List of usage examples for org.apache.commons.net.ftp FTPClient enterLocalPassiveMode
public void enterLocalPassiveMode()
PASSIVE_LOCAL_DATA_CONNECTION_MODE . From source file:com.maxl.java.aips2sqlite.AllDown.java
public void downZurRose() { String fl = ""; String fp = ""; String fs = ""; try {/*from w ww. j av a 2 s. c om*/ FileInputStream access = new FileInputStream(Constants.DIR_ZURROSE + "/access.ami.csv"); BufferedReader br = new BufferedReader(new InputStreamReader(access, "UTF-8")); String line; while ((line = br.readLine()) != null) { // Semicolon is used as a separator String[] gln = line.split(";"); if (gln.length > 2) { if (gln[0].equals("P_ywesee")) { fl = gln[0]; fp = gln[1]; fs = gln[2]; } } } br.close(); } catch (Exception e) { e.printStackTrace(); } FTPClient ftp_client = new FTPClient(); try { ftp_client.connect(fs, 21); ftp_client.login(fl, fp); ftp_client.enterLocalPassiveMode(); ftp_client.setFileType(FTP.BINARY_FILE_TYPE); System.out.println("- Connected to server " + fs + "..."); String[] working_dir = { "ywesee out", "../ywesee in" }; for (int i = 0; i < working_dir.length; ++i) { // Set working directory ftp_client.changeWorkingDirectory(working_dir[i]); int reply = ftp_client.getReplyCode(); if (!FTPReply.isPositiveCompletion(reply)) { ftp_client.disconnect(); System.err.println("FTP server refused connection."); return; } // Get list of filenames FTPFile[] ftpFiles = ftp_client.listFiles(); if (ftpFiles != null && ftpFiles.length > 0) { // ... then download all csv files for (FTPFile f : ftpFiles) { String remote_file = f.getName(); if (remote_file.endsWith("csv")) { String local_file = remote_file; if (remote_file.startsWith("Artikelstamm")) local_file = Constants.CSV_FILE_DISPO_ZR; OutputStream os = new FileOutputStream(Constants.DIR_ZURROSE + "/" + local_file); System.out.print("- Downloading " + remote_file + " from server " + fs + "... "); boolean done = ftp_client.retrieveFile(remote_file, os); if (done) System.out.println("success."); else System.out.println("error."); os.close(); } } } } } catch (IOException ex) { System.out.println("Error: " + ex.getMessage()); ex.printStackTrace(); } finally { try { if (ftp_client.isConnected()) { ftp_client.logout(); ftp_client.disconnect(); } } catch (IOException ex) { ex.printStackTrace(); } } }
From source file:it.baywaylabs.jumpersumo.twitter.TwitterListener.java
/** * @param host FTP Host name./*ww w .ja v a2 s .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:net.audumla.climate.bom.BOMDataLoader.java
private synchronized FTPClient getFTPClient(String host) { FTPClient ftp = ftpClients.get(host); if (ftp == null || !ftp.isAvailable() || !ftp.isConnected()) { ftp = new FTPClient(); FTPClientConfig config = new FTPClientConfig(); ftp.configure(config);/*from w w w . j av a 2 s.c o m*/ try { ftp.setControlKeepAliveTimeout(30); ftp.setControlKeepAliveReplyTimeout(5); ftp.setDataTimeout(3000); ftp.setDefaultTimeout(1000); int reply; ftp.connect(host); LOG.debug("Connected to " + host); reply = ftp.getReplyCode(); if (!FTPReply.isPositiveCompletion(reply)) { ftp.disconnect(); LOG.error("FTP server '" + host + "' refused connection."); } else { if (!ftp.login("anonymous", "guest")) { LOG.error("Unable to login to server " + host); } ftp.setSoTimeout(60000); ftp.enterLocalPassiveMode(); ftp.setFileType(FTPClient.BINARY_FILE_TYPE); } } catch (IOException e) { LOG.error("Unable to connect to " + host, e); } ftpClients.put(host, ftp); } if (!ftp.isConnected() || !ftp.isAvailable()) { throw new UnsupportedOperationException("Cannot connect to " + host); } return ftp; }
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 ww w . j ava2 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:convcao.com.agent.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 w w . j ava 2s . co m*/ 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:com.rvl.android.getnzb.LocalNZB.java
