Examples with OutputFunctionContext cbit.vcell.solver.OutputFunctionContext used on opensource projects

Example 1 with OutputFunctionContext

use of cbit.vcell.solver.OutputFunctionContext in project vcell by virtualcell.

the class OutputFunctionsListTableModel method propertyChange.

/**
 * This method gets called when a bound property is changed.
 * @param evt A PropertyChangeEvent object describing the event source
 *   	and the property that has changed.
 */
public void propertyChange(java.beans.PropertyChangeEvent evt) {
    OutputFunctionContext fc = getOutputFunctionContext();
    SimulationOwner so = null;
    if (fc != null) {
        so = fc.getSimulationOwner();
    }
    if (evt.getSource() == fc && evt.getPropertyName().equals(OutputFunctionContext.PROPERTY_OUTPUT_FUNCTIONS)) {
        setData(outputFunctionContext.getOutputFunctionsList());
    }
    if (evt.getSource() instanceof SimulationContext && evt.getSource() == so && evt.getPropertyName().equals(Model.PROPERTY_NAME_MODEL_ENTITY_NAME)) {
        SimulationContext simulationContext = (SimulationContext) so;
        if (fc.getOutputFunctionsList() == null || fc.getOutputFunctionsList().isEmpty()) {
            return;
        }
        Hashtable<String, Object> hashTable = new Hashtable<String, Object>();
        // 
        // WARNING: this should NOT be used under any circumstance for batch renaming
        // MathDescription, MathMapping, expressions are NOT thread safe
        // 
        AsynchClientTask task0 = new AsynchClientTask("Renaming Functions", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING, false, false) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                MathMappingCallback callback = new MathMappingCallback() {

                    @Override
                    public void setProgressFraction(float fractionDone) {
                    }

                    @Override
                    public void setMessage(String message) {
                    }

                    @Override
                    public boolean isInterrupted() {
                        return false;
                    }
                };
                MathMapping mathMapping = simulationContext.createNewMathMapping(callback, NetworkGenerationRequirements.ComputeFullNoTimeout);
                MathDescription mathDesc = null;
                try {
                    mathDesc = mathMapping.getMathDescription(callback);
                } catch (MappingException | MathException | MatrixException | ExpressionException | ModelException e1) {
                    e1.printStackTrace();
                }
                String oldName = (String) evt.getOldValue();
                String newName = (String) evt.getNewValue();
                ArrayList<AnnotatedFunction> afList = fc.getOutputFunctionsList();
                List<Expression> changedExpressions = new ArrayList<>();
                for (AnnotatedFunction af : afList) {
                    if (af == null) {
                        continue;
                    }
                    Expression exp = af.getExpression();
                    if (exp == null || exp.getSymbols() == null || exp.getSymbols().length == 0) {
                        continue;
                    }
                    String errMsg = "Failed to rename symbol '" + oldName + "' with '" + newName + "' in the Expression of Function '" + af.getName() + "'.";
                    for (String symbol : exp.getSymbols()) {
                        if (symbol.contentEquals(oldName)) {
                            try {
                                exp.substituteInPlace(new Expression(oldName), new Expression(newName));
                                changedExpressions.add(exp);
                            } catch (ExpressionException e) {
                                e.printStackTrace();
                                throw new RuntimeException(errMsg);
                            }
                        }
                    }
                }
                if (changedExpressions.size() > 0) {
                    try {
                        simulationContext.setMathDescription(mathDesc);
                        for (Expression exp : changedExpressions) {
                            exp.bindExpression(outputFunctionContext);
                        }
                    } catch (ExpressionException | PropertyVetoException e) {
                        e.printStackTrace();
                    }
                }
            }
        };
        ClientTaskDispatcher.dispatch(ownerTable, hashTable, new AsynchClientTask[] { task0 }, false);
    }
    if (evt.getPropertyName().equals(GeometryOwner.PROPERTY_NAME_GEOMETRY)) {
        Geometry oldGeometry = (Geometry) evt.getOldValue();
        Geometry newGeometry = (Geometry) evt.getNewValue();
        // changing from ode to pde
        if (oldGeometry.getDimension() == 0 && newGeometry.getDimension() > 0) {
            fireTableStructureChanged();
            setData(getOutputFunctionContext().getOutputFunctionsList());
        }
    }
}

Example 2 with OutputFunctionContext

use of cbit.vcell.solver.OutputFunctionContext in project vcell by virtualcell.

the class OutputFunctionsPanel method setOutputFunctionContext.

private void setOutputFunctionContext(OutputFunctionContext argOutputFnContext) {
    OutputFunctionContext oldValue = this.outputFunctionContext;
    this.outputFunctionContext = argOutputFnContext;
    firePropertyChange("outputFunctionContext", oldValue, argOutputFnContext);
}

Example 3 with OutputFunctionContext

use of cbit.vcell.solver.OutputFunctionContext in project vcell by virtualcell.

the class XmlReader method getMathModel.

