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

Example 81 with DataAccessException

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

the class SimulationData method getParticleDataBlock.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.simdata.ParticleDataBlock
 * @param double time
 */
public synchronized ParticleDataBlock getParticleDataBlock(double time) throws DataAccessException, IOException {
    refreshLogFile();
    File particleFile = getParticleDataFile(time);
    if (particleFile == null) {
        throw new DataAccessException("particle data doesn't exist for time = " + time);
    }
    File zipFile = null;
    try {
        zipFile = getPDEDataZipFile(time);
    } catch (DataAccessException ex) {
        zipFile = null;
    }
    ParticleDataBlock particleDataBlock = new ParticleDataBlock(vcDataId.getOwner(), vcDataId.getID(), time, particleFile, zipFile);
    return particleDataBlock;
}

Example 82 with DataAccessException

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

the class SimulationData method getSimDataBlock.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.simdata.DataBlock
 * @param user cbit.vcell.server.User
 * @param simID java.lang.String
 */
public synchronized SimDataBlock getSimDataBlock(OutputContext outputContext, String varName, double time) throws DataAccessException, IOException {
    refreshLogFile();
    try {
        getFunctionDataIdentifiers(outputContext);
    } catch (Exception ex) {
        ex.printStackTrace(System.out);
    }
    try {
        if (isPostProcessing(outputContext, varName)) {
            PDEDataInfo pdeDataInfo = new PDEDataInfo(vcDataId.getOwner(), vcDataId.getID(), varName, time, lastDataProcessingOutputInfoTime);
            DataProcessingOutputDataValuesOP dataProcessingOutputDataValuesOP = new DataProcessingOutputDataValuesOP(vcDataId, varName, TimePointHelper.createSingleTimeTimePointHelper(extractClosestPostProcessTime(time)), DataIndexHelper.createAllDataIndexesDataIndexHelper(), outputContext, null);
            DataProcessingOutputDataValues dataProcessingOutputDataValues = (DataProcessingOutputDataValues) DataSetControllerImpl.getDataProcessingOutput(dataProcessingOutputDataValuesOP, getDataProcessingOutputSourceFileHDF5());
            return new SimDataBlock(pdeDataInfo, dataProcessingOutputDataValues.getDataValues()[0], /*1 time only*/
            VariableType.POSTPROCESSING);
        }
    } catch (Exception e) {
        // ignore
        e.printStackTrace();
    }
    File pdeFile = getPDEDataFile(time);
    if (pdeFile == null) {
        return null;
    }
    DataSet dataSet = getPDEDataSet(pdeFile, time);
    File zipFile = null;
    try {
        zipFile = getPDEDataZipFile(time);
    } catch (DataAccessException ex) {
        zipFile = null;
    }
    long lastModified = getLastModified(pdeFile, zipFile);
    DataSetIdentifier dsi = getDataSetIdentifier(varName);
    if (dsi == null) {
        throw new DataAccessException("data not found for variable " + varName);
    }
    final String varNameInDataSet = dsi.getQualifiedName();
    double[] data = dataSet.getData(varNameInDataSet, zipFile, time, amplistorHelper.solverDataType);
    int varTypeInt = dataSet.getVariableTypeInteger(varNameInDataSet);
    VariableType variableType = null;
    try {
        variableType = VariableType.getVariableTypeFromInteger(varTypeInt);
    } catch (IllegalArgumentException e) {
        e.printStackTrace(System.out);
        System.out.println("invalid varTypeInt = " + varTypeInt + " for variable " + varName + " at time " + time);
        try {
            variableType = SimulationData.getVariableTypeFromLength(getMesh(), data.length);
        } catch (MathException ex) {
            ex.printStackTrace(System.out);
            throw new DataAccessException(ex.getMessage());
        }
    }
    PDEDataInfo pdeDataInfo = new PDEDataInfo(vcDataId.getOwner(), vcDataId.getID(), varName, time, lastModified);
    if (data != null) {
        return new SimDataBlock(pdeDataInfo, data, variableType);
    } else {
        return null;
    }
}

Example 83 with DataAccessException

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

the class SimulationData method removeAllResults.

