C# SBMLDocument.getErrorLog方法代码示例

 public void test_internal_consistency_check_20307()
 {
     SBMLDocument d = new SBMLDocument(3,1);
       long errors;
       Model m = d.createModel();
       FunctionDefinition fd = m.createFunctionDefinition();
       ASTNode ast = libsbml.parseFormula("lambda(x, 2*x)");
       fd.setMath(ast);
       errors = d.checkInternalConsistency();
       assertTrue( errors == 1 );
       assertTrue( d.getError(0).getErrorId() == 20307 );
       fd.setId("fd");
       d.getErrorLog().clearLog();
       errors = d.checkInternalConsistency();
       assertTrue( errors == 0 );
       d = null;
 }

 public void test_internal_consistency_check_20421()
 {
     SBMLDocument d = new SBMLDocument(3,1);
       long errors;
       Model m = d.createModel();
       UnitDefinition ud = m.createUnitDefinition();
       ud.setId("ud");
       Unit u = ud.createUnit();
       errors = d.checkInternalConsistency();
       assertTrue( errors == 4 );
       assertTrue( d.getError(0).getErrorId() == 20421 );
       assertTrue( d.getError(1).getErrorId() == 20421 );
       assertTrue( d.getError(2).getErrorId() == 20421 );
       assertTrue( d.getError(3).getErrorId() == 20421 );
       u.setKind(libsbml.UNIT_KIND_MOLE);
       d.getErrorLog().clearLog();
       errors = d.checkInternalConsistency();
       assertTrue( errors == 3 );
       assertTrue( d.getError(0).getErrorId() == 20421 );
       assertTrue( d.getError(1).getErrorId() == 20421 );
       assertTrue( d.getError(2).getErrorId() == 20421 );
       u.setExponent(1.0);
       d.getErrorLog().clearLog();
       errors = d.checkInternalConsistency();
       assertTrue( errors == 2 );
       assertTrue( d.getError(0).getErrorId() == 20421 );
       assertTrue( d.getError(1).getErrorId() == 20421 );
       u.setScale(0);
       d.getErrorLog().clearLog();
       errors = d.checkInternalConsistency();
       assertTrue( errors == 1 );
       assertTrue( d.getError(0).getErrorId() == 20421 );
       u.setMultiplier(1.0);
       d.getErrorLog().clearLog();
       errors = d.checkInternalConsistency();
       assertTrue( errors == 0 );
       d = null;
 }

 public void test_internal_consistency_check_20419()
 {
     SBMLDocument d = new SBMLDocument(3,1);
       long errors;
       Model m = d.createModel();
       UnitDefinition ud = m.createUnitDefinition();
       errors = d.checkInternalConsistency();
       assertTrue( errors == 1 );
       assertTrue( d.getError(0).getErrorId() == 20419 );
       ud.setId("ud");
       d.getErrorLog().clearLog();
       errors = d.checkInternalConsistency();
       assertTrue( errors == 0 );
       d = null;
 }

 public void test_internal_consistency_check_21231()
 {
     SBMLDocument d = new SBMLDocument(3,1);
       long errors;
       Model m = d.createModel();
       Event r = m.createEvent();
       r.setUseValuesFromTriggerTime(true);
       ASTNode ast = libsbml.parseFormula("2*x");
       Trigger t = r.createTrigger();
       t.setMath(ast);
       t.setPersistent(true);
       t.setInitialValue(false);
       EventAssignment ea = r.createEventAssignment();
       ea.setVariable("ea");
       ea.setMath(ast);
       Priority prior = r.createPriority();
       d.getErrorLog().clearLog();
       errors = d.checkInternalConsistency();
       assertTrue( errors == 1 );
       assertTrue( d.getError(0).getErrorId() == 21231 );
       prior.setMath(ast);
       d.getErrorLog().clearLog();
       errors = d.checkInternalConsistency();
       assertTrue( errors == 0 );
       d = null;
 }

