List of usage examples for org.apache.commons.net.ftp FTPClient FTPClient
public FTPClient()
From source file:edu.wisc.ssec.mcidasv.data.cyclone.AtcfStormDataSource.java
/** * _more_/*from w ww . ja v a 2 s .c om*/ * * @param file * _more_ * @param ignoreErrors * _more_ * * @return _more_ * * @throws Exception * _more_ */ private byte[] readFile(String file, boolean ignoreErrors) throws Exception { if (new File(file).exists()) { return IOUtil.readBytes(IOUtil.getInputStream(file, getClass())); } if (!file.startsWith("ftp:")) { if (ignoreErrors) { return null; } throw new FileNotFoundException("Could not read file: " + file); } URL url = new URL(file); FTPClient ftp = new FTPClient(); try { ftp.connect(url.getHost()); ftp.login("anonymous", "password"); ftp.setFileType(FTP.IMAGE_FILE_TYPE); ftp.enterLocalPassiveMode(); ByteArrayOutputStream bos = new ByteArrayOutputStream(); if (ftp.retrieveFile(url.getPath(), bos)) { return bos.toByteArray(); } else { throw new IOException("Unable to retrieve file:" + url); } } catch (org.apache.commons.net.ftp.FTPConnectionClosedException fcce) { System.err.println("ftp error:" + fcce); System.err.println(ftp.getReplyString()); if (!ignoreErrors) { throw fcce; } return null; } catch (Exception exc) { if (!ignoreErrors) { throw exc; } return null; } finally { try { ftp.logout(); } catch (Exception exc) { } try { ftp.disconnect(); } catch (Exception exc) { } } }
From source file:it.baywaylabs.jumpersumo.twitter.TwitterListener.java
/** * @param host FTP Host name./*from ww w.j av a2s . co m*/ * @param port FTP port. * @param user FTP User. * @param pswd FTP Password. * @param c Context * @return Downloaded name file or blank list if something was going wrong. */ private String FTPDownloadFile(String host, Integer port, String user, String pswd, Context c) { String result = ""; FTPClient mFTPClient = null; try { mFTPClient = new FTPClient(); // connecting to the host mFTPClient.connect(host, port); // Now check the reply code, if positive mean connection success if (FTPReply.isPositiveCompletion(mFTPClient.getReplyCode())) { // Login using username & password boolean status = mFTPClient.login(user, pswd); mFTPClient.setFileType(FTP.BINARY_FILE_TYPE); mFTPClient.enterLocalPassiveMode(); mFTPClient.changeWorkingDirectory(Constants.DIR_ROBOT_MEDIA); FTPFile[] fileList = mFTPClient.listFiles(); long timestamp = 0l; String nameFile = ""; for (int i = 0; i < fileList.length; i++) { if (fileList[i].isFile() && fileList[i].getTimestamp().getTimeInMillis() > timestamp) { timestamp = fileList[i].getTimestamp().getTimeInMillis(); nameFile = fileList[i].getName(); } } Log.d(TAG, "File da scaricare: " + nameFile); mFTPClient.enterLocalActiveMode(); File folder = new File(Constants.DIR_ROBOT_IMG); OutputStream outputStream = null; boolean success = true; if (!folder.exists()) { success = folder.mkdir(); } try { outputStream = new FileOutputStream(folder.getAbsolutePath() + "/" + nameFile); success = mFTPClient.retrieveFile(nameFile, outputStream); } catch (Exception e) { return e.getMessage(); } finally { if (outputStream != null) { outputStream.close(); } } if (success) { result = nameFile; mFTPClient.deleteFile(nameFile); } } } catch (Exception e) { Log.e(TAG, e.getMessage()); } finally { if (mFTPClient != null) { try { mFTPClient.logout(); mFTPClient.disconnect(); } catch (IOException e) { Log.e(TAG, e.getMessage()); } } } return result; }
From source file:com.clickha.nifi.processors.util.FTPTransferV2.java
private FTPClient getClient(final FlowFile flowFile) throws IOException { if (client != null) { String desthost = ctx.getProperty(HOSTNAME).evaluateAttributeExpressions(flowFile).getValue(); if (remoteHostName.equals(desthost)) { // destination matches so we can keep our current session resetWorkingDirectory();/*from w ww .j a v a2 s . c o m*/ return client; } else { // this flowFile is going to a different destination, reset session close(); } } final Proxy.Type proxyType = Proxy.Type.valueOf(ctx.getProperty(PROXY_TYPE).getValue()); final String proxyHost = ctx.getProperty(PROXY_HOST).getValue(); final Integer proxyPort = ctx.getProperty(PROXY_PORT).asInteger(); FTPClient client; if (proxyType == Proxy.Type.HTTP) { client = new FTPHTTPClient(proxyHost, proxyPort, ctx.getProperty(HTTP_PROXY_USERNAME).getValue(), ctx.getProperty(HTTP_PROXY_PASSWORD).getValue()); } else { client = new FTPClient(); if (proxyType == Proxy.Type.SOCKS) { client.setSocketFactory(new SocksProxySocketFactory( new Proxy(proxyType, new InetSocketAddress(proxyHost, proxyPort)))); } } this.client = client; client.setDataTimeout(ctx.getProperty(DATA_TIMEOUT).asTimePeriod(TimeUnit.MILLISECONDS).intValue()); client.setDefaultTimeout( ctx.getProperty(CONNECTION_TIMEOUT).asTimePeriod(TimeUnit.MILLISECONDS).intValue()); client.setRemoteVerificationEnabled(false); final String remoteHostname = ctx.getProperty(HOSTNAME).evaluateAttributeExpressions(flowFile).getValue(); this.remoteHostName = remoteHostname; InetAddress inetAddress = null; try { inetAddress = InetAddress.getByAddress(remoteHostname, null); } catch (final UnknownHostException uhe) { } if (inetAddress == null) { inetAddress = InetAddress.getByName(remoteHostname); } client.connect(inetAddress, ctx.getProperty(PORT).evaluateAttributeExpressions(flowFile).asInteger()); this.closed = false; client.setDataTimeout(ctx.getProperty(DATA_TIMEOUT).asTimePeriod(TimeUnit.MILLISECONDS).intValue()); client.setSoTimeout(ctx.getProperty(CONNECTION_TIMEOUT).asTimePeriod(TimeUnit.MILLISECONDS).intValue()); final String username = ctx.getProperty(USERNAME).evaluateAttributeExpressions(flowFile).getValue(); final String password = ctx.getProperty(PASSWORD).evaluateAttributeExpressions(flowFile).getValue(); final boolean loggedIn = client.login(username, password); if (!loggedIn) { throw new IOException("Could not login for user '" + username + "'"); } final String connectionMode = ctx.getProperty(CONNECTION_MODE).getValue(); if (connectionMode.equalsIgnoreCase(CONNECTION_MODE_ACTIVE)) { client.enterLocalActiveMode(); } else { client.enterLocalPassiveMode(); } // additional FTPClientConfig ftpConfig = new FTPClientConfig(FTPClientConfig.SYST_UNIX); final String ftpClientConfig = ctx.getProperty(FTP_CLIENT_CONFIG_SYST).getValue(); if (ftpClientConfig.equalsIgnoreCase(FTP_CLIENT_CONFIG_SYST_UNIX)) { this.ftpConfig = ftpConfig; client.configure(ftpConfig); } else if (ftpClientConfig.equalsIgnoreCase(FTP_CLIENT_CONFIG_SYST_NT)) { this.ftpConfig = ftpConfig; client.configure(ftpConfig); } final String transferMode = ctx.getProperty(TRANSFER_MODE).getValue(); final int fileType = (transferMode.equalsIgnoreCase(TRANSFER_MODE_ASCII)) ? FTPClient.ASCII_FILE_TYPE : FTPClient.BINARY_FILE_TYPE; if (!client.setFileType(fileType)) { throw new IOException("Unable to set transfer mode to type " + transferMode); } this.homeDirectory = client.printWorkingDirectory(); return client; }
From source file:madkitgroupextension.export.Export.java
private static void sendToWebSite() throws IOException { System.out.println("Enter your password :"); byte b[] = new byte[100]; int l = System.in.read(b); String pwd = new String(b, 0, l); boolean reconnect = true; long time = System.currentTimeMillis(); File current_file_transfert = null; File current_directory_transfert = null; while (reconnect) { FTPClient ftpClient = new FTPClient(); ftpClient.connect(FTPURL, 21);/*from w ww . j a v a 2 s . c om*/ try { if (ftpClient.isConnected()) { System.out.println("Connected to server " + FTPURL + " (Port: " + FTPPORT + ") !"); if (ftpClient.login(FTPLOGIN, pwd)) { ftpClient.setFileTransferMode(FTP.BINARY_FILE_TYPE); System.out.println("Logged as " + FTPLOGIN + " !"); System.out.print("Updating..."); FTPFile files[] = ftpClient.listFiles(""); FTPFile downloadroot = null; FTPFile docroot = null; for (FTPFile f : files) { if (f.getName().equals("downloads")) { downloadroot = f; if (docroot != null) break; } if (f.getName().equals("doc")) { docroot = f; if (downloadroot != null) break; } } if (downloadroot == null) { //ftpClient.changeWorkingDirectory("/"); if (!ftpClient.makeDirectory("downloads")) { System.err.println("Impossible to create directory: downloads"); } } if (docroot == null) { //ftpClient.changeWorkingDirectory("/"); if (!ftpClient.makeDirectory("doc")) { System.err.println("Impossible to create directory: doc"); } } updateFTP(ftpClient, "downloads/", new File(ExportPathFinal), current_file_transfert, current_directory_transfert); updateFTP(ftpClient, "doc/", new File("./doc"), current_file_transfert, current_directory_transfert); reconnect = false; System.out.println("[OK]"); if (ftpClient.logout()) { System.out.println("Logged out from " + FTPLOGIN + " succesfull !"); } else System.err.println("Logged out from " + FTPLOGIN + " FAILED !"); } else System.err.println("Impossible to log as " + FTPLOGIN + " !"); ftpClient.disconnect(); System.out.println("Disconnected from " + FTPURL + " !"); } else { System.err.println("Impossible to get a connection to the server " + FTPURL + " !"); } reconnect = false; } catch (TransfertException e) { if (System.currentTimeMillis() - time > 30000) { System.err.println("A problem occured during the transfert..."); System.out.println("Reconnection in progress..."); try { ftpClient.disconnect(); } catch (Exception e2) { } current_file_transfert = e.current_file_transfert; current_directory_transfert = e.current_directory_transfert; time = System.currentTimeMillis(); } else { System.err.println("A problem occured during the transfert. Transfert aborded."); throw e.original_exception; } } } }
From source file:au.com.infiniterecursion.vidiom.utils.PublishingUtils.java
public Thread videoUploadToFTPserver(final Activity activity, final Handler handler, final String latestVideoFile_filename, final String latestVideoFile_absolutepath, final String emailAddress, final long sdrecord_id) { Log.d(TAG, "doVideoFTP starting"); // Make the progress bar view visible. ((VidiomActivity) activity).startedUploading(PublishingUtils.TYPE_FTP); final Resources res = activity.getResources(); Thread t = new Thread(new Runnable() { public void run() { // Do background task. // FTP; connect preferences here! ///*w ww.j a v a 2 s . c om*/ SharedPreferences prefs = PreferenceManager.getDefaultSharedPreferences(activity.getBaseContext()); String ftpHostName = prefs.getString("defaultFTPhostPreference", null); String ftpUsername = prefs.getString("defaultFTPusernamePreference", null); String ftpPassword = prefs.getString("defaultFTPpasswordPreference", null); // use name of local file. String ftpRemoteFtpFilename = latestVideoFile_filename; // FTP FTPClient ftpClient = new FTPClient(); InetAddress uploadhost = null; try { uploadhost = InetAddress.getByName(ftpHostName); } catch (UnknownHostException e1) { // If DNS resolution fails then abort immediately - show // dialog to // inform user first. e1.printStackTrace(); Log.e(TAG, " got exception resolving " + ftpHostName + " - video uploading failed."); uploadhost = null; } if (uploadhost == null) { // Use the handler to execute a Runnable on the // main thread in order to have access to the // UI elements. mainapp.removeSDFileRecordIDfromUploadingTrack(sdrecord_id, TYPE_FTP); handler.postDelayed(new Runnable() { public void run() { // Update UI // Hide the progress bar ((VidiomActivity) activity).finishedUploading(false); ((VidiomActivity) activity) .createNotification(res.getString(R.string.upload_to_ftp_host_failed_)); new AlertDialog.Builder(activity).setMessage(R.string.cant_find_upload_host) .setPositiveButton(R.string.yes, new DialogInterface.OnClickListener() { public void onClick(DialogInterface dialog, int whichButton) { } }).show(); } }, 0); return; } boolean connected = false; try { ftpClient.connect(uploadhost); connected = true; } catch (SocketException e) { e.printStackTrace(); connected = false; } catch (UnknownHostException e) { // e.printStackTrace(); connected = false; } catch (IOException e) { // e.printStackTrace(); connected = false; } if (!connected) { // Use the handler to execute a Runnable on the // main thread in order to have access to the // UI elements. mainapp.removeSDFileRecordIDfromUploadingTrack(sdrecord_id, TYPE_FTP); handler.postDelayed(new Runnable() { public void run() { // Update UI // Hide the progress bar ((VidiomActivity) activity).finishedUploading(false); ((VidiomActivity) activity) .createNotification(res.getString(R.string.upload_to_ftp_host_failed_)); new AlertDialog.Builder(activity).setMessage(R.string.cant_login_upload_host) .setPositiveButton(R.string.yes, new DialogInterface.OnClickListener() { public void onClick(DialogInterface dialog, int whichButton) { } }).show(); } }, 0); return; } boolean reply = false; try { reply = ftpClient.login(ftpUsername, ftpPassword); } catch (IOException e) { // e.printStackTrace(); Log.e(TAG, " got exception on ftp.login - video uploading failed."); } // check