Examples with Namespace org.jdom.Namespace used on opensource projects

Example 11 with Namespace

use of org.jdom.Namespace in project vcell by virtualcell.

the class XmlHelper method XMLToImage.

static VCImage XMLToImage(String xmlString, boolean printKeys) throws XmlParseException {
    Namespace ns = Namespace.getNamespace(XMLTags.VCML_NS);
    if (xmlString == null || xmlString.length() == 0) {
        throw new XmlParseException("Invalid xml for Image: " + xmlString);
    }
    // default parser and no validation
    Element root = (XmlUtil.stringToXML(xmlString, null)).getRootElement();
    Element extentElement = root.getChild(XMLTags.ExtentTag, ns);
    Element imageElement = root.getChild(XMLTags.ImageTag, ns);
    // Element extentElement = root.getChild(XMLTags.ExtentTag);
    // Element imageElement = root.getChild(XMLTags.ImageTag);
    XmlReader reader = new XmlReader(printKeys, ns);
    Extent extent = reader.getExtent(extentElement);
    VCImage vcImage = reader.getVCImage(imageElement, extent);
    vcImage.refreshDependencies();
    return vcImage;
}

Example 12 with Namespace

use of org.jdom.Namespace in project vcell by virtualcell.

the class XmlHelper method XMLToDocument.

/**
 * Insert the method's description here.
 * Creation date: (2/7/2006 4:45:26 PM)
 * @return cbit.vcell.document.VCDocument
 * @param xmlString java.lang.String
 */
public static VCDocument XMLToDocument(VCLogger vcLogger, String xmlString) throws Exception {
    VCDocument doc = null;
    XMLSource xmlSource = new XMLSource(xmlString);
    // some overhead.
    org.jdom.Element rootElement = xmlSource.getXmlDoc().getRootElement();
    String xmlType = rootElement.getName();
    if (xmlType.equals(XMLTags.VcmlRootNodeTag)) {
        // For now, assuming that <vcml> element has only one child (biomodel, mathmodel or geometry).
        // Will deal with multiple children of <vcml> Element when we get to model composition.
        java.util.List<?> childElementList = rootElement.getChildren();
        // assuming first child is the biomodel, mathmodel or geometry.
        Element modelElement = (Element) childElementList.get(0);
        xmlType = modelElement.getName();
    }
    if (xmlType.equals(XMLTags.BioModelTag)) {
        doc = XmlHelper.XMLToBioModel(xmlSource);
    } else if (xmlType.equals(XMLTags.MathModelTag)) {
        doc = XmlHelper.XMLToMathModel(xmlSource);
    } else if (xmlType.equals(XMLTags.GeometryTag)) {
        doc = XmlHelper.XMLToGeometry(xmlSource);
    } else if (xmlType.equals(XMLTags.SbmlRootNodeTag)) {
        Namespace namespace = rootElement.getNamespace(XMLTags.SBML_SPATIAL_NS_PREFIX);
        boolean bIsSpatial = (namespace == null) ? false : true;
        doc = XmlHelper.importSBML(vcLogger, xmlSource, bIsSpatial);
    } else if (xmlType.equals(XMLTags.CellmlRootNodeTag)) {
        doc = XmlHelper.importMathCellML(vcLogger, xmlSource);
    } else {
        // unknown XML format
        throw new RuntimeException("unsupported XML format, first element tag is <" + rootElement.getName() + ">");
    }
    return doc;
}

Example 13 with Namespace

use of org.jdom.Namespace in project vcell by virtualcell.

the class XmlHelper method XMLToSim.