/**
 * This method was created in VisualAge.
 */
private synchronized void removeAllResults(File logFile, File meshFile) {
    // 
    // remove data files
    // 
    double[] times = null;
    try {
        times = getDataTimes();
    } catch (DataAccessException exc) {
        System.out.println("<<EXCEPTION>> SimResults:removeAllResults() " + exc.getMessage());
    }
    // 
    if (isODEData) {
        File odeFile = null;
        try {
            odeFile = getODEDataFile();
        } catch (DataAccessException e) {
            System.out.println("<<EXCEPTION>> SimResults:removeAllResults() removing .ode file: " + e.getMessage());
        }
        if (odeFile != null && odeFile.exists()) {
            odeFile.delete();
        }
    } else {
        // 
        if (times != null) {
            for (int i = 0; i < times.length; i++) {
                File zipFile = null;
                try {
                    zipFile = getPDEDataZipFile(times[i]);
                } catch (DataAccessException exc) {
                    System.out.println("<<EXCEPTION>> SimResults:removeAllResults() removing .zip file " + exc.getMessage());
                }
                if (zipFile != null && zipFile.exists()) {
                    zipFile.delete();
                }
                File dataFile = null;
                try {
                    dataFile = getPDEDataFile(times[i]);
                } catch (DataAccessException exc) {
                    System.out.println("<<EXCEPTION>> SimResults:removeAllResults() removing .sim file " + exc.getMessage());
                }
                if (dataFile != null && dataFile.exists()) {
                    dataFile.delete();
                }
                File particleFile = null;
                try {
                    particleFile = getParticleDataFile(times[i]);
                } catch (DataAccessException exc) {
                    System.out.println("<<EXCEPTION>> SimResults:removeAllResults() removing .particle file " + exc.getMessage());
                }
                if (particleFile != null && particleFile.exists()) {
                    particleFile.delete();
                }
            }
        }
    }
    // 
    if (logFile != null) {
        if (logFile.exists()) {
            logFile.delete();
        }
    }
    // 
    if (meshFile != null) {
        if (meshFile.exists()) {
            meshFile.delete();
        }
    }
    // 
    // clear cached info
    // 
    dataFilenames = null;
    zipFilenames = null;
    dataTimes = null;
    chomboFileIterationIndices = null;
    annotatedFunctionList.removeAllElements();
    mesh = null;
    logFileLastModified = 0;
    logFileLength = 0;
    meshFileLastModified = 0;
}