public void uploadLocalFileFTP(String filename) { UPLOADFILENAME = filename;/*from w w w . j a v a 2s . c om*/ UPLOADDIALOG = ProgressDialog.show(this, "Please wait...", "Uploading '" + filename + "' to FTP server."); SharedPreferences prefs = GetNZB.preferences; if (prefs.getString("FTPHostname", "") == "") { uploadDialogHandler.sendEmptyMessage(0); Toast.makeText(this, "Upload to FTP server not possible. Please check FTP preferences.", Toast.LENGTH_LONG).show(); return; } new Thread() { public void run() { SharedPreferences prefs = GetNZB.preferences; FTPClient ftp = new FTPClient(); String replycode = ""; String FTPHostname = prefs.getString("FTPHostname", ""); String FTPUsername = prefs.getString("FTPUsername", "anonymous"); String FTPPassword = prefs.getString("FTPPassword", "my@email.address"); String FTPPort = prefs.getString("FTPPort", "21"); String FTPUploadPath = prefs.getString("FTPUploadPath", "~/"); if (!FTPUploadPath.matches("$/")) { Log.d(Tags.LOG, "Adding trailing slash"); FTPUploadPath += "/"; } String targetFile = FTPUploadPath + UPLOADFILENAME; try { ftp.connect(FTPHostname, Integer.parseInt(FTPPort)); if (ftp.login(FTPUsername, FTPPassword)) { ftp.setFileType(FTP.BINARY_FILE_TYPE); ftp.enterLocalPassiveMode(); File file = new File(getFilesDir() + "/" + UPLOADFILENAME); BufferedInputStream buffIn = new BufferedInputStream(new FileInputStream(file)); Log.d(Tags.LOG, "Saving file to:" + targetFile); if (ftp.storeFile(targetFile, buffIn)) { Log.d(Tags.LOG, "FTP: File should be uploaded. Replycode: " + Integer.toString(ftp.getReplyCode())); isUploadedFTP = true; } else { Log.d(Tags.LOG, "FTP: Could not upload file Replycode: " + Integer.toString(ftp.getReplyCode())); FTPErrorCode = Integer.toString(ftp.getReplyCode()); isUploadedFTP = false; } buffIn.close(); ftp.logout(); ftp.disconnect(); } else { Log.d(Tags.LOG, "No ftp login"); } } catch (SocketException e) { Log.d(Tags.LOG, "ftp(): " + e.getMessage()); return; } catch (IOException e) { Log.d(Tags.LOG, "ftp(): " + e.getMessage()); return; } if (isUploadedFTP) { removeLocalNZBFile(UPLOADFILENAME); } UPLOADFILENAME = ""; uploadDialogHandlerFTP.sendEmptyMessage(0); } }.start(); }
From source file:edu.lternet.pasta.dml.download.DownloadHandler.java
/** * Gets content from given source and writes it to DataStorageInterface * to store them. This method will be called by run() * /* ww w . ja v a 2 s. co m*/ * @param resourceName the URL to the source data to be retrieved */ protected boolean getContentFromSource(String resourceName) { boolean successFlag = false; QualityCheck onlineURLsQualityCheck = null; boolean onlineURLsException = false; // used to determine status of onlineURLs quality check if (resourceName != null) { resourceName = resourceName.trim(); } if (resourceName != null && (resourceName.startsWith("http://") || resourceName.startsWith("https://") || resourceName.startsWith("file://") || resourceName.startsWith("ftp://"))) { // get the data from a URL int responseCode = 0; String responseMessage = null; try { URL url = new URL(resourceName); boolean isFTP = false; if (entity != null) { String contentType = null; // Find the right MIME type and set it as content type if (resourceName.startsWith("http")) { HttpURLConnection httpURLConnection = (HttpURLConnection) url.openConnection(); httpURLConnection.setRequestMethod("HEAD"); httpURLConnection.connect(); contentType = httpURLConnection.getContentType(); responseCode = httpURLConnection.getResponseCode(); responseMessage = httpURLConnection.getResponseMessage(); } else if (resourceName.startsWith("file")) { URLConnection urlConnection = url.openConnection(); urlConnection.connect(); contentType = urlConnection.getContentType(); } else { // FTP isFTP = true; contentType = "application/octet-stream"; } entity.setUrlContentType(contentType); } if (!isFTP) { // HTTP(S) or FILE InputStream filestream = url.openStream(); try { successFlag = this.writeRemoteInputStreamIntoDataStorage(filestream); } catch (IOException e) { exception = e; String errorMessage = e.getMessage(); if (errorMessage.startsWith(ONLINE_URLS_EXCEPTION_MESSAGE)) { onlineURLsException = true; } } finally { filestream.close(); } } else { // FTP String[] urlParts = resourceName.split("/"); String address = urlParts[2]; String dir = "/"; for (int i = 3; i < urlParts.length - 1; i++) { dir += urlParts[i] + "/"; } String fileName = urlParts[urlParts.length - 1]; FTPClient ftpClient = new FTPClient(); ftpClient.connect(address); ftpClient.login(ANONYMOUS, anonymousFtpPasswd); ftpClient.changeWorkingDirectory(dir); ftpClient.setFileType(FTP.BINARY_FILE_TYPE); ftpClient.enterLocalPassiveMode(); // necessary to avoid firewall blocking InputStream filestream = ftpClient.retrieveFileStream(fileName); try { successFlag = this.writeRemoteInputStreamIntoDataStorage(filestream); } catch (IOException e) { exception = e; String errorMessage = e.getMessage(); if (errorMessage.startsWith(ONLINE_URLS_EXCEPTION_MESSAGE)) { onlineURLsException = true; } } finally { try { filestream.close(); } catch (IOException e) { exception = new DataSourceNotFoundException(String .format("Error closing local file '%s': %s", resourceName, e.getMessage())); onlineURLsException = true; } } // logout and disconnect if FTP session if (resourceName.startsWith("ftp") && ftpClient != null) { try { ftpClient.enterLocalActiveMode(); ftpClient.logout(); ftpClient.disconnect(); } catch (IOException e) { exception = new DataSourceNotFoundException( String.format("Error disconnecting from FTP with resource '%s': %s", resourceName, e.getMessage())); onlineURLsException = true; } } } } catch (MalformedURLException e) { String eClassName = e.getClass().getName(); String eMessage = String.format("%s: %s", eClassName, e.getMessage()); onlineURLsException = true; exception = new DataSourceNotFoundException( String.format("The URL '%s' is a malformed URL: %s", resourceName, eMessage)); } catch (IOException e) { String eClassName = e.getClass().getName(); String eMessage = String.format("%s: %s", eClassName, e.getMessage()); if (responseCode > 0) { eMessage = String.format("Response Code: %d %s; %s", responseCode, responseMessage, eMessage); } onlineURLsException = true; exception = new DataSourceNotFoundException( String.format("The URL '%s' is not reachable: %s", resourceName, eMessage)); } // Initialize the "Online URLs are live" quality check String qualityCheckIdentifier = "onlineURLs"; QualityCheck qualityCheckTemplate = QualityReport.getQualityCheckTemplate(qualityCheckIdentifier); onlineURLsQualityCheck = new QualityCheck(qualityCheckIdentifier, qualityCheckTemplate); if (QualityCheck.shouldRunQualityCheck(entity, onlineURLsQualityCheck)) { String resourceNameEscaped = embedInCDATA(resourceName); if (!onlineURLsException) { onlineURLsQualityCheck.setStatus(Status.valid); onlineURLsQualityCheck.setFound("true"); onlineURLsQualityCheck.setExplanation("Succeeded in accessing URL: " + resourceNameEscaped); } else { onlineURLsQualityCheck.setFailedStatus(); onlineURLsQualityCheck.setFound("false"); String explanation = "Failed to access URL: " + resourceNameEscaped; explanation = explanation + "; " + embedInCDATA(exception.getMessage()); onlineURLsQualityCheck.setExplanation(explanation); } entity.addQualityCheck(onlineURLsQualityCheck); } return successFlag; } else if (resourceName != null && resourceName.startsWith("ecogrid://")) { // get the docid from url int start = resourceName.indexOf("/", 11) + 1; //log.debug("start: " + start); int end = resourceName.indexOf("/", start); if (end == -1) { end = resourceName.length(); } //log.debug("end: " + end); String ecogridIdentifier = resourceName.substring(start, end); // pass this docid and get data item //System.out.println("the endpoint is "+ECOGRIDENDPOINT); //System.out.println("The identifier is "+ecogridIdentifier); //return false; return getContentFromEcoGridSource(ecogridEndPoint, ecogridIdentifier); } else if (resourceName != null && resourceName.startsWith("srb://")) { // get srb docid from the url String srbIdentifier = transformSRBurlToDocid(resourceName); // reset endpoint for srb (This is hack we need to figure ou // elegent way to do this //mEndPoint = Config.getValue("//ecogridService/srb/endPoint"); // pass this docid and get data item //log.debug("before get srb data"); return getContentFromEcoGridSource(SRBENDPOINT, srbIdentifier); } else { successFlag = false; return successFlag; } }