public static Simulation XMLToSim(String xmlString) throws XmlParseException {
    Simulation sim = null;
    Namespace ns = Namespace.getNamespace(XMLTags.VCML_NS);
    try {
        if (xmlString == null || xmlString.length() == 0) {
            throw new XmlParseException("Invalid xml for Simulation: " + xmlString);
        }
        // default parser and no validation
        Element root = (XmlUtil.stringToXML(xmlString, null)).getRootElement();
        Element simElement = root.getChild(XMLTags.SimulationTag, ns);
        Element mdElement = root.getChild(XMLTags.MathDescriptionTag, ns);
        Element geomElement = root.getChild(XMLTags.GeometryTag, ns);
        XmlReader reader = new XmlReader(true, ns);
        Geometry geom = null;
        if (geomElement != null) {
            geom = reader.getGeometry(geomElement);
        }
        MathDescription md = reader.getMathDescription(mdElement, geom);
        sim = reader.getSimulation(simElement, md);
    } catch (Exception pve) {
        pve.printStackTrace();
        throw new XmlParseException("Unable to parse simulation string.", pve);
    }
    sim.refreshDependencies();
    return sim;
}

Example 14 with Namespace

use of org.jdom.Namespace in project vcell by virtualcell.

the class XmlHelper method XMLToSimTask.

public static SimulationTask XMLToSimTask(String xmlString) throws XmlParseException, ExpressionException {
    Namespace ns = Namespace.getNamespace(XMLTags.VCML_NS);
    try {
        if (xmlString == null || xmlString.length() == 0) {
            throw new XmlParseException("Invalid xml for Simulation: " + xmlString);
        }
        // default parser and no validation
        Element root = (XmlUtil.stringToXML(xmlString, null)).getRootElement();
        if (!root.getName().equals(SimulationTask_tag)) {
            throw new RuntimeException("expecting top level element to be " + SimulationTask_tag);
        }
        int taskId = Integer.parseInt(root.getAttributeValue(TaskId_attr));
        int jobIndex = Integer.parseInt(root.getAttributeValue(JobIndex_attr));
        String computeResource = root.getChildTextTrim(ComputeResource_tag, ns);
        List<?> children = root.getChildren(FieldFunctionIdentifierSpec_tag, ns);
        ArrayList<FieldDataIdentifierSpec> fdisArrayList = new ArrayList<FieldDataIdentifierSpec>();
        for (Object child : children) {
            if (child instanceof Element) {
                String fdisText = ((Element) child).getTextTrim();
                FieldDataIdentifierSpec fdis = FieldDataIdentifierSpec.fromCSVString(fdisText);
                fdisArrayList.add(fdis);
            }
        }
        FieldDataIdentifierSpec[] fdisArray = fdisArrayList.toArray(new FieldDataIdentifierSpec[0]);
        Element simElement = root.getChild(XMLTags.SimulationTag, ns);
        Element mdElement = root.getChild(XMLTags.MathDescriptionTag, ns);
        Element geomElement = root.getChild(XMLTags.GeometryTag, ns);
        XmlReader reader = new XmlReader(true, ns);
        Geometry geom = null;
        if (geomElement != null) {
            geom = reader.getGeometry(geomElement);
        }
        MathDescription md = reader.getMathDescription(mdElement, geom);
        Simulation sim = reader.getSimulation(simElement, md);
        sim.refreshDependencies();
        SimulationJob simJob = new SimulationJob(sim, jobIndex, fdisArray);
        SimulationTask simTask = new SimulationTask(simJob, taskId, computeResource);
        return simTask;
    } catch (Exception pve) {
        pve.printStackTrace();
        throw new XmlParseException("Unable to parse simulation string.", pve);
    }
}

Example 15 with Namespace

use of org.jdom.Namespace in project vcell by virtualcell.

the class ParameterEstimationTaskXMLPersistence method getParameterEstimationTask.

