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

Example 1 with XmlReader

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

the class TMLPanel method processComparisonResult.

// process events for loading the model displayed in the comparison panel
public VCDocument processComparisonResult() throws Exception {
    try {
        NodeInfo root = (NodeInfo) getTree().getModel().getRoot();
        // if (!isNormal(root)) {
        // displayMessage(this, "Please resolve all tagged elements/attributes before proceeding.");
        // }
        String xmlStr = root.toXmlString();
        // System.out.println(xmlStr);
        Element rootElement = (XmlUtil.stringToXML(xmlStr, null)).getRootElement();
        // ?
        XmlReader reader = new XmlReader(true);
        String rootName = rootElement.getName();
        Document doc = rootElement.getDocument();
        VCDocument vcDoc = null;
        if (rootName.equals(XMLTags.BioModelTag)) {
            String docSoftwareVersion = rootElement.getAttributeValue(XMLTags.SoftwareVersionAttrTag);
            vcDoc = reader.getBioModel(rootElement, (docSoftwareVersion == null ? null : VCellSoftwareVersion.fromString(docSoftwareVersion)));
        } else if (rootName.equals(XMLTags.MathModelTag)) {
            vcDoc = reader.getMathModel(rootElement);
        } else if (rootName.equals(XMLTags.GeometryTag)) {
            vcDoc = reader.getGeometry(rootElement);
        } else {
            throw new Exception("Invalid root for the tree");
        }
        return vcDoc;
    } catch (java.lang.Exception ivjExc) {
        handleException(ivjExc);
        throw ivjExc;
    }
}

Example 2 with XmlReader

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

the class ModelTable method readRbmElement.

public static void readRbmElement(Connection con, Model model, DatabaseSyntax dbSyntax) throws SQLException, DataAccessException {
    Statement stmt = null;
    try {
        stmt = con.createStatement();
        ResultSet rset = stmt.executeQuery("SELECT * FROM " + ModelTable.table.getTableName() + " WHERE " + ModelTable.table.id.getUnqualifiedColName() + " = " + model.getVersion().getVersionKey().toString());
        if (rset.next()) {
            String rbmXMLStr = DbDriver.varchar2_CLOB_get(rset, ModelTable.table.rbmSmall, ModelTable.table.rbmLarge, dbSyntax);
            rset.close();
            if (rbmXMLStr != null) {
                Element rbmElement = XmlUtil.stringToXML(rbmXMLStr, null).getRootElement();
                XmlReader reader = new XmlReader(false);
                try {
                    reader.getRbmModelContainer(rbmElement, model);
                } catch (ModelException | PropertyVetoException | XmlParseException e) {
                    throw new DataAccessException(e.getMessage(), e);
                }
            }
        }
    } finally {
        if (stmt != null) {
            try {
                stmt.close();
            } catch (Exception e) {
                e.printStackTrace();
            }
        }
    }
}

Example 3 with XmlReader

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

the class ModelTable method getModel.

/**
 * This method was created in VisualAge.
 * @return Model
 * @param rset ResultSet
 * @param log SessionLog
 */
public Model getModel(ResultSet rset, Connection con) throws SQLException, DataAccessException {
    java.math.BigDecimal groupid = rset.getBigDecimal(VersionTable.privacy_ColumnName);
    Version version = getVersion(rset, DbDriver.getGroupAccessFromGroupID(con, groupid));
    ModelUnitSystem modelUnitSystem = ModelUnitSystem.createDefaultVCModelUnitSystem();
    String unitSystemXML = rset.getString(ModelTable.table.unitSystemXML.toString());
    if (!rset.wasNull()) {
        unitSystemXML = org.vcell.util.TokenMangler.getSQLRestoredString(unitSystemXML);
        XmlReader xmlReader = new XmlReader(false);
        modelUnitSystem = xmlReader.getUnitSystem(XmlUtil.stringToXML(unitSystemXML, null).getRootElement());
    }
    return new Model(version, modelUnitSystem);
}

Example 4 with XmlReader

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

the class SimContextTable method readAppComponents.

