Examples with Model cbit.vcell.model.Model used on opensource projects

Example 56 with Model

use of cbit.vcell.model.Model in project vcell by virtualcell.

the class ModelDbDriver method getModel.

/**
 * getModel method comment.
 */
private cbit.vcell.model.Model getModel(QueryHashtable dbc, Connection con, User user, KeyValue modelKey) throws SQLException, DataAccessException, ObjectNotFoundException {
    if (user == null || modelKey == null) {
        throw new IllegalArgumentException("Improper parameters for getModel");
    }
    // log.print("ModelDbDriver.getModel(user=" + user + ", id=" + modelKey + ")");
    String sql;
    Field[] f = { new cbit.sql.StarField(modelTable), userTable.userid };
    Table[] t = { modelTable, userTable };
    String condition = modelTable.id.getQualifiedColName() + " = " + modelKey + " AND " + userTable.id.getQualifiedColName() + " = " + modelTable.ownerRef.getQualifiedColName();
    sql = DatabasePolicySQL.enforceOwnershipSelect(user, f, t, (OuterJoin) null, condition, null, dbSyntax);
    Statement stmt = con.createStatement();
    Model model = null;
    try {
        ResultSet rset = stmt.executeQuery(sql);
        if (rset.next()) {
            model = getModel(dbc, rset, con, user);
        } else {
            throw new org.vcell.util.ObjectNotFoundException("Model id=" + modelKey + " not found for user '" + user + "'");
        }
    } finally {
        // Release resources include resultset
        stmt.close();
    }
    // GlobalModelParameterTable.table.setModelParameters(con, model);
    return model;
}

Example 57 with Model

use of cbit.vcell.model.Model 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 58 with Model

use of cbit.vcell.model.Model in project vcell by virtualcell.

the class ServerDocumentManager method getBioModelUnresolved.