/**
 * Insert the method's description here.
 * Creation date: (5/5/2006 4:50:36 PM)
 * @return cbit.vcell.modelopt.ParameterEstimationTask
 * @param element org.jdom.Element
 * @param simContext cbit.vcell.mapping.SimulationContext
 */
public static ParameterEstimationTask getParameterEstimationTask(Element parameterEstimationTaskElement, SimulationContext simContext) throws ExpressionException, MappingException, MathException, java.beans.PropertyVetoException {
    Namespace ns = parameterEstimationTaskElement.getNamespace();
    ParameterEstimationTask parameterEstimationTask = new ParameterEstimationTask(simContext);
    String name = parameterEstimationTaskElement.getAttributeValue(NameAttribute);
    parameterEstimationTask.setName(name);
    Element annotationElement = parameterEstimationTaskElement.getChild(AnnotationTag, ns);
    if (annotationElement != null) {
        String annotationText = annotationElement.getText();
        parameterEstimationTask.setAnnotation(annotationText);
    }
    // 
    // read ParameterMappingSpecs
    // 
    Element parameterMappingSpecListElement = parameterEstimationTaskElement.getChild(ParameterMappingSpecListTag, ns);
    if (parameterMappingSpecListElement != null) {
        List<Element> parameterMappingSpecElementList = parameterMappingSpecListElement.getChildren(ParameterMappingSpecTag, ns);
        for (Element parameterMappingSpecElement : parameterMappingSpecElementList) {
            String parameterName = parameterMappingSpecElement.getAttributeValue(ParameterReferenceAttribute);
            SymbolTableEntry ste = getSymbolTableEntry(simContext, parameterName);
            if (ste instanceof Parameter) {
                Parameter parameter = (Parameter) ste;
                ParameterMappingSpec parameterMappingSpec = parameterEstimationTask.getModelOptimizationSpec().getParameterMappingSpec(parameter);
                if (parameterMappingSpec != null) {
                    String lowLimitString = parameterMappingSpecElement.getAttributeValue(LowLimitAttribute);
                    if (lowLimitString != null) {
                        parameterMappingSpec.setLow(parseDouble(lowLimitString));
                    }
                    String highLimitString = parameterMappingSpecElement.getAttributeValue(HighLimitAttribute);
                    if (highLimitString != null) {
                        parameterMappingSpec.setHigh(parseDouble(highLimitString));
                    }
                    String currentValueString = parameterMappingSpecElement.getAttributeValue(CurrentValueAttribute);
                    if (currentValueString != null) {
                        parameterMappingSpec.setCurrent(Double.parseDouble(currentValueString));
                    }
                    String selectedString = parameterMappingSpecElement.getAttributeValue(SelectedAttribute);
                    if (selectedString != null) {
                        parameterMappingSpec.setSelected(Boolean.valueOf(selectedString).booleanValue());
                    }
                }
            } else {
                System.out.println("couldn't read parameterMappingSpec '" + parameterName + "', ste=" + ste);
            }
        }
    }
    // 
    // read ReferenceData
    // 
    Element referenceDataElement = parameterEstimationTaskElement.getChild(ReferenceDataTag, ns);
    if (referenceDataElement != null) {
        String numRowsText = referenceDataElement.getAttributeValue(NumRowsAttribute);
        String numColsText = referenceDataElement.getAttributeValue(NumColumnsAttribute);
        // int numRows = Integer.parseInt(numRowsText);
        int numCols = Integer.parseInt(numColsText);
        // 
        // read columns
        // 
        String[] columnNames = new String[numCols];
        double[] columnWeights = new double[numCols];
        int columnCounter = 0;
        Element dataColumnListElement = referenceDataElement.getChild(DataColumnListTag, ns);
        List<Element> dataColumnList = dataColumnListElement.getChildren(DataColumnTag, ns);
        for (Element dataColumnElement : dataColumnList) {
            columnNames[columnCounter] = dataColumnElement.getAttributeValue(NameAttribute);
