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

Example 6 with XmlReader

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

the class VFrapXmlHelper method VFRAPToBioModel.

public static BioModel VFRAPToBioModel(Hashtable<String, Object> hashTable, XMLSource xmlSource, DocumentManager documentManager, final TopLevelWindowManager requester) throws XmlParseException, IOException, DataAccessException, MathException, DivideByZeroException, ExpressionException, ImageException, UtilCancelException {
    Component requesterComponent = requester.getComponent();
    File vFrapFile = xmlSource.getXmlFile();
    // ---
    // ex  ccc8.vfrap
    String vFrapFileNameExtended = vFrapFile.getName();
    {
        // we want to make sure to reload these strings from the hash later on
        String initialFieldDataName = vFrapFileNameExtended.substring(0, vFrapFileNameExtended.indexOf(".vfrap"));
        // we'll save here the "special" vFrap images (prebleach_avg, ...)
        String mixedFieldDataName = initialFieldDataName + "Mx";
        hashTable.put("mixedFieldDataName", mixedFieldDataName);
        hashTable.put("initialFieldDataName", initialFieldDataName);
    }
    if (vFrapFileNameExtended.indexOf(".vfrap") < 0) {
        throw new RuntimeException("File extension must be .vfrap");
    }
    // VFrapXmlHelper vFrapXmlHelper = new VFrapXmlHelper();
    checkNameAvailability(hashTable, true, documentManager, requesterComponent);
    System.out.println("Loading " + vFrapFileNameExtended + " ...");
    String xmlString = XmlUtil.getXMLString(vFrapFile.getAbsolutePath());
    MicroscopyXmlReader xmlReader = new MicroscopyXmlReader(true);
    Element vFrapRoot = XmlUtil.stringToXML(xmlString, null).getRootElement();
    // ----- read the biomodel from Virtual FRAP xml file ----------
    BioModel bioModel = null;
    XmlReader vcellXMLReader = new XmlReader(true);
    Element bioModelElement = vFrapRoot.getChild(XMLTags.BioModelTag);
    if (bioModelElement == null) {
        throw new RuntimeException("Unable to load biomodel.");
    }
    String docSoftwareVersion = vFrapRoot.getAttributeValue(XMLTags.SoftwareVersionAttrTag);
    bioModel = vcellXMLReader.getBioModel(bioModelElement, (docSoftwareVersion == null ? null : VCellSoftwareVersion.fromString(docSoftwareVersion)));
    // ------ locate the special images within the vFrap files and load them in memory
    if (!LoadVFrapSpecialImages(hashTable, vFrapRoot)) {
        // just return the biomodel if image loading fails for some reason
        return bioModel;
    }
    // ------- save the special images in the database as field data ------------
    ExternalDataIdentifier vfrapMisc = SaveVFrapSpecialImagesAsFieldData(hashTable, documentManager);
    // ------- create and save data symbols for the vFrap "special" images -----------
    CreateSaveVFrapDataSymbols(hashTable, bioModel, vfrapMisc);
    // -------- replace vFrap default names in field function arguments with data symbol names -----
    ReplaceVFrapNamesWithSymbolNames(bioModel);
    return bioModel;
}

Example 7 with XmlReader

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

the class GlobalModelParameterTable method setModelParameters.

public void setModelParameters(Connection con, Model model) throws SQLException, DataAccessException {
    String sql = " SELECT " + GlobalModelParameterTable.table.xmlFragment.getQualifiedColName() + " FROM " + GlobalModelParameterTable.table.getTableName() + " WHERE " + GlobalModelParameterTable.table.modelRef.getQualifiedColName() + " = " + model.getVersion().getVersionKey() + " ORDER BY " + GlobalModelParameterTable.table.id.getUnqualifiedColName();
    Statement stmt = con.createStatement();
    try {
        ResultSet rset = stmt.executeQuery(sql);
        StringBuffer modelParameeterXMLSB = new StringBuffer();
        while (rset.next()) {
            String modelParameeterXMLS = rset.getString(GlobalModelParameterTable.table.xmlFragment.toString());
            if (!rset.wasNull()) {
                modelParameeterXMLS = org.vcell.util.TokenMangler.getSQLRestoredString(modelParameeterXMLS);
                modelParameeterXMLSB.append(modelParameeterXMLS);
            }
        }
        if (modelParameeterXMLSB.length() > 0) {
            XmlReader xmlReader = new XmlReader(true);
            Element modelParameeterXMLElement = XmlUtil.stringToXML(modelParameeterXMLSB.toString(), null).getRootElement();
            try {
                Model.ModelParameter[] modelParameterArr = xmlReader.getModelParams(modelParameeterXMLElement, model);
                model.setModelParameters(modelParameterArr);
            } catch (Exception e) {
                throw new DataAccessException("error reading ModelParameters for model " + model.getName(), e);
            }
        }
    } finally {
        // Release resources include resultset
        stmt.close();
    }
}

Example 8 with XmlReader

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

the class ApplicationMathTable method convertOutputFunctionXMLToFuncList.

private ArrayList<AnnotatedFunction> convertOutputFunctionXMLToFuncList(String outputFunctionsXML) throws XmlParseException {
    Element outputFunctionElement = XmlUtil.stringToXML(outputFunctionsXML, null).getRootElement();
    ArrayList<AnnotatedFunction> outputFunctionList = (new XmlReader(false)).getOutputFunctions(outputFunctionElement);
    return outputFunctionList;
}