Examples with SimulationContext cbit.vcell.mapping.SimulationContext used on opensource projects

Example 81 with SimulationContext

use of cbit.vcell.mapping.SimulationContext in project vcell by virtualcell.

the class DbDriver method setVersioned.

/**
 * This method was created in VisualAge.
 * @param vTable cbit.sql.VersionTable
 * @param versionKey cbit.sql.KeyValue
 */
protected void setVersioned(Connection con, User user, Versionable versionable) throws ObjectNotFoundException, SQLException, DataAccessException {
    String sql;
    if (versionable instanceof SimulationContext) {
        SimulationContext sc = (SimulationContext) versionable;
        setVersioned(con, user, sc.getGeometryContext().getGeometry());
        setVersioned(con, user, sc.getGeometryContext().getModel());
        if (sc.getMathDescription() != null) {
            setVersioned(con, user, sc.getMathDescription());
        }
    } else if (versionable instanceof MathDescription) {
        MathDescription math = (MathDescription) versionable;
        setVersioned(con, user, math.getGeometry());
    } else if (versionable instanceof Geometry) {
        Geometry geo = (Geometry) versionable;
        if (geo.getGeometrySpec().getImage() != null) {
            setVersioned(con, user, geo.getGeometrySpec().getImage());
        }
    }
    // 
    if (versionable.getVersion().getOwner().compareEqual(user)) {
        VersionTable vTable = VersionTable.getVersionTable(versionable);
        sql = "UPDATE " + vTable.getTableName() + " SET " + vTable.versionFlag + " = " + VersionFlag.Archived.getIntValue() + " WHERE " + vTable.id + " = " + versionable.getVersion().getVersionKey() + // " AND " + vTable.versionFlag + " = " + VersionFlag.CURRENT +
        " AND " + vTable.ownerRef + " = " + user.getID();
        if (updateCleanSQL(con, sql) != 1) {
            throw new DataAccessException("setVersioned failed for :" + versionable.getVersion());
        }
    }
}

Example 82 with SimulationContext

use of cbit.vcell.mapping.SimulationContext 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 83 with SimulationContext

use of cbit.vcell.mapping.SimulationContext 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 84 with SimulationContext

use of cbit.vcell.mapping.SimulationContext in project vcell by virtualcell.

the class SimulationContextDbDriver method getSimulationContextSQL.

/**
 * getModel method comment.
 */
private SimulationContext getSimulationContextSQL(QueryHashtable dbc, Connection con, User user, KeyValue simContextKey) throws /*, ReactStepDbDriver reactStepDB*/
SQLException, DataAccessException, IllegalMappingException, PropertyVetoException {
    SimulationContext simContext = null;
    String sql;
    Field[] f = { new cbit.sql.StarField(simContextTable), userTable.userid };
    Table[] t = { simContextTable, userTable };
    String condition = simContextTable.id.getQualifiedColName() + " = " + simContextKey + " AND " + simContextTable.ownerRef.getQualifiedColName() + " = " + userTable.id.getQualifiedColName();
    sql = DatabasePolicySQL.enforceOwnershipSelect(user, f, t, (OuterJoin) null, condition, null, dbSyntax);
    // System.out.println(sql);
    Statement stmt = con.createStatement();
    try {
        ResultSet rset = stmt.executeQuery(sql);
        if (rset.next()) {
            simContext = simContextTable.getSimContext(dbc, con, user, rset, geomDB, modelDB, mathDescDB);
        } else {
            throw new ObjectNotFoundException("SimulationContext id=" + simContextKey + " not found for user '" + user + "'");
        }
    } finally {
        stmt.close();
    }
    DataSymbolTable.table.populateDataSymbols(con, simContextKey, simContext.getDataContext(), user, simContext.getModel().getUnitSystem());
    ArrayList<AnnotatedFunction> outputFunctionList = ApplicationMathTable.table.getOutputFunctionsSimcontext(con, simContextKey, dbSyntax);
    if (outputFunctionList != null) {
        OutputFunctionContext outputFnContext = simContext.getOutputFunctionContext();
        outputFnContext.setOutputFunctions(outputFunctionList);
    }
    SimContextTable.table.readAppComponents(con, simContext, dbSyntax);
    assignStimuliSQL(con, simContextKey, simContext);
    assignStructureMappingsSQL(dbc, con, simContextKey, simContext);
    assignSpeciesContextSpecsSQL(con, simContextKey, simContext);
    assignReactionSpecsSQL(con, simContextKey, simContext);
    for (GeometryClass gc : simContext.getGeometry().getGeometryClasses()) {
        try {
            StructureSizeSolver.updateUnitStructureSizes(simContext, gc);
        } catch (Exception e) {
            e.printStackTrace(System.out);
        }
    }
    simContext.getGeometryContext().enforceHierarchicalBoundaryConditions(simContext.getModel().getStructureTopology());
    simContext.getModel().refreshDependencies();
    assignAnalysisTasksSQL(con, simContextKey, simContext);
    // really needed to calculate MembraneMapping parameters that are not stored (inside/outside flux correction factors).
    simContext.refreshDependencies();
    return simContext;
}

Example 85 with SimulationContext

use of cbit.vcell.mapping.SimulationContext in project vcell by virtualcell.

the class ElectricalStimulusPanel method setsimulationContext1.

/**
 * Set the simulationContext1 to a new value.
 * @param newValue cbit.vcell.mapping.SimulationContext
 */
/* WARNING: THIS METHOD WILL BE REGENERATED. */
private void setsimulationContext1(SimulationContext newValue) {
    if (ivjsimulationContext1 != newValue) {
        try {
            SimulationContext oldValue = getsimulationContext1();
            /* Stop listening for events from the current object */
            if (ivjsimulationContext1 != null) {
                ivjsimulationContext1.removePropertyChangeListener(ivjEventHandler);
            }
            ivjsimulationContext1 = newValue;
            /* Listen for events from the new object */
            if (ivjsimulationContext1 != null) {
                ivjsimulationContext1.addPropertyChangeListener(ivjEventHandler);
            }
            connPtoP1SetSource();
            connEtoM1(ivjsimulationContext1);
            connEtoM3(ivjsimulationContext1);
            connEtoM8(ivjsimulationContext1);
            connEtoM11(ivjsimulationContext1);
            connEtoC1(ivjsimulationContext1);
            connEtoC7(ivjsimulationContext1);
            setupElectrodeFeatureListProvider();
            firePropertyChange("simulationContext", oldValue, newValue);
        // user code begin {1}
        // user code end
        } catch (java.lang.Throwable ivjExc) {
            // user code begin {2}
            // user code end
            handleException(ivjExc);
        }
    }
    ;
// user code begin {3}
// user code end
}