 public void test_internal_consistency_check_21172()
 {
     SBMLDocument d = new SBMLDocument(3,1);
       long errors;
       Model m = d.createModel();
       Reaction r = m.createReaction();
       r.setId("r");
       r.setReversible(true);
       r.setFast(false);
       SpeciesReference sr = r.createReactant();
       sr.setSpecies("s");
       sr.setConstant(true);
       KineticLaw kl = r.createKineticLaw();
       ASTNode ast = libsbml.parseFormula("2*x");
       kl.setMath(ast);
       LocalParameter lp = kl.createLocalParameter();
       errors = d.checkInternalConsistency();
       assertTrue( errors == 1 );
       assertTrue( d.getError(0).getErrorId() == 21172 );
       lp.setId("pp");
       d.getErrorLog().clearLog();
       errors = d.checkInternalConsistency();
       assertTrue( errors == 0 );
       d = null;
 }

 public void test_internal_consistency_check_21007()
 {
     SBMLDocument d = new SBMLDocument(3,1);
       long errors;
       Model m = d.createModel();
       Constraint r = m.createConstraint();
       errors = d.checkInternalConsistency();
       assertTrue( errors == 1 );
       assertTrue( d.getError(0).getErrorId() == 21007 );
       ASTNode ast = libsbml.parseFormula("lambda(x, 2*x)");
       r.setMath(ast);
       d.getErrorLog().clearLog();
       errors = d.checkInternalConsistency();
       assertTrue( errors == 0 );
       d = null;
 }

//.........这里部分代码省略.........
            sr.setStoichiometry(1);
            sr.setSpecies("S");
            rxn.addReactant(sr);
            sr.setSpecies("D");
            rxn.addProduct(sr);

            mod1.addReaction(rxn);

            var mod1plug = (CompModelPlugin)(mod1.getPlugin("comp"));
            var port = new Port();
            port.setId("S_port");
            port.setIdRef("S");
            mod1plug.addPort(port);

            var port2 = mod1plug.createPort();
            port2.setId("D_port");
            port2.setIdRef("D");

            port.setId("comp_port");
            port.setIdRef("comp");
            mod1plug.addPort(port);

            port.setId("J0_port");
            port.setIdRef("J0");
            mod1plug.addPort(port);

            // create the Model
            var model = document.createModel();
            model.setId("complexified");

            // Set the submodels
            var mplugin = (CompModelPlugin)(model.getPlugin("comp"));
            var submod1 = mplugin.createSubmodel();
            submod1.setId("A");
            submod1.setModelRef("ExtMod1");
            var submod2 = mplugin.createSubmodel();
            submod2.setId("B");
            submod2.setModelRef("simple");
            var del = submod2.createDeletion();
            del.setPortRef("J0_port");

            // Synchronize the compartments
            var mcomp = model.createCompartment();
            mcomp.setSpatialDimensions(3);
            mcomp.setConstant(true);
            mcomp.setId("comp");
            mcomp.setSize(1L);
            var compartplug = (CompSBasePlugin)(mcomp.getPlugin("comp"));
            var re = new ReplacedElement();
            re.setIdRef("comp");
            re.setSubmodelRef("A");
            compartplug.addReplacedElement(re);
            re.setSubmodelRef("B");
            re.unsetIdRef();
            re.setPortRef("comp_port");
            compartplug.addReplacedElement(re);

            //Synchronize the species
            spec.setId("S");
            spec.setInitialConcentration(5);
            var specplug = (CompSBasePlugin)(spec.getPlugin("comp"));
            var sre = specplug.createReplacedElement();
            sre.setSubmodelRef("A");
            sre.setIdRef("S");
            var sre2 = specplug.createReplacedElement();
            sre2.setSubmodelRef("B");
            sre2.setPortRef("S_port");
            model.addSpecies(spec);

            spec.setId("D");
            spec.setInitialConcentration(10);
            sre.setIdRef("D");
            sre2.setPortRef("D_port");
            model.addSpecies(spec);

            libsbml.writeSBMLToFile(document, "spec_example3.xml");
            document = libsbml.readSBMLFromFile("spec_example3.xml");
            if (document == null)
            {
                Console.WriteLine("Error reading back in file.");