/*
public RateRuleVariable[] getRateRuleVariables(Element rateRuleVarsElement, Model model) throws XmlParseException  {
	Iterator<Element> rateRuleVarsIterator = rateRuleVarsElement.getChildren(XMLTags.RateRuleVariableTag, vcNamespace).iterator();
	Vector<RateRuleVariable> rateRuleVarsVector = new Vector<RateRuleVariable>();
	while (rateRuleVarsIterator.hasNext()) {
		Element rrvElement = (Element) rateRuleVarsIterator.next();

		RateRuleVariable newRateRuleVar = null;
		try {
			String rrvName = unMangle(rrvElement.getAttributeValue(XMLTags.NameAttrTag));
		    String rrvStructureName = unMangle(rrvElement.getAttributeValue(XMLTags.StructureAttrTag));
		    // structure can be null
		    Structure rrvStructure = null;
		    if (rrvStructureName != null) {
		    	rrvStructure = (Structure) model.getStructure(rrvStructureName);
		    }
//		    if (structureref == null) {
//		    	throw new XmlParseException("The structure " + rrvStructureName + "could not be resolved!");
//		    }
		    String rrvRoleStr = rrvElement.getAttributeValue(XMLTags.ParamRoleAttrTag);
		    int rrvRole = RateRuleVariable.getParamRoleFromDesc(rrvRoleStr);
		    Element rrvParamElement = rrvElement.getChild(XMLTags.ParameterTag, vcNamespace);
		    ModelParameter rrvParameter = getModelParameter(rrvParamElement, model);
		    newRateRuleVar = new RateRuleVariable(rrvName, rrvStructure, rrvParameter, rrvRole);
			newRateRuleVar.bind();
		} catch (ExpressionBindingException e) {
			e.printStackTrace(System.out);
			throw new XmlParseException(e.getMessage());
		}
		if (newRateRuleVar != null) {
			rateRuleVarsVector.add(newRateRuleVar);
		}
	}
	
	return ((RateRuleVariable[])BeanUtils.getArray(rateRuleVarsVector, RateRuleVariable.class));
}
*/
/**
 * This method returns a MathModel object from a XML Element.
 * Creation date: (3/13/2001 12:35:00 PM)
 * @return cbit.vcell.mathmodel.MathModel
 * @param param org.jdom.Element
 */
public MathModel getMathModel(Element param) throws XmlParseException {
    // Create it
    // set Metadata (version), if any
    Version versionObject = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace));
    MathModel mathmodel = new MathModel(versionObject);
    // Set attributes
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    try {
        mathmodel.setName(name);
        // String annotation = param.getAttributeValue(XMLTags.AnnotationAttrTag);
        // if (annotation!=null) {
        // mathmodel.setDescription(unMangle(annotation));
        // }
        // Add annotation
        String annotationText = param.getChildText(XMLTags.AnnotationTag, vcNamespace);
        if (annotationText != null && annotationText.length() > 0) {
            mathmodel.setDescription(unMangle(annotationText));
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("An error occurred while trying to set the name " + param.getAttributeValue(XMLTags.NameAttrTag) + "to a MathModel!", e);
    }
    // set Geometry (if any)
    Element tempElem = param.getChild(XMLTags.GeometryTag, vcNamespace);
    Geometry tempGeometry = getGeometry(tempElem);
    // set MathDescription
    tempElem = param.getChild(XMLTags.MathDescriptionTag, vcNamespace);
    MathDescription mathDesc = getMathDescription(tempElem, tempGeometry);
    if (tempElem != null) {
        mathmodel.setMathDescription(mathDesc);
    } else {
        throw new XmlParseException("MathDescription missing in this MathModel!");
    }
    // set output functions (outputfunctionContext)
    Element outputFunctionsElement = param.getChild(XMLTags.OutputFunctionsTag, vcNamespace);
    if (outputFunctionsElement != null) {
        ArrayList<AnnotatedFunction> outputFunctions = getOutputFunctions(outputFunctionsElement);
        try {
            // construct OutputFnContext from mathmodel and add output functions that were read in from XML.
            OutputFunctionContext outputFnContext = mathmodel.getOutputFunctionContext();
            for (AnnotatedFunction outputFunction : outputFunctions) {
                outputFnContext.addOutputFunction(outputFunction);
            }
        } catch (PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException(e);
        }
    }
    // Set simulations contexts (if any)
    List<Element> childList = param.getChildren(XMLTags.SimulationTag, vcNamespace);
    Simulation[] simList = new Simulation[childList.size()];
    int simCounter = 0;
    for (Element simElement : childList) {
        simList[simCounter] = getSimulation(simElement, mathDesc);
        simCounter++;
    }
    try {
        mathmodel.setSimulations(simList);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("A PropertyVetoException occurred when adding the Simulations to the MathModel " + name, e);
    }
    return mathmodel;
}