the reply code here // If we cant login, abort after showing user a dialog. if (!reply) { try { ftpClient.disconnect(); } catch (IOException e) { // e.printStackTrace(); } // Use the handler to execute a Runnable on the // main thread in order to have access to the // UI elements. mainapp.removeSDFileRecordIDfromUploadingTrack(sdrecord_id, TYPE_FTP); handler.postDelayed(new Runnable() { public void run() { // Update UI // Hide the progress bar ((VidiomActivity) activity).finishedUploading(false); ((VidiomActivity) activity) .createNotification(res.getString(R.string.upload_to_ftp_host_failed_)); new AlertDialog.Builder(activity).setMessage(R.string.cant_login_upload_host) .setPositiveButton(R.string.yes, new DialogInterface.OnClickListener() { public void onClick(DialogInterface dialog, int whichButton) { } }).show(); } }, 0); return; } // Set File type to binary try { ftpClient.setFileType(FTP.BINARY_FILE_TYPE); } catch (IOException e) { // e.printStackTrace(); // keep going?! } // BEYOND HERE DONT USE DIALOGS! // Construct the input stream to send to Ftp server, from the // local // video file on the sd card BufferedInputStream buffIn = null; File file = new File(latestVideoFile_absolutepath); try { buffIn = new BufferedInputStream(new FileInputStream(file)); } catch (FileNotFoundException e) { // e.printStackTrace(); Log.e(TAG, " got exception on local video file - video uploading failed."); // Use the handler to execute a Runnable on the // main thread in order to have access to the // UI elements. mainapp.removeSDFileRecordIDfromUploadingTrack(sdrecord_id, TYPE_FTP); handler.postDelayed(new Runnable() { public void run() { // Update UI // Hide the progress bar ((VidiomActivity) activity).finishedUploading(false); ((VidiomActivity) activity) .createNotification(res.getString(R.string.upload_to_ftp_host_failed_)); } }, 0); // This is a bad error, lets abort. // user dialog ?! shouldnt happen, but still... return; } ftpClient.enterLocalPassiveMode(); try { // UPLOAD THE LOCAL VIDEO FILE. ftpClient.storeFile(ftpRemoteFtpFilename, buffIn); } catch (IOException e) { // e.printStackTrace(); Log.e(TAG, " got exception on storeFile - video uploading failed."); // This is a bad error, lets abort. // user dialog ?! shouldnt happen, but still... // Use the handler to execute a Runnable on the // main thread in order to have access to the // UI elements. mainapp.removeSDFileRecordIDfromUploadingTrack(sdrecord_id, TYPE_FTP); handler.postDelayed(new Runnable() { public void run() { // Update UI // Hide the progress bar ((VidiomActivity) activity).finishedUploading(false); ((VidiomActivity) activity) .createNotification(res.getString(R.string.upload_to_ftp_host_failed_)); } }, 0); return; } try { buffIn.close(); } catch (IOException e) { // e.printStackTrace(); Log.e(TAG, " got exception on buff.close - video uploading failed."); // Use the handler to execute a Runnable on the // main thread in order to have access to the // UI elements. mainapp.removeSDFileRecordIDfromUploadingTrack(sdrecord_id, TYPE_FTP); handler.postDelayed(new Runnable() { public void run() { // Update UI // Hide the progress bar ((VidiomActivity) activity).finishedUploading(false); ((VidiomActivity) activity) .createNotification(res.getString(R.string.upload_to_ftp_host_failed_)); } }, 0); return; } try { ftpClient.logout(); } catch (IOException e) { // e.printStackTrace(); Log.e(TAG, " got exception on ftp logout - video uploading failed."); // Use the handler to execute a Runnable on the // main thread in order to have access to the // UI elements. mainapp.removeSDFileRecordIDfromUploadingTrack(sdrecord_id, TYPE_FTP); handler.postDelayed(new Runnable() { public void run() { // Update UI // Hide the progress bar ((VidiomActivity) activity).finishedUploading(false); ((VidiomActivity) activity) .createNotification(res.getString(R.string.upload_to_ftp_host_failed_)); } }, 0); return; } try { ftpClient.disconnect(); } catch (IOException e) { // e.printStackTrace(); Log.e(TAG, " got exception on ftp disconnect - video uploading failed."); // Use the handler to execute a Runnable on the // main thread in order to have access to the // UI elements. mainapp.removeSDFileRecordIDfromUploadingTrack(sdrecord_id, TYPE_FTP); handler.postDelayed(new Runnable() { public void