Examples with ObjectNotFoundException org.vcell.util.ObjectNotFoundException used on opensource projects

Example 21 with ObjectNotFoundException

use of org.vcell.util.ObjectNotFoundException in project vcell by virtualcell.

the class GeomDbDriver method getVCImage.

/**
 * getModel method comment.
 */
private VCImage getVCImage(QueryHashtable dbc, Connection con, User user, KeyValue imageKey, boolean bCheckPermission) throws SQLException, DataAccessException, ObjectNotFoundException {
    // log.print("GeomDbDriver.getImage(user="+user+", id="+imageKey+")");
    String sql;
    Field[] f = { new StarField(imageTable), userTable.userid, imageDataTable.data, new StarField(extentTable) };
    Table[] t = { imageTable, userTable, imageDataTable, extentTable };
    String condition = imageTable.id.getQualifiedColName() + " = " + imageKey + " AND " + imageTable.ownerRef.getQualifiedColName() + " = " + userTable.id.getQualifiedColName() + " AND " + imageTable.id.getQualifiedColName() + " = " + imageDataTable.imageRef.getQualifiedColName() + " AND " + imageTable.extentRef.getQualifiedColName() + " = " + extentTable.id.getQualifiedColName();
    sql = DatabasePolicySQL.enforceOwnershipSelect(user, f, t, (OuterJoin) null, condition, null, dbSyntax, bCheckPermission);
    // System.out.println(sql);
    // Connection con = conFact.getConnection();
    VCImage vcImage = null;
    Statement stmt = con.createStatement();
    try {
        ResultSet rset = stmt.executeQuery(sql);
        if (rset.next()) {
            vcImage = imageTable.getImage(rset, con, imageDataTable, dbSyntax);
            getImageRegionsForVCImage(dbc, con, vcImage);
        } else {
            throw new ObjectNotFoundException("Image id=" + imageKey + " not found for user '" + user + "'");
        }
    } finally {
        // Release resources include resultset
        stmt.close();
    }
    return vcImage;
}

Example 22 with ObjectNotFoundException

use of org.vcell.util.ObjectNotFoundException in project vcell by virtualcell.

the class ServerDocumentManager method getBioModelXML.

/**
 * Insert the method's description here.
 * Creation date: (3/29/2004 4:04:16 PM)
 * @return java.lang.String
 * @param vType cbit.sql.VersionableType
 * @param vKey cbit.sql.KeyValue
 */
public String getBioModelXML(QueryHashtable dbc, User user, KeyValue bioModelKey, boolean bRegenerateXML) throws DataAccessException {
    String bioModelXML = null;
    try {
        bioModelXML = dbServer.getDBTopLevel().getBioModelXML(user, bioModelKey, true);
        if (bioModelXML != null) {
            if (bRegenerateXML) {
                try {
                    BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML));
                    return cbit.vcell.xml.XmlHelper.bioModelToXML(bioModel);
                } catch (XmlParseException e) {
                    e.printStackTrace();
                    throw new DataAccessException(e.getMessage(), e);
                }
            } else {
                return bioModelXML;
            }
        }
    } catch (java.sql.SQLException e) {
        e.printStackTrace(System.out);
        throw new DataAccessException(e.getMessage());
    } catch (ObjectNotFoundException e) {
    // 
    // not stored as XML currently, retrieve traditional way.
    // 
    }
    try {
        bioModelXML = getBioModelUnresolved(dbc, user, bioModelKey);
        dbServer.insertVersionableXML(user, VersionableType.BioModelMetaData, bioModelKey, bioModelXML);
        return bioModelXML;
    } catch (java.sql.SQLException e) {
        e.printStackTrace(System.out);
        throw new DataAccessException(e.getMessage());
    } catch (cbit.vcell.xml.XmlParseException e) {
        e.printStackTrace(System.out);
        throw new DataAccessException(e.getMessage());
    }
}

Example 23 with ObjectNotFoundException

use of org.vcell.util.ObjectNotFoundException in project vcell by virtualcell.

the class ServerDocumentManager method isChanged.

