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

Example 1 with XmlParseException

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

the class SEDMLExporter method translateBioModelToSedML.

private void translateBioModelToSedML(String savePath) {
    sbmlFilePathStrAbsoluteList.clear();
    // models
    try {
        SimulationContext[] simContexts = vcBioModel.getSimulationContexts();
        cbit.vcell.model.Model vcModel = vcBioModel.getModel();
        // "urn:sedml:language:sbml";
        String sbmlLanguageURN = SUPPORTED_LANGUAGE.SBML_GENERIC.getURN();
        String bioModelName = TokenMangler.mangleToSName(vcBioModel.getName());
        // String usrHomeDirPath = ResourceUtil.getUserHomeDir().getAbsolutePath();
        // to get Xpath string for variables.
        SBMLSupport sbmlSupport = new SBMLSupport();
        // for model count, task subcount
        int simContextCnt = 0;
        // for dtaGenerator count.
        int varCount = 0;
        boolean bSpeciesAddedAsDataGens = false;
        String sedmlNotesStr = "";
        for (SimulationContext simContext : simContexts) {
            String simContextName = simContext.getName();
            // export all applications that are not spatial stochastic
            if (!(simContext.getGeometry().getDimension() > 0 && simContext.isStoch())) {
                // to compute and set the sizes of the remaining structures.
                if (!simContext.getGeometryContext().isAllSizeSpecifiedPositive()) {
                    Structure structure = simContext.getModel().getStructure(0);
                    double structureSize = 1.0;
                    StructureMapping structMapping = simContext.getGeometryContext().getStructureMapping(structure);
                    StructureSizeSolver.updateAbsoluteStructureSizes(simContext, structure, structureSize, structMapping.getSizeParameter().getUnitDefinition());
                }
                // Export the application itself to SBML, with default overrides
                String sbmlString = null;
                int level = 2;
                int version = 4;
                boolean isSpatial = simContext.getGeometry().getDimension() > 0 ? true : false;
                SimulationJob simJob = null;
                // if (simContext.getGeometry().getDimension() > 0) {
                // sbmlString = XmlHelper.exportSBML(vcBioModel, 2, 4, 0, true, simContext, null);
                // } else {
                // sbmlString = XmlHelper.exportSBML(vcBioModel, 2, 4, 0, false, simContext, null);
                // }
                // 
                // TODO: we need to salvage from the SBMLExporter info about the fate of local parameters
                // some of them may stay as locals, some others may become globals
                // Any of these, if used in a repeated task or change or whatever, needs to be used in a consistent way,
                // that is, if a param becomes a global in SBML, we need to refer at it in SEDML as the same global
                // 
                // We'll use:
                // Map<Pair <String reaction, String param>, String global>		- if local converted to global
                // Set<Pair <String reaction, String param>>	(if needed?)	- if local stays local
                // 
                // local to global translation map
                Map<Pair<String, String>, String> l2gMap = null;
                if (vcBioModel instanceof BioModel) {
                    try {
                        // check if model to be exported to SBML has units compatible with SBML default units (default units in SBML can be assumed only until SBML Level2)
                        ModelUnitSystem forcedModelUnitSystem = simContext.getModel().getUnitSystem();
                        if (level < 3 && !ModelUnitSystem.isCompatibleWithDefaultSBMLLevel2Units(forcedModelUnitSystem)) {
                            forcedModelUnitSystem = ModelUnitSystem.createDefaultSBMLLevel2Units();
                        }
                        // create new Biomodel with new (SBML compatible)  unit system
                        BioModel modifiedBiomodel = ModelUnitConverter.createBioModelWithNewUnitSystem(simContext.getBioModel(), forcedModelUnitSystem);
                        // extract the simContext from new Biomodel. Apply overrides to *this* modified simContext
                        SimulationContext simContextFromModifiedBioModel = modifiedBiomodel.getSimulationContext(simContext.getName());
                        SBMLExporter sbmlExporter = new SBMLExporter(modifiedBiomodel, level, version, isSpatial);
                        sbmlExporter.setSelectedSimContext(simContextFromModifiedBioModel);
                        // no sim job
                        sbmlExporter.setSelectedSimulationJob(null);
                        sbmlString = sbmlExporter.getSBMLFile();
                        l2gMap = sbmlExporter.getLocalToGlobalTranslationMap();
                    } catch (ExpressionException | SbmlException e) {
                        e.printStackTrace(System.out);
                        throw new XmlParseException(e);
                    }
                } else {
                    throw new RuntimeException("unsupported Document Type " + vcBioModel.getClass().getName() + " for SBML export");
                }
                String sbmlFilePathStrAbsolute = savePath + FileUtils.WINDOWS_SEPARATOR + bioModelName + "_" + simContextName + ".xml";
                String sbmlFilePathStrRelative = bioModelName + "_" + simContextName + ".xml";
                XmlUtil.writeXMLStringToFile(sbmlString, sbmlFilePathStrAbsolute, true);
                sbmlFilePathStrAbsoluteList.add(sbmlFilePathStrRelative);
                String simContextId = TokenMangler.mangleToSName(simContextName);
                sedmlModel.addModel(new Model(simContextId, simContextName, sbmlLanguageURN, sbmlFilePathStrRelative));
                // required for mathOverrides, if any
                MathMapping mathMapping = simContext.createNewMathMapping();
                MathSymbolMapping mathSymbolMapping = mathMapping.getMathSymbolMapping();
                // create sedml simulation objects and tasks (mapping each sim with current simContext)
                int simCount = 0;
                String taskRef = null;
                int overrideCount = 0;
                for (Simulation vcSimulation : simContext.getSimulations()) {
                    List<DataGenerator> dataGeneratorsOfSim = new ArrayList<DataGenerator>();
                    // if simContext is non-spatial stochastic, check if sim is histogram
                    SolverTaskDescription simTaskDesc = vcSimulation.getSolverTaskDescription();
                    if (simContext.getGeometry().getDimension() == 0 && simContext.isStoch()) {
                        long numOfTrials = simTaskDesc.getStochOpt().getNumOfTrials();
                        if (numOfTrials > 1) {
                            String msg = "\n\t" + simContextName + " ( " + vcSimulation.getName() + " ) : export of non-spatial stochastic simulation with histogram option to SEDML not supported at this time.";
                            sedmlNotesStr += msg;
                            continue;
                        }
                    }
                    // create Algorithm and sedmlSimulation (UniformtimeCourse)
                    SolverDescription vcSolverDesc = simTaskDesc.getSolverDescription();
                    // String kiSAOIdStr = getKiSAOIdFromSimulation(vcSolverDesc);	// old way of doing it, going directly to the web site
                    String kiSAOIdStr = vcSolverDesc.getKisao();
                    Algorithm sedmlAlgorithm = new Algorithm(kiSAOIdStr);
                    TimeBounds vcSimTimeBounds = simTaskDesc.getTimeBounds();