Example 4 with OutputFunctionContext

use of cbit.vcell.solver.OutputFunctionContext in project vcell by virtualcell.

the class IonItems method saveVCMLRemoveSimsWithNoData.

private static void saveVCMLRemoveSimsWithNoData(Connection con, File dirToSaveVCML, File usersDir, long startSimKey, long endSimKey) {
    // select id from vc_biomodel where versionflag=3 and privacy=0;
    String bmsql = "SELECT " + BioModelTable.table.id.getQualifiedColName() + " modelkey" + "," + UserTable.table.id.getQualifiedColName() + " userkey" + "," + UserTable.table.userid.getQualifiedColName() + " userid" + " FROM " + BioModelTable.table.getTableName() + "," + UserTable.table.getTableName() + " WHERE " + BioModelTable.table.versionFlag.getQualifiedColName() + "=" + VersionFlag.Published.getIntValue() + " AND " + BioModelTable.table.privacy.getQualifiedColName() + "=" + GroupAccess.GROUPACCESS_ALL.intValue() + " AND " + BioModelTable.table.ownerRef.getQualifiedColName() + "=" + UserTable.table.id.getQualifiedColName() + " AND " + BioModelTable.table.id.getQualifiedColName() + " IN " + "(SELECT " + PublicationModelLinkTable.table.bioModelRef.getQualifiedColName() + " FROM " + PublicationModelLinkTable.table.getTableName() + " WHERE " + PublicationModelLinkTable.table.bioModelRef.getQualifiedColName() + " IS NOT NULL)" + " ORDER BY modelKey";
    String mmsql = "SELECT " + MathModelTable.table.id.getQualifiedColName() + " modelkey" + "," + UserTable.table.id.getQualifiedColName() + " userkey" + "," + UserTable.table.userid.getQualifiedColName() + " userid" + " FROM " + MathModelTable.table.getTableName() + "," + UserTable.table.getTableName() + " WHERE " + MathModelTable.table.versionFlag.getQualifiedColName() + "=" + VersionFlag.Published.getIntValue() + " AND " + MathModelTable.table.privacy.getQualifiedColName() + "=" + GroupAccess.GROUPACCESS_ALL.intValue() + " AND " + MathModelTable.table.ownerRef.getQualifiedColName() + "=" + UserTable.table.id.getQualifiedColName() + " AND " + MathModelTable.table.id.getQualifiedColName() + " IN " + // vc_publicationmodellink.biomodelref
    "(SELECT " + PublicationModelLinkTable.table.mathModelRef.getQualifiedColName() + " FROM " + PublicationModelLinkTable.table.getTableName() + " WHERE " + PublicationModelLinkTable.table.mathModelRef.getQualifiedColName() + " IS NOT NULL)" + " ORDER BY modelKey";
    Statement stmt = null;
    try {
        stmt = con.createStatement();
        // ArrayList<VCDocument> successDocs = new ArrayList<VCDocument>();
        DatabaseServerImpl databaseServerImpl = new DatabaseServerImpl(connFac, null);
        // ServerDocumentManager serverDocManager = new ServerDocumentManager(databaseServerImpl);
        // QueryHashtable qht = new QueryHashtable();
        DataSetControllerImpl dsci = new DataSetControllerImpl(new Cachetable(Cachetable.minute * 3, 30000000L), usersDir, null);
        ArrayList<Object[]> modeKeyAndUser = new ArrayList<Object[]>();
        for (int i = 0; i < 2; i++) {
            String sql = (i == 0 ? bmsql : mmsql);
            ResultSet rset = stmt.executeQuery(sql);
            while (rset.next()) {
                BigDecimal modelKeyBigDecimal = rset.getBigDecimal("modelkey");
                KeyValue modelKey = new KeyValue(modelKeyBigDecimal);
                if (startSimKey == 0 || (modelKeyBigDecimal.longValue() >= startSimKey && modelKeyBigDecimal.longValue() <= endSimKey)) {
                    User user = new User(rset.getString("userid"), new KeyValue(rset.getBigDecimal("userkey")));
                    modeKeyAndUser.add(new Object[] { (i == 0 ? VCDocumentType.BIOMODEL_DOC : VCDocumentType.MATHMODEL_DOC), modelKey, user });
                }
            }
            rset.close();
        }
        stmt.close();
        VCDocument vcDoc = null;
        for (int ii = 0; ii < modeKeyAndUser.size(); ii++) {
            try {
                VCDocumentType vcDocType = (VCDocumentType) modeKeyAndUser.get(ii)[0];
                KeyValue modelKey = (KeyValue) modeKeyAndUser.get(ii)[1];
                User user = (User) modeKeyAndUser.get(ii)[2];
                // -----NOTE: (privacy, versionflag) may not match between xml and database (because privacy and versionflag can be set without saving model)
                // some models regenerated from xml will not have same privacy and versionflag matched in query from database (the database values are correct, ignore the xml values)
                BigString modelXML = (vcDocType == VCDocumentType.BIOMODEL_DOC ? databaseServerImpl.getBioModelXML(user, modelKey) : databaseServerImpl.getMathModelXML(user, modelKey));
                Simulation[] sims = null;
                vcDoc = null;
                if (vcDocType == VCDocumentType.BIOMODEL_DOC) {
