Examples with XMLSource cbit.vcell.xml.XMLSource used on opensource projects

Example 51 with XMLSource

use of cbit.vcell.xml.XMLSource in project vcell by virtualcell.

the class SBMLSpatialTest method test.

// @Test
public void test() throws Exception {
    // BioModel bioModel1 = BioModelTest.getExampleWithImage();
    URL vcmlURL = SBMLSpatialTest.class.getResource("Solver_Suite_6_2.vcml");
    File vcmlFile = new File(vcmlURL.toURI());
    BioModel bioModel1 = XmlHelper.XMLToBioModel(new XMLSource(vcmlFile));
    bioModel1.refreshDependencies();
    // for (int i = 0; i<bioModel1.getNumSimulationContexts(); i++){
    for (int i = 5; i == 5; i++) {
        SimulationContext sc1 = bioModel1.getSimulationContext(i);
        if (sc1.getApplicationType() != Application.NETWORK_DETERMINISTIC) {
            System.err.println(sc1.getName() + " is not a network determistic application");
            continue;
        }
        boolean isSpatial = sc1.getGeometry().getDimension() > 0;
        SBMLExporter exporter = new SBMLExporter(bioModel1, 3, 1, isSpatial);
        sc1.refreshMathDescription(null, NetworkGenerationRequirements.ComputeFullNoTimeout);
        exporter.setSelectedSimContext(sc1);
        String sbmlString = exporter.getSBMLString();
        File tempFile = File.createTempFile("sbmlSpatialTest_SBML_", ".sbml.xml");
        FileUtils.write(tempFile, sbmlString);
        System.out.println(tempFile);
        try {
            VCLogger argVCLogger = new TLogger();
            SBMLImporter importer = new SBMLImporter(tempFile.getAbsolutePath(), argVCLogger, isSpatial);
            BioModel bioModel2 = importer.getBioModel();
            File tempFile2 = File.createTempFile("sbmlSpatialTest_Biomodel_", ".vcml.xml");
            FileUtils.write(tempFile2, XmlHelper.bioModelToXML(bioModel2));
            System.out.println(tempFile2);
            // if (true) { throw new RuntimeException("stop"); }
            bioModel2.refreshDependencies();
            SimulationContext sc2 = bioModel2.getSimulationContext(0);
            // sc2.refreshMathDescription(null, NetworkGenerationRequirements.ComputeFullNoTimeout);
            sc2.setMathDescription(sc2.createNewMathMapping(null, NetworkGenerationRequirements.ComputeFullNoTimeout).getMathDescription());
            if (!sc1.getMathDescription().isValid()) {
                throw new RuntimeException("sc1.math is not valid");
            }
            if (!sc2.getMathDescription().isValid()) {
                throw new RuntimeException("sc2.math is not valid");
            }
            MathCompareResults mathCompareResults = MathDescription.testEquivalency(SimulationSymbolTable.createMathSymbolTableFactory(), sc1.getMathDescription(), sc2.getMathDescription());
            if (!mathCompareResults.isEquivalent()) {
                System.out.println("MATH DESCRIPTION 1 <UNCHANGED>");
                System.out.println(sc1.getMathDescription().getVCML_database());
                System.out.println("MATH DESCRIPTION 2 <UNCHANGED>");
                System.out.println(sc2.getMathDescription().getVCML_database());
                // if (mathCompareResults.decision  == Decision.MathDifferent_SUBDOMAINS_DONT_MATCH){
                // BioModel bioModel1_copy = XmlHelper.XMLToBioModel(new XMLSource(vcmlFile));
                // bioModel1_copy.refreshDependencies();
                // SimulationContext sc1_copy = bioModel1_copy.getSimulationContext(i);
                // VCImage image = sc1_copy.getGeometry().getGeometrySpec().getImage();
                // if (image!=null){
                // ArrayList<VCPixelClass> pcList = new ArrayList<VCPixelClass>();
                // for (VCPixelClass pc : image.getPixelClasses()){
                // pcList.add(new VCPixelClass(pc.getKey(),SBMLExporter.DOMAIN_TYPE_PREFIX+pc.getPixelClassName(),pc.getPixel()));
                // }
                // image.setPixelClasses(pcList.toArray(new VCPixelClass[0]));
                // }
                // for (GeometryClass gc : sc1_copy.getGeometry().getGeometryClasses()){
                // System.out.println("name before "+gc.getName());
                // gc.setName(SBMLExporter.DOMAIN_TYPE_PREFIX+gc.getName());
                // System.out.println("name after "+gc.getName());
                // }
                // sc1_copy.checkValidity();
                // bioModel1_copy.refreshDependencies();
                // sc1_copy.getGeometry().precomputeAll(new GeometryThumbnailImageFactoryAWT(), true, true);
                // sc1_copy.setMathDescription(sc1_copy.createNewMathMapping(null, NetworkGenerationRequirements.ComputeFullNoTimeout).getMathDescription());
                // MathCompareResults mathCompareResults_renamedSubdomains = MathDescription.testEquivalency(SimulationSymbolTable.createMathSymbolTableFactory(),sc1_copy.getMathDescription(), sc2.getMathDescription());
                // if (!mathCompareResults_renamedSubdomains.isEquivalent()){
                // System.out.println("MATH DESCRIPTION 1 <RENAMED>");
                // System.out.println(sc1_copy.getMathDescription().getVCML_database());
                // Assert.fail(mathCompareResults_renamedSubdomains.decision+" "+mathCompareResults_renamedSubdomains.details);
                // }
                // }else{
                System.err.println(mathCompareResults.decision + " " + mathCompareResults.details);
            // }
            } else {
                System.out.println("MATHS WERE EQUIVALENT");
            }
        } finally {
            tempFile.delete();
        }
    }
    // loop over determinstic applications
    System.out.println("done");
}