From source file:fr.bmartel.speedtest.SpeedTestTask.java
/** * start FTP download with specific port, user, password. * * @param hostname ftp host/*from w w w .j a v a 2 s. co m*/ * @param uri ftp uri * @param user ftp username * @param password ftp password */ public void startFtpDownload(final String hostname, final int port, final String uri, final String user, final String password) { mSpeedTestMode = SpeedTestMode.DOWNLOAD; mErrorDispatched = false; mForceCloseSocket = false; if (mReadExecutorService == null || mReadExecutorService.isShutdown()) { mReadExecutorService = Executors.newSingleThreadExecutor(); } mReadExecutorService.execute(new Runnable() { @Override public void run() { final FTPClient ftpclient = new FTPClient(); try { ftpclient.connect(hostname, port); ftpclient.login(user, password); ftpclient.enterLocalPassiveMode(); ftpclient.setFileType(FTP.BINARY_FILE_TYPE); mDownloadTemporaryPacketSize = 0; mTimeStart = System.currentTimeMillis(); mTimeEnd = 0; if (mRepeatWrapper.isFirstDownload()) { mRepeatWrapper.setFirstDownloadRepeat(false); mRepeatWrapper.setStartDate(mTimeStart); } mDownloadPckSize = new BigDecimal(getFileSize(ftpclient, uri)); if (mRepeatWrapper.isRepeatDownload()) { mRepeatWrapper.updatePacketSize(mDownloadPckSize); } mFtpInputstream = ftpclient.retrieveFileStream(uri); if (mFtpInputstream != null) { final byte[] bytesArray = new byte[SpeedTestConst.READ_BUFFER_SIZE]; int read; while ((read = mFtpInputstream.read(bytesArray)) != -1) { mDownloadTemporaryPacketSize += read; if (mRepeatWrapper.isRepeatDownload()) { mRepeatWrapper.updateTempPacketSize(read); } if (!mReportInterval) { final SpeedTestReport report = mSocketInterface.getLiveDownloadReport(); for (int i = 0; i < mListenerList.size(); i++) { mListenerList.get(i).onDownloadProgress(report.getProgressPercent(), report); } } if (mDownloadTemporaryPacketSize == mDownloadPckSize.longValueExact()) { break; } } mFtpInputstream.close(); mTimeEnd = System.currentTimeMillis(); mReportInterval = false; final SpeedTestReport report = mSocketInterface.getLiveDownloadReport(); for (int i = 0; i < mListenerList.size(); i++) { mListenerList.get(i).onDownloadFinished(report); } } else { mReportInterval = false; SpeedTestUtils.dispatchError(mForceCloseSocket, mListenerList, true, "cant create stream " + "from uri " + uri + " with reply code : " + ftpclient.getReplyCode()); } if (!mRepeatWrapper.isRepeatDownload()) { closeExecutors(); } } catch (IOException e) { //e.printStackTrace(); mReportInterval = false; catchError(true, e.getMessage()); } finally { mErrorDispatched = false; mSpeedTestMode = SpeedTestMode.NONE; disconnectFtp(ftpclient); } } }); }
From source file:ddf.test.itests.catalog.TestFtp.java
private FTPClient createInsecureClient() throws Exception { FTPClient ftp = new FTPClient(); int attempts = 0; while (true) { try {/* w w w .j a v a 2s. c o m*/ ftp.connect(FTP_SERVER, Integer.parseInt(FTP_PORT.getPort())); break; } catch (SocketException e) { // a socket exception can be thrown if the ftp server is still in the process of coming up // or down Thread.sleep(1000); if (attempts++ > 30) { throw e; } } } showServerReply(ftp); int connectionReply = ftp.getReplyCode(); if (!FTPReply.isPositiveCompletion(connectionReply)) { fail("FTP server refused connection: " + connectionReply); } boolean success = ftp.login(USERNAME, PASSWORD); showServerReply(ftp); if (!success) { fail("Could not log in to the FTP server."); } ftp.enterLocalPassiveMode(); ftp.setControlKeepAliveTimeout(300); ftp.setFileType(FTP.BINARY_FILE_TYPE); return ftp; }
From source file:base.BasePlayer.AddGenome.java
static void updateEnsemblList() { try {/* w w w .j av a 2 s. c o 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(); } }