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();
}
}
/**
* Convenience method for creating a local temporary file DataBean with content. Content stream is
* read into a temp file and location of the file is stored to DataBean.
*
* @throws IOException
*/
public DataBean createDataBean(String name, InputStream content)
throws MicroarrayException, IOException {
// copy the data from the input stream to the file in repository
File contentFile;
contentFile = createNewRepositoryFile(name);
InputStream input = new BufferedInputStream(content);
OutputStream output = new BufferedOutputStream(new FileOutputStream(contentFile));
try {
IO.copy(input, output);
output.flush();
} finally {
IOUtils.closeIfPossible(input);
IOUtils.closeIfPossible(output);
}
// create and return the bean
DataBean bean = createDataBean(name);
try {
addContentLocationForDataBean(bean, StorageMethod.LOCAL_TEMP, contentFile.toURI().toURL());
} catch (MalformedURLException e) {
throw new MicroarrayException(e);
} catch (ContentLengthException e) {
// shouldn't happen, because newly created bean doesn't have size set
logger.error(e, e);
}
return bean;
}
/**
* 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 parseMetadata() throws ZipException, IOException, JAXBException, SAXException {
ZipFile zipFile = null;
try {
// get the session.xml zip entry
zipFile = new ZipFile(sessionFile);
InputStream metadataStream =
zipFile.getInputStream(zipFile.getEntry(UserSession.SESSION_DATA_FILENAME));
// validate
// ClientSession.getSchema().newValidator().validate(new StreamSource(metadataStream));
// parse the metadata xml to java objects using jaxb
Unmarshaller unmarshaller = UserSession.getPreviousJAXBContext().createUnmarshaller();
unmarshaller.setSchema(UserSession.getPreviousSchema());
NonStoppingValidationEventHandler validationEventHandler =
new NonStoppingValidationEventHandler();
unmarshaller.setEventHandler(validationEventHandler);
this.sessionType =
unmarshaller.unmarshal(new StreamSource(metadataStream), SessionType.class).getValue();
if (validationEventHandler.hasEvents()) {
throw new JAXBException(
"Invalid session file:\n" + validationEventHandler.getValidationEventsAsString());
}
} finally {
IOUtils.closeIfPossible(zipFile);
}
}
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();
}
@Override
public boolean isAvailable(
String dataId, Long contentLength, String checksum, FileBrokerArea area)
throws FileBrokerException {
try {
InputStream inStream = download(getSessionId(), dataId);
IOUtils.closeIfPossible(inStream);
return true;
} catch (NotFoundException e) {
return false;
}
}
/**
* A convenience method for gathering streamed binary content into a byte array. Gathers only
* maxLength first bytes. Returns null if none of the content locations are available.
*
* @throws IOException
* @see #getContentStream()
*/
public byte[] getContentBytes(DataBean bean, long maxLength, DataNotAvailableHandling naHandling)
throws IOException {
InputStream in = null;
try {
in = getContentStream(bean, naHandling);
if (in != null) {
return Files.inputStreamToBytes(in, maxLength);
} else {
return null;
}
} finally {
IOUtils.closeIfPossible(in);
}
}