/**
* Get a local copy of a file. If the dataId matches any of the files found from local filebroker
* paths (given in constructor of this class), then it is symlinked or copied locally. Otherwise
* the file pointed by the dataId is downloaded.
*
* @throws JMSException
* @throws ChecksumException
* @see fi.csc.microarray.filebroker.FileBrokerClient#getFile(File, URL)
*/
@Override
public void getFile(UUID sessionId, String dataId, File destFile)
throws IOException, FileBrokerException, ChecksumException {
InputStream inStream = download(sessionId, dataId);
IOUtils.copy(inStream, destFile);
}
private void convertToLocalTempDataBean(DataBean bean) throws IOException {
try {
// copy contents to new file
File newFile = this.createNewRepositoryFile(bean.getName());
BufferedOutputStream out = new BufferedOutputStream(new FileOutputStream(newFile));
ChecksumInputStream inputStream =
getContentStream(bean, DataNotAvailableHandling.EXCEPTION_ON_NA);
BufferedInputStream in = new BufferedInputStream(inputStream);
try {
IOUtils.copy(in, out);
setOrVerifyChecksum(bean, inputStream.verifyChecksums());
} finally {
IOUtils.closeIfPossible(in);
IOUtils.closeIfPossible(out);
}
// update url, type and handler in the bean
URL newURL = newFile.toURI().toURL();
addContentLocationForDataBean(bean, StorageMethod.LOCAL_TEMP, newURL);
} catch (ChecksumException | ContentLengthException e) {
// corrupted data
throw new IOException();
}
}
private String getSourceCode(String sourceCodeFileName) throws ZipException, IOException {
ZipFile zipFile = null;
InputStream sourceCodeInputStream = null;
StringWriter stringWriter = null;
try {
zipFile = new ZipFile(sessionFile);
sourceCodeInputStream = zipFile.getInputStream(zipFile.getEntry(sourceCodeFileName));
stringWriter = new StringWriter();
IOUtils.copy(sourceCodeInputStream, new WriterOutputStream(stringWriter));
stringWriter.flush();
} finally {
IOUtils.closeIfPossible(sourceCodeInputStream);
IOUtils.closeIfPossible(stringWriter);
if (zipFile != null) {
zipFile.close();
}
}
return stringWriter.toString();
}