            columnWeights[columnCounter] = Double.parseDouble(dataColumnElement.getAttributeValue(WeightAttribute));
            columnCounter++;
        }
        // 
        // read rows
        // 
        Vector<double[]> rowDataVector = new Vector<double[]>();
        Element dataRowListElement = referenceDataElement.getChild(DataRowListTag, ns);
        List<Element> dataRowList = dataRowListElement.getChildren(DataRowTag, ns);
        for (Element dataRowElement : dataRowList) {
            String rowText = dataRowElement.getText();
            CommentStringTokenizer tokens = new CommentStringTokenizer(rowText);
            double[] rowData = new double[numCols];
            for (int j = 0; j < numCols; j++) {
                if (tokens.hasMoreTokens()) {
                    String token = tokens.nextToken();
                    rowData[j] = Double.parseDouble(token);
                } else {
                    throw new RuntimeException("failed to read row data for ReferenceData");
                }
            }
            rowDataVector.add(rowData);
        }
        ReferenceData referenceData = new SimpleReferenceData(columnNames, columnWeights, rowDataVector);
        parameterEstimationTask.getModelOptimizationSpec().setReferenceData(referenceData);
    }
    // 
    // read ReferenceDataMappingSpecs
    // 
    Element referenceDataMappingSpecListElement = parameterEstimationTaskElement.getChild(ReferenceDataMappingSpecListTag, ns);
    if (referenceDataMappingSpecListElement != null) {
        List<Element> referenceDataMappingSpecList = referenceDataMappingSpecListElement.getChildren(ReferenceDataMappingSpecTag, ns);
        for (Element referenceDataMappingSpecElement : referenceDataMappingSpecList) {
            String referenceDataColumnName = referenceDataMappingSpecElement.getAttributeValue(ReferenceDataColumnNameAttribute);
            String referenceDataModelSymbolName = referenceDataMappingSpecElement.getAttributeValue(ReferenceDataModelSymbolAttribute);
            ReferenceDataMappingSpec referenceDataMappingSpec = parameterEstimationTask.getModelOptimizationSpec().getReferenceDataMappingSpec(referenceDataColumnName);
            SymbolTableEntry modelSymbolTableEntry = null;
            if (referenceDataModelSymbolName != null) {
                modelSymbolTableEntry = getSymbolTableEntry(simContext, referenceDataModelSymbolName);
                if (referenceDataMappingSpec != null && modelSymbolTableEntry != null) {
                    referenceDataMappingSpec.setModelObject(modelSymbolTableEntry);
                }
            }
        }
    }
    // 
    // read OptimizationSolverSpec
    // 
    Element optimizationSolverSpecElement = parameterEstimationTaskElement.getChild(OptimizationSolverSpecTag, ns);
    if (optimizationSolverSpecElement != null) {
        OptimizationSolverSpec optSolverSpec = null;
        String optimizationSolverTypeName = optimizationSolverSpecElement.getAttributeValue(OptimizationSolverTypeAttribute);
        // getting parameters
        Element optimizationSolverParameterList = optimizationSolverSpecElement.getChild(OptimizationListOfParametersTag, ns);
        if (optimizationSolverParameterList != null) {
            List<Element> listOfSolverParams = optimizationSolverParameterList.getChildren(OptimizationParameterTag, ns);
            CopasiOptimizationMethod copasiOptMethod = null;
            if (listOfSolverParams != null && listOfSolverParams.size() > 0) {
                List<CopasiOptimizationParameter> copasiSolverParams = new ArrayList<CopasiOptimizationParameter>();
                for (Element solverParam : listOfSolverParams) {
                    String paramName = solverParam.getAttributeValue(OptimizationParameterNameAttribute);
                    double paramValue = Double.parseDouble(solverParam.getAttributeValue(OptimizationParameterValueAttribute));
                    CopasiOptimizationParameter copasiParam = new CopasiOptimizationParameter(getCopasiOptimizationParameterTypeByName(paramName), paramValue);
                    copasiSolverParams.add(copasiParam);
                }