run() { // Update UI // Hide the progress bar ((VidiomActivity) activity).finishedUploading(false); ((VidiomActivity) activity) .createNotification(res.getString(R.string.upload_to_ftp_host_failed_)); } }, 0); return; } if (emailAddress != null && ftpHostName != null) { // EmailSender through IR controlled gmail system. SSLEmailSender sender = new SSLEmailSender( activity.getString(R.string.automatic_email_username), activity.getString(R.string.automatic_email_password)); // consider // this // public // knowledge. try { sender.sendMail(activity.getString(R.string.vidiom_automatic_email), // subject.getText().toString(), activity.getString(R.string.url_of_hosted_video_is_) + " " + ftpHostName, // body.getText().toString(), activity.getString(R.string.automatic_email_from), // from.getText().toString(), emailAddress // to.getText().toString() ); } catch (Exception e) { Log.e(TAG, e.getMessage(), e); } } // Log record of this URL in POSTs table dbutils.creatHostDetailRecordwithNewVideoUploaded(sdrecord_id, ftpHostName, ftpHostName, ""); mainapp.removeSDFileRecordIDfromUploadingTrack(sdrecord_id, TYPE_FTP); // Use the handler to execute a Runnable on the // main thread in order to have access to the // UI elements. handler.postDelayed(new Runnable() { public void run() { // Update UI // Indicate back to calling activity the result! // update uploadInProgress state also. ((VidiomActivity) activity).finishedUploading(true); ((VidiomActivity) activity) .createNotification(res.getString(R.string.upload_to_ftp_host_succeeded_)); } }, 0); } }); t.start(); return t; }
From source file:convcao.com.caoAgent.convcaoNeptusInteraction.java
private void Upload(String ftpServer, String pathDirectory, String SourcePathDirectory, String userName, String password, String filename) { FTPClient client = new FTPClient(); FileInputStream fis = null;//from w ww.ja v a2 s . c om try { client.connect(ftpServer); client.login(userName, password); client.enterLocalPassiveMode(); client.setFileType(FTP.BINARY_FILE_TYPE); fis = new FileInputStream(SourcePathDirectory + filename); client.changeWorkingDirectory("/" + pathDirectory); client.storeFile(filename, fis); System.out.println( "The file " + SourcePathDirectory + " was stored to " + "/" + pathDirectory + "/" + filename); client.logout(); //Report = "File: " + filename + " Uploaded Successfully "; } catch (Exception exp) { exp.printStackTrace(); Report = "Server Error"; jLabel6.setText(Report); } finally { try { if (fis != null) { fis.close(); } client.disconnect(); } catch (IOException e) { e.printStackTrace(); } } }
From source file:base.BasePlayer.AddGenome.java
static void updateEnsemblList() { try {//from www .ja v a 2 s.co m menu = new JPopupMenu(); area = new JTextArea(); menuscroll = new JScrollPane(); area.setFont(Main.menuFont); menu.add(menuscroll); //menu.setPreferredSize(new Dimension(menu.getFontMetrics(Main.menuFont).stringWidth("0000000000000000000000000000000000000000000000000")+Main.defaultFontSize*10, (int)menu.getFontMetrics(Main.menuFont).getHeight()*4)); menu.setPreferredSize(new Dimension(300, 200)); //area.setMaximumSize(new Dimension(300, 600)); //area.setLineWrap(true); //area.setWrapStyleWord(true); //area.setPreferredSize(new Dimension(300,200)); area.revalidate(); menuscroll.getViewport().add(area); menu.pack(); menu.show(AddGenome.treescroll, 0, 0); /* area.addMouseListener(new MouseListener() { @Override public void mouseClicked(MouseEvent arg0) { // TODO Auto-generated method stub } @Override public void mouseEntered(MouseEvent arg0) { // TODO Auto-generated method stub } @Override public void mouseExited(MouseEvent arg0) { // TODO Auto-generated method stub } @Override public void mousePressed(MouseEvent arg0) { StringBuffer buf = new StringBuffer(""); for(int i= 0; i<(int)(Math.random()*100); i++) { buf.append("O"); } AddGenome.area.append(buf.toString() +"\n"); AddGenome.area.setCaretPosition(AddGenome.area.getText().length()); AddGenome.area.revalidate(); } @Override public void mouseReleased(MouseEvent arg0) { // TODO Auto-generated method stub } });*/ FTPClient f = new FTPClient(); news = new ArrayList<String[]>(); area.append("Connecting to Ensembl...\n"); //System.out.println("Connecting to Ensembl..."); f.connect("ftp.ensembl.org"); f.enterLocalPassiveMode(); f.login("anonymous", ""); //System.out.println("Connected."); area.append("Connected.