                    BioModel bm = cbit.vcell.xml.XmlHelper.XMLToBioModel(new XMLSource(modelXML.toString()));
                    bm.refreshDependencies();
                    sims = bm.getSimulations().clone();
                    vcDoc = bm;
                } else {
                    MathModel mm = cbit.vcell.xml.XmlHelper.XMLToMathModel(new XMLSource(modelXML.toString()));
                    mm.refreshDependencies();
                    sims = mm.getSimulations().clone();
                    vcDoc = mm;
                }
                // if(true) {
                // System.out.println(modelKey+" "+user+" "+vcDoc);
                // continue;
                // }
                boolean bRemovedSims = false;
                for (int j = 0; sims != null && j < sims.length; j++) {
                    try {
                        // public FoundSimDataInfo(long simID, int lastTaskID, int jobIndex, String userid) {
                        File foundLog = findSimLogFile(usersDir, new FoundSimDataInfo(Long.parseLong(sims[j].getKey().toString()), -1, 0, user.getName()), true, vcDocType);
                        if (foundLog == null) {
                            throw new Exception("Logfile not found for sim " + sims[j].getKey().toString());
                        } else {
                            VCSimulationIdentifier vcsi = new VCSimulationIdentifier(sims[j].getKey(), user);
                            VCSimulationDataIdentifier vcdID = new VCSimulationDataIdentifier(vcsi, 0);
                            OutputFunctionContext outputFunctionContext = sims[j].getSimulationOwner().getOutputFunctionContext();
                            OutputContext outputContext = new OutputContext(outputFunctionContext.getOutputFunctionsList().toArray(new AnnotatedFunction[0]));
                            DataIdentifier[] dataIdentifiers = dsci.getDataIdentifiers(outputContext, vcdID);
                            double[] dataSetTimes = dsci.getDataSetTimes(vcdID);
                            if (sims[j].getMathDescription().getGeometry().getDimension() == 0) {
                                ODEDataBlock odeDataBlock = dsci.getODEDataBlock(vcdID);
                            } else {
                                // for(int k=0;k<dataIdentifiers.length;k++){
                                SimDataBlock simDataBlock = dsci.getSimDataBlock(outputContext, vcdID, dataIdentifiers[0].getName(), dataSetTimes[dataSetTimes.length - 1]);
                            // }
                            }
                        }
                    } catch (Exception e) {
                        System.out.println("-----SIMERROR " + vcDoc.getVersion().getVersionKey() + "\n-----Sim=" + sims[j].getVersion());
                        e.printStackTrace();
                        if (e.getMessage().contains("HDF5")) {
                            return;
                        }
                        bRemovedSims = true;
                        if (vcDoc.getDocumentType() == VCDocument.VCDocumentType.BIOMODEL_DOC) {
                            ((BioModel) vcDoc).removeSimulation(sims[j]);
                        } else {
                            ((MathModel) vcDoc).removeSimulation(sims[j]);
                        }
                    }
                }
                String docXml = null;
                if (vcDoc.getDocumentType() == VCDocument.VCDocumentType.BIOMODEL_DOC) {
                    docXml = XmlHelper.bioModelToXML(((BioModel) vcDoc));
                } else {
                    docXml = XmlHelper.mathModelToXML(((MathModel) vcDoc));
                }
                PrintWriter pw = new PrintWriter(new File(dirToSaveVCML, vcDoc.getVersion().getVersionKey().toString() + "_" + (bRemovedSims) + ".xml"));
                pw.write(docXml);
                pw.close();
            // }
            } catch (Exception e) {
                System.out.println("----------GENERALERROR " + vcDoc.getVersion().getVersionKey());
                e.printStackTrace();
                if (vcDoc != null) {
                    PrintWriter pw = new PrintWriter(new File(dirToSaveVCML, vcDoc.getVersion().getVersionKey().toString() + "_exception.xml"));
                    pw.write("");
                    pw.close();
                }
            }
        }
    // for(VCDocument successDoc:successDocs) {
    // if(successDoc.getDocumentType() == VCDocument.VCDocumentType.BIOMODEL_DOC) {
    // ((BioModel)vcDoc).removeSimulation(sims[i]);
    // }else {
    // ((MathModel)vcDoc).removeSimulation(sims[i]);
    // }
    // 
    // }
    } catch (Exception e) {
        e.printStackTrace();
    } finally {
        if (stmt != null) {
            try {
                stmt.close();
            } catch (Exception e) {
                e.printStackTrace();
            }
        }
    }
}