/**
 * Insert the method's description here.
 * Creation date: (11/14/00 4:02:44 PM)
 * @return cbit.vcell.biomodel.BioModel
 * @param bioModelInfo cbit.vcell.biomodel.BioModelInfo
 */
// 
// this returns a BioModel that contains multiple instances of objects.
// 
public String getBioModelUnresolved(QueryHashtable dbc, User user, KeyValue bioModelKey) throws DataAccessException, XmlParseException, java.sql.SQLException {
    // 
    // get meta data associated with BioModel
    // 
    BioModelMetaData bioModelMetaData = dbServer.getDBTopLevel().getBioModelMetaData(dbc, user, bioModelKey);
    // 
    // get list of appropriate child components
    // 
    KeyValue modelKey = bioModelMetaData.getModelKey();
    KeyValue[] simKeys = getKeyArrayFromEnumeration(bioModelMetaData.getSimulationKeys());
    KeyValue[] scKeys = getKeyArrayFromEnumeration(bioModelMetaData.getSimulationContextKeys());
    Model model = dbServer.getDBTopLevel().getModel(dbc, user, modelKey);
    Simulation[] simArray = new Simulation[simKeys.length];
    for (int i = 0; i < simKeys.length; i++) {
        Simulation sim = dbServer.getDBTopLevel().getSimulation(dbc, user, simKeys[i]);
        // 
        try {
            simArray[i] = (Simulation) BeanUtils.cloneSerializable(sim);
        } catch (Throwable e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("exception cloning Simulation: " + e.getMessage());
        }
    }
    SimulationContext[] scArray = new SimulationContext[scKeys.length];
    for (int i = 0; i < scKeys.length; i++) {
        SimulationContext sc = dbServer.getDBTopLevel().getSimulationContext(dbc, user, scKeys[i]);
        // 
        try {
            scArray[i] = (SimulationContext) BeanUtils.cloneSerializable(sc);
            scArray[i].getModel().refreshDependencies();
            scArray[i].refreshDependencies();
            scArray[i].setModel(model);
        } catch (Throwable e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("exception cloning Application: " + e.getMessage());
        }
        if (!scArray[i].getModel().getKey().compareEqual(modelKey)) {
            // throw new DataAccessException("simulationContext("+scKeys[i]+").model = "+scArray[i].getModel().getKey()+", BioModel.model = "+modelKey);
            System.out.println("simulationContext(" + scKeys[i] + ").model = " + scArray[i].getModel().getKey() + ", BioModel.model = " + modelKey);
        }
    }
    // 
    // create new BioModel according to loaded BioModelMetaData
    // 
    BioModel newBioModel = new BioModel(bioModelMetaData.getVersion());
    try {
        // newBioModel.setMIRIAMAnnotation(bioModelMetaData.getMIRIAMAnnotation());
        System.err.println("< < < < NEED TO GET VCMETADATA FROM METADATA TABLE ... METADATA IS EMPTY. > > > >");
        newBioModel.setModel(model);
        newBioModel.setSimulationContexts(scArray);
        // 
        for (int i = 0; i < simArray.length; i++) {
            boolean bMathFound = false;
            for (int j = 0; j < scArray.length; j++) {
                if (simArray[i].getMathDescription().getVersion().getVersionKey().compareEqual(scArray[j].getMathDescription().getVersion().getVersionKey())) {
                    simArray[i].setMathDescription(scArray[j].getMathDescription());
                    bMathFound = true;
                    break;
                }
            }
            if (!bMathFound) {
                System.out.println("<<<<WARNING>>>>> ClientDocumentManager.getBioModel(), Simulation " + simArray[i].getName() + " is orphaned, Math(" + simArray[i].getMathDescription().getName() + ") not found in Applications");
                simArray = (Simulation[]) BeanUtils.removeElement(simArray, simArray[i]);
                i--;
            }
        }
        newBioModel.setSimulations(simArray);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace(System.out);
        throw new DataAccessException("PropertyVetoException caught " + e.getMessage());
    }
    // 
    // The BioModel is no longer cloned because the reference to this BioModel is no longer returned to the calling method.
    // the only possible side effect is the "BioModel:refreshDependencies()" method call.
    // this will reconnect internal listeners and other transient fields, and is not going to harm the cache integrity.
    // 
    // //
    // // clone BioModel (so that children can't be corrupted in the cache)
    // //
    // try {
    // newBioModel = (BioModel)BeanUtils.cloneSerializable(newBioModel);
    // }catch (Exception e){
    // e.printStackTrace(System.out);
    // throw new DataAccessException("BioModel clone failed: "+e.getMessage());
    // }
    newBioModel.refreshDependencies();
    // 
    return cbit.vcell.xml.XmlHelper.bioModelToXML(newBioModel);
}

Example 59 with Model

use of cbit.vcell.model.Model in project vcell by virtualcell.

the class SimContextTable method getSimContext.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.mapping.SimulationContext
 * @param rset java.sql.ResultSet
 * @param log cbit.vcell.server.SessionLog
 * @deprecated shouldn't do recursive query
 */
public SimulationContext getSimContext(QueryHashtable dbc, Connection con, User user, ResultSet rset, GeomDbDriver geomDB, ModelDbDriver modelDB, MathDescriptionDbDriver mathDB) throws SQLException, DataAccessException, java.beans.PropertyVetoException {
    java.math.BigDecimal groupid = rset.getBigDecimal(VersionTable.privacy_ColumnName);
    Version version = getVersion(rset, DbDriver.getGroupAccessFromGroupID(con, groupid));
    KeyValue geomKey = new KeyValue(rset.getBigDecimal(SimContextTable.table.geometryRef.toString()));
    Geometry geom = (Geometry) geomDB.getVersionable(dbc, con, user, VersionableType.Geometry, geomKey, false);
    KeyValue modelKey = new KeyValue(rset.getBigDecimal(SimContextTable.table.modelRef.toString()));
    Model model = (Model) modelDB.getVersionable(dbc, con, user, VersionableType.Model, modelKey);
    // 
    // read characteristic size (may be null)
    // 
    Double characteristicSize = null;
    BigDecimal size = rset.getBigDecimal(charSize.toString());
    if (!rset.wasNull() && size != null) {
        characteristicSize = new Double(size.doubleValue());
    }
    // 
    // get mathKey (may be null)
    // 
    MathDescription mathDesc = null;
    BigDecimal mathKeyValue = rset.getBigDecimal(SimContextTable.table.mathRef.toString());
    if (!rset.wasNull()) {
        KeyValue mathKey = new KeyValue(mathKeyValue);
        mathDesc = (MathDescription) mathDB.getVersionable(dbc, con, user, VersionableType.MathDescription, mathKey);
    }
    boolean bStochastic = mathDesc.isNonSpatialStoch() || mathDesc.isSpatialStoch() || mathDesc.isSpatialHybrid();
    boolean bRuleBased = mathDesc.isRuleBased();
    SimulationContext simContext = new SimulationContext(model, geom, mathDesc, version, bStochastic, bRuleBased);
    if (characteristicSize != null) {
        simContext.setCharacteristicSize(characteristicSize);
    }
    return simContext;
}