                    double startingTime = vcSimTimeBounds.getStartingTime();
                    String simName = vcSimulation.getName();
                    UniformTimeCourse utcSim = new UniformTimeCourse(TokenMangler.mangleToSName(simName), simName, startingTime, startingTime, vcSimTimeBounds.getEndingTime(), (int) simTaskDesc.getExpectedNumTimePoints(), sedmlAlgorithm);
                    // if solver is not CVODE, add a note to utcSim to indicate actual solver name
                    if (!vcSolverDesc.equals(SolverDescription.CVODE)) {
                        String simNotesStr = "Actual Solver Name : '" + vcSolverDesc.getDisplayLabel() + "'.";
                        utcSim.addNote(createNotesElement(simNotesStr));
                    }
                    sedmlModel.addSimulation(utcSim);
                    // add SEDML tasks (map simulation to model:simContext)
                    // repeated tasks
                    MathOverrides mathOverrides = vcSimulation.getMathOverrides();
                    if (mathOverrides != null && mathOverrides.hasOverrides()) {
                        String[] overridenConstantNames = mathOverrides.getOverridenConstantNames();
                        String[] scannedConstantsNames = mathOverrides.getScannedConstantNames();
                        HashMap<String, String> scannedParamHash = new HashMap<String, String>();
                        HashMap<String, String> unscannedParamHash = new HashMap<String, String>();
                        for (String name : scannedConstantsNames) {
                            scannedParamHash.put(name, name);
                        }
                        for (String name : overridenConstantNames) {
                            if (!scannedParamHash.containsKey(name)) {
                                unscannedParamHash.put(name, name);
                            }
                        }
                        if (!unscannedParamHash.isEmpty() && scannedParamHash.isEmpty()) {
                            // only parameters with simple overrides (numeric/expression) no scans
                            // create new model with change for each parameter that has override; add simple task
                            String overriddenSimContextId = simContextId + "_" + overrideCount;
                            String overriddenSimContextName = simContextName + " modified";
                            Model sedModel = new Model(overriddenSimContextId, overriddenSimContextName, sbmlLanguageURN, simContextId);
                            overrideCount++;
                            for (String unscannedParamName : unscannedParamHash.values()) {
                                SymbolTableEntry ste = getSymbolTableEntryForModelEntity(mathSymbolMapping, unscannedParamName);
                                Expression unscannedParamExpr = mathOverrides.getActualExpression(unscannedParamName, 0);
                                if (unscannedParamExpr.isNumeric()) {
                                    // if expression is numeric, add ChangeAttribute to model created above
                                    XPathTarget targetXpath = getTargetAttributeXPath(ste, l2gMap);
                                    ChangeAttribute changeAttribute = new ChangeAttribute(targetXpath, unscannedParamExpr.infix());
                                    sedModel.addChange(changeAttribute);
                                } else {
                                    // non-numeric expression : add 'computeChange' to modified model
                                    ASTNode math = Libsedml.parseFormulaString(unscannedParamExpr.infix());
                                    XPathTarget targetXpath = getTargetXPath(ste, l2gMap);
                                    ComputeChange computeChange = new ComputeChange(targetXpath, math);
                                    String[] exprSymbols = unscannedParamExpr.getSymbols();
                                    for (String symbol : exprSymbols) {
                                        String symbolName = TokenMangler.mangleToSName(symbol);
                                        SymbolTableEntry ste1 = vcModel.getEntry(symbol);
                                        if (ste != null) {
                                            if (ste1 instanceof SpeciesContext || ste1 instanceof Structure || ste1 instanceof ModelParameter) {
                                                XPathTarget ste1_XPath = getTargetXPath(ste1, l2gMap);
                                                org.jlibsedml.Variable sedmlVar = new org.jlibsedml.Variable(symbolName, symbolName, taskRef, ste1_XPath.getTargetAsString());
                                                computeChange.addVariable(sedmlVar);
                                            } else {
                                                double doubleValue = 0.0;
                                                if (ste1 instanceof ReservedSymbol) {
                                                    doubleValue = getReservedSymbolValue(ste1);
                                                }
                                                Parameter sedmlParameter = new Parameter(symbolName, symbolName, doubleValue);
                                                computeChange.addParameter(sedmlParameter);
                                            }
                                        } else {
                                            throw new RuntimeException("Symbol '" + symbol + "' used in expression for '" + unscannedParamName + "' not found in model.");
                                        }
                                    }
                                    sedModel.addChange(computeChange);
                                }
                            }
                            sedmlModel.addModel(sedModel);
                            String taskId = "tsk_" + simContextCnt + "_" + simCount;
                            Task sedmlTask = new Task(taskId, taskId, sedModel.getId(), utcSim.getId());
                            sedmlModel.addTask(sedmlTask);
                            // to be used later to add dataGenerators : one set of DGs per model (simContext).
                            taskRef = taskId;
                        } else if (!scannedParamHash.isEmpty() && unscannedParamHash.isEmpty()) {
                            // only parameters with scans : only add 1 Task and 1 RepeatedTask
                            String taskId = "tsk_" + simContextCnt + "_" + simCount;
                            Task sedmlTask = new Task(taskId, taskId, simContextId, utcSim.getId());
                            sedmlModel.addTask(sedmlTask);
                            String repeatedTaskId = "repTsk_" + simContextCnt + "_" + simCount;
                            // TODO: temporary solution - we use as range here the first range
                            String scn = scannedConstantsNames[0];
                            String rId = "range_" + simContextCnt + "_" + simCount + "_" + scn;
                            RepeatedTask rt = new RepeatedTask(repeatedTaskId, repeatedTaskId, true, rId);
                            // to be used later to add dataGenerators - in our case it has to be the repeated task
                            taskRef = repeatedTaskId;
                            SubTask subTask = new SubTask("0", taskId);
                            rt.addSubtask(subTask);
                            for (String scannedConstName : scannedConstantsNames) {
                                ConstantArraySpec constantArraySpec = mathOverrides.getConstantArraySpec(scannedConstName);
                                String rangeId = "range_" + simContextCnt + "_" + simCount + "_" + scannedConstName;
                                // list of Ranges, if sim is parameter scan.