Example 52 with XMLSource

use of cbit.vcell.xml.XMLSource in project vcell by virtualcell.

the class ModelUnitConverter method createBioModelWithNewUnitSystem.

public static BioModel createBioModelWithNewUnitSystem(BioModel oldBioModel, ModelUnitSystem newUnitSystem) throws ExpressionException, XmlParseException {
    // new BioModel has new unit system applied to all built-in units ... but expressions still need to be corrected (see below).
    String biomodelXMLString = XmlHelper.bioModelToXML(oldBioModel);
    XMLSource newXMLSource = new XMLSource(biomodelXMLString);
    BioModel newBioModel = XmlHelper.XMLToBioModel(newXMLSource, true, newUnitSystem);
    Model newModel = newBioModel.getModel();
    Model oldModel = oldBioModel.getModel();
    for (Parameter p : newBioModel.getModel().getModelParameters()) {
        convertVarsWithUnitFactors(oldBioModel.getModel(), newBioModel.getModel(), p);
    }
    for (ReactionStep reactionStep : newBioModel.getModel().getReactionSteps()) {
        SymbolTable oldSymbolTable = oldBioModel.getModel().getReactionStep(reactionStep.getName());
        SymbolTable newSymbolTable = reactionStep;
        for (Parameter p : reactionStep.getKinetics().getUnresolvedParameters()) {
            convertVarsWithUnitFactors(oldSymbolTable, newSymbolTable, p);
        }
        for (Parameter p : reactionStep.getKinetics().getKineticsParameters()) {
            convertVarsWithUnitFactors(oldSymbolTable, newSymbolTable, p);
        }
        Kinetics kinetics = reactionStep.getKinetics();
        KineticsParameter kineticsParameter = null;
        if (kinetics.getKineticsParameterFromRole(Kinetics.ROLE_ReactionRate) != null) {
            kineticsParameter = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_ReactionRate);
        } else if (kinetics.getKineticsParameterFromRole(Kinetics.ROLE_LumpedReactionRate) != null) {
            kineticsParameter = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_LumpedReactionRate);
        } else {
            throw new RuntimeException("Role 'reaction rate' or role 'lumped reaction rate' expected");
        }
        Expression rateExpression = kineticsParameter.getExpression();
        jscl.math.Expression jsclExpression = null;
        String jsclExpressionString = rateExpression.infix_JSCL();
        try {
            jsclExpression = jscl.math.Expression.valueOf(jsclExpressionString);
        } catch (jscl.text.ParseException e) {
            e.printStackTrace(System.out);
            System.out.println("JSCL couldn't parse \"" + jsclExpressionString + "\"");
            return null;
        }
        jscl.math.Generic g1 = jsclExpression.expand().simplify();
        Expression newRate = new Expression(SymbolUtils.getRestoredStringJSCL(g1.toString()));
        newRate.bindExpression(reactionStep);
        // reactionStep.getKinetics().getKineticsParameterFromRole(Kinetics.ROLE_ReactionRate).setExpression(newRate.flatten());
        if (reactionStep.getKinetics().getKineticsParameterFromRole(Kinetics.ROLE_ReactionRate) != null) {
            reactionStep.getKinetics().getKineticsParameterFromRole(Kinetics.ROLE_ReactionRate).setExpression(newRate.flatten());
        }
    }
    for (ReactionRule reactionRule : newBioModel.getModel().getRbmModelContainer().getReactionRuleList()) {
        SymbolTable oldSymbolTable = oldBioModel.getModel().getRbmModelContainer().getReactionRule(reactionRule.getName()).getKineticLaw().getScopedSymbolTable();
        SymbolTable newSymbolTable = reactionRule.getKineticLaw().getScopedSymbolTable();
        for (Parameter p : reactionRule.getKineticLaw().getUnresolvedParameters()) {
            convertVarsWithUnitFactors(oldSymbolTable, newSymbolTable, p);
        }
        for (Parameter p : reactionRule.getKineticLaw().getLocalParameters()) {
            convertVarsWithUnitFactors(oldSymbolTable, newSymbolTable, p);
        }
    }
    for (SimulationContext simContext : newBioModel.getSimulationContexts()) {
        SimulationContext oldSimContext = oldBioModel.getSimulationContext(simContext.getName());
        // ArrayList<Parameter> parameterList = new ArrayList<Parameter>();
        for (StructureMapping mapping : simContext.getGeometryContext().getStructureMappings()) {
            Structure oldStructure = oldModel.getStructure(mapping.getStructure().getName());
            StructureMapping oldMapping = oldSimContext.getGeometryContext().getStructureMapping(oldStructure);
            for (Parameter p : mapping.computeApplicableParameterList()) {
                convertVarsWithUnitFactors(oldMapping, mapping, p);
            }
