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

Example 1 with CacheException

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

the class DataSetControllerImpl method getChomboExtrapolatedValues.

private SimDataBlock getChomboExtrapolatedValues(VCDataIdentifier vcdID, String varName, double time) throws DataAccessException {
    final String methodName = "DataSetControllerImpl.getSimDataBlock(" + varName + ", " + time + ")";
    VCMongoMessage.sendTrace(methodName + " <<ENTER>>");
    try {
        // 
        // check if already cached for non-function variables
        // 
        VCData vcData = getVCData(vcdID);
        if (vcData == null || !(vcData instanceof SimulationData)) {
            return null;
        }
        SimulationData simData = (SimulationData) vcData;
        VCMongoMessage.sendTrace(methodName + " got VCData");
        long dataBlockTimeStamp = simData.getDataBlockTimeStamp(PDE_DATA, time);
        VCMongoMessage.sendTrace(methodName + " got dataBlockTimeStamp");
        PDEDataInfo pdeDataInfo = new PDEDataInfo(vcdID.getOwner(), vcdID.getID(), varName, time, dataBlockTimeStamp);
        SimDataBlock simDataBlock = null;
        if (dataCachingEnabled && chomboExtrapolatedValuesCache == null) {
            chomboExtrapolatedValuesCache = new Cachetable(MessageConstants.MINUTE_IN_MS * 10, 1000000L);
        }
        simDataBlock = chomboExtrapolatedValuesCache.get(pdeDataInfo);
        if (simDataBlock == null) {
            VCMongoMessage.sendTrace(methodName + " read chombo extrapolated values");
            simDataBlock = simData.getChomboExtrapolatedValues(varName, time);
            if (simDataBlock != null && dataCachingEnabled) {
                if (chomboExtrapolatedValuesCache != null) {
                    try {
                        chomboExtrapolatedValuesCache.put(pdeDataInfo, simDataBlock);
                    } catch (CacheException e) {
                        // if can't cache the data, it is ok
                        e.printStackTrace();
                    }
                }
            }
        }
        if (simDataBlock != null) {
            VCMongoMessage.sendTrace(methodName + "  <<EXIT-Success>>");
            return simDataBlock;
        }
        String msg = "failure reading " + varName + " at t=" + time + " for " + vcdID.getOwner().getName() + "'s " + vcdID.getID();
        if (lg.isWarnEnabled())
            lg.warn(methodName + msg);
        throw new DataAccessException(msg);
    } catch (Exception e) {
        lg.error(e.getMessage(), e);
        VCMongoMessage.sendTrace(methodName + "  <<EXIT-Exception>>");
        throw new DataAccessException(e.getMessage());
    }
}

Example 2 with CacheException

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

the class DataSetControllerImpl method getSimDataBlock.