Example 5 with OutputFunctionContext

use of cbit.vcell.solver.OutputFunctionContext in project vcell by virtualcell.

the class XmlReader method getSimulationContext.

/**
 * This method returns a SimulationContext from a XML representation.
 * Creation date: (4/2/2001 3:19:01 PM)
 * @return cbit.vcell.mapping.SimulationContext
 * @param param org.jdom.Element
 */
private SimulationContext getSimulationContext(Element param, BioModel biomodel) throws XmlParseException {
    // get the attributes
    // name
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    boolean bStoch = false;
    boolean bRuleBased = false;
    boolean bUseConcentration = true;
    boolean bRandomizeInitCondition = false;
    boolean bInsufficientIterations = false;
    boolean bInsufficientMaxMolecules = false;
    // default is true for now
    boolean bMassConservationModelReduction = true;
    NetworkConstraints nc = null;
    Element ncElement = param.getChild(XMLTags.RbmNetworkConstraintsTag, vcNamespace);
    if (ncElement != null) {
        // one network constraint element
        nc = getAppNetworkConstraints(ncElement, biomodel.getModel());
    } else {
        if (legacyNetworkConstraints != null) {
            nc = legacyNetworkConstraints;
        }
    }
    if ((param.getAttributeValue(XMLTags.StochAttrTag) != null) && (param.getAttributeValue(XMLTags.StochAttrTag).equals("true"))) {
        bStoch = true;
    }
    if (bStoch) {
        // stochastic and using concentration vs amount
        if ((param.getAttributeValue(XMLTags.ConcentrationAttrTag) != null) && (param.getAttributeValue(XMLTags.ConcentrationAttrTag).equals("false"))) {
            bUseConcentration = false;
        }
        // stochastic and randomizing initial conditions or not (for non-spatial)
        if ((param.getAttributeValue(XMLTags.RandomizeInitConditionTag) != null) && (param.getAttributeValue(XMLTags.RandomizeInitConditionTag).equals("true"))) {
            bRandomizeInitCondition = true;
        }
    }
    if ((param.getAttributeValue(XMLTags.MassConservationModelReductionTag) != null) && (param.getAttributeValue(XMLTags.MassConservationModelReductionTag).equals("false"))) {
        bMassConservationModelReduction = false;
    }
    if ((param.getAttributeValue(XMLTags.InsufficientIterationsTag) != null) && (param.getAttributeValue(XMLTags.InsufficientIterationsTag).equals("true"))) {
        bInsufficientIterations = true;
    }
    if ((param.getAttributeValue(XMLTags.InsufficientMaxMoleculesTag) != null) && (param.getAttributeValue(XMLTags.InsufficientMaxMoleculesTag).equals("true"))) {
        bInsufficientMaxMolecules = true;
    }
    if ((param.getAttributeValue(XMLTags.RuleBasedAttrTag) != null) && (param.getAttributeValue(XMLTags.RuleBasedAttrTag).equals("true"))) {
        bRuleBased = true;
        if ((param.getAttributeValue(XMLTags.ConcentrationAttrTag) != null) && (param.getAttributeValue(XMLTags.ConcentrationAttrTag).equals("false"))) {
            bUseConcentration = false;
        }
        if ((param.getAttributeValue(XMLTags.RandomizeInitConditionTag) != null) && (param.getAttributeValue(XMLTags.RandomizeInitConditionTag).equals("true"))) {
            // we propagate the flag but we don't use it for now
            bRandomizeInitCondition = true;
        }
    }
    // Retrieve Geometry
    Geometry newgeometry = null;
    try {
        newgeometry = getGeometry(param.getChild(XMLTags.GeometryTag, vcNamespace));
    } catch (Throwable e) {
        e.printStackTrace();
        String stackTrace = null;
        try {
            java.io.ByteArrayOutputStream bos = new java.io.ByteArrayOutputStream();
            java.io.PrintStream ps = new java.io.PrintStream(bos);
            e.printStackTrace(ps);
            ps.flush();
            bos.flush();
            stackTrace = new String(bos.toByteArray());
            ps.close();
            bos.close();
        } catch (Exception e2) {
        // do Nothing
        }
        throw new XmlParseException("A Problem occurred while retrieving the geometry for the simulationContext " + name, e);
    }
    // Retrieve MathDescription(if there is no MathDescription skip it)
    MathDescription newmathdesc = null;
    Element xmlMathDescription = param.getChild(XMLTags.MathDescriptionTag, vcNamespace);
    if (xmlMathDescription != null) {
        newmathdesc = getMathDescription(xmlMathDescription, newgeometry);
        if (biomodel.getVersion() != null && biomodel.getVersion().getVersionKey() != null) {
            Long lpcBMKey = Long.valueOf(biomodel.getVersion().getVersionKey().toString());
            // MathDescription.originalHasLowPrecisionConstants.remove(lpcBMKey);
            try {
                Enumeration<Constant> myenum = newmathdesc.getConstants();
                while (myenum.hasMoreElements()) {
                    Constant nextElement = myenum.nextElement();