                retval = -1;
            }
            else
            {
                document.setConsistencyChecks(libsbml.LIBSBML_CAT_UNITS_CONSISTENCY, false);
                document.checkConsistency();
                if (document.getErrorLog().getNumFailsWithSeverity(2) > 0 ||
                    document.getErrorLog().getNumFailsWithSeverity(3) > 0)
                {
                    var stream = new OStringStream();
                    document.printErrors(stream);
                    Console.WriteLine("Errors encoutered when round-tripping  SBML file: \n" +
                                      stream.str());
                    retval = -1;
                }
                libsbml.writeSBMLToFile(document, "spec_example3_rt.xml");
            }
            return retval;
        }

 public void test_internal_consistency_check_20805()
 {
     SBMLDocument d = new SBMLDocument(3,1);
       long errors;
       Model m = d.createModel();
       InitialAssignment ia = m.createInitialAssignment();
       ASTNode ast = libsbml.parseFormula("lambda(x, 2*x)");
       ia.setMath(ast);
       errors = d.checkInternalConsistency();
       assertTrue( errors == 1 );
       assertTrue( d.getError(0).getErrorId() == 20805 );
       ia.setSymbol("fd");
       d.getErrorLog().clearLog();
       errors = d.checkInternalConsistency();
       assertTrue( errors == 0 );
       d = null;
 }

 public void test_internal_consistency_check_20908()
 {
     SBMLDocument d = new SBMLDocument(3,1);
       long errors;
       Model m = d.createModel();
       AssignmentRule r = m.createAssignmentRule();
       ASTNode ast = libsbml.parseFormula("lambda(x, 2*x)");
       r.setMath(ast);
       errors = d.checkInternalConsistency();
       assertTrue( errors == 1 );
       assertTrue( d.getError(0).getErrorId() == 20908 );
       r.setVariable("fd");
       d.getErrorLog().clearLog();
       errors = d.checkInternalConsistency();
       assertTrue( errors == 0 );
       d = null;
 }

 public void test_internal_consistency_check_20706()
 {
     SBMLDocument d = new SBMLDocument(3,1);
       long errors;
       Model m = d.createModel();
       Parameter p = m.createParameter();
       errors = d.checkInternalConsistency();
       assertTrue( errors == 2 );
       assertTrue( d.getError(0).getErrorId() == 20706 );
       assertTrue( d.getError(1).getErrorId() == 20706 );
       p.setId("c");
       d.getErrorLog().clearLog();
       errors = d.checkInternalConsistency();
       assertTrue( errors == 1 );
       assertTrue( d.getError(0).getErrorId() == 20706 );
       p.setConstant(true);
       d.getErrorLog().clearLog();
       errors = d.checkInternalConsistency();
       assertTrue( errors == 0 );
       d = null;
 }

 public void test_internal_consistency_check_20623()
 {
     SBMLDocument d = new SBMLDocument(3,1);
       long errors;
       Model m = d.createModel();
       Compartment c = m.createCompartment();
       c.setId("c");
       c.setConstant(true);
       Species s = m.createSpecies();
       errors = d.checkInternalConsistency();
       assertTrue( errors == 5 );
       assertTrue( d.getError(0).getErrorId() == 20623 );
       assertTrue( d.getError(1).getErrorId() == 20614 );
       assertTrue( d.getError(2).getErrorId() == 20623 );
       assertTrue( d.getError(3).getErrorId() == 20623 );
       assertTrue( d.getError(4).getErrorId() == 20623 );
       s.setId("s");
       d.getErrorLog().clearLog();
       errors = d.checkInternalConsistency();
       assertTrue( errors == 4 );
       assertTrue( d.getError(0).getErrorId() == 20614 );
       assertTrue( d.getError(1).getErrorId() == 20623 );
       assertTrue( d.getError(2).getErrorId() == 20623 );
       assertTrue( d.getError(3).getErrorId() == 20623 );
       s.setCompartment("c");
       d.getErrorLog().clearLog();
       errors = d.checkInternalConsistency();
       assertTrue( errors == 3 );
       assertTrue( d.getError(0).getErrorId() == 20623 );
       assertTrue( d.getError(1).getErrorId() == 20623 );
       assertTrue( d.getError(2).getErrorId() == 20623 );
       s.setHasOnlySubstanceUnits(true);
       d.getErrorLog().clearLog();
       errors = d.checkInternalConsistency();
       assertTrue( errors == 2 );
       assertTrue( d.getError(0).getErrorId() == 20623 );
       assertTrue( d.getError(1).getErrorId() == 20623 );
       s.setBoundaryCondition(true);
       d.getErrorLog().clearLog();
       errors = d.checkInternalConsistency();
       assertTrue( errors == 1 );
       assertTrue( d.getError(0).getErrorId() == 20623 );
       s.setConstant(true);
       d.getErrorLog().clearLog();
       errors = d.checkInternalConsistency();
       assertTrue( errors == 0 );
       d = null;
 }

