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

Example 16 with ObjectNotFoundException

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

the class ReactStepDbDriver method getSpecies.

/**
 * getModel method comment.
 */
public Species getSpecies(QueryHashtable dbc, Connection con, KeyValue speciesID) throws SQLException, DataAccessException, ObjectNotFoundException {
    // 
    // try to get Species from the object cache
    // 
    Species species = (Species) dbc.get(speciesID);
    if (species != null) {
        return species;
    }
    if (speciesID == null) {
        throw new IllegalArgumentException("Improper parameters for getSpecies");
    }
    // log.print("ReactStepDbDriver.getSpecies(speciesID=" + speciesID + ")");
    String sql;
    sql = " SELECT * " + " FROM " + speciesTable.getTableName() + " WHERE " + speciesTable.id + " = " + speciesID;
    // System.out.println(sql);
    Statement stmt = con.createStatement();
    try {
        ResultSet rset = stmt.executeQuery(sql);
        if (rset.next()) {
            species = getSpecies(dbc, rset, con);
        } else {
            throw new org.vcell.util.ObjectNotFoundException("Species id=" + speciesID + " not found");
        }
    } finally {
        // Release resources include resultset
        stmt.close();
    }
    // MIRIAMTable.table.setMIRIAMAnnotation(con, species, speciesID);
    return species;
}

Example 17 with ObjectNotFoundException

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

the class DatabaseServerImpl method getVersionInfos.

/**
 * This method was created in VisualAge.
 * @return GeometryInfo
 * @param key KeyValue
 * @exception org.vcell.util.DataAccessException The exception description.
 * @exception java.rmi.RemoteException The exception description.
 */
private VersionInfo[] getVersionInfos(User user, KeyValue key, VersionableType vType, boolean bAll, boolean bCheckPermission) throws DataAccessException {
    try {
        if (lg.isTraceEnabled())
            lg.trace("DatabaseServerImpl.getVersionInfos(User=" + user + ",vType=" + vType + ",bAll=" + bAll + ")");
        Vector<VersionInfo> vector = dbTop.getVersionableInfos(user, key, vType, bAll, bCheckPermission, true);
        if (vType.equals(VersionableType.BioModelMetaData)) {
            BioModelInfo[] bioModelInfos = new BioModelInfo[vector.size()];
            vector.copyInto(bioModelInfos);
            return bioModelInfos;
        } else if (vType.equals(VersionableType.Geometry)) {
            GeometryInfo[] geoInfos = new GeometryInfo[vector.size()];
            vector.copyInto(geoInfos);
            return geoInfos;
        } else if (vType.equals(VersionableType.MathModelMetaData)) {
            MathModelInfo[] mathInfos = new MathModelInfo[vector.size()];
            vector.copyInto(mathInfos);
            return mathInfos;
        } else if (vType.equals(VersionableType.VCImage)) {
            VCImageInfo[] imgInfos = new VCImageInfo[vector.size()];
            vector.copyInto(imgInfos);
            return imgInfos;
        } else if (vType.equals(VersionableType.Simulation)) {
            SimulationInfo[] simInfos = new SimulationInfo[vector.size()];
            vector.copyInto(simInfos);
            return simInfos;
        } else {
            throw new IllegalArgumentException("Wrong VersinableType vType:" + vType);
        }
    } catch (SQLException e) {
        lg.error(e.getMessage(), e);
        throw new DataAccessException(e.getMessage());
    } catch (ObjectNotFoundException e) {
        lg.error(e.getMessage(), e);
        throw new ObjectNotFoundException(e.getMessage());
    } catch (Throwable e) {
        lg.error(e.getMessage(), e);
        throw new DataAccessException(e.getMessage());
    }
}

Example 18 with ObjectNotFoundException

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

the class DatabaseServerImpl method groupAddUser.

/**
 * This method was created in VisualAge.
 * @return void
 * @param key KeyValue
 * @exception org.vcell.util.DataAccessException The exception description.
 * @exception java.rmi.RemoteException The exception description.
 */
public VersionInfo groupAddUser(User user, VersionableType vType, KeyValue key, String addUserToGroup, boolean isHidden) throws DataAccessException, ObjectNotFoundException {
    try {
        if (lg.isTraceEnabled())
            lg.trace("DatabaseServerImpl.groupAddUser(vType=" + vType.getTypeName() + ", Key=" + key + ", userToAdd=" + addUserToGroup + ", isHidden=" + isHidden + ")");
        dbTop.groupAddUser(user, vType, key, true, addUserToGroup, isHidden);
        VersionInfo newVersionInfo = (VersionInfo) (dbTop.getVersionableInfos(user, key, vType, false, true, true).elementAt(0));
        return newVersionInfo;
    } catch (SQLException e) {
        lg.error(e.getMessage(), e);
        throw new DataAccessException(e.getMessage());
    } catch (ObjectNotFoundException e) {
        lg.error(e.getMessage(), e);
        throw new ObjectNotFoundException(e.getMessage());
    } catch (Throwable e) {
        lg.error(e.getMessage(), e);
        throw new DataAccessException(e.getMessage());
    }
}

Example 19 with ObjectNotFoundException

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

the class DatabaseServerImpl method getVCImageXML.

/**
 * getVersionable method comment.
 */
public BigString getVCImageXML(User user, KeyValue key) throws DataAccessException, ObjectNotFoundException {
    try {
        if (lg.isTraceEnabled())
            lg.trace("DatabaseServerImpl.getVCImageXML(user=" + user + ", Key=" + key + ")");
        boolean bCheckPermission = true;
        VCImage image = dbTop.getVCImage(new QueryHashtable(), user, key, bCheckPermission);
        return new BigString(XmlHelper.imageToXML(image));
    } catch (ObjectNotFoundException e) {
        lg.error(e.getMessage(), e);
        throw new ObjectNotFoundException(e.getMessage());
    } catch (Throwable e) {
        lg.error(e.getMessage(), e);
        throw new DataAccessException(e.getMessage());
    }
}

Example 20 with ObjectNotFoundException

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

the class GeomDbDriver method getExtentRefKeyFromGeometry.

/**
 * getModel method comment.
 */
private KeyValue getExtentRefKeyFromGeometry(Connection con, KeyValue geomKey) throws SQLException, DataAccessException, ObjectNotFoundException {
    if (geomKey == null) {
        throw new IllegalArgumentException("Improper parameters for getSizeKeyFromGeometry");
    }
    // log.print("GeomDbDriver.getSizeKeyFromGeometry(id="+geomKey+")");
    String sql;
    sql = " SELECT " + geomTable.extentRef + " FROM " + geomTable.getTableName() + " WHERE " + geomTable.id + " = " + geomKey;
    // System.out.println(sql);
    // Connection con = conFact.getConnection();
    Statement stmt = con.createStatement();
    try {
        ResultSet rset = stmt.executeQuery(sql);
        if (rset.next()) {
            return new KeyValue(rset.getBigDecimal(geomTable.extentRef.toString()));
        } else {
            throw new ObjectNotFoundException("getSizeKeyFromGeometry for Image id=" + geomKey + " not found");
        }
    } finally {
        // Release resources include resultset
        stmt.close();
    }
}