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

Example 16 with ZipFile

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

the class ConfigUtils method copyDefaultConfig.

/**
     * Initialises the default configuration for the SolrYard based on data in the parsed bundle. The
     * configuration will be copied to the parsed root directory.
     * 
     * @param clazzInArchive
     *            This class is used to identify the archive containing the default configuration. Parsing
     *            <code>null</code> causes this class to be used and therefore initialises the default
     *            configuration contained by the SolrYard bundle.
     * @param rootDir
     *            the target directory for the configuration.
     * @param override
     *            if true existing configurations are overridden.
     * @return the root directory of the solr configuration (same as parsed as rootDir)
     * @throws IOException
     *             On any IO error while coping the configuration
     * @throws IllegalStateException
     *             If the parsed rootDir does exist but is not a directory.
     * @throws IllegalArgumentException
     *             iIf <code>null</code> is parsed as rootDir or if the parsed bundle does not contain the
     *             required information to set up an configuration
     */
public static File copyDefaultConfig(Class<?> clazzInArchive, File rootDir, boolean override) throws IOException, IllegalStateException, IllegalArgumentException {
    if (rootDir == null) {
        throw new IllegalArgumentException("The parsed root directory MUST NOT be NULL!");
    }
    if (rootDir.exists() && !rootDir.isDirectory()) {
        throw new IllegalStateException("The parsed root directory " + rootDir.getAbsolutePath() + " extists but is not a directory!");
    }
    File sourceRoot = getSource(clazzInArchive != null ? clazzInArchive : ConfigUtils.class);
    log.info("Init Solr Managed Directory form {} to {} (override={})", new Object[] { sourceRoot, rootDir, override });
    if (sourceRoot.isFile()) {
        ZipFile archive = new ZipFile(sourceRoot);
        log.info("  - read from jar-file");
        try {
            for (@SuppressWarnings("unchecked") Enumeration<ZipArchiveEntry> entries = archive.getEntries(); entries.hasMoreElements(); ) {
                ZipArchiveEntry entry = entries.nextElement();
                if (!entry.isDirectory() && entry.getName().startsWith(CONFIG_DIR)) {
                    copyResource(rootDir, archive, entry, CONFIG_DIR, override);
                }
            }
        } finally {
            // regardless what happens we need to close the archive!
            ZipFile.closeQuietly(archive);
        }
    } else {
        // load from file
        log.info("  - read from directory");
        File source = new File(sourceRoot, CONFIG_DIR);
        if (source.exists() && source.isDirectory()) {
            FileUtils.copyDirectory(source, rootDir);
        } else {
            throw new FileNotFoundException("The SolrIndex default config was not found in directory " + source.getAbsolutePath());
        }
    }
    return rootDir;
}

Example 17 with ZipFile

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

the class DataSet method read.

/**
 * This method was created by a SmartGuide.
 */
public void read(File file, File zipFile) throws IOException, OutOfMemoryError {
    ZipFile zipZipFile = null;
    DataInputStream dataInputStream = null;
    try {
        this.fileName = file.getPath();
        InputStream is = null;
        long length = 0;
        if (zipFile != null) {
            System.out.println("DataSet.read() open " + zipFile + " for " + file.getName());
            zipZipFile = openZipFile(zipFile);
            java.util.zip.ZipEntry dataEntry = zipZipFile.getEntry(file.getName());
            is = zipZipFile.getInputStream((ZipArchiveEntry) dataEntry);
            length = dataEntry.getSize();
        } else {
            if (!file.exists()) {
                File compressedFile = new File(fileName + ".Z");
                if (compressedFile.exists()) {
                    Runtime.getRuntime().exec("uncompress " + fileName + ".Z");
                    file = new File(fileName);
                    if (!file.exists()) {
                        throw new IOException("file " + fileName + ".Z could not be uncompressed");
                    }
                } else {
                    throw new FileNotFoundException("file " + fileName + " does not exist");
                }
            }
            System.out.println("DataSet.read() open '" + fileName + "'");
            is = new FileInputStream(file);
            length = file.length();
        }
        if (is != null && zipFile != null && isChombo(zipFile)) {
            try {
                readHdf5SolutionMetaData(is);
            } catch (Exception e) {
                e.printStackTrace();
                throw new IOException(e.getMessage(), e);
            }
        } else {
            BufferedInputStream bis = new BufferedInputStream(is);
            dataInputStream = new DataInputStream(bis);
            fileHeader.read(dataInputStream);
            for (int i = 0; i < fileHeader.numBlocks; i++) {
                DataBlock dataBlock = new DataBlock();
                dataBlock.readBlockHeader(dataInputStream);
                dataBlockList.addElement(dataBlock);
            }
        }
    } finally {
        if (dataInputStream != null) {
            try {
                dataInputStream.close();
            } catch (Exception e) {
                e.printStackTrace();
            }
        }
        if (zipZipFile != null) {
            try {
                zipZipFile.close();
            } catch (Exception e) {
                e.printStackTrace();
            }
        }
    }
}

Example 18 with ZipFile

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

the class DataSet method getData.