                    String name2 = nextElement.getName();
                    ReservedSymbol reservedSymbolByName = biomodel.getModel().getReservedSymbolByName(name2);
                    if (reservedSymbolByName != null && nextElement.getExpression() != null && reservedSymbolByName.getExpression() != null) {
                        // System.out.println(name2);
                        boolean equals = nextElement.getExpression().infix().equals(reservedSymbolByName.getExpression().infix());
                        // System.out.println("--"+" "+nextElement.getExpression().infix() +" "+reservedSymbolByName.getExpression().infix()+" "+equals);
                        if (!equals) {
                            TreeSet<String> treeSet = MathDescription.originalHasLowPrecisionConstants.get(lpcBMKey);
                            if (treeSet == null) {
                                treeSet = new TreeSet<>();
                                MathDescription.originalHasLowPrecisionConstants.put(lpcBMKey, treeSet);
                            }
                            treeSet.add(newmathdesc.getVersion().getVersionKey().toString());
                            break;
                        }
                    }
                }
            } catch (Exception e) {
                // TODO Auto-generated catch block
                e.printStackTrace();
            }
        }
    }
    // Retrieve Version (Metada)
    Version version = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace));
    // ------ Create SimContext ------
    SimulationContext newsimcontext = null;
    try {
        newsimcontext = new SimulationContext(biomodel.getModel(), newgeometry, newmathdesc, version, bStoch, bRuleBased);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace(System.out);
        throw new XmlParseException("A propertyveto exception was generated when creating the new SimulationContext " + name, e);
    }
    // set attributes
    try {
        newsimcontext.setName(name);
        // Add annotation
        String annotation = param.getChildText(XMLTags.AnnotationTag, vcNamespace);
        if (annotation != null) /* && annotation.length()>0*/
        {
            newsimcontext.setDescription(unMangle(annotation));
        }
        // set if using concentration
        newsimcontext.setUsingConcentration(bUseConcentration);
        // set mass conservation model reduction flag
        newsimcontext.setUsingMassConservationModelReduction(bMassConservationModelReduction);
        // set if randomizing init condition or not (for stochastic applications
        if (bStoch) {
            newsimcontext.setRandomizeInitConditions(bRandomizeInitCondition);
        }
        if (bInsufficientIterations) {
            newsimcontext.setInsufficientIterations(bInsufficientIterations);
        }
        if (bInsufficientMaxMolecules) {
            newsimcontext.setInsufficientMaxMolecules(bInsufficientMaxMolecules);
        }
        if (nc != null) {
            newsimcontext.setNetworkConstraints(nc);
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace(System.out);
        throw new XmlParseException("Exception", e);
    }
    String tempchar = param.getAttributeValue(XMLTags.CharacteristicSizeTag);
    if (tempchar != null) {
        try {
            newsimcontext.setCharacteristicSize(Double.valueOf(tempchar));
        } catch (java.beans.PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException("A PropertyVetoException was fired when setting the CharacteristicSize " + tempchar, e);
        }
    }
    // Retrieve DataContext
    Element dataContextElement = param.getChild(XMLTags.DataContextTag, vcNamespace);
    if (dataContextElement != null) {
        DataContext dataContext = newsimcontext.getDataContext();
        ArrayList<DataSymbol> dataSymbols = getDataSymbols(dataContextElement, dataContext, newsimcontext.getModel().getUnitSystem());
        for (int i = 0; i < dataSymbols.size(); i++) {
            dataContext.addDataSymbol(dataSymbols.get(i));
        }
    }
    // Retrieve spatialObjects and add to simContext
    Element spatialObjectsElement = param.getChild(XMLTags.SpatialObjectsTag, vcNamespace);
    if (spatialObjectsElement != null) {
        SpatialObject[] spatialObjects = getSpatialObjects(newsimcontext, spatialObjectsElement);
        try {
            newsimcontext.setSpatialObjects(spatialObjects);
        } catch (PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error adding spatialObjects to simulationContext", e);
        }
    }
    // Retrieve application parameters and add to simContext
    Element appParamsElement = param.getChild(XMLTags.ApplicationParametersTag, vcNamespace);
    if (appParamsElement != null) {
        SimulationContextParameter[] appParameters = getSimulationContextParams(appParamsElement, newsimcontext);
        try {