                                if (constantArraySpec != null) {
                                    Range r = null;
                                    System.out.println("     " + constantArraySpec.toString());
                                    if (constantArraySpec.getType() == ConstantArraySpec.TYPE_INTERVAL) {
                                        // ------ Uniform Range
                                        r = new UniformRange(rangeId, constantArraySpec.getMinValue(), constantArraySpec.getMaxValue(), constantArraySpec.getNumValues());
                                        rt.addRange(r);
                                    } else {
                                        // ----- Vector Range
                                        cbit.vcell.math.Constant[] cs = constantArraySpec.getConstants();
                                        ArrayList<Double> values = new ArrayList<Double>();
                                        for (int i = 0; i < cs.length; i++) {
                                            String value = cs[i].getExpression().infix();
                                            values.add(Double.parseDouble(value));
                                        }
                                        r = new VectorRange(rangeId, values);
                                        rt.addRange(r);
                                    }
                                    // list of Changes
                                    SymbolTableEntry ste = getSymbolTableEntryForModelEntity(mathSymbolMapping, scannedConstName);
                                    XPathTarget target = getTargetXPath(ste, l2gMap);
                                    // ASTNode math1 = new ASTCi(r.getId());		// was scannedConstName
                                    ASTNode math1 = Libsedml.parseFormulaString(r.getId());
                                    SetValue setValue = new SetValue(target, r.getId(), simContextId);
                                    setValue.setMath(math1);
                                    rt.addChange(setValue);
                                } else {
                                    throw new RuntimeException("No scan ranges found for scanned parameter : '" + scannedConstName + "'.");
                                }
                            }
                            sedmlModel.addTask(rt);
                        } else {
                            // both scanned and simple parameters : create new model with change for each simple override; add RepeatedTask
                            // create new model with change for each unscanned parameter that has override
                            String overriddenSimContextId = simContextId + "_" + overrideCount;
                            String overriddenSimContextName = simContextName + " modified";
                            Model sedModel = new Model(overriddenSimContextId, overriddenSimContextName, sbmlLanguageURN, simContextId);
                            overrideCount++;
                            String taskId = "tsk_" + simContextCnt + "_" + simCount;
                            Task sedmlTask = new Task(taskId, taskId, overriddenSimContextId, utcSim.getId());
                            sedmlModel.addTask(sedmlTask);
                            // scanned parameters
                            String repeatedTaskId = "repTsk_" + simContextCnt + "_" + simCount;
                            // TODO: temporary solution - we use as range here the first range
                            String scn = scannedConstantsNames[0];
                            String rId = "range_" + simContextCnt + "_" + simCount + "_" + scn;
                            RepeatedTask rt = new RepeatedTask(repeatedTaskId, repeatedTaskId, true, rId);
                            // to be used later to add dataGenerators - in our case it has to be the repeated task
                            taskRef = repeatedTaskId;
                            SubTask subTask = new SubTask("0", taskId);
                            rt.addSubtask(subTask);
                            for (String scannedConstName : scannedConstantsNames) {
                                ConstantArraySpec constantArraySpec = mathOverrides.getConstantArraySpec(scannedConstName);
                                String rangeId = "range_" + simContextCnt + "_" + simCount + "_" + scannedConstName;
                                // list of Ranges, if sim is parameter scan.
                                if (constantArraySpec != null) {
                                    Range r = null;
                                    System.out.println("     " + constantArraySpec.toString());
                                    if (constantArraySpec.getType() == ConstantArraySpec.TYPE_INTERVAL) {
                                        // ------ Uniform Range
                                        r = new UniformRange(rangeId, constantArraySpec.getMinValue(), constantArraySpec.getMaxValue(), constantArraySpec.getNumValues());
                                        rt.addRange(r);
                                    } else {
                                        // ----- Vector Range
                                        cbit.vcell.math.Constant[] cs = constantArraySpec.getConstants();
                                        ArrayList<Double> values = new ArrayList<Double>();
                                        for (int i = 0; i < cs.length; i++) {
                                            String value = cs[i].getExpression().infix() + ", ";
                                            values.add(Double.parseDouble(value));
                                        }
                                        r = new VectorRange(rangeId, values);
                                        rt.addRange(r);
                                    }
                                    // use scannedParamHash to store rangeId for that param, since it might be needed if unscanned param has a scanned param in expr.
                                    if (scannedParamHash.get(scannedConstName).equals(scannedConstName)) {
                                        // the hash was originally populated as <scannedParamName, scannedParamName>. Replace 'value' with rangeId for scannedParam
                                        scannedParamHash.put(scannedConstName, r.getId());
                                    }
                                    // create setValue for scannedConstName
                                    SymbolTableEntry ste2 = getSymbolTableEntryForModelEntity(mathSymbolMapping, scannedConstName);
                                    XPathTarget target1 = getTargetXPath(ste2, l2gMap);
                                    ASTNode math1 = new ASTCi(scannedConstName);
                                    SetValue setValue1 = new SetValue(target1, r.getId(), sedModel.getId());
                                    setValue1.setMath(math1);
                                    rt.addChange(setValue1);
                                } else {
                                    throw new RuntimeException("No scan ranges found for scanned parameter : '" + scannedConstName + "'.");
                                }
                            }
                            // for unscanned parameter overrides
                            for (String unscannedParamName : unscannedParamHash.values()) {
                                SymbolTableEntry ste = getSymbolTableEntryForModelEntity(mathSymbolMapping, unscannedParamName);
                                Expression unscannedParamExpr = mathOverrides.getActualExpression(unscannedParamName, 0);
                                if (unscannedParamExpr.isNumeric()) {
                                    // if expression is numeric, add ChangeAttribute to model created above
