Examples with DataContext cbit.vcell.data.DataContext used on opensource projects

Example 1 with DataContext

use of cbit.vcell.data.DataContext 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;
}