Example 84 with DataAccessException

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

the class SimulationData method getSimDataTimeSeries0.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.simdata.DataBlock
 * @param user cbit.vcell.server.User
 * @param simID java.lang.String
 */
synchronized double[][][] getSimDataTimeSeries0(OutputContext outputContext, String[] varNames, int[][] indexes, boolean[] wantsThisTime, DataSetControllerImpl.SpatialStatsInfo spatialStatsInfo, DataSetControllerImpl.ProgressListener progressListener) throws DataAccessException, IOException {
    refreshLogFile();
    try {
        getFunctionDataIdentifiers(outputContext);
    } catch (Exception ex) {
        ex.printStackTrace(System.out);
    }
    int resultsCounter = 0;
    for (int i = 0; i < wantsThisTime.length; i += 1) {
        if (wantsThisTime[i]) {
            resultsCounter += 1;
        }
    }
    // min,max,mean,wmean
    final int NUM_STATS = 4;
    // Create results buffer
    // [timePoints][varNames][dataIndexes]
    double[][][] results = new double[resultsCounter][][];
    for (int i = 0; i < results.length; i += 1) {
        results[i] = new double[varNames.length][];
        for (int j = 0; j < results[i].length; j += 1) {
            if (spatialStatsInfo != null) {
                // min,max.mean,wmean
                results[i][j] = new double[NUM_STATS];
            } else {
                results[i][j] = new double[indexes[j].length];
            }
        }
    }
    try {
        if (varNames.length > 0 && isPostProcessing(outputContext, varNames[0])) {
            double[] specificTimePoints = new double[results.length];
            int counter = 0;
            for (int i = 0; i < dataProcessingOutputInfo.getVariableTimePoints().length; i++) {
                if (wantsThisTime[i]) {
                    specificTimePoints[counter] = dataProcessingOutputInfo.getVariableTimePoints()[i];
                    counter++;
                }
            }
            // PDEDataInfo pdeDataInfo = new PDEDataInfo(vcDataId.getOwner(),vcDataId.getID(),varName,time,lastDataProcessingOutputInfoTime);
            for (int i = 0; i < varNames.length; i++) {
                DataProcessingOutputDataValuesOP dataProcessingOutputDataValuesOP = new DataProcessingOutputDataValuesOP(vcDataId, varNames[i], TimePointHelper.createSpecificTimePointHelper(specificTimePoints), DataIndexHelper.createSpecificDataIndexHelper(indexes[i]), outputContext, null);
                DataProcessingOutputDataValues dataProcessingOutputDataValues = (DataProcessingOutputDataValues) DataSetControllerImpl.getDataProcessingOutput(dataProcessingOutputDataValuesOP, getDataProcessingOutputSourceFileHDF5());
                for (int j = 0; j < specificTimePoints.length; j++) {
                    results[j][i] = dataProcessingOutputDataValues.getDataValues()[j];
                }
            }
            return results;
        }
    } catch (Exception e) {
        // ignore
        e.printStackTrace();
    }
    String[] varNamesInDataSet = new String[varNames.length];
    for (int i = 0; i < varNamesInDataSet.length; i++) {
        varNamesInDataSet[i] = getDataSetIdentifier(varNames[i]).getQualifiedName();
    }
    // Setup parameters for SimDataReader
    double[] tempDataTimes = dataTimes.clone();
    String[] tempZipFileNames = null;
    if (bZipFormat2) {
        tempZipFileNames = new String[tempDataTimes.length];
    }
    String[] tempSimDataFileNames = new String[tempDataTimes.length];
    for (int i = 0; i < tempDataTimes.length; i += 1) {
        if (bZipFormat2 || bZipFormat1) {
            if (bZipFormat2) {
                tempZipFileNames[i] = getPDEDataZipFile(tempDataTimes[i]).getAbsolutePath();
            }
            tempSimDataFileNames[i] = dataFilenames[i];
        } else {
            // userDirectory.getAbsolutePath()+"\\"+dataFilenames[i];//getPDEDataFile(dataTimes[i]).getAbsolutePath();
            tempSimDataFileNames[i] = amplistorHelper.getFile(dataFilenames[i]).getName();
        }
    }
    SimDataReader sdr = null;
    double[][] singleTimePointResultsBuffer = new double[varNamesInDataSet.length][];
    for (int i = 0; i < singleTimePointResultsBuffer.length; i += 1) {
        singleTimePointResultsBuffer[i] = new double[indexes[i].length];
    }
    // In case sim files have been updated since "wantsThisTime" was calculated
    if (wantsThisTime.length < tempDataTimes.length) {
        double[] tempTempDataTimes = new double[wantsThisTime.length];
        System.arraycopy(tempDataTimes, 0, tempTempDataTimes, 0, wantsThisTime.length);
        tempDataTimes = tempTempDataTimes;
        String[] tempTempZipFileNames = new String[wantsThisTime.length];
        System.arraycopy(tempZipFileNames, 0, tempTempZipFileNames, 0, wantsThisTime.length);
        tempZipFileNames = tempTempZipFileNames;
        String[] tempTempSimDataFileNames = new String[wantsThisTime.length];
        System.arraycopy(tempSimDataFileNames, 0, tempTempSimDataFileNames, 0, wantsThisTime.length);
        tempSimDataFileNames = tempTempSimDataFileNames;
    }
    try {
        sdr = new SimDataReader(wantsThisTime, tempDataTimes, tempZipFileNames, tempSimDataFileNames, varNamesInDataSet, indexes, isChombo());
        int counter = 0;
        int progressCounter = 0;
        while (sdr.hasMoreData()) {
            sdr.getNextDataAtCurrentTime(singleTimePointResultsBuffer);
            // Copy data to timeSeries format
            if (wantsThisTime[counter]) {
                for (int i = 0; i < varNamesInDataSet.length; i += 1) {
                    if (spatialStatsInfo != null) {
                        results[progressCounter][i] = calcSpaceStats(singleTimePointResultsBuffer[i], i, spatialStatsInfo);
                    } else {
                        for (int j = 0; j < indexes[i].length; j += 1) {
                            results[progressCounter][i][j] = singleTimePointResultsBuffer[i][j];
                        }
                    }
                }
                progressCounter += 1;
                if (progressListener != null) {
                    progressListener.updateProgress(100.0 * (double) progressCounter / (double) resultsCounter);
                }
            }
            counter += 1;
        }
        return results;
    } catch (DataAccessException e) {
        throw e;
    } catch (IOException e) {
        throw e;
    } catch (Throwable e) {
        throw new DataAccessException(e.getMessage(), e);
    } finally {
        if (sdr != null) {
            sdr.close();
        }
    }
}