                                    XPathTarget targetXpath = getTargetAttributeXPath(ste, l2gMap);
                                    ChangeAttribute changeAttribute = new ChangeAttribute(targetXpath, unscannedParamExpr.infix());
                                    sedModel.addChange(changeAttribute);
                                } else {
                                    // check for any scanned parameter in unscanned parameter expression
                                    ASTNode math = Libsedml.parseFormulaString(unscannedParamExpr.infix());
                                    String[] exprSymbols = unscannedParamExpr.getSymbols();
                                    boolean bHasScannedParameter = false;
                                    String scannedParamNameInUnscannedParamExp = null;
                                    for (String symbol : exprSymbols) {
                                        if (scannedParamHash.get(symbol) != null) {
                                            bHasScannedParameter = true;
                                            scannedParamNameInUnscannedParamExp = new String(symbol);
                                            // @TODO check for multiple scannedParameters in expression.
                                            break;
                                        }
                                    }
                                    // (scanned parameter in expr) ? (add setValue for unscanned param in repeatedTask) : (add computeChange to modifiedModel)
                                    if (bHasScannedParameter && scannedParamNameInUnscannedParamExp != null) {
                                        // create setValue for unscannedParamName (which contains a scanned param in its expression)
                                        SymbolTableEntry entry = getSymbolTableEntryForModelEntity(mathSymbolMapping, unscannedParamName);
                                        XPathTarget target = getTargetXPath(entry, l2gMap);
                                        String rangeId = scannedParamHash.get(scannedParamNameInUnscannedParamExp);
                                        // @TODO: we have no range??
                                        SetValue setValue = new SetValue(target, rangeId, sedModel.getId());
                                        setValue.setMath(math);
                                        rt.addChange(setValue);
                                    } else {
                                        // non-numeric expression : add 'computeChange' to modified model
                                        XPathTarget targetXpath = getTargetXPath(ste, l2gMap);
                                        ComputeChange computeChange = new ComputeChange(targetXpath, math);
                                        for (String symbol : exprSymbols) {
                                            String symbolName = TokenMangler.mangleToSName(symbol);
                                            SymbolTableEntry ste1 = vcModel.getEntry(symbol);
                                            // ste1 could be a math parameter, hence the above could return null
                                            if (ste1 == null) {
                                                ste1 = simContext.getMathDescription().getEntry(symbol);
                                            }
                                            if (ste1 != null) {
                                                if (ste1 instanceof SpeciesContext || ste1 instanceof Structure || ste1 instanceof ModelParameter) {
                                                    XPathTarget ste1_XPath = getTargetXPath(ste1, l2gMap);
                                                    org.jlibsedml.Variable sedmlVar = new org.jlibsedml.Variable(symbolName, symbolName, taskRef, ste1_XPath.getTargetAsString());
                                                    computeChange.addVariable(sedmlVar);
                                                } else {
                                                    double doubleValue = 0.0;
                                                    if (ste1 instanceof ReservedSymbol) {
                                                        doubleValue = getReservedSymbolValue(ste1);
                                                    } else if (ste instanceof Function) {
                                                        try {
                                                            doubleValue = ste.getExpression().evaluateConstant();
                                                        } catch (Exception e) {
                                                            e.printStackTrace(System.out);
                                                            throw new RuntimeException("Unable to evaluate function '" + ste.getName() + "' used in '" + unscannedParamName + "' expression : ", e);
                                                        }
                                                    } else {
                                                        doubleValue = ste.getConstantValue();
                                                    }
                                                    // TODO: shouldn't be s1_init_uM which is a math symbol, should be s0 (so use the ste-something from above)
                                                    // TODO: revert to Variable, not Parameter
                                                    Parameter sedmlParameter = new Parameter(symbolName, symbolName, doubleValue);
                                                    computeChange.addParameter(sedmlParameter);
                                                }
                                            } else {
                                                throw new RuntimeException("Symbol '" + symbol + "' used in expression for '" + unscannedParamName + "' not found in model.");
                                            }
                                        }
                                        sedModel.addChange(computeChange);
                                    }
                                }
                            }
                            sedmlModel.addModel(sedModel);
                            sedmlModel.addTask(rt);
                        }
                    } else {
                        // no math overrides, add basic task.
                        String taskId = "tsk_" + simContextCnt + "_" + simCount;
                        Task sedmlTask = new Task(taskId, taskId, simContextId, utcSim.getId());
                        sedmlModel.addTask(sedmlTask);
                        // to be used later to add dataGenerators : one set of DGs per model (simContext).
                        taskRef = taskId;
                    }
                    // add one dataGenerator for 'time' for entire SEDML model.
                    // (using the id of the first task in model for 'taskRef' field of var since
                    String timeDataGenPrefix = DATAGENERATOR_TIME_NAME + "_" + taskRef;
                    DataGenerator timeDataGen = sedmlModel.getDataGeneratorWithId(timeDataGenPrefix);
                    if (timeDataGen == null) {
                        // org.jlibsedml.Variable timeVar = new org.jlibsedml.Variable(DATAGENERATOR_TIME_SYMBOL, DATAGENERATOR_TIME_SYMBOL, sedmlModel.getTasks().get(0).getId(), VariableSymbol.TIME);
                        org.jlibsedml.Variable timeVar = new org.jlibsedml.Variable(DATAGENERATOR_TIME_SYMBOL, DATAGENERATOR_TIME_SYMBOL, taskRef, VariableSymbol.TIME);
                        ASTNode math = Libsedml.parseFormulaString(DATAGENERATOR_TIME_SYMBOL);
                        timeDataGen = new DataGenerator(timeDataGenPrefix, timeDataGenPrefix, math);