        }
        for (SpeciesContextSpec spec : simContext.getReactionContext().getSpeciesContextSpecs()) {
            SpeciesContext oldSpeciesContext = oldModel.getSpeciesContext(spec.getSpeciesContext().getName());
            SpeciesContextSpec oldSpec = oldSimContext.getReactionContext().getSpeciesContextSpec(oldSpeciesContext);
            for (Parameter p : spec.computeApplicableParameterList()) {
                convertVarsWithUnitFactors(oldSpec, spec, p);
            }
        }
        for (int i = 0; i < simContext.getElectricalStimuli().length; i++) {
            ElectricalStimulus newElectricalStimulus = simContext.getElectricalStimuli()[i];
            ElectricalStimulus oldElectricalStimulus = oldSimContext.getElectricalStimuli()[i];
            for (Parameter p : newElectricalStimulus.getParameters()) {
                convertVarsWithUnitFactors(oldElectricalStimulus.getNameScope().getScopedSymbolTable(), newElectricalStimulus.getNameScope().getScopedSymbolTable(), p);
            }
        }
        // convert events : trigger and delay parameters and event assignments
        for (int i = 0; simContext.getBioEvents() != null && oldSimContext.getBioEvents() != null && i < simContext.getBioEvents().length; i++) {
            BioEvent newBioEvent = simContext.getBioEvents()[i];
            BioEvent oldBioEvent = oldSimContext.getBioEvent(newBioEvent.getName());
            for (Parameter p : newBioEvent.getEventParameters()) {
                convertVarsWithUnitFactors(oldBioEvent.getNameScope().getScopedSymbolTable(), newBioEvent.getNameScope().getScopedSymbolTable(), p);
            }
            // for each event assignment expression
            for (int e = 0; e < newBioEvent.getEventAssignments().size(); e++) {
                ScopedSymbolTable newSymbolTable = newBioEvent.getNameScope().getScopedSymbolTable();
                ScopedSymbolTable oldSymbolTable = oldBioEvent.getNameScope().getScopedSymbolTable();
                EventAssignment newEventAssignment = newBioEvent.getEventAssignments().get(e);
                EventAssignment oldEventAssignment = oldBioEvent.getEventAssignments().get(e);
                VCUnitDefinition oldTargetUnit = oldEventAssignment.getTarget().getUnitDefinition();
                VCUnitDefinition newTargetUnit = newEventAssignment.getTarget().getUnitDefinition();
                Expression eventAssgnExpr = newEventAssignment.getAssignmentExpression();
                convertExprWithUnitFactors(oldSymbolTable, newSymbolTable, oldTargetUnit, newTargetUnit, eventAssgnExpr);
            }
        }
        /**
         * @TODO: If rate rule variable unit is TBD, we still need to handle the rate expression unit.
         */
        // convert rate rules
        RateRule[] rateRules = simContext.getRateRules();
        if (rateRules != null && rateRules.length > 0) {
            for (RateRule rateRule : rateRules) {
                RateRule oldRateRule = oldSimContext.getRateRule(rateRule.getName());
                ScopedSymbolTable oldSymbolTable = oldRateRule.getSimulationContext();
                ScopedSymbolTable newSymbolTable = rateRule.getSimulationContext();
                VCUnitDefinition oldTargetUnit = oldRateRule.getRateRuleVar().getUnitDefinition();
                VCUnitDefinition newTargetUnit = rateRule.getRateRuleVar().getUnitDefinition();
                Expression rateRuleExpr = rateRule.getRateRuleExpression();
                convertExprWithUnitFactors(oldSymbolTable, newSymbolTable, oldTargetUnit, newTargetUnit, rateRuleExpr);
            }
        }
        AssignmentRule[] assignmentRules = simContext.getAssignmentRules();
        if (assignmentRules != null && assignmentRules.length > 0) {
            for (AssignmentRule assignmentRule : assignmentRules) {
                AssignmentRule oldAssignRule = oldSimContext.getAssignmentRule(assignmentRule.getName());
                ScopedSymbolTable oldSymbolTable = oldAssignRule.getSimulationContext();
                ScopedSymbolTable newSymbolTable = assignmentRule.getSimulationContext();
                VCUnitDefinition oldTargetUnit = oldAssignRule.getAssignmentRuleVar().getUnitDefinition();
                VCUnitDefinition newTargetUnit = assignmentRule.getAssignmentRuleVar().getUnitDefinition();
                Expression assignmentRuleExpr = assignmentRule.getAssignmentRuleExpression();
                convertExprWithUnitFactors(oldSymbolTable, newSymbolTable, oldTargetUnit, newTargetUnit, assignmentRuleExpr);
            }
        }
    }
    // end  for - simulationContext
    return newBioModel;
}