            newsimcontext.setSimulationContextParameters(appParameters);
        } catch (PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error adding application parameters to simulationContext", e);
        }
    }
    // 
    // -Process the GeometryContext-
    // 
    Element tempelement = param.getChild(XMLTags.GeometryContextTag, vcNamespace);
    LinkedList<StructureMapping> maplist = new LinkedList<StructureMapping>();
    // Retrieve FeatureMappings
    Iterator<Element> iterator = tempelement.getChildren(XMLTags.FeatureMappingTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        maplist.add(getFeatureMapping((Element) (iterator.next()), newsimcontext));
    }
    // Retrieve MembraneMappings
    iterator = tempelement.getChildren(XMLTags.MembraneMappingTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        maplist.add(getMembraneMapping((Element) (iterator.next()), newsimcontext));
    }
    // Add these mappings to the internal geometryContext of this simcontext
    StructureMapping[] structarray = new StructureMapping[maplist.size()];
    maplist.toArray(structarray);
    try {
        newsimcontext.getGeometryContext().setStructureMappings(structarray);
        newsimcontext.getGeometryContext().refreshStructureMappings();
        newsimcontext.refreshSpatialObjects();
    } catch (MappingException e) {
        e.printStackTrace();
        throw new XmlParseException("A MappingException was fired when trying to set the StructureMappings array to the Geometrycontext of the SimContext " + name, e);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace(System.out);
        throw new XmlParseException("A PopertyVetoException was fired when trying to set the StructureMappings array to the Geometrycontext of the SimContext " + name, e);
    }
    // 
    // -Process the ReactionContext-
    // 
    tempelement = param.getChild(XMLTags.ReactionContextTag, vcNamespace);
    // Retrieve ReactionSpecs
    List<Element> children = tempelement.getChildren(XMLTags.ReactionSpecTag, vcNamespace);
    if (children.size() != 0) {
        if (children.size() != biomodel.getModel().getReactionSteps().length) {
            throw new XmlParseException("The number of reactions is not consistent.\n" + "Model reactions=" + biomodel.getModel().getReactionSteps().length + ", Reaction specs=" + children.size());
        }
        // *NOTE: Importing a model from other languages does not generates reaction specs.
        // A more robust code will read the reactions in the source file and replace the ones created by the default by the VirtualCell framework.
        ReactionSpec[] reactionSpecs = new ReactionSpec[children.size()];
        int rSpecCounter = 0;
        for (Element rsElement : children) {
            reactionSpecs[rSpecCounter] = getReactionSpec(rsElement, newsimcontext);
            rSpecCounter++;
        }
        try {
            newsimcontext.getReactionContext().setReactionSpecs(reactionSpecs);
        } catch (java.beans.PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException("A PropertyVetoException occurred while setting the ReactionSpecs to the SimContext " + name, e);
        }
    }
    // Retrieve ReactionRuleSpecs
    Element reactionRuleSpecsElement = tempelement.getChild(XMLTags.ReactionRuleSpecsTag, vcNamespace);
    if (reactionRuleSpecsElement != null) {
        ReactionRuleSpec[] reactionRuleSpecs = getReactionRuleSpecs(newsimcontext, reactionRuleSpecsElement);
        try {
            newsimcontext.getReactionContext().setReactionRuleSpecs(reactionRuleSpecs);
        } catch (PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException("A PropertyVetoException occurred while setting the ReactionRuleSpecs to the SimContext " + name, e);
        }
    }
    children = tempelement.getChildren(XMLTags.SpeciesContextSpecTag, vcNamespace);
    getSpeciesContextSpecs(children, newsimcontext.getReactionContext(), biomodel.getModel());
    // Retrieve output functions
    Element outputFunctionsElement = param.getChild(XMLTags.OutputFunctionsTag, vcNamespace);
    if (outputFunctionsElement != null) {
        ArrayList<AnnotatedFunction> outputFunctions = getOutputFunctions(outputFunctionsElement);
        try {
            // construct OutputFnContext from mathDesc in newSimContext and add output functions that were read in from XML.
            OutputFunctionContext outputFnContext = newsimcontext.getOutputFunctionContext();
            for (AnnotatedFunction outputFunction : outputFunctions) {
                outputFnContext.addOutputFunction(outputFunction);
            }
        } catch (PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException(e);
        }
    }
    // Retrieve Electrical context
    org.jdom.Element electElem = param.getChild(XMLTags.ElectricalContextTag, vcNamespace);
    // this information is optional!
    if (electElem != null) {