Example 85 with DataAccessException

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

the class SimulationData method getVarAndFunctionDataIdentifiers.

/**
 * This method was created in VisualAge.
 * @return java.lang.String[]
 */
public synchronized DataIdentifier[] getVarAndFunctionDataIdentifiers(OutputContext outputContext) throws IOException, DataAccessException {
    // Is this zip format?
    boolean bIsChombo = false;
    try {
        bIsChombo = isChombo();
    } catch (FileNotFoundException e) {
        e.printStackTrace(System.out);
    }
    File zipFile1 = getZipFile(bIsChombo, null);
    File zipFile2 = getZipFile(bIsChombo, 0);
    bZipFormat1 = false;
    bZipFormat2 = false;
    if (zipFile1.exists()) {
        bZipFormat1 = true;
    } else if (zipFile2.exists()) {
        bZipFormat2 = true;
    }
    refreshLogFile();
    if (!isComsol()) {
        try {
            refreshMeshFile();
        } catch (MathException e) {
            e.printStackTrace(System.out);
            throw new DataAccessException(e.getMessage());
        }
    }
    if (!isRulesData && !getIsODEData() && !isComsol() && dataFilenames != null) {
        // read variables only when I have never read the file since variables don't change
        if (dataSetIdentifierList.size() == 0) {
            File file = getPDEDataFile(0.0);
            DataSet dataSet = getPDEDataSet(file, 0.0);
            String[] varNames = dataSet.getDataNames();
            int[] varTypeInts = dataSet.getVariableTypeIntegers();
            if (varNames == null) {
                return null;
            }
            dataSetIdentifierList.clear();
            for (int i = 0; i < varNames.length; i++) {
                VariableType varType = null;
                try {
                    varType = VariableType.getVariableTypeFromInteger(varTypeInts[i]);
                } catch (IllegalArgumentException e) {
                    if (LG.isEnabledFor(Level.WARN)) {
                        LG.warn("Exception typing " + varNames[i] + " has unsupported type " + varTypeInts[i] + ": " + e.getMessage());
                    }
                    varType = SimulationData.getVariableTypeFromLength(mesh, dataSet.getDataLength(varNames[i]));
                }
                Domain domain = Variable.getDomainFromCombinedIdentifier(varNames[i]);
                String varName = Variable.getNameFromCombinedIdentifier(varNames[i]);
                dataSetIdentifierList.addElement(new DataSetIdentifier(varName, varType, domain));
            }
            refreshDataProcessingOutputInfo(outputContext);
            if (dataProcessingOutputInfo != null) {
                for (int i = 0; i < dataProcessingOutputInfo.getVariableNames().length; i++) {
                    if (dataProcessingOutputInfo.getPostProcessDataType(dataProcessingOutputInfo.getVariableNames()[i]).equals(DataProcessingOutputInfo.PostProcessDataType.image)) {
                        dataSetIdentifierList.addElement(new DataSetIdentifier(dataProcessingOutputInfo.getVariableNames()[i], VariableType.POSTPROCESSING, null));
                    }
                }
            }
        }
        // always read functions file since functions might change
        getFunctionDataIdentifiers(outputContext);
    }
    if ((isRulesData || getIsODEData()) && dataSetIdentifierList.size() == 0) {
        ODEDataBlock odeDataBlock = getODEDataBlock();
        if (odeDataBlock == null) {
            throw new DataAccessException("Results are not availabe yet. Please try again later.");
        }
        ODESimData odeSimData = odeDataBlock.getODESimData();
        int colCount = odeSimData.getColumnDescriptionsCount();
        // assume index=0 is time "t"
        int DATA_OFFSET = 1;
        dataSetIdentifierList.clear();
        for (int i = 0; i < (colCount - DATA_OFFSET); i++) {
            String varName = odeSimData.getColumnDescriptions(i + DATA_OFFSET).getDisplayName();
            // TODO domain
            Domain domain = null;