\n"); FTPFile[] files = f.listFiles("pub"); String releasedir = ""; String releasenro; for (int i = 0; i < files.length; i++) { if (files[i].isDirectory() && files[i].getName().contains("release")) { releasedir = files[i].getName(); } } files = f.listFiles("pub/" + releasedir + "/fasta/"); releasenro = releasedir.substring(releasedir.indexOf("-") + 1); area.append("Searching for new genomes"); for (int i = 0; i < files.length; i++) { if (files[i].isDirectory()) { FTPFile[] fastafiles = f .listFiles("pub/" + releasedir + "/fasta/" + files[i].getName() + "/dna/"); String[] urls = new String[5]; for (int j = 0; j < fastafiles.length; j++) { if (fastafiles[j].getName().contains(".dna.toplevel.")) { urls[0] = "ftp://ftp.ensembl.org/pub/" + releasedir + "/fasta/" + files[i].getName() + "/dna/" + fastafiles[j].getName(); String filePath = "/pub/" + releasedir + "/fasta/" + files[i].getName() + "/dna/" + fastafiles[j].getName(); f.sendCommand("SIZE", filePath); String reply = f.getReplyString().split("\\s+")[1]; urls[1] = reply; break; } } if (urls[0] == null) { continue; } FTPFile[] annofiles = f.listFiles("pub/" + releasedir + "/gff3/" + files[i].getName()); for (int j = 0; j < annofiles.length; j++) { if (annofiles[j].getName().contains("." + releasenro + ".gff3.gz")) { urls[2] = "ftp://ftp.ensembl.org/pub/" + releasedir + "/gff3/" + files[i].getName() + "/" + annofiles[j].getName(); String filePath = "/pub/" + releasedir + "/gff3/" + files[i].getName() + "/" + annofiles[j].getName(); f.sendCommand("SIZE", filePath); String reply = f.getReplyString().split("\\s+")[1]; urls[3] = reply; break; } } if (urls[2] == null) { continue; } if (files[i].getName().contains("homo_sapiens")) { urls[4] = "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz"; } else if (files[i].getName().contains("mus_musculus")) { urls[4] = "http://hgdownload.cse.ucsc.edu/goldenPath/mm10/database/cytoBand.txt.gz"; } String name = urls[0].substring(urls[0].lastIndexOf("/") + 1, urls[0].indexOf(".dna.")); //System.out.print(urls[0]+"\t" +urls[1] +"\t" +urls[2] +"\t" +urls[3]); if (genomeHash.containsKey(name) || AddGenome.removables.contains(name)) { //System.out.println(name +" already in the list."); area.append("."); } else { area.append("\nNew genome " + name + " added.\n"); AddGenome.area.setCaretPosition(AddGenome.area.getText().length()); AddGenome.area.revalidate(); //System.out.println("New reference " +name +" found."); organisms.add(name); news.add(urls); if (urls[4] != null) { //System.out.println(urls[0] +" " + urls[2] +" " +urls[4]); URL[] newurls = { new URL(urls[0]), new URL(urls[2]), new URL(urls[4]) }; genomeHash.put(name, newurls); } else { URL[] newurls = { new URL(urls[0]), new URL(urls[2]) }; genomeHash.put(name, newurls); } Integer[] sizes = { Integer.parseInt(urls[1]), Integer.parseInt(urls[3]) }; sizeHash.put(name, sizes); } /*if(urls[4] != null) { System.out.print("\t" +urls[4]); } System.out.println(); */ } } checkGenomes(); if (news.size() > 0) { try { //File file = new File(); FileWriter fw = new FileWriter(Main.genomeDir.getCanonicalPath() + "/ensembl_fetched.txt"); BufferedWriter bw = new BufferedWriter(fw); for (int i = 0; i < news.size(); i++) { for (int j = 0; j < news.get(i).length; j++) { if (news.get(i)[j] == null) { break; } if (j > 0) { bw.write("\t"); } bw.write(news.get(i)[j]); } bw.write("\n"); } bw.close(); fw.close(); } catch (IOException e) { e.printStackTrace(); } } } catch (Exception e) { Main.showError(e.getMessage(), "Error"); e.printStackTrace(); } }
From source file:convcao.com.agent.ConvcaoNeptusInteraction.java
private void connectButtonActionPerformed(ActionEvent evt) throws SocketException, IOException { String[] vehicles = controlledVehicles.split(","); jTextArea1.setText(""); jTextArea1.repaint();//from w w w . j a v a 2 s. c om showText("Initializing Control Structures"); try { startLocalStructures(vehicles); } catch (Exception e) { GuiUtils.errorMessage(getConsole(), e); return; } auvs = positions.keySet().size(); showText("Initializing server connection"); FTPClient client = new FTPClient(); boolean PathNameCreated = false; try { client.connect("www.convcao.com", 21); client.login(jTextField1.getText(), new String(jPasswordField1.getPassword())); PathNameCreated = client.makeDirectory("/NEPTUS/" + sessionID); client.logout(); } catch (IOException e) { jLabel6.setText("Connection Error"); throw e; } showText("Sending session data"); InputData initialState = new InputData(); initialState.DateTime = new SimpleDateFormat("dd/MM/yyyy HH:mm:ss").format(new Date()); initialState.SessionID = sessionID; initialState.DemoMode = "1"; initialState.AUVs = "" + positions.keySet().size(); String fileName = sessionID + ".txt"; Gson gson = new Gson(); String json = gson.toJson(initialState); PrintWriter writer = new PrintWriter(fileName, "UTF-8"); writer.write(json); writer.close(); if (PathNameCreated) { jLabel6.setText("Connection Established"); jLabel1.setVisible(true); System.out.println("Uploading first file"); upload("www.convcao.com", "NEPTUS", "", jTextField1.getText(), new String(jPasswordField1.getPassword()), fileName); // send first file System.out.println("Uploading second file"); String mapFxStr = FileUtil.getResourceAsFileKeepName("convcao/com/caoAgent/mapPortoSparse.txt"); File mapFx = new File(mapFxStr); upload("www.convcao.com", "NEPTUS/" + sessionID, mapFx.getParent(), jTextField1.getText(), new String(jPasswordField1.getPassword()), "mapPortoSparse.txt"); // send sparse map System.out.println("Both files uploaded"); jButton1.setEnabled(true); jButton2.setEnabled(true); jTextPane1.setEditable(false); jTextField1.setEditable(false); jPasswordField1.setEditable(false); connectButton.setEnabled(false); renewButton.setEnabled(false); } else { jLabel6.setText(client.getReplyString()); jLabel1.setVisible(false); } myDeleteFile(fileName); showText("ConvCAO control has started"); }
From source file:com.ephesoft.gxt.batchinstance.server.BatchInfoDownloadServlet.java
/** * This method uploads the folder containing information related to a batch on a ftp server. * /*from w w w . ja v a2 s . c o m*/ * @param batchInstance {@link BatchInstance} * @param batchSchemaService {@link BatchSchemaService} * @param batchClass {@link BatchClass} * @param response {@link HttpServletResponse} * * @return {@link String} the path where file is uploaded */ private String uploadToFTPPath(final BatchInstance batchInstance, final BatchSchemaService batchSchemaService, final BatchClass batchClass, final HttpServletResponse response) { File zipFolder = null; String ftpFolderPath = null; String batchInstanceIdentifier = null; if (null != batchInstance) { batchInstanceIdentifier = batchInstance.getIdentifier(); } File tempFolder = new File(createDownloadFolderPathName(batchInstanceIdentifier, baseFolderPath)); tempFolder.mkdirs(); if (tempFolder.exists()) { FileOutputStream fout = null; ZipOutputStream zout = null; try { PrintWriter writer = response.getWriter(); response.setContentType(IUtilCommonConstants.CONTENT_TYPE_HTML); String zipFileName = createZipFileName(batchInstanceIdentifier); String zipFolderPath = EphesoftStringUtil.concatenate(baseFolderPath, File.separator, TROUBLESHOOT, File.separator, zipFileName); String zipFilePath = EphesoftStringUtil.concatenate(zipFolderPath, File.separator, zipFileName, ZIP_EXT); zipFolder = new File(zipFolderPath); zipFolder.mkdirs(); fout = new FileOutputStream(zipFilePath); zout = new ZipOutputStream(fout); Properties properties = getFTPProperties(); if (null != properties) { ftpFolderPath = EphesoftStringUtil.concatenate(TROUBLESHOOT, File.separator, zipFileName, ZIP_EXT); FTPInformation ftpInformation = new FTPInformation(ftpServerURL, username, password, properties.getProperty(UPLOAD_BASE_DIR), Integer.parseInt(properties.getProperty(NUM_OF_RETRIES)), properties.getProperty(DATA_TIMEOUT), zipFolderPath, TROUBLESHOOT, 2); try { FTPClient client = new FTPClient(); FTPUtil.createConnection(client, ftpServerURL, username, password, properties.getProperty(DATA_TIMEOUT)); client.disconnect(); copySelectedFolders(batchInstance, batchSchemaService, batchClass, tempFolder.getPath(), tempFolder); if (null != tempFolder.list()) { FileUtils.zipDirectoryWithFullName(tempFolder.getPath(), zout); FTPUtil.uploadDirectory(ftpInformation, false); } writer.write(copyTroubleshootingArtifacts.getFoldersNotCopied()); } catch (SocketException socketException) { LOGGER.error("Could not connect to the FTP client. Socket Exception", socketException.getMessage()); ftpFolderPath = null; // Removed response.sendError code to fix JIRA bug id EPHESOFT-12355. Did not returned expected results. } catch (final IOException ioException) { LOGGER.error(" Invalid Credentials. Could not connect to the FTP client.", ioException.getMessage()); ftpFolderPath = null; writer.write("INVALID_CREDENTIALS"); response.setStatus(HttpServletResponse.SC_OK); // Removed response.sendError code to fix JIRA bug id EPHESOFT-12355. Did not returned expected results. } } } catch (FTPDataUploadException e) { LOGGER.error(EphesoftStringUtil.concatenate("Error occured in uploading the file to path ", ftpFolderPath)); response.setStatus(HttpServletResponse.SC_INTERNAL_SERVER_ERROR); } catch (IOException e) { LOGGER.error(EphesoftStringUtil.concatenate("Error occured in getting writer from response.", e.getMessage())); } catch (NumberFormatException e) { LOGGER.error(EphesoftStringUtil.concatenate("Exception occured in parsing number of retries.", e.getMessage())); } finally { try { closeResources(null, zout, fout, null); if (tempFolder != null) { FileUtils.deleteDirectoryAndContentsRecursive(tempFolder); } if (zipFolder != null) { FileUtils.deleteDirectoryAndContentsRecursive(zipFolder); } } catch (IOException e) { LOGGER.error(EphesoftStringUtil.concatenate("Exception occured while closing outputstream.", e.getMessage())); } } } else { LOGGER.error("Could not create the folder for copying the required folders."); } return ftpFolderPath; }
From source file:com.cladonia.xngreditor.URLUtilities.java
public static InputStream open(URL url) throws IOException { // System.out.println( "URLUtilities.open( "+url+")"); InputStream stream = null;/*from w w w . jav a 2 s.c om*/ String password = URLUtilities.getPassword(url); String username = URLUtilities.getUsername(url); String protocol = url.getProtocol(); if (protocol.equals("http") || protocol.equals("https")) { try { DefaultAuthenticator authenticator = Main.getDefaultAuthenticator(); URL newURL = new URL(URLUtilities.toString(url)); if (authenticator != null && password != null && username != null) { authenticator.setPasswordAuthentication( new PasswordAuthentication(username, password.toCharArray())); } stream = newURL.openStream(); if (authenticator != null && password != null && username != null) { authenticator.setPasswordAuthentication(null); } } catch (Exception e) { // System.out.println( "Could not use normal http connection, because of:\n"+e.getMessage()); // try it with webdav WebdavResource webdav = createWebdavResource(toString(url), username, password); stream = webdav.getMethodData(toString(url)); webdav.close(); } } else if (protocol.equals("ftp")) { FTPClient client = null; String host = url.getHost(); try { // System.out.println( "Connecting to: "+host+" ..."); client = new FTPClient(); client.connect(host); // System.out.println( "Connected."); // After connection attempt, you should check the reply code to verify // success. int reply = client.getReplyCode(); if (!FTPReply.isPositiveCompletion(reply)) { // System.out.println( "Could not connect."); client.disconnect(); throw new IOException("FTP Server \"" + host + "\" refused connection."); } // System.out.println( "Logging in using: "+username+", "+password+" ..."); if (!client.login(username, password)) { // System.out.println( "Could not log in."); // TODO bring up login dialog? client.disconnect(); throw new IOException("Could not login to FTP Server \"" + host + "\"."); } // System.out.println( "Logged in."); client.setFileType(FTP.BINARY_FILE_TYPE); client.enterLocalPassiveMode(); // System.out.println( "Opening file \""+url.getFile()+"\" ..."); stream = client.retrieveFileStream(url.getFile()); // System.out.println( "File opened."); // System.out.println( "Disconnecting ..."); client.disconnect(); // System.out.println( "Disconnected."); } catch (IOException e) { if (client.isConnected()) { try { client.disconnect(); } catch (IOException f) { // do nothing e.printStackTrace(); } } throw new IOException("Could not connect to FTP Server \"" + host + "\"."); } } else if (protocol.equals("file")) { stream = url.openStream(); } else { //unknown protocol but try anyways try { stream = url.openStream(); } catch (IOException ioe) { throw new IOException("The \"" + protocol + "\" protocol is not supported."); } } return stream; }