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

Example 1 with UnzipUtility

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

the class BioModelsNetPanel method download.

private ExternalDocInfo download(String name, String id) throws Exception {
    // C:\Users\vasilescu\.vcell\simdata
    String simDataDir = ResourceUtil.getLocalRootDir().getAbsolutePath();
    String tempDir = simDataDir + File.separator + "temp";
    String destDirectory = tempDir + File.separator + id;
    String zipFilePath = destDirectory + ".zip";
    Path tempDirPath = Paths.get(tempDir);
    // temp may not be there, we make it
    Files.createDirectories(tempDirPath);
    byte[] responseContent = null;
    URL url = new URL(BeanUtils.getDynamicClientProperties().getProperty(PropertyLoader.BMDB_DOWNLOAD_URL) + id);
    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    InputStream is = null;
    try {
        try {
            is = url.openStream();
        } catch (Exception e) {
            e.printStackTrace();
            if (is != null) {
                is.close();
            }
            // Try with http instead of https
            String newUrlString = url.toString().replaceFirst("^https", "http");
            url = new URL(newUrlString);
            is = url.openStream();
        }
        // Or whatever size you want to read in at a time.
        byte[] byteChunk = new byte[4096];
        int n;
        while ((n = is.read(byteChunk)) > 0) {
            baos.write(byteChunk, 0, n);
        }
        responseContent = baos.toByteArray();
    } catch (IOException e) {
        System.err.printf("Failed while reading bytes from %s: %s", url.toExternalForm(), e.getMessage());
        // e.printStackTrace ();
        throw new RuntimeException("Failed while reading bytes from: " + url.toExternalForm());
    } finally {
        if (is != null) {
            is.close();
        }
    }
    if (responseContent == null) {
        throw new RuntimeException("Failed while reading bytes from: " + url.toExternalForm());
    }
    try {
        File file = new File(zipFilePath);
        Files.write(file.toPath(), responseContent, StandardOpenOption.CREATE, StandardOpenOption.WRITE, StandardOpenOption.TRUNCATE_EXISTING);
        UnzipUtility uu = new UnzipUtility();
        uu.unzip(zipFilePath, destDirectory);
    } catch (IOException e) {
        e.printStackTrace();
    }
    String unzippedPath = destDirectory + File.separator + id + ".xml";
    String bioModelSBML = new String(Files.readAllBytes(Paths.get(unzippedPath)), StandardCharsets.UTF_8);
    // bioModelSBML = bioModelSBML.replace("<notanumber/>", "<ci> a </ci>");
    try {
        // the original zip file
        Files.deleteIfExists(Paths.get(zipFilePath));
        // the unzipped SBML file
        Files.deleteIfExists(Paths.get(unzippedPath));
        // its directory
        Files.deleteIfExists(Paths.get(destDirectory));
    // Files.deleteIfExists(Paths.get(prettyXML));			// the pretty xml
    } catch (IOException e) {
        e.printStackTrace();
    }
    ExternalDocInfo externalDocInfo = ExternalDocInfo.createBioModelsNetExternalDocInfo(bioModelSBML, name);
    return externalDocInfo;
}