        if (electElem.getChild(XMLTags.ClampTag, vcNamespace) != null) {
            // read clamp
            ElectricalStimulus[] electArray = new ElectricalStimulus[1];
            electArray[0] = getElectricalStimulus(electElem.getChild(XMLTags.ClampTag, vcNamespace), newsimcontext);
            try {
                newsimcontext.setElectricalStimuli(electArray);
            } catch (java.beans.PropertyVetoException e) {
                e.printStackTrace(System.out);
                throw new XmlParseException(e);
            }
        }
        // read ground electrode
        if (electElem.getChild(XMLTags.ElectrodeTag, vcNamespace) != null) {
            Electrode groundElectrode = getElectrode(electElem.getChild(XMLTags.ElectrodeTag, vcNamespace), newsimcontext);
            try {
                newsimcontext.setGroundElectrode(groundElectrode);
            } catch (java.beans.PropertyVetoException e) {
                e.printStackTrace(System.out);
                throw new XmlParseException(e);
            }
        }
    }
    // Retrieve (bio)events and add to simContext
    tempelement = param.getChild(XMLTags.BioEventsTag, vcNamespace);
    if (tempelement != null) {
        BioEvent[] bioEvents = getBioEvents(newsimcontext, tempelement);
        try {
            newsimcontext.setBioEvents(bioEvents);
        } catch (PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error adding events to simulationContext", e);
        }
    }
    // Retrieve spatialProcesses and add to simContext
    tempelement = param.getChild(XMLTags.SpatialProcessesTag, vcNamespace);
    if (tempelement != null) {
        SpatialProcess[] spatialProcesses = getSpatialProcesses(newsimcontext, tempelement);
        try {
            newsimcontext.setSpatialProcesses(spatialProcesses);
        } catch (PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error adding spatialProcesses to simulationContext", e);
        }
    }
    // Retrieve rate rules and add to simContext
    tempelement = param.getChild(XMLTags.RateRulesTag, vcNamespace);
    if (tempelement != null) {
        RateRule[] rateRules = getRateRules(newsimcontext, tempelement);
        try {
            newsimcontext.setRateRules(rateRules);
        } catch (PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error adding rate rules to simulationContext", e);
        }
    }
    tempelement = param.getChild(XMLTags.AssignmentRulesTag, vcNamespace);
    if (tempelement != null) {
        AssignmentRule[] assignmentRules = getAssignmentRules(newsimcontext, tempelement);
        try {
            newsimcontext.setAssignmentRules(assignmentRules);
        } catch (PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error adding assignment rules to simulationContext", e);
        }
    }
    org.jdom.Element analysisTaskListElement = param.getChild(XMLTags.AnalysisTaskListTag, vcNamespace);
    if (analysisTaskListElement != null) {
        children = analysisTaskListElement.getChildren(XMLTags.ParameterEstimationTaskTag, vcNamespace);
        if (children.size() != 0) {
            Vector<ParameterEstimationTask> analysisTaskList = new Vector<ParameterEstimationTask>();
            for (Element parameterEstimationTaskElement : children) {
                try {
                    ParameterEstimationTask parameterEstimationTask = ParameterEstimationTaskXMLPersistence.getParameterEstimationTask(parameterEstimationTaskElement, newsimcontext);
                    analysisTaskList.add(parameterEstimationTask);
                } catch (Exception e) {
                    e.printStackTrace(System.out);
                    throw new XmlParseException("An Exception occurred when parsing AnalysisTasks of SimContext " + name, e);
                }
            }
            try {
                AnalysisTask[] analysisTasks = (AnalysisTask[]) BeanUtils.getArray(analysisTaskList, AnalysisTask.class);
                newsimcontext.setAnalysisTasks(analysisTasks);
            } catch (java.beans.PropertyVetoException e) {
                e.printStackTrace(System.out);
                throw new XmlParseException("A PropertyVetoException occurred when setting the AnalysisTasks of the SimContext " + name, e);
            }
        }
    }
    // Microscope Measurement
    org.jdom.Element element = param.getChild(XMLTags.MicroscopeMeasurement, vcNamespace);
    if (element != null) {
        getMicroscopeMeasurement(element, newsimcontext);
    }
    for (GeometryClass gc : newsimcontext.getGeometry().getGeometryClasses()) {
        try {
            StructureSizeSolver.updateUnitStructureSizes(newsimcontext, gc);
        } catch (Exception e) {
            e.printStackTrace();
        }
    }
    newsimcontext.getGeometryContext().enforceHierarchicalBoundaryConditions(newsimcontext.getModel().getStructureTopology());
    return newsimcontext;
}