Examples with ZipFile org.apache.commons.compress.archivers.zip.ZipFile used on opensource projects

Example 41 with ZipFile

use of org.apache.commons.compress.archivers.zip.ZipFile in project vcell by virtualcell.

the class SimDataReader method getNextDataAtCurrentTimeChombo.

private void getNextDataAtCurrentTimeChombo(double[][] returnValues) throws Exception {
    if (zipFilenNames == null || zipFilenNames[masterTimeIndex] == null) {
        return;
    }
    if (currentZipFile == null || !currentZipFileName.equals(zipFilenNames[masterTimeIndex])) {
        close();
        currentZipFile = new ZipFile(zipFilenNames[masterTimeIndex]);
        currentZipFileName = zipFilenNames[masterTimeIndex];
    }
    File tempFile = null;
    FileFormat solFile = null;
    try {
        tempFile = DataSet.createTempHdf5File(currentZipFile, simDataFileNames[masterTimeIndex]);
        FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5);
        solFile = fileFormat.createInstance(tempFile.getAbsolutePath(), FileFormat.READ);
        solFile.open();
        for (int k = 0; k < varNames.length; ++k) {
            try {
                boolean bExtrapolatedValue = false;
                String varName = varNames[k];
                if (varName.endsWith(InsideVariable.INSIDE_VARIABLE_SUFFIX)) {
                    bExtrapolatedValue = true;
                    varName = varName.substring(0, varName.lastIndexOf(InsideVariable.INSIDE_VARIABLE_SUFFIX));
                } else if (varName.endsWith(OutsideVariable.OUTSIDE_VARIABLE_SUFFIX)) {
                    bExtrapolatedValue = true;
                    varName = varName.substring(0, varName.lastIndexOf(OutsideVariable.OUTSIDE_VARIABLE_SUFFIX));
                }
                double[] sol = null;
                if (bExtrapolatedValue) {
                    sol = DataSet.readChomboExtrapolatedValues(varName, solFile);
                } else {
                    String varPath = Hdf5Utils.getVarSolutionPath(varNames[k]);
                    HObject solObj = FileFormat.findObject(solFile, varPath);
                    if (solObj instanceof Dataset) {
                        Dataset dataset = (Dataset) solObj;
                        sol = (double[]) dataset.read();
                    }
                }
                if (sol != null) {
                    for (int l = 0; l < varIndexes[k].length; ++l) {
                        int idx = varIndexes[k][l];
                        double val = sol[idx];
                        returnValues[k][l] = val;
                    }
                }
            } catch (Exception e) {
                e.printStackTrace(System.out);
                throw new DataAccessException(e.getMessage(), e);
            }
        }
    } finally {
        try {
            if (solFile != null) {
                solFile.close();
            }
            if (tempFile != null) {
                if (!tempFile.delete()) {
                    System.err.println("couldn't delete temp file " + tempFile.getAbsolutePath());
                }
            }
        } catch (Exception e) {
        // ignore
        }
    }
    ++masterTimeIndex;
    if (masterTimeIndex >= times.length) {
        close();
    }
}

Example 42 with ZipFile

use of org.apache.commons.compress.archivers.zip.ZipFile in project vcell by virtualcell.

the class SimulationData method getVCellSimFiles.

@Override
public VCellSimFiles getVCellSimFiles() throws FileNotFoundException, DataAccessException {
    File cartesianMeshFile = getMeshFile();
    File meshMetricsFile = getMembraneMeshMetricsFile();
    File subdomainFile = getSubdomainFile();
    File logFile = getLogFile();
    File postprocessingFile = getDataProcessingOutputSourceFileHDF5();
    if (!(vcDataId instanceof VCSimulationDataIdentifier)) {
        throw new RuntimeException("cannot process vtk, vcDataId not " + VCSimulationDataIdentifier.class.getSimpleName());
    }
    VCSimulationDataIdentifier vcSimDataID = (VCSimulationDataIdentifier) vcDataId;
    VCellSimFiles vcellSimFiles = new VCellSimFiles(vcSimDataID.getSimulationKey(), vcSimDataID.getJobIndex(), cartesianMeshFile, meshMetricsFile, subdomainFile, logFile, postprocessingFile);
    refreshLogFile();
    double[] times = getDataTimes();
    for (int i = 0; i < times.length; i++) {
        File pdeDataFile = getPDEDataFile(times[i]);
        File zipFile = getPDEDataZipFile(times[i]);
        vcellSimFiles.addDataFileEntry(zipFile, pdeDataFile, times[i]);
    }
    return vcellSimFiles;
}

Example 43 with ZipFile

use of org.apache.commons.compress.archivers.zip.ZipFile in project vcell by virtualcell.

the class SimulationData method getChomboExtrapolatedValues.

public synchronized SimDataBlock getChomboExtrapolatedValues(String varName, double time) throws DataAccessException, IOException {
    refreshLogFile();
    File pdeFile = getPDEDataFile(time);
    if (pdeFile == null) {
        return null;
    }
    DataSet dataSet = new DataSet();
    File zipFile = null;
    try {
        zipFile = getPDEDataZipFile(time);
    } catch (DataAccessException ex) {
        zipFile = null;
    }
    try {
        dataSet.read(pdeFile, zipFile);
    } catch (IOException ex) {
        ex.printStackTrace();
        throw new DataAccessException("data at time=" + time + " read error", ex);
    }
    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.readChomboExtrapolatedValues(varNameInDataSet, pdeFile, zipFile);
    VariableType variableType = VariableType.MEMBRANE;
    PDEDataInfo pdeDataInfo = new PDEDataInfo(vcDataId.getOwner(), vcDataId.getID(), varName, time, lastModified);
    return data == null ? null : new SimDataBlock(pdeDataInfo, data, variableType);
}

Example 44 with ZipFile

use of org.apache.commons.compress.archivers.zip.ZipFile in project vcell by virtualcell.

the class SimulationData method getPDEDataZipFile.

/**
 * This method was created by a SmartGuide.
 * @return java.lang.String
 * @param time double
 */
private synchronized File getPDEDataZipFile(double time) throws DataAccessException {
    // 
    if (bZipFormat1) {
        File zipFile = getZipFile(false, null);
        if (zipFile.exists()) {
            return zipFile;
        } else {
            return null;
        }
    }
    if (!bZipFormat2) {
        return null;
    }
    double[] times = getDataTimes();
    if (times == null) {
        return null;
    }
    if (zipFilenames == null || times.length != zipFilenames.length) {
        return null;
    }
    Integer index = pdeDataMap.get(time);
    if (index != null) {
        String zipFileName = FilenameUtils.getName(zipFilenames[index]);
        // new File(userDirectory,zipFileName);
        File zipFile = amplistorHelper.getFile(zipFileName);
        if (zipFile.exists()) {
            return zipFile;
        } else {
            return null;
        }
    }
    return null;
}