                        timeDataGen.addVariable(timeVar);
                        sedmlModel.addDataGenerator(timeDataGen);
                        dataGeneratorsOfSim.add(timeDataGen);
                    }
                    // add dataGenerators for species
                    // get species list from SBML model.
                    String dataGenIdPrefix = "dataGen_" + taskRef;
                    String[] varNamesList = SimSpec.fromSBML(sbmlString).getVarsList();
                    for (String varName : varNamesList) {
                        org.jlibsedml.Variable sedmlVar = new org.jlibsedml.Variable(varName, varName, taskRef, sbmlSupport.getXPathForSpecies(varName));
                        ASTNode varMath = Libsedml.parseFormulaString(varName);
                        // "dataGen_" + varCount; - old code
                        String dataGenId = dataGenIdPrefix + "_" + TokenMangler.mangleToSName(varName);
                        DataGenerator dataGen = new DataGenerator(dataGenId, dataGenId, varMath);
                        dataGen.addVariable(sedmlVar);
                        sedmlModel.addDataGenerator(dataGen);
                        dataGeneratorsOfSim.add(dataGen);
                        varCount++;
                    }
                    // add DataGenerators for output functions here
                    ArrayList<AnnotatedFunction> outputFunctions = simContext.getOutputFunctionContext().getOutputFunctionsList();
                    for (AnnotatedFunction annotatedFunction : outputFunctions) {
                        Expression functionExpr = annotatedFunction.getExpression();
                        ASTNode funcMath = Libsedml.parseFormulaString(functionExpr.infix());
                        // "dataGen_" + varCount; - old code
                        String dataGenId = dataGenIdPrefix + "_" + TokenMangler.mangleToSName(annotatedFunction.getName());
                        DataGenerator dataGen = new DataGenerator(dataGenId, dataGenId, funcMath);
                        String[] functionSymbols = functionExpr.getSymbols();
                        for (String symbol : functionSymbols) {
                            String symbolName = TokenMangler.mangleToSName(symbol);
                            // try to get symbol from model, if null, try simContext.mathDesc
                            SymbolTableEntry ste = vcModel.getEntry(symbol);
                            if (ste == null) {
                                ste = simContext.getMathDescription().getEntry(symbol);
                            }
                            if (ste instanceof SpeciesContext || ste instanceof Structure || ste instanceof ModelParameter) {
                                XPathTarget targetXPath = getTargetXPath(ste, l2gMap);
                                org.jlibsedml.Variable sedmlVar = new org.jlibsedml.Variable(symbolName, symbolName, taskRef, targetXPath.getTargetAsString());
                                dataGen.addVariable(sedmlVar);
                            } else {
                                double value = 0.0;
                                if (ste instanceof Function) {
                                    try {
                                        value = ste.getExpression().evaluateConstant();
                                    } catch (Exception e) {
                                        e.printStackTrace(System.out);
                                        throw new RuntimeException("Unable to evaluate function '" + ste.getName() + "' for output function '" + annotatedFunction.getName() + "'.", e);
                                    }
                                } else {
                                    value = ste.getConstantValue();
                                }
                                Parameter sedmlParameter = new Parameter(symbolName, symbolName, value);
                                dataGen.addParameter(sedmlParameter);
                            }
                        }
                        sedmlModel.addDataGenerator(dataGen);
                        dataGeneratorsOfSim.add(dataGen);
                        varCount++;
                    }
                    simCount++;
                    // ignoring output for spatial deterministic (spatial stochastic is not exported to SEDML) and non-spatial stochastic applications with histogram
                    if (!(simContext.getGeometry().getDimension() > 0)) {
                        // ignore Output (Plot2d)  for non-spatial stochastic simulation with histogram.
                        boolean bSimHasHistogram = false;
                        if (simContext.isStoch()) {
                            long numOfTrials = simTaskDesc.getStochOpt().getNumOfTrials();
                            if (numOfTrials > 1) {
                                // not histogram {
                                bSimHasHistogram = true;
                            }
                        }
                        if (!bSimHasHistogram) {
                            String plot2dId = "plot2d_" + TokenMangler.mangleToSName(vcSimulation.getName());
                            Plot2D sedmlPlot2d = new Plot2D(plot2dId, simContext.getName() + "plots");
                            sedmlPlot2d.addNote(createNotesElement("Plot of all variables and output functions from application '" + simContext.getName() + "' ; simulation '" + vcSimulation.getName() + "' in VCell model"));
                            List<DataGenerator> dataGenerators = sedmlModel.getDataGenerators();
                            String xDataRef = sedmlModel.getDataGeneratorWithId(DATAGENERATOR_TIME_NAME + "_" + taskRef).getId();
                            // add a curve for each dataGenerator in SEDML model
                            int curveCnt = 0;
                            for (DataGenerator dataGenerator : dataGeneratorsOfSim) {
                                // no curve for time, since time is xDateReference
                                if (dataGenerator.getId().equals(xDataRef)) {
                                    continue;
                                }
                                String curveId = "curve_" + curveCnt++;
                                Curve curve = new Curve(curveId, curveId, false, false, xDataRef, dataGenerator.getId());
                                sedmlPlot2d.addCurve(curve);
                            }
                            sedmlModel.addOutput(sedmlPlot2d);
                        }
                    }
                }
            // end - for 'sims'
            } else {
                // end if (!(simContext.getGeometry().getDimension() > 0 && simContext.isStoch()))
                String msg = "\n\t" + simContextName + " : export of spatial stochastic (Smoldyn solver) applications to SEDML not supported at this time.";
                sedmlNotesStr += msg;
            }
            // end : if-else simContext is not spatial stochastic
            simContextCnt++;
        }
        // if sedmlNotesStr is not null, there were some applications that could not be exported to SEDML (eg., spatial stochastic). Create a notes element and add it to sedml Model.
        if (sedmlNotesStr.length() > 0) {
            sedmlNotesStr = "\n\tThe following applications in the VCell model were not exported to VCell : " + sedmlNotesStr;
            sedmlModel.addNote(createNotesElement(sedmlNotesStr));
        }
        // error check : if there are no non-spatial deterministic applications (=> no models in SEDML document), complain.
        if (sedmlModel.getModels().isEmpty()) {
            throw new RuntimeException("No applications in biomodel to export to Sedml.");
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new RuntimeException("Error adding model to SEDML document : " + e.getMessage());
    }
}