 public void test_internal_consistency_check_20517()
 {
     SBMLDocument d = new SBMLDocument(3,1);
       long errors;
       Model m = d.createModel();
       Compartment c = m.createCompartment();
       errors = d.checkInternalConsistency();
       assertTrue( errors == 2 );
       assertTrue( d.getError(0).getErrorId() == 20517 );
       assertTrue( d.getError(1).getErrorId() == 20517 );
       c.setId("c");
       d.getErrorLog().clearLog();
       errors = d.checkInternalConsistency();
       assertTrue( errors == 1 );
       assertTrue( d.getError(0).getErrorId() == 20517 );
       c.setConstant(true);
       d.getErrorLog().clearLog();
       errors = d.checkInternalConsistency();
       assertTrue( errors == 0 );
       d = null;
 }

        private static int Main(string[] args)
        {
            var sbmlns = new SBMLNamespaces(3, 1, "comp", 1);

            // create the document
            var document = new SBMLDocument(sbmlns);

            //Define the external model definitions
            var compdoc = (CompSBMLDocumentPlugin)(document.getPlugin("comp"));
            compdoc.setRequired(true);
            var extmod = compdoc.createExternalModelDefinition();
            extmod.setId("ExtMod1");
            extmod.setSource("enzyme_model.xml");
            extmod.setModelRef("enzyme");

            // create the main Model
            var model = document.createModel();

            // Set the submodels
            var mplugin = (CompModelPlugin)(model.getPlugin("comp"));
            var submod1 = mplugin.createSubmodel();
            submod1.setId("A");
            submod1.setModelRef("ExtMod1");
            var submod2 = mplugin.createSubmodel();
            submod2.setId("B");
            submod2.setModelRef("ExtMod1");

            // create a replacement compartment
            var comp = model.createCompartment();
            comp.setSpatialDimensions(3);
            comp.setConstant(true);
            comp.setId("comp");
            comp.setSize(1L);

            //Tell the model that this compartment replaces both of the inside ones.
            var compartplug = (CompSBasePlugin)(comp.getPlugin("comp"));
            var re = new ReplacedElement();
            re.setIdRef("comp");
            re.setSubmodelRef("A");
            compartplug.addReplacedElement(re);
            re.setSubmodelRef("B");
            compartplug.addReplacedElement(re);

            // create a replacement species
            var spec = model.createSpecies();
            spec.setCompartment("comp");
            spec.setHasOnlySubstanceUnits(false);
            spec.setConstant(false);
            spec.setBoundaryCondition(false);
            spec.setId("S");

            //Tell the model that this species replaces both of the inside ones.
            var spp = (CompSBasePlugin)(spec.getPlugin("comp"));
            re.setIdRef("S");
            re.setSubmodelRef("A");
            spp.addReplacedElement(re);
            re.setSubmodelRef("B");
            spp.addReplacedElement(re);

