/**
* Set the import log file's size in the database to its current size on the filesystem.
*
* @throws ServerError if the import log's size could not be updated in the database
*/
private void setLogFileSize() throws ServerError {
final OriginalFile logFile =
(OriginalFile)
sf.getQueryService().get(OriginalFile.class.getSimpleName(), logPath.getId());
logFile.setSize(omero.rtypes.rlong(logPath.size()));
sf.getUpdateService().saveObject(logFile);
}
/** Opens the file. */
private void openFile() {
if (!(data instanceof FileAnnotationData)) return;
FileAnnotationData fa = (FileAnnotationData) data;
Registry reg = MetadataViewerAgent.getRegistry();
UserNotifier un = reg.getUserNotifier();
OriginalFile f = (OriginalFile) fa.getContent();
Environment env = (Environment) reg.lookup(LookupNames.ENV);
DownloadAndLaunchActivityParam activity;
final long dataId = fa.getId();
final File dir =
new File(env.getOmeroFilesHome() + File.separatorChar + "file annotation " + dataId);
if (!dir.exists()) {
dir.mkdir();
}
if (f != null && f.isLoaded()) {
activity = new DownloadAndLaunchActivityParam(f, dir, null);
} else {
activity =
new DownloadAndLaunchActivityParam(
dataId, DownloadAndLaunchActivityParam.FILE_ANNOTATION, dir, null);
}
un.notifyActivity(model.getSecurityContext(), activity);
return;
}
public List<String> list(String path, Current __current) throws ServerError {
List<OriginalFile> ofiles = listFiles(path, __current);
List<String> contents = new ArrayList<String>(ofiles.size());
for (OriginalFile ofile : ofiles) {
contents.add(ofile.getPath().getValue() + ofile.getName().getValue());
}
return contents;
}
/**
* Get an {@link OriginalFile} object based on its id. Returns null if the file does not exist or
* does not belong to this repo.
*
* @param id long, db id of original file.
* @return OriginalFile object.
*/
private CheckedPath checkId(final long id, final Ice.Current curr)
throws SecurityViolation, ValidationException {
// TODO: could getOriginalFile and getFile be reduced to a single call?
final FsFile file = this.repositoryDao.getFile(id, curr, this.repoUuid);
if (file == null) {
throw new SecurityViolation(null, null, "FileNotFound: " + id);
}
final OriginalFile originalFile = this.repositoryDao.getOriginalFile(id, curr);
if (originalFile == null) {
/* reachable even if file != null because getFile uses SQL,
* evading the filter on the HQL used here by getOriginalFile */
throw new SecurityViolation(null, null, "FileNotAccessible: " + id);
}
final CheckedPath checked =
new CheckedPath(
this.serverPaths, file.toString(), checksumProviderFactory, originalFile.getHasher());
checked.setId(id);
return checked;
}
protected OriginalFile findOrCreateInDb(
CheckedPath checked, String mode, String mimetype, Ice.Current curr) throws ServerError {
OriginalFile ofile = findInDb(checked, mode, curr);
if (ofile != null) {
return ofile;
}
if (checked.exists()) {
omero.grid.UnregisteredFileException ufe = new omero.grid.UnregisteredFileException();
ofile = (OriginalFile) new IceMapper().map(checked.asOriginalFile(mimetype));
ufe.file = ofile;
throw ufe;
}
ofile = repositoryDao.register(repoUuid, checked, null, curr);
final long originalFileId = ofile.getId().getValue();
setOriginalFileHasherToSHA1(originalFileId, curr);
checked.setId(originalFileId);
return ofile;
}
/**
* Find the given path in the DB or create.
*
* <p>"requiresWrite" is set to true unless the mode is "r". If requiresWrite is true, then the
* caller needs the file to be modifiable (both on disk and the DB). If this doesn't hold, then a
* SecurityViolation will be thrown.
*/
protected OriginalFile findInDb(CheckedPath checked, String mode, Ice.Current current)
throws ServerError {
final OriginalFile ofile = repositoryDao.findRepoFile(repoUuid, checked, null, current);
if (ofile == null) {
return null; // EARLY EXIT!
}
boolean requiresWrite = true;
if ("r".equals(mode)) {
requiresWrite = false;
}
checked.setId(ofile.getId().getValue());
boolean canUpdate = repositoryDao.canUpdate(ofile, current);
if (requiresWrite && !canUpdate) {
throw new omero.SecurityViolation(null, null, "requiresWrite is true but cannot modify");
}
return ofile;
}
/**
* Downloads the file.
*
* @see EditorLoader#cancel()
*/
public void load() {
if (data != null) {
OriginalFile f = ((FileAnnotation) data.asAnnotation()).getFile();
if (f.isLoaded()) {
handle = mhView.loadFile(file, f.getId().getValue(), f.getSize().getValue(), this);
}
} else {
Entry entry;
Iterator i = files.entrySet().iterator();
FileAnnotationData fa;
filesMap = new HashMap<FileAnnotationData, File>(files.size());
File f;
// int index = 0;
String dir = MetadataViewerAgent.getTmpDir();
while (i.hasNext()) {
entry = (Entry) i.next();
fa = (FileAnnotationData) entry.getKey();
f = new File(dir + File.separator + fa.getFileID() + "_" + fa.getFileName());
f.deleteOnExit();
filesMap.put(fa, f);
}
handle = mhView.loadFiles(filesMap, this);
}
}
