUnitDef, unitSystem);
            if (!vcUnit.getSymbol().equals(new_vcUnit.getSymbol())) {
                System.err.println("orig vcUnit '" + vcUnit.getSymbol() + "' doesn't match new vcUnit '" + new_vcUnit.getSymbol() + "'");
            }
            // System.out.println("sbmlUnit = "+sbmlUnitDef.toString()+", vcUnit = "+vcUnit.getSymbol());
            System.out.println("sbmlUnit(" + sbmlUnitDef.getClass().getName() + ", builtin=" + sbmlUnitDef.isVariantOfSubstance() + ") = " + sbmlUnitDef.toString() + ", id=" + sbmlUnitDef.getId() + ",  name=" + sbmlUnitDef.getName() + ",   vcUnit = " + vcUnit.getSymbol());
            if (sbmlUnitDef.getNumUnits() > 1) {
                System.out.println("vcUnit = " + vcUnit.getSymbol());
                for (Unit unit : sbmlUnitDef.getListOfUnits()) {
                    try {
                        // VCUnitDefinition vcUnit = unitSystem.getInstance(unit.getKind().getName());
                        System.out.println("    vcUnit = " + unit);
                    } catch (Exception e) {
                        e.printStackTrace();
                    }
                }
                System.out.println("found bigger unit, " + sbmlUnitDef);
            }
        }
        if (sbmlFile == sbmlFiles[0]) {
            System.out.println("sbml length unit = " + sbmlModel.getLengthUnitsInstance() + ", idref=" + sbmlModel.getLengthUnits());
            System.out.println("sbml area unit = " + sbmlModel.getAreaUnitsInstance() + ", idref=" + sbmlModel.getAreaUnits());
            System.out.println("sbml volume unit = " + sbmlModel.getVolumeUnitsInstance() + ", idref=" + sbmlModel.getVolumeUnits());
            System.out.println("sbml time unit = " + sbmlModel.getTimeUnitsInstance() + ", idref=" + sbmlModel.getTimeUnits());
            System.out.println("sbml extent unit = " + sbmlModel.getExtentUnitsInstance() + ", idref=" + sbmlModel.getExtentUnits());
            System.out.println("sbml substance unit = " + sbmlModel.getSubstanceUnitsInstance() + ", idref=" + sbmlModel.getSubstanceUnits());
            for (UnitDefinition sbmlUnitDef : sbmlModel.getListOfPredefinedUnitDefinitions()) {
                if (sbmlUnitDef.getNumUnits() == 1 && sbmlUnitDef.getUnit(0).isAvogadro()) {
                    continue;
                }
                if (sbmlUnitDef.getNumUnits() == 1 && sbmlUnitDef.getUnit(0).isKatal()) {
                    continue;
                }
                VCUnitDefinition vcUnit = SBMLUnitTranslator.getVCUnitDefinition(sbmlUnitDef, unitSystem);
                // System.out.println("sbmlUnit = "+sbmlUnitDef.toString()+", vcUnit = "+vcUnit.getSymbol());
                System.out.println("sbmlUnit(" + sbmlUnitDef.getClass().getName() + ", builtin=" + sbmlUnitDef.isVariantOfSubstance() + ") = " + sbmlUnitDef.toString() + ", id=" + sbmlUnitDef.getId() + ",  name=" + sbmlUnitDef.getName() + ",   vcUnit = " + vcUnit.getSymbol());
            // for (Unit unit : sbmlUnitDef.getListOfUnits()){
            // try {
            // VCUnitDefinition vcUnit = unitSystem.getInstance(unit.getKind().getName());
            // System.out.println("    vcUnit = "+vcUnit.getSymbol());
            // }catch (Exception e){
            // e.printStackTrace();
            // }
            // }
            }
        }
    }
}