Example 53 with XMLSource

use of cbit.vcell.xml.XMLSource in project vcell by virtualcell.

the class SEDMLExporter method main.

public static void main(String[] args) {
    // if (args.length != 1) {
    // System.out.println("Usage:\n\t path_of_vcml_file\n" );
    // System.exit(1);
    // }
    // String pathName = args[0];
    String pathName = "c:\\dan\\SEDML\\SEDML2.vcml";
    try {
        String biomodelXmlStr = XmlUtil.getXMLString(pathName);
        BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(biomodelXmlStr.toString()));
        bioModel.refreshDependencies();
        // invoke the SEDMLEXporter
        SEDMLExporter sedmlExporter = new SEDMLExporter(bioModel, 1, 1, null);
        String absolutePath = "c:\\dan\\SEDML";
        String sedmlStr = sedmlExporter.getSEDMLFile(absolutePath, "SEDML2", false, false, false);
        // String absolutePath = ResourceUtil.getUserHomeDir().getAbsolutePath();
        String outputName = absolutePath + "\\" + TokenMangler.mangleToSName(bioModel.getName()) + ".sedml";
        XmlUtil.writeXMLStringToFile(sedmlStr, outputName, true);
    } catch (IOException e) {
        e.printStackTrace(System.out);
        throw new RuntimeException("Unable to read VCML file '" + pathName + "' into string.");
    } catch (XmlParseException e) {
        e.printStackTrace(System.out);
        throw new RuntimeException("Unable to convert VCML file '" + pathName + "' to a biomodel.");
    }
}

Example 54 with XMLSource

use of cbit.vcell.xml.XMLSource in project vcell by virtualcell.

the class SBMLStandaloneImporter method attemptImport.

private BioModel attemptImport(File sbmlFile) throws ExecutableException, IOException, ClassNotFoundException, XmlParseException {
    if (subProcess == null || subProcess.getStatus() != LiveProcessStatus.RUNNING) {
        subProcess = createProcess();
    }
    toChildProcess.writeObject(sbmlFile);
    Object back = fromChildProcess.readObject();
    if (back instanceof String) {
        String xml = (String) back;
        if (lg.isDebugEnabled()) {
            try (FileWriter fw = new FileWriter(sbmlFile.getAbsolutePath() + ".dump")) {
                fw.append(xml);
            }
        }
        XMLSource source = new XMLSource(xml);
        return XmlHelper.XMLToBioModel(source);
    }
    if (back instanceof Exception) {
        try {
            throw (Exception) back;
        } catch (SBMLImportException sie) {
            throw sie;
        } catch (Exception e) {
            throw new ExecutableException("child process exception", e);
        }
    }
    throw new ExecutableException("unexpected object from child process:  " + back.getClass().getName() + " " + back.toString());
}

Example 55 with XMLSource

use of cbit.vcell.xml.XMLSource in project vcell by virtualcell.

the class ProfileLikelihood method main.

// main
public static void main(String[] args) {
    try {
        File newXML = new File(args[0]);
        XMLSource source = new XMLSource(newXML);
        BioModel biomodel = XmlHelper.XMLToBioModel(source);
        SimulationContext app = biomodel.getSimulationContext("Deterministic");
        AnalysisTask[] task = app.getAnalysisTasks();
        // ParestRun.bFakeOptimization = true;
        final ProfileLikelihoodCallback callback = new ProfileLikelihoodCallback() {

            @Override
            public void report(String msg) {
                System.out.println(msg);
            }
        };
        ProfileLikelihood pl = new ProfileLikelihood(callback);
        pl.run((ParameterEstimationTask) task[0]);
    } catch (XmlParseException e) {
        e.printStackTrace();
    } catch (Exception e) {
        e.printStackTrace();
    }
}