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

Example 26 with ObjectNotFoundException

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

the class DBTopLevel method getBioModelXML.

/**
 * This method was created in VisualAge.
 * @return cbit.sql.Versionable
 * @param object cbit.sql.Versionable
 * @param name java.lang.String
 * @param bVersion boolean
 * @exception org.vcell.util.DataAccessException The exception description.
 * @exception java.sql.SQLException The exception description.
 * @exception cbit.sql.RecordChangedException The exception description.
 */
String getBioModelXML(User user, KeyValue key, boolean bEnableRetry) throws DataAccessException, java.sql.SQLException, ObjectNotFoundException {
    Object lock = new Object();
    Connection con = conFactory.getConnection(lock);
    DbDriver driver = getDbDriver(VersionableType.BioModelMetaData);
    try {
        // 
        // Getting the corresponding VersionInfo will fail if you don't have permission to the object.
        // This is needed because the DbDriver-level services can return objects directly from the
        // cache without checking for permissions first.
        // 
        // This check is placed in DbTopLevel because this is the client API entry point.
        // Child objects (of the requested object) are given permission by reachablity anyway,
        // so if the user is allowed permission to the parent, no further checks are necessary.
        // 
        Vector<VersionInfo> vInfos = getVersionableInfos(user, key, VersionableType.BioModelMetaData, true, true, false);
        if (vInfos.size() == 0) {
            throw new ObjectNotFoundException(VersionableType.BioModelMetaData.getTypeName() + " not found");
        }
        return driver.getVersionableXML(con, VersionableType.BioModelMetaData, key);
    } catch (Throwable e) {
        lg.error(e.getMessage(), e);
        if (bEnableRetry && isBadConnection(con)) {
            conFactory.failed(con, lock);
            return getBioModelXML(user, key, false);
        } else {
            handle_DataAccessException_SQLException(e);
            // never gets here;
            return null;
        }
    } finally {
        conFactory.release(con, lock);
    }
}

Example 27 with ObjectNotFoundException

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

the class ODESolverPlotSpecificationPanel method getSensitivityParameter.

/**
 * // Method to obtain the sensitivity parameter (if applicable). The method checks the column description names in the
 * // result set to find any column description that begins with the substring "sens" and contains the substring "wrt_".
 * // If there is, then the last portion of that column description name is the parameter name. The sensitivity parameter
 * // is also stored as a function column description in the result set (as a constant function). The value is extracted
 * // from the result set, and a new Constant is created (with the name and value of the parameter) and returned. If no
 * // column description starts with the substring "sens" or if the column for the parameter does not exist in the result
 * // set, the method returns null.
 */
private Constant getSensitivityParameter() throws ExpressionException {
    String sensParamName = "";
    ColumnDescription[] fcds = getMyDataInterface().getAllColumnDescriptions();
    // Check for any column description name that starts with the substring "sens" and contains "wrt_".
    for (int i = 0; i < fcds.length; i++) {
        if (fcds[i].getName().startsWith("sens_")) {
            int c = fcds[i].getName().indexOf("wrt_");
            sensParamName = fcds[i].getName().substring(c + 4);
            if (!sensParamName.equals(null) || !sensParamName.equals("")) {
                break;
            }
        }
    }
    double sensParamValue = 0.0;
    if (sensParamName.equals("")) {
        return null;
    }
    // If the sens param column exists in the result set, create a Constant and return it, else return null.
    try {
        sensParamValue = getMyDataInterface().extractColumn(sensParamName)[1];
    } catch (ObjectNotFoundException e) {
        // System.out.println("REUSULT SET DOES NOT HAVE SENSITIVITY ANALYSIS");
        return null;
    }
    Constant sensParam = new Constant(sensParamName, new Expression(sensParamValue));
    return sensParam;
}

Example 28 with ObjectNotFoundException

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

the class ClientDocumentManager method getGeometryInfo.

/**
 * Insert the method's description here.
 * Creation date: (11/14/00 2:50:07 PM)
 * @return cbit.sql.Versionable
 * @param vType cbit.sql.VersionableType
 * @param key cbit.sql.KeyValue
 */
public synchronized GeometryInfo getGeometryInfo(KeyValue key) throws DataAccessException {
    if (key == null) {
        System.out.println("<<<NULL>>>> ClientDocumentManager.getGeometryInfo(" + key + ")");
        return null;
    }
    // 
    // first look in local cache for the Info object
    // 
    GeometryInfo geometryInfo = (GeometryInfo) geoInfoHash.get(key);
    if (geometryInfo != null) {
        // System.out.println("<<<IN CACHE>>> ClientDocumentManager.getGeometryInfo("+key+")");
        return geometryInfo;
    }
    // 
    // else get new list of info objects from database and stick in cache
    // 
    reloadGeometryInfos();
    // bGeometryInfosDirty = false;
    // 
    // now look in cache again (should be in there unless it was deleted from database).
    // 
    geometryInfo = (GeometryInfo) geoInfoHash.get(key);
    if (geometryInfo != null) {
        return geometryInfo;
    } else {
        throw new ObjectNotFoundException("GeometryInfo(" + key + ") not found");
    }
}

Example 29 with ObjectNotFoundException

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

the class ClientDocumentManager 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
 */
private XMLHolder<BioModel> getBioModelXML(KeyValue vKey) throws DataAccessException {
    try {
        String xmlString = (String) xmlHash.get(vKey);
        if (xmlString == null) {
            BigString xmlBS = sessionManager.getUserMetaDbServer().getBioModelXML(vKey);
            xmlString = (xmlBS != null ? xmlBS.toString() : null);
            if (xmlString != null) {
                BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(xmlString));
                String newXmlString = XmlHelper.bioModelToXML(bioModel);
                xmlHash.put(vKey, newXmlString);
                return new XMLHolder<BioModel>(newXmlString, bioModel);
            } else {
                throw new RuntimeException("unexpected: UserMetaDbServer.getBioModelXML() returned null");
            }
        } else {
            return new XMLHolder<BioModel>(xmlString);
        }
    } catch (ObjectNotFoundException e) {
        throw new DataAccessException("BioModel (id=" + vKey + ") does not exist. It either " + "has been deleted or its reference is outdated. Please use menu 'Server->Reconnect' to update document references.");
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw FailToLoadDocumentExc.createException(e, vKey, this);
    }
}

Example 30 with ObjectNotFoundException

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

the class ClientDocumentManager method getMathModelXML.

/**
 * 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
 */
private XMLHolder<MathModel> getMathModelXML(KeyValue vKey) throws DataAccessException {
    try {
        String xmlString = (String) xmlHash.get(vKey);
        if (xmlString == null) {
            xmlString = sessionManager.getUserMetaDbServer().getMathModelXML(vKey).toString();
            if (xmlString != null) {
                MathModel mathModel = XmlHelper.XMLToMathModel(new XMLSource(xmlString));
                String newXmlString = XmlHelper.mathModelToXML(mathModel);
                xmlHash.put(vKey, newXmlString);
                return new XMLHolder<MathModel>(newXmlString, mathModel);
            } else {
                throw new RuntimeException("unexpected: UserMetaDbServer.getMathModelXML() returned null");
            }
        } else {
            return new XMLHolder<MathModel>(xmlString);
        }
    } catch (ObjectNotFoundException e) {
        throw new DataAccessException("MathModel (id=" + vKey + ") does not exist. It either " + "has been deleted or its reference is outdated. Please use menu 'Server->Reconnect' to update document references.");
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw FailToLoadDocumentExc.createException(e, vKey, this);
    }
}