Example 60 with Model

use of cbit.vcell.model.Model in project vcell by virtualcell.

the class ReactionCartoonTool method lineAction.

private void lineAction(SpeciesContext speciesContextStart, SpeciesContext speciesContextEnd) throws Exception {
    Structure endStructure = speciesContextEnd.getStructure();
    Structure startStructure = speciesContextStart.getStructure();
    Model model = getModel();
    ReactionStep reaction = null;
    Point startPos = edgeShape.getStart();
    Point endPos = edgeShape.getEnd();
    Structure reactionStructure = null;
    boolean bLumpedKinetics = false;
    if (startStructure != endStructure) {
        if (startStructure instanceof Feature && endStructure instanceof Feature) {
            // Feature-speciesContext ==> Feature-speciesContext
            Membrane membraneBetween = model.getStructureTopology().getMembrane((Feature) startStructure, (Feature) endStructure);
            // Feature-speciesContext ==> Feature-speciesContext with membrane in between : add reaction in Membrane (scStart : reactant; scEnd : pdt)
            if (membraneBetween != null) {
                reactionStructure = membraneBetween;
            } else {
                // Feature-speciesContext ==> Feature-speciesContext with no membrane between : create a lumped reaction in startFeature
                reactionStructure = startStructure;
                bLumpedKinetics = true;
            }
        } else if (startStructure instanceof Feature && endStructure instanceof Membrane) {
            // Feature-speciesContext ==> Membrane-speciesContext : create membrane reaction ; add scStart : reactant and scEnd : pdt.
            reactionStructure = endStructure;
        } else if (startStructure instanceof Membrane && endStructure instanceof Feature) {
            // Membrane-speciesContext ==> Feature-speciesContext : create reaction in membrane; scStart : reactant, scEnd : pdt.
            reactionStructure = startStructure;
        } else if (startStructure instanceof Membrane && endStructure instanceof Membrane) {
            // Membrane-speciesContext ==> Membrane-speciesContext : the 2 membranes are different : create lumped reaction in endMembrane
            reactionStructure = endStructure;
            bLumpedKinetics = true;
        }
    } else {
        // startStructure == endStructure : create reaction in structure
        reactionStructure = startStructure;
    }
    reaction = model.createSimpleReaction(reactionStructure);
    if (bLumpedKinetics) {
        reaction.setKinetics(new GeneralLumpedKinetics(reaction));
    }
    reaction.addReactant(speciesContextStart, 1);
    reaction.addProduct(speciesContextEnd, 1);
    positionShapeForObject(reactionStructure, reaction, new Point((startPos.x + endPos.x) / 2, (startPos.y + endPos.y) / 2));
    getReactionCartoon().notifyChangeEvent();
    getGraphModel().clearSelection();
    getGraphModel().select(reaction);
}