            libsbml.writeSBMLToFile(document, "spec_example2.xml");
            document = libsbml.readSBMLFromFile("spec_example2.xml");
            if (document == null)
            {
                Console.WriteLine("Error reading back in file.");
                return -1;
            }
            else
            {
                document.setConsistencyChecks(libsbml.LIBSBML_CAT_UNITS_CONSISTENCY, false);
                document.checkConsistency();
                if (document.getErrorLog().getNumFailsWithSeverity(2) > 0 ||
                    document.getErrorLog().getNumFailsWithSeverity(3) > 0)
                {
                    var stream = new OStringStream();
                    document.printErrors(stream);
                    Console.WriteLine("Errors encoutered when round-tripping  SBML file: \n" +
                                      stream.str());
                    return -1;
                }
                libsbml.writeSBMLToFile(document, "spec_example2_rt.xml");
            }

            return 0;
        }

 public void test_internal_consistency_check_21117()
 {
     SBMLDocument d = new SBMLDocument(3,1);
       long errors;
       Model m = d.createModel();
       Reaction r = m.createReaction();
       r.setId("r");
       r.setReversible(true);
       r.setFast(false);
       SpeciesReference sr = r.createReactant();
       sr.setSpecies("s");
       sr.setConstant(true);
       ModifierSpeciesReference msr = r.createModifier();
       d.getErrorLog().clearLog();
       errors = d.checkInternalConsistency();
       assertTrue( errors == 1 );
       assertTrue( d.getError(0).getErrorId() == 21117 );
       msr.setSpecies("s");
       d.getErrorLog().clearLog();
       errors = d.checkInternalConsistency();
       assertTrue( errors == 0 );
       d = null;
 }

    //===============================================================================
    //
    //
    // Helper functions for writing/validating the given SBML documents.
    //
    //
    //===============================================================================
    /**
     *
     *  Validates the given SBMLDocument.
     *
     *   This function is based on validateSBML.cpp implemented by
     *   Sarah Keating, Ben Bornstein, and Michael Hucka.
     *
     */
    private static bool validateExampleSBML(SBMLDocument sbmlDoc)
    {
        if (sbmlDoc == null)
        {
            Console.Error.WriteLine("validateExampleSBML: given a null SBML Document");
            return false;
        }

        string consistencyMessages = "";
        string validationMessages = "";
        bool noProblems = true;
        int numCheckFailures = 0;
        int numConsistencyErrors = 0;
        int numConsistencyWarnings = 0;
        int numValidationErrors = 0;
        int numValidationWarnings = 0;

        // LibSBML 3.3 is lenient when generating models from scratch using the
        // API for creating objects.  Once the whole model is done and before it
        // gets written out, it's important to check that the whole model is in
        // fact complete, consistent and valid.

        numCheckFailures = (int)sbmlDoc.checkInternalConsistency();
        if (numCheckFailures > 0)
        {
            noProblems = false;
            for (int i = 0;
            i < numCheckFailures;
            i++)
            {
                SBMLError sbmlErr = sbmlDoc.getError(i);
                if (sbmlErr.isFatal() || sbmlErr.isError())
                {
                    ++numConsistencyErrors;
                }
                else
                {
                    ++numConsistencyWarnings;
                }
            }
            consistencyMessages = sbmlDoc.getErrorLog().toString();
        }

        // If the internal checks fail, it makes little sense to attempt
        // further validation, because the model may be too compromised to
        // be properly interpreted.

        if (numConsistencyErrors > 0)
        {
            consistencyMessages += "Further validation aborted.";
        }
        else
        {
            numCheckFailures = (int)sbmlDoc.checkConsistency();
            if (numCheckFailures > 0)
            {
                noProblems = false;
                for (int i = 0;
                i < numCheckFailures;
                i++)
                {
                    SBMLError sbmlErr = sbmlDoc.getError(i);
                    if (sbmlErr.isFatal() || sbmlErr.isError())
                    {
                        ++numValidationErrors;
                    }
                    else
                    {
                        ++numValidationWarnings;
                    }
                }

                validationMessages = sbmlDoc.getErrorLog().toString();
            }
        }

        if (noProblems)
            return true;
        else
        {
            if (numConsistencyErrors > 0)
            {
                Console.WriteLine("ERROR: encountered " + numConsistencyErrors
                + " consistency error" + (numConsistencyErrors == 1 ? "" : "s")
                + " in model '" + sbmlDoc.getModel().getId() + "'.");
//.........这里部分代码省略.........