                copasiOptMethod = new CopasiOptimizationMethod(getCopasiOptimizationMethodTypeByName(optimizationSolverTypeName), copasiSolverParams.toArray(new CopasiOptimizationParameter[copasiSolverParams.size()]));
            } else // no parameters
            {
                copasiOptMethod = new CopasiOptimizationMethod(getCopasiOptimizationMethodTypeByName(optimizationSolverTypeName), new CopasiOptimizationParameter[0]);
            }
            optSolverSpec = new OptimizationSolverSpec(copasiOptMethod);
            // add number of runs attribute
            String numOfRunsStr = optimizationSolverSpecElement.getAttributeValue(OptimizationSolverNumOfRunsAttribute);
            if (numOfRunsStr != null) {
                int numOfRuns = Integer.parseInt(numOfRunsStr);
                optSolverSpec.setNumOfRuns(numOfRuns);
            }
        }
        parameterEstimationTask.setOptimizationSolverSpec(optSolverSpec);
    }
    if (// optimization solver spec is null create a default copasi evolutionary programming
    optimizationSolverSpecElement == null || parameterEstimationTask.getOptimizationSolverSpec() == null) {
        OptimizationSolverSpec optSolverSpec = new OptimizationSolverSpec(new CopasiOptimizationMethod(CopasiOptimizationMethodType.EvolutionaryProgram));
        parameterEstimationTask.setOptimizationSolverSpec(optSolverSpec);
    }
    // read optimization solver result set
    Element optimizationResultSetElement = parameterEstimationTaskElement.getChild(OptXmlTags.OptimizationResultSet_Tag, ns);
    if (optimizationResultSetElement != null) {
        OptimizationResultSet optResultSet = null;
        // read optsolverResultSet
        if (optimizationResultSetElement.getChild(OptXmlTags.bestOptRunResultSet_Tag, ns) != null) {
            Element optSolverResultSetElement = optimizationResultSetElement.getChild(OptXmlTags.bestOptRunResultSet_Tag, ns);
            OptSolverResultSet optSolverResultSet = null;
            // get best parameters, best func value, number of evaluations and construct an optRunResultSet
            Element paramListElement = optSolverResultSetElement.getChild(OptimizationListOfParametersTag, ns);
            OptRunResultSet optRunResultSet = null;
            List<String> paramNames = new ArrayList<String>();
            List<Double> paramValues = new ArrayList<Double>();
            if (paramListElement != null && !paramListElement.getChildren().isEmpty()) {
                List<Element> paramElements = paramListElement.getChildren(OptimizationParameterTag, ns);
                if (paramElements != null) {
                    for (Element paramElement : paramElements) {
                        String paramName = paramElement.getAttributeValue(OptimizationParameterNameAttribute);
                        double paramValue = Double.parseDouble(paramElement.getAttributeValue(OptimizationParameterValueAttribute));
                        paramNames.add(paramName);
                        paramValues.add(paramValue);
                    }
                }
            }
            Element bestFuncValueElement = optSolverResultSetElement.getChild(OptXmlTags.ObjectiveFunction_Tag, ns);
            double bestFuncValue = Double.parseDouble(bestFuncValueElement.getAttributeValue(OptimizationParameterValueAttribute));
            Element numEvaluationsElement = optSolverResultSetElement.getChild(OptXmlTags.OptSolverResultSetFunctionEvaluations_Tag, ns);
            long numEvaluations = Long.parseLong(numEvaluationsElement.getAttributeValue(OptimizationParameterValueAttribute));
            // change List<Double> to double[]
            double[] values = new double[paramValues.size()];
            int index = 0;
            for (Double value : paramValues) {
                values[index++] = value;
            }
            optRunResultSet = new OptRunResultSet(values, bestFuncValue, numEvaluations, null);
            // create optSolverResultSet
            optSolverResultSet = new OptSolverResultSet(paramNames.toArray(new String[paramNames.size()]), optRunResultSet);
            // create optimization result set
            optResultSet = new OptimizationResultSet(optSolverResultSet, null);
        }
        parameterEstimationTask.setOptimizationResultSet(optResultSet);
    }
    return parameterEstimationTask;
}