public double[] getData(String varName, File zipFile) throws IOException {
    double[] data = null;
    if (zipFile != null && isChombo(zipFile)) {
        throw new RuntimeException("chombo files not read with " + getClass().getName() + ", should use Chombo utilities");
    } else {
        for (int i = 0; i < dataBlockList.size(); i++) {
            DataBlock dataBlock = (DataBlock) dataBlockList.elementAt(i);
            if (varName.trim().equals(dataBlock.getVarName().trim())) {
                File pdeFile = new File(fileName);
                InputStream is = null;
                long length = 0;
                ZipFile zipZipFile = null;
                if (zipFile == null && !pdeFile.exists()) {
                    throw new FileNotFoundException("file " + fileName + " does not exist");
                }
                if (zipFile != null) {
                    zipZipFile = openZipFile(zipFile);
                    java.util.zip.ZipEntry dataEntry = zipZipFile.getEntry(pdeFile.getName());
                    length = dataEntry.getSize();
                    is = zipZipFile.getInputStream((ZipArchiveEntry) dataEntry);
                } else {
                    length = pdeFile.length();
                    is = new FileInputStream(pdeFile);
                }
                // read data from zip file
                DataInputStream dis = null;
                try {
                    BufferedInputStream bis = new BufferedInputStream(is);
                    dis = new DataInputStream(bis);
                    dis.skip(dataBlock.getDataOffset());
                    int size = dataBlock.getSize();
                    data = new double[size];
                    for (int j = 0; j < size; j++) {
                        data[j] = dis.readDouble();
                    }
                } finally {
                    try {
                        if (dis != null) {
                            dis.close();
                        }
                        if (zipZipFile != null) {
                            zipZipFile.close();
                        }
                    } catch (Exception ex) {
                    // ignore
                    }
                }
                break;
            }
        }
    }
    if (data == null) {
        throw new IOException("DataSet.getData(), data not found for variable '" + varName + "'");
    }
    return data;
}

Example 19 with ZipFile

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

the class DataSet method getData.

double[] getData(String varName, File zipFile, Double time, SolverDataType solverDataType) throws IOException {
    double[] data = null;
    if (solverDataType == SolverDataType.MBSData) {
        try {
            data = readMBSData(varName, time);
        } catch (Exception e) {
            throw new IOException(e.getMessage(), e);
        }
    } else {
        if (zipFile != null && isChombo(zipFile)) {
            try {
                data = readHdf5VariableSolution(zipFile, new File(fileName).getName(), varName);
            } catch (Exception e) {
                throw new IOException(e.getMessage(), e);
            }
        } else {
            for (int i = 0; i < dataBlockList.size(); i++) {
                DataBlock dataBlock = (DataBlock) dataBlockList.elementAt(i);
                if (varName.trim().equals(dataBlock.getVarName().trim())) {
                    File pdeFile = new File(fileName);
                    InputStream is = null;
                    long length = 0;
                    org.apache.commons.compress.archivers.zip.ZipFile zipZipFile = null;
                    if (zipFile == null && !pdeFile.exists()) {
                        throw new FileNotFoundException("file " + fileName + " does not exist");
                    }
                    if (zipFile != null) {
                        zipZipFile = openZipFile(zipFile);
                        java.util.zip.ZipEntry dataEntry = zipZipFile.getEntry(pdeFile.getName());
                        length = dataEntry.getSize();
                        is = zipZipFile.getInputStream((ZipArchiveEntry) dataEntry);
                    } else {
                        length = pdeFile.length();
                        is = new FileInputStream(pdeFile);
                    }
                    // read data from zip file
                    DataInputStream dis = null;
                    try {
                        BufferedInputStream bis = new BufferedInputStream(is);
                        dis = new DataInputStream(bis);
                        dis.skip(dataBlock.getDataOffset());
                        int size = dataBlock.getSize();
                        data = new double[size];
                        for (int j = 0; j < size; j++) {
                            data[j] = dis.readDouble();
                        }
                    } finally {
                        try {
                            if (dis != null) {
                                dis.close();
                            }
                            if (zipZipFile != null) {
                                zipZipFile.close();
                            }
                        } catch (Exception ex) {
                        // ignore
                        }
                    }
                    break;
                }
            }
        }
    }
    if (data == null) {
        throw new IOException("DataSet.getData(), data not found for variable '" + varName + "'");
    }
    return data;
}

Example 20 with ZipFile

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

the class DataSet method readHdf5VariableSolution.

static double[] readHdf5VariableSolution(File zipfile, String fileName, String varName) throws Exception {
    File tempFile = null;
    FileFormat solFile = null;
    try {
        tempFile = createTempHdf5File(zipfile, fileName);
        FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5);
        solFile = fileFormat.createInstance(tempFile.getAbsolutePath(), FileFormat.READ);
        solFile.open();
        if (varName != null) {
            String varPath = Hdf5Utils.getVarSolutionPath(varName);
            HObject solObj = FileFormat.findObject(solFile, varPath);
            if (solObj instanceof Dataset) {
                Dataset dataset = (Dataset) solObj;
                return (double[]) dataset.read();
            }
        }
    } 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
        }
    }
    return null;
}