/**
 * This method was created by a SmartGuide.
 * @return double[]
 * @param varName java.lang.String
 * @param time double
 */
public SimDataBlock getSimDataBlock(OutputContext outputContext, VCDataIdentifier vcdID, String varName, double time) throws DataAccessException {
    VCMongoMessage.sendTrace("DataSetControllerImpl.getSimDataBlock(" + varName + ", " + time + ")  <<ENTER>>");
    try {
        // 
        // check if already cached for non-function variables
        // 
        VCData simData = getVCData(vcdID);
        VCMongoMessage.sendTrace("DataSetControllerImpl.getSimDataBlock(" + varName + ", " + time + ") got VCData");
        long dataBlockTimeStamp = simData.getDataBlockTimeStamp(PDE_DATA, time);
        VCMongoMessage.sendTrace("DataSetControllerImpl.getSimDataBlock(" + varName + ", " + time + ") got dataBlockTimeStamp");
        PDEDataInfo pdeDataInfo = new PDEDataInfo(vcdID.getOwner(), vcdID.getID(), varName, time, dataBlockTimeStamp);
        SimDataBlock simDataBlock = null;
        AnnotatedFunction function = getFunction(outputContext, vcdID, varName);
        VCMongoMessage.sendTrace("DataSetControllerImpl.getSimDataBlock(" + varName + ", " + time + ") got function");
        if (function == null) {
            simDataBlock = (cacheTable0 != null ? cacheTable0.get(pdeDataInfo) : null);
            if (simDataBlock == null) {
                simDataBlock = simData.getSimDataBlock(outputContext, varName, time);
                if (simDataBlock != null && dataCachingEnabled) {
                    // cacheTable.put(pdeDataInfo,simDataBlock);
                    if (cacheTable0 != null) {
                        try {
                            cacheTable0.put(pdeDataInfo, simDataBlock);
                        } catch (CacheException e) {
                            // if can't cache the data, it is ok
                            e.printStackTrace();
                        }
                    }
                }
            }
        } else {
            if (simData instanceof SimulationData) {
                function = ((SimulationData) simData).simplifyFunction(function);
            }
            VCMongoMessage.sendTrace("DataSetControllerImpl.getSimDataBlock(" + varName + ", " + time + ") evaluating function");
            simDataBlock = evaluateFunction(outputContext, vcdID, simData, function, time);
        }
        CartesianMesh mesh = getMesh(vcdID);
        if (mesh != null && mesh.isChomboMesh()) {
            for (int i = 0; i < simDataBlock.getData().length; i++) {
                if (simDataBlock.getData()[i] == 1.23456789e300) {
                    simDataBlock.getData()[i] = Double.NaN;
                }
            }
        }
        if (simDataBlock != null) {
            VCMongoMessage.sendTrace("DataSetControllerImpl.getSimDataBlock(" + varName + ", " + time + ")  <<EXIT-simDataBlock not null>>");
            return simDataBlock;
        } else {
            String msg = "failure reading " + varName + " at t=" + time + " for " + vcdID.getOwner().getName() + "'s " + vcdID.getID();
            if (lg.isWarnEnabled())
                lg.warn("DataSetControllerImpl.getDataBlockValues(): " + msg);
            VCMongoMessage.sendTrace("DataSetControllerImpl.getSimDataBlock(" + varName + ", " + time + ")  <<EXIT-Exception>>");
            throw new DataAccessException(msg);
        }
    } catch (MathException e) {
        lg.error(e.getMessage(), e);
        VCMongoMessage.sendTrace("DataSetControllerImpl.getSimDataBlock(" + varName + ", " + time + ")  <<EXIT-Exception>>");
        throw new DataAccessException(e.getMessage());
    } catch (IOException e) {
        lg.error(e.getMessage(), e);
        VCMongoMessage.sendTrace("DataSetControllerImpl.getSimDataBlock(" + varName + ", " + time + ")  <<EXIT-Exception>>");
        throw new DataAccessException(e.getMessage());
    } catch (ExpressionException e) {
        lg.error(e.getMessage(), e);
        VCMongoMessage.sendTrace("DataSetControllerImpl.getSimDataBlock(" + varName + ", " + time + ")  <<EXIT-Exception>>");
        throw new DataAccessException(e.getMessage());
    }
}

Example 3 with CacheException

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

the class DBCacheTable method putProtected.

public void putProtected(KeyValue key, Cacheable cacheable) throws CacheException {
    if (!((cacheable instanceof Cloneable) || (cacheable instanceof Immutable) || (cacheable instanceof Serializable))) {
        throw new CacheException("put:Object not Cloneable, Immutable or Serializable");
    }
    if (key == null) {
        throw new CacheException("put: key == null");
    }
    long dataSize = 1000;
    byte[] objData = null;
    try {
        objData = org.vcell.util.BeanUtils.toSerialized(cacheable);
        // 
        // dataSize is length*3 because three copies are stored in DbObjectWrapper (reference/bytes/working).
        // 
        dataSize = objData.length * 3;
    } catch (IOException e) {
        e.printStackTrace(System.out);
        throw new CacheException(e.getMessage());
    }
    TimeWrapper oldTimeWrapper = put(key, new TimeWrapper(new DbObjectWrapper(cacheable, objData), dataSize, key));
    // 
    if (oldTimeWrapper != null) {
        System.out.println("replacing object ALREADY IN DATABASE_CACHE " + oldTimeWrapper.getObject() + " at key " + key);
    }
    // 
    // checking to see if same object (using compareEqual) already in hash
    // 
    // if (cacheable instanceof cbit.vcell.model.Species){
    // Enumeration enum1 = hashTable.elements();
    // while (enum1.hasMoreElements()){
    // TimeWrapper timeWrapper = (TimeWrapper) enum1.nextElement();
    // DbObjectWrapper objWrapper = (DbObjectWrapper) timeWrapper.getObject();
    // Cacheable cacheObj = objWrapper.getWorkingCopy();
    // if (cacheable != cacheObj && cacheable.compareEqual(cacheObj)){
    // //	throw new RuntimeException("DBCacheTable.put("+cacheable+"), already in cache as ("+cacheObj+")");
    // System.out.println("DBCacheTable.put("+cacheable+"), already in cache as ("+cacheObj+")");
    // }
    // }
    // }
    // System.out.print("put(cacheable="+cacheable+") ");
    show();
}