Example 2 with XmlParseException

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

the class PathwayBiopax3Test method bioModelToXML.

static String bioModelToXML(PathwayModel pathwayModel) throws XmlParseException {
    String xmlString = null;
    try {
        if (pathwayModel == null) {
            throw new IllegalArgumentException("Invalid input for pathwayModel: " + pathwayModel);
        }
        String biopaxVersion = "3.0";
        // create root element
        Element rootElement = new Element("RDF", rdf);
        rootElement.setAttribute("version", biopaxVersion);
        // get element from producer and add it to root element
        PathwayProducerBiopax3 xmlProducer = new PathwayProducerBiopax3(new RDFXMLContext());
        // here is work done
        xmlProducer.getXML(pathwayModel, rootElement);
        // create xml doc and convert to string
        Document bioDoc = new Document();
        Comment docComment = new Comment("This pathway model was generated in Biopax Version " + biopaxVersion);
        bioDoc.addContent(docComment);
        bioDoc.setRootElement(rootElement);
        xmlString = XmlUtil.xmlToString(bioDoc, false);
        System.out.println(xmlString);
    } catch (Exception e) {
        e.printStackTrace();
        throw new XmlParseException("Unable to generate PathwayModel XML", e);
    }
    return xmlString;
}

Example 3 with XmlParseException

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

the class MicroscopyXmlproducer method getXML.