            dataSetIdentifierList.addElement(new DataSetIdentifier(varName, VariableType.NONSPATIAL, domain));
        }
    }
    if (isComsol() && dataSetIdentifierList.size() == 0) {
        ComsolSimFiles comsolSimFiles = getComsolSimFiles();
        if (comsolSimFiles.simTaskXMLFile != null) {
            try {
                String xmlString = FileUtils.readFileToString(comsolSimFiles.simTaskXMLFile);
                SimulationTask simTask = XmlHelper.XMLToSimTask(xmlString);
                Enumeration<Variable> variablesEnum = simTask.getSimulation().getMathDescription().getVariables();
                while (variablesEnum.hasMoreElements()) {
                    Variable var = variablesEnum.nextElement();
                    if (var instanceof VolVariable) {
                        dataSetIdentifierList.addElement(new DataSetIdentifier(var.getName(), VariableType.VOLUME, var.getDomain()));
                    } else if (var instanceof MemVariable) {
                        dataSetIdentifierList.addElement(new DataSetIdentifier(var.getName(), VariableType.MEMBRANE, var.getDomain()));
                    } else if (var instanceof Function) {
                        VariableType varType = VariableType.UNKNOWN;
                        if (var.getDomain() != null && var.getDomain().getName() != null) {
                            SubDomain subDomain = simTask.getSimulation().getMathDescription().getSubDomain(var.getDomain().getName());
                            if (subDomain instanceof CompartmentSubDomain) {
                                varType = VariableType.VOLUME;
                            } else if (subDomain instanceof MembraneSubDomain) {
                                varType = VariableType.MEMBRANE;
                            } else if (subDomain instanceof FilamentSubDomain) {
                                throw new RuntimeException("filament subdomains not supported");
                            } else if (subDomain instanceof PointSubDomain) {
                                varType = VariableType.POINT_VARIABLE;
                            }
                        }
                        dataSetIdentifierList.addElement(new DataSetIdentifier(var.getName(), varType, var.getDomain()));
                    } else if (var instanceof Constant) {
                        System.out.println("ignoring Constant " + var.getName());
                    } else if (var instanceof InsideVariable) {
                        System.out.println("ignoring InsideVariable " + var.getName());
                    } else if (var instanceof OutsideVariable) {
                        System.out.println("ignoring OutsideVariable " + var.getName());
                    } else {
                        throw new RuntimeException("unexpected variable " + var.getName() + " of type " + var.getClass().getName());
                    }
                }
            } catch (XmlParseException | ExpressionException e) {
                e.printStackTrace();
                throw new RuntimeException("failed to read sim task file, msg: " + e.getMessage(), e);
            }
        }
    }
    DataIdentifier[] dis = new DataIdentifier[dataSetIdentifierList.size()];
    for (int i = 0; i < dataSetIdentifierList.size(); i++) {
        DataSetIdentifier dsi = (DataSetIdentifier) dataSetIdentifierList.elementAt(i);
        String displayName = dsi.getName();
        if (dsi.isFunction()) {
            AnnotatedFunction f = null;
            for (int j = 0; j < annotatedFunctionList.size(); j++) {
                AnnotatedFunction function = (AnnotatedFunction) annotatedFunctionList.elementAt(j);
                if (function.getName().equals(dsi.getName())) {
                    f = function;
                    break;
                }
            }
            if (f != null) {
                displayName = f.getDisplayName();
            }
        }
        dis[i] = new DataIdentifier(dsi.getName(), dsi.getVariableType(), dsi.getDomain(), dsi.isFunction(), displayName);
    }
    return dis;
}