/**
 * Insert the method's description here.
 * Creation date: (2/5/01 4:58:40 PM)
 */
boolean isChanged(QueryHashtable dbc, User user, cbit.image.VCImage vcImage) throws org.vcell.util.DataAccessException {
    // 
    // identify versionable as it was last loaded from the database
    // 
    KeyValue key = (vcImage.getVersion() != null) ? (vcImage.getVersion().getVersionKey()) : null;
    if (key == null) {
        return true;
    }
    Versionable savedVersionable = null;
    // 
    try {
        savedVersionable = dbServer.getDBTopLevel().getVCImage(dbc, user, key, true);
    } catch (ObjectNotFoundException e) {
        // 
        return true;
    } catch (Throwable e) {
        // 
        // loaded version has been deleted
        // 
        e.printStackTrace(System.out);
        return true;
    }
    return isChanged0(user, vcImage, savedVersionable);
}

Example 24 with ObjectNotFoundException

use of org.vcell.util.ObjectNotFoundException 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 25 with ObjectNotFoundException

use of org.vcell.util.ObjectNotFoundException in project vcell by virtualcell.

the class BioModelDbDriver method getBioModelMetaData.

/**
 * getModel method comment.
 */
private BioModelMetaData getBioModelMetaData(Connection con, User user, KeyValue bioModelKey, DatabaseSyntax dbSyntax) throws SQLException, DataAccessException, ObjectNotFoundException {
    if (user == null || bioModelKey == null) {
        throw new IllegalArgumentException("Improper parameters for getBioModelMetaData");
    }
    // if (lg.isTraceEnabled()) lg.trace("BioModelDbDriver.getBioModelMetaData(user=" + user + ", id=" + bioModelKey + ")");
    // 
    // to construct a BioModelMetaData as an immutable object, lets collect all keys first
    // (even before authentication).  If the user doesn't authenticate, then throw away the
    // child keys (from link tables).
    // 
    // 
    // get Simulation Keys for bioModelKey
    // 
    KeyValue[] simKeys = getSimulationEntriesFromBioModel(con, bioModelKey);
    // 
    // get SimulationContext Keys for bioModelKey
    // 
    KeyValue[] simContextKeys = getSimContextEntriesFromBioModel(con, bioModelKey);
    // 
    // get BioModelMetaData object for bioModelKey
    // 
    String sql;
    VCMetaDataTable vcMetadataTable = VCMetaDataTable.table;
    Field[] f = { new StarField(bioModelTable), userTable.userid, new StarField(vcMetadataTable) };
    Table[] t = { bioModelTable, userTable, vcMetadataTable };
    switch(dbSyntax) {
        case ORACLE:
            {
                String condition = bioModelTable.id.getQualifiedColName() + " = " + bioModelKey + " AND " + userTable.id.getQualifiedColName() + " = " + bioModelTable.ownerRef.getQualifiedColName() + " AND " + vcMetadataTable.bioModelRef.getQualifiedColName() + "(+) = " + bioModelTable.id.getQualifiedColName();
                sql = DatabasePolicySQL.enforceOwnershipSelect(user, f, t, null, condition, null, dbSyntax, true);
                break;
            }
        case POSTGRES:
            {
                String condition = bioModelTable.id.getQualifiedColName() + " = " + bioModelKey + " AND " + userTable.id.getQualifiedColName() + " = " + bioModelTable.ownerRef.getQualifiedColName() + " ";
                // " AND "+ VCMetaDataTable.table.bioModelRef.getQualifiedColName() + "(+) = " + bioModelTable.id.getQualifiedColName();
                OuterJoin outerJoin = new OuterJoin(vcMetadataTable, bioModelTable, JoinOp.RIGHT_OUTER_JOIN, vcMetadataTable.bioModelRef, bioModelTable.id);
                sql = DatabasePolicySQL.enforceOwnershipSelect(user, f, t, outerJoin, condition, null, dbSyntax, true);
                break;
            }
        default:
            {
                throw new RuntimeException("unexpected DatabaseSyntax " + dbSyntax);
            }
    }
    Statement stmt = con.createStatement();
    BioModelMetaData bioModelMetaData = null;
    try {
        ResultSet rset = stmt.executeQuery(sql);
        if (rset.next()) {
            bioModelMetaData = bioModelTable.getBioModelMetaData(rset, con, simContextKeys, simKeys, dbSyntax);
        } else {
            throw new ObjectNotFoundException("BioModel id=" + bioModelKey + " not found for user '" + user + "'");
        }
    } finally {
        // Release resources include resultset
        stmt.close();
    }
    return bioModelMetaData;
}