/**
 * This methods returns a XML represnetation of a VCImage object.
 * Creation date: (3/1/2001 3:02:37 PM)
 * @param param cbit.image.VCImage
 * @return Element
 * @throws XmlParseException
 */
private static Element getXML(UShortImage param, Xmlproducer vcellXMLProducer, boolean bSaveCompressed) throws XmlParseException {
    Element image = new Element(MicroscopyXMLTags.UShortImageTag);
    // add atributes
    if (param.getName() != null && param.getName().length() > 0) {
        image.setAttribute(XMLTags.NameAttrTag, mangle(param.getName()));
    }
    // Add annotation
    if (param.getDescription() != null && param.getDescription().length() > 0) {
        Element annotationElement = new Element(XMLTags.AnnotationTag);
        annotationElement.setText(mangle(param.getDescription()));
        image.addContent(annotationElement);
    }
    // Add extent
    if (param.getExtent() != null) {
        image.addContent(vcellXMLProducer.getXML(param.getExtent()));
    }
    // Add Origin
    if (param.getOrigin() != null) {
        image.addContent(vcellXMLProducer.getXML(param.getOrigin()));
    }
    final int BYTES_PER_SHORT = 2;
    int aNumX = param.getNumX();
    int aNumY = param.getNumY();
    int aNumZ = param.getNumZ();
    // Add Imagedata subelement
    int UNCOMPRESSED_SIZE_BYTES = aNumX * aNumY * aNumZ * BYTES_PER_SHORT;
    short[] pixelsShort = param.getPixels();
    byte[] compressedPixels = null;
    boolean bForceUncompressed = false;
    while (true) {
        ByteArrayOutputStream bos = new ByteArrayOutputStream();
        OutputStream dos = bos;
        if (bSaveCompressed && !bForceUncompressed) {
            dos = new DeflaterOutputStream(bos);
        }
        ByteBuffer byteBuffer = ByteBuffer.allocate(UNCOMPRESSED_SIZE_BYTES);
        for (int i = 0; i < pixelsShort.length; i++) {
            byteBuffer.putShort(pixelsShort[i]);
        }
        try {
            dos.write(byteBuffer.array());
        } catch (IOException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException("failed to create compressed pixel data");
        } finally {
            if (dos != null) {
                try {
                    dos.close();
                } catch (Exception e2) {
                    e2.printStackTrace();
                }
            }
        }
        compressedPixels = bos.toByteArray();
        if (!bSaveCompressed || bForceUncompressed) {
            if (UNCOMPRESSED_SIZE_BYTES != compressedPixels.length) {
                throw new XmlParseException("failed to create uncompressed pixel data");
            }
        } else if (!bForceUncompressed) {
            if (UNCOMPRESSED_SIZE_BYTES <= compressedPixels.length) {
                // Compression didn't compress
                // Save uncompressed so reader not confused
                bForceUncompressed = true;
                continue;
            }
        }
        break;
    }
    Element imagedata = new Element(XMLTags.ImageDataTag);
    // Get imagedata attributes
    imagedata.setAttribute(XMLTags.XAttrTag, String.valueOf(aNumX));
    imagedata.setAttribute(XMLTags.YAttrTag, String.valueOf(aNumY));
    imagedata.setAttribute(XMLTags.ZAttrTag, String.valueOf(aNumZ));
    imagedata.setAttribute(XMLTags.CompressedSizeTag, String.valueOf(compressedPixels.length));
    // Get imagedata content
    // encode
    imagedata.addContent(org.vcell.util.Hex.toString(compressedPixels));
    // Add imagedata to VCImage element
    image.addContent(imagedata);
    return image;
}

Example 4 with XmlParseException

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

the class SimulationTaskMessage method toMessage.

/**
 * Insert the method's description here.
 * Creation date: (12/31/2003 11:08:17 AM)
 * @return javax.jms.Message
 * @param session cbit.vcell.messaging.VCellSession
 * @throws VCMessagingException
 */
private VCMessage toMessage(VCMessageSession session) throws VCMessagingException {
    VCMessage message;
    try {
        message = session.createTextMessage(XmlHelper.simTaskToXML(simTask));
    } catch (XmlParseException e) {
        e.printStackTrace(System.out);
        throw new VCMessagingException("failed to restore Simulation Task from XML", e);
    }
    // must have
    message.setStringProperty(VCMessagingConstants.MESSAGE_TYPE_PROPERTY, MessageConstants.MESSAGE_TYPE_SIMULATION_JOB_VALUE);
    // must have
    message.setIntProperty(MessageConstants.JOBINDEX_PROPERTY, simTask.getSimulationJob().getJobIndex());
    // must have
    message.setIntProperty(MessageConstants.TASKID_PROPERTY, simTask.getTaskID());
    // might be used to remove from the job queue when do stopSimulation
    message.setStringProperty(VCMessagingConstants.USERNAME_PROPERTY, simTask.getUserName());
    // might be used to remove from the job queue when do stopSimulation
    message.setLongProperty(MessageConstants.SIMKEY_PROPERTY, Long.parseLong(simTask.getSimKey() + ""));
    // for worker message filter
    message.setDoubleProperty(MessageConstants.SIZE_MB_PROPERTY, simTask.getEstimatedMemorySizeMB());
    if (simTask.getComputeResource() != null) {
        // for worker message filter
        message.setStringProperty(MessageConstants.COMPUTE_RESOURCE_PROPERTY, simTask.getComputeResource());
    }
    FieldDataIdentifierSpec[] fieldDataIDs = simTask.getSimulationJob().getFieldDataIdentifierSpecs();
    if (fieldDataIDs != null && fieldDataIDs.length > 0) {
        StringBuffer sb = new StringBuffer();
        for (int i = 0; i < fieldDataIDs.length; i++) {
            sb.append(fieldDataIDs[i].toCSVString() + "\n");
        }
        message.setStringProperty(MessageConstants.FIELDDATAID_PROPERTY, sb.toString());
    }
    return message;
}

