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Orbit, a versatile image analysis software for biological image-based quantification
/*
* Orbit, a versatile image analysis software for biological image-based quantification.
* Copyright (C) 2009 - 2018 Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland.
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see listFilenames(String remoteFolder) throws IOException {
List flist = new ArrayList<>();
SmbFile file = new SmbFile(share + "/" + remoteFolder + "/", auth);
SmbFile[] files = file.listFiles();
if (files != null && files.length > 0) {
for (SmbFile f : files) {
flist.add(f.getName());
}
}
return flist;
}
@Override
public List listFilenames(String remoteFolder, boolean sortByDate) throws IOException {
List flist = new ArrayList<>();
SmbFile file = new SmbFile(share + "/" + remoteFolder + "/", auth);
SmbFile[] files = file.listFiles();
if (sortByDate) {
Arrays.sort(files, new Comparator() {
@Override
public int compare(SmbFile o1, SmbFile o2) {
return (int) (o1.getDate() - o2.getDate());
}
});
}
if (files != null && files.length > 0) {
for (SmbFile f : files) {
RemoteFile rf = new RemoteFile(f.getName());
rf.setDate(f.getDate());
rf.setLength(f.length());
SID sid = f.getOwnerUser();
if (sid!=null) {
rf.setUser(sid.getAccountName());
}
flist.add(rf);
}
}
return flist;
}
public SmbFile[] listFilenames(String remoteFolder, final String filter) throws IOException {
List flist = new ArrayList<>();
SmbFile file = new SmbFile(share + "/" + remoteFolder + "/",auth);
SmbFile[] files = file.listFiles(new SmbFilenameFilter() {
@Override
public boolean accept(SmbFile dir, String name) throws SmbException {
if (filter==null||filter.length()==0) return true;
return name.endsWith(filter);
}
});
return files;
}
private byte[] readFromRemote(String remoteFile, int buffersize) throws IOException {
return readFromRemote(remoteFile, buffersize, false);
}
private byte[] readFromRemote(String remoteFile, int buffersize, boolean zipped) throws IOException {
SmbFileInputStream smbfis = null;
ByteArrayOutputStream bsos = null;
GZIPInputStream zip = null;
String fname = share + File.separator + remoteFile;
fname = fname.replace('\\', '/');
SmbFile smbFile = new SmbFile(fname, auth);
smbfis = new SmbFileInputStream(smbFile);
bsos = new ByteArrayOutputStream();
if (zipped) zip = new GZIPInputStream(smbfis);
try {
byte[] buffer = new byte[buffersize];
int bytesRead = 0;
if (zipped) {
while ((bytesRead = zip.read(buffer)) > 0) {
bsos.write(buffer, 0, bytesRead);
}
} else {
while ((bytesRead = smbfis.read(buffer)) > 0) {
bsos.write(buffer, 0, bytesRead);
}
}
} catch (IOException e) {
e.printStackTrace();
}
bsos.flush();
byte[] b = bsos.toByteArray();
bsos.close();
smbfis.close();
if (zipped) zip.close();
return b;
}
private boolean writeRemote(String path, byte[] data) throws IOException {
return writeRemote(path, data, false);
}
private boolean writeRemote(String path, byte[] data, boolean zipped) throws IOException {
String fname = share + File.separator + path;
fname = fname.replace('\\', '/');
jcifs.smb.SmbFile file = new jcifs.smb.SmbFile(fname, auth);
jcifs.smb.SmbFile dir = new jcifs.smb.SmbFile(file.getParent(), auth);
if (!dir.exists()) dir.mkdirs();
jcifs.smb.SmbFileOutputStream bos = null;
GZIPOutputStream zip = null;
bos = new jcifs.smb.SmbFileOutputStream(file);
boolean err = true;
int cnt = 0;
while (err && cnt<5) {
err = false;
try {
if (zipped) {
zip = new GZIPOutputStream(bos);
zip.write(data);
zip.flush();
zip.close();
} else {
bos.write(data);
}
bos.flush();
bos.close();
} catch (Exception e) {
err = true;
cnt++;
logger.error("samba error ["+cnt+"], trying again in 2s...", e);
try {
Thread.sleep(2000l);
} catch (InterruptedException e1) {
e1.printStackTrace();
}
}
}
return true;
}
}