/**
 * readAppComponents : reads the additional simContext components like bioevents/application related flags (for stochastic, at the moment), if present, and sets them on simContext.
 * @param con
 * @param simContext
 * @return
 * @throws SQLException
 * @throws DataAccessException
 * @throws PropertyVetoException
 */
public void readAppComponents(Connection con, SimulationContext simContext, DatabaseSyntax dbSyntax) throws SQLException, DataAccessException, PropertyVetoException {
    try {
        Element appComponentsElement = getAppComponentsElement(con, simContext.getVersion().getVersionKey(), dbSyntax);
        if (appComponentsElement != null) {
            Element appRelatedFlags = appComponentsElement.getChild(XMLTags.ApplicationSpecificFlagsTag);
            if (appRelatedFlags != null) {
                // for now, only reading the 'randomizeInitCondition' attribute, since 'isStoch' and 'isUsingconcentration' are read in by other means; so not messing with those fields of simContext.
                boolean bRandomizeInitCondition = false;
                if ((appRelatedFlags.getAttributeValue(XMLTags.RandomizeInitConditionTag) != null) && (appRelatedFlags.getAttributeValue(XMLTags.RandomizeInitConditionTag).equals("true"))) {
                    bRandomizeInitCondition = true;
                }
                simContext.setRandomizeInitConditions(bRandomizeInitCondition);
            }
            if ((appComponentsElement.getAttributeValue(XMLTags.InsufficientIterationsTag) != null) && (appComponentsElement.getAttributeValue(XMLTags.InsufficientIterationsTag).equals("true"))) {
                simContext.setInsufficientIterations(true);
            } else {
                simContext.setInsufficientIterations(false);
            }
            if ((appComponentsElement.getAttributeValue(XMLTags.InsufficientMaxMoleculesTag) != null) && (appComponentsElement.getAttributeValue(XMLTags.InsufficientMaxMoleculesTag).equals("true"))) {
                simContext.setInsufficientMaxMolecules(true);
            } else {
                simContext.setInsufficientMaxMolecules(false);
            }
            XmlReader xmlReader = new XmlReader(false);
            NetworkConstraints nc = null;
            Element ncElement = appComponentsElement.getChild(XMLTags.RbmNetworkConstraintsTag);
            if (ncElement != null) {
                // one network constraint element
                nc = xmlReader.getAppNetworkConstraints(ncElement, simContext.getModel());
            }
            simContext.setNetworkConstraints(nc);
            // get spatial objects
            Element spatialObjectsElement = appComponentsElement.getChild(XMLTags.SpatialObjectsTag);
            if (spatialObjectsElement != null) {
                SpatialObject[] spatialObjects = xmlReader.getSpatialObjects(simContext, spatialObjectsElement);
                simContext.setSpatialObjects(spatialObjects);
            }
            // get application parameters
            Element appParamsElement = appComponentsElement.getChild(XMLTags.ApplicationParametersTag);
            if (appParamsElement != null) {
                SimulationContextParameter[] appParams = xmlReader.getSimulationContextParams(appParamsElement, simContext);
                simContext.setSimulationContextParameters(appParams);
            }
            // get bioEvents
            Element bioEventsElement = appComponentsElement.getChild(XMLTags.BioEventsTag);
            if (bioEventsElement != null) {
                BioEvent[] bioEvents = xmlReader.getBioEvents(simContext, bioEventsElement);
                simContext.setBioEvents(bioEvents);
            }
            // get spatial processes
            Element spatialProcessesElement = appComponentsElement.getChild(XMLTags.SpatialProcessesTag);
            if (spatialProcessesElement != null) {
                SpatialProcess[] spatialProcesses = xmlReader.getSpatialProcesses(simContext, spatialProcessesElement);
                simContext.setSpatialProcesses(spatialProcesses);
            }
            // get microscope measurements
            Element element = appComponentsElement.getChild(XMLTags.MicroscopeMeasurement);
            if (element != null) {
                xmlReader.getMicroscopeMeasurement(element, simContext);
            }
            // get rate rules
            Element rateRulesElement = appComponentsElement.getChild(XMLTags.RateRulesTag);
            if (rateRulesElement != null) {
                RateRule[] rateRules = xmlReader.getRateRules(simContext, rateRulesElement);
                simContext.setRateRules(rateRules);
            }
            // get reaction rule specs
            Element reactionRuleSpecsElement = appComponentsElement.getChild(XMLTags.ReactionRuleSpecsTag);
            if (reactionRuleSpecsElement != null) {
                ReactionRuleSpec[] reactionRuleSpecs = xmlReader.getReactionRuleSpecs(simContext, reactionRuleSpecsElement);
                simContext.getReactionContext().setReactionRuleSpecs(reactionRuleSpecs);
            }
        }
    } catch (XmlParseException e) {
        e.printStackTrace(System.out);
        throw new DataAccessException("Error retrieving bioevents : " + e.getMessage());
    }
}

Example 5 with XmlReader

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

the class SubVolumeTable method getAnalyticOrCompartmentSubVolume.

/**
 * This method was created in VisualAge.
 * @return Model
 * @param rset ResultSet
 * @param log SessionLog
 */
public SubVolume getAnalyticOrCompartmentSubVolume(KeyValue key, ResultSet rset) throws SQLException, ExpressionException, DataAccessException {
    // KeyValue key = new KeyValue(rset.getBigDecimal(id.toString(),0));
    String svName = rset.getString(name.toString());
    int handleValue = rset.getInt(handle.toString());
    String expString = rset.getString(expression.toString());
    if (rset.wasNull()) {
        return new CompartmentSubVolume(key, handleValue);
    } else {
        try {
            if (expString.startsWith("<") && expString.endsWith(">")) {
                String xmlStr = TokenMangler.getSQLRestoredString(expString);
                XmlReader xmlReader = new XmlReader(true);
                Element csgObjElement = (XmlUtil.stringToXML(xmlStr, null)).getRootElement();
                try {
                    CSGObject csgObject = xmlReader.getCSGObject(csgObjElement, key);
                    return csgObject;
                } catch (Exception e1) {
                    e1.printStackTrace(System.out);
                    throw new DataAccessException(e1.getMessage(), e1);
                }
            }
            Expression exp = new Expression(expString);
            return new AnalyticSubVolume(key, svName, exp, handleValue);
        } catch (Exception e) {
            e.printStackTrace(System.out);
            throw new DataAccessException(e.getMessage(), e);
        }
    }
}