Example 5 with XmlParseException

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

the class XMLMetaDataReader method readFromElement.

@SuppressWarnings("unchecked")
public static void readFromElement(VCMetaData metaData, IdentifiableProvider identifiableProvider, Element metadataElement) throws XmlParseException {
    Element bindingElement = metadataElement.getChild(XMLMetaData.URI_BINDING_LIST_TAG, VCMetaData.nsVCML);
    if (bindingElement != null) {
        // read binding
        List<Element> entryElements = bindingElement.getChildren(XMLMetaData.URI_BINDING_TAG, VCMetaData.nsVCML);
        for (Iterator<Element> iterator = entryElements.iterator(); iterator.hasNext(); ) {
            Element entryElement = iterator.next();
            try {
                String uri = entryElement.getAttributeValue(XMLMetaData.URI_ATTR_TAG);
                String vcidString = entryElement.getAttributeValue(XMLMetaData.VCID_ATTR_TAG);
                // make new entry based on URI
                // create VCID
                VCID vcid = VCID.fromString(vcidString);
                // lookup Identifiable object using VCID ... add to entry.
                metaData.getRegistry().newEntry(metaData.getRdfData(), identifiableProvider.getIdentifiableObject(vcid), uri);
            } catch (VCID.InvalidVCIDException e) {
                e.printStackTrace();
                throw new XmlParseException(e);
            }
        }
    }
    Element rdfElement = metadataElement.getChild(XMLRDF.tagRDF, XMLRDF.nsRDF);
    if (rdfElement != null) {
        // read RDF
        try {
            metaData.addToModelFromElement(rdfElement);
        } catch (RDFParseException e) {
            e.printStackTrace();
            throw new XmlParseException(e.getMessage());
        } catch (RDFHandlerException e) {
            e.printStackTrace();
            throw new XmlParseException(e.getMessage());
        } catch (IOException e) {
            e.printStackTrace();
            throw new XmlParseException(e.getMessage());
        }
    }
    Element nonRDFAnnotationListElement = metadataElement.getChild(XMLMetaData.NONRDF_ANNOTATION_LIST_TAG, VCMetaData.nsVCML);
    if (nonRDFAnnotationListElement != null) {
        List<Element> nonRDFAnnotationElements = nonRDFAnnotationListElement.getChildren(XMLMetaData.NONRDF_ANNOTATION_TAG, VCMetaData.nsVCML);
        for (Element nonRDFAnnotationElement : nonRDFAnnotationElements) {
            String vcidString = nonRDFAnnotationElement.getAttributeValue(XMLMetaData.VCID_ATTR_TAG);
            VCID vcid = null;
            try {
                vcid = VCID.fromString(vcidString);
            } catch (InvalidVCIDException e) {
                e.printStackTrace();
                throw new XmlParseException(e.getMessage());
            }
            Identifiable identifiable = identifiableProvider.getIdentifiableObject(vcid);
            if (identifiable != null) {
                // populate the annotation
                Element freeTextAnnotationElement = nonRDFAnnotationElement.getChild(XMLMetaData.FREETEXT_TAG, VCMetaData.nsVCML);
                if (freeTextAnnotationElement != null) {
                    String freeText = freeTextAnnotationElement.getText();
                    metaData.setFreeTextAnnotation(identifiable, freeText);
                }
                Element xhtmlNotesElement = nonRDFAnnotationElement.getChild(XMLMetaData.NOTES_TAG, VCMetaData.nsVCML);
                if (xhtmlNotesElement != null) {
                    metaData.setXhtmlNotes(identifiable, xhtmlNotesElement);
                }
                Element annotationListElement = nonRDFAnnotationElement.getChild(XMLMetaData.ANNOTATION_LIST_TAG, VCMetaData.nsVCML);
                if (annotationListElement != null) {
                    List<?> annotationContents = annotationListElement.getContent();
                    List<Element> annotationElements = new ArrayList<Element>();
                    for (int i = 0; i < annotationContents.size(); i++) {
                        if (annotationContents.get(i) instanceof Element) {
                            annotationElements.add((Element) annotationContents.get(i));
                        }
                    }
                    metaData.setXmlAnnotations(identifiable, annotationElements.toArray(new Element[annotationElements.size()]));
                }
            } else {
                System.err.println("Cannot find identifiable for vcid : " + vcidString);
            }
        }
    }
}