Example 4 with CacheException

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

the class DataSetControllerImpl method getVCData.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.simdata.SimResults
 * @param user User
 * @param simID java.lang.String
 */
public VCData getVCData(VCDataIdentifier vcdID) throws DataAccessException, IOException {
    VCMongoMessage.sendTrace("DataSetControllerImpl.getVCData(" + vcdID.getID() + ") ... <<ENTER>>");
    VCData vcData = (cacheTable0 != null ? cacheTable0.get(vcdID) : null);
    // 
    if (vcData == null) {
        // System.out.println("getVCData " + vcdID);
        if (vcdID instanceof MergedDataInfo) {
            try {
                User user = vcdID.getOwner();
                VCDataIdentifier[] vcdIdentifiers = ((MergedDataInfo) vcdID).getDataIDs();
                VCMongoMessage.sendTrace("DataSetControllerImpl.getVCData(" + vcdID.getID() + ") : creating new MergedData : <<BEGIN>>");
                vcData = new MergedData(user, getPrimaryUserDir(vcdID.getOwner(), false), getSecondaryUserDir(vcdID.getOwner()), this, vcdIdentifiers, ((MergedDataInfo) vcdID).getDataSetPrefix());
                VCMongoMessage.sendTrace("DataSetControllerImpl.getVCData(" + vcdID.getID() + ") : creating new MergedData : <<END>>");
            } catch (IOException e) {
                e.printStackTrace(System.out);
                throw new RuntimeException(e.getMessage());
            }
        } else {
            // assume vcdID instanceof cbit.vcell.solver.SimulationInfo or a test adapter
            VCMongoMessage.sendTrace("DataSetControllerImpl.getVCData(" + vcdID.getID() + ") : creating new SimulationData : <<BEGIN>>");
            SimulationData.SimDataAmplistorInfo simDataAmplistorInfo = AmplistorUtils.getSimDataAmplistorInfoFromPropertyLoader();
            vcData = new SimulationData(vcdID, getPrimaryUserDir(vcdID.getOwner(), false), getSecondaryUserDir(vcdID.getOwner()), simDataAmplistorInfo);
            VCMongoMessage.sendTrace("DataSetControllerImpl.getVCData(" + vcdID.getID() + ") : creating new SimulationData : <<END>>");
        }
        if (cacheTable0 != null) {
            try {
                VCMongoMessage.sendTrace("DataSetControllerImpl.getVCData(" + vcdID.getID() + ") : caching vcData : <<BEGIN>>");
                cacheTable0.put(vcdID, vcData);
                VCMongoMessage.sendTrace("DataSetControllerImpl.getVCData(" + vcdID.getID() + ") : caching vcData : <<END>>");
            } catch (CacheException e) {
                // if  can't cache the data, it is ok
                e.printStackTrace();
            }
        }
    }
    VCMongoMessage.sendTrace("DataSetControllerImpl.getVCData(" + vcdID.getID() + ") ... <<EXIT>>");
    return vcData;
}

Example 5 with CacheException

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

the class Cachetable method put.

private synchronized TimeWrapper put(Object key, TimeWrapper timeWrapper) throws CacheException {
    long dataMemSize = timeWrapper.getSize();
    if (dataMemSize >= maxMemSize) {
        throw new CacheException("data item " + key + " with memSize=" + dataMemSize + " too large, maxCacheSize=" + maxMemSize);
    }
    // 
    if (dataMemSize + currMemSize >= maxMemSize) {
        resize(Math.min((long) (maxMemSize * cleanupFraction), maxMemSize - dataMemSize));
    }
    TimeWrapper oldTimeWrapper = (TimeWrapper) hashTable.put(key, timeWrapper);
    currMemSize += dataMemSize;
    if (oldTimeWrapper != null) {
        currMemSize -= oldTimeWrapper.getSize();
    }
    if (currMemSize < 0 || currMemSize >= maxMemSize) {
        throw new CacheException("Error: adding data item " + key + ". currMemSize=" + currMemSize + " maxMemSize=" + maxMemSize);
    }
    // System.out.println("........Cachetable.put(key="+key+